Nonrandom community assembly and high temporal turnover promote regional coexistence in tropics but not temperate zone.

PubMed

Freestone, Amy L; Inouye, Brian D

2015-01-01

A persistent challenge for ecologists is understanding the ecological mechanisms that maintain global patterns of biodiversity, particularly the latitudinal diversity gradient of peak species richness in the tropics. Spatial and temporal variation in community composition contribute to these patterns of biodiversity, but how this variation and its underlying processes change across latitude remains unresolved. Using a model system of sessile marine invertebrates across 25 degrees of latitude, from the temperate zone to the tropics, we tested the prediction that spatial and temporal patterns of taxonomic richness and composition, and the community assembly processes underlying these patterns, will differ across latitude. Specifically, we predicted that high beta diversity (spatial variation in composition) and high temporal turnover contribute to the high species richness of the tropics. Using a standardized experimental approach that controls for several confounding factors that hinder interpretation of prior studies, we present results that support our predictions. In the temperate zone, communities were more similar across spatial scales from centimeters to tens of kilometers and temporal scales up to one year than at lower latitudes. Since the patterns at northern latitudes were congruent with a null model, stochastic assembly processes are implicated. In contrast, the communities in the tropics were a dynamic spatial and temporal mosaic, with low similarity even across small spatial scales and high temporal turnover at both local and regional scales. Unlike the temperate zone, deterministic community assembly processes such as predation likely contributed to the high beta diversity in the tropics. Our results suggest that community assembly processes and temporal dynamics vary across latitude and help structure and maintain latitudinal patterns of diversity.

Altitudinal Patterns of Species Diversity and Phylogenetic Diversity across Temperate Mountain Forests of Northern China.

PubMed

Zhang, Wenxin; Huang, Dizhou; Wang, Renqing; Liu, Jian; Du, Ning

2016-01-01

The spatial patterns of biodiversity and their underlying mechanisms have been an active area of research for a long time. In this study, a total of 63 samples (20m × 30m) were systematically established along elevation gradients on Mount Tai and Mount Lao, China. We explored altitudinal patterns of plant diversity in the two mountain systems. In order to understand the mechanisms driving current diversity patterns, we used phylogenetic approaches to detect the spatial patterns of phylogenetic diversity and phylogenetic structure along two elevation gradients. We found that total species richness had a monotonically decreasing pattern and tree richness had a unimodal pattern along the elevation gradients in the two study areas. However, altitudinal patterns in shrub richness and herbs richness were not consistent on the two mountains. At low elevation, anthropogenic disturbances contributed to the increase of plant diversity, especially for shrubs and herbs in understory layers, which are more sensitive to changes in microenvironment. The phylogenetic structure of plant communities exhibited an inverted hump-shaped pattern along the elevation gradient on Mount Tai, which demonstrates that environmental filtering is the main driver of plant community assembly at high and low elevations and inter-specific competition may be the main driver of plant community assembly in the middle elevations. However, the phylogenetic structure of plant communities did not display a clear pattern on Mount Lao where the climate is milder. Phylogenetic beta diversity and species beta diversity consistently increased with increasing altitudinal divergence in the two study areas. However, the altitudinal patterns of species richness did not completely mirror phylogenetic diversity patterns. Conservation areas should be selected taking into consideration the preservation of high species richness, while maximizing phylogenetic diversity to improve the potential for diversification in the future.

Microbes on mountainsides: Contrasting elevational patterns of bacterial and plant diversity

PubMed Central

Bryant, Jessica A.; Lamanna, Christine; Morlon, Hélène; Kerkhoff, Andrew J.; Enquist, Brian J.; Green, Jessica L.

2008-01-01

The study of elevational diversity gradients dates back to the foundation of biogeography. Although elevational patterns of plant and animal diversity have been studied for centuries, such patterns have not been reported for microorganisms and remain poorly understood. Here, in an effort to assess the generality of elevational diversity patterns, we examined soil bacterial and plant diversity along an elevation gradient. To gain insight into the forces that structure these patterns, we adopted a multifaceted approach to incorporate information about the structure, diversity, and spatial turnover of montane communities in a phylogenetic context. We found that observed patterns of plant and bacterial diversity were fundamentally different. While bacterial taxon richness and phylogenetic diversity decreased monotonically from the lowest to highest elevations, plants followed a unimodal pattern, with a peak in richness and phylogenetic diversity at mid-elevations. At all elevations bacterial communities had a tendency to be phylogenetically clustered, containing closely related taxa. In contrast, plant communities did not exhibit a uniform phylogenetic structure across the gradient: they became more overdispersed with increasing elevation, containing distantly related taxa. Finally, a metric of phylogenetic beta-diversity showed that bacterial lineages were not randomly distributed, but rather exhibited significant spatial structure across the gradient, whereas plant lineages did not exhibit a significant phylogenetic signal. Quantifying the influence of sample scale in intertaxonomic comparisons remains a challenge. Nevertheless, our findings suggest that the forces structuring microorganism and macroorganism communities along elevational gradients differ. PMID:18695215

A metric for quantifying El Niño pattern diversity with implications for ENSO-mean state interaction

NASA Astrophysics Data System (ADS)

Lemmon, Danielle E.; Karnauskas, Kristopher B.

2018-04-01

Recent research on the El Niño-Southern Oscillation (ENSO) phenomenon increasingly reveals the highly complex and diverse nature of ENSO variability. A method of quantifying ENSO spatial pattern uniqueness and diversity is presented, which enables (1) formally distinguishing between unique and "canonical" El Niño events, (2) testing whether historical model simulations aptly capture ENSO diversity by comparing with instrumental observations, (3) projecting future ENSO diversity using future model simulations, (4) understanding the dynamics that give rise to ENSO diversity, and (5) analyzing the associated diversity of ENSO-related atmospheric teleconnection patterns. Here we develop a framework for measuring El Niño spatial SST pattern uniqueness and diversity for a given set of El Niño events using two indices, the El Niño Pattern Uniqueness (EPU) index and El Niño Pattern Diversity (EPD) index, respectively. By applying this framework to instrumental records, we independently confirm a recent regime shift in El Niño pattern diversity with an increase in unique El Niño event sea surface temperature patterns. However, the same regime shift is not observed in historical CMIP5 model simulations; moreover, a comparison between historical and future CMIP5 model scenarios shows no robust change in future ENSO diversity. Finally, we support recent work that asserts a link between the background cooling of the eastern tropical Pacific and changes in ENSO diversity. This robust link between an eastern Pacific cooling mode and ENSO diversity is observed not only in instrumental reconstructions and reanalysis, but also in historical and future CMIP5 model simulations.

A phylogenetic perspective on species diversity, β-diversity and biogeography for the microbial world.

PubMed

Barberán, Albert; Casamayor, Emilio O

2014-12-01

There is an increasing interest to combine phylogenetic data with distributional and ecological records to assess how natural communities arrange under an evolutionary perspective. In the microbial world, there is also a need to go beyond the problematic species definition to deeply explore ecological patterns using genetic data. We explored links between evolution/phylogeny and community ecology using bacterial 16S rRNA gene information from a high-altitude lakes district data set. We described phylogenetic community composition, spatial distribution, and β-diversity and biogeographical patterns applying evolutionary relatedness without relying on any particular operational taxonomic unit definition. High-altitude lakes districts usually contain a large mosaic of highly diverse small water bodies and conform a fine biogeographical model of spatially close but environmentally heterogeneous ecosystems. We sampled 18 lakes in the Pyrenees with a selection criteria focused on capturing the maximum environmental variation within the smallest geographical area. The results showed highly diverse communities nonrandomly distributed with phylogenetic β-diversity patterns mainly shaped by the environment and not by the spatial distance. Community similarity based on both bacterial taxonomic composition and phylogenetic β-diversity shared similar patterns and was primarily structured by similar environmental drivers. We observed a positive relationship between lake area and phylogenetic diversity with a slope consistent with highly dispersive planktonic organisms. The phylogenetic approach incorporated patterns of common ancestry into bacterial community analysis and emerged as a very convenient analytical tool for direct inter- and intrabiome biodiversity comparisons and sorting out microbial habitats with potential application in conservation studies. © 2014 John Wiley & Sons Ltd.

Small-scale spatial variability of soil microbial community composition and functional diversity in a mixed forest

NASA Astrophysics Data System (ADS)

Wang, Qiufeng; Tian, Jing; Yu, Guirui

2014-05-01

Patterns in the spatial distribution of organisms provide important information about mechanisms that regulate the diversity and complexity of soil ecosystems. Therefore, information on spatial distribution of microbial community composition and functional diversity is urgently necessary. The spatial variability on a 26×36 m plot and vertical distribution (0-10 cm and 10-20 cm) of soil microbial community composition and functional diversity were studied in a natural broad-leaved Korean pine (Pinus koraiensis) mixed forest soil in Changbai Mountain. The phospholipid fatty acid (PLFA) pattern was used to characterize the soil microbial community composition and was compared with the community substrate utilization pattern using Biolog. Bacterial biomass dominated and showed higher variability than fungal biomass at all scales examined. The microbial biomass decreased with soil depths increased and showed less variability in lower 10-20 cm soil layer. The Shannon-Weaver index value for microbial functional diversity showed higher variability in upper 0-10 cm than lower 10-20 cm soil layer. Carbohydrates, carboxylic acids, polymers and amino acids are the main carbon sources possessing higher utilization efficiency or utilization intensity. At the same time, the four carbon source types contributed to the differentiation of soil microbial communities. This study suggests the higher diversity and complexity for this mix forest ecosystem. To determine the driving factors that affect this spatial variability of microorganism is the next step for our study.

Mitochondrial phylogeography of a Beringian relict: the endemic freshwater genus of blackfish Dallia (Esociformes).

PubMed

Campbell, M A; Lopéz, J A

2014-02-01

Mitochondrial genetic variability among populations of the blackfish genus Dallia (Esociformes) across Beringia was examined. Levels of divergence and patterns of geographic distribution of mitochondrial DNA lineages were characterized using phylogenetic inference, median-joining haplotype networks, Bayesian skyline plots, mismatch analysis and spatial analysis of molecular variance (SAMOVA) to infer genealogical relationships and to assess patterns of phylogeography among extant mitochondrial lineages in populations of species of Dallia. The observed variation includes extensive standing mitochondrial genetic diversity and patterns of distinct spatial segregation corresponding to historical and contemporary barriers with minimal or no mixing of mitochondrial haplotypes between geographic areas. Mitochondrial diversity is highest in the common delta formed by the Yukon and Kuskokwim Rivers where they meet the Bering Sea. Other regions sampled in this study host comparatively low levels of mitochondrial diversity. The observed levels of mitochondrial diversity and the spatial distribution of that diversity are consistent with persistence of mitochondrial lineages in multiple refugia through the last glacial maximum. © 2014 The Fisheries Society of the British Isles.

Metacommunity versus Biogeography: A Case Study of Two Groups of Neotropical Vegetation-Dwelling Arthropods

PubMed Central

Gonçalves-Souza, Thiago; Romero, Gustavo Q.; Cottenie, Karl

2014-01-01

Biogeography and metacommunity ecology provide two different perspectives on species diversity. Both are spatial in nature but their spatial scales do not necessarily match. With recent boom of metacommunity studies, we see an increasing need for clear discrimination of spatial scales relevant for both perspectives. This discrimination is a necessary prerequisite for improved understanding of ecological phenomena across scales. Here we provide a case study to illustrate some spatial scale-dependent concepts in recent metacommunity studies and identify potential pitfalls. We presented here the diversity patterns of Neotropical lepidopterans and spiders viewed both from metacommunity and biogeographical perspectives. Specifically, we investigated how the relative importance of niche- and dispersal-based processes for community assembly change at two spatial scales: metacommunity scale, i.e. within a locality, and biogeographical scale, i.e. among localities widely scattered along a macroclimatic gradient. As expected, niche-based processes dominated the community assembly at metacommunity scale, while dispersal-based processes played a major role at biogeographical scale for both taxonomical groups. However, we also observed small but significant spatial effects at metacommunity scale and environmental effects at biogeographical scale. We also observed differences in diversity patterns between the two taxonomical groups corresponding to differences in their dispersal modes. Our results thus support the idea of continuity of processes interactively shaping diversity patterns across scales and emphasize the necessity of integration of metacommunity and biogeographical perspectives. PMID:25549332

Metacommunity composition of web-spiders in a fragmented neotropical forest: relative importance of environmental and spatial effects.

PubMed

Baldissera, Ronei; Rodrigues, Everton N L; Hartz, Sandra M

2012-01-01

The distribution of beta diversity is shaped by factors linked to environmental and spatial control. The relative importance of both processes in structuring spider metacommunities has not yet been investigated in the Atlantic Forest. The variance explained by purely environmental, spatially structured environmental, and purely spatial components was compared for a metacommunity of web spiders. The study was carried out in 16 patches of Atlantic Forest in southern Brazil. Field work was done in one landscape mosaic representing a slight gradient of urbanization. Environmental variables encompassed plot- and patch-level measurements and a climatic matrix, while principal coordinates of neighbor matrices (PCNMs) acted as spatial variables. A forward selection procedure was carried out to select environmental and spatial variables influencing web-spider beta diversity. Variation partitioning was used to estimate the contribution of pure environmental and pure spatial effects and their shared influence on beta-diversity patterns, and to estimate the relative importance of selected environmental variables. Three environmental variables (bush density, land use in the surroundings of patches, and shape of patches) and two spatial variables were selected by forward selection procedures. Variation partitioning revealed that 15% of the variation of beta diversity was explained by a combination of environmental and PCNM variables. Most of this variation (12%) corresponded to pure environmental and spatially environmental structure. The data indicated that (1) spatial legacy was not important in explaining the web-spider beta diversity; (2) environmental predictors explained a significant portion of the variation in web-spider composition; (3) one-third of environmental variation was due to a spatial structure that jointly explains variation in species distributions. We were able to detect important factors related to matrix management influencing the web-spider beta-diversity patterns, which are probably linked to historical deforestation events.

Scale dependency of forest functional diversity assessed using imaging spectroscopy and airborne laser scanning

NASA Astrophysics Data System (ADS)

Schneider, F. D.; Morsdorf, F.; Schmid, B.; Petchey, O. L.; Hueni, A.; Schimel, D.; Schaepman, M. E.

2016-12-01

Forest functional traits offer a mechanistic link between ecological processes and community structure and assembly rules. However, measuring functional traits of forests in a continuous and consistent way is particularly difficult due to the complexity of in-situ measurements and geo-referencing. New imaging spectroscopy measurements overcome these limitations allowing to map physiological traits on broad spatial scales. We mapped leaf chlorophyll, carotenoids and leaf water content over 900 ha of temperate mixed forest (Fig. 1a). The selected traits are functionally important because they are indicating the photosynthetic potential of trees, leaf longevity and protection, as well as tree water and drought stress. Spatially continuous measurements on the scale of individual tree crowns allowed to assess functional diversity patterns on a range of ecological extents. We used indexes of functional richness, divergence and evenness to map different aspects of diversity. Fig. 1b shows an example of physiological richness at an extent of 240 m radius. We compared physiological to morphological diversity patterns, derived based on plant area index, canopy height and foliage height diversity. Our results show that patterns of physiological and morphological diversity generally agree, independently measured by airborne imaging spectroscopy and airborne laser scanning, respectively. The occurrence of disturbance areas and mixtures of broadleaf and needle trees were the main drivers of the observed diversity patterns. Spatial patterns at varying extents and richness-area relationships indicated that environmental filtering is the predominant community assembly process. Our results demonstrate the potential for mapping physiological and morphological diversity in a temperate mixed forest between and within species on scales relevant to study community assembly and structure from space and test the corresponding measurement schemes.

A MULTI-LOCUS, MULTI-TAXA PHYLOGEOGRAPHICAL ANALYSIS OF GENETIC DIVERSITY

EPA Science Inventory

In addition to measuring spatial patterns of genetic diversity, population genetic measures of biological resources should include temporal data that indicate whether the observed patterns are the result of historical or contemporary processes. In general, genetic measures focus...

A modeling study of the impacts of Mississippi River diversion and sea-level rise on water quality of a deltaic estuary

USGS Publications Warehouse

Wang, Hongqing; Chen, Qin; Hu, Kelin; LaPeyre, Megan K.

2017-01-01

Freshwater and sediment management in estuaries affects water quality, particularly in deltaic estuaries. Furthermore, climate change-induced sea-level rise (SLR) and land subsidence also affect estuarine water quality by changing salinity, circulation, stratification, sedimentation, erosion, residence time, and other physical and ecological processes. However, little is known about how the magnitudes and spatial and temporal patterns in estuarine water quality variables will change in response to freshwater and sediment management in the context of future SLR. In this study, we applied the Delft3D model that couples hydrodynamics and water quality processes to examine the spatial and temporal variations of salinity, total suspended solids, and chlorophyll-α concentration in response to small (142 m3 s−1) and large (7080 m3 s−1) Mississippi River (MR) diversions under low (0.38 m) and high (1.44 m) relative SLR (RSLR = eustatic SLR + subsidence) scenarios in the Breton Sound Estuary, Louisiana, USA. The hydrodynamics and water quality model were calibrated and validated via field observations at multiple stations across the estuary. Model results indicate that the large MR diversion would significantly affect the magnitude and spatial and temporal patterns of the studied water quality variables across the entire estuary, whereas the small diversion tends to influence water quality only in small areas near the diversion. RSLR would also play a significant role on the spatial heterogeneity in estuary water quality by acting as an opposite force to river diversions; however, RSLR plays a greater role than the small-scale diversion on the magnitude and spatial pattern of the water quality parameters in this deltaic estuary.

Modeling α- and β-diversity in a tropical forest from remotely sensed and spatial data

NASA Astrophysics Data System (ADS)

Hernández-Stefanoni, J. Luis; Gallardo-Cruz, J. Alberto; Meave, Jorge A.; Rocchini, Duccio; Bello-Pineda, Javier; López-Martínez, J. Omar

2012-10-01

Comprehensive information on species distribution and species composition patterns of plant communities is required for effective conservation and management of biodiversity. Remote sensing offers an inexpensive means of attaining complete spatial coverage for large areas, at regular time intervals, and can therefore be extremely useful for estimating both species richness and spatial variation of species composition (α- and β-diversity). An essential step to map such attributes is to identify and understand their main drivers. We used remotely sensed data as a surrogate of plant productivity and habitat structure variables for explaining α- and β-diversity, and evaluated the relative roles of productivity-habitat structure and spatial variables in explaining observed patterns of α- and β-diversity by using a Principal Coordinates of Neighbor Matrices analysis. We also examined the relationship between remotely sensed and field data, in order to map α- and β-diversity at the landscape-level in the Yucatan Peninsula, using a regression kriging procedure. These two procedures integrate the relationship of species richness and spatial species turnover both with remotely sensed data and spatial structure. The empirical models so obtained can be used to predict species richness and variation in species composition, and they can be regarded as valuable tools not only for identifying areas with high local species richness (α-diversity), but also areas with high species turnover (β-diversity). Ultimately, information obtained in this way can help maximize the number of species preserved in a landscape.

Demographic mechanisms underpinning genetic assimilation of remnant groups of a large carnivore

USGS Publications Warehouse

Mikle, Nathaniel; Graves, Tabitha A.; Kovach, Ryan P.; Kendall, Katherine C.; Macleod, Amy C.

2016-01-01

Current range expansions of large terrestrial carnivores are occurring following human-induced range contraction. Contractions are often incomplete, leaving small remnant groups in refugia throughout the former range. Little is known about the underlying ecological and evolutionary processes that influence how remnant groups are affected during range expansion. We used data from a spatially explicit, long-term genetic sampling effort of grizzly bears (Ursus arctos) in the Northern Continental Divide Ecosystem (NCDE), USA, to identify the demographic processes underlying spatial and temporal patterns of genetic diversity. We conducted parentage analysis to evaluate how reproductive success and dispersal contribute to spatio-temporal patterns of genetic diversity in remnant groups of grizzly bears existing in the southwestern (SW), southeastern (SE) and east-central (EC) regions of the NCDE. A few reproductively dominant individuals and local inbreeding caused low genetic diversity in peripheral regions that may have persisted for multiple generations before eroding rapidly (approx. one generation) during population expansion. Our results highlight that individual-level genetic and reproductive dynamics play critical roles during genetic assimilation, and show that spatial patterns of genetic diversity on the leading edge of an expansion may result from historical demographic patterns that are highly ephemeral.

Demographic mechanisms underpinning genetic assimilation of remnant groups of a large carnivore

PubMed Central

Kovach, Ryan; Kendall, Katherine C.; Macleod, Amy C.

2016-01-01

Current range expansions of large terrestrial carnivores are occurring following human-induced range contraction. Contractions are often incomplete, leaving small remnant groups in refugia throughout the former range. Little is known about the underlying ecological and evolutionary processes that influence how remnant groups are affected during range expansion. We used data from a spatially explicit, long-term genetic sampling effort of grizzly bears (Ursus arctos) in the Northern Continental Divide Ecosystem (NCDE), USA, to identify the demographic processes underlying spatial and temporal patterns of genetic diversity. We conducted parentage analysis to evaluate how reproductive success and dispersal contribute to spatio-temporal patterns of genetic diversity in remnant groups of grizzly bears existing in the southwestern (SW), southeastern (SE) and east-central (EC) regions of the NCDE. A few reproductively dominant individuals and local inbreeding caused low genetic diversity in peripheral regions that may have persisted for multiple generations before eroding rapidly (approx. one generation) during population expansion. Our results highlight that individual-level genetic and reproductive dynamics play critical roles during genetic assimilation, and show that spatial patterns of genetic diversity on the leading edge of an expansion may result from historical demographic patterns that are highly ephemeral. PMID:27655768

Patterns of fish community composition along a river affected by agricultural and urban disturbance in south-central Chile

DOE Office of Scientific and Technical Information (OSTI.GOV)

Orrego, Rodrigo; Barra, Ricardo; Chiang, Gustavo

2008-03-01

Patterns of fish community composition in a south-central Chile river were investigated along the altitudinal-spatial and environmental gradient and as a function of anthropogenic factors. The spatial pattern of fish communities in different biocoenotic zones of the Chillan River is influenced by both natural factors such a hydrologic features, habitat, and feeding types, and also by water quality variables which can reduce the diversity and abundance of sensitive species. A principal component analysis incorporating both water quality parameters and biomarker responses of representative fish species was used to evaluate the status of fish communities along the spatial gradient of themore » stream. The abundance and diversity of the fish community changed from a low in the upper reaches where the low pollution-tolerant species such as salmonid dominated, to a reduced diversity in the lower reaches of the river where tolerant browser species such as cypriniformes dominated. Even though the spatial pattern of fish community structure is similar to that found for the Chilean Rivers, the structure of these communities is highly influenced by human disturbance, particularly along the lower reaches of the river.« less

The rich get richer: Patterns of plant invasions in the United States

USGS Publications Warehouse

Stohlgren, T.J.; Barnett, D.T.; Kartesz, J.T.

2003-01-01

Observations from islands, small-scale experiments, and mathematical models have generally supported the paradigm that habitats of low plant diversity are more vulnerable to plant invasions than areas of high plant diversity. We summarize two independent data sets to show exactly the opposite pattern at multiple spatial scales. More significant, and alarming, is that hotspots of native plant diversity have been far more heavily invaded than areas of low plant diversity in most parts of the United States when considered at larger spatial scales. Our findings suggest that we cannot expect such hotspots to repel invasions, and that the threat of invasion is significant and predictably greatest in these areas.

Temporally variable environments maintain more beta-diversity in Mediterranean landscapes

NASA Astrophysics Data System (ADS)

Martin, Beatriz; Ferrer, Miguel

2015-10-01

We examined the relationships between different environmental factors and the alpha and beta-diversity of terrestrial vertebrates (birds, mammals, amphibians and reptiles) in a Mediterranean region at the landscape level. We investigated whether the mechanisms underlying alpha and beta-diversity patterns are influenced by energy availability, habitat heterogeneity and temporal variability and if the drivers of the diversity patterns differed between both components of diversity. We defined alpha-diversity as synonym of species richness whereas beta-diversity was measured as distinctiveness. We evaluated a total of 13 different predictors using generalized linear mixed model (GLMM) analysis. Habitat spatial heterogeneity increased alpha-diversity, but contrastingly, it did not significantly affect beta-diversity among sites. Disturbed landscapes may show higher habitat spatial variation and higher alpha-diversity due to the contribution of highly generalist species that are wide-distributed and do not differ in composition (beta-diversity) among different sites within the region. Contrastingly, higher beta-diversity levels were negatively related to more stable sites in terms of temporal environmental variation. This negative relationship between environmental stability and beta-diversity levels is explained in terms of species adaptation to the local environmental conditions. Our study highlights the importance of temporal environmental variability in maintaining beta-diversity patterns under highly variable environmental conditions.

Contrasting spatial patterns in active-fire and fire-suppressed Mediterranean climate old-growth mixed conifer forests

Treesearch

Danny L. Fry; Scott L. Stephens; Brandon M. Collins; Malcolm North; Ernesto Franco-Vizcaino; Samantha J. Gill

2014-01-01

In Mediterranean environments in western North America, historic fire regimes in frequent-fire conifer forests are highly variable both temporally and spatially. This complexity influenced forest structure and spatial patterns, but some of this diversity has been lost due to anthropogenic disruption of ecosystem processes, including fire. Information from reference...

Implications of recurrent disturbance for genetic diversity.

PubMed

Davies, Ian D; Cary, Geoffrey J; Landguth, Erin L; Lindenmayer, David B; Banks, Sam C

2016-02-01

Exploring interactions between ecological disturbance, species' abundances and community composition provides critical insights for ecological dynamics. While disturbance is also potentially an important driver of landscape genetic patterns, the mechanisms by which these patterns may arise by selective and neutral processes are not well-understood. We used simulation to evaluate the relative importance of disturbance regime components, and their interaction with demographic and dispersal processes, on the distribution of genetic diversity across landscapes. We investigated genetic impacts of variation in key components of disturbance regimes and spatial patterns that are likely to respond to climate change and land management, including disturbance size, frequency, and severity. The influence of disturbance was mediated by dispersal distance and, to a limited extent, by birth rate. Nevertheless, all three disturbance regime components strongly influenced spatial and temporal patterns of genetic diversity within subpopulations, and were associated with changes in genetic structure. Furthermore, disturbance-induced changes in temporal population dynamics and the spatial distribution of populations across the landscape resulted in disrupted isolation by distance patterns among populations. Our results show that forecast changes in disturbance regimes have the potential to cause major changes to the distribution of genetic diversity within and among populations. We highlight likely scenarios under which future changes to disturbance size, severity, or frequency will have the strongest impacts on population genetic patterns. In addition, our results have implications for the inference of biological processes from genetic data, because the effects of dispersal on genetic patterns were strongly mediated by disturbance regimes.

Spatial extent of analysis influences observed patterns of population genetic structure in a widespread darter species (Percidae)

USGS Publications Warehouse

Argentina, Jane E.; Angermeier, Paul L.; Hallerman, Eric M.; Welsh, Stuart A.

2018-01-01

Connectivity among stream fish populations allows for exchange of genetic material and helps maintain genetic diversity, adaptive potential and population stability over time. Changes in species demographics and population connectivity have the potential to permanently alter the genetic patterns of stream fish, although these changes through space and time are variable and understudied in small‐bodied freshwater fish.As a spatially widespread, common species of benthic freshwater fish, the variegate darter (Etheostoma variatum) is a model species for documenting how patterns of genetic structure and diversity respond to increasing isolation due to large dams and how scale of study may shape our understanding of these patterns. We sampled variegate darters from 34 sites across their range in the North American Ohio River basin and examined how patterns of genetic structure and diversity within and between populations responded to historical population changes and dams within and between populations.Spatial scale and configuration of genetic structure varied across the eight identified populations, from tributaries within a watershed, to a single watershed, to multiple watersheds that encompass Ohio River mainstem habitats. This multiwatershed pattern of population structuring suggests genetic dispersal across large distances was and may continue to be common, although some populations remain isolated despite no apparent structural dispersal barriers. Populations with low effective population sizes and evidence of past population bottlenecks showed low allelic richness, but diversity patterns were not related to watershed size, a surrogate for habitat availability. Pairwise genetic differentiation (FST) increased with fluvial distance and was related to both historic and contemporary processes. Genetic diversity changes were influenced by underlying population size and stability, and while instream barriers were not strong determinants of genetic structuring or loss of genetic diversity, they reduce population connectivity and may impact long‐term population persistence.The broad spatial scale of this study demonstrated the large spatial extent of some variegate darter populations and indicated that dispersal is more extensive than expected given the movement patterns typically observed for small‐bodied, benthic fish. Dam impacts depended on underlying population size and stability, with larger populations more resilient to genetic drift and allelic richness loss than smaller populations.Other darters that inhabit large river habitats may show similar patterns in landscape‐scale studies, and large river barriers may impact populations of small‐bodied fish more than previously expected. Estimation of dispersal rates and behaviours is critical to conservation of imperilled riverine species such as darters.

Fish assemblage in a semi-arid Neotropical reservoir: composition, structure and patterns of diversity and abundance.

PubMed

Novaes, J L C; Moreira, S I L; Freire, C E C; Sousa, M M O; Costa, R S

2014-05-01

The aim of this study was to analyse the composition, structure and spatial and temporal patterns of diversity and abundance of the ichthyofauna of the Santa Cruz Reservoir in semi-arid Brazil. Data were collected quarterly at eight sampling locations on the reservoir between February 2010 and November 2011 using gillnets from 12- to 70-mm mesh that were left in the water for 12h00min during the night. We evaluated the composition, structure and assemblage descriptors (Shannon-Wiener diversity index and equitability, respectively) and catch per unit effort by the number (CPUEn) and biomass (CPUEb) of the ichthyofauna. The 6,047 individuals (399,211.6 g) captured represented three orders, ten families and 20 species, of which four belonged to introduced species. The family Characidae was the most abundant with a total of 2,772 (45.8%) individuals captured. The species-abundance curve fit the log-normal model. In the spatial analysis of diversity, there were significant differences between sampling sites in the lacustrine and fluvial regions, and the highest values were found in the lacustrine region. In the temporal analysis of diversity, significant differences were also observed between the rainy and dry seasons, and the higher values were found during the dry season. Equitability followed the same spatiotemporal pattern as diversity. The Spearman correlation was significantly negative between diversity and rainfall. A cluster analysis spatially separated the ichthyofauna into two groups: one group formed by sampling sites in the fluvial region and another group formed by the remainder of the points in the lacustrine region. Both the CPUEn and CPUEb values were higher at point 8 (fluvial region) and during the rainy season. A two-way ANOVA showed that the CPUEn and CPUEb values were spatially and temporally significant. We conclude that the spatial and temporal trends of diversity in the Santa Cruz reservoir differ from those of other Brazilian reservoirs but that the fish community composition and spatiotemporal patterns of abundance were similar.

Additive Partitioning of Coral Reef Fish Diversity across Hierarchical Spatial Scales throughout the Caribbean

PubMed Central

Francisco-Ramos, Vanessa; Arias-González, Jesús Ernesto

2013-01-01

There is an increasing need to examine regional patterns of diversity in coral-reef systems since their biodiversity is declining globally. In this sense, additive partitioning might be useful since it quantifies the contribution of alpha and beta to total diversity across different scales. We applied this approach using an unbalanced design across four hierarchical scales (80 sites, 22 subregions, six ecoregions, and the Caribbean basin). Reef-fish species were compiled from the Reef Environmental Education Foundation (REEF) database and distributions were confirmed with published data. Permutation tests were used to compare observed values to those expected by chance. The primary objective was to identify patterns of reef-fish diversity across multiple spatial scales under different scenarios, examining factors such as fisheries and demographic connectivity. Total diversity at the Caribbean scale was attributed to β-diversity (nearly 62% of the species), with the highest β-diversity at the site scale. α¯-diversity was higher than expected by chance in all scenarios and at all studied scales. This suggests that fish assemblages are more homogenous than expected, particularly at the ecoregion scale. Within each ecoregion, diversity was mainly attributed to alpha, except for the Southern ecoregion where there was a greater difference in species among sites. β-components were lower than expected in all ecoregions, indicating that fishes within each ecoregion are a subsample of the same species pool. The scenario involving the effects of fisheries showed a shift in dominance for β-diversity from regions to subregions, with no major changes to the diversity patterns. In contrast, demographic connectivity partially explained the diversity pattern. β-components were low within connectivity regions and higher than expected by chance when comparing between them. Our results highlight the importance of ecoregions as a spatial scale to conserve local and regional coral reef-fish diversity. PMID:24205311

Spatial patterns of littoral zooplankton assemblages along a salinity gradient in a brackish sea: A functional diversity perspective

NASA Astrophysics Data System (ADS)

Helenius, Laura K.; Leskinen, Elina; Lehtonen, Hannu; Nurminen, Leena

2017-11-01

The distribution patterns and diversity of littoral zooplankton are both key baseline information for understanding the functioning of coastal ecosystems, and for identifying the mechanisms by which the impacts of recently increased eutrophication are transferred through littoral food webs. In this study, zooplankton community structure and diversity along a shallow coastal area of the northern Baltic Sea were determined in terms of horizontal environmental gradients. Spatial heterogeneity of the zooplankton community was examined along the gradient. Altogether 31 sites in shallow sandy bays on the coast of southwest Finland were sampled in the summer periods of 2009 and 2010 for zooplankton and environmental variables (surface water temperature, salinity, turbidity, wave exposure, macrophyte coverage, chlorophyll a and nutrients). Zooplankton diversity was measured as both taxonomic as well as functional diversity, using trait-based classification of planktonic crustaceans. Salinity, and to a lesser extent turbidity and temperature, were found to be the main predictors of the spatial patterns and functional diversity of the zooplankton community. Occurrence of cyclopoid copepods, as well as abundances of the calanoid copepod genus Acartia and the rotifer genus Keratella were found to be key factors in differentiating sites along the gradient. As far as we know, this is the first extensive study of functional diversity in Baltic Sea coastal zooplankton communities.

Dispersal responses override density effects on genetic diversity during post-disturbance succession

PubMed Central

Landguth, Erin L.; Bull, C. Michael; Banks, Sam C.; Gardner, Michael G.; Driscoll, Don A.

2016-01-01

Dispersal fundamentally influences spatial population dynamics but little is known about dispersal variation in landscapes where spatial heterogeneity is generated predominantly by disturbance and succession. We tested the hypothesis that habitat succession following fire inhibits dispersal, leading to declines over time in genetic diversity in the early successional gecko Nephrurus stellatus. We combined a landscape genetics field study with a spatially explicit simulation experiment to determine whether successional patterns in genetic diversity were driven by habitat-mediated dispersal or demographic effects (declines in population density leading to genetic drift). Initial increases in genetic structure following fire were likely driven by direct mortality and rapid population expansion. Subsequent habitat succession increased resistance to gene flow and decreased dispersal and genetic diversity in N. stellatus. Simulated changes in population density alone did not reproduce these results. Habitat-mediated reductions in dispersal, combined with changes in population density, were essential to drive the field-observed patterns. Our study provides a framework for combining demographic, movement and genetic data with simulations to discover the relative influence of demography and dispersal on patterns of landscape genetic structure. Our results suggest that succession can inhibit connectivity among individuals, opening new avenues for understanding how disturbance regimes influence spatial population dynamics. PMID:27009225

Habitat history improves prediction of biodiversity in rainforest fauna

PubMed Central

Graham, Catherine H.; Moritz, Craig; Williams, Stephen E.

2006-01-01

Patterns of biological diversity should be interpreted in light of both contemporary and historical influences; however, to date, most attempts to explain diversity patterns have largely ignored history or have been unable to quantify the influence of historical processes. The historical effects on patterns of diversity have been hypothesized to be most important for taxonomic groups with poor dispersal abilities. We quantified the relative stability of rainforests over the late Quaternary period by modeling rainforest expansion and contraction in 21 biogeographic subregions in northeast Australia across four time periods. We demonstrate that historical habitat stability can be as important, and in endemic low-dispersal taxa even more important, than current habitat area in explaining spatial patterns of species richness. In contrast, patterns of endemic species richness for taxa with high dispersal capacity are best predicted by using current environmental parameters. We also show that contemporary patterns of species turnover across the region are best explained by historical patterns of habitat connectivity. These results clearly demonstrate that spatially explicit analyses of the historical processes of persistence and colonization are both effective and necessary for understanding observed patterns of biodiversity. PMID:16407139

A STATISTICAL THERMODYNAMIC MODEL OF THE ORGANIZATIONAL ORDER OF VEGETATION. (R827676)

EPA Science Inventory

The complex pattern of vegetation is the macroscopic manifestation of biological diversity and the ecological order in space and time. How is this overwhelmingly diverse, yet wonderfully ordered spatial pattern formed, and how does it evolve? To answer these questions, most tr...

Modeling Effects of Local Extinctions on Culture Change and Diversity in the Paleolithic

PubMed Central

Premo, L. S.; Kuhn, Steven L.

2010-01-01

The persistence of early stone tool technologies has puzzled archaeologists for decades. Cognitively based explanations, which presume either lack of ability to innovate or extreme conformism, do not account for the totality of the empirical patterns. Following recent research, this study explores the effects of demographic factors on rates of culture change and diversification. We investigate whether the appearance of stability in early Paleolithic technologies could result from frequent extinctions of local subpopulations within a persistent metapopulation. A spatially explicit agent-based model was constructed to test the influence of local extinction rate on three general cultural patterns that archaeologists might observe in the material record: total diversity, differentiation among spatially defined groups, and the rate of cumulative change. The model shows that diversity, differentiation, and the rate of cumulative cultural change would be strongly affected by local extinction rates, in some cases mimicking the results of conformist cultural transmission. The results have implications for understanding spatial and temporal patterning in ancient material culture. PMID:21179418

Spatial Distribution Patterns in the Very Rare and Species-Rich Picea chihuahuana Tree Community (Mexico).

PubMed

Wehenkel, Christian; Brazão-Protázio, João Marcelo; Carrillo-Parra, Artemio; Martínez-Guerrero, José Hugo; Crecente-Campo, Felipe

2015-01-01

The very rare Mexican Picea chihuahuana tree community covers an area of no more than 300 ha in the Sierra Madre Occidental. This special tree community has been the subject of several studies aimed at learning more about the genetic structure and ecology of the species and the potential effects of climate change. The spatial distribution of trees is a result of many ecological processes and can affect the degree of competition between neighbouring trees, tree density, variability in size and distribution, regeneration, survival, growth, mortality, crown formation and the biological diversity within forest communities. Numerous scale-dependent measures have been established in order to describe spatial forest structure. The overall aim of most of these studies has been to obtain data to help design preservation and conservation strategies. In this study, we examined the spatial distribution pattern of trees in the P. chihuahuana tree community in 12 localities, in relation to i) tree stand density, ii) diameter distribution (vertical structure), iii) tree species diversity, iv) geographical latitude and v) tree dominance at a fine scale (in 0.25 ha plots), with the aim of obtaining a better understanding of the complex ecosystem processes and biological diversity. Because of the strongly mixed nature of this tree community, which often produces low population densities of each tree species and random tree fall gaps caused by tree death, we expect aggregated patterns in individual Picea chihuahuana trees and in the P. chihuahuana tree community, repulsive Picea patterns to other tree species and repulsive patterns of young to adult trees. Each location was represented by one plot of 50 x 50 m (0.25 ha) established in the centre of the tree community. The findings demonstrate that the hypothesis of aggregated tree pattern is not applicable to the mean pattern measured by Clark-Evans index, Uniform Angle index and Mean Directional index of the uneven-aged P. chihuahuana trees and P. chihuahuana tree community and but to specific spatial scales measured by the univariate L-function. The spatial distribution pattern of P. chihuahuana trees was found to be independent of patches of other tree species measured by the bivariate L-function. The spatial distribution was not significantly related to tree density, diameter distribution or tree species diversity. The index of Clark and Evans decreased significantly from the southern to northern plots containing all tree species. Self-thinning due to intra and inter-specific competition-induced mortality is probably the main cause of the decrease in aggregation intensity during the course of population development in this tree community. We recommend the use of larger sampling plots (> 0.25 ha) in uneven-aged and species-rich forest ecosystems to detect less obvious, but important, relationships between spatial tree pattern and functioning and diversity in these forests.

Spatial Distribution Patterns in the Very Rare and Species-Rich Picea chihuahuana Tree Community (Mexico)

PubMed Central

Wehenkel, Christian; Brazão-Protázio, João Marcelo; Carrillo-Parra, Artemio; Martínez-Guerrero, José Hugo; Crecente-Campo, Felipe

2015-01-01

The very rare Mexican Picea chihuahuana tree community covers an area of no more than 300 ha in the Sierra Madre Occidental. This special tree community has been the subject of several studies aimed at learning more about the genetic structure and ecology of the species and the potential effects of climate change. The spatial distribution of trees is a result of many ecological processes and can affect the degree of competition between neighbouring trees, tree density, variability in size and distribution, regeneration, survival, growth, mortality, crown formation and the biological diversity within forest communities. Numerous scale-dependent measures have been established in order to describe spatial forest structure. The overall aim of most of these studies has been to obtain data to help design preservation and conservation strategies. In this study, we examined the spatial distribution pattern of trees in the P. chihuahuana tree community in 12 localities, in relation to i) tree stand density, ii) diameter distribution (vertical structure), iii) tree species diversity, iv) geographical latitude and v) tree dominance at a fine scale (in 0.25 ha plots), with the aim of obtaining a better understanding of the complex ecosystem processes and biological diversity. Because of the strongly mixed nature of this tree community, which often produces low population densities of each tree species and random tree fall gaps caused by tree death, we expect aggregated patterns in individual Picea chihuahuana trees and in the P. chihuahuana tree community, repulsive Picea patterns to other tree species and repulsive patterns of young to adult trees. Each location was represented by one plot of 50 x 50 m (0.25 ha) established in the centre of the tree community. The findings demonstrate that the hypothesis of aggregated tree pattern is not applicable to the mean pattern measured by Clark-Evans index, Uniform Angle index and Mean Directional index of the uneven-aged P. chihuahuana trees and P. chihuahuana tree community and but to specific spatial scales measured by the univariate L-function. The spatial distribution pattern of P. chihuahuana trees was found to be independent of patches of other tree species measured by the bivariate L-function. The spatial distribution was not significantly related to tree density, diameter distribution or tree species diversity. The index of Clark and Evans decreased significantly from the southern to northern plots containing all tree species. Self-thinning due to intra and inter-specific competition-induced mortality is probably the main cause of the decrease in aggregation intensity during the course of population development in this tree community. We recommend the use of larger sampling plots (> 0.25 ha) in uneven-aged and species-rich forest ecosystems to detect less obvious, but important, relationships between spatial tree pattern and functioning and diversity in these forests. PMID:26496189

Latitude delineates patterns of biogeography in terrestrial Streptomyces.

PubMed

Choudoir, Mallory J; Doroghazi, James R; Buckley, Daniel H

2016-12-01

The biogeography of Streptomyces was examined at regional spatial scales to identify factors that govern patterns of microbial diversity. Streptomyces are spore forming filamentous bacteria which are widespread in soil. Streptomyces strains were isolated from perennial grass habitats sampled across a spatial scale of more than 6000 km. Previous analysis of this geographically explicit culture collection provided evidence for a latitudinal diversity gradient in Streptomyces species. Here the hypothesis that this latitudinal diversity gradient is a result of evolutionary dynamics associated with historical demographic processes was evaluated. Historical demographic phenomena have genetic consequences that can be evaluated through analysis of population genetics. Population genetic approaches were applied to analyze population structure in six of the most numerically abundant and geographically widespread Streptomyces phylogroups from our culture collection. Streptomyces population structure varied at regional spatial scales, and allelic diversity correlated with geographic distance. In addition, allelic diversity and gene flow are partitioned by latitude. Finally, it was found that nucleotide diversity within phylogroups was negatively correlated with latitude. These results indicate that phylogroup diversification is constrained by dispersal limitation at regional spatial scales, and they are consistent with the hypothesis that historical demographic processes have influenced the contemporary biogeography of Streptomyces. © 2016 Society for Applied Microbiology and John Wiley & Sons Ltd.

Baseflow physical characteristics differ at multiple spatial scales in stream networks across diverse biomes

Treesearch

Janine Ruegg; Walter K. Dodds; Melinda D. Daniels; Ken R. Sheehan; Christina L. Baker; William B. Bowden; Kaitlin J. Farrell; Michael B. Flinn; Tamara K. Harms; Jeremy B. Jones; Lauren E. Koenig; John S. Kominoski; William H. McDowell; Samuel P. Parker; Amy D. Rosemond; Matt T. Trentman; Matt Whiles; Wilfred M. Wollheim

2016-01-01

ContextSpatial scaling of ecological processes is facilitated by quantifying underlying habitat attributes. Physical and ecological patterns are often measured at disparate spatial scales limiting our ability to quantify ecological processes at broader spatial scales using physical attributes.

The assembly of ecological communities inferred from taxonomic and functional composition

Treesearch

Eric R. Sokol; E.F. Benfield; Lisa K. Belden; H. Maurice. Valett

2011-01-01

Among-site variation in metacommunities (beta diversity) is typically correlated with the distance separating the sites (spatial lag). This distance decay in similarity pattern has been linked to both niche-based and dispersal-based community assembly hypotheses. Here we show that beta diversity patterns in community composition, when supplemented with functional-trait...

The beta-diversity of species interactions: Untangling the drivers of geographic variation in plant-pollinator diversity and function across scales.

PubMed

Burkle, Laura A; Myers, Jonathan A; Belote, R Travis

2016-01-01

Geographic patterns of biodiversity have long inspired interest in processes that shape the assembly, diversity, and dynamics of communities at different spatial scales. To study mechanisms of community assembly, ecologists often compare spatial variation in community composition (beta-diversity) across environmental and spatial gradients. These same patterns inspired evolutionary biologists to investigate how micro- and macro-evolutionary processes create gradients in biodiversity. Central to these perspectives are species interactions, which contribute to community assembly and geographic variation in evolutionary processes. However, studies of beta-diversity have predominantly focused on single trophic levels, resulting in gaps in our understanding of variation in species-interaction networks (interaction beta-diversity), especially at scales most relevant to evolutionary studies of geographic variation. We outline two challenges and their consequences in scaling-up studies of interaction beta-diversity from local to biogeographic scales using plant-pollinator interactions as a model system in ecology, evolution, and conservation. First, we highlight how variation in regional species pools may contribute to variation in interaction beta-diversity among biogeographic regions with dissimilar evolutionary history. Second, we highlight how pollinator behavior (host-switching) links ecological networks to geographic patterns of plant-pollinator interactions and evolutionary processes. Third, we outline key unanswered questions regarding the role of geographic variation in plant-pollinator interactions for conservation and ecosystem services (pollination) in changing environments. We conclude that the largest advances in the burgeoning field of interaction beta-diversity will come from studies that integrate frameworks in ecology, evolution, and conservation to understand the causes and consequences of interaction beta-diversity across scales. © 2016 Botanical Society of America.

Nematode Spatial and Ecological Patterns from Tropical and Temperate Rainforests

PubMed Central

Porazinska, Dorota L.; Giblin-Davis, Robin M.; Powers, Thomas O.; Thomas, W. Kelley

2012-01-01

Large scale diversity patterns are well established for terrestrial macrobiota (e.g. plants and vertebrates), but not for microscopic organisms (e.g. nematodes). Due to small size, high abundance, and extensive dispersal, microbiota are assumed to exhibit cosmopolitan distributions with no biogeographical patterns. This assumption has been extrapolated from local spatial scale studies of a few taxonomic groups utilizing morphological approaches. Recent molecularly-based studies, however, suggest something quite opposite. Nematodes are the most abundant metazoans on earth, but their diversity patterns are largely unknown. We conducted a survey of nematode diversity within three vertical strata (soil, litter, and canopy) of rainforests at two contrasting latitudes in the North American meridian (temperate: the Olympic National Forest, WA, U.S.A and tropical: La Selva Biological Station, Costa Rica) using standardized sampling designs and sample processing protocols. To describe nematode diversity, we applied an ecometagenetic approach using 454 pyrosequencing. We observed that: 1) nematode communities were unique without even a single common species between the two rainforests, 2) nematode communities were unique among habitats in both rainforests, 3) total species richness was 300% more in the tropical than in the temperate rainforest, 4) 80% of the species in the temperate rainforest resided in the soil, whereas only 20% in the tropics, 5) more than 90% of identified species were novel. Overall, our data provided no support for cosmopolitanism at both local (habitats) and large (rainforests) spatial scales. In addition, our data indicated that biogeographical patterns typical of macrobiota also exist for microbiota. PMID:22984536

Using climate, energy, and spatial-based hypotheses to interpret macroecological patterns of North America chelonians

USGS Publications Warehouse

Ennen, Joshua R.; Agha, Mickey; Matamoros, Wilfredo A.; Hazzard, Sarah C.; Lovich, Jeffrey E.

2016-01-01

Our study investigates how factors, such as latitude, productivity, and several environmental variables, influence contemporary patterns of the species richness in North American turtles. In particular, we test several hypotheses explaining broad-scale species richness patterns on several species richness data sets: (i) total turtles, (ii) freshwater turtles only, (iii) aquatic turtles, (iv) terrestrial turtles only, (v) Emydidae, and (vi) Kinosternidae. In addition to spatial data, we used a combination of 25 abiotic variables in spatial regression models to predict species richness patterns. Our results provide support for multiple hypotheses related to broad-scale patterns of species richness, and in particular, hypotheses related to climate, productivity, water availability, topography, and latitude. In general, species richness patterns were positively associated with temperature, precipitation, diversity of streams, coefficient of variation of elevation, and net primary productivity. We also found that North America turtles follow the general latitudinal diversity gradient pattern (i.e., increasing species richness towards equator) by exhibiting a negative association with latitude. Because of the incongruent results among our six data sets, our study highlights the importance of considering phylogenetic constraints and guilds when interpreting species richness patterns, especially for taxonomic groups that occupy a myriad of habitats.

Large-scale diversity of slope fishes: pattern inconsistency between multiple diversity indices.

PubMed

Gaertner, Jean-Claude; Maiorano, Porzia; Mérigot, Bastien; Colloca, Francesco; Politou, Chrissi-Yianna; Gil De Sola, Luis; Bertrand, Jacques A; Murenu, Matteo; Durbec, Jean-Pierre; Kallianiotis, Argyris; Mannini, Alessandro

2013-01-01

Large-scale studies focused on the diversity of continental slope ecosystems are still rare, usually restricted to a limited number of diversity indices and mainly based on the empirical comparison of heterogeneous local data sets. In contrast, we investigate large-scale fish diversity on the basis of multiple diversity indices and using 1454 standardized trawl hauls collected throughout the upper and middle slope of the whole northern Mediterranean Sea (36°3'- 45°7' N; 5°3'W - 28°E). We have analyzed (1) the empirical relationships between a set of 11 diversity indices in order to assess their degree of complementarity/redundancy and (2) the consistency of spatial patterns exhibited by each of the complementary groups of indices. Regarding species richness, our results contrasted both the traditional view based on the hump-shaped theory for bathymetric pattern and the commonly-admitted hypothesis of a large-scale decreasing trend correlated with a similar gradient of primary production in the Mediterranean Sea. More generally, we found that the components of slope fish diversity we analyzed did not always show a consistent pattern of distribution according either to depth or to spatial areas, suggesting that they are not driven by the same factors. These results, which stress the need to extend the number of indices traditionally considered in diversity monitoring networks, could provide a basis for rethinking not only the methodological approach used in monitoring systems, but also the definition of priority zones for protection. Finally, our results call into question the feasibility of properly investigating large-scale diversity patterns using a widespread approach in ecology, which is based on the compilation of pre-existing heterogeneous and disparate data sets, in particular when focusing on indices that are very sensitive to sampling design standardization, such as species richness.

Spatial organization of bacterial chromosomes

PubMed Central

Wang, Xindan; Rudner, David Z.

2014-01-01

Bacterial chromosomes are organized in stereotypical patterns that are faithfully and robustly regenerated in daughter cells. Two distinct spatial patterns were described almost a decade ago in our most tractable model organisms. In recent years, analysis of chromosome organization in a larger and more diverse set of bacteria and a deeper characterization of chromosome dynamics in the original model systems have provided a broader and more complete picture of both chromosome organization and the activities that generate the observed spatial patterns. Here, we summarize these different patterns highlighting similarities and differences and discuss the protein factors that help establish and maintain them. PMID:25460798

Seed dispersal increases local species richness and reduces spatial turnover of tropical tree seedlings

PubMed Central

Dunham, Amy E.; Duncan, Richard P.; Rogers, Haldre S.

2017-01-01

Dispersal is thought to be a key process underlying the high spatial diversity of tropical forests. Just how important dispersal is in structuring plant communities is nevertheless an open question because it is very difficult to isolate dispersal from other processes, and thereby measure its effect. Using a unique situation, the loss of vertebrate seed dispersers on the island of Guam and their presence on the neighboring islands of Saipan and Rota, we quantify the contribution of vertebrate seed dispersal to spatial patterns of diversity of tree seedlings in treefall gaps. The presence of vertebrate seed dispersers approximately doubled seedling species richness within canopy gaps and halved species turnover among gaps. Our study demonstrates that dispersal plays a key role in maintaining local and regional patterns of diversity, and highlights the potential for ongoing declines in vertebrate seed dispersers to profoundly alter tropical forest composition. PMID:28847937

Seed dispersal increases local species richness and reduces spatial turnover of tropical tree seedlings.

PubMed

Wandrag, Elizabeth M; Dunham, Amy E; Duncan, Richard P; Rogers, Haldre S

2017-10-03

Dispersal is thought to be a key process underlying the high spatial diversity of tropical forests. Just how important dispersal is in structuring plant communities is nevertheless an open question because it is very difficult to isolate dispersal from other processes, and thereby measure its effect. Using a unique situation, the loss of vertebrate seed dispersers on the island of Guam and their presence on the neighboring islands of Saipan and Rota, we quantify the contribution of vertebrate seed dispersal to spatial patterns of diversity of tree seedlings in treefall gaps. The presence of vertebrate seed dispersers approximately doubled seedling species richness within canopy gaps and halved species turnover among gaps. Our study demonstrates that dispersal plays a key role in maintaining local and regional patterns of diversity, and highlights the potential for ongoing declines in vertebrate seed dispersers to profoundly alter tropical forest composition.

Spatial reconstruction of single-cell gene expression data.

PubMed

Satija, Rahul; Farrell, Jeffrey A; Gennert, David; Schier, Alexander F; Regev, Aviv

2015-05-01

Spatial localization is a key determinant of cellular fate and behavior, but methods for spatially resolved, transcriptome-wide gene expression profiling across complex tissues are lacking. RNA staining methods assay only a small number of transcripts, whereas single-cell RNA-seq, which measures global gene expression, separates cells from their native spatial context. Here we present Seurat, a computational strategy to infer cellular localization by integrating single-cell RNA-seq data with in situ RNA patterns. We applied Seurat to spatially map 851 single cells from dissociated zebrafish (Danio rerio) embryos and generated a transcriptome-wide map of spatial patterning. We confirmed Seurat's accuracy using several experimental approaches, then used the strategy to identify a set of archetypal expression patterns and spatial markers. Seurat correctly localizes rare subpopulations, accurately mapping both spatially restricted and scattered groups. Seurat will be applicable to mapping cellular localization within complex patterned tissues in diverse systems.

Spatial reconstruction of single-cell gene expression

PubMed Central

Satija, Rahul; Farrell, Jeffrey A.; Gennert, David; Schier, Alexander F.; Regev, Aviv

2015-01-01

Spatial localization is a key determinant of cellular fate and behavior, but spatial RNA assays traditionally rely on staining for a limited number of RNA species. In contrast, single-cell RNA-seq allows for deep profiling of cellular gene expression, but established methods separate cells from their native spatial context. Here we present Seurat, a computational strategy to infer cellular localization by integrating single-cell RNA-seq data with in situ RNA patterns. We applied Seurat to spatially map 851 single cells from dissociated zebrafish (Danio rerio) embryos, inferring a transcriptome-wide map of spatial patterning. We confirmed Seurat’s accuracy using several experimental approaches, and used it to identify a set of archetypal expression patterns and spatial markers. Additionally, Seurat correctly localizes rare subpopulations, accurately mapping both spatially restricted and scattered groups. Seurat will be applicable to mapping cellular localization within complex patterned tissues in diverse systems. PMID:25867923

Twenty-million-year relationship between mammalian diversity and primary productivity

NASA Astrophysics Data System (ADS)

Fritz, Susanne A.; Eronen, Jussi T.; Schnitzler, Jan; Hof, Christian; Janis, Christine M.; Mulch, Andreas; Böhning-Gaese, Katrin; Graham, Catherine H.

2016-09-01

At global and regional scales, primary productivity strongly correlates with richness patterns of extant animals across space, suggesting that resource availability and climatic conditions drive patterns of diversity. However, the existence and consistency of such diversity-productivity relationships through geological history is unclear. Here we provide a comprehensive quantitative test of the diversity-productivity relationship for terrestrial large mammals through time across broad temporal and spatial scales. We combine >14,000 occurrences for 690 fossil genera through the Neogene (23-1.8 Mya) with regional estimates of primary productivity from fossil plant communities in North America and Europe. We show a significant positive diversity-productivity relationship through the 20-million-year record, providing evidence on unprecedented spatial and temporal scales that this relationship is a general pattern in the ecology and paleo-ecology of our planet. Further, we discover that genus richness today does not match the fossil relationship, suggesting that a combination of human impacts and Pleistocene climate variability has modified the 20-million-year ecological relationship by strongly reducing primary productivity and driving many mammalian species into decline or to extinction.

Partitioning the impact of environment and spatial structure on alpha and beta components of taxonomic, functional, and phylogenetic diversity in European ants.

PubMed

Arnan, Xavier; Cerdá, Xim; Retana, Javier

2015-01-01

We analyze the relative contribution of environmental and spatial variables to the alpha and beta components of taxonomic (TD), phylogenetic (PD), and functional (FD) diversity in ant communities found along different climate and anthropogenic disturbance gradients across western and central Europe, in order to assess the mechanisms structuring ant biodiversity. To this aim we calculated alpha and beta TD, PD, and FD for 349 ant communities, which included a total of 155 ant species; we examined 10 functional traits and phylogenetic relatedness. Variation partitioning was used to examine how much variation in ant diversity was explained by environmental and spatial variables. Autocorrelation in diversity measures and each trait's phylogenetic signal were also analyzed. We found strong autocorrelation in diversity measures. Both environmental and spatial variables significantly contributed to variation in TD, PD, and FD at both alpha and beta scales; spatial structure had the larger influence. The different facets of diversity showed similar patterns along environmental gradients. Environment explained a much larger percentage of variation in FD than in TD or PD. All traits demonstrated strong phylogenetic signals. Our results indicate that environmental filtering and dispersal limitations structure all types of diversity in ant communities. Strong dispersal limitations appear to have led to clustering of TD, PD, and FD in western and central Europe, probably because different historical and evolutionary processes generated different pools of species. Remarkably, these three facets of diversity showed parallel patterns along environmental gradients. Trait-mediated species sorting and niche conservatism appear to structure ant diversity, as evidenced by the fact that more variation was explained for FD and that all traits had strong phylogenetic signals. Since environmental variables explained much more variation in FD than in PD, functional diversity should be a better indicator of community assembly processes than phylogenetic diversity.

Fine-scale spatial patterns in the demersal fish and invertebrate community in a northwest Atlantic ecosystem

NASA Astrophysics Data System (ADS)

Malek, Anna J.; Collie, Jeremy S.; Gartland, James

2014-06-01

The abundance, biomass, diversity, and species composition of the demersal fish and invertebrate community in Rhode Island Sound and Block Island Sound, an area identified for offshore renewable energy development, were evaluated for spatial and seasonal structure. We conducted 58 otter trawls and 51 beam trawls in the spring, summer and fall of 2009-2012, and incorporated additional data from 88 otter trawls conducted by the Northeast Area Monitoring and Assessment Program. We used regionally-grouped abundance, biomass, diversity, and size spectra to assess spatial patterns in the aggregate fish community, and hierarchical cluster analysis to evaluate trends in species assemblages. Our analyses revealed coherent gradients in fish community biomass, diversity and species composition extending from inshore to offshore waters, as well as patterns related to the differing bathymetry of Rhode Island and Block Island Sounds. The fish communities around Block Island and Cox's Ledge are particularly diverse, suggesting that the proximity of hard bottom habitat may be important in structuring fish communities in this area. Species assemblages in Rhode Island and Block Island Sounds are characterized by a combination of piscivores (silver hake, summer flounder, spiny dogfish), benthivores (American lobster, black sea bass, Leucoraja spp. skates, scup) and planktivores (sea scallop), and exhibit geographic patterns that are persistent from year to year, yet variable by season. Such distributions reflect the cross-shelf migration of fish and invertebrate species in the spring and fall, highlighting the importance of considering seasonal fish behavior when planning construction schedules for offshore development projects. The fine spatial scale (10 s of kms) of this research makes it especially valuable for local marine spatial planning efforts by identifying local-scale patterns in fish community structure that will enable future assessment of the ecological impacts of offshore development. As such, this knowledge of the spatial and temporal structure of the demersal fish community in Rhode Island and Block Island Sounds will help to guide the placement of offshore structures so as to preserve the ecological and economic value of the area.

Estimating planktonic diversity through spatial dominance patterns in a model ocean.

PubMed

Soccodato, Alice; d'Ovidio, Francesco; Lévy, Marina; Jahn, Oliver; Follows, Michael J; De Monte, Silvia

2016-10-01

In the open ocean, the observation and quantification of biodiversity patterns is challenging. Marine ecosystems are indeed largely composed by microbial planktonic communities whose niches are affected by highly dynamical physico-chemical conditions, and whose observation requires advanced methods for morphological and molecular classification. Optical remote sensing offers an appealing complement to these in-situ techniques. Global-scale coverage at high spatiotemporal resolution is however achieved at the cost of restrained information on the local assemblage. Here, we use a coupled physical and ecological model ocean simulation to explore one possible metrics for comparing measures performed on such different scales. We show that a large part of the local diversity of the virtual plankton ecosystem - corresponding to what accessible by genomic methods - can be inferred from crude, but spatially extended, information - as conveyed by remote sensing. Shannon diversity of the local community is indeed highly correlated to a 'seascape' index, which quantifies the surrounding spatial heterogeneity of the most abundant functional group. The error implied in drastically reducing the resolution of the plankton community is shown to be smaller in frontal regions as well as in regions of intermediate turbulent energy. On the spatial scale of hundreds of kms, patterns of virtual plankton diversity are thus largely sustained by mixing communities that occupy adjacent niches. We provide a proof of principle that in the open ocean information on spatial variability of communities can compensate for limited local knowledge, suggesting the possibility of integrating in-situ and satellite observations to monitor biodiversity distribution at the global scale. Copyright © 2016 Elsevier B.V. All rights reserved.

Spatial Pattern of Standing Timber Value across the Brazilian Amazon

PubMed Central

Ahmed, Sadia E.; Ewers, Robert M.

2012-01-01

The Amazon is a globally important system, providing a host of ecosystem services from climate regulation to food sources. It is also home to a quarter of all global diversity. Large swathes of forest are removed each year, and many models have attempted to predict the spatial patterns of this forest loss. The spatial patterns of deforestation are determined largely by the patterns of roads that open access to frontier areas and expansion of the road network in the Amazon is largely determined by profit seeking logging activities. Here we present predictions for the spatial distribution of standing value of timber across the Amazon. We show that the patterns of timber value reflect large-scale ecological gradients, determining the spatial distribution of functional traits of trees which are, in turn, correlated with timber values. We expect that understanding the spatial patterns of timber value across the Amazon will aid predictions of logging movements and thus predictions of potential future road developments. These predictions in turn will be of great use in estimating the spatial patterns of deforestation in this globally important biome. PMID:22590520

Generation of Earth's First-Order Biodiversity Pattern

NASA Astrophysics Data System (ADS)

Krug, Andrew Z.; Jablonski, David; Valentine, James W.; Roy, Kaustuv

2009-02-01

The first-order biodiversity pattern on Earth today and at least as far back as the Paleozoic is the latitudinal diversity gradient (LDG), a decrease in richness of species and higher taxa from the equator to the poles. LDGs are produced by geographic trends in origination, extinction, and dispersal over evolutionary timescales, so that analyses of static patterns will be insufficient to reveal underlying processes. The fossil record of marine bivalve genera, a model system for the analysis of biodiversity dynamics over large temporal and spatial scales, shows that an origination and range-expansion gradient plays a major role in generating the LDG. Peak origination rates and peak diversities fall within the tropics, with range expansion out of the tropics the predominant spatial dynamic thereafter. The origination-diversity link occurs even in a "contrarian" group whose diversity peaks at midlatitudes, an exception proving the rule that spatial variations in origination are key to latitudinal diversity patterns. Extinction rates are lower in polar latitudes (≥60°) than in temperate zones and thus cannot create the observed gradient alone. They may, however, help to explain why origination and immigration are evidently damped in higher latitudes. We suggest that species require more resources in higher latitudes, for the seasonality of primary productivity increases by more than an order of magnitude from equatorial to polar regions. Higher-latitude species are generalists that, unlike potential immigrants, are adapted to garner the large share of resources required for incumbency in those regions. When resources are opened up by extinctions, lineages spread chiefly poleward and chiefly through speciation.

Generation of Earth's first-order biodiversity pattern.

PubMed

Krug, Andrew Z; Jablonski, David; Valentine, James W; Roy, Kaustuv

2009-01-01

The first-order biodiversity pattern on Earth today and at least as far back as the Paleozoic is the latitudinal diversity gradient (LDG), a decrease in richness of species and higher taxa from the equator to the poles. LDGs are produced by geographic trends in origination, extinction, and dispersal over evolutionary timescales, so that analyses of static patterns will be insufficient to reveal underlying processes. The fossil record of marine bivalve genera, a model system for the analysis of biodiversity dynamics over large temporal and spatial scales, shows that an origination and range-expansion gradient plays a major role in generating the LDG. Peak origination rates and peak diversities fall within the tropics, with range expansion out of the tropics the predominant spatial dynamic thereafter. The origination-diversity link occurs even in a "contrarian" group whose diversity peaks at midlatitudes, an exception proving the rule that spatial variations in origination are key to latitudinal diversity patterns. Extinction rates are lower in polar latitudes (> or =60 degrees ) than in temperate zones and thus cannot create the observed gradient alone. They may, however, help to explain why origination and immigration are evidently damped in higher latitudes. We suggest that species require more resources in higher latitudes, for the seasonality of primary productivity increases by more than an order of magnitude from equatorial to polar regions. Higher-latitude species are generalists that, unlike potential immigrants, are adapted to garner the large share of resources required for incumbency in those regions. When resources are opened up by extinctions, lineages spread chiefly poleward and chiefly through speciation.

Biodiversity patterns along ecological gradients: unifying β-diversity indices.

PubMed

Szava-Kovats, Robert C; Pärtel, Meelis

2014-01-01

Ecologists have developed an abundance of conceptions and mathematical expressions to define β-diversity, the link between local (α) and regional-scale (γ) richness, in order to characterize patterns of biodiversity along ecological (i.e., spatial and environmental) gradients. These patterns are often realized by regression of β-diversity indices against one or more ecological gradients. This practice, however, is subject to two shortcomings that can undermine the validity of the biodiversity patterns. First, many β-diversity indices are constrained to range between fixed lower and upper limits. As such, regression analysis of β-diversity indices against ecological gradients can result in regression curves that extend beyond these mathematical constraints, thus creating an interpretational dilemma. Second, despite being a function of the same measured α- and γ-diversity, the resultant biodiversity pattern depends on the choice of β-diversity index. We propose a simple logistic transformation that rids beta-diversity indices of their mathematical constraints, thus eliminating the possibility of an uninterpretable regression curve. Moreover, this transformation results in identical biodiversity patterns for three commonly used classical beta-diversity indices. As a result, this transformation eliminates the difficulties of both shortcomings, while allowing the researcher to use whichever beta-diversity index deemed most appropriate. We believe this method can help unify the study of biodiversity patterns along ecological gradients.

Biodiversity Patterns along Ecological Gradients: Unifying β-Diversity Indices

PubMed Central

Szava-Kovats, Robert C.; Pärtel, Meelis

2014-01-01

Ecologists have developed an abundance of conceptions and mathematical expressions to define β-diversity, the link between local (α) and regional-scale (γ) richness, in order to characterize patterns of biodiversity along ecological (i.e., spatial and environmental) gradients. These patterns are often realized by regression of β-diversity indices against one or more ecological gradients. This practice, however, is subject to two shortcomings that can undermine the validity of the biodiversity patterns. First, many β-diversity indices are constrained to range between fixed lower and upper limits. As such, regression analysis of β-diversity indices against ecological gradients can result in regression curves that extend beyond these mathematical constraints, thus creating an interpretational dilemma. Second, despite being a function of the same measured α- and γ-diversity, the resultant biodiversity pattern depends on the choice of β-diversity index. We propose a simple logistic transformation that rids beta-diversity indices of their mathematical constraints, thus eliminating the possibility of an uninterpretable regression curve. Moreover, this transformation results in identical biodiversity patterns for three commonly used classical beta-diversity indices. As a result, this transformation eliminates the difficulties of both shortcomings, while allowing the researcher to use whichever beta-diversity index deemed most appropriate. We believe this method can help unify the study of biodiversity patterns along ecological gradients. PMID:25330181

Incorporating historical ecosystem diversity into conservation planning efforts in grass and shrub ecosystems

Treesearch

Amy C. Ganguli; Johathan B. Haufler; Carolyn A. Mehl; Jimmie D. Chew

2011-01-01

Understanding historical ecosystem diversity and wildlife habitat quality can provide a useful reference for managing and restoring rangeland ecosystems. We characterized historical ecosystem diversity using available empirical data, expert opinion, and the spatially explicit vegetation dynamics model SIMPPLLE (SIMulating Vegetative Patterns and Processes at Landscape...

Disturbance History,Spatial Variability, and Patterns of Biodiversity

NASA Astrophysics Data System (ADS)

Bendix, J.; Wiley, J. J.; Commons, M.

2012-12-01

The intermediate disturbance hypothesis predicts that species diversity will be maximized in environments experiencing intermediate intensity disturbance, after an intermediate timespan. Because many landscapes comprise mosaics with complex disturbance histories, the theory implies that each patch in those mosaics should have a distinct level of diversity reflecting combined impact of the magnitude of disturbance and the time since it occurred. We modeled the changing patterns of species richness across a landscape experiencing varied scenarios of simulated disturbance. Model outputs show that individual landscape patches have highly variable species richness through time, with the details reflecting the timing, intensity and sequence of their disturbance history. When the results are mapped across the landscape, the resulting temporal and spatial complexity illustrates both the contingent nature of diversity and the danger of generalizing about the impacts of disturbance.

Plant diversity predicts beta but not alpha diversity of soil microbes across grasslands worldwide

USGS Publications Warehouse

Prober, Suzanne M.; Leff, Jonathan W.; Bates, Scott T.; Borer, Elizabeth T.; Firn, Jennifer; Harpole, W. Stanley; Lind, Eric M.; Seabloom, Eric W.; Adler, Peter B.; Bakker, Jonathan D.; Cleland, Elsa E.; DeCrappeo, Nicole; DeLorenze, Elizabeth; Hagenah, Nicole; Hautier, Yann; Hofmockel, Kirsten S.; Kirkman, Kevin P.; Knops, Johannes M. H.; La Pierre, Kimberly J.; MacDougall, Andrew S.; McCulley, Rebecca L.; Mitchell, Charles E.; Risch, Anita C.; Schuetz, Martin; Stevens, Carly J.; Williams, Ryan J.; Fierer, Noah

2015-01-01

Aboveground–belowground interactions exert critical controls on the composition and function of terrestrial ecosystems, yet the fundamental relationships between plant diversity and soil microbial diversity remain elusive. Theory predicts predominantly positive associations but tests within single sites have shown variable relationships, and associations between plant and microbial diversity across broad spatial scales remain largely unexplored. We compared the diversity of plant, bacterial, archaeal and fungal communities in one hundred and forty-five 1 m2 plots across 25 temperate grassland sites from four continents. Across sites, the plant alpha diversity patterns were poorly related to those observed for any soil microbial group. However, plant beta diversity (compositional dissimilarity between sites) was significantly correlated with the beta diversity of bacterial and fungal communities, even after controlling for environmental factors. Thus, across a global range of temperate grasslands, plant diversity can predict patterns in the composition of soil microbial communities, but not patterns in alpha diversity.

Large-scale spatio-temporal monitoring highlights hotspots of demersal fish diversity in the Mediterranean Sea

NASA Astrophysics Data System (ADS)

Granger, Victoria; Fromentin, Jean-Marc; Bez, Nicolas; Relini, Giulio; Meynard, Christine N.; Gaertner, Jean-Claude; Maiorano, Porzia; Garcia Ruiz, Cristina; Follesa, Cristina; Gristina, Michele; Peristeraki, Panagiota; Brind'Amour, Anik; Carbonara, Pierluigi; Charilaou, Charis; Esteban, Antonio; Jadaud, Angélique; Joksimovic, Aleksandar; Kallianiotis, Argyris; Kolitari, Jerina; Manfredi, Chiara; Massuti, Enric; Mifsud, Roberta; Quetglas, Antoni; Refes, Wahid; Sbrana, Mario; Vrgoc, Nedo; Spedicato, Maria Teresa; Mérigot, Bastien

2015-01-01

Increasing human pressures and global environmental change may severely affect the diversity of species assemblages and associated ecosystem services. Despite the recent interest in phylogenetic and functional diversity, our knowledge on large spatio-temporal patterns of demersal fish diversity sampled by trawling remains still incomplete, notably in the Mediterranean Sea, one of the most threatened marine regions of the world. We investigated large spatio-temporal diversity patterns by analysing a dataset of 19,886 hauls from 10 to 800 m depth performed annually during the last two decades by standardised scientific bottom trawl field surveys across the Mediterranean Sea, within the MEDITS program. A multi-component (eight diversity indices) and multi-scale (local assemblages, biogeographic regions to basins) approach indicates that only the two most traditional components (species richness and evenness) were sufficient to reflect patterns in taxonomic, phylogenetic or functional richness and divergence. We also put into question the use of widely computed indices that allow comparing directly taxonomic, phylogenetic and functional diversity within a unique mathematical framework. In addition, demersal fish assemblages sampled by trawl do not follow a continuous decreasing longitudinal/latitudinal diversity gradients (spatial effects explained up to 70.6% of deviance in regression tree and generalised linear models), for any of the indices and spatial scales analysed. Indeed, at both local and regional scales species richness was relatively high in the Iberian region, Malta, the Eastern Ionian and Aegean seas, meanwhile the Adriatic Sea and Cyprus showed a relatively low level. In contrast, evenness as well as taxonomic, phylogenetic and functional divergences did not show regional hotspots. All studied diversity components remained stable over the last two decades. Overall, our results highlight the need to use complementary diversity indices through different spatial scales when developing conservation strategies and defining delimitations for protected areas.

Impact factors identification of spatial heterogeneity of herbaceous plant diversity on five southern islands of Miaodao Archipelago in North China

NASA Astrophysics Data System (ADS)

Chi, Yuan; Shi, Honghua; Wang, Xiaoli; Qin, Xuebo; Zheng, Wei; Peng, Shitao

2016-09-01

Herbaceous plants are widely distributed on islands and where they exhibit spatial heterogeneity. Accurately identifying the impact factors that drive spatial heterogeneity can reveal typical island biodiversity patterns. Five southern islands in the Miaodao Archipelago, North China were studied herein. The spatial distribution of herbaceous plant diversity on these islands was analyzed, and the impact factors and their degree of impact on spatial heterogeneity were identified using CCA ordination and ANOVA. The results reveal 114 herbaceous plant species, belonging to 94 genera from 34 families in the 50 plots sampled. The total species numbers on different islands were significantly positively correlated with island area, and the average α diversity was correlated with human activities, while the β diversity among islands was more affected by island area than mutual distances. Spatial heterogeneity within islands indicated that the diversities were generally high in areas with higher altitude, slope, total nitrogen, total carbon, and canopy density, and lower moisture content, pH, total phosphorus, total potassium, and aspect. Among the environmental factors, pH, canopy density, total K, total P, moisture content, altitude, and slope had significant gross effects, but only canopy density exhibited a significant net effect. Terrain affected diversity by restricting plantation, plantation in turn influenced soil properties and the two together affected diversity. Therefore, plantation was ultimately the fundamental driving factor for spatial heterogeneity in herbaceous plant diversity on the five islands.

The fin-to-limb transition as the re-organization of a Turing pattern

PubMed Central

Onimaru, Koh; Marcon, Luciano; Musy, Marco; Tanaka, Mikiko; Sharpe, James

2016-01-01

A Turing mechanism implemented by BMP, SOX9 and WNT has been proposed to control mouse digit patterning. However, its generality and contribution to the morphological diversity of fins and limbs has not been explored. Here we provide evidence that the skeletal patterning of the catshark Scyliorhinus canicula pectoral fin is likely driven by a deeply conserved Bmp–Sox9–Wnt Turing network. In catshark fins, the distal nodular elements arise from a periodic spot pattern of Sox9 expression, in contrast to the stripe pattern in mouse digit patterning. However, our computer model shows that the Bmp–Sox9–Wnt network with altered spatial modulation can explain the Sox9 expression in catshark fins. Finally, experimental perturbation of Bmp or Wnt signalling in catshark embryos produces skeletal alterations which match in silico predictions. Together, our results suggest that the broad morphological diversity of the distal fin and limb elements arose from the spatial re-organization of a deeply conserved Turing mechanism. PMID:27211489

Comparing spatial diversification and meta-population models in the Indo-Australian Archipelago

PubMed Central

Chalmandrier, Loïc; Albouy, Camille; Descombes, Patrice; Sandel, Brody; Faurby, Soren; Svenning, Jens-Christian; Zimmermann, Niklaus E.

2018-01-01

Reconstructing the processes that have shaped the emergence of biodiversity gradients is critical to understand the dynamics of diversification of life on Earth. Islands have traditionally been used as model systems to unravel the processes shaping biological diversity. MacArthur and Wilson's island biogeographic model predicts diversity to be based on dynamic interactions between colonization and extinction rates, while treating islands themselves as geologically static entities. The current spatial configuration of islands should influence meta-population dynamics, but long-term geological changes within archipelagos are also expected to have shaped island biodiversity, in part by driving diversification. Here, we compare two mechanistic models providing inferences on species richness at a biogeographic scale: a mechanistic spatial-temporal model of species diversification and a spatial meta-population model. While the meta-population model operates over a static landscape, the diversification model is driven by changes in the size and spatial configuration of islands through time. We compare the inferences of both models to floristic diversity patterns among land patches of the Indo-Australian Archipelago. Simulation results from the diversification model better matched observed diversity than a meta-population model constrained only by the contemporary landscape. The diversification model suggests that the dynamic re-positioning of islands promoting land disconnection and reconnection induced an accumulation of particularly high species diversity on Borneo, which is central within the island network. By contrast, the meta-population model predicts a higher diversity on the mainlands, which is less compatible with empirical data. Our analyses highlight that, by comparing models with contrasting assumptions, we can pinpoint the processes that are most compatible with extant biodiversity patterns. PMID:29657753

Comparing spatial diversification and meta-population models in the Indo-Australian Archipelago.

PubMed

Chalmandrier, Loïc; Albouy, Camille; Descombes, Patrice; Sandel, Brody; Faurby, Soren; Svenning, Jens-Christian; Zimmermann, Niklaus E; Pellissier, Loïc

2018-03-01

Reconstructing the processes that have shaped the emergence of biodiversity gradients is critical to understand the dynamics of diversification of life on Earth. Islands have traditionally been used as model systems to unravel the processes shaping biological diversity. MacArthur and Wilson's island biogeographic model predicts diversity to be based on dynamic interactions between colonization and extinction rates, while treating islands themselves as geologically static entities. The current spatial configuration of islands should influence meta-population dynamics, but long-term geological changes within archipelagos are also expected to have shaped island biodiversity, in part by driving diversification. Here, we compare two mechanistic models providing inferences on species richness at a biogeographic scale: a mechanistic spatial-temporal model of species diversification and a spatial meta-population model. While the meta-population model operates over a static landscape, the diversification model is driven by changes in the size and spatial configuration of islands through time. We compare the inferences of both models to floristic diversity patterns among land patches of the Indo-Australian Archipelago. Simulation results from the diversification model better matched observed diversity than a meta-population model constrained only by the contemporary landscape. The diversification model suggests that the dynamic re-positioning of islands promoting land disconnection and reconnection induced an accumulation of particularly high species diversity on Borneo, which is central within the island network. By contrast, the meta-population model predicts a higher diversity on the mainlands, which is less compatible with empirical data. Our analyses highlight that, by comparing models with contrasting assumptions, we can pinpoint the processes that are most compatible with extant biodiversity patterns.

Large-Scale Diversity of Slope Fishes: Pattern Inconsistency between Multiple Diversity Indices

PubMed Central

Gaertner, Jean-Claude; Colloca, Francesco; Politou, Chrissi-Yianna; Gil De Sola, Luis; Bertrand, Jacques A.; Murenu, Matteo; Durbec, Jean-Pierre; Kallianiotis, Argyris; Mannini, Alessandro

2013-01-01

Large-scale studies focused on the diversity of continental slope ecosystems are still rare, usually restricted to a limited number of diversity indices and mainly based on the empirical comparison of heterogeneous local data sets. In contrast, we investigate large-scale fish diversity on the basis of multiple diversity indices and using 1454 standardized trawl hauls collected throughout the upper and middle slope of the whole northern Mediterranean Sea (36°3′- 45°7′ N; 5°3′W - 28°E). We have analyzed (1) the empirical relationships between a set of 11 diversity indices in order to assess their degree of complementarity/redundancy and (2) the consistency of spatial patterns exhibited by each of the complementary groups of indices. Regarding species richness, our results contrasted both the traditional view based on the hump-shaped theory for bathymetric pattern and the commonly-admitted hypothesis of a large-scale decreasing trend correlated with a similar gradient of primary production in the Mediterranean Sea. More generally, we found that the components of slope fish diversity we analyzed did not always show a consistent pattern of distribution according either to depth or to spatial areas, suggesting that they are not driven by the same factors. These results, which stress the need to extend the number of indices traditionally considered in diversity monitoring networks, could provide a basis for rethinking not only the methodological approach used in monitoring systems, but also the definition of priority zones for protection. Finally, our results call into question the feasibility of properly investigating large-scale diversity patterns using a widespread approach in ecology, which is based on the compilation of pre-existing heterogeneous and disparate data sets, in particular when focusing on indices that are very sensitive to sampling design standardization, such as species richness. PMID:23843962

Spatial genetic structure in Beta vulgaris subsp. maritima and Beta macrocarpa reveals the effect of contrasting mating system, influence of marine currents, and footprints of postglacial recolonization routes.

PubMed

Leys, Marie; Petit, Eric J; El-Bahloul, Yasmina; Liso, Camille; Fournet, Sylvain; Arnaud, Jean-François

2014-05-01

Understanding the factors that contribute to population genetic divergence across a species' range is a long-standing goal in evolutionary biology and ecological genetics. We examined the relative importance of historical and ecological features in shaping the present-day spatial patterns of genetic structure in two related plant species, Beta vulgaris subsp. maritima and Beta macrocarpa. Using nuclear and mitochondrial markers, we surveyed 93 populations from Brittany (France) to Morocco - the southern limit of their species' range distribution. Whereas B. macrocarpa showed a genotypic structure and a high level of genetic differentiation indicative of selfing, the population genetic structure of B. vulgaris subsp. maritima was consistent with an outcrossing mating system. We further showed (1) a strong geographic clustering in coastal B. vulgaris subsp. maritima populations that highlighted the influence of marine currents in shaping different lineages and (2) a peculiar genetic structure of inland B. vulgaris subsp. maritima populations that could indicate the admixture of distinct evolutionary lineages and recent expansions associated with anthropogenic disturbances. Spatial patterns of nuclear diversity and differentiation also supported a stepwise recolonization of Europe from Atlantic-Mediterranean refugia after the last glacial period, with leading-edge expansions. However, cytoplasmic diversity was not impacted by postglacial recolonization: stochastic long-distance seed dispersal mediated by major oceanic currents may mitigate the common patterns of reduced cytoplasmic diversity observed for edge populations. Overall, the patterns we documented here challenge the general view of reduced genetic diversity at the edge of a species' range distribution and provide clues for understanding how life-history and major geographic features interact to shape the distribution of genetic diversity.

Spatial genetic structure in Beta vulgaris subsp. maritima and Beta macrocarpa reveals the effect of contrasting mating system, influence of marine currents, and footprints of postglacial recolonization routes

PubMed Central

Leys, Marie; Petit, Eric J; El-Bahloul, Yasmina; Liso, Camille; Fournet, Sylvain; Arnaud, Jean-François

2014-01-01

Understanding the factors that contribute to population genetic divergence across a species' range is a long-standing goal in evolutionary biology and ecological genetics. We examined the relative importance of historical and ecological features in shaping the present-day spatial patterns of genetic structure in two related plant species, Beta vulgaris subsp. maritima and Beta macrocarpa. Using nuclear and mitochondrial markers, we surveyed 93 populations from Brittany (France) to Morocco – the southern limit of their species' range distribution. Whereas B. macrocarpa showed a genotypic structure and a high level of genetic differentiation indicative of selfing, the population genetic structure of B. vulgaris subsp. maritima was consistent with an outcrossing mating system. We further showed (1) a strong geographic clustering in coastal B. vulgaris subsp. maritima populations that highlighted the influence of marine currents in shaping different lineages and (2) a peculiar genetic structure of inland B. vulgaris subsp. maritima populations that could indicate the admixture of distinct evolutionary lineages and recent expansions associated with anthropogenic disturbances. Spatial patterns of nuclear diversity and differentiation also supported a stepwise recolonization of Europe from Atlantic-Mediterranean refugia after the last glacial period, with leading-edge expansions. However, cytoplasmic diversity was not impacted by postglacial recolonization: stochastic long-distance seed dispersal mediated by major oceanic currents may mitigate the common patterns of reduced cytoplasmic diversity observed for edge populations. Overall, the patterns we documented here challenge the general view of reduced genetic diversity at the edge of a species' range distribution and provide clues for understanding how life-history and major geographic features interact to shape the distribution of genetic diversity. PMID:24963380

Mapping multi-scale vascular plant richness in a forest landscape with integrated LiDAR and hyperspectral remote-sensing.

PubMed

Hakkenberg, C R; Zhu, K; Peet, R K; Song, C

2018-02-01

The central role of floristic diversity in maintaining habitat integrity and ecosystem function has propelled efforts to map and monitor its distribution across forest landscapes. While biodiversity studies have traditionally relied largely on ground-based observations, the immensity of the task of generating accurate, repeatable, and spatially-continuous data on biodiversity patterns at large scales has stimulated the development of remote-sensing methods for scaling up from field plot measurements. One such approach is through integrated LiDAR and hyperspectral remote-sensing. However, despite their efficiencies in cost and effort, LiDAR-hyperspectral sensors are still highly constrained in structurally- and taxonomically-heterogeneous forests - especially when species' cover is smaller than the image resolution, intertwined with neighboring taxa, or otherwise obscured by overlapping canopy strata. In light of these challenges, this study goes beyond the remote characterization of upper canopy diversity to instead model total vascular plant species richness in a continuous-cover North Carolina Piedmont forest landscape. We focus on two related, but parallel, tasks. First, we demonstrate an application of predictive biodiversity mapping, using nonparametric models trained with spatially-nested field plots and aerial LiDAR-hyperspectral data, to predict spatially-explicit landscape patterns in floristic diversity across seven spatial scales between 0.01-900 m 2 . Second, we employ bivariate parametric models to test the significance of individual, remotely-sensed predictors of plant richness to determine how parameter estimates vary with scale. Cross-validated results indicate that predictive models were able to account for 15-70% of variance in plant richness, with LiDAR-derived estimates of topography and forest structural complexity, as well as spectral variance in hyperspectral imagery explaining the largest portion of variance in diversity levels. Importantly, bivariate tests provide evidence of scale-dependence among predictors, such that remotely-sensed variables significantly predict plant richness only at spatial scales that sufficiently subsume geolocational imprecision between remotely-sensed and field data, and best align with stand components including plant size and density, as well as canopy gaps and understory growth patterns. Beyond their insights into the scale-dependent patterns and drivers of plant diversity in Piedmont forests, these results highlight the potential of remotely-sensible essential biodiversity variables for mapping and monitoring landscape floristic diversity from air- and space-borne platforms. © 2017 by the Ecological Society of America.

Patterns and predictors of β-diversity in the fragmented Brazilian Atlantic forest: a multiscale analysis of forest specialist and generalist birds.

PubMed

Morante-Filho, José Carlos; Arroyo-Rodríguez, Víctor; Faria, Deborah

2016-01-01

Biodiversity maintenance in human-altered landscapes (HALs) depends on the species turnover among localities, but the patterns and determinants of β-diversity in HALs are poorly known. In fact, declines, increases and neutral shifts in β-diversity have all been documented, depending on the landscape, ecological group and spatial scale of analysis. We shed some light on this controversy by assessing the patterns and predictors of bird β-diversity across multiple spatial scales considering forest specialist and habitat generalist bird assemblages. We surveyed birds from 144 point counts in 36 different forest sites across two landscapes with different amount of forest cover in the Brazilian Atlantic forest. We analysed β-diversity among points, among sites and between landscapes with multiplicative diversity partitioning of Hill numbers. We tested whether β-diversity among points was related to within-site variations in vegetation structure, and whether β-diversity among sites was related to site location and/or to differences among sites in vegetation structure and landscape composition (i.e. per cent forest and pasture cover surrounding each site). β-diversity between landscapes was lower than among sites and among points in both bird assemblages. In forest specialist birds, the landscape with less forest cover showed the highest β-diversity among sites (bird differentiation among sites), but generalist birds showed the opposite pattern. At the local scale, however, the less forested landscape showed the lowest β-diversity among points (bird homogenization within sites), independently of the bird assemblage. β-diversity among points was weakly related to vegetation structure, but higher β-diversity values were recorded among sites that were more isolated from each other, and among sites with higher differences in landscape composition, particularly in the less forested landscape. Our findings indicate that patterns of bird β-diversity vary across scales and are strongly related to landscape composition. Bird assemblages are shaped by both environmental filtering and dispersal limitation, particularly in less forested landscapes. Conservation and management strategies should therefore prevent deforestation in this biodiversity hotspot. © 2015 The Authors. Journal of Animal Ecology © 2015 British Ecological Society.

Landscape pattern of seed banks and anthropogenic impacts in forested wetlands of the northern Mississippi River Alluvial Valley

USGS Publications Warehouse

Middleton, B.; Wu, X.B.

2008-01-01

Agricultural development on floodplains contributes to hydrologic alteration and forest fragmentation, which may alter landscape-level processes. These changes may be related to shifts in the seed bank composition of floodplain wetlands. We examined the patterns of seed bank composition across a floodplain watershed by looking at the number of seeds germinating per m2 by species in 60 farmed and intact forested wetlands along the Cache River watershed in Illinois. The seed bank composition was compared above and below a water diversion (position), which artificially subdivides the watershed. Position of these wetlands represented the most variability of Axis I in a Nonmetric Multidimensional Scaling (NMS) analysis of site environmental variables and their relationship to seed bank composition (coefficient of determination for Axis 1: r2 = 0.376; Pearson correlation of position to Axis 1: r = 0.223). The 3 primary axes were also represented by other site environmental variables, including farming status (farmed or unfarmed), distance from the mouth of the river, latitude, and longitude. Spatial analysis based on Mantel correlograms showed that both water-dispersed and wind/water-dispersed seed assemblages had strong spatial structure in the upper Cache (above the water diversion), bur the spatial structure of water-dispersed seed assemblage was diminished in the lower Cache (below the water diversion), which lost floodpulsing. Bearing analysis also Suggested that water-dispersal process had a stronger influence on the overall spatial pattern of seed assemblage in the upper Cache, while wind/water-dispersal process had a stronger influence in the lower Cache. An analysis of the landscapes along the river showed that the mid-lower Cache (below the water diversion) had undergone greater land cover changes associated with agriculture than did the upper Cache watershed. Thus, the combination of forest fragmentation and hydrologic changes in the surrounding landscape may have had an influence on the seed bank composition and spatial distribution of the seed banks of the Cache River watershed. Our study suggests that the spatial pattern of seed bank composition may be influenced by landscape-level factors and processes.

Biodiversity, molecular ecology and phylogeography of marine sponges: patterns, implications and outlooks.

PubMed

Wörheide, Gert; Solé-Cava, Antonio M; Hooper, John N A

2005-04-01

Marine sponges are an ecologically important and highly diverse component of marine benthic communities, found in all the world's oceans, at all depths. Although their commercial potential and evolutionary importance is increasingly recognized, many pivotal aspects of their basic biology remain enigmatic. Knowledge of historical biogeographic affinities and biodiversity patterns is rudimentary, and there are still few data about genetic variation among sponge populations and spatial patterns of this variation. Biodiversity analyses of tropical Australasian sponges revealed spatial trends not universally reflected in the distributions of other marine phyla within the Indo-West Pacific region. At smaller spatial scales sponges frequently form heterogeneous, spatially patchy assemblages, with some empirical evidence suggesting that environmental variables such as light and/or turbidity strongly contribute to local distributions. There are no apparent latitudinal diversity gradients at larger spatial scales but stochastic processes, such as changing current patterns, the presence or absence of major carbonate platforms and historical biogeography, may determine modern day distributions. Studies on Caribbean oceanic reefs have revealed similar patterns, only weakly correlated with environmental factors. However, several questions remain where molecular approaches promise great potential, e.g., concerning connectivity and biogeographic relationships. Studies to date have helped to reveal that sponge populations are genetically highly structured and that historical processes might play an important role in determining such structure. Increasingly sophisticated molecular tools are now being applied, with results contributing significantly to a better understanding of poriferan microevolutionary processes and molecular ecology.

Patterns of species diversity in estuarine benthic communities along teh US west coast

EPA Science Inventory

Estuaries in the Pacific North West (PNW) were recently classified by whether the estuary is river- or ocean-dominated, the extent of intertidal to subtidal environments, and spatial salinity patterns. We examine whether these characteristics predict patterns of soft-sediment, m...

Consumer preference for seeds and seedlings of rare species impacts tree diversity at multiple scales.

PubMed

Young, Hillary S; McCauley, Douglas J; Guevara, Roger; Dirzo, Rodolfo

2013-07-01

Positive density-dependent seed and seedling predation, where herbivores selectively eat seeds or seedlings of common species, is thought to play a major role in creating and maintaining plant community diversity. However, many herbivores and seed predators are known to exhibit preferences for rare foods, which could lead to negative density-dependent predation. In this study, we first demonstrate the occurrence of increased predation of locally rare tree species by a widespread group of insular seed and seedling predators, land crabs. We then build computer simulations based on these empirical data to examine the effects of such predation on diversity patterns. Simulations show that herbivore preferences for locally rare species are likely to drive scale-dependent effects on plant community diversity: at small scales these foraging patterns decrease plant community diversity via the selective consumption of rare plant species, while at the landscape level they should increase diversity, at least for short periods, by promoting clustered local dominance of a variety of species. Finally, we compared observed patterns of plant diversity at the site to those obtained via computer simulations, and found that diversity patterns generated under simulations were highly consistent with observed diversity patterns. We posit that preference for rare species by herbivores may be prevalent in low- or moderate-diversity systems, and that these effects may help explain diversity patterns across different spatial scales in such ecosystems.

Developing spectral, structural, and phenological diversity proxies for monitoring biodiversity change across space and time using ESA's Sentinel satellites

NASA Astrophysics Data System (ADS)

Ma, X.; Mahecha, M. D.; Migliavacca, M.; Luo, Y.; Urban, M.; Bohn, F. J.; Huth, A.; Reichstein, M.

2017-12-01

A key challenge for monitoring biodiversity change is the lack of consistent measures of biodiversity across space and time. This challenge may be addressed by exploring the potentials provided by novel remote sensing observations. By continuously observing broad-scale patterns of vegetation and land surface parameters, remote sensing can complement the restricted coverage afforded by field measurements. Here we develop methods to infer spatial patterns of biodiversity at ecosystem level from ESA's next-generation Sentinel sensors (Sentinel-1: C-band radar & Sentinel-2: multispectral). Both satellites offer very high spatial (10 m) and temporal resolutions (5 days) measurements with global coverage. We propose and test several ecosystem biodiversity proxies, including landscape spectral diversity, phenological diversity, and canopy structural diversity. These diversity proxies are highly related to some key aspects of essential biodiversity variables (EBVs) as defined by GEO-BON, such as habitat structure, community composition, ecosystem function and structure. We verify spaceborne retrievals of these biodiversity proxies with in situ measurements from drone (spectral diversity), phenocam (phenological diversity), and airborne LiDAR (canopy structural diversity) over multiple flux tower sites within the Mediterranean region. We further compare our remote sensing retrievals of biodiversity proxies against several biodiversity indices as derived from field measurements (incl. ⍺-/β- diversity and Shannon-index) to explore the limitations and potentials of extending the RS proxies to a greater spatial extent. We expect the new concept as to maximize the potential of remote sensing information might help to monitor key aspects of EBVs on a global scale.

Patterns of Racial Diversity and Segregation in the United States: 1990–2010*

PubMed Central

Wright, Richard; Ellis, Mark; Holloway, Steven R.; Wong, Sandy

2014-01-01

The growing ethnic and racial diversity of the United States is evident at all spatial scales. One of the striking features of this new mixture of peoples, however, is that this new diversity often occurs in tandem with racial concentration. This article surveys these new geographies from four points of view: the nation as a whole, states, large metropolitan areas, and neighborhoods. The analysis at each scale relies on a new taxonomy of racial composition that simultaneously appraises both diversity and the lack thereof (Holloway, Wright, and Ellis 2012). Urban analysis often posits neighborhood racial segregation and diversity as either endpoints on a continuum of racial dominance or mirror images of one another. We disturb that perspective and stress that segregation and diversity must be jointly understood—they are necessarily related, although not as inevitable binary opposites. Using census data from 1990, 2000, and 2010, the research points to how patterns of racial diversity and dominance interact across varying spatial scales. This investigation helps answer some basic questions about the changing geographies of racialized groups, setting the stage for the following articles that explore the relationship between geography and the participation of underrepresented groups in higher education. PMID:25083001

Taxonomic and Phylogenetic Determinants of Functional Composition of Bolivian Bat Assemblages

PubMed Central

Aguirre, Luis F.; Montaño-Centellas, Flavia A.; Gavilanez, M. Mercedes; Stevens, Richard D.

2016-01-01

Understanding diversity patterns and the potential mechanisms driving them is a fundamental goal in ecology. Examination of different dimensions of biodiversity can provide insights into the relative importance of different processes acting upon biotas to shape communities. Unfortunately, patterns of diversity are still poorly understood in hyper-diverse tropical countries. Here, we assess spatial variation of taxonomic, functional and phylogenetic diversity of bat assemblages in one of the least studied Neotropical countries, Bolivia, and determine whether changes in biodiversity are explained by the replacement of species or functional groups, or by differences in richness (i.e., gain or loss of species or functional groups). Further, we evaluate the contribution of phylogenetic and taxonomic changes in the resulting patterns of functional diversity of bats. Using well-sampled assemblages from published studies we examine noctilionoid bats at ten study sites across five ecoregions in Bolivia. Bat assemblages differed from each other in all dimensions of biodiversity considered; however, diversity patterns for each dimension were likely structured by different mechanisms. Within ecoregions, differences were largely explained by species richness, suggesting that the gain or loss of species or functional groups (as opposed to replacement) was driving dissimilarity patterns. Overall, our results suggest that whereas evolutionary processes (i.e., historical connection and dispersal routes across Bolivia) create a template of diversity patterns across the country, ecological mechanisms modify these templates, decoupling the observed patterns of functional, taxonomic and phylogenetic diversity in Bolivian bats. Our results suggests that elevation represents an important source of variability among diversity patterns for each dimension of diversity considered. Further, we found that neither phylogenetic nor taxonomic diversity can fully account for patterns of functional diversity, highlighting the need for examining different dimensions of biodiversity of bats in hyperdiverse ecosystems. PMID:27384441

Taxonomic and Phylogenetic Determinants of Functional Composition of Bolivian Bat Assemblages.

PubMed

Aguirre, Luis F; Montaño-Centellas, Flavia A; Gavilanez, M Mercedes; Stevens, Richard D

2016-01-01

Understanding diversity patterns and the potential mechanisms driving them is a fundamental goal in ecology. Examination of different dimensions of biodiversity can provide insights into the relative importance of different processes acting upon biotas to shape communities. Unfortunately, patterns of diversity are still poorly understood in hyper-diverse tropical countries. Here, we assess spatial variation of taxonomic, functional and phylogenetic diversity of bat assemblages in one of the least studied Neotropical countries, Bolivia, and determine whether changes in biodiversity are explained by the replacement of species or functional groups, or by differences in richness (i.e., gain or loss of species or functional groups). Further, we evaluate the contribution of phylogenetic and taxonomic changes in the resulting patterns of functional diversity of bats. Using well-sampled assemblages from published studies we examine noctilionoid bats at ten study sites across five ecoregions in Bolivia. Bat assemblages differed from each other in all dimensions of biodiversity considered; however, diversity patterns for each dimension were likely structured by different mechanisms. Within ecoregions, differences were largely explained by species richness, suggesting that the gain or loss of species or functional groups (as opposed to replacement) was driving dissimilarity patterns. Overall, our results suggest that whereas evolutionary processes (i.e., historical connection and dispersal routes across Bolivia) create a template of diversity patterns across the country, ecological mechanisms modify these templates, decoupling the observed patterns of functional, taxonomic and phylogenetic diversity in Bolivian bats. Our results suggests that elevation represents an important source of variability among diversity patterns for each dimension of diversity considered. Further, we found that neither phylogenetic nor taxonomic diversity can fully account for patterns of functional diversity, highlighting the need for examining different dimensions of biodiversity of bats in hyperdiverse ecosystems.

Consistent patterns of high alpha and low beta diversity in tropical parasitic and free-living protists.

PubMed

Lentendu, Guillaume; Mahé, Frédéric; Bass, David; Rueckert, Sonja; Stoeck, Thorsten; Dunthorn, Micah

2018-05-30

Tropical animals and plants are known to have high alpha diversity within forests, but low beta diversity between forests. By contrast, it is unknown whether microbes inhabiting the same ecosystems exhibit similar biogeographic patterns. To evaluate the biogeographies of tropical protists, we used metabarcoding data of species sampled in the soils of three lowland Neotropical rainforests. Taxa-area and distance-decay relationships for three of the dominant protist taxa and their subtaxa were estimated at both the OTU and phylogenetic levels, with presence-absence and abundance-based measures. These estimates were compared to null models. High local alpha and low regional beta diversity patterns were consistently found for both the parasitic Apicomplexa and the largely free-living Cercozoa and Ciliophora. Similar to animals and plants, the protists showed spatial structures between forests at the OTU and phylogenetic levels, and only at the phylogenetic level within forests. These results suggest that the biogeographies of macro- and micro-organismal eukaryotes in lowland Neotropical rainforests are partially structured by the same general processes. However, and unlike the animals and plants, the protist OTUs did not exhibit spatial structures within forests, which hinders our ability to estimate the local and regional diversity of protists in tropical forests. © 2018 John Wiley & Sons Ltd.

Fungal biogeography. Global diversity and geography of soil fungi.

PubMed

Tedersoo, Leho; Bahram, Mohammad; Põlme, Sergei; Kõljalg, Urmas; Yorou, Nourou S; Wijesundera, Ravi; Villarreal Ruiz, Luis; Vasco-Palacios, Aída M; Thu, Pham Quang; Suija, Ave; Smith, Matthew E; Sharp, Cathy; Saluveer, Erki; Saitta, Alessandro; Rosas, Miguel; Riit, Taavi; Ratkowsky, David; Pritsch, Karin; Põldmaa, Kadri; Piepenbring, Meike; Phosri, Cherdchai; Peterson, Marko; Parts, Kaarin; Pärtel, Kadri; Otsing, Eveli; Nouhra, Eduardo; Njouonkou, André L; Nilsson, R Henrik; Morgado, Luis N; Mayor, Jordan; May, Tom W; Majuakim, Luiza; Lodge, D Jean; Lee, Su See; Larsson, Karl-Henrik; Kohout, Petr; Hosaka, Kentaro; Hiiesalu, Indrek; Henkel, Terry W; Harend, Helery; Guo, Liang-dong; Greslebin, Alina; Grelet, Gwen; Geml, Jozsef; Gates, Genevieve; Dunstan, William; Dunk, Chris; Drenkhan, Rein; Dearnaley, John; De Kesel, André; Dang, Tan; Chen, Xin; Buegger, Franz; Brearley, Francis Q; Bonito, Gregory; Anslan, Sten; Abell, Sandra; Abarenkov, Kessy

2014-11-28

Fungi play major roles in ecosystem processes, but the determinants of fungal diversity and biogeographic patterns remain poorly understood. Using DNA metabarcoding data from hundreds of globally distributed soil samples, we demonstrate that fungal richness is decoupled from plant diversity. The plant-to-fungus richness ratio declines exponentially toward the poles. Climatic factors, followed by edaphic and spatial variables, constitute the best predictors of fungal richness and community composition at the global scale. Fungi show similar latitudinal diversity gradients to other organisms, with several notable exceptions. These findings advance our understanding of global fungal diversity patterns and permit integration of fungi into a general macroecological framework. Copyright © 2014, American Association for the Advancement of Science.

Regional patterns of genetic diversity in swine influenza A viruses in the United States from 2010 to 2016.

PubMed

Walia, Rasna R; Anderson, Tavis K; Vincent, Amy L

2018-04-06

Regular spatial and temporal analyses of the genetic diversity and evolutionary patterns of influenza A virus (IAV) in swine informs control efforts and improves animal health. Initiated in 2009, the USDA passively surveils IAV in U.S. swine, with a focus on subtyping clinical respiratory submissions, sequencing at minimum the hemagglutinin (HA) and neuraminidase (NA) genes, and sharing these data publicly. In this study, our goal was to quantify and describe regional and national patterns in the genetic diversity and evolution of IAV in U.S. swine from 2010 to 2016. A comprehensive phylogenetic and epidemiological analysis of publicly available HA and NA genes generated by the USDA surveillance system collected from January 2010 to December 2016 was conducted. The dominant subtypes and genetic clades detected during the study period were H1N1 (H1-γ/1A.3.3.3, N1-classical, 29%), H1N2 (H1-δ1/1B.2.2, N2-2002, 27%), and H3N2 (H3-IV-A, N2-2002, 15%), but many other minor clades were also maintained. Year-round circulation was observed, with a primary epidemic peak in October-November and a secondary epidemic peak in March-April. Partitioning these data into 5 spatial zones revealed that genetic diversity varied regionally and was not correlated with aggregated national patterns of HA/NA diversity. These data suggest that vaccine composition and control efforts should consider IAV diversity within swine production regions in addition to aggregated national patterns. This article is protected by copyright. All rights reserved. This article is protected by copyright. All rights reserved.

Contrasting diversity patterns of soil mites and nematodes in secondary succession

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kardol, Paul; Newton, Jeffrey S.; Bezemer, T Martijn

2009-01-01

Soil biodiversity has been recognized as a key feature of ecosystem functioning and stability. However, soil biodiversity is strongly impaired by agriculture and relatively little is known on how and at what spatial and temporal scales soil biodiversity is restored after the human disturbances have come to an end. Here, a multi-scale approach was used to compare diversity patterns of soil mites and nematodes at four stages (early, mid, late, reference site) along a secondary succession chronosequence from abandoned arable land to heath land. In each field four soil samples were taken during four successive seasons. We determined soil diversitymore » within samples ({alpha}-diversity), between samples ({beta}-diversity) and within field sites ({gamma}-diversity). The patterns of {alpha}- and {gamma}-diversity developed similarly along the chronosequence for oribatid mites, but not for nematodes. Nematode {alpha}-diversity was highest in mid- and late-successional sites, while {gamma}-diversity was constant along the chronosequence. Oribatid mite {beta}-diversity was initially high, but decreased thereafter, whereas nematode {beta}-diversity increased when succession proceeded; indicating that patterns of within-site heterogeneity diverged for oribatid mites and nematodes. The spatio-temporal diversity patterns after land abandonment suggest that oribatid mite community development depends predominantly on colonization of new taxa, whereas nematode community development depends on shifts in dominance patterns. This would imply that at old fields diversity patterns of oribatid mites are mainly controlled by dispersal, whereas diversity patterns of nematodes are mainly controlled by changing abiotic or biotic soil conditions. Our study shows that the restoration of soil biodiversity along secondary successional gradients can be both scale- and phylum-dependent.« less

Legacy of Pre-Disturbance Spatial Pattern Determines Early Structural Diversity following Severe Disturbance in Montane Spruce Forests

PubMed Central

Bače, Radek; Svoboda, Miroslav; Janda, Pavel; Morrissey, Robert C.; Wild, Jan; Clear, Jennifer L.; Čada, Vojtěch; Donato, Daniel C.

2015-01-01

Background Severe canopy-removing disturbances are native to many temperate forests and radically alter stand structure, but biotic legacies (surviving elements or patterns) can lend continuity to ecosystem function after such events. Poorly understood is the degree to which the structural complexity of an old-growth forest carries over to the next stand. We asked how pre-disturbance spatial pattern acts as a legacy to influence post-disturbance stand structure, and how this legacy influences the structural diversity within the early-seral stand. Methods Two stem-mapped one-hectare forest plots in the Czech Republic experienced a severe bark beetle outbreak, thus providing before-and-after data on spatial patterns in live and dead trees, crown projections, down logs, and herb cover. Results Post-disturbance stands were dominated by an advanced regeneration layer present before the disturbance. Both major species, Norway spruce (Picea abies) and rowan (Sorbus aucuparia), were strongly self-aggregated and also clustered to former canopy trees, pre-disturbance snags, stumps and logs, suggesting positive overstory to understory neighbourhood effects. Thus, although the disturbance dramatically reduced the stand’s height profile with ~100% mortality of the canopy layer, the spatial structure of post-disturbance stands still closely reflected the pre-disturbance structure. The former upper tree layer influenced advanced regeneration through microsite and light limitation. Under formerly dense canopies, regeneration density was high but relatively homogeneous in height; while in former small gaps with greater herb cover, regeneration density was lower but with greater heterogeneity in heights. Conclusion These findings suggest that pre-disturbance spatial patterns of forests can persist through severe canopy-removing disturbance, and determine the spatial structure of the succeeding stand. Such patterns constitute a subtle but key legacy effect, promoting structural complexity in early-seral forests as well as variable successional pathways and rates. This influence suggests a continuity in spatial ecosystem structure that may well persist through multiple forest generations. PMID:26421726

Consistently inconsistent drivers of microbial diversity and abundance at macroecological scales.

PubMed

Hendershot, John Nicholas; Read, Quentin D; Henning, Jeremiah A; Sanders, Nathan J; Classen, Aimée T

2017-07-01

Macroecology seeks to understand broad-scale patterns in the diversity and abundance of organisms, but macroecologists typically study aboveground macroorganisms. Belowground organisms regulate numerous ecosystem functions, yet we lack understanding of what drives their diversity. Here, we examine the controls on belowground diversity along latitudinal and elevational gradients. We performed a global meta-analysis of 325 soil communities across 20 studies conducted along temperature and soil pH gradients. Belowground taxa, whether bacterial or fungal, observed along a given gradient of temperature or soil pH were equally likely to show a linear increase, linear decrease, humped pattern, trough-shaped pattern, or no pattern in diversity along the gradient. Land-use intensity weakly affected the diversity-temperature relationship, but no other factor did so. Our study highlights disparities among diversity patterns of soil microbial communities. Belowground diversity may be controlled by the associated climatic and historical contexts of particular gradients, by factors not typically measured in community-level studies, or by processes operating at scales that do not match the temporal and spatial scales under study. Because these organisms are responsible for a suite of key processes, understanding the drivers of their distribution and diversity is fundamental to understanding the functioning of ecosystems. © 2017 by the Ecological Society of America.

Global marine bacterial diversity peaks at high latitudes in winter

PubMed Central

Ladau, Joshua; Sharpton, Thomas J; Finucane, Mariel M; Jospin, Guillaume; Kembel, Steven W; O'Dwyer, James; Koeppel, Alexander F; Green, Jessica L; Pollard, Katherine S

2013-01-01

Genomic approaches to characterizing bacterial communities are revealing significant differences in diversity and composition between environments. But bacterial distributions have not been mapped at a global scale. Although current community surveys are way too sparse to map global diversity patterns directly, there is now sufficient data to fit accurate models of how bacterial distributions vary across different environments and to make global scale maps from these models. We apply this approach to map the global distributions of bacteria in marine surface waters. Our spatially and temporally explicit predictions suggest that bacterial diversity peaks in temperate latitudes across the world's oceans. These global peaks are seasonal, occurring 6 months apart in the two hemispheres, in the boreal and austral winters. This pattern is quite different from the tropical, seasonally consistent diversity patterns observed for most macroorganisms. However, like other marine organisms, surface water bacteria are particularly diverse in regions of high human environmental impacts on the oceans. Our maps provide the first picture of bacterial distributions at a global scale and suggest important differences between the diversity patterns of bacteria compared with other organisms. PMID:23514781

Patterns of genetic variability and habitat occupancy in Crepis triasii (Asteraceae) at different spatial scales: insights on evolutionary processes leading to diversification in continental islands.

PubMed

Mayol, Maria; Palau, Carles; Rosselló, Josep A; González-Martínez, Santiago C; Molins, Arántzazu; Riba, Miquel

2012-02-01

Archipelagos are unique systems for studying evolutionary processes promoting diversification and speciation. The islands of the Mediterranean basin are major areas of plant richness, including a high proportion of narrow endemics. Many endemic plants are currently found in rocky habitats, showing varying patterns of habitat occupancy at different spatial scales throughout their range. The aim of the present study was to understand the impact of varying patterns of population distribution on genetic diversity and structure to shed light on demographic and evolutionary processes leading to population diversification in Crepis triasii, an endemic plant from the eastern Balearic Islands. Using allozyme and chloroplast markers, we related patterns of genetic structure and diversity to those of habitat occupancy at a regional (between islands and among populations within islands) and landscape (population size and connectivity) scale. Genetic diversity was highly structured both at the regional and at the landscape level, and was positively correlated with population connectivity in the landscape. Populations located in small isolated mountains and coastal areas, with restricted patterns of regional occupancy, were genetically less diverse and much more differentiated. In addition, more isolated populations had stronger fine-scale genetic structure than well-connected ones. Changes in habitat availability and quality arising from marine transgressions during the Quaternary, as well as progressive fragmentation associated with the aridification of the climate since the last glaciation, are the most plausible factors leading to the observed patterns of genetic diversity and structure. Our results emphasize the importance of gene flow in preventing genetic erosion and maintaining the evolutionary potential of populations. They also agree with recent studies highlighting the importance of restricted gene flow and genetic drift as drivers of plant evolution in Mediterranean continental islands.

Disturbance, neutral theory, and patterns of beta diversity in soil communities.

PubMed

Maaß, Stefanie; Migliorini, Massimo; Rillig, Matthias C; Caruso, Tancredi

2014-12-01

Beta diversity describes how local communities within an area or region differ in species composition/abundance. There have been attempts to use changes in beta diversity as a biotic indicator of disturbance, but lack of theory and methodological caveats have hampered progress. We here propose that the neutral theory of biodiversity plus the definition of beta diversity as the total variance of a community matrix provide a suitable, novel, starting point for ecological applications. Observed levels of beta diversity (BD) can be compared to neutral predictions with three possible outcomes: Observed BD equals neutral prediction or is larger (divergence) or smaller (convergence) than the neutral prediction. Disturbance might lead to either divergence or convergence, depending on type and strength. We here apply these ideas to datasets collected on oribatid mites (a key, very diverse soil taxon) under several regimes of disturbances. When disturbance is expected to increase the heterogeneity of soil spatial properties or the sampling strategy encompassed a range of diverging environmental conditions, we observed diverging assemblages. On the contrary, we observed patterns consistent with neutrality when disturbance could determine homogenization of soil properties in space or the sampling strategy encompassed fairly homogeneous areas. With our method, spatial and temporal changes in beta diversity can be directly and easily monitored to detect significant changes in community dynamics, although the method itself cannot inform on underlying mechanisms. However, human-driven disturbances and the spatial scales at which they operate are usually known. In this case, our approach allows the formulation of testable predictions in terms of expected changes in beta diversity, thereby offering a promising monitoring tool.

Quantifying Spatial Genetic Structuring in Mesophotic Populations of the Precious Coral Corallium rubrum

PubMed Central

Costantini, Federica; Carlesi, Lorenzo; Abbiati, Marco

2013-01-01

While shallow water red coral populations have been overharvested in the past, nowadays, commercial harvesting shifted its pressure on mesophotic organisms. An understanding of red coral population structure, particularly larval dispersal patterns and connectivity among harvested populations is paramount to the viability of the species. In order to determine patterns of genetic spatial structuring of deep water Corallium rubrum populations, for the first time, colonies found between 58–118 m depth within the Tyrrhenian Sea were collected and analyzed. Ten microsatellite loci and two regions of mitochondrial DNA (mtMSH and mtC) were used to quantify patterns of genetic diversity within populations and to define population structuring at spatial scales from tens of metres to hundreds of kilometres. Microsatellites showed heterozygote deficiencies in all populations. Significant levels of genetic differentiation were observed at all investigated spatial scales, suggesting that populations are likely to be isolated. This differentiation may by the results of biological interactions, occurring within a small spatial scale and/or abiotic factors acting at a larger scale. Mitochondrial markers revealed significant genetic structuring at spatial scales greater then 100 km showing the occurrence of a barrier to gene flow between northern and southern Tyrrhenian populations. These findings provide support for the establishment of marine protected areas in the deep sea and off-shore reefs, in order to effectively maintain genetic diversity of mesophotic red coral populations. PMID:23646109

Quantifying spatial genetic structuring in mesophotic populations of the precious coral Corallium rubrum.

PubMed

Costantini, Federica; Carlesi, Lorenzo; Abbiati, Marco

2013-01-01

While shallow water red coral populations have been overharvested in the past, nowadays, commercial harvesting shifted its pressure on mesophotic organisms. An understanding of red coral population structure, particularly larval dispersal patterns and connectivity among harvested populations is paramount to the viability of the species. In order to determine patterns of genetic spatial structuring of deep water Corallium rubrum populations, for the first time, colonies found between 58-118 m depth within the Tyrrhenian Sea were collected and analyzed. Ten microsatellite loci and two regions of mitochondrial DNA (mtMSH and mtC) were used to quantify patterns of genetic diversity within populations and to define population structuring at spatial scales from tens of metres to hundreds of kilometres. Microsatellites showed heterozygote deficiencies in all populations. Significant levels of genetic differentiation were observed at all investigated spatial scales, suggesting that populations are likely to be isolated. This differentiation may by the results of biological interactions, occurring within a small spatial scale and/or abiotic factors acting at a larger scale. Mitochondrial markers revealed significant genetic structuring at spatial scales greater then 100 km showing the occurrence of a barrier to gene flow between northern and southern Tyrrhenian populations. These findings provide support for the establishment of marine protected areas in the deep sea and off-shore reefs, in order to effectively maintain genetic diversity of mesophotic red coral populations.

Mechanism underlying the diverse collective behavior in the swarm oscillator model

NASA Astrophysics Data System (ADS)

Iwasa, Masatomo; Tanaka, Dan

2017-09-01

The swarm oscillator model describes the long-time behavior of interacting chemotactic particles, and it shows numerous types of macroscopic patterns. However, the reason why so many kinds of patterns emerge is not clear. In this study, we elucidate the mechanism underlying the diversity of the pattens by analyzing the model for two particles. Focusing on the behavior when the two particles are spatially close, we find that the dynamics is classified into eight types, which explain most of the observed 13 types of patterns.

Analysis of sea use landscape pattern based on GIS: a case study in Huludao, China.

PubMed

Suo, Anning; Wang, Chen; Zhang, Minghui

2016-01-01

This study aims to analyse sea use landscape patterns on a regional scale based on methods of landscape ecology integrated with sea use spatial characteristics. Several landscape-level analysis indices, such as the dominance index, complex index, intensivity index, diversity index and sea congruency index, were established using Geographic Information System (GIS) and applied in Huludao, China. The results indicated that sea use landscape analysis indices, which were created based on the characteristics of sea use spatial patterns using GIS, are suitable to quantitatively describe the landscape patterns of sea use. They are operable tools for the landscape analysis of sea use. The sea use landscape in Huludao was dominated by fishing use with a landscape dominance index of 0.724. The sea use landscape is a complex mosaic with high diversity and plenty of fishing areas, as shown by the landscape complex index of 27.21 and the landscape diversity index of 1.25. Most sea use patches correspond to the marine functional zonation plan and the sea use congruency index is 0.89 in the fishing zone and 0.92 in the transportation zone.

Genetic patterns of habitat fragmentation and past climate-change effects in the Mediterranean high-mountain plant Armeria caespitosa (Plumbaginaceae).

PubMed

García-Fernández, Alfredo; Iriondo, Jose M; Escudero, Adrián; Aguilar, Javier Fuertes; Feliner, Gonzalo Nieto

2013-08-01

Mountain plants are among the species most vulnerable to global warming, because of their isolation, narrow geographic distribution, and limited geographic range shifts. Stochastic and selective processes can act on the genome, modulating genetic structure and diversity. Fragmentation and historical processes also have a great influence on current genetic patterns, but the spatial and temporal contexts of these processes are poorly known. We aimed to evaluate the microevolutionary processes that may have taken place in Mediterranean high-mountain plants in response to changing historical environmental conditions. Genetic structure, diversity, and loci under selection were analyzed using AFLP markers in 17 populations distributed over the whole geographic range of Armeria caespitosa, an endemic plant that inhabits isolated mountains (Sierra de Guadarrama, Spain). Differences in altitude, geographic location, and climate conditions were considered in the analyses, because they may play an important role in selective and stochastic processes. Bayesian clustering approaches identified nine genetic groups, although some discrepancies in assignment were found between alternative analyses. Spatially explicit analyses showed a weak relationship between genetic parameters and spatial or environmental distances. However, a large proportion of outlier loci were detected, and some outliers were related to environmental variables. A. caespitosa populations exhibit spatial patterns of genetic structure that cannot be explained by the isolation-by-distance model. Shifts along the altitude gradient in response to Pleistocene climatic oscillations and environmentally mediated selective forces might explain the resulting structure and genetic diversity values found.

Detection of forest stand-level spatial structure in ectomycorrhizal fungal communities.

PubMed

Lilleskov, Erik A; Bruns, Thomas D; Horton, Thomas R; Taylor, D; Grogan, Paul

2004-08-01

Ectomycorrhizal fungal (EMF) communities are highly diverse at the stand level. To begin to understand what might lead to such diversity, and to improve sampling designs, we investigated the spatial structure of these communities. We used EMF community data from a number of studies carried out in seven mature and one recently fire-initiated forest stand. We applied various measures of spatial pattern to characterize distributions at EMF community and species levels: Mantel tests, Mantel correlograms, variance/mean and standardized variograms. Mantel tests indicated that in four of eight sites community similarity decreased with distance, whereas Mantel correlograms also found spatial autocorrelation in those four plus two additional sites. In all but one of these sites elevated similarity was evident only at relatively small spatial scales (< 2.6 m), whereas one exhibited a larger scale pattern ( approximately 25 m). Evenness of biomass distribution among cores varied widely among taxa. Standardized variograms indicated that most of the dominant taxa showed patchiness at a scale of less than 3 m, with a range from 0 to < or =17 m. These results have implications for both sampling scale and intensity to achieve maximum efficiency of community sampling. In the systems we examined, cores should be at least 3 m apart to achieve the greatest sampling efficiency for stand-level community analysis. In some cases even this spacing may result in reduced sampling efficiency arising from patterns of spatial autocorrelation. Interpretation of the causes and significance of these patterns requires information on the genetic identity of individuals in the communities.

Multilocus sequence analysis of Thermoanaerobacter isolates reveals recombining, but differentiated, populations from geothermal springs of the Uzon Caldera, Kamchatka, Russia

PubMed Central

Wagner, Isaac D.; Varghese, Litty B.; Hemme, Christopher L.; Wiegel, Juergen

2013-01-01

Thermal environments have island-like characteristics and provide a unique opportunity to study population structure and diversity patterns of microbial taxa inhabiting these sites. Strains having ≥98% 16S rRNA gene sequence similarity to the obligately anaerobic Firmicutes Thermoanaerobacter uzonensis were isolated from seven geothermal springs, separated by up to 1600 m, within the Uzon Caldera (Kamchatka, Russian Far East). The intraspecies variation and spatial patterns of diversity for this taxon were assessed by multilocus sequence analysis (MLSA) of 106 strains. Analysis of eight protein-coding loci (gyrB, lepA, leuS, pyrG, recA, recG, rplB, and rpoB) revealed that all loci were polymorphic and that nucleotide substitutions were mostly synonymous. There were 148 variable nucleotide sites across 8003 bp concatenates of the protein-coding loci. While pairwise FST values indicated a small but significant level of genetic differentiation between most subpopulations, there was a negligible relationship between genetic divergence and spatial separation. Strains with the same allelic profile were only isolated from the same hot spring, occasionally from consecutive years, and single locus variant (SLV) sequence types were usually derived from the same spring. While recombination occurred, there was an “epidemic” population structure in which a particular T. uzonensis sequence type rose in frequency relative to the rest of the population. These results demonstrate spatial diversity patterns for an anaerobic bacterial species in a relative small geographic location and reinforce the view that terrestrial geothermal springs are excellent places to look for biogeographic diversity patterns regardless of the involved distances. PMID:23801987

A comparative analysis reveals weak relationships between ecological factors and beta diversity of stream insect metacommunities at two spatial levels.

PubMed

Heino, Jani; Melo, Adriano S; Bini, Luis Mauricio; Altermatt, Florian; Al-Shami, Salman A; Angeler, David G; Bonada, Núria; Brand, Cecilia; Callisto, Marcos; Cottenie, Karl; Dangles, Olivier; Dudgeon, David; Encalada, Andrea; Göthe, Emma; Grönroos, Mira; Hamada, Neusa; Jacobsen, Dean; Landeiro, Victor L; Ligeiro, Raphael; Martins, Renato T; Miserendino, María Laura; Md Rawi, Che Salmah; Rodrigues, Marciel E; Roque, Fabio de Oliveira; Sandin, Leonard; Schmera, Denes; Sgarbi, Luciano F; Simaika, John P; Siqueira, Tadeu; Thompson, Ross M; Townsend, Colin R

2015-03-01

The hypotheses that beta diversity should increase with decreasing latitude and increase with spatial extent of a region have rarely been tested based on a comparative analysis of multiple datasets, and no such study has focused on stream insects. We first assessed how well variability in beta diversity of stream insect metacommunities is predicted by insect group, latitude, spatial extent, altitudinal range, and dataset properties across multiple drainage basins throughout the world. Second, we assessed the relative roles of environmental and spatial factors in driving variation in assemblage composition within each drainage basin. Our analyses were based on a dataset of 95 stream insect metacommunities from 31 drainage basins distributed around the world. We used dissimilarity-based indices to quantify beta diversity for each metacommunity and, subsequently, regressed beta diversity on insect group, latitude, spatial extent, altitudinal range, and dataset properties (e.g., number of sites and percentage of presences). Within each metacommunity, we used a combination of spatial eigenfunction analyses and partial redundancy analysis to partition variation in assemblage structure into environmental, shared, spatial, and unexplained fractions. We found that dataset properties were more important predictors of beta diversity than ecological and geographical factors across multiple drainage basins. In the within-basin analyses, environmental and spatial variables were generally poor predictors of variation in assemblage composition. Our results revealed deviation from general biodiversity patterns because beta diversity did not show the expected decreasing trend with latitude. Our results also call for reconsideration of just how predictable stream assemblages are along ecological gradients, with implications for environmental assessment and conservation decisions. Our findings may also be applicable to other dynamic systems where predictability is low.

Mapping genetic diversity of cherimoya (Annona cherimola Mill.): application of spatial analysis for conservation and use of plant genetic resources.

PubMed

Zonneveld, Maarten van; Scheldeman, Xavier; Escribano, Pilar; Viruel, María A; Van Damme, Patrick; Garcia, Willman; Tapia, César; Romero, José; Sigueñas, Manuel; Hormaza, José I

2012-01-01

There is a growing call for inventories that evaluate geographic patterns in diversity of plant genetic resources maintained on farm and in species' natural populations in order to enhance their use and conservation. Such evaluations are relevant for useful tropical and subtropical tree species, as many of these species are still undomesticated, or in incipient stages of domestication and local populations can offer yet-unknown traits of high value to further domestication. For many outcrossing species, such as most trees, inbreeding depression can be an issue, and genetic diversity is important to sustain local production. Diversity is also crucial for species to adapt to environmental changes. This paper explores the possibilities of incorporating molecular marker data into Geographic Information Systems (GIS) to allow visualization and better understanding of spatial patterns of genetic diversity as a key input to optimize conservation and use of plant genetic resources, based on a case study of cherimoya (Annona cherimola Mill.), a Neotropical fruit tree species. We present spatial analyses to (1) improve the understanding of spatial distribution of genetic diversity of cherimoya natural stands and cultivated trees in Ecuador, Bolivia and Peru based on microsatellite molecular markers (SSRs); and (2) formulate optimal conservation strategies by revealing priority areas for in situ conservation, and identifying existing diversity gaps in ex situ collections. We found high levels of allelic richness, locally common alleles and expected heterozygosity in cherimoya's putative centre of origin, southern Ecuador and northern Peru, whereas levels of diversity in southern Peru and especially in Bolivia were significantly lower. The application of GIS on a large microsatellite dataset allows a more detailed prioritization of areas for in situ conservation and targeted collection across the Andean distribution range of cherimoya than previous studies could do, i.e. at province and department level in Ecuador and Peru, respectively.

Mapping Genetic Diversity of Cherimoya (Annona cherimola Mill.): Application of Spatial Analysis for Conservation and Use of Plant Genetic Resources

PubMed Central

van Zonneveld, Maarten; Scheldeman, Xavier; Escribano, Pilar; Viruel, María A.; Van Damme, Patrick; Garcia, Willman; Tapia, César; Romero, José; Sigueñas, Manuel; Hormaza, José I.

2012-01-01

There is a growing call for inventories that evaluate geographic patterns in diversity of plant genetic resources maintained on farm and in species' natural populations in order to enhance their use and conservation. Such evaluations are relevant for useful tropical and subtropical tree species, as many of these species are still undomesticated, or in incipient stages of domestication and local populations can offer yet-unknown traits of high value to further domestication. For many outcrossing species, such as most trees, inbreeding depression can be an issue, and genetic diversity is important to sustain local production. Diversity is also crucial for species to adapt to environmental changes. This paper explores the possibilities of incorporating molecular marker data into Geographic Information Systems (GIS) to allow visualization and better understanding of spatial patterns of genetic diversity as a key input to optimize conservation and use of plant genetic resources, based on a case study of cherimoya (Annona cherimola Mill.), a Neotropical fruit tree species. We present spatial analyses to (1) improve the understanding of spatial distribution of genetic diversity of cherimoya natural stands and cultivated trees in Ecuador, Bolivia and Peru based on microsatellite molecular markers (SSRs); and (2) formulate optimal conservation strategies by revealing priority areas for in situ conservation, and identifying existing diversity gaps in ex situ collections. We found high levels of allelic richness, locally common alleles and expected heterozygosity in cherimoya's putative centre of origin, southern Ecuador and northern Peru, whereas levels of diversity in southern Peru and especially in Bolivia were significantly lower. The application of GIS on a large microsatellite dataset allows a more detailed prioritization of areas for in situ conservation and targeted collection across the Andean distribution range of cherimoya than previous studies could do, i.e. at province and department level in Ecuador and Peru, respectively. PMID:22253801

Herbivory and drought interact to enhance spatial patterning and diversity in a savanna understory.

PubMed

Porensky, Lauren M; Wittman, Sarah E; Riginos, Corinna; Young, Truman P

2013-10-01

The combination of abiotic stress and consumer stress can have complex impacts on plant community structure. Effective conservation and management of semi-arid ecosystems requires an understanding of how different stresses interact to structure plant communities. We explored the separate and combined impacts of episodic drought, livestock grazing, and wild ungulate herbivory on species co-occurrence and diversity patterns in a relatively productive, semi-arid Acacia savanna. Specifically, we analyzed 9 years of biannual plant community data from the Kenya long-term exclosure experiment, a broad-scale manipulative experiment that has excluded different combinations of large mammalian herbivores from 18 4-ha plots since 1995. During droughts, we observed low species diversity and random species co-occurrence patterns. However, when rain followed a major drought, areas exposed to moderate cattle grazing displayed high species diversity and evidence of significant species aggregation. These patterns were not apparent in the absence of cattle, even if other large herbivores were present. To explore possible mechanisms, we examined patterns separately for common and rare species. We found that aggregation patterns were likely driven by rare species responding similarly to the availability of open micro-sites. Our results indicate that in a productive, fire-suppressed savanna, the combination of periodic drought and moderate cattle grazing can enhance plant biodiversity and fine-scale spatial heterogeneity by opening up space for species that are otherwise rare or cryptic. Our findings also emphasize that domestic herbivores can have significantly stronger impacts on plant community dynamics than wild herbivores, even in an ecosystem with a long history of grazing.

Distribution, abundance, and diversity of stream fishes under variable environmental conditions

Treesearch

Christopher M. Taylor; Thomas L. Holder; Richard A. Fiorillo; Lance R. Williams; R. Brent Thomas; Melvin L. Warren

2006-01-01

The effects of stream size and flow regime on spatial and temporal variability of stream fish distribution, abundance, and diversity patterns were investigated. Assemblage variability and species richness were each significantly associated with a complex environmental gradient contrasting smaller, hydrologically variable stream localities with larger localities...

sGD: software for estimating spatially explicit indices of genetic diversity.

PubMed

Shirk, A J; Cushman, S A

2011-09-01

Anthropogenic landscape changes have greatly reduced the population size, range and migration rates of many terrestrial species. The small local effective population size of remnant populations favours loss of genetic diversity leading to reduced fitness and adaptive potential, and thus ultimately greater extinction risk. Accurately quantifying genetic diversity is therefore crucial to assessing the viability of small populations. Diversity indices are typically calculated from the multilocus genotypes of all individuals sampled within discretely defined habitat patches or larger regional extents. Importantly, discrete population approaches do not capture the clinal nature of populations genetically isolated by distance or landscape resistance. Here, we introduce spatial Genetic Diversity (sGD), a new spatially explicit tool to estimate genetic diversity based on grouping individuals into potentially overlapping genetic neighbourhoods that match the population structure, whether discrete or clinal. We compared the estimates and patterns of genetic diversity using patch or regional sampling and sGD on both simulated and empirical populations. When the population did not meet the assumptions of an island model, we found that patch and regional sampling generally overestimated local heterozygosity, inbreeding and allelic diversity. Moreover, sGD revealed fine-scale spatial heterogeneity in genetic diversity that was not evident with patch or regional sampling. These advantages should provide a more robust means to evaluate the potential for genetic factors to influence the viability of clinal populations and guide appropriate conservation plans. © 2011 Blackwell Publishing Ltd.

Evolutionary history of Lissotriton helveticus: multilocus assessment of ancestral vs. recent colonization of the Iberian Peninsula.

PubMed

Recuero, Ernesto; García-París, Mario

2011-07-01

The Pleistocene was characterized by climatic changes that greatly altered the distribution of organisms. Population extinctions, bottlenecks, isolation, range expansions and contractions were often associated with glaciations, leaving signatures in the spatial patterns of genetic diversity across species. Lissotriton helveticus belongs to a Pan-European lineage of newts that were strongly affected by glaciations and represent an excellent model to analyse the effect of generalized climatic changes in phylogeographic patterns. We studied the genetic diversity of the species using data from two mitochondrial and three nuclear genes analyzed in a Bayesian phylogenetic framework to investigate the historical processes shaping spatial patterns of genetic diversity. Mitochondrial haplotypes cluster in four different groups present in the Iberian Peninsula and of Pleistocene origin, probably by allopatric fragmentation. Nuclear genes present no obvious geographic structure patterns, suggesting gene flow and generalized incomplete lineage sorting. Populations north of the Pyrenees are closely related to those from northeastern Iberia, suggesting recent range expansion from this region. Historical demographic analyses indicate a demographic expansion starting about 100,000years ago and more recent population declines. Compared to other Lissotriton species, L. helveticus includes only relatively young genetic lineages, suggesting a Central European pre-Pleistocene distribution followed by complete extirpation of the species during glaciations in that area. Historical demographic trends in the Iberian Peninsula are reversed with respect to the more Mediterranean species Lissotriton boscai, indicating different responses of both species to climate changes. Diversity patterns among Lissotriton species seem to be defined by four main factors: ancestral distributions, colonization capabilities, interactions with other species and effective population sizes. Differences in these factors define two types of species, referred to as "R" (refugia) and "S" (sanctuaries) that explain part of the diversity in patterns of genetic diversity created by glaciations in Western Europe. Copyright © 2011 Elsevier Inc. All rights reserved.

Shrub expansion in northern Chihuahuan Desert grasslands: Spatial patterns of transition and biophysical constraints

USDA-ARS?s Scientific Manuscript database

Among the greatest contemporary threats to the structure, function and biological diversity of desert grassland and shrub savanna ecosystems of the southwestern United States is the displacement of mesophytic grasses by xerophytic woody plants. Through a combination of field sampling and spatial mod...

Characterizing fire-related spatial patterns in fire-prone ecosystems using optical and microwave remote sensing

NASA Astrophysics Data System (ADS)

Henry, Mary Catherine

The use of active and passive remote sensing systems for relating forest spatial patterns to fire history was tested over one of the Arizona Sky Islands. Using Landsat Thematic Mapper (TM), Shuttle Imaging Radar (SIR-C), and data fusion I examined the relationship between landscape metrics and a range of fire history characteristics. Each data type (TM, SIR-C, and fused) was processed in the following manner: each band, channel, or derived feature was simplified to a thematic layer and landscape statistics were calculated for plots with known fire history. These landscape metrics were then correlated with fire history characteristics, including number of fire-free years in a given time period, mean fire-free interval, and time since fire. Results from all three case studies showed significant relationships between fire history and forest spatial patterns. Data fusion performed as well or better than Landsat TM alone, and better than SIR-C alone. These comparisons were based on number and strength of significant correlations each method achieved. The landscape metric that was most consistent and obtained the greatest number of significant correlations was Shannon's Diversity Index. Results also agreed with field-based research that has linked higher fire frequency to increased landscape diversity and patchiness. An additional finding was that the fused data seem to detect fire-related spatial patterns over a range of scales.

Global patterns of evolutionary distinct and globally endangered amphibians and mammals.

PubMed

Safi, Kamran; Armour-Marshall, Katrina; Baillie, Jonathan E M; Isaac, Nick J B

2013-01-01

Conservation of phylogenetic diversity allows maximising evolutionary information preserved within fauna and flora. The "EDGE of Existence" programme is the first institutional conservation initiative that prioritises species based on phylogenetic information. Species are ranked in two ways: one according to their evolutionary distinctiveness (ED) and second, by including IUCN extinction status, their evolutionary distinctiveness and global endangerment (EDGE). Here, we describe the global patterns in the spatial distribution of priority ED and EDGE species, in order to identify conservation areas for mammalian and amphibian communities. In addition, we investigate whether environmental conditions can predict the observed spatial pattern in ED and EDGE globally. Priority zones with high concentrations of ED and EDGE scores were defined using two different methods. The overlap between mammal and amphibian zones was very small, reflecting the different phylo-biogeographic histories. Mammal ED zones were predominantly found on the African continent and the neotropical forests, whereas in amphibians, ED zones were concentrated in North America. Mammal EDGE zones were mainly in South-East Asia, southern Africa and Madagascar; for amphibians they were in central and south America. The spatial pattern of ED and EDGE was poorly described by a suite of environmental variables. Mapping the spatial distribution of ED and EDGE provides an important step towards identifying priority areas for the conservation of mammalian and amphibian phylogenetic diversity in the EDGE of existence programme.

Bird diversity along a gradient of fragmented habitats of the Cerrado.

PubMed

Jesus, Shayana DE; Pedro, Wagner A; Bispo, Arthur A

2018-01-01

Understanding the factors that affect biodiversity is of central interest to ecology, and essential to species conservation and ecosystems management. We sampled bird communities in 17 forest fragments in the Cerrado biome, the Central-West region of Brazil. We aimed to know the communities structure pattern and the influence of geographical distance and environmental variables on them, along a gradient of fragmented habitats at both local and landscape scales. Eight structural variables of the fragments served as an environmental distance measurement at the local scale while five metrics served as an environmental distance measurement at the landscape scale. Species presence-absence data were used to calculate the dissimilarity index. Beta diversity was calculated using three indices (βsim, βnes and βsor), representing the spatial species turnover, nestedness and total beta diversity, respectively. Spatial species turnover was the predominant pattern in the structure of the communities. Variations in beta diversity were explained only by the environmental variables of the landscape with spatial configuration being more important than the composition. This fact indicates that, in Cerrado of Goiás avian communities structure, deterministic ecological processes associated to differences in species responses to landscape fragmentation are more important than stochastic processes driven by species dispersal.

Putting Beta-Diversity on the Map: Broad-Scale Congruence and Coincidence in the Extremes

PubMed Central

McKnight, Meghan W; White, Peter S; McDonald, Robert I; Lamoreux, John F; Sechrest, Wes; Ridgely, Robert S; Stuart, Simon N

2007-01-01

Beta-diversity, the change in species composition between places, is a critical but poorly understood component of biological diversity. Patterns of beta-diversity provide information central to many ecological and evolutionary questions, as well as to conservation planning. Yet beta-diversity is rarely studied across large extents, and the degree of similarity of patterns among taxa at such scales remains untested. To our knowledge, this is the first broad-scale analysis of cross-taxon congruence in beta-diversity, and introduces a new method to map beta-diversity continuously across regions. Congruence between amphibian, bird, and mammal beta-diversity in the Western Hemisphere varies with both geographic location and spatial extent. We demonstrate that areas of high beta-diversity for the three taxa largely coincide, but areas of low beta-diversity exhibit little overlap. These findings suggest that similar processes lead to high levels of differentiation in amphibian, bird, and mammal assemblages, while the ecological and biogeographic factors influencing homogeneity in vertebrate assemblages vary. Knowledge of beta-diversity congruence can help formulate hypotheses about the mechanisms governing regional diversity patterns and should inform conservation, especially as threat from global climate change increases. PMID:17927449

Multiple spatial scale analyses provide new clues on patterns and drivers of deep-sea nematode diversity

NASA Astrophysics Data System (ADS)

Danovaro, Roberto; Carugati, Laura; Corinaldesi, Cinzia; Gambi, Cristina; Guilini, Katja; Pusceddu, Antonio; Vanreusel, Ann

2013-08-01

The deep sea is the largest biome of the biosphere. The knowledge of the spatial variability of deep-sea biodiversity is one of the main challenges of marine ecology and evolutionary biology. The choice of the observational spatial scale is assumed to play a key role for understanding processes structuring the deep-sea benthic communities and one of the most typical features of marine biodiversity distribution is the existence of bathymetric gradients. However, the analysis of biodiversity bathymetric gradients and the associated changes in species composition (beta diversity) typically compared large depth ranges (with intervals of 500 to 1000 or even 2000 m depth among sites). To test whether significant changes in alpha and beta diversity occur also at fine-scale bathymetric gradients (i.e., within few hundred-meter depth intervals) the variability of deep-sea nematode biodiversity and assemblage composition along a bathymetric transect (200-1200 m depth) with intervals of 200 m among sampling depths, was investigated. A hierarchical sampling strategy for the analysis of nematode species richness, beta diversity, functional (trophic) diversity, and related environmental variables, was used. The results indicate the lack of significant differences in taxonomic and functional diversity across sampling depths, but the presence of high beta diversity at all spatial scales investigated: between cores collected from the same box corer (on average 56%), among deployments at the same depth (58%), and between all sampling depths (62%). Such high beta diversity is influenced by the presence of small-scale patchiness in the deep sea and is also related to the large number of rare or very rare species (typically accounting for >80% of total species richness). Moreover, the number of ubiquitous nematode species across all sampling depths is quite low (ca. 15%). Multiple regression analyses provide evidence that such patterns could be related to the different availability, composition and size spectra of food particles in the sediments. Additionally, though to a lesser extent, our results indicate, that selective predation can influence the nematode trophic composition. These findings suggest that a multiple scale analysis based on a nested sampling design could significantly improve our knowledge of bathymetric patterns of deep-sea biodiversity and its drivers.

Spatial patterns in land cover of exurbanizing watersheds in southeastern Michigan

Treesearch

Rebecca L. Cifaldi; David Allan; J. D. Duh; Daniel G. Brown

2003-01-01

Recent research into landscape composition and configuration, or pattern, seeks to identify a core set of metrics and determine whether these describe unique gradients or dimensions of pattern across diverse settings. Prior work generally has examined relatively large units, and it is uncertain whether this approach will prove useful with small (50-100 km2...

Area-based tests for association between spatial patterns

NASA Astrophysics Data System (ADS)

Maruca, Susan L.; Jacquez, Geoffrey M.

Edge effects pervade natural systems, and the processes that determine spatial heterogeneity (e.g. physical, geochemical, biological, ecological factors) occur on diverse spatial scales. Hence, tests for association between spatial patterns should be unbiased by edge effects and be based on null spatial models that incorporate the spatial heterogeneity characteristic of real-world systems. This paper develops probabilistic pattern association tests that are appropriate when edge effects are present, polygon size is heterogeneous, and the number of polygons varies from one classification to another. The tests are based on the amount of overlap between polygons in each of two partitions. Unweighted and area-weighted versions of the statistics are developed and verified using scenarios representing both polygon overlap and avoidance at different spatial scales and for different distributions of polygon sizes. These statistics were applied to Soda Butte Creek, Wyoming, to determine whether stream microhabitats, such as riffles, pools and glides, can be identified remotely using high spatial resolution hyperspectral imagery. These new ``spatially explicit'' techniques provide information and insights that cannot be obtained from the spectral information alone.

Spatial and temporal variation at major histocompatibility complex class IIB genes in the endangered Blakiston's fish owl.

PubMed

Kohyama, Tetsuo I; Omote, Keita; Nishida, Chizuko; Takenaka, Takeshi; Saito, Keisuke; Fujimoto, Satoshi; Masuda, Ryuichi

2015-01-01

Quantifying intraspecific genetic variation in functionally important genes, such as those of the major histocompatibility complex (MHC), is important in the establishment of conservation plans for endangered species. The MHC genes play a crucial role in the vertebrate immune system and generally show high levels of diversity, which is likely due to pathogen-driven balancing selection. The endangered Blakiston's fish owl (Bubo blakistoni) has suffered marked population declines on Hokkaido Island, Japan, during the past several decades due to human-induced habitat loss and fragmentation. We investigated the spatial and temporal patterns of genetic diversity in MHC class IIβ genes in Blakiston's fish owl, using massively parallel pyrosequencing. We found that the Blakiston's fish owl genome contains at least eight MHC class IIβ loci, indicating recent gene duplications. An analysis of sequence polymorphism provided evidence that balancing selection acted in the past. The level of MHC variation, however, was low in the current fish owl populations in Hokkaido: only 19 alleles were identified from 174 individuals. We detected considerable spatial differences in MHC diversity among the geographically isolated populations. We also detected a decline of MHC diversity in some local populations during the past decades. Our study demonstrated that the current spatial patterns of MHC variation in Blakiston's fish owl populations have been shaped by loss of variation due to the decline and fragmentation of populations, and that the short-term effects of genetic drift have counteracted the long-term effects of balancing selection.

Gap formation following climatic events in spatially structured plant communities

PubMed Central

Liao, Jinbao; De Boeck, Hans J.; Li, Zhenqing; Nijs, Ivan

2015-01-01

Gaps play a crucial role in maintaining species diversity, yet how community structure and composition influence gap formation is still poorly understood. We apply a spatially structured community model to predict how species diversity and intraspecific aggregation shape gap patterns emerging after climatic events, based on species-specific mortality responses. In multispecies communities, average gap size and gap-size diversity increased rapidly with increasing mean mortality once a mortality threshold was exceeded, greatly promoting gap recolonization opportunity. This result was observed at all levels of species richness. Increasing interspecific difference likewise enhanced these metrics, which may promote not only diversity maintenance but also community invasibility, since more diverse niches for both local and exotic species are provided. The richness effects on gap size and gap-size diversity were positive, but only expressed when species were sufficiently different. Surprisingly, while intraspecific clumping strongly promoted gap-size diversity, it hardly influenced average gap size. Species evenness generally reduced gap metrics induced by climatic events, so the typical assumption of maximum evenness in many experiments and models may underestimate community diversity and invasibility. Overall, understanding the factors driving gap formation in spatially structured assemblages can help predict community secondary succession after climatic events. PMID:26114803

Patterns of genetic diversity in the polymorphic ground snake (Sonora semiannulata).

PubMed

Cox, Christian L; Chippindale, Paul T

2014-08-01

We evaluated the genetic diversity of a snake species with color polymorphism to understand the evolutionary processes that drive genetic structure across a large geographic region. Specifically, we analyzed genetic structure of the highly polymorphic ground snake, Sonora semiannulata, (1) among populations, (2) among color morphs (3) at regional and local spatial scales, using an amplified fragment length polymorphism dataset and multiple population genetic analyses, including FST-based and clustering analytical techniques. Based upon these methods, we found that there was moderate to low genetic structure among populations. However, this diversity was not associated with geographic locality at either spatial scale. Similarly, we found no evidence for genetic divergence among color morphs at either spatial scale. These results suggest that despite dramatic color polymorphism, this phenotypic diversity is not a major driver of genetic diversity within or among populations of ground snakes. We suggest that there are two mechanisms that could explain existing genetic diversity in ground snakes: recent range expansion from a genetically diverse founder population and current or recent gene flow among populations. Our findings have further implications for the types of color polymorphism that may generate genetic diversity in snakes.

Revealing Beta-Diversity Patterns of Breeding Bird and Lizard Communities on Inundated Land-Bridge Islands by Separating the Turnover and Nestedness Components

PubMed Central

Si, Xingfeng; Baselga, Andrés; Ding, Ping

2015-01-01

Beta diversity describes changes in species composition among sites in a region and has particular relevance for explaining ecological patterns in fragmented habitats. However, it is difficult to reveal the mechanisms if broad sense beta-diversity indices (i.e. yielding identical values under nestedness and species replacement) are used. Partitioning beta diversity into turnover (caused by species replacement from site to site) and nestedness-resultant components (caused by nested species losses) could provide a unique way to understand the variation of species composition in fragmented habitats. Here, we collected occupancy data of breeding birds and lizards on land-bridge islands in an inundated lake in eastern China. We decomposed beta diversity of breeding bird and lizard communities into spatial turnover and nestedness-resultant components to assess their relative contributions and respective relationships to differences in island area, isolation, and habitat richness. Our results showed that spatial turnover contributed more to beta diversity than the nestedness-resultant component. The degree of isolation had no significant effect on overall beta diversity or its components, neither for breeding birds nor for lizards. In turn, in both groups the nestedness-resultant component increased with larger differences in island area and habitat richness, respectively, while turnover component decreased with them. The major difference among birds and lizards was a higher relevance of nestedness-resultant dissimilarity in lizards, suggesting that they are more prone to local extinctions derived from habitat fragmentation. The dominance of the spatial turnover component of beta diversity suggests that all islands have potential conservation value for breeding bird and lizard communities. PMID:25992559

Long-term trends in the structure of eastern Adriatic littoral fish assemblages: Consequences for fisheries management

NASA Astrophysics Data System (ADS)

Stagličić, N.; Matić-Skoko, S.; Pallaoro, A.; Grgičević, R.; Kraljević, M.; Tutman, P.; Dragičević, B.; Dulčić, J.

2011-09-01

Long-term interannual changes in abundance, biomass, diversity and structure of littoral fish assemblages were examined between 1993 and 2009 by experimental trammel net fishing up to six times per year, within the warm period - May to September, at multiple areas along the eastern Adriatic coast with the aim of testing for the consistency of patterns of change across a large spatial scale (˜600 km). The results revealed spatially consistent increasing trends of total fish abundance and biomass growing at an average rate of 15 and 14% per year, respectively. Of the diversity indices analysed, the same pattern of variability was observed for Shannon diversity, while Pielou evenness and average taxonomic distinctness measures Δ ∗ and Δ + showed spatial variability with no obvious temporal trends. Multivariate fish assemblage structure underwent a directional change displaying a similar pattern through time for all the areas. The structural change in fish assemblages generally involved most of the species present in trammel net catches. A large pool of fish species responsible for producing the temporal pattern of assemblage change was relatively different in each of the areas reflecting a large geographic range covered by the study. An analysis of 4 fish species ( Symphodus tinca, Pagellus erythrinus, Mullus surmuletus, Scorpaena porcus) common to each of the study areas as the ones driving the temporal change indicated that there were clear increasing trends of their mean catches across the years at all the study areas. A common pattern among time trajectories across the spatial scale studied implies that the factor affecting the littoral fish assemblages is not localised but regional in nature. As an underlying factor having the potential to induce such widespread and consistent improvements in littoral fish assemblages, a more restrictive artisanal fishery management that has progressively been put in place during the study period, is suggested and discussed.

Species-area relationships in coral communities: evaluating mechanisms for a commonly observed pattern

NASA Astrophysics Data System (ADS)

Huntington, B. E.; Lirman, D.

2012-12-01

Landscape-scale attributes of patch size, spatial isolation, and topographic complexity are known to influence diversity and abundance in terrestrial and marine systems, but remain collectively untested for reef-building corals. To investigate the relationship between the coral assemblage and seascape variation in reef habitats, we took advantage of the distinct boundaries, spatial configurations, and topographic complexities among artificial reef patches to overcome the difficulties of manipulating natural reefs. Reef size (m2) was found to be the foremost predictor of coral richness in accordance with species-area relationship predictions. Larger reefs were also found to support significantly higher colony densities, enabling us to reject the null hypothesis of random placement (a sampling artifact) in favor of target area predictions that suggest greater rates of immigration on larger reefs. Unlike the pattern previously documented for reef fishes, topographic complexity was not a significant predictor of any coral assemblage response variable, despite the range of complexity values sampled. Lastly, coral colony density was best explained by both increasing reef size and decreasing reef spatial isolation, a pattern found exclusively among brooding species with shorter larval dispersal distances. We conclude that seascape attributes of reef size and spatial configuration within the seascape can influence the species richness and abundance of the coral community at relatively small spatial scales (<1 km). Specifically, we demonstrate how patterns in the coral communities that have naturally established on these manipulated reefs agree with the target area and island biogeography mechanisms to drive species-area relationships in reef-building corals. Based on the patterns documented in artificial reefs, habitat degradation that results in smaller, more isolated natural reefs may compromise coral diversity.

Consequences of extensive habitat fragmentation in landscape-level patterns of genetic diversity and structure in the Mediterranean esparto grasshopper

PubMed Central

Ortego, Joaquín; Aguirre, María P; Noguerales, Víctor; Cordero, Pedro J

2015-01-01

Anthropogenic habitat fragmentation has altered the distribution and population sizes in many organisms worldwide. For this reason, understanding the demographic and genetic consequences of this process is necessary to predict the fate of populations and establish management practices aimed to ensure their viability. In this study, we analyse whether the spatial configuration of remnant semi-natural habitat patches within a chronically fragmented landscape has shaped the patterns of genetic diversity and structure in the habitat-specialist esparto grasshopper (Ramburiella hispanica). In particular, we predict that agricultural lands constitute barriers to gene flow and hypothesize that fragmentation has restricted interpopulation dispersal and reduced local levels of genetic diversity. Our results confirmed the expectation that isolation and habitat fragmentation have reduced the genetic diversity of local populations. Landscape genetic analyses based on circuit theory showed that agricultural land offers ∽1000 times more resistance to gene flow than semi-natural habitats, indicating that patterns of dispersal are constrained by the spatial configuration of remnant patches of suitable habitat. Overall, this study shows that semi-natural habitat patches act as corridors for interpopulation gene flow and should be preserved due to the disproportionately large ecological function that they provide considering their insignificant area within these human-modified landscapes. PMID:26136826

Spatial scaling patterns and functional redundancies in a changing boreal lake landscape

USGS Publications Warehouse

Angeler, David G.; Allen, Craig R.; Uden, Daniel R.; Johnson, Richard K.

2015-01-01

Global transformations extend beyond local habitats; therefore, larger-scale approaches are needed to assess community-level responses and resilience to unfolding environmental changes. Using longterm data (1996–2011), we evaluated spatial patterns and functional redundancies in the littoral invertebrate communities of 85 Swedish lakes, with the objective of assessing their potential resilience to environmental change at regional scales (that is, spatial resilience). Multivariate spatial modeling was used to differentiate groups of invertebrate species exhibiting spatial patterns in composition and abundance (that is, deterministic species) from those lacking spatial patterns (that is, stochastic species). We then determined the functional feeding attributes of the deterministic and stochastic invertebrate species, to infer resilience. Between one and three distinct spatial patterns in invertebrate composition and abundance were identified in approximately one-third of the species; the remainder were stochastic. We observed substantial differences in metrics between deterministic and stochastic species. Functional richness and diversity decreased over time in the deterministic group, suggesting a loss of resilience in regional invertebrate communities. However, taxon richness and redundancy increased monotonically in the stochastic group, indicating the capacity of regional invertebrate communities to adapt to change. Our results suggest that a refined picture of spatial resilience emerges if patterns of both the deterministic and stochastic species are accounted for. Spatially extensive monitoring may help increase our mechanistic understanding of community-level responses and resilience to regional environmental change, insights that are critical for developing management and conservation agendas in this current period of rapid environmental transformation.

Biogeographic patterns of soil diazotrophic communities across six forests in the North America.

PubMed

Tu, Qichao; Deng, Ye; Yan, Qingyun; Shen, Lina; Lin, Lu; He, Zhili; Wu, Liyou; Van Nostrand, Joy D; Buzzard, Vanessa; Michaletz, Sean T; Enquist, Brian J; Weiser, Michael D; Kaspari, Michael; Waide, Robert B; Brown, James H; Zhou, Jizhong

2016-06-01

Soil diazotrophs play important roles in ecosystem functioning by converting atmospheric N2 into biologically available ammonium. However, the diversity and distribution of soil diazotrophic communities in different forests and whether they follow biogeographic patterns similar to macroorganisms still remain unclear. By sequencing nifH gene amplicons, we surveyed the diversity, structure and biogeographic patterns of soil diazotrophic communities across six North American forests (126 nested samples). Our results showed that each forest harboured markedly different soil diazotrophic communities and that these communities followed traditional biogeographic patterns similar to plant and animal communities, including the taxa-area relationship (TAR) and latitudinal diversity gradient. Significantly higher community diversity and lower microbial spatial turnover rates (i.e. z-values) were found for rainforests (~0.06) than temperate forests (~0.1). The gradient pattern of TARs and community diversity was strongly correlated (r(2)  > 0.5) with latitude, annual mean temperature, plant species richness and precipitation, and weakly correlated (r(2)  < 0.25) with pH and soil moisture. This study suggests that even microbial subcommunities (e.g. soil diazotrophs) follow general biogeographic patterns (e.g. TAR, latitudinal diversity gradient), and indicates that the metabolic theory of ecology and habitat heterogeneity may be the major underlying ecological mechanisms shaping the biogeographic patterns of soil diazotrophic communities. © 2016 John Wiley & Sons Ltd.

Eco-geophysical imaging of watershed-scale soil patterns links with plant community spatial patterns

USDA-ARS?s Scientific Manuscript database

The extent to which soil resource availability, nutrients or 1 moisture, control the structure, function and diversity of plant communities has aroused considerable interest in the past decade, and remains topical in light of global change. Numerous plant communities are controlled either by water o...

Small-scale topography modulates elevational α-, β- and γ-diversity of Andean leaf beetles.

PubMed

Thormann, Birthe; Ahrens, Dirk; Espinosa, Carlos Iván; Armijos, Diego Marín; Wagner, Thomas; Wägele, Johann W; Peters, Marcell K

2018-05-01

Elevational diversity gradients are typically studied without considering the complex small-scale topography of large mountains, which generates habitats of strongly different environmental conditions within the same elevational zones. Here we analyzed the importance of small-scale topography for elevational diversity patterns of hyperdiverse tropical leaf beetles (Coleoptera: Chrysomelidae). We compared patterns of elevational diversity and species composition of beetles in two types of forests (on mountain ridges and in valleys) and analyzed whether differences in the rate of species turnover among forest habitats lead to shifts in patterns of elevational diversity when scaling up from the local study site to the elevational belt level. We sampled beetle assemblages at 36 sites in the Podocarpus National Park, Ecuador, which were equally distributed over two forest habitats and three elevational levels. DNA barcoding and Poisson tree processes modelling were used to delimitate putative species. On average, local leaf beetle diversity showed a clear hump-shaped pattern. However, only diversity in forests on mountain ridges peaked at mid-elevation, while beetle diversity in valleys was similarly high at low- and mid-elevation and only declined at highest elevations. A higher turnover of species assemblages at lower than at mid-elevations caused a shift from a hump-shaped diversity pattern found at the local level to a low-elevation plateau pattern (with similar species numbers at low and mid-elevation) at the elevational belt level. Our study reveals an important role of small-scale topography and spatial scale for the inference on gradients of elevational species diversity.

The Emerging Spatial Organization of the Metropolis: Zones of Diversity and Minority Enclaves in Chicago

PubMed Central

Zhang, Wenquan; Logan, John R.

2018-01-01

The rapid growth of Asian and Hispanic populations in urban areas is superceding traditional classifications of neighborhoods (for example as white, transitional, or minority). The “global neighborhood” that includes all groups (white, black, Hispanic and Asian) is one important new category. We examine the emerging spatial pattern of racial/ethnic composition in the Chicago metropolis, documenting an expansion of all-minority neighborhoods in the city and just beyond its borders, a shrinking set of all-white neighborhoods in the outer suburbs, and more diverse neighborhoods including whites mainly in between. The most novel element of this pattern is how large the zone of diversity has become and how far it extends into suburbia, upending the old dichotomy of “chocolate city” and “vanilla suburbs.” In addition to comparing the distance of different kinds of neighborhoods from the urban core, we also analyze their adjacency to neighborhoods of the same type or other types. There is a strong tendency toward spatial clustering of each neighborhood type and also for transitions on the boundaries of clusters either to expand or to contract their territory. PMID:29430517

Multispecies genetic objectives in spatial conservation planning.

PubMed

Nielsen, Erica S; Beger, Maria; Henriques, Romina; Selkoe, Kimberly A; von der Heyden, Sophie

2017-08-01

Growing threats to biodiversity and global alteration of habitats and species distributions make it increasingly necessary to consider evolutionary patterns in conservation decision making. Yet, there is no clear-cut guidance on how genetic features can be incorporated into conservation-planning processes, despite multiple molecular markers and several genetic metrics for each marker type to choose from. Genetic patterns differ between species, but the potential tradeoffs among genetic objectives for multiple species in conservation planning are currently understudied. We compared spatial conservation prioritizations derived from 2 metrics of genetic diversity (nucleotide and haplotype diversity) and 2 metrics of genetic isolation (private haplotypes and local genetic differentiation) in mitochondrial DNA of 5 marine species. We compared outcomes of conservation plans based only on habitat representation with plans based on genetic data and habitat representation. Fewer priority areas were selected for conservation plans based solely on habitat representation than on plans that included habitat and genetic data. All 4 genetic metrics selected approximately similar conservation-priority areas, which is likely a result of prioritizing genetic patterns across a genetically diverse array of species. Largely, our results suggest that multispecies genetic conservation objectives are vital to creating protected-area networks that appropriately preserve community-level evolutionary patterns. © 2016 Society for Conservation Biology.

Drivers of coastal bacterioplankton community diversity and structure along a nutrient gradient in the East China Sea

NASA Astrophysics Data System (ADS)

He, Jiaying; Wang, Kai; Xiong, Jinbo; Guo, Annan; Zhang, Demin; Fei, Yuejun; Ye, Xiansen

2017-04-01

Anthropogenic nutrient discharge poses widespread threats to coastal ecosystems and has increased environmental gradients from coast to sea. Bacterioplankton play crucial roles in coastal biogeochemical cycling, and a variety of factors affect bacterial community diversity and structure. We used 16S rRNA gene pyrosequencing to investigate the spatial variation in bacterial community composition (BCC) across five sites on a coast-offshore gradient in the East China Sea. Overall, bacterial alpha-diversity did not differ across sites, except that richness and phylogenetic diversity were lower in the offshore sites, and the highest alpha-diversity was found in the most landward site, with Chl-a being the main factor. BCCs generally clustered into coastal and offshore groups. Chl-a explained 12.3% of the variation in BCCs, more than that explained by either the physicochemical (5.7%) or spatial (8.5%) variables. Nutrients (particularly nitrate and phosphate), along with phytoplankton abundance, were more important than other physicochemical factors, co-explaining 20.0% of the variation in BCCs. Additionally, a series of discriminant families (primarily affiliated with Gammaproteobacteria and Alphaproteobacteria), whose relative abundances correlated with Chl-a, DIN, and phosphate concentrations, were identified, implying their potential to indicate phytoplankton blooms and nutrient enrichment in this marine ecosystem. This study provides insight into bacterioplankton response patterns along a coast-offshore gradient, with phytoplankton abundance increasing in the offshore sites. Time-series sampling across multiple transects should be performed to determine the seasonal and spatial patterns in bacterial diversity and community structure along this gradient.

Drivers of coastal bacterioplankton community diversity and structure along a nutrient gradient in the East China Sea

NASA Astrophysics Data System (ADS)

He, Jiaying; Wang, Kai; Xiong, Jinbo; Guo, Annan; Zhang, Demin; Fei, Yuejun; Ye, Xiansen

2018-03-01

Anthropogenic nutrient discharge poses widespread threats to coastal ecosystems and has increased environmental gradients from coast to sea. Bacterioplankton play crucial roles in coastal biogeochemical cycling, and a variety of factors affect bacterial community diversity and structure. We used 16S rRNA gene pyrosequencing to investigate the spatial variation in bacterial community composition (BCC) across five sites on a coast-offshore gradient in the East China Sea. Overall, bacterial alpha-diversity did not differ across sites, except that richness and phylogenetic diversity were lower in the offshore sites, and the highest alpha-diversity was found in the most landward site, with Chl-a being the main factor. BCCs generally clustered into coastal and offshore groups. Chl-a explained 12.3% of the variation in BCCs, more than that explained by either the physicochemical (5.7%) or spatial (8.5%) variables. Nutrients (particularly nitrate and phosphate), along with phytoplankton abundance, were more important than other physicochemical factors, co-explaining 20.0% of the variation in BCCs. Additionally, a series of discriminant families (primarily affiliated with Gammaproteobacteria and Alphaproteobacteria), whose relative abundances correlated with Chl-a, DIN, and phosphate concentrations, were identified, implying their potential to indicate phytoplankton blooms and nutrient enrichment in this marine ecosystem. This study provides insight into bacterioplankton response patterns along a coast-offshore gradient, with phytoplankton abundance increasing in the offshore sites. Time-series sampling across multiple transects should be performed to determine the seasonal and spatial patterns in bacterial diversity and community structure along this gradient.

Environmental characteristics drive variation in Amazonian understorey bird assemblages

PubMed Central

Magnusson, William E.; Anderson, Marti J.; Schlegel, Martin; Pe’er, Guy; Henle, Klaus

2017-01-01

Tropical bird assemblages display patterns of high alpha and beta diversity and, as tropical birds exhibit strong habitat specificity, their spatial distributions are generally assumed to be driven primarily by environmental heterogeneity and interspecific interactions. However, spatial distributions of some Amazonian forest birds are also often restricted by large rivers and other large-scale topographic features, suggesting that dispersal limitation may also play a role in driving species’ turnover. In this study, we evaluated the effects of environmental characteristics, topographic and spatial variables on variation in local assemblage structure and diversity of birds in an old-growth forest in central Amazonia. Birds were mist-netted in 72 plots distributed systematically across a 10,000 ha reserve in each of three years. Alpha diversity remained stable through time, but species composition changed. Spatial variation in bird-assemblage structure was significantly related to environmental and topographic variables but not strongly related to spatial variables. At a broad scale, we found bird assemblages to be significantly distinct between two watersheds that are divided by a central ridgeline. We did not detect an effect of the ridgeline per se in driving these patterns, indicating that most birds are able to fly across it, and that differences in assemblage structure between watersheds may be due to unmeasured environmental variables or unique combinations of measured variables. Our study indicates that complex geography and landscape features can act together with environmental variables to drive changes in the diversity and composition of tropical bird assemblages at local scales, but highlights that we still know very little about what makes different parts of tropical forest suitable for different species. PMID:28225774

Evaluating population expansion of black bears using spatial capture-recapture

USGS Publications Warehouse

Sun, Catherine C.; Fuller, Angela K.; Hare, Matthew P.; Hurst, Jeremy E.

2017-01-01

The population of American black bears (Ursus americanus) in southern New York, USA has been growing and expanding in range since the 1990s. This has motivated a need to anticipate future patterns of range expansion. We conducted a non-invasive, genetic, spatial capture-recapture (SCR) study to estimate black bear density and identify spatial patterns of population density that are potentially associated with range expansion. We collected hair samples in a 2,519-km2 study area in southern New York with barbed-wire hair snares and identified individuals and measured genetic diversity using 7 microsatellite loci and 1 sex-linked marker. We estimated a mean density of black bears in the region of 13.7 bears/100 km2, and detected a slight latitudinal gradient in density consistent with the documented range expansion. However, elevation and the amounts of forest, crop, and developed landcover types did not influence density, suggesting that bears are using a diversity of resources in this heterogeneous landscape outside their previously described distribution. These results provide the first robust baseline estimates for population density and distribution associated with different landcover types in the expanded bear range. Further, genetic diversity was comparable to that of non-expanding black bear populations in the eastern United States, and in combination with the latitudinal density gradient, suggest that the study area is not at the colonizing front of the range expansion. In addition, the diversity of landcover types used by bears in the study area implies a possible lack of constraints for further northern expansion of the black bear range. Our non-invasive, genetic, spatial capture-recapture approach has utility for studying populations of other species that may be expanding in range because SCR allows for the testing of explicit, spatial ecological hypotheses. 

Intensive agriculture erodes β-diversity at large scales.

PubMed

Karp, Daniel S; Rominger, Andrew J; Zook, Jim; Ranganathan, Jai; Ehrlich, Paul R; Daily, Gretchen C

2012-09-01

Biodiversity is declining from unprecedented land conversions that replace diverse, low-intensity agriculture with vast expanses under homogeneous, intensive production. Despite documented losses of species richness, consequences for β-diversity, changes in community composition between sites, are largely unknown, especially in the tropics. Using a 10-year data set on Costa Rican birds, we find that low-intensity agriculture sustained β-diversity across large scales on a par with forest. In high-intensity agriculture, low local (α) diversity inflated β-diversity as a statistical artefact. Therefore, at small spatial scales, intensive agriculture appeared to retain β-diversity. Unlike in forest or low-intensity systems, however, high-intensity agriculture also homogenised vegetation structure over large distances, thereby decoupling the fundamental ecological pattern of bird communities changing with geographical distance. This ~40% decline in species turnover indicates a significant decline in β-diversity at large spatial scales. These findings point the way towards multi-functional agricultural systems that maintain agricultural productivity while simultaneously conserving biodiversity. © 2012 Blackwell Publishing Ltd/CNRS.

The relationship between satellite-derived indices and species diversity across African savanna ecosystems

NASA Astrophysics Data System (ADS)

Mapfumo, Ratidzo B.; Murwira, Amon; Masocha, Mhosisi; Andriani, R.

2016-10-01

The ability to use remotely sensed diversity is important for the management of ecosystems at large spatial extents. However, to achieve this, there is still need to develop robust methods and approaches that enable large-scale mapping of species diversity. In this study, we tested the relationship between species diversity measured in situ with the Normalized Difference Vegetation Index (NDVI) and the Coefficient of Variation in the NDVI (CVNDVI) derived from high and medium spatial resolution satellite data at dry, wet and coastal savanna woodlands. We further tested the effect of logging on NDVI along the transects and between transects as disturbance may be a mechanism driving the patterns observed. Overall, the results of this study suggest that high tree species diversity is associated with low and high NDVI and at intermediate levels is associated with low tree species diversity and NDVI. High tree species diversity is associated with high CVNDVI and vice versa and at intermediate levels is associated with high tree species diversity and CVNDVI.

Coexistence of species with different dispersal across landscapes: a critical role of spatial correlation in disturbance.

PubMed

Liao, Jinbao; Ying, Zhixia; Woolnough, Daelyn A; Miller, Adam D; Li, Zhenqing; Nijs, Ivan

2016-05-11

Disturbance is key to maintaining species diversity in plant communities. Although the effects of disturbance frequency and extent on species diversity have been studied, we do not yet have a mechanistic understanding of how these aspects of disturbance interact with spatial structure of disturbance to influence species diversity. Here we derive a novel pair approximation model to explore competitive outcomes in a two-species system subject to spatially correlated disturbance. Generally, spatial correlation in disturbance favoured long-range dispersers, while distance-limited dispersers were greatly suppressed. Interestingly, high levels of spatial aggregation of disturbance promoted long-term species coexistence that is not possible in the absence of disturbance, but only when the local disperser was intrinsically competitively superior. However, spatial correlation in disturbance led to different competitive outcomes, depending on the disturbed area. Concerning ecological conservation and management, we theoretically demonstrate that introducing a spatially correlated disturbance to the system or altering an existing disturbance regime can be a useful strategy either to control species invasion or to promote species coexistence. Disturbance pattern analysis may therefore provide new insights into biodiversity conservation. © 2016 The Author(s).

Macroecology of unicellular organisms - patterns and processes.

PubMed

Soininen, Janne

2012-02-01

Macroecology examines the relationship between organisms and their environment at large spatial (and temporal) scales. Typically, macroecologists explain the large-scale patterns of abundance, distribution and diversity. Despite the difficulties in sampling and characterizing microbial diversity, macroecologists have recently also been interested in unicellular organisms. Here, I review the current advances made in microbial macroecology, as well as discuss related ecosystem functions. Overall, it seems that microorganisms suit surprisingly well to known species abundance distributions and show positive relationship between distribution and adundance. Microbial species-area and distance-decay relationships tend to be weaker than for macroorganisms, but nonetheless significant. Few findings on altitudinal gradients in unicellular taxa seem to differ greatly from corresponding findings for larger taxa, whereas latitudinal gradients among microorganisms have either been clearly evident or absent depending on the context. Literature also strongly emphasizes the role of spatial scale for the patterns of diversity and suggests that patterns are affected by species traits as well as ecosystem characteristics. Finally, I discuss the large role of local biotic and abiotic variables driving the community assembly in unicellular taxa and eventually dictating how multiple ecosystem processes are performed. Present review highlights the fact that most microorganisms may not differ fundamentally from larger taxa in their large-scale distribution patterns. Yet, review also shows that many aspects of microbial macroecology are still relatively poorly understood and specific patterns depend on focal taxa and ecosystem concerned. © 2011 Society for Applied Microbiology and Blackwell Publishing Ltd.

Higher speciation and lower extinction rates influence mammal diversity gradients in Asia.

PubMed

Tamma, Krishnapriya; Ramakrishnan, Uma

2015-02-04

Little is known about the patterns and correlates of mammal diversity gradients in Asia. In this study, we examine patterns of species distributions and phylogenetic diversity in Asia and investigate if the observed diversity patterns are associated with differences in diversification rates between the tropical and non-tropical regions. We used species distribution maps and phylogenetic trees to generate species and phylogenetic diversity measures for 1° × 1° cells across mainland Asia. We constructed lineage-through-time plots and estimated diversification shift-times to examine the temporal patterns of diversifications across orders. Finally, we tested if the observed gradients in Asia could be associated with geographical differences in diversification rates across the tropical and non-tropical biomes. We estimated speciation, extinction and dispersal rates across these two regions for mammals, both globally and for Asian mammals. Our results demonstrate strong latitudinal and longitudinal gradients of species and phylogenetic diversity with Southeast Asia and the Himalayas showing highest diversity. Importantly, our results demonstrate that differences in diversification (speciation, extinction and dispersal) rates between the tropical and the non-tropical biomes influence the observed diversity gradients globally and in Asia. For the first time, we demonstrate that Asian tropics act as both cradles and museums of mammalian diversity. Temporal and spatial variation in diversification rates across different lineages of mammals is an important correlate of species diversity gradients observed in Asia.

Genomic patterns in Acropora cervicornis show extensive population structure and variable genetic diversity.

PubMed

Drury, Crawford; Schopmeyer, Stephanie; Goergen, Elizabeth; Bartels, Erich; Nedimyer, Ken; Johnson, Meaghan; Maxwell, Kerry; Galvan, Victor; Manfrino, Carrie; Lirman, Diego

2017-08-01

Threatened Caribbean coral communities can benefit from high-resolution genetic data used to inform management and conservation action. We use Genotyping by Sequencing (GBS) to investigate genetic patterns in the threatened coral, Acropora cervicornis , across the Florida Reef Tract (FRT) and the western Caribbean. Results show extensive population structure at regional scales and resolve previously unknown structure within the FRT. Different regions also exhibit up to threefold differences in genetic diversity (He), suggesting targeted management based on the goals and resources of each population is needed. Patterns of genetic diversity have a strong spatial component, and our results show Broward and the Lower Keys are among the most diverse populations in Florida. The genetic diversity of Caribbean staghorn coral is concentrated within populations and within individual reefs (AMOVA), highlighting the complex mosaic of population structure. This variance structure is similar over regional and local scales, which suggests that in situ nurseries are adequately capturing natural patterns of diversity, representing a resource that can replicate the average diversity of wild assemblages, serving to increase intraspecific diversity and potentially leading to improved biodiversity and ecosystem function. Results presented here can be translated into specific goals for the recovery of A. cervicornis , including active focus on low diversity areas, protection of high diversity and connectivity, and practical thresholds for responsible restoration.

Macroecological factors shape local-scale spatial patterns in agriculturalist settlements.

PubMed

Tao, Tingting; Abades, Sebastián; Teng, Shuqing; Huang, Zheng Y X; Reino, Luís; Chen, Bin J W; Zhang, Yong; Xu, Chi; Svenning, Jens-Christian

2017-11-15

Macro-scale patterns of human systems ranging from population distribution to linguistic diversity have attracted recent attention, giving rise to the suggestion that macroecological rules shape the assembly of human societies. However, in which aspects the geography of our own species is shaped by macroecological factors remains poorly understood. Here, we provide a first demonstration that macroecological factors shape strong local-scale spatial patterns in human settlement systems, through an analysis of spatial patterns in agriculturalist settlements in eastern mainland China based on high-resolution Google Earth images. We used spatial point pattern analysis to show that settlement spatial patterns are characterized by over-dispersion at fine spatial scales (0.05-1.4 km), consistent with territory segregation, and clumping at coarser spatial scales beyond the over-dispersion signals, indicating territorial clustering. Statistical modelling shows that, at macroscales, potential evapotranspiration and topographic heterogeneity have negative effects on territory size, but positive effects on territorial clustering. These relationships are in line with predictions from territory theory for hunter-gatherers as well as for many animal species. Our results help to disentangle the complex interactions between intrinsic spatial processes in agriculturalist societies and external forcing by macroecological factors. While one may speculate that humans can escape ecological constraints because of unique abilities for environmental modification and globalized resource transportation, our work highlights that universal macroecological principles still shape the geography of current human agricultural societies. © 2017 The Author(s).

Spatial variability of macrobenthic zonation on exposed sandy beaches

NASA Astrophysics Data System (ADS)

Veiga, Puri; Rubal, Marcos; Cacabelos, Eva; Maldonado, Cristina; Sousa-Pinto, Isabel

2014-07-01

We analysed the consistence of vertical patterns of distribution (i.e. zonation) for macrofauna at different spatial scales on four intermediate exposed beaches in the North of Portugal. We tested the hypothesis that biological zonation on exposed sandy beaches would vary at the studied spatial scales. For this aim, abundance, diversity and structure of macrobenthic assemblages were examined at the scales of transect and beach. Moreover, the main environmental factors that could potentially drive zonation patterns were investigated. Univariate and multivariate analyses revealed that the number of biological zones ranged from two to three depending on the beach and from indistinct zonation to three zones at the scale of transect. Therefore, results support our working hypothesis because zonation patterns were not consistent at the studied spatial scales. The median particle size, sorting coefficient and water content were significantly correlated with zonation patterns of macrobenthic assemblages. However, a high degree of correlation was not reached when the total structure of the assemblage was considered.

Patterns of genetic variability and habitat occupancy in Crepis triasii (Asteraceae) at different spatial scales: insights on evolutionary processes leading to diversification in continental islands

PubMed Central

Mayol, Maria; Palau, Carles; Rosselló, Josep A.; González-Martínez, Santiago C.; Molins, Arántzazu; Riba, Miquel

2012-01-01

Background and Aims Archipelagos are unique systems for studying evolutionary processes promoting diversification and speciation. The islands of the Mediterranean basin are major areas of plant richness, including a high proportion of narrow endemics. Many endemic plants are currently found in rocky habitats, showing varying patterns of habitat occupancy at different spatial scales throughout their range. The aim of the present study was to understand the impact of varying patterns of population distribution on genetic diversity and structure to shed light on demographic and evolutionary processes leading to population diversification in Crepis triasii, an endemic plant from the eastern Balearic Islands. Methods Using allozyme and chloroplast markers, we related patterns of genetic structure and diversity to those of habitat occupancy at a regional (between islands and among populations within islands) and landscape (population size and connectivity) scale. Key Results Genetic diversity was highly structured both at the regional and at the landscape level, and was positively correlated with population connectivity in the landscape. Populations located in small isolated mountains and coastal areas, with restricted patterns of regional occupancy, were genetically less diverse and much more differentiated. In addition, more isolated populations had stronger fine-scale genetic structure than well-connected ones. Changes in habitat availability and quality arising from marine transgressions during the Quaternary, as well as progressive fragmentation associated with the aridification of the climate since the last glaciation, are the most plausible factors leading to the observed patterns of genetic diversity and structure. Conclusions Our results emphasize the importance of gene flow in preventing genetic erosion and maintaining the evolutionary potential of populations. They also agree with recent studies highlighting the importance of restricted gene flow and genetic drift as drivers of plant evolution in Mediterranean continental islands. PMID:22167790

Patterns of seed bank and vegetation diversity along a tidal freshwater river.

PubMed

Elsey-Quirk, Tracy; Leck, Mary Allessio

2015-12-01

Species richness and diversity may increase with spatial scale related to increased area and heterogeneity of habitat. Yet, in bidirectional hydrologically connected tidal ecosystems, secondary dispersal via hydrochory has the potential to homogenize seed banks, and both life history characteristics and tolerances to environmental conditions influence the composition of plant communities. How species richness, diversity, and composition of seed banks and vegetation change along environmental gradients and at different spatial scales is not well understood. We explored the relationships of seed bank and vegetation diversity across 135 plots along a tidal freshwater river in the Delaware Estuary, USA. Species richness and diversity were partitioned across three hierarchical spatial scales: individual plots, transects perpendicular to the tidal channel, and river kilometers. Community structure was also examined as it related to distance from the tidal channel and location along the tidal river. Species richness was 89 in the seed bank and 54 in the vegetation. Species-area relationships revealed that species richness reached a near maximum asymptote inland (20 m from channel) for the seed bank and at the edge (0 m) for the vegetation. Rare occurrences of species in the seed bank and vegetation were greatest 5 m from the channel edge. As spatial scale increased, seed bank richness increased, associated with the progressive accumulation of species. Seed bank diversity, however, was maximized within small plot areas and along the river. Diversity of the vegetation was maximized locally due to the abundance of a few common species. These findings suggest that suites of common species contributed to high localized vegetation diversity, yet large spatial scales maximized the number and diversity of species in the seed bank and vegetation through rare encounters, as well as the complexity of the landscape. © 2015 Botanical Society of America.

Spatial aspects of tree mortality strongly differ between young and old-growth forests.

PubMed

Larson, Andrew J; Lutz, James A; Donato, Daniel C; Freund, James A; Swanson, Mark E; HilleRisLambers, Janneke; Sprugel, Douglas G; Franklin, Jerry F

2015-11-01

Rates and spatial patterns of tree mortality are predicted to change during forest structural development. In young forests, mortality should be primarily density dependent due to competition for light, leading to an increasingly spatially uniform pattern of surviving trees. In contrast, mortality in old-growth forests should be primarily caused by contagious and spatially autocorrelated agents (e.g., insects, wind), causing spatial aggregation of surviving trees to increase through time. We tested these predictions by contrasting a three-decade record of tree mortality from replicated mapped permanent plots located in young (< 60-year-old) and old-growth (> 300-year-old) Abies amabilis forests. Trees in young forests died at a rate of 4.42% per year, whereas trees in old-growth forests died at 0.60% per year. Tree mortality in young forests was significantly aggregated, strongly density dependent, and caused live tree patterns to become more uniform through time. Mortality in old-growth forests was spatially aggregated, but was density independent and did not change the spatial pattern of surviving trees. These results extend current theory by demonstrating that density-dependent competitive mortality leading to increasingly uniform tree spacing in young forests ultimately transitions late in succession to a more diverse tree mortality regime that maintains spatial heterogeneity through time.

Climatic suitability, isolation by distance and river resistance explain genetic variation in a Brazilian whiptail lizard.

PubMed

Oliveira, Eliana Faria; Martinez, Pablo Ariel; São-Pedro, Vinícius Avelar; Gehara, Marcelo; Burbrink, Frank Thomas; Mesquita, Daniel Oliveira; Garda, Adrian Antonio; Colli, Guarino Rinaldi; Costa, Gabriel Correa

2018-03-01

Spatial patterns of genetic variation can help understand how environmental factors either permit or restrict gene flow and create opportunities for regional adaptations. Organisms from harsh environments such as the Brazilian semiarid Caatinga biome may reveal how severe climate conditions may affect patterns of genetic variation. Herein we combine information from mitochondrial DNA with physical and environmental features to study the association between different aspects of the Caatinga landscape and spatial genetic variation in the whiptail lizard Ameivula ocellifera. We investigated which of the climatic, environmental, geographical and/or historical components best predict: (1) the spatial distribution of genetic diversity, and (2) the genetic differentiation among populations. We found that genetic variation in A. ocellifera has been influenced mainly by temperature variability, which modulates connectivity among populations. Past climate conditions were important for shaping current genetic diversity, suggesting a time lag in genetic responses. Population structure in A. ocellifera was best explained by both isolation by distance and isolation by resistance (main rivers). Our findings indicate that both physical and climatic features are important for explaining the observed patterns of genetic variation across the xeric Caatinga biome.

Spatial and temporal drivers of phenotypic diversity in polymorphic snakes.

PubMed

Cox, Christian L; Davis Rabosky, Alison R

2013-08-01

Color polymorphism in natural populations presents an ideal opportunity to study the evolutionary drivers of phenotypic diversity. Systems with striking spatial, temporal, and qualitative variation in color can be leveraged to study the mechanisms promoting the distribution of different types of variation in nature. We used the highly polymorphic ground snake (Sonora semiannulata), a putative coral snake mimic with both cryptic and conspicuous morphs, to compare patterns of neutral genetic variation and variation over space and time in color polymorphism to investigate the mechanistic drivers of phenotypic variation across scales. We found that strong selection promotes color polymorphism across spatial and temporal scales, with morph frequencies differing markedly between juvenile and adult age classes within a single population, oscillating over time within multiple populations, and varying drastically over the landscape despite minimal population genetic structure. However, we found no evidence that conspicuousness of morphs was related to which color pattern was favored by selection or to any geographic factors, including sympatry with coral snakes. We suggest that complex patterns of phenotypic variation in polymorphic systems may be a fundamental outcome of the conspicuousness of morphs and that explicit tests of temporal and geographic variation are critical to the interpretation of conspicuousness and mimicry.

Evolutionary history and functional traits determine the spatial pattern of multifaceted plant diversity in a typical temperate desert disturbed by an expressway.

PubMed

Li, Shuai; Dong, Shikui; Zhang, Xiangfeng; Liu, Shiliang; Shi, Jianbin; Gao, Xiaoxia; Swift, David; Xu, Yudan; Shen, Hao; Yang, Mingyue; Margarida, Canhoto Coxixo Ana

2018-04-20

Temperate desert is one of the globally important biomes with unique and valuable biodiversity, which might be threatened by environmental stresses and human disturbance associated with rapid development. However, few studies have documented the spatial distribution of the multifaceted plant diversity of the temperate desert and their relationships with external impacting factors. We sampled multifaceted plant species diversity including taxonomic diversity, functional diversity and phylogenetic diversity in the Alashan Desert along Beijing-Xinjiang Expressway (G6) in Northern China to identify the key factors and process which regulate the multifaceted plant diversity of the temperate desert. We found that the dynamics of species richness, functional richness, and phylogenetic richness along the elevational gradient corresponded to the unimodal model. Species phylogenetic development shifted from aggregation to divergence, while species functional traits were the opposite along the elevational gradient. The sites at an elevation around 1200-1400 m were the key habitats for the occurrence of high plant diversity including species richness, functional richness and phylogenetic richness. There were no significant differences (p > 0.05) in plant diversity at different distances from the road (500 m, 1000 m and 1500 m) and human disturbances (the distance from the nearest human settlements). Temperature, temperature variability, precipitation, precipitation variability, soil physical and chemistry properties showed no significant effects on plant diversity. It was concluded that evolutionary history and functional traits, not environmental or anthropogenic factors were the key determinants of the pattern of multifaceted plant diversity. Copyright © 2018 Elsevier B.V. All rights reserved.

Using Laser-Induced Thermal Voxels to Pattern Diverse Materials at the Solid-Liquid Interface.

PubMed

Zarzar, Lauren D; Swartzentruber, B S; Donovan, Brian F; Hopkins, Patrick E; Kaehr, Bryan

2016-08-24

We describe a high-resolution patterning approach that combines the spatial control inherent to laser direct writing with the versatility of benchtop chemical synthesis. By taking advantage of the steep thermal gradient that occurs while laser heating a metal edge in contact with solution, diverse materials comprising transition metals are patterned with feature size resolution nearing 1 μm. We demonstrate fabrication of reduced metallic nickel in one step and examine electrical properties and air stability through direct-write integration onto a device platform. This strategy expands the chemistries and materials that can be used in combination with laser direct writing.

Using laser-induced thermal voxels to pattern diverse materials at the solid–liquid interface

DOE PAGES

Zarzar, Lauren D.; Swartzentruber, B. S.; Donovan, Brian F.; ...

2016-08-05

We describe a high-resolution patterning approach that combines the spatial control inherent to laser direct writing with the versatility of benchtop chemical synthesis. By taking advantage of the steep thermal gradient that occurs while laser heating a metal edge in contact with solution, diverse materials comprising transition metals are patterned with feature size resolution nearing 1 μm. We demonstrate fabrication of reduced metallic nickel in one step and examine electrical properties and air stability through direct-write integration onto a device platform. In conclusion, this strategy expands the chemistries and materials that can be used in combination with laser direct writing.

Spatial patterns of distribution, abundance, and species diversity of small odontocetes estimated using density surface modeling with line transect sampling

NASA Astrophysics Data System (ADS)

Kanaji, Yu; Okazaki, Makoto; Miyashita, Tomio

2017-06-01

Spatial patterns of distribution, abundance, and species diversity of small odontocetes including species in the Delphinidae and Phocoenidae families were investigated using long-term dedicated sighting survey data collected between 1983 and 2006 in the North Pacific. Species diversity indices were calculated from abundance estimated using density surface modeling of line-transect data. The estimated abundance ranged from 19,521 individuals in killer whale to 1,886,022 in pantropical spotted dolphin. The predicted density maps showed that the habitats of small odontocetes corresponded well with distinct oceanic domains. Species richness was estimated to be highest between 30 and 40°N where warm- and cold-water currents converge. Simpson's Diversity Index showed latitudinal diversity gradients of decreasing species numbers toward the poles. Higher diversity was also estimated in the coastal areas and the zonal areas around 35-42°N. Coastal-offshore gradients and latitudinal gradients are known for many taxa. The zonal areas around 35°N and 40°N coincide with the Kuroshio Current and its extension and the subarctic boundary, respectively. These results suggest that the species diversity of small odontocetes primarily follows general patterns of latitudinal and longitudinal gradients, while the confluence of faunas originating in distinct water masses increases species diversify in frontal waters around 30-40°N. Population densities tended to be higher for the species inhabiting higher latitudes, but were highest for intermediate latitudes at approximately 35-40°N. According to latitudinal gradients in water temperature and biological productivity, the costs for thermoregulation will decrease in warmer low latitudes, while feeding efficiency will increase in colder high latitudes. These trade-offs could optimize population density in intermediate latitudes.

Learning place cells, grid cells and invariances with excitatory and inhibitory plasticity

PubMed Central

2018-01-01

Neurons in the hippocampus and adjacent brain areas show a large diversity in their tuning to location and head direction, and the underlying circuit mechanisms are not yet resolved. In particular, it is unclear why certain cell types are selective to one spatial variable, but invariant to another. For example, place cells are typically invariant to head direction. We propose that all observed spatial tuning patterns – in both their selectivity and their invariance – arise from the same mechanism: Excitatory and inhibitory synaptic plasticity driven by the spatial tuning statistics of synaptic inputs. Using simulations and a mathematical analysis, we show that combined excitatory and inhibitory plasticity can lead to localized, grid-like or invariant activity. Combinations of different input statistics along different spatial dimensions reproduce all major spatial tuning patterns observed in rodents. Our proposed model is robust to changes in parameters, develops patterns on behavioral timescales and makes distinctive experimental predictions. PMID:29465399

Present spatial diversity patterns of Theobroma cacao L. in the neotropics reflect genetic differentiation in pleistocene refugia followed by human-influenced dispersal.

PubMed

Thomas, Evert; van Zonneveld, Maarten; Loo, Judy; Hodgkin, Toby; Galluzzi, Gea; van Etten, Jacob

2012-01-01

Cacao (Theobroma cacao L.) is indigenous to the Amazon basin, but is generally believed to have been domesticated in Mesoamerica for the production of chocolate beverage. However, cacao's distribution of genetic diversity in South America is also likely to reflect pre-Columbian human influences that were superimposed on natural processes of genetic differentiation. Here we present the results of a spatial analysis of the intra-specific diversity of cacao in Latin America, drawing on a dataset of 939 cacao trees genotypically characterized by means of 96 SSR markers. To assess continental diversity patterns we performed grid-based calculations of allelic richness, Shannon diversity and Nei gene diversity, and distinguished different spatially coherent genetic groups by means of cluster analysis. The highest levels of genetic diversity were observed in the Upper Amazon areas from southern Peru to the Ecuadorian Amazon and the border areas between Colombia, Peru and Brazil. On the assumption that the last glaciation (22,000-13,000 BP) had the greatest pre-human impact on the current distribution and diversity of cacao, we modeled the species' Pleistocene niche suitability and overlaid this with present-day diversity maps. The results suggest that cacao was already widely distributed in the Western Amazon before the onset of glaciation. During glaciations, cacao populations were likely to have been restricted to several refugia where they probably underwent genetic differentiation, resulting in a number of genetic clusters which are representative for, or closest related to, the original wild cacao populations. The analyses also suggested that genetic differentiation and geographical distribution of a number of other clusters seem to have been significantly affected by processes of human management and accompanying genetic bottlenecks. We discuss the implications of these results for future germplasm collection and in situ, on farm and ex situ conservation of cacao.

Present Spatial Diversity Patterns of Theobroma cacao L. in the Neotropics Reflect Genetic Differentiation in Pleistocene Refugia Followed by Human-Influenced Dispersal

PubMed Central

Thomas, Evert; van Zonneveld, Maarten; Loo, Judy; Hodgkin, Toby; Galluzzi, Gea; van Etten, Jacob

2012-01-01

Cacao (Theobroma cacao L.) is indigenous to the Amazon basin, but is generally believed to have been domesticated in Mesoamerica for the production of chocolate beverage. However, cacao’s distribution of genetic diversity in South America is also likely to reflect pre-Columbian human influences that were superimposed on natural processes of genetic differentiation. Here we present the results of a spatial analysis of the intra-specific diversity of cacao in Latin America, drawing on a dataset of 939 cacao trees genotypically characterized by means of 96 SSR markers. To assess continental diversity patterns we performed grid-based calculations of allelic richness, Shannon diversity and Nei gene diversity, and distinguished different spatially coherent genetic groups by means of cluster analysis. The highest levels of genetic diversity were observed in the Upper Amazon areas from southern Peru to the Ecuadorian Amazon and the border areas between Colombia, Peru and Brazil. On the assumption that the last glaciation (22,000–13,000 BP) had the greatest pre-human impact on the current distribution and diversity of cacao, we modeled the species’ Pleistocene niche suitability and overlaid this with present-day diversity maps. The results suggest that cacao was already widely distributed in the Western Amazon before the onset of glaciation. During glaciations, cacao populations were likely to have been restricted to several refugia where they probably underwent genetic differentiation, resulting in a number of genetic clusters which are representative for, or closest related to, the original wild cacao populations. The analyses also suggested that genetic differentiation and geographical distribution of a number of other clusters seem to have been significantly affected by processes of human management and accompanying genetic bottlenecks. We discuss the implications of these results for future germplasm collection and in situ, on farm and ex situ conservation of cacao. PMID:23112832

Genetic diversity in Capsicum baccatum is significantly influenced by its ecogeographical distribution.

PubMed

Albrecht, Elena; Zhang, Dapeng; Mays, Anne Deslattes; Saftner, Robert A; Stommel, John R

2012-08-06

The exotic pepper species Capsicum baccatum, also known as the aji or Peruvian hot pepper, is comprised of wild and domesticated botanical forms. The species is a valuable source of new genes useful for improving fruit quality and disease resistance in C. annuum sweet bell and hot chile pepper. However, relatively little research has been conducted to characterize the species, thus limiting its utilization. The structure of genetic diversity in a plant germplasm collection is significantly influenced by its ecogeographical distribution. Together with DNA fingerprints derived from AFLP markers, we evaluated variation in fruit and plant morphology of plants collected across the species native range in South America and evaluated these characters in combination with the unique geography, climate and ecology at different sites where plants originated. The present study mapped the ecogeographic distribution, analyzed the spatial genetic structure, and assessed the relationship between the spatial genetic pattern and the variation of morphological traits in a diverse C. baccatum germplasm collection spanning the species distribution. A combined diversity analysis was carried out on the USDA-ARS C. baccatum germplasm collection using data from GIS, morphological traits and AFLP markers. The results demonstrate that the C. baccatum collection covers wide geographic areas and is adapted to divergent ecological conditions in South America ranging from cool Andean highland to Amazonia rainforest. A high level of morphological diversity was evident in the collection, with fruit weight the leading variable. The fruit weight distribution pattern was compatible to AFLP-based clustering analysis for the collection. A significant spatial structure was observed in the C. baccatum gene pool. Division of the domesticated germplasm into two major regional groups (Western and Eastern) was further supported by the pattern of spatial population structure. The results reported improve our understanding of the combined effects of geography, ecology and human intervention on organization of the C. baccatum genepool. The results will facilitate utilization of C. baccatum for crop improvement and species conservation by providing a framework for efficient germplasm collection management and guidance for future plant acquisitions.

Genetic diversity in Capsicum baccatum is significantly influenced by its ecogeographical distribution

PubMed Central

2012-01-01

Background The exotic pepper species Capsicum baccatum, also known as the aji or Peruvian hot pepper, is comprised of wild and domesticated botanical forms. The species is a valuable source of new genes useful for improving fruit quality and disease resistance in C. annuum sweet bell and hot chile pepper. However, relatively little research has been conducted to characterize the species, thus limiting its utilization. The structure of genetic diversity in a plant germplasm collection is significantly influenced by its ecogeographical distribution. Together with DNA fingerprints derived from AFLP markers, we evaluated variation in fruit and plant morphology of plants collected across the species native range in South America and evaluated these characters in combination with the unique geography, climate and ecology at different sites where plants originated. Results The present study mapped the ecogeographic distribution, analyzed the spatial genetic structure, and assessed the relationship between the spatial genetic pattern and the variation of morphological traits in a diverse C. baccatum germplasm collection spanning the species distribution. A combined diversity analysis was carried out on the USDA-ARS C. baccatum germplasm collection using data from GIS, morphological traits and AFLP markers. The results demonstrate that the C. baccatum collection covers wide geographic areas and is adapted to divergent ecological conditions in South America ranging from cool Andean highland to Amazonia rainforest. A high level of morphological diversity was evident in the collection, with fruit weight the leading variable. The fruit weight distribution pattern was compatible to AFLP-based clustering analysis for the collection. A significant spatial structure was observed in the C. baccatum gene pool. Division of the domesticated germplasm into two major regional groups (Western and Eastern) was further supported by the pattern of spatial population structure. Conclusions The results reported improve our understanding of the combined effects of geography, ecology and human intervention on organization of the C. baccatum genepool. The results will facilitate utilization of C. baccatum for crop improvement and species conservation by providing a framework for efficient germplasm collection management and guidance for future plant acquisitions. PMID:22866868

Stair-Step Pattern of Soil Bacterial Diversity Mainly Driven by pH and Vegetation Types Along the Elevational Gradients of Gongga Mountain, China

PubMed Central

Li, Jiabao; Shen, Zehao; Li, Chaonan; Kou, Yongping; Wang, Yansu; Tu, Bo; Zhang, Shiheng; Li, Xiangzhen

2018-01-01

Ecological understandings of soil bacterial community succession and assembly mechanism along elevational gradients in mountains remain not well understood. Here, by employing the high-throughput sequencing technique, we systematically examined soil bacterial diversity patterns, the driving factors, and community assembly mechanisms along the elevational gradients of 1800–4100 m on Gongga Mountain in China. Soil bacterial diversity showed an extraordinary stair-step pattern along the elevational gradients. There was an abrupt decrease of bacterial diversity between 2600 and 2800 m, while no significant change at either lower (1800–2600 m) or higher (2800–4100 m) elevations, which coincided with the variation in soil pH. In addition, the community structure differed significantly between the lower and higher elevations, which could be primarily attributed to shifts in soil pH and vegetation types. Although there was no direct effect of MAP and MAT on bacterial community structure, our partial least squares path modeling analysis indicated that bacterial communities were indirectly influenced by climate via the effect on vegetation and the derived effect on soil properties. As for bacterial community assembly mechanisms, the null model analysis suggested that environmental filtering played an overwhelming role in the assembly of bacterial communities in this region. In addition, variation partition analysis indicated that, at lower elevations, environmental attributes explained much larger fraction of the β-deviation than spatial attributes, while spatial attributes increased their contributions at higher elevations. Our results highlight the importance of environmental filtering, as well as elevation-related spatial attributes in structuring soil bacterial communities in mountain ecosystems. PMID:29636740

Insights into the Genetic History of French Cattle from Dense SNP Data on 47 Worldwide Breeds

PubMed Central

Gautier, Mathieu; Laloë, Denis; Moazami-Goudarzi, Katayoun

2010-01-01

Background Modern cattle originate from populations of the wild extinct aurochs through a few domestication events which occurred about 8,000 years ago. Newly domesticated populations subsequently spread worldwide following breeder migration routes. The resulting complex historical origins associated with both natural and artificial selection have led to the differentiation of numerous different cattle breeds displaying a broad phenotypic variety over a short period of time. Methodology/Principal Findings This study gives a detailed assessment of cattle genetic diversity based on 1,121 individuals sampled in 47 populations from different parts of the world (with a special focus on French cattle) genotyped for 44,706 autosomal SNPs. The analyzed data set consisted of new genotypes for 296 individuals representing 14 French cattle breeds which were combined to those available from three previously published studies. After characterizing SNP polymorphism in the different populations, we performed a detailed analysis of genetic structure at both the individual and population levels. We further searched for spatial patterns of genetic diversity among 23 European populations, most of them being of French origin, under the recently developed spatial Principal Component analysis framework. Conclusions/Significance Overall, such high throughput genotyping data confirmed a clear partitioning of the cattle genetic diversity into distinct breeds. In addition, patterns of differentiation among the three main groups of populations—the African taurine, the European taurine and zebus—may provide some additional support for three distinct domestication centres. Finally, among the European cattle breeds investigated, spatial patterns of genetic diversity were found in good agreement with the two main migration routes towards France, initially postulated based on archeological evidence. PMID:20927341

Evaluating patterns and drivers of spatial change in the recreational guided fishing sector in Alaska

PubMed Central

2017-01-01

Understanding the impacts of recreational fishing on habitats and species, as well as the social and ecological importance of place to anglers, requires information on the spatial distribution of fishing activities. This study documented long-term changes in core fishing areas of a major recreational fishery in Alaska and identified biological, regulatory, social, and economic drivers of spatial fishing patterns by charter operators. Using participatory mapping and in-person interviews, we characterized the spatial footprint of 46 charter operators in the communities of Sitka and Homer since the 1990s. The spatial footprint differed between Homer and Sitka respondents, with Homer operators consistently using larger areas for Pacific halibut than Sitka operators. Homer and Sitka showed opposite trends in core fishing location area over time, with an overall decrease in Homer and an overall increase in Sitka. For both Sitka and Homer respondents, the range of areas fished was greater for Pacific halibut than for rockfish/lingcod or Pacific salmon. Spatial patterns were qualitatively different between businesses specializing in single species trips and those that operated multispecies trips and between businesses with one vessel and those with multiple vessels. In Homer, the most frequently cited reasons for changes in the location and/or extent of fishing were changes in trip type and the price of fuel, while in Sitka, the most frequently cited reasons for spatial shifts were changes to Pacific halibut regulations and gaining experience or exploring new locations. The diversity of charter fishing strategies in Alaska may allow individual charter operators to respond differently to perturbations and thus maintain resilience of the industry as a whole to social, environmental, and regulatory change. This research also highlights the importance of understanding fishers’ diverse portfolio of activities to effective ecosystem-based management. PMID:28632745

Evaluating patterns and drivers of spatial change in the recreational guided fishing sector in Alaska.

PubMed

Chan, Maggie N; Beaudreau, Anne H; Loring, Philip A

2017-01-01

Understanding the impacts of recreational fishing on habitats and species, as well as the social and ecological importance of place to anglers, requires information on the spatial distribution of fishing activities. This study documented long-term changes in core fishing areas of a major recreational fishery in Alaska and identified biological, regulatory, social, and economic drivers of spatial fishing patterns by charter operators. Using participatory mapping and in-person interviews, we characterized the spatial footprint of 46 charter operators in the communities of Sitka and Homer since the 1990s. The spatial footprint differed between Homer and Sitka respondents, with Homer operators consistently using larger areas for Pacific halibut than Sitka operators. Homer and Sitka showed opposite trends in core fishing location area over time, with an overall decrease in Homer and an overall increase in Sitka. For both Sitka and Homer respondents, the range of areas fished was greater for Pacific halibut than for rockfish/lingcod or Pacific salmon. Spatial patterns were qualitatively different between businesses specializing in single species trips and those that operated multispecies trips and between businesses with one vessel and those with multiple vessels. In Homer, the most frequently cited reasons for changes in the location and/or extent of fishing were changes in trip type and the price of fuel, while in Sitka, the most frequently cited reasons for spatial shifts were changes to Pacific halibut regulations and gaining experience or exploring new locations. The diversity of charter fishing strategies in Alaska may allow individual charter operators to respond differently to perturbations and thus maintain resilience of the industry as a whole to social, environmental, and regulatory change. This research also highlights the importance of understanding fishers' diverse portfolio of activities to effective ecosystem-based management.

Incongruent genetic connectivity patterns for VME indicator taxa: implications for the management of New Zealand's vulnerable marine ecosystems

NASA Astrophysics Data System (ADS)

Clark, M. R.; Gardner, J.; Holland, L.; Zeng, C.; Hamilton, J. S.; Rowden, A. A.

2016-02-01

In the New Zealand region vulnerable marine ecosystems (VMEs) are at risk from commercial fishing activity and future seabed mining. Understanding connectivity among VMEs is important for the design of effective spatial management strategies, i.e. a network of protected areas. To date however, genetic connectivity in the New Zealand region has rarely been documented. As part of a project developing habitat suitability models and spatial management options for VMEs we used DNA sequence data and microsatellite genotyping to assess genetic connectivity for a range of VME indicator taxa, including the coral Desmophyllum dianthus, and the sponges Poecilastra laminaris and Penares palmatoclada. Overall, patterns of connectivity were inconsistent amonst taxa. Nonetheless, genetic data from each taxon were relevant to inform management at a variety of spatial scales. D. dianthus populations in the Kermadec volcanic arc and the Louisville Seamount Chain were indistinguishable, highlighting the importance of considering source-sink dynamics between populations beyond the EEZ in conservation planning. Poecilastra laminaris populations showed significant divergence across the Chatham Rise, in contrast to P. palmatoclada, which had a uniform haplotypic distribution. However, both sponge species exhibited the highest genetic diversity on the Chatham Rise, suggesting that this area is a genetic hotspot. The spatial heterogeneity of genetic patterns of structure suggest that inclusion of several taxa is necessary to facilitate understanding of regional connectivity patterns, variation in which may be attributed to alternate life history strategies, local hydrodynamic regimes, or in some cases, suboptimal sample sizes. Our findings provide important information for use by environmental managers, including summary maps of genetic diversity and barriers to gene flow, which will be used in spatial management decision-support tools.

Elevational Gradients in β-Diversity Reflect Variation in the Strength of Local Community Assembly Mechanisms across Spatial Scales

PubMed Central

Tello, J. Sebastián; Myers, Jonathan A.; Macía, Manuel J.; Fuentes, Alfredo F.; Cayola, Leslie; Arellano, Gabriel; Loza, M. Isabel; Torrez, Vania; Cornejo, Maritza; Miranda, Tatiana B.; Jørgensen, Peter M.

2015-01-01

Despite long-standing interest in elevational-diversity gradients, little is known about the processes that cause changes in the compositional variation of communities (β-diversity) across elevations. Recent studies have suggested that β-diversity gradients are driven by variation in species pools, rather than by variation in the strength of local community assembly mechanisms such as dispersal limitation, environmental filtering, or local biotic interactions. However, tests of this hypothesis have been limited to very small spatial scales that limit inferences about how the relative importance of assembly mechanisms may change across spatial scales. Here, we test the hypothesis that scale-dependent community assembly mechanisms shape biogeographic β-diversity gradients using one of the most well-characterized elevational gradients of tropical plant diversity. Using an extensive dataset on woody plant distributions along a 4,000-m elevational gradient in the Bolivian Andes, we compared observed patterns of β-diversity to null-model expectations. β-deviations (standardized differences from null values) were used to measure the relative effects of local community assembly mechanisms after removing sampling effects caused by variation in species pools. To test for scale-dependency, we compared elevational gradients at two contrasting spatial scales that differed in the size of local assemblages and regions by at least an order of magnitude. Elevational gradients in β-diversity persisted after accounting for regional variation in species pools. Moreover, the elevational gradient in β-deviations changed with spatial scale. At small scales, local assembly mechanisms were detectable, but variation in species pools accounted for most of the elevational gradient in β-diversity. At large spatial scales, in contrast, local assembly mechanisms were a dominant force driving changes in β-diversity. In contrast to the hypothesis that variation in species pools alone drives β-diversity gradients, we show that local community assembly mechanisms contribute strongly to systematic changes in β-diversity across elevations. We conclude that scale-dependent variation in community assembly mechanisms underlies these iconic gradients in global biodiversity. PMID:25803846

Geographic distance and ecosystem size determine the distribution of smallest protists in lacustrine ecosystems.

PubMed

Lepère, Cécile; Domaizon, Isabelle; Taïb, Najwa; Mangot, Jean-François; Bronner, Gisèle; Boucher, Delphine; Debroas, Didier

2013-07-01

Understanding the spatial distribution of aquatic microbial diversity and the underlying mechanisms causing differences in community composition is a challenging and central goal for ecologists. Recent insights into protistan diversity and ecology are increasing the debate over their spatial distribution. In this study, we investigate the importance of spatial and environmental factors in shaping the small protists community structure in lakes. We analyzed small protists community composition (beta-diversity) and richness (alpha-diversity) at regional scale by different molecular methods targeting the gene coding for 18S rRNA gene (T-RFLP and 454 pyrosequencing). Our results show a distance-decay pattern for rare and dominant taxa and the spatial distribution of the latter followed the prediction of the island biogeography theory. Furthermore, geographic distances between lakes seem to be the main force shaping the protists community composition in the lakes studied here. Finally, the spatial distribution of protists was discussed at the global scale (11 worldwide distributed lakes) by comparing these results with those present in the public database. UniFrac analysis showed 18S rRNA gene OTUs compositions significantly different among most of lakes, and this difference does not seem to be related to the trophic status. © 2013 Federation of European Microbiological Societies. Published by Blackwell Publishing Ltd. All rights reserved.

Spatial and temporal genetic diversity of lake whitefish (Coregonus clupeaformis (Mitchill)) from Lake Huron and Lake Erie

USGS Publications Warehouse

Stott, Wendylee; Ebener, Mark P.; Mohr, Lloyd; Hartman, Travis; Johnson, Jim; Roseman, Edward F.

2013-01-01

Lake whitefish (Coregonus clupeaformis (Mitchill)) are important commercially, culturally, and ecologically in the Laurentian Great Lakes. Stocks of lake whitefish in the Great Lakes have recovered from low levels of abundance in the 1960s. Reductions in abundance, loss of habitat and environmental degradation can be accompanied by losses of genetic diversity and overall fitness that may persist even as populations recover demographically. Therefore, it is important to be able to identify stocks that have reduced levels of genetic diversity. In this study, we investigated patterns of genetic diversity at microsatellite DNA loci in lake whitefish collected between 1927 and 1929 (historical period) and between 1997 and 2005 (contemporary period) from Lake Huron and Lake Erie. Genetic analysis of lake whitefish from Lakes Huron and Erie shows that the amount of population structuring varies from lake to lake. Greater genetic divergences among collections from Lake Huron may be the result of sampling scale, migration patterns and demographic processes. Fluctuations in abundance of lake whitefish populations may have resulted in periods of increased genetic drift that have resulted in changes in allele frequencies over time, but periodic genetic drift was not severe enough to result in a significant loss of genetic diversity. Migration among stocks may have decreased levels of genetic differentiation while not completely obscuring stock boundaries. Recent changes in spatial boundaries to stocks, the number of stocks and life history characteristics of stocks further demonstrate the potential of coregonids for a swift and varied response to environmental change and emphasise the importance of incorporating both spatial and temporal considerations into management plans to ensure that diversity is preserved.

Tree growth and competition in an old-growth Picea abies forest of boreal Sweden: influence of tree spatial patterning

USGS Publications Warehouse

Fraver, Shawn; D'Amato, Anthony W.; Bradford, John B.; Jonsson, Bengt Gunnar; Jönsson, Mari; Esseen, Per-Anders

2013-01-01

Question: What factors best characterize tree competitive environments in this structurally diverse old-growth forest, and do these factors vary spatially within and among stands? Location: Old-growth Picea abies forest of boreal Sweden. Methods: Using long-term, mapped permanent plot data augmented with dendrochronological analyses, we evaluated the effect of neighbourhood competition on focal tree growth by means of standard competition indices, each modified to include various metrics of trees size, neighbour mortality weighting (for neighbours that died during the inventory period), and within-neighbourhood tree clustering. Candidate models were evaluated using mixed-model linear regression analyses, with mean basal area increment as the response variable. We then analysed stand-level spatial patterns of competition indices and growth rates (via kriging) to determine if the relationship between these patterns could further elucidate factors influencing tree growth. Results: Inter-tree competition clearly affected growth rates, with crown volume being the size metric most strongly influencing the neighbourhood competitive environment. Including neighbour tree mortality weightings in models only slightly improved descriptions of competitive interactions. Although the within-neighbourhood clustering index did not improve model predictions, competition intensity was influenced by the underlying stand-level tree spatial arrangement: stand-level clustering locally intensified competition and reduced tree growth, whereas in the absence of such clustering, inter-tree competition played a lesser role in constraining tree growth. Conclusions: Our findings demonstrate that competition continues to influence forest processes and structures in an old-growth system that has not experienced major disturbances for at least two centuries. The finding that the underlying tree spatial pattern influenced the competitive environment suggests caution in interpreting traditional tree competition studies, in which tree spatial patterning is typically not taken into account. Our findings highlight the importance of forest structure – particularly the spatial arrangement of trees – in regulating inter-tree competition and growth in structurally diverse forests, and they provide insight into the causes and consequences of heterogeneity in this old-growth system.

Clinal patterns of human Y chromosomal diversity in continental Italy and Greece are dominated by drift and founder effects.

PubMed

Di Giacomo, F; Luca, F; Anagnou, N; Ciavarella, G; Corbo, R M; Cresta, M; Cucci, F; Di Stasi, L; Agostiano, V; Giparaki, M; Loutradis, A; Mammi', C; Michalodimitrakis, E N; Papola, F; Pedicini, G; Plata, E; Terrenato, L; Tofanelli, S; Malaspina, P; Novelletto, A

2003-09-01

We explored the spatial distribution of human Y chromosomal diversity on a microgeographic scale, by typing 30 population samples from closely spaced locations in Italy and Greece for 9 haplogroups and their internal microsatellite variation. We confirm a significant difference in the composition of the Y chromosomal gene pools of the two countries. However, within each country, heterogeneity is not organized along the lines of clinal variation deduced from studies on larger spatial scales. Microsatellite data indicate that local increases of haplogroup frequencies can be often explained by a limited number of founders. We conclude that local founder or drift effects are the main determinants in shaping the microgeographic Y chromosomal diversity.

Disentangling the drivers of taxonomic and phylogenetic beta diversities in disturbed and undisturbed subtropical forests

NASA Astrophysics Data System (ADS)

Liu, Jinliang; Qian, Hong; Jin, Yi; Wu, Chuping; Chen, Jianhua; Yu, Shuquan; Wei, Xinliang; Jin, Xiaofeng; Liu, Jiajia; Yu, Mingjian

2016-10-01

Understanding the relative importance of dispersal limitation and environmental filtering processes in structuring the beta diversities of subtropical forests in human disturbed landscapes is still limited. Here we used taxonomic (TBD) and phylogenetic (PBD), including terminal PBD (PBDt) and basal PBD (PBDb), beta diversity indices to quantify the taxonomic and phylogenetic turnovers at different depths of evolutionary history in disturbed and undisturbed subtropical forests. Multiple linear regression model and distance-based redundancy analysis were used to disentangle the relative importance of environmental and spatial variables. Environmental variables were significantly correlated with TBD and PBDt metrics. Temperature and precipitation were major environmental drivers of beta diversity patterns, which explained 7-27% of the variance in TBD and PBDt, whereas the spatial variables independently explained less than 1% of the variation for all forests. The relative importance of environmental and spatial variables differed between disturbed and undisturbed forests (e.g., when Bray-Curtis was used as a beta diversity metric, environmental variable had a significant effect on beta diversity for disturbed forests but had no effect on undisturbed forests). We conclude that environmental filtering plays a more important role than geographical limitation and disturbance history in driving taxonomic and terminal phylogenetic beta diversity.

Disentangling the drivers of taxonomic and phylogenetic beta diversities in disturbed and undisturbed subtropical forests

PubMed Central

Liu, Jinliang; Qian, Hong; Jin, Yi; Wu, Chuping; Chen, Jianhua; Yu, Shuquan; Wei, Xinliang; Jin, Xiaofeng; Liu, Jiajia; Yu, Mingjian

2016-01-01

Understanding the relative importance of dispersal limitation and environmental filtering processes in structuring the beta diversities of subtropical forests in human disturbed landscapes is still limited. Here we used taxonomic (TBD) and phylogenetic (PBD), including terminal PBD (PBDt) and basal PBD (PBDb), beta diversity indices to quantify the taxonomic and phylogenetic turnovers at different depths of evolutionary history in disturbed and undisturbed subtropical forests. Multiple linear regression model and distance-based redundancy analysis were used to disentangle the relative importance of environmental and spatial variables. Environmental variables were significantly correlated with TBD and PBDt metrics. Temperature and precipitation were major environmental drivers of beta diversity patterns, which explained 7–27% of the variance in TBD and PBDt, whereas the spatial variables independently explained less than 1% of the variation for all forests. The relative importance of environmental and spatial variables differed between disturbed and undisturbed forests (e.g., when Bray-Curtis was used as a beta diversity metric, environmental variable had a significant effect on beta diversity for disturbed forests but had no effect on undisturbed forests). We conclude that environmental filtering plays a more important role than geographical limitation and disturbance history in driving taxonomic and terminal phylogenetic beta diversity. PMID:27775021

Mating system and early viability resistance to habitat fragmentation in a bird-pollinated eucalypt

PubMed Central

Breed, M F; Ottewell, K M; Gardner, M G; Marklund, M H K; Stead, M G; Harris, J B C; Lowe, A J

2015-01-01

Habitat fragmentation has been shown to disrupt ecosystem processes such as plant-pollinator mutualisms. Consequently, mating patterns in remnant tree populations are expected to shift towards increased inbreeding and reduced pollen diversity, with fitness consequences for future generations. However, mating patterns and phenotypic assessments of open-pollinated progeny have rarely been combined in a single study. Here, we collected seeds from 37 Eucalyptus incrassata trees from contrasting stand densities following recent clearance in a single South Australian population (intact woodland=12.6 trees ha−1; isolated pasture=1.7 trees ha−1; population area=10 km2). 649 progeny from these trees were genotyped at eight microsatellite loci. We estimated genetic diversity, spatial genetic structure, indirect contemporary pollen flow and mating patterns for adults older than the clearance events and open-pollinated progeny sired post-clearance. A proxy of early stage progeny viability was assessed in a common garden experiment. Density had no impact on mating patterns, adult and progeny genetic diversity or progeny growth, but was associated with increased mean pollen dispersal. Weak spatial genetic structure among adults suggests high historical gene flow. We observed preliminary evidence for inbreeding depression related to stress caused by fungal infection, but which was not associated with density. Higher observed heterozygosities in adults compared with progeny may relate to weak selection on progeny and lifetime-accumulated mortality of inbred adults. E. incrassata appears to be resistant to the negative mating pattern and fitness changes expected within fragmented landscapes. This pattern is likely explained by strong outcrossing and regular long-distance pollen flow. PMID:23188172

Symbiodinium biogeography tracks environmental patterns rather than host genetics in a key Caribbean reef-builder, Orbicella annularis.

PubMed

Kennedy, Emma V; Tonk, Linda; Foster, Nicola L; Chollett, Iliana; Ortiz, Juan-Carlos; Dove, Sophie; Hoegh-Guldberg, Ove; Mumby, Peter J; Stevens, Jamie R

2016-11-16

The physiological performance of a reef-building coral is a combined outcome of both the coral host and its algal endosymbionts, Symbiodinium While Orbicella annularis-a dominant reef-building coral in the Wider Caribbean-is known to be a flexible host in terms of the diversity of Symbiodinium types it can associate with, it is uncertain how this diversity varies across the Caribbean, and whether spatial variability in the symbiont community is related to either O. annularis genotype or environment. Here, we target the Symbiodinium-ITS2 gene to characterize and map dominant Symbiodinium hosted by O. annularis at an unprecedented spatial scale. We reveal northwest-southeast partitioning across the Caribbean, both in terms of the dominant symbiont taxa hosted and in assemblage diversity. Multivariate regression analyses incorporating a suite of environmental and genetic factors reveal that observed spatial patterns are predominantly explained by chronic thermal stress (summer temperatures) and are unrelated to host genotype. Furthermore, we were able to associate the presence of specific Symbiodinium types with local environmental drivers (for example, Symbiodinium C7 with areas experiencing cooler summers, B1j with nutrient loading and B17 with turbidity), associations that have not previously been described. © 2016 The Authors.

Symbiodinium biogeography tracks environmental patterns rather than host genetics in a key Caribbean reef-builder, Orbicella annularis

PubMed Central

Tonk, Linda; Chollett, Iliana; Ortiz, Juan-Carlos; Dove, Sophie; Hoegh-Guldberg, Ove; Mumby, Peter J.

2016-01-01

The physiological performance of a reef-building coral is a combined outcome of both the coral host and its algal endosymbionts, Symbiodinium. While Orbicella annularis—a dominant reef-building coral in the Wider Caribbean—is known to be a flexible host in terms of the diversity of Symbiodinium types it can associate with, it is uncertain how this diversity varies across the Caribbean, and whether spatial variability in the symbiont community is related to either O. annularis genotype or environment. Here, we target the Symbiodinium-ITS2 gene to characterize and map dominant Symbiodinium hosted by O. annularis at an unprecedented spatial scale. We reveal northwest–southeast partitioning across the Caribbean, both in terms of the dominant symbiont taxa hosted and in assemblage diversity. Multivariate regression analyses incorporating a suite of environmental and genetic factors reveal that observed spatial patterns are predominantly explained by chronic thermal stress (summer temperatures) and are unrelated to host genotype. Furthermore, we were able to associate the presence of specific Symbiodinium types with local environmental drivers (for example, Symbiodinium C7 with areas experiencing cooler summers, B1j with nutrient loading and B17 with turbidity), associations that have not previously been described. PMID:27807263

Frugivores bias seed-adult tree associations through nonrandom seed dispersal: a phylogenetic approach.

PubMed

Razafindratsima, Onja H; Dunham, Amy E

2016-08-01

Frugivores are the main seed dispersers in many ecosystems, such that behaviorally driven, nonrandom patterns of seed dispersal are a common process; but patterns are poorly understood. Characterizing these patterns may be essential for understanding spatial organization of fruiting trees and drivers of seed-dispersal limitation in biodiverse forests. To address this, we studied resulting spatial associations between dispersed seeds and adult tree neighbors in a diverse rainforest in Madagascar, using a temporal and phylogenetic approach. Data show that by using fruiting trees as seed-dispersal foci, frugivores bias seed dispersal under conspecific adults and under heterospecific trees that share dispersers and fruiting time with the dispersed species. Frugivore-mediated seed dispersal also resulted in nonrandom phylogenetic associations of dispersed seeds with their nearest adult neighbors, in nine out of the 16 months of our study. However, these nonrandom phylogenetic associations fluctuated unpredictably over time, ranging from clustered to overdispersed. The spatial and phylogenetic template of seed dispersal did not translate to similar patterns of association in adult tree neighborhoods, suggesting the importance of post-dispersal processes in structuring plant communities. Results suggest that frugivore-mediated seed dispersal is important for structuring early stages of plant-plant associations, setting the template for post-dispersal processes that influence ultimate patterns of plant recruitment. Importantly, if biased patterns of dispersal are common in other systems, frugivores may promote tree coexistence in biodiverse forests by limiting the frequency and diversity of heterospecific interactions of seeds they disperse. © 2016 by the Ecological Society of America.

The spatial sensitivity of the spectral diversity-biodiversity relationship: an experimental test in a prairie grassland.

PubMed

Wang, Ran; Gamon, John A; Cavender-Bares, Jeannine; Townsend, Philip A; Zygielbaum, Arthur I

2018-03-01

Remote sensing has been used to detect plant biodiversity in a range of ecosystems based on the varying spectral properties of different species or functional groups. However, the most appropriate spatial resolution necessary to detect diversity remains unclear. At coarse resolution, differences among spectral patterns may be too weak to detect. In contrast, at fine resolution, redundant information may be introduced. To explore the effect of spatial resolution, we studied the scale dependence of spectral diversity in a prairie ecosystem experiment at Cedar Creek Ecosystem Science Reserve, Minnesota, USA. Our study involved a scaling exercise comparing synthetic pixels resampled from high-resolution images within manipulated diversity treatments. Hyperspectral data were collected using several instruments on both ground and airborne platforms. We used the coefficient of variation (CV) of spectral reflectance in space as the indicator of spectral diversity and then compared CV at different scales ranging from 1 mm 2 to 1 m 2 to conventional biodiversity metrics, including species richness, Shannon's index, Simpson's index, phylogenetic species variation, and phylogenetic species evenness. In this study, higher species richness plots generally had higher CV. CV showed higher correlations with Shannon's index and Simpson's index than did species richness alone, indicating evenness contributed to the spectral diversity. Correlations with species richness and Simpson's index were generally higher than with phylogenetic species variation and evenness measured at comparable spatial scales, indicating weaker relationships between spectral diversity and phylogenetic diversity metrics than with species diversity metrics. High resolution imaging spectrometer data (1 mm 2 pixels) showed the highest sensitivity to diversity level. With decreasing spatial resolution, the difference in CV between diversity levels decreased and greatly reduced the optical detectability of biodiversity. The optimal pixel size for distinguishing α diversity in these prairie plots appeared to be around 1 mm to 10 cm, a spatial scale similar to the size of an individual herbaceous plant. These results indicate a strong scale-dependence of the spectral diversity-biodiversity relationships, with spectral diversity best able to detect a combination of species richness and evenness, and more weakly detecting phylogenetic diversity. These findings can be used to guide airborne studies of biodiversity and develop more effective large-scale biodiversity sampling methods. ©2018 The Authors Ecological Applications published by Wiley Periodicals, Inc. on behalf of Ecological Society of America.

Neighborhood diversity of large trees shows independent species patterns in a mixed dipterocarp forest in Sri Lanka.

PubMed

Punchi-Manage, Ruwan; Wiegand, Thorsten; Wiegand, Kerstin; Getzin, Stephan; Huth, Andreas; Gunatilleke, C V Savitri; Gunatilleke, I A U Nimal

2015-07-01

Interactions among neighboring individuals influence plant performance and should create spatial patterns in local community structure. In order to assess the role of large trees in generating spatial patterns in local species richness, we used the individual species-area relationship (ISAR) to evaluate the species richness of trees of different size classes (and dead trees) in circular neighborhoods with varying radius around large trees of different focal species. To reveal signals of species interactions, we compared the ISAR function of the individuals of focal species with that of randomly selected nearby locations. We expected that large trees should strongly affect the community structure of smaller trees in their neighborhood, but that these effects should fade away with increasing size class. Unexpectedly, we found that only few focal species showed signals of species interactions with trees of the different size classes and that this was less likely for less abundant focal species. However, the few and relatively weak departures from independence were consistent with expectations of the effect of competition for space and the dispersal syndrome on spatial patterns. A noisy signal of competition for space found for large trees built up gradually with increasing life stage; it was not yet present for large saplings but detectable for intermediates. Additionally, focal species with animal-dispersed seeds showed higher species richness in their neighborhood than those with gravity- and gyration-dispersed seeds. Our analysis across the entire ontogeny from recruits to large trees supports the hypothesis that stochastic effects dilute deterministic species interactions in highly diverse communities. Stochastic dilution is a consequence of the stochastic geometry of biodiversity in species-rich communities where the identities of the nearest neighbors of a given plant are largely unpredictable. While the outcome of local species interactions is governed for each plant by deterministic fitness and niche differences, the large variability of competitors causes also a large variability in the outcomes of interactions and does not allow for strong directed responses at the species level. Collectively, our results highlight the critical effect of the stochastic geometry of biodiversity in structuring local spatial patterns of tropical forest diversity.

Diversity patterns of microbial eukaryotes mirror those of bacteria in Antarctic cryoconite holes.

PubMed

Sommers, Pacifica; Darcy, John L; Gendron, Eli M S; Stanish, Lee F; Bagshaw, Elizabeth A; Porazinska, Dorota L; Schmidt, Steven K

2018-01-01

Ice-lidded cryoconite holes on glaciers in the Taylor Valley, Antarctica, provide a unique system of natural mesocosms for studying community structure and assembly. We used high-throughput DNA sequencing to characterize both microbial eukaryotic communities and bacterial communities within cryoconite holes across three glaciers to study similarities in their spatial patterns. We expected that the alpha (phylogenetic diversity) and beta (pairwise community dissimilarity) diversity patterns of eukaryotes in cryoconite holes would be related to those of bacteria, and that they would be related to the biogeochemical gradient within the Taylor Valley. We found that eukaryotic alpha and beta diversity were strongly related to those of bacteria across scales ranging from 140 m to 41 km apart. Alpha diversity of both was significantly related to position in the valley and surface area of the cryoconite hole, with pH also significantly correlated with the eukaryotic diversity. Beta diversity for both bacteria and eukaryotes was significantly related to position in the valley, with bacterial beta diversity also related to nitrate. These results are consistent with transport of sediments onto glaciers occurring primarily at local scales relative to the size of the valley, thus creating feedbacks in local chemistry and diversity. © FEMS 2017. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Factors influencing geographic patterns in diversity of forest bird communities of eastern Connecticut, USA

USGS Publications Warehouse

Craig, Robert J.; Klaver, Robert W.

2012-01-01

At regional scales, the most important variables associated with diversity are latitudinally-based temperature and net primary productivity, although diversity is also influenced by habitat. We examined bird species richness, community density and community evenness in forests of eastern Connecticut to determine whether: 1) spatial and seasonal patterns exist in diversity, 2) energy explains the greatest proportion of variation in diversity parameters, 3) variation in habitat explains remaining diversity variance, and 4) seasonal shifts in diversity provide clues about how environmental variables shape communities. We sought to discover if our data supported predictions of the species–energy hypothesis. We used the variable circular plot technique to estimate bird populations and quantified the location, elevation, forest type, vegetation type, canopy cover, moisture regime, understory density and primary production for the study sites. We found that 1) summer richness and population densities are roughly equal in northeastern and southeastern Connecticut, whereas in winter both concentrate toward the coast, 2) variables linked with temperature explained much of the patterns in winter diversity, but energy-related variables showed little relationship to summer diversity, 3) the effect of habitat variables on diversity parameters predominated in summer, although their effect was weak, 4) contrary to theory, evenness increased from summer to winter, and 5) support for predictions of species–energy theory was primarily restricted to winter data. Although energy and habitat played a role in explaining community patterns, they left much of the variance in regional diversity unexplained, suggesting that a large stochastic component to diversity also may exist.

Ecological and evolutionary drivers of the elevational gradient of diversity.

PubMed

Laiolo, Paola; Pato, Joaquina; Obeso, José Ramón

2018-05-02

Ecological, evolutionary, spatial and neutral theories make distinct predictions and provide distinct explanations for the mechanisms that control the relationship between diversity and the environment. Here, we test predictions of the elevational diversity gradient focusing on Iberian bumblebees, grasshoppers and birds. Processes mediated by local abundance and regional diversity concur in explaining local diversity patterns along elevation. Effects expressed through variation in abundance were similar among taxa and point to the overriding role of a physical factor, temperature. This determines how energy is distributed among individuals and ultimately how the resulting pattern of abundance affects species incidence. Effects expressed through variation in regional species pools depended instead on taxon-specific evolutionary history, and lead to diverging responses under similar environmental pressures. Local filters and regional variation also explain functional diversity gradients, in line with results from species richness that indicate an (local) ecological and (regional) historical unfolding of diversity-elevation relationships. © 2018 John Wiley & Sons Ltd/CNRS.

Spatial patterns in vegetation fires in the Indian region.

PubMed

Vadrevu, Krishna Prasad; Badarinath, K V S; Anuradha, Eaturu

2008-12-01

In this study, we used fire count datasets derived from Along Track Scanning Radiometer (ATSR) satellite to characterize spatial patterns in fire occurrences across highly diverse geographical, vegetation and topographic gradients in the Indian region. For characterizing the spatial patterns of fire occurrences, observed fire point patterns were tested against the hypothesis of a complete spatial random (CSR) pattern using three different techniques, the quadrat analysis, nearest neighbor analysis and Ripley's K function. Hierarchical nearest neighboring technique was used to depict the 'hotspots' of fire incidents. Of the different states, highest fire counts were recorded in Madhya Pradesh (14.77%) followed by Gujarat (10.86%), Maharastra (9.92%), Mizoram (7.66%), Jharkhand (6.41%), etc. With respect to the vegetation categories, highest number of fires were recorded in agricultural regions (40.26%) followed by tropical moist deciduous vegetation (12.72), dry deciduous vegetation (11.40%), abandoned slash and burn secondary forests (9.04%), tropical montane forests (8.07%) followed by others. Analysis of fire counts based on elevation and slope range suggested that maximum number of fires occurred in low and medium elevation types and in very low to low-slope categories. Results from three different spatial techniques for spatial pattern suggested clustered pattern in fire events compared to CSR. Most importantly, results from Ripley's K statistic suggested that fire events are highly clustered at a lag-distance of 125 miles. Hierarchical nearest neighboring clustering technique identified significant clusters of fire 'hotspots' in different states in northeast and central India. The implications of these results in fire management and mitigation were discussed. Also, this study highlights the potential of spatial point pattern statistics in environmental monitoring and assessment studies with special reference to fire events in the Indian region.

Soil bacterial diversity patterns and drivers along an elevational gradient on Shennongjia Mountain, China

PubMed Central

Zhang, Yuguang; Cong, Jing; Lu, Hui; Li, Guangliang; Xue, Yadong; Deng, Ye; Li, Hui; Zhou, Jizhong; Li, Diqiang

2015-01-01

Understanding biological diversity elevational pattern and the driver factors are indispensable to develop the ecological theories. Elevational gradient may minimize the impact of environmental factors and is the ideal places to study soil microbial elevational patterns. In this study, we selected four typical vegetation types from 1000 to 2800 m above the sea level on the northern slope of Shennongjia Mountain in central China, and analysed the soil bacterial community composition, elevational patterns and the relationship between soil bacterial diversity and environmental factors by using the 16S rRNA Illumina sequencing and multivariate statistical analysis. The results revealed that the dominant bacterial phyla were Acidobacteria, Actinobacteria, Alphaproteobacteria, Betaproteobacteria, Gammaproteobacteria and Verrucomicrobia, which accounted for over 75% of the bacterial sequences obtained from tested samples, and the soil bacterial operational taxonomic unit (OTU) richness was a significant monotonous decreasing (P < 0.01) trend with the elevational increasing. The similarity of soil bacterial population composition decreased significantly (P < 0.01) with elevational distance increased as measured by the Jaccard and Bray–Curtis index. Canonical correspondence analysis and Mantel test analysis indicated that plant diversity and soil pH were significantly correlated (P < 0.01) with the soil bacterial community. Therefore, the soil bacterial diversity on Shennongjia Mountain had a significant and different elevational pattern, and plant diversity and soil pH may be the key factors in shaping the soil bacterial spatial pattern. PMID:26032124

The road to higher permanence and biodiversity in exurban wetlands.

PubMed

Urban, Mark C; Roehm, Robert

2018-01-01

Exurban areas are expanding throughout the world, yet their effects on local biodiversity remain poorly understood. Wetlands, in particular, face ongoing and substantial threats from exurban development. We predicted that exurbanization would reduce the diversity of wetland amphibian and invertebrate communities and that more spatially aggregated residential development would leave more undisturbed natural land, thereby promoting greater local diversity. Using structural equation models, we tested a series of predictions about the direct and indirect pathways by which exurbanization extent, spatial pattern, and wetland characteristics might affect diversity patterns in 38 wetlands recorded during a growing season. We used redundancy, indicator species, and nested community analyses to evaluate how exurbanization affected species composition. In contrast to expectations, we found higher diversity in exurban wetlands. We also found that housing aggregation did not significantly affect diversity. Exurbanization affected biodiversity indirectly by increasing roads and development, which promoted permanent wetlands with less canopy cover and more aquatic vegetation. These pond characteristics supported greater diversity. However, exurbanization was associated with fewer temporary wetlands and fewer of the species that depend on these habitats. Moreover, the best indicator species for an exurban wetland was the ram's head snail, a common disease vector in disturbed ponds. Overall, results suggest that exurbanization is homogenizing wetlands into more permanent water bodies. These more permanent, exurban ponds support higher overall animal diversity, but exclude temporary wetland specialists. Conserving the full assemblage of wetland species in expanding exurban regions throughout the world will require protecting and creating temporary wetlands.

Digging up the roots of an insular hotspot of genetic diversity: decoupled mito-nuclear histories in the evolution of the Corsican-Sardinian endemic lizard Podarcis tiliguerta.

PubMed

Salvi, Daniele; Pinho, Catarina; Harris, D James

2017-03-02

Mediterranean islands host a disproportionately high level of biodiversity and endemisms. Growing phylogeographic evidence on island endemics has unveiled unexpectedly complex patterns of intra-island diversification, which originated at diverse spatial and temporal scales. We investigated multilocus genetic variation of the Corsican-Sardinian endemic lizard Podarcis tiliguerta with the aim of shedding more light on the evolutionary processes underlying the origin of Mediterranean island biodiversity. We analysed DNA sequences of mitochondrial (12S and nd4) and nuclear (acm4 and mc1r) gene fragments in 174 individuals of P. tiliguerta from 81 localities across the full range of the species in a geographic and genealogical framework. We found surprisingly high genetic diversity both at mitochondrial and nuclear loci. Seventeen reciprocally monophyletic allopatric mitochondrial haplogroups were sharply divided into four main mitochondrial lineages (two in Corsica and two in Sardinia) of Miocene origin. In contrast, shallow divergence and shared diversity within and between islands was observed at the nuclear loci. We evaluated alternative biogeographic and evolutionary scenarios to explain such profound discordance in spatial and phylogenetic patterning between mitochondrial and nuclear genomes. While neutral models provided unparsimonious explanations for the observed pattern, the hypothesis of environmental selection driving mitochondrial divergence in the presence of nuclear gene flow is favoured. Our study on the genetic variation of P. tiliguerta reveals surprising levels of diversity underlining a complex phylogeographic pattern with a striking example of mito-nuclear discordance. These findings have profound implications, not only for the taxonomy and conservation of P. tiliguerta. Growing evidence on deep mitochondrial breaks in absence of geographic barriers and of climatic factors associated to genetic variation of Corsican-Sardinian endemics warrants additional investigation on the potential role of environmental selection driving the evolution of diversity hotspots within Mediterranean islands.

Influence of Ethnolinguistic Diversity on the Sorghum Genetic Patterns in Subsistence Farming Systems in Eastern Kenya

PubMed Central

Labeyrie, Vanesse; Deu, Monique; Barnaud, Adeline; Calatayud, Caroline; Buiron, Marylène; Wambugu, Peterson; Manel, Stéphanie; Glaszmann, Jean-Christophe; Leclerc, Christian

2014-01-01

Understanding the effects of actions undertaken by human societies on crop evolution processes is a major challenge for the conservation of genetic resources. This study investigated the mechanisms whereby social boundaries associated with patterns of ethnolinguistic diversity have influenced the on-farm distribution of sorghum diversity. Social boundaries limit the diffusion of planting material, practices and knowledge, thus shaping crop diversity in situ. To assess the effect of social boundaries, this study was conducted in the contact zone between the Chuka, Mbeere and Tharaka ethnolinguistic groups in eastern Kenya. Sorghum varieties were inventoried and samples collected in 130 households. In all, 297 individual plants derived from seeds collected under sixteen variety names were characterized using a set of 18 SSR molecular markers and 15 morphological descriptors. The genetic structure was investigated using both a Bayesian assignment method and distance-based clustering. Principal Coordinates Analysis was used to describe the structure of the morphological diversity of the panicles. The distribution of the varieties and the main genetic clusters across ethnolinguistic groups was described using a non-parametric MANOVA and pairwise Fisher tests. The spatial distribution of landrace names and the overall genetic spatial patterns were significantly correlated with ethnolinguistic partition. However, the genetic structure inferred from molecular makers did not discriminate the short-cycle landraces despite their morphological distinctness. The cases of two improved varieties highlighted possible fates of improved materials. The most recent one was often given the name of local landraces. The second one, that was introduced a dozen years ago, displays traces of admixture with local landraces with differential intensity among ethnic groups. The patterns of congruence or discordance between the nomenclature of farmers’ varieties and the structure of both genetic and morphological diversity highlight the effects of the social organization of communities on the diffusion of seed, practices, and variety nomenclature. PMID:24637745

Species turnover drives β-diversity patterns across multiple spatial scales of plant-galling interactions in mountaintop grasslands.

PubMed

Coelho, Marcel Serra; Carneiro, Marco Antônio Alves; Branco, Cristina Alves; Borges, Rafael Augusto Xavier; Fernandes, Geraldo Wilson

2018-01-01

This study describes differences in species richness and composition of the assemblages of galling insects and their host plants at different spatial scales. Sampling was conducted along altitudinal gradients composed of campos rupestres and campos de altitude of two mountain complexes in southeastern Brazil: Espinhaço Range and Mantiqueira Range. The following hypotheses were tested: i) local and regional richness of host plants and galling insects are positively correlated; ii) beta diversity is the most important component of regional diversity of host plants and galling insects; and iii) Turnover is the main mechanism driving beta diversity of both host plants and galling insects. Local richness of galling insects and host plants increased with increasing regional richness of species, suggesting a pattern of unsaturated communities. The additive partition of regional richness (γ) into local and beta components shows that local richnesses (α) of species of galling insects and host plants are low relative to regional richness; the beta (β) component incorporates most of the regional richness. The multi-scale analysis of additive partitioning showed similar patterns for galling insects and host plants with the local component (α) incorporated a small part of regional richness. Beta diversity of galling insects and host plants were mainly the result of turnover, with little contribution from nesting. Although the species composition of galling insects and host plant species varied among sample sites, mountains and even mountain ranges, local richness remained relatively low. In this way, the addition of local habitats with different landscapes substantially affects regional richness. Each mountain contributes fundamentally to the composition of regional diversity of galling insects and host plants, and so the design of future conservation strategies should incorporate multiple scales.

Hydrological and environmental variables outperform spatial factors in structuring species, trait composition, and beta diversity of pelagic algae.

PubMed

Wu, Naicheng; Qu, Yueming; Guse, Björn; Makarevičiūtė, Kristė; To, Szewing; Riis, Tenna; Fohrer, Nicola

2018-03-01

There has been increasing interest in algae-based bioassessment, particularly, trait-based approaches are increasingly suggested. However, the main drivers, especially the contribution of hydrological variables, of species composition, trait composition, and beta diversity of algae communities are less studied. To link species and trait composition to multiple factors (i.e., hydrological variables, local environmental variables, and spatial factors) that potentially control species occurrence/abundance and to determine their relative roles in shaping species composition, trait composition, and beta diversities of pelagic algae communities, samples were collected from a German lowland catchment, where a well-proven ecohydrological modeling enabled to predict long-term discharges at each sampling site. Both trait and species composition showed significant correlations with hydrological, environmental, and spatial variables, and variation partitioning revealed that the hydrological and local environmental variables outperformed spatial variables. A higher variation of trait composition (57.0%) than species composition (37.5%) could be explained by abiotic factors. Mantel tests showed that both species and trait-based beta diversities were mostly related to hydrological and environmental heterogeneity with hydrological contributing more than environmental variables, while purely spatial impact was less important. Our findings revealed the relative importance of hydrological variables in shaping pelagic algae community and their spatial patterns of beta diversities, emphasizing the need to include hydrological variables in long-term biomonitoring campaigns and biodiversity conservation or restoration. A key implication for biodiversity conservation was that maintaining the instream flow regime and keeping various habitats among rivers are of vital importance. However, further investigations at multispatial and temporal scales are greatly needed.

Grain-dependent responses of mammalian diversity to land use and the implications for conservation set-aside.

PubMed

Wearn, Oliver R; Carbone, Chris; Rowcliffe, J Marcus; Bernard, Henry; Ewers, Robert M

2016-07-01

Diversity responses to land-use change are poorly understood at local scales, hindering our ability to make forecasts and management recommendations at scales which are of practical relevance. A key barrier in this has been the underappreciation of grain-dependent diversity responses and the role that β-diversity (variation in community composition across space) plays in this. Decisions about the most effective spatial arrangement of conservation set-aside, for example high conservation value areas, have also neglected β-diversity, despite its role in determining the complementarity of sites. We examined local-scale mammalian species richness and β-diversity across old-growth forest, logged forest, and oil palm plantations in Borneo, using intensive camera- and live-trapping. For the first time, we were able to investigate diversity responses, as well as β-diversity, at multiple spatial grains, and across the whole terrestrial mammal community (large and small mammals); β-diversity was quantified by comparing observed β-diversity with that obtained under a null model, in order to control for sampling effects, and we refer to this as the β-diversity signal. Community responses to land use were grain dependent, with large mammals showing reduced richness in logged forest compared to old-growth forest at the grain of individual sampling points, but no change at the overall land-use level. Responses varied with species group, however, with small mammals increasing in richness at all grains in logged forest compared to old-growth forest. Both species groups were significantly depauperate in oil palm. Large mammal communities in old-growth forest became more heterogeneous at coarser spatial grains and small mammal communities became more homogeneous, while this pattern was reversed in logged forest. Both groups, however, showed a significant β-diversity signal at the finest grain in logged forest, likely due to logging-induced environmental heterogeneity. The β-diversity signal in oil palm was weak, but heterogeneity at the coarsest spatial grain was still evident, likely due to variation in landscape forest cover. Our findings suggest that the most effective spatial arrangement of set-aside will involve trade-offs between conserving large and small mammals. Greater consideration in the conservation and management of tropical landscapes needs to be given to β-diversity at a range of spatial grains. © 2016 by the Ecological Society of America.

Environmental Predictors of Diversity in Recent Planktonic Foraminifera as Recorded in Marine Sediments

PubMed Central

Pearson, Paul N.; Dunkley Jones, Tom; Purvis, Andy

2016-01-01

Global diversity patterns are thought to result from a combination of environmental and historical factors. This study tests the set of ecological and evolutionary hypotheses proposed to explain the global variation in present-day coretop diversity in the macroperforate planktonic foraminifera, a clade with an exceptional fossil record. Within this group, marine surface sediment assemblages are thought to represent an accurate, although centennial to millennial time-averaged, representation of recent diversity patterns. Environmental variables chosen to capture ocean temperature, structure, productivity and seasonality were used to model a range of diversity measures across the world’s oceans. Spatial autoregressive models showed that the same broad suite of environmental variables were important in shaping each of the four largely independent diversity measures (rarefied species richness, Simpson’s evenness, functional richness and mean evolutionary age). Sea-surface temperature explains the largest portion of diversity in all four diversity measures, but not in the way predicted by the metabolic theory of ecology. Vertical structure could be linked to increased diversity through the strength of stratification, but not through the depth of the mixed layer. There is limited evidence that seasonal turnover explains diversity patterns. There is evidence for functional redundancy in the low-latitude sites. The evolutionary mechanism of deep-time stability finds mixed support whilst there is relatively little evidence for an out-of-the-tropics model. These results suggest the diversity patterns of planktonic foraminifera cannot be explained by any one environmental variable or proposed mechanism, but instead reflect multiple processes acting in concert. PMID:27851751

Environmental Predictors of Diversity in Recent Planktonic Foraminifera as Recorded in Marine Sediments.

PubMed

Fenton, Isabel S; Pearson, Paul N; Dunkley Jones, Tom; Purvis, Andy

2016-01-01

Global diversity patterns are thought to result from a combination of environmental and historical factors. This study tests the set of ecological and evolutionary hypotheses proposed to explain the global variation in present-day coretop diversity in the macroperforate planktonic foraminifera, a clade with an exceptional fossil record. Within this group, marine surface sediment assemblages are thought to represent an accurate, although centennial to millennial time-averaged, representation of recent diversity patterns. Environmental variables chosen to capture ocean temperature, structure, productivity and seasonality were used to model a range of diversity measures across the world's oceans. Spatial autoregressive models showed that the same broad suite of environmental variables were important in shaping each of the four largely independent diversity measures (rarefied species richness, Simpson's evenness, functional richness and mean evolutionary age). Sea-surface temperature explains the largest portion of diversity in all four diversity measures, but not in the way predicted by the metabolic theory of ecology. Vertical structure could be linked to increased diversity through the strength of stratification, but not through the depth of the mixed layer. There is limited evidence that seasonal turnover explains diversity patterns. There is evidence for functional redundancy in the low-latitude sites. The evolutionary mechanism of deep-time stability finds mixed support whilst there is relatively little evidence for an out-of-the-tropics model. These results suggest the diversity patterns of planktonic foraminifera cannot be explained by any one environmental variable or proposed mechanism, but instead reflect multiple processes acting in concert.

Comparative riverscape genetics reveals reservoirs of genetic diversity for conservation and restoration of Great Plains fishes.

PubMed

Osborne, Megan J; Perkin, Joshuah S; Gido, Keith B; Turner, Thomas F

2014-12-01

We used comparative landscape genetics to examine the relative roles of historical events, intrinsic traits and landscape factors in determining the distribution of genetic diversity of river fishes across the North American Great Plains. Spatial patterns of diversity were overlaid on a patch-based graphical model and then compared within and among three species that co-occurred across five Great Plains watersheds. Species differing in reproductive strategy (benthic vs. pelagic-spawning) were hypothesized to have different patterns of genetic diversity, but the overriding factor shaping contemporary patterns of diversity was the signature of past climates and geological history. Allelic diversity was significantly higher at southern latitudes for Cyprinella lutrensis and Hybognathus placitus, consistent with northward expansion from southern Pleistocene refugia. Within the historical context, all species exhibited lowered occupancy and abundance in heavily fragmented and drier upstream reaches, particularly H. placitus; a pelagic-spawning species, suggesting rates of extirpation have outpaced losses of genetic diversity in this species. Within most tributary basins, genetically diverse populations of each species persisted. Hence, reconnecting genetically diverse populations with those characterized by reduced diversity (regardless of their position within the riverine network) would provide populations with greater genetic and demographic resilience. We discuss cases where cross-basin transfer may be appropriate to enhance genetic diversity and mitigate negative effects of climate change. Overall, striking similarities in genetic patterns and in response to fragmentation and dewatering suggest a common strategy for genetic resource management in this unique riverine fish assemblage. © 2014 John Wiley & Sons Ltd.

Geostatistics and Geographic Information System to Analyze the Spatial Distribution of the Diversity of Anastrepha Species (Diptera: Tephritidae): the Effect of Forest Fragments in an Urban Area.

PubMed

Garcia, A G; Araujo, M R; Uramoto, K; Walder, J M M; Zucchi, R A

2017-12-08

Fruit flies are among the most damaging insect pests of commercial fruit in Brazil. It is important to understand the landscape elements that may favor these flies. In the present study, spatial data from surveys of species of Anastrepha Schiner (Diptera: Tephritidae) in an urban area with forest fragments were analyzed, using geostatistics and Geographic Information System (GIS) to map the diversity of insects and evaluate how the forest fragments drive the spatial patterns. The results indicated a high diversity of species associated with large fragments, and a trend toward lower diversity in the more urbanized area, as the fragment sizes decreased. We concluded that the diversity of Anastrepha species is directly and positively related to large and continuous forest fragments in urbanized areas, and that combining geostatistics and GIS is a promising method for use in insect-pest management and sampling involving fruit flies. © The Authors 2017. Published by Oxford University Press on behalf of Entomological Society of America. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Derivation of two well-behaved theoretical contagion indices and their sampling properties and application for assessing forest landscape diversity

Treesearch

Bernard R. Parresol

2011-01-01

Studies of spatial patterns of landscapes are useful to quantify human impact, predict wildlife effects, or describe variability of landscape features. A common approach to identify and quantify landscape structure is with a landscape scale model known as a contagion index. A contagion index quantifies two distinct components of landscape diversity: composition and...

Characterizing and Comparing Landscape Diversity Using GIS and a Contagion Index

Treesearch

Bernard R. Parresol; Joseph McCollum

1997-01-01

The purpose of this study was to examine the pattern land changes in forestcover types over the last two decades on three landscape level physiographic provinces of the state of Alabama, USA: (i) The Great Appalachian Valley Province, (ii) The Blue Ridge Talladega Mountain Province, and (iii) The Piedmont Province. Studies of spatial patterns of landscapes are useful...

Mapping and determinism of soil microbial community distribution across an agricultural landscape

PubMed Central

Constancias, Florentin; Terrat, Sébastien; Saby, Nicolas P A; Horrigue, Walid; Villerd, Jean; Guillemin, Jean-Philippe; Biju-Duval, Luc; Nowak, Virginie; Dequiedt, Samuel; Ranjard, Lionel; Chemidlin Prévost-Bouré, Nicolas

2015-01-01

Despite the relevance of landscape, regarding the spatial patterning of microbial communities and the relative influence of environmental parameters versus human activities, few investigations have been conducted at this scale. Here, we used a systematic grid to characterize the distribution of soil microbial communities at 278 sites across a monitored agricultural landscape of 13 km². Molecular microbial biomass was estimated by soil DNA recovery and bacterial diversity by 16S rRNA gene pyrosequencing. Geostatistics provided the first maps of microbial community at this scale and revealed a heterogeneous but spatially structured distribution of microbial biomass and diversity with patches of several hundreds of meters. Variance partitioning revealed that both microbial abundance and bacterial diversity distribution were highly dependent of soil properties and land use (total variance explained ranged between 55% and 78%). Microbial biomass and bacterial richness distributions were mainly explained by soil pH and texture whereas bacterial evenness distribution was mainly related to land management. Bacterial diversity (richness, evenness, and Shannon index) was positively influenced by cropping intensity and especially by soil tillage, resulting in spots of low microbial diversity in soils under forest management. Spatial descriptors also explained a small but significant portion of the microbial distribution suggesting that landscape configuration also shapes microbial biomass and bacterial diversity. PMID:25833770

Beta diversity at different spatial scales: plant communities in organic and conventional agriculture.

PubMed

Gabriel, Doreen; Roschewitz, Indra; Tscharntke, Teja; Thies, Carsten

2006-10-01

Biodiversity studies that guide agricultural subsidy policy have generally compared farming systems at a single spatial scale: the field. However, diversity patterns vary across spatial scales. Here, we examined the effects of farming system (organic vs. conventional) and position in the field (edge vs. center) on plant species richness in wheat fields at three spatial scales. We quantified alpha-, beta-, and gamma-diversity at the microscale in 800 plots, at the mesoscale in 40 fields, and at the macroscale in three regions using the additive partitioning approach, and evaluated the relative contribution of beta-diversity at each spatial scale to total observed species richness. We found that alpha-, beta-, and gamma-diversity were higher in organic than conventional fields and higher at the field edge than in the field center at all spatial scales. In both farming systems, beta-diversity at the meso- and macroscale explained most of the overall species richness (up to 37% and 25%, respectively), indicating considerable differences in community composition among fields and regions due to environmental heterogeneity. The spatial scale at which beta-diversity contributed the most to overall species richness differed between rare and common species. Total richness of rare species (present in < or = 5% of total samples) was mainly explained by differences in community composition at the meso- and macroscale (up to 27% and 48%, respectively), but only in organic fields. Total richness of common species (present in > or = 25% of total samples) was explained by differences in community composition at the micro- and mesoscale (up to 29% and 47%, respectively), i.e., among plots and fields, independent of farming system. Our results show that organic farming made the greatest contribution to total species richness at the meso (among fields) and macro (among regions) scale due to environmental heterogeneity. Hence, agri-environment schemes should exploit this large-scale contribution of beta-diversity by tailoring schemes at regional scales to maximize dissimilarity between conservation areas using geographic information systems rather than focusing entirely at the classical local-field scale, which is the current practice.

Different responses of functional traits and diversity of stream macroinvertebrates to environmental and spatial factors in the Xishuangbanna watershed of the upper Mekong River Basin, China.

PubMed

Ding, Ning; Yang, Weifang; Zhou, Yunlei; González-Bergonzoni, Ivan; Zhang, Jie; Chen, Kai; Vidal, Nicolas; Jeppesen, Erik; Liu, Zhengwen; Wang, Beixin

2017-01-01

Functional traits and diversity indices have provided new insights into community responses to stressors. Most traits of aquatic organisms have frequently been tested for predictability and geographical stability in response to environmental variables, but such tests of functional diversity indices are rare. We sampled macroinvertebrates at 18 reference sites (RS) and 35 disturbed sites (DS) from headwater streams in the upper Mekong River Basin, Xishuangbanna (XSBN), China. We selected 29 qualitative categories of eight traits and then calculated five functional diversity indices, namely functional richness (FRic), functional evenness (FEve), functional dispersion (FDis), functional divergence (FDiv) and Rao's Quadratic Entropy (RaoQ), and two trait diversity indices, namely trait richness (TR) and trait diversity (TD). We used combination of RLQ and fourth-corner to examine the response of traits and functional diversity to the disturbance and environmental variables. We used variance partitioning to explore the relative role of environmental variables and spatial factors in constraining trait composition and functional diversity. We found that the relative frequency of ten trait categories, and the values of TD, TR, FRic and FDis in RS were significantly different (p<0.05) from DS. In addition, the seven traits (except for "habit") demonstrated a predictable response of trait patterns along the integrative environmental gradients. Environmental variables significantly contributed to most of the traits, functional diversity and trait diversity. However, spatial variables were mainly significant in shaping ecological traits, FRic and FEve. Our results confirm the dominant role of environmental variables in the determination of community trait composition and functional diversity, and substantiate the contribution of spatial vectors in explaining the variance of functional traits and diversity. We conclude that the traits "Refuge", "External protection", "Respiration" and "Body shape", and diversity indices FDis, TD, and TR are promising indicators of stream conditions at XSBN. Copyright © 2016 Elsevier B.V. All rights reserved.

Regional variation in the hierarchical partitioning of diversity in coral-dwelling fishes.

PubMed

Belmaker, Jonathan; Ziv, Yaron; Shashar, Nadav; Connolly, Sean R

2008-10-01

The size of the regional species pool may influence local patterns of diversity. However, it is unclear whether certain spatial scales are less sensitive to regional influences than others. Additive partitioning was used to separate coral-dwelling fish diversity to its alpha and beta components, at multiple scales, in several regions across the Indo-Pacific. We then examined how the relative contribution of these components changes with increased regional diversity. By employing specific random-placement null models, we overcome methodological problems with local-regional regressions. We show that, although alpha and beta diversities within each region are consistently different from random-placement null models, the increase in beta diversities among regions was similar to that predicted once heterogeneity in coral habitat was accounted for. In contrast, alpha diversity within single coral heads was limited and increased less than predicted by the null models. This was correlated with increased intraspecific aggregation in more diverse regions and is consistent with ecological limitations on the number of coexisting species at the local scale. These results suggest that, apart from very small spatial scales, variation in the partitioning of fish diversity along regional species richness gradients is driven overwhelmingly by the corresponding gradients in coral assemblage structure.

Violent crime in San Antonio, Texas: an application of spatial epidemiological methods.

PubMed

Sparks, Corey S

2011-12-01

Violent crimes are rarely considered a public health problem or investigated using epidemiological methods. But patterns of violent crime and other health conditions are often affected by similar characteristics of the built environment. In this paper, methods and perspectives from spatial epidemiology are used in an analysis of violent crimes in San Antonio, TX. Bayesian statistical methods are used to examine the contextual influence of several aspects of the built environment. Additionally, spatial regression models using Bayesian model specifications are used to examine spatial patterns of violent crime risk. Results indicate that the determinants of violent crime depend on the model specification, but are primarily related to the built environment and neighborhood socioeconomic conditions. Results are discussed within the context of a rapidly growing urban area with a diverse population. Copyright © 2011 Elsevier Ltd. All rights reserved.

Shaping the Latitudinal Diversity Gradient: New Perspectives from a Synthesis of Paleobiology and Biogeography.

PubMed

Jablonski, David; Huang, Shan; Roy, Kaustuv; Valentine, James W

2017-01-01

An impediment to understanding the origin and dynamics of the latitudinal diversity gradient (LDG)-the most pervasive large-scale biotic pattern on Earth-has been the tendency to focus narrowly on a single causal factor when a more synthetic, integrative approach is needed. Using marine bivalves as a model system and drawing on other systems where possible, we review paleobiologic and biogeographic support for two supposedly opposing views, that the LDG is shaped primarily by (a) local environmental factors that determine the number of species and higher taxa at a given latitude (in situ hypotheses) or (b) the entry of lineages arising elsewhere into a focal region (spatial dynamics hypotheses). Support for in situ hypotheses includes the fit of present-day diversity trends in many clades to such environmental factors as temperature and the correlation of extinction intensities in Pliocene bivalve faunas with net regional temperature changes. Support for spatial dynamics hypotheses includes the age-frequency distribution of bivalve genera across latitudes, which is consistent with an out-of-the-tropics dynamic, as are the higher species diversities in temperate southeastern Australia and southeastern Japan than in the tropical Caribbean. Thus, both in situ and spatial dynamics processes must shape the bivalve LDG and are likely to operate in other groups as well. The relative strengths of the two processes may differ among groups showing similar LDGs, but dissecting their effects will require improved methods of integrating fossil data with molecular phylogenies. We highlight several potential research directions and argue that many of the most dramatic biotic patterns, past and present, are likely to have been generated by diverse, mutually reinforcing drivers.

A test of multiple hypotheses for the species richness gradient of South American owls.

PubMed

Diniz-Filho, José Alexandre Felizola; Rangel, Thiago F L V B; Hawkins, Bradford A

2004-08-01

Many mechanisms have been proposed to explain broad scale spatial patterns in species richness. In this paper, we evaluate five explanations for geographic gradients in species richness, using South American owls as a model. We compared the explanatory power of contemporary climate, landcover diversity, spatial climatic heterogeneity, evolutionary history, and area. An important aspect of our analyses is that very different hypotheses, such as history and area, can be quantified at the same observation scale and, consequently can be incorporated into a single analytical framework. Both area effects and owl phylogenetic history were poorly associated with richness, whereas contemporary climate, climatic heterogeneity at the mesoscale and landcover diversity explained ca. 53% of the variation in species richness. We conclude that both climate and environmental heterogeneity should be retained as plausible explanations for the diversity gradient. Turnover rates and scaling effects, on the other hand, although perhaps useful for detecting faunal changes and beta diversity at local and regional scales, are not strong explanations for the owl diversity gradient.

Twenty-million-year relationship between mammalian diversity and primary productivity

PubMed Central

Fritz, Susanne A.; Eronen, Jussi T.; Schnitzler, Jan; Hof, Christian; Janis, Christine M.; Mulch, Andreas; Böhning-Gaese, Katrin; Graham, Catherine H.

2016-01-01

At global and regional scales, primary productivity strongly correlates with richness patterns of extant animals across space, suggesting that resource availability and climatic conditions drive patterns of diversity. However, the existence and consistency of such diversity–productivity relationships through geological history is unclear. Here we provide a comprehensive quantitative test of the diversity–productivity relationship for terrestrial large mammals through time across broad temporal and spatial scales. We combine >14,000 occurrences for 690 fossil genera through the Neogene (23–1.8 Mya) with regional estimates of primary productivity from fossil plant communities in North America and Europe. We show a significant positive diversity–productivity relationship through the 20-million-year record, providing evidence on unprecedented spatial and temporal scales that this relationship is a general pattern in the ecology and paleo-ecology of our planet. Further, we discover that genus richness today does not match the fossil relationship, suggesting that a combination of human impacts and Pleistocene climate variability has modified the 20-million-year ecological relationship by strongly reducing primary productivity and driving many mammalian species into decline or to extinction. PMID:27621451

The effects of habitat connectivity and regional heterogeneity on artificial pond metacommunities.

PubMed

Pedruski, Michael T; Arnott, Shelley E

2011-05-01

Habitat connectivity and regional heterogeneity represent two factors likely to affect biodiversity across different spatial scales. We performed a 3 × 2 factorial design experiment to investigate the effects of connectivity, heterogeneity, and their interaction on artificial pond communities of freshwater invertebrates at the local (α), among-community (β), and regional (γ) scales. Despite expectations that the effects of connectivity would depend on levels of regional heterogeneity, no significant interactions were found for any diversity index investigated at any spatial scale. While observed responses of biodiversity to connectivity and heterogeneity depended to some extent on the diversity index and spatial partitioning formula used, the general pattern shows that these factors largely act at the β scale, as opposed to the α or γ scales. We conclude that the major role of connectivity in aquatic invertebrate communities is to act as a homogenizing force with relatively little effect on diversity at the α or γ levels. Conversely, heterogeneity acts as a force maintaining differences between communities.

Stand Structure and Substrate Diversity as Two Major Drivers for Bryophyte Distribution in a Temperate Montane Ecosystem

PubMed Central

Chen, Yun; Niu, Shuai; Li, Peikun; Jia, Hongru; Wang, Hailiang; Ye, Yongzhong; Yuan, Zhiliang

2017-01-01

Elucidating the major drivers of bryophyte distribution is the first step to protecting bryophyte diversity. Topography, forest, substrates (ground, tree trunks, roots, rocks, and rotten wood), and spatial factor, which factors are the major drivers of bryophyte distribution? In this study, 53 plots were set in 400 m2 along the elevation gradient in Xiaoqinling, China. All bryophytes in the plots were collected and identified. Regression analysis was used to examine the relationship between bryophyte and substrate diversity. We compared the patterns of overall bryophyte diversity and diversity of bryophytes found on the ground, tree, and rock along elevational gradients. Canonical correspondence analysis was applied to relate species composition to selected environmental variables. The importance of topography, forest, substrates, and spatial factors was determined by variance partitioning. A total of 1378 bryophyte specimens were collected, and 240 species were identified. Bryophyte diversity was closely related to substrate diversity. The overall bryophyte diversity significantly increased with elevation; however, the response varied among ground, tree, and rock bryophytes. Tree diversity and herb layer were considered important environmental factors in determining bryophyte distribution. Species abundance was best explained by stand structure (17%), and species diversity was best explained by stand structure (35%) and substrate (40%). Results directly indicated that substrate diversity can improve bryophyte species diversity. The effects of micro-habitat formed by stand structure and substrate diversity were higher than those of spatial processes and topography factors on bryophyte distribution. This study proved that the determinant factors influencing bryophyte diversity reflect the trends in recent forest management, providing a real opportunity to improve forest biodiversity conservation. PMID:28603535

Stand Structure and Substrate Diversity as Two Major Drivers for Bryophyte Distribution in a Temperate Montane Ecosystem.

PubMed

Chen, Yun; Niu, Shuai; Li, Peikun; Jia, Hongru; Wang, Hailiang; Ye, Yongzhong; Yuan, Zhiliang

2017-01-01

Elucidating the major drivers of bryophyte distribution is the first step to protecting bryophyte diversity. Topography, forest, substrates (ground, tree trunks, roots, rocks, and rotten wood), and spatial factor, which factors are the major drivers of bryophyte distribution? In this study, 53 plots were set in 400 m 2 along the elevation gradient in Xiaoqinling, China. All bryophytes in the plots were collected and identified. Regression analysis was used to examine the relationship between bryophyte and substrate diversity. We compared the patterns of overall bryophyte diversity and diversity of bryophytes found on the ground, tree, and rock along elevational gradients. Canonical correspondence analysis was applied to relate species composition to selected environmental variables. The importance of topography, forest, substrates, and spatial factors was determined by variance partitioning. A total of 1378 bryophyte specimens were collected, and 240 species were identified. Bryophyte diversity was closely related to substrate diversity. The overall bryophyte diversity significantly increased with elevation; however, the response varied among ground, tree, and rock bryophytes. Tree diversity and herb layer were considered important environmental factors in determining bryophyte distribution. Species abundance was best explained by stand structure (17%), and species diversity was best explained by stand structure (35%) and substrate (40%). Results directly indicated that substrate diversity can improve bryophyte species diversity. The effects of micro-habitat formed by stand structure and substrate diversity were higher than those of spatial processes and topography factors on bryophyte distribution. This study proved that the determinant factors influencing bryophyte diversity reflect the trends in recent forest management, providing a real opportunity to improve forest biodiversity conservation.

Spatial variability in community composition on a granite breakwater versus natural rocky shores: lack of microhabitats suppresses intertidal biodiversity.

PubMed

Aguilera, Moisés A; Broitman, Bernardo R; Thiel, Martin

2014-10-15

Strong differences have been observed between the assemblages on artificial reefs and on natural hard-bottom habitats worldwide, but little is known about the mechanisms that cause contrasting biodiversity patterns. We examined the influence of spatial attributes in relation to both biogenic and topographic microhabitats, in the distribution and composition of intertidal species on both artificial and natural reefs. We found higher small-scale spatial heterogeneity on the natural reef compared with the study breakwater. Species richness and diversity were associated with a higher availability of crevices, rock pools and mussels in natural habitats. Spatial distribution of certain grazers corresponded well with the spatial structure of microhabitats. In contrast, the lack of microhabitats on the breakwater resulted in the absence of several grazers reflected in lower species richness. Biogenic and topographic microhabitats can have interactive effects providing niche opportunities for multiple species, explaining differences in species diversity between artificial versus natural reefs. Copyright © 2014 Elsevier Ltd. All rights reserved.

Species richness effects on ecosystem multifunctionality depend on evenness, composition and spatial pattern

USGS Publications Warehouse

Maestre, F.T.; Castillo-Monroy, A. P.; Bowker, M.A.; Ochoa-Hueso, R.

2012-01-01

1. Recent studies have suggested that the simultaneous maintenance of multiple ecosystem functions (multifunctionality) is positively supported by species richness. However, little is known regarding the relative importance of other community attributes (e.g. spatial pattern, species evenness) as drivers of multifunctionality. 2. We conducted two microcosm experiments using model biological soil crust communities dominated by lichens to: (i) evaluate the joint effects and relative importance of changes in species composition, spatial pattern (clumped and random distribution of lichens), evenness (maximal and low evenness) and richness (from two to eight species) on soil functions related to nutrient cycling (β-glucosidase, urease and acid phosphatase enzymes, in situ N availability, total N, organic C, and N fixation), and (ii) assess how these community attributes affect multifunctionality. 3. Species richness, composition and spatial pattern affected multiple ecosystem functions (e.g. organic C, total N, N availability, β-glucosidase activity), albeit the magnitude and direction of their effects varied with the particular function, experiment and soil depth considered. Changes in species composition had effects on organic C, total N and the activity of β-glucosidase. Significant species richness × evenness and spatial pattern × evenness interactions were found when analysing functions such as organic C, total N and the activity of phosphatase. 4. The probability of sustaining multiple ecosystem functions increased with species richness, but this effect was largely modulated by attributes such as species evenness, composition and spatial pattern. Overall, we found that model communities with high species richness, random spatial pattern and low evenness increased multifunctionality. 5. Synthesis. Our results illustrate how different community attributes have a diverse impact on ecosystem functions related to nutrient cycling, and provide new experimental evidence illustrating the importance of the spatial pattern of organisms on ecosystem functioning. They also indicate that species richness is not the only biotic driver of multifunctionality, and that particular combinations of community attributes may be required to maximize it.

Trophic interactions induce spatial self-organization of microbial consortia on rough surfaces.

PubMed

Wang, Gang; Or, Dani

2014-10-24

The spatial context of microbial interactions common in natural systems is largely absent in traditional pure culture-based microbiology. The understanding of how interdependent microbial communities assemble and coexist in limited spatial domains remains sketchy. A mechanistic model of cell-level interactions among multispecies microbial populations grown on hydrated rough surfaces facilitated systematic evaluation of how trophic dependencies shape spatial self-organization of microbial consortia in complex diffusion fields. The emerging patterns were persistent irrespective of initial conditions and resilient to spatial and temporal perturbations. Surprisingly, the hydration conditions conducive for self-assembly are extremely narrow and last only while microbial cells remain motile within thin aqueous films. The resulting self-organized microbial consortia patterns could represent optimal ecological templates for the architecture that underlie sessile microbial colonies on natural surfaces. Understanding microbial spatial self-organization offers new insights into mechanisms that sustain small-scale soil microbial diversity; and may guide the engineering of functional artificial microbial consortia.

Environmental Filtering Process Has More Important Roles than Dispersal Limitation in Shaping Large-Scale Prokaryotic Beta Diversity Patterns of Grassland Soils.

PubMed

Cao, Peng; Wang, Jun-Tao; Hu, Hang-Wei; Zheng, Yuan-Ming; Ge, Yuan; Shen, Ju-Pei; He, Ji-Zheng

2016-07-01

Despite the utmost importance of microorganisms in maintaining ecosystem functioning and their ubiquitous distribution, our knowledge of the large-scale pattern of microbial diversity is limited, particularly in grassland soils. In this study, the microbial communities of 99 soil samples spanning over 3000 km across grassland ecosystems in northern China were investigated using high-throughput sequencing to analyze the beta diversity pattern and the underlying ecological processes. The microbial communities were dominated by Proteobacteria, Actinobacteria, Acidobacteria, Chloroflexi, and Planctomycetes across all the soil samples. Spearman's correlation analysis indicated that climatic factors and soil pH were significantly correlated with the dominant microbial taxa, while soil microbial richness was positively linked to annual precipitation. The environmental divergence-dissimilarity relationship was significantly positive, suggesting the importance of environmental filtering processes in shaping soil microbial communities. Structural equation modeling found that the deterministic process played a more important role than the stochastic process on the pattern of soil microbial beta diversity, which supported the predictions of niche theory. Partial mantel test analysis have showed that the contribution of independent environmental variables has a significant effect on beta diversity, while independent spatial distance has no such relationship, confirming that the deterministic process was dominant in structuring soil microbial communities. Overall, environmental filtering process has more important roles than dispersal limitation in shaping microbial beta diversity patterns in the grassland soils.

High variability of dung beetle diversity patterns at four mountains of the Trans-Mexican Volcanic Belt

PubMed Central

Arriaga-Jiménez, Alfonsina; Halffter, Gonzalo

2018-01-01

Insect diversity patterns of high mountain ecosystems remain poorly studied in the tropics. Sampling dung beetles of the subfamilies Aphodiinae, Scarabaeinae, and Geotrupinae was carried out at four volcanoes in the Trans-Mexican Volcanic Belt (TMVB) in the Mexican transition zone at 2,700 and 3,400 MASL, and on the windward and leeward sides. Sampling units represented a forest–shrubland–pasture (FSP) mosaic typical of this mountain region. A total of 3,430 individuals of 29 dung beetle species were collected. Diversity, abundance and compositional similarity (CS) displayed a high variability at all scales; elevation, cardinal direction, or FSP mosaics did not show any patterns of higher or lower values of those measures. The four mountains were different regarding dispersion patterns and taxonomic groups, both for species and individuals. Onthophagus chevrolati dominated all four mountains with an overall relative abundance of 63%. CS was not related to distance among mountains, but when O. chevrolati was excluded from the analysis, CS values based on species abundance decreased with increasing distance. Speciation, dispersion, and environmental instability are suggested as the main drivers of high mountain diversity patterns, acting together at different spatial and temporal scales. Three species new to science were collected (>10% of all species sampled). These discoveries may indicate that speciation rate is high among these volcanoes—a hypothesis that is also supported by the elevated number of collected species with a restricted montane distribution. Dispersion is an important factor in driving species composition, although naturally limited between high mountains; horizontal colonization events at different time scales may best explain the observed species composition in the TMVB, complemented by vertical colonization events to a lesser extent. Environmental instability may be the main factor causing the high variability of diversity and abundance patterns found during sampling. Together, we interpret these results as indicating that species richness and composition in the high mountains of the TMVB may be driven by biogeographical history while variability in diversity is determined by ecological factors. We argue that current conservation strategies do not focus sufficiently on protecting high mountain fauna, and that there is a need for developing and applying new conservation concepts that take into account the high spatial and temporal variability of this system. PMID:29507842

Spatial pattern affects diversity-productivity relationships in experimental meadow communities

NASA Astrophysics Data System (ADS)

Lamošová, Tereza; Doležal, Jiří; Lanta, Vojtěch; Lepš, Jan

2010-05-01

Plant species create aggregations of conspecifics as a consequence of limited seed dispersal, clonal growth and heterogeneous environment. Such intraspecific aggregation increases the importance of intraspecific competition relative to interspecific competition which may slow down competitive exclusion and promote species coexistence. To examine how spatial aggregation impacts the functioning of experimental assemblages of varying species richness, eight perennial grassland species of different growth form were grown in random and aggregated patterns in monocultures, two-, four-, and eight-species mixtures. In mixtures with an aggregated pattern, monospecific clumps were interspecifically segregated. Mixed model ANOVA was used to test (i) how the total productivity and productivity of individual species is affected by the number of species in a mixture, and (ii) how these relationships are affected by spatial pattern of sown plants. The main patterns of productivity response to species richness conform to other studies: non-transgressive overyielding is omnipresent (the productivity of mixtures is higher than the average of its constituent species so that the net diversity, selection and complementarity effects are positive), whereas transgressive overyielding is found only in a minority of cases (average of log(overyielding) being close to zero or negative). The theoretical prediction that plants in a random pattern should produce more than in an aggregated pattern (the distances to neighbours are smaller and consequently the competition among neighbours stronger) was confirmed in monocultures of all the eight species. The situation is more complicated in mixtures, probably as a consequence of complicated interplay between interspecific and intraspecific competition. The most productive species ( Achillea, Holcus, Plantago) were competitively superior and increased their relative productivity with mixture richness. The intraspecific competition of these species is stronger than that of most other species. The aggregated pattern in the full mixture increased the survival of subordinate species, and consequently, we conclude that an aggregated pattern can promote species coexistence (or at least postpone competitive exclusion), particularly in comparison with homogeneously sown mixtures.

Geothermal activity helps life survive glacial cycles

PubMed Central

Fraser, Ceridwen I.; Terauds, Aleks; Smellie, John; Convey, Peter; Chown, Steven L.

2014-01-01

Climate change has played a critical role in the evolution and structure of Earth’s biodiversity. Geothermal activity, which can maintain ice-free terrain in glaciated regions, provides a tantalizing solution to the question of how diverse life can survive glaciations. No comprehensive assessment of this “geothermal glacial refugia” hypothesis has yet been undertaken, but Antarctica provides a unique setting for doing so. The continent has experienced repeated glaciations that most models indicate blanketed the continent in ice, yet many Antarctic species appear to have evolved in almost total isolation for millions of years, and hence must have persisted in situ throughout. How could terrestrial species have survived extreme glaciation events on the continent? Under a hypothesis of geothermal glacial refugia and subsequent recolonization of nongeothermal regions, we would expect to find greater contemporary diversity close to geothermal sites than in nongeothermal regions, and significant nestedness by distance of this diversity. We used spatial modeling approaches and the most comprehensive, validated terrestrial biodiversity dataset yet created for Antarctica to assess spatial patterns of diversity on the continent. Models clearly support our hypothesis, indicating that geothermally active regions have played a key role in structuring biodiversity patterns in Antarctica. These results provide critical insights into the evolutionary importance of geothermal refugia and the history of Antarctic species. PMID:24616489

Identifying Genetic Hotspots by Mapping Molecular Diversity of Widespread Trees: When Commonness Matters.

PubMed

Souto, Cintia P; Mathiasen, Paula; Acosta, María Cristina; Quiroga, María Paula; Vidal-Russell, Romina; Echeverría, Cristian; Premoli, Andrea C

2015-01-01

Conservation planning requires setting priorities at the same spatial scale at which decision-making processes are undertaken considering all levels of biodiversity, but current methods for identifying biodiversity hotspots ignore its genetic component. We developed a fine-scale approach based on the definition of genetic hotspots, which have high genetic diversity and unique variants that represent their evolutionary potential and evolutionary novelties. Our hypothesis is that wide-ranging taxa with similar ecological tolerances, yet of phylogenetically independent lineages, have been and currently are shaped by ecological and evolutionary forces that result in geographically concordant genetic patterns. We mapped previously published genetic diversity and unique variants of biparentally inherited markers and chloroplast sequences for 9 species from 188 and 275 populations, respectively, of the 4 woody dominant families of the austral temperate forest, an area considered a biodiversity hotspot. Spatial distribution patterns of genetic polymorphisms differed among taxa according to their ecological tolerances. Eight genetic hotspots were detected and we recommend conservation actions for some in the southern Coastal Range in Chile. Existing spatially explicit genetic data from multiple populations and species can help to identify biodiversity hotspots and guide conservation actions to establish science-based protected areas that will preserve the evolutionary potential of key habitats and species. © The American Genetic Association 2015. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Tracing Mississippi River influences in estuarine food webs of coastal Louisiana.

PubMed

Wissel, Björn; Fry, Brian

2005-08-01

The Breton Sound estuary in southern Louisiana receives large amounts of Mississippi River water via a controlled diversion structure at the upstream end of the estuary. We used stable isotopes to trace spatial and seasonal responses of the downstream food web to winter and spring introductions of river water. Analysis of delta13C, delta15N, and delta34S in the common local consumers such as grass shrimp (Palaemonetes sp.), barnacles (Balanus sp.), and small plankton-feeding fish (bay anchovies, Anchoa mitchilli) showed that the diversion was associated with two of the five major source regimes that were supporting food webs: a river regime near the diversion and a river-influenced productive marsh regime farther away from the diversion. Mixing models identified a third river-influenced source regime at the marine end of the estuary where major natural discharge from the Bird's Foot Delta wraps around into estuarine waters. The remaining two source regimes represented typical estuarine conditions: local freshwater sources especially from precipitation and a brackish source regime representing higher salinity marine influences. Overall, the Mississippi River diversion accounted for 75% of food web support in the upper estuary and 25% in the middle estuary, with influence strongest along known flow pathways and closest to the diversion. Isotopes also traced seasonal changes in river contributions, and indicated increased plant community productivity along the major flow path of diversion water. In the Breton Sound estuary, bottom-up forcing of food webs is strongly linked to river introductions and discharge, occurring in spatial and temporal patterns predictable from known river input regimes and known hydrologic circulation patterns.

Comparative phylogeography of eight herbs and lianas (Marantaceae) in central African rainforests.

PubMed

Ley, Alexandra C; Dauby, Gilles; Köhler, Julia; Wypior, Catherina; Röser, Martin; Hardy, Olivier J

2014-01-01

Vegetation history in tropical Africa is still to date hardly known and the drivers of population differentiation and speciation processes are little documented. It has often been postulated that population fragmentations following climate changes have played a key role in shaping the geographic distribution patterns of genetic diversity and in driving speciation. Here we analyzed phylogeographic patterns (chloroplast-DNA sequences) within and between eight (sister) species of widespread rainforest herbs and lianas from four genera of Marantaceae (Halopegia, Haumania, Marantochloa, Megaphrynium), searching for concordant patterns across species and concordance with the Pleistocene refuge hypothesis. Using 1146 plastid DNA sequences sampled across African tropical lowland rainforest, particularly in the Lower Guinean (LG) phytogeographic region, we analyzed intra- and interspecific patterns of genetic diversity, endemism and distinctiveness. Intraspecific patterns of haplotype diversity were concordant among most species as well as with the species-level diversity pattern of Marantaceae. Highest values were found in the hilly areas of Cameroon and Gabon. However, the spatial distribution of endemic haplotypes, an indicator for refuge areas in general, was not congruent across species. Each proposed refuge exhibited high values of endemism for one or a few species indicating their potential role as area of retraction for the respective species only. Thus, evolutionary histories seem to be diverse across species. In fact, areas of high diversity might have been both refuge and/or crossing zone of recolonization routes i.e., secondary contact zone. We hypothesize that retraction of species into one or the other refuge happened by chance depending on the species' distribution range at the time of climate deterioration. The idiosyncratic patterns found in Marantaceae species are similar to those found among tropical tree species, especially in southern LG.

Comparative phylogeography of eight herbs and lianas (Marantaceae) in central African rainforests

PubMed Central

Ley, Alexandra C.; Dauby, Gilles; Köhler, Julia; Wypior, Catherina; Röser, Martin; Hardy, Olivier J.

2014-01-01

Vegetation history in tropical Africa is still to date hardly known and the drivers of population differentiation and speciation processes are little documented. It has often been postulated that population fragmentations following climate changes have played a key role in shaping the geographic distribution patterns of genetic diversity and in driving speciation. Here we analyzed phylogeographic patterns (chloroplast-DNA sequences) within and between eight (sister) species of widespread rainforest herbs and lianas from four genera of Marantaceae (Halopegia, Haumania, Marantochloa, Megaphrynium), searching for concordant patterns across species and concordance with the Pleistocene refuge hypothesis. Using 1146 plastid DNA sequences sampled across African tropical lowland rainforest, particularly in the Lower Guinean (LG) phytogeographic region, we analyzed intra- and interspecific patterns of genetic diversity, endemism and distinctiveness. Intraspecific patterns of haplotype diversity were concordant among most species as well as with the species-level diversity pattern of Marantaceae. Highest values were found in the hilly areas of Cameroon and Gabon. However, the spatial distribution of endemic haplotypes, an indicator for refuge areas in general, was not congruent across species. Each proposed refuge exhibited high values of endemism for one or a few species indicating their potential role as area of retraction for the respective species only. Thus, evolutionary histories seem to be diverse across species. In fact, areas of high diversity might have been both refuge and/or crossing zone of recolonization routes i.e., secondary contact zone. We hypothesize that retraction of species into one or the other refuge happened by chance depending on the species' distribution range at the time of climate deterioration. The idiosyncratic patterns found in Marantaceae species are similar to those found among tropical tree species, especially in southern LG. PMID:25477901

Modelling patterns of pollinator species richness and diversity using satellite image texture.

PubMed

Hofmann, Sylvia; Everaars, Jeroen; Schweiger, Oliver; Frenzel, Mark; Bannehr, Lutz; Cord, Anna F

2017-01-01

Assessing species richness and diversity on the basis of standardised field sampling effort represents a cost- and time-consuming method. Satellite remote sensing (RS) can help overcome these limitations because it facilitates the collection of larger amounts of spatial data using cost-effective techniques. RS information is hence increasingly analysed to model biodiversity across space and time. Here, we focus on image texture measures as a proxy for spatial habitat heterogeneity, which has been recognized as an important determinant of species distributions and diversity. Using bee monitoring data of four years (2010-2013) from six 4 × 4 km field sites across Central Germany and a multimodel inference approach we test the ability of texture features derived from Landsat-TM imagery to model local pollinator biodiversity. Textures were shown to reflect patterns of bee diversity and species richness to some extent, with the first-order entropy texture and terrain roughness being the most relevant indicators. However, the texture measurements accounted for only 3-5% of up to 60% of the variability that was explained by our final models, although the results are largely consistent across different species groups (bumble bees, solitary bees). While our findings provide indications in support of the applicability of satellite imagery textures for modeling patterns of bee biodiversity, they are inconsistent with the high predictive power of texture metrics reported in previous studies for avian biodiversity. We assume that our texture data captured mainly heterogeneity resulting from landscape configuration, which might be functionally less important for wild bees than compositional diversity of plant communities. Our study also highlights the substantial variability among taxa in the applicability of texture metrics for modelling biodiversity.

Modelling patterns of pollinator species richness and diversity using satellite image texture

PubMed Central

Everaars, Jeroen; Schweiger, Oliver; Frenzel, Mark; Bannehr, Lutz; Cord, Anna F.

2017-01-01

Assessing species richness and diversity on the basis of standardised field sampling effort represents a cost- and time-consuming method. Satellite remote sensing (RS) can help overcome these limitations because it facilitates the collection of larger amounts of spatial data using cost-effective techniques. RS information is hence increasingly analysed to model biodiversity across space and time. Here, we focus on image texture measures as a proxy for spatial habitat heterogeneity, which has been recognized as an important determinant of species distributions and diversity. Using bee monitoring data of four years (2010–2013) from six 4 × 4 km field sites across Central Germany and a multimodel inference approach we test the ability of texture features derived from Landsat-TM imagery to model local pollinator biodiversity. Textures were shown to reflect patterns of bee diversity and species richness to some extent, with the first-order entropy texture and terrain roughness being the most relevant indicators. However, the texture measurements accounted for only 3–5% of up to 60% of the variability that was explained by our final models, although the results are largely consistent across different species groups (bumble bees, solitary bees). While our findings provide indications in support of the applicability of satellite imagery textures for modeling patterns of bee biodiversity, they are inconsistent with the high predictive power of texture metrics reported in previous studies for avian biodiversity. We assume that our texture data captured mainly heterogeneity resulting from landscape configuration, which might be functionally less important for wild bees than compositional diversity of plant communities. Our study also highlights the substantial variability among taxa in the applicability of texture metrics for modelling biodiversity. PMID:28973006

Niger-wide assessment of in situ sorghum genetic diversity with microsatellite markers.

PubMed

Deu, M; Sagnard, F; Chantereau, J; Calatayud, C; Hérault, D; Mariac, C; Pham, J-L; Vigouroux, Y; Kapran, I; Traore, P S; Mamadou, A; Gerard, B; Ndjeunga, J; Bezançon, G

2008-05-01

Understanding the geographical, environmental and social patterns of genetic diversity on different spatial scales is key to the sustainable in situ management of genetic resources. However, few surveys have been conducted on crop genetic diversity using exhaustive in situ germplasm collections on a country scale and such data are missing for sorghum in sub-Saharan Africa, its centre of origin. We report here a genetic analysis of 484 sorghum varieties collected in 79 villages evenly distributed across Niger, using 28 microsatellite markers. We found a high level of SSR diversity in Niger. Diversity varied between eastern and western Niger, and allelic richness was lower in the eastern part of the country. Genetic differentiation between botanical races was the first structuring factor (Fst = 0.19), but the geographical distribution and the ethnic group to which farmers belonged were also significantly associated with genetic diversity partitioning. Gene pools are poorly differentiated among climatic zones. The geographical situation of Niger, where typical western African (guinea), central African (caudatum) and eastern Sahelian African (durra) sorghum races converge, explained the high observed genetic diversity and was responsible for the interactions among the ethnic, geographical and botanical structure revealed in our study. After correcting for the structure of botanical races, spatial correlation of genetic diversity was still detected within 100 km, which may hint at limited seed exchanges between farmers. Sorghum domestication history, in relation to the spatial organisation of human societies, is therefore key information for sorghum in situ conservation programs in sub-Saharan Africa.

Species richness, distribution and genetic diversity of Caenorhabditis nematodes in a remote tropical rainforest

PubMed Central

2013-01-01

Background In stark contrast to the wealth of detail about C. elegans developmental biology and molecular genetics, biologists lack basic data for understanding the abundance and distribution of Caenorhabditis species in natural areas that are unperturbed by human influence. Methods Here we report the analysis of dense sampling from a small, remote site in the Amazonian rain forest of the Nouragues Natural Reserve in French Guiana. Results Sampling of rotting fruits and flowers revealed proliferating populations of Caenorhabditis, with up to three different species co-occurring within a single substrate sample, indicating remarkable overlap of local microhabitats. We isolated six species, representing the highest local species richness for Caenorhabditis encountered to date, including both tropically cosmopolitan and geographically restricted species not previously isolated elsewhere. We also documented the structure of within-species molecular diversity at multiple spatial scales, focusing on 57 C. briggsae isolates from French Guiana. Two distinct genetic subgroups co-occur even within a single fruit. However, the structure of C. briggsae population genetic diversity in French Guiana does not result from strong local patterning but instead presents a microcosm of global patterns of differentiation. We further integrate our observations with new data from nearly 50 additional recently collected C. briggsae isolates from both tropical and temperate regions of the world to re-evaluate local and global patterns of intraspecific diversity, providing the most comprehensive analysis to date for C. briggsae population structure across multiple spatial scales. Conclusions The abundance and species richness of Caenorhabditis nematodes is high in a Neotropical rainforest habitat that is subject to minimal human interference. Microhabitat preferences overlap for different local species, although global distributions include both cosmopolitan and geographically restricted groups. Local samples for the cosmopolitan C. briggsae mirror its pan-tropical patterns of intraspecific polymorphism. It remains an important challenge to decipher what drives Caenorhabditis distributions and diversity within and between species. PMID:23311925

Functional diversity patterns of abyssal nematodes in the Eastern Mediterranean: A comparison between cold seeps and typical deep sea sediments

NASA Astrophysics Data System (ADS)

Kalogeropoulou, V.; Keklikoglou, K.; Lampadariou, N.

2015-04-01

Spatial patterns in deep sea nematode biological trait composition and functional diversity were investigated between chemosynthetic and typical deep sea ecosystems as well as between different microhabitats within the chemosynthetic ecosystems, in the Eastern Mediterranean. The chemosynthetic ecosystems chosen were two mud volcanoes, Napoli at 1950 m depth and Amsterdam at 2040 m depth which are cold seeps characterized by high chemosynthetic activity and spatial heterogeneity. Typical deep sea ecosystems consisted of fine-grained silt-clay sediments which were collected from three areas located in the south Ionian Sea at 2765 to 2840 m depth, the southern Cretan margin at 1089 to 1998 m depth and the Levantine Sea at 3055 to 3870 m depth. A range of biological traits (9 traits; 31 categories) related to buccal morphology, tail shape, body size, body shape, life history strategy, sediment position, cuticle morphology, amphid shape and presence of somatic setae were combined to identify patterns in the functional composition of nematode assemblages between the two habitats, the two mud volcanoes (macroscale) and between the microhabitats within the mud volcanoes (microscale). Data on trait correspondence was provided by biological information on species and genera. A total of 170 nematode species were allocated in 67 different trait combinations, i.e. functional groups, based on taxonomic, morphological and behavioral characteristics. The Biological Trait Analysis (BTA) revealed significant differences between the mud volcanoes and the typical deep sea sediments indicating the presence of different biological functions in ecologically very different environments. Moreover, chemosynthetic activity and habitat heterogeneity within mud volcanoes enhance the presence of different biological and ecological functions in nematode assemblages of different microhabitats. Functional diversity and species richness patterns varied significantly across the different environmental gradients prevailing in the study areas. Biological trait analysis, with the addition of newly introduced trait categories, and functional diversity outcomes provided greater explanatory power of ecosystem functioning than species richness and taxonomic diversity.

Metacommunity ecology meets biogeography: effects of geographical region, spatial dynamics and environmental filtering on community structure in aquatic organisms.

PubMed

Heino, Jani; Soininen, Janne; Alahuhta, Janne; Lappalainen, Jyrki; Virtanen, Risto

2017-01-01

Metacommunity patterns and underlying processes in aquatic organisms have typically been studied within a drainage basin. We examined variation in the composition of six freshwater organismal groups across various drainage basins in Finland. We first modelled spatial structures within each drainage basin using Moran eigenvector maps. Second, we partitioned variation in community structure among three groups of predictors using constrained ordination: (1) local environmental variables, (2) spatial variables, and (3) dummy variable drainage basin identity. Third, we examined turnover and nestedness components of multiple-site beta diversity, and tested the best fit patterns of our datasets using the "elements of metacommunity structure" analysis. Our results showed that basin identity and local environmental variables were significant predictors of community structure, whereas within-basin spatial effects were typically negligible. In half of the organismal groups (diatoms, bryophytes, zooplankton), basin identity was a slightly better predictor of community structure than local environmental variables, whereas the opposite was true for the remaining three organismal groups (insects, macrophytes, fish). Both pure basin and local environmental fractions were, however, significant after accounting for the effects of the other predictor variable sets. All organismal groups exhibited high levels of beta diversity, which was mostly attributable to the turnover component. Our results showed consistent Clementsian-type metacommunity structures, suggesting that subgroups of species responded similarly to environmental factors or drainage basin limits. We conclude that aquatic communities across large scales are mostly determined by environmental and basin effects, which leads to high beta diversity and prevalence of Clementsian community types.

From broadscale patterns to fine-scale processes: habitat structure influences genetic differentiation in the pitcher plant midge across multiple spatial scales.

PubMed

Rasic, Gordana; Keyghobadi, Nusha

2012-01-01

The spatial scale at which samples are collected and analysed influences the inferences that can be drawn from landscape genetic studies. We examined genetic structure and its landscape correlates in the pitcher plant midge, Metriocnemus knabi, an inhabitant of the purple pitcher plant, Sarracenia purpurea, across several spatial scales that are naturally delimited by the midge's habitat (leaf, plant, cluster of plants, bog and system of bogs). We analysed 11 microsatellite loci in 710 M. knabi larvae from two systems of bogs in Algonquin Provincial Park (Canada) and tested the hypotheses that variables related to habitat structure are associated with genetic differentiation in this midge. Up to 54% of variation in individual-based genetic distances at several scales was explained by broadscale landscape variables of bog size, pitcher plant density within bogs and connectivity of pitcher plant clusters. Our results indicate that oviposition behaviour of females at fine scales, as inferred from the spatial locations of full-sib larvae, and spatially limited gene flow at broad scales represent the important processes underlying observed genetic patterns in M. knabi. Broadscale landscape features (bog size and plant density) appear to influence oviposition behaviour of midges, which in turn influences the patterns of genetic differentiation observed at both fine and broad scales. Thus, we inferred linkages among genetic patterns, landscape patterns and ecological processes across spatial scales in M. knabi. Our results reinforce the value of exploring such links simultaneously across multiple spatial scales and landscapes when investigating genetic diversity within a species. © 2011 Blackwell Publishing Ltd.

Diversity and Spatial-Temporal Distribution of Soil Macrofauna Communities Along Elevation in the Changbai Mountain, China.

PubMed

Yin, Xiuqin; Qiu, Lili; Jiang, Yunfeng; Wang, Yeqiao

2017-06-01

The understanding of patterns of vertical variation and diversity of flora and fauna along elevational change has been well established over the past century. However, it is unclear whether there is an elevational distribution pattern for soil fauna. This study revealed the diversity and spatial-temporal distribution of soil macrofauna communities in different vegetation zones from forest to alpine tundra along elevation of the Changbai Mountain, China. The abundance, richness, and Shannon-Wiener diversity index of soil macrofauna communities were compared in four distinguished vegetation zones including the coniferous and broadleaved mixed forest zone, the coniferous forest zone, the subalpine dwarf birch (Betula ermanii) forest zone, and the alpine tundra zone. Soil macrofauna were extracted in May, July, and September of 2009. In each season, the abundance and richness of the soil macrofauna decreased with the ascending elevation. The Shannon-Wiener diversity indices of the soil macrofauna were higher in the vegetation zones of lower elevation than of higher elevation. Significant differences were observed in the abundance, richness, and Shannon-Wiener diversity index for the studied vegetation zones. Soil macrofauna congregated mainly to the litter layer in the low-elevation areas and in the 0-5 cm soil layer of the higher elevation areas. The results emphasized that the diversity of soil macrofauna communities decreased as the elevation increased and possess the distinct characteristics of zonation in the mountain ecosystem. The diversity and distribution of soil macrofauna communities were influenced by mean annual precipitation, altitude, annual radiation quantity, and mean annual temperature. © The Authors 2017. Published by Oxford University Press on behalf of Entomological Society of America. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

Subtle Ecological Gradient in the Tropics Triggers High Species-Turnover in a Local Geographical Scale

PubMed Central

Nguyen, Dinh T.

2016-01-01

Our perception of diversity, including both alpha- and beta-diversity components, depends on spatial scale. Studies of spatial variation of the latter are just starting, with a paucity of research on beta-diversity patterns at smaller scales. Understanding these patterns and the processes shaping the distribution of diversity is critical to describe this diversity, but it is paramount in conservation too. Here, we investigate the diversity and structure of a tropical community of herbivorous beetles at a reduced local scale of some 10 km2, evaluating the effect of a small, gradual ecological change on this structure. We sampled leaf beetles in the Núi Chúa National Park (S Vietnam), studying changes in alpha- and beta-diversity across an elevation gradient up to 500 m, encompassing the ecotone between critically endangered lowland dry deciduous forest and mixed evergreen forest at higher elevations. Leaf beetle diversity was assessed using several molecular tree-based species delimitation approaches (with mtDNA cox1 data), species richness using rarefaction and incidence-based diversity indexes, and beta-diversity was investigated decomposing the contribution of species turnover and nestedness. We documented 155 species in the area explored and species-richness estimates 1.5–2.0x higher. Species diversity was similar in both forest types and changes in alpha-diversity along the elevation gradient showed an expected local increase of diversity in the ecotone. Beta-diversity was high among forest paths (average Sørensen's dissimilarity = 0.694) and, tentatively fixing at 300 m the boundary between otherwise continuous biomes, demonstrated similarly high beta-diversity (Sørensen's dissimilarity = 0.581), with samples clustering according to biome/elevation. Highly relevant considering the local scale of the study, beta-diversity had a high contribution of species replacement among locales (54.8%) and between biomes (79.6%), suggesting environmental heterogeneity as the dominant force shaping diversity at such small scale, directly and indirectly on the plant communities. Protection actions in the Park, especially these addressed at the imperative conservation of dry forest, must ponder the small scale at which processes shape species diversity and community structure for inconspicuous, yet extraordinarily diverse organisms such as the leaf beetles. PMID:27276228

Ecosystem variability along the estuarine salinity gradient: Examples from long-term study of San Francisco Bay

USGS Publications Warehouse

Cloern, James E.; Jassby, Alan D.; Schraga, Tara; Kress, Erica S.; Martin, Charles A.

2017-01-01

The salinity gradient of estuaries plays a unique and fundamental role in structuring spatial patterns of physical properties, biota, and biogeochemical processes. We use variability along the salinity gradient of San Francisco Bay to illustrate some lessons about the diversity of spatial structures in estuaries and their variability over time. Spatial patterns of dissolved constituents (e.g., silicate) can be linear or nonlinear, depending on the relative importance of river-ocean mixing and internal sinks (diatom uptake). Particles have different spatial patterns because they accumulate in estuarine turbidity maxima formed by the combination of sinking and estuarine circulation. Some constituents have weak or no mean spatial structure along the salinity gradient, reflecting spatially distributed sources along the estuary (nitrate) or atmospheric exchanges that buffer spatial variability of ecosystem metabolism (dissolved oxygen). The density difference between freshwater and seawater establishes stratification in estuaries stronger than the thermal stratification of lakes and oceans. Stratification is strongest around the center of the salinity gradient and when river discharge is high. Spatial distributions of motile organisms are shaped by species-specific adaptations to different salinity ranges (shrimp) and by behavioral responses to environmental variability (northern anchovy). Estuarine spatial patterns change over time scales of events (intrusions of upwelled ocean water), seasons (river inflow), years (annual weather anomalies), and between eras separated by ecosystem disturbances (a species introduction). Each of these lessons is a piece in the puzzle of how estuarine ecosystems are structured and how they differ from the river and ocean ecosystems they bridge.

Development of spatially diverse and complex dune-field patterns: Gran Desierto Dune Field, Sonora, Mexico

USGS Publications Warehouse

Beveridge, C.; Kocurek, G.; Ewing, R.C.; Lancaster, N.; Morthekai, P.; Singhvi, A.K.; Mahan, S.A.

2006-01-01

The pattern of dunes within the Gran Desierto of Sonora, Mexico, is both spatially diverse and complex. Identification of the pattern components from remote-sensing images, combined with statistical analysis of their measured parameters demonstrate that the composite pattern consists of separate populations of simple dune patterns. Age-bracketing by optically stimulated luminescence (OSL) indicates that the simple patterns represent relatively short-lived aeolian constructional events since ???25 ka. The simple dune patterns consist of: (i) late Pleistocene relict linear dunes; (ii) degraded crescentic dunes formed at ???12 ka; (iii) early Holocene western crescentic dunes; (iv) eastern crescentic dunes emplaced at ???7 ka; and (v) star dunes formed during the last 3 ka. Recognition of the simple patterns and their ages allows for the geomorphic backstripping of the composite pattern. Palaeowind reconstructions, based upon the rule of gross bedform-normal transport, are largely in agreement with regional proxy data. The sediment state over time for the Gran Desierto is one in which the sediment supply for aeolian constructional events is derived from previously stored sediment (Ancestral Colorado River sediment), and contemporaneous influx from the lower Colorado River valley and coastal influx from the Bahia del Adair inlet. Aeolian constructional events are triggered by climatic shifts to greater aridity, changes in the wind regime, and the development of a sediment supply. The rate of geomorphic change within the Gran Desierto is significantly greater than the rate of subsidence and burial of the accumulation surface upon which it rests. ?? 2006 The Authors. Journal compilation 2006 International Association of Sedimentologists.

Topographic influences on vegetation mosaics and tree diversity in the Chihuahuan Desert Borderlands.

PubMed

Poulos, Helen M; Camp, Ann E

2010-04-01

The abundance and distribution of species reflect how the niche requirements of species and the dynamics of populations interact with spatial and temporal variation in the environment. This study investigated the influence of geographical variation in environmental site conditions on tree dominance and diversity patterns in three topographically dissected mountain ranges in west Texas, USA, and northern Mexico. We measured tree abundance and basal area using a systematic sampling design across the forested areas of three mountain ranges and related these data to a suite of environmental parameters derived from field and digital elevation model data. We employed cluster analysis, classification and regression trees (CART), and rarefaction to identify (1) the dominant forest cover types across the three study sites and (2) environmental influences on tree distribution and diversity patterns. Elevation, topographic position, and incident solar radiation were the major influences on tree dominance and diversity. Mesic valley bottoms hosted high-diversity vegetation types, while hotter and drier mid-slopes and ridgetops supported lower tree diversity. Valley bottoms and other topographic positions shared few species, indicating high species turnover at the landscape scale. Mountain ranges with high topographic complexity also had higher species richness, suggesting that geographical variability in environmental conditions was a major influence on tree diversity. This study stressed the importance of landscape- and regional-scale topographic variability as a key factor controlling vegetation pattern and diversity in southwestern North America.

Spatially variable natural selection and the divergence between parapatric subspecies of lodgepole pine (Pinus contorta, Pinaceae).

PubMed

Eckert, Andrew J; Shahi, Hurshbir; Datwyler, Shannon L; Neale, David B

2012-08-01

Plant populations arrayed across sharp environmental gradients are ideal systems for identifying the genetic basis of ecologically relevant phenotypes. A series of five uplifted marine terraces along the northern coast of California represents one such system where morphologically distinct populations of lodgepole pine (Pinus contorta) are distributed across sharp soil gradients ranging from fertile soils near the coast to podzolic soils ca. 5 km inland. A total of 92 trees was sampled across four coastal marine terraces (N = 10-46 trees/terrace) located in Mendocino County, California and sequenced for a set of 24 candidate genes for growth and responses to various soil chemistry variables. Statistical analyses relying on patterns of nucleotide diversity were employed to identify genes whose diversity patterns were inconsistent with three null models. Most genes displayed patterns of nucleotide diversity that were consistent with null models (N = 19) or with the presence of paralogs (N = 3). Two genes, however, were exceptional: an aluminum responsive ABC-transporter with F(ST) = 0.664 and an inorganic phosphate transporter characterized by divergent haplotypes segregating at intermediate frequencies in most populations. Spatially variable natural selection along gradients of aluminum and phosphate ion concentrations likely accounted for both outliers. These results shed light on some of the genetic components comprising the extended phenotype of this ecosystem, as well as highlight ecotones as fruitful study systems for the detection of adaptive genetic variants.

Soil CO2 efflux and water use efficiency across diverse cover types in southern Appalachian hardwood forests

Treesearch

Ruba C. Bilal; John R. Seiler; Brian D. Strahm; John A. Peterson

2016-01-01

We are investigating biogeochemical cycling in a mixed hardwood forest in the Ridge and Valley physiographic province in Montgomery County, Virginia. The broad aim of the study is to understand how carbon, water and nutrient cycles vary among diverse stand types in a relatively small spatial area. The specific objectives here are to determine patterns in soil CO2...

How large is large enough for insects? Forest fragmentation effects at three spatial scales

NASA Astrophysics Data System (ADS)

Ribas, C. R.; Sobrinho, T. G.; Schoereder, J. H.; Sperber, C. F.; Lopes-Andrade, C.; Soares, S. M.

2005-02-01

Several mechanisms may lead to species loss in fragmented habitats, such as edge and shape effects, loss of habitat and heterogeneity. Ants and crickets were sampled in 18 forest remnants in south-eastern Brazil, to test whether a group of small remnants maintains the same insect species richness as similar sized large remnants, at three spatial scales. We tested hypotheses about alpha and gamma diversity to explain the results. Groups of remnants conserve as many species of ants as a single one. Crickets, however, showed a scale-dependent pattern: at small scales there was no significant or important difference between groups of remnants and a single one, while at the larger scale the group of remnants maintained more species. Alpha diversity (local species richness) was similar in a group of remnants and in a single one, at the three spatial scales, both for ants and crickets. Gamma diversity, however, varied both with taxa (ants and crickets) and spatial scale, which may be linked to insect mobility, remnant isolation, and habitat heterogeneity. Biological characteristics of the organisms involved have to be considered when studying fragmentation effects, as well as spatial scale at which it operates. Mobility of the organisms influences fragmentation effects, and consequently conservation strategies.

Up, Down, and All Around: Scale-Dependent Spatial Variation in Rocky-Shore Communities of Fildes Peninsula, King George Island, Antarctica

PubMed Central

Valdivia, Nelson; Díaz, María J.; Holtheuer, Jorge; Garrido, Ignacio; Huovinen, Pirjo; Gómez, Iván

2014-01-01

Understanding the variation of biodiversity along environmental gradients and multiple spatial scales is relevant for theoretical and management purposes. Hereby, we analysed the spatial variability in diversity and structure of intertidal and subtidal macrobenthic Antarctic communities along vertical environmental stress gradients and across multiple horizontal spatial scales. Since biotic interactions and local topographic features are likely major factors for coastal assemblages, we tested the hypothesis that fine-scale processes influence the effects of the vertical environmental stress gradients on the macrobenthic diversity and structure. We used nested sampling designs in the intertidal and subtidal habitats, including horizontal spatial scales ranging from few centimetres to 1000s of metres along the rocky shore of Fildes Peninsula, King George Island. In both intertidal and subtidal habitats, univariate and multivariate analyses showed a marked vertical zonation in taxon richness and community structure. These patterns depended on the horizontal spatial scale of observation, as all analyses showed a significant interaction between height (or depth) and the finer spatial scale analysed. Variance and pseudo-variance components supported our prediction for taxon richness, community structure, and the abundance of dominant species such as the filamentous green alga Urospora penicilliformis (intertidal), the herbivore Nacella concinna (intertidal), the large kelp-like Himantothallus grandifolius (subtidal), and the red crustose red alga Lithothamnion spp. (subtidal). We suggest that in coastal ecosystems strongly governed by physical factors, fine-scale processes (e.g. biotic interactions and refugia availability) are still relevant for the structuring and maintenance of the local communities. The spatial patterns found in this study serve as a necessary benchmark to understand the dynamics and adaptation of natural assemblages in response to observed and predicted environmental changes in Antarctica. PMID:24956114

Mapping and determinism of soil microbial community distribution across an agricultural landscape.

PubMed

Constancias, Florentin; Terrat, Sébastien; Saby, Nicolas P A; Horrigue, Walid; Villerd, Jean; Guillemin, Jean-Philippe; Biju-Duval, Luc; Nowak, Virginie; Dequiedt, Samuel; Ranjard, Lionel; Chemidlin Prévost-Bouré, Nicolas

2015-06-01

Despite the relevance of landscape, regarding the spatial patterning of microbial communities and the relative influence of environmental parameters versus human activities, few investigations have been conducted at this scale. Here, we used a systematic grid to characterize the distribution of soil microbial communities at 278 sites across a monitored agricultural landscape of 13 km². Molecular microbial biomass was estimated by soil DNA recovery and bacterial diversity by 16S rRNA gene pyrosequencing. Geostatistics provided the first maps of microbial community at this scale and revealed a heterogeneous but spatially structured distribution of microbial biomass and diversity with patches of several hundreds of meters. Variance partitioning revealed that both microbial abundance and bacterial diversity distribution were highly dependent of soil properties and land use (total variance explained ranged between 55% and 78%). Microbial biomass and bacterial richness distributions were mainly explained by soil pH and texture whereas bacterial evenness distribution was mainly related to land management. Bacterial diversity (richness, evenness, and Shannon index) was positively influenced by cropping intensity and especially by soil tillage, resulting in spots of low microbial diversity in soils under forest management. Spatial descriptors also explained a small but significant portion of the microbial distribution suggesting that landscape configuration also shapes microbial biomass and bacterial diversity. © 2015 The Authors. MicrobiologyOpen published by John Wiley & Sons Ltd.

Species Pool Functional Diversity Plays a Hidden Role in Generating β-Diversity.

PubMed

Patrick, Christopher J; Brown, Bryan L

2018-05-01

Functional trait diversity is used as a way to infer mechanistic processes that drive community assembly. While functional diversity within communities is often viewed as a response variable, here we present and test a framework for how functional diversity among taxa in the regional species pool drives the assembly of communities among habitats. We predicted that species pool functional diversity should work with environmental heterogeneity to drive β-diversity. We tested these predictions by modeling empirical patterns in invertebrate communities from 570 streams in 52 watersheds. Our analysis of the field data provided strong support for the inclusion of both functional diversity and environmental heterogeneity in the models, and our predictions were supported when the community was analyzed all together. However, analyses within individual functional feeding guilds revealed strong context dependency in the relative importance of functional diversity, γ-richness, and environmental heterogeneity to β-diversity. We interpret the results to mean that functional diversity can play an important role in driving β-diversity; however, within guilds the nature of interspecific interactions and species pool size complicate the relationship. Future research should test this conceptual model across different ecosystems and in experimental settings using metacommunity mesocosms to enhance our understanding of the role that functional variation plays in generating spatial biodiversity patterns.

spads 1.0: a toolbox to perform spatial analyses on DNA sequence data sets.

PubMed

Dellicour, Simon; Mardulyn, Patrick

2014-05-01

SPADS 1.0 (for 'Spatial and Population Analysis of DNA Sequences') is a population genetic toolbox for characterizing genetic variability within and among populations from DNA sequences. In view of the drastic increase in genetic information available through sequencing methods, spads was specifically designed to deal with multilocus data sets of DNA sequences. It computes several summary statistics from populations or groups of populations, performs input file conversions for other population genetic programs and implements locus-by-locus and multilocus versions of two clustering algorithms to study the genetic structure of populations. The toolbox also includes two MATLAB and r functions, GDISPAL and GDIVPAL, to display differentiation and diversity patterns across landscapes. These functions aim to generate interpolating surfaces based on multilocus distance and diversity indices. In the case of multiple loci, such surfaces can represent a useful alternative to multiple pie charts maps traditionally used in phylogeography to represent the spatial distribution of genetic diversity. These coloured surfaces can also be used to compare different data sets or different diversity and/or distance measures estimated on the same data set. © 2013 John Wiley & Sons Ltd.

Species dispersal rates alter diversity and ecosystem stability in pond metacommunities.

PubMed

Howeth, Jennifer G; Leibold, Mathew A

2010-09-01

Metacommunity theory suggests that relationships between diversity and ecosystem stability can be determined by the rate of species dispersal among local communities. The predicted relationships, however, may depend upon the relative strength of local environmental processes and disturbance. Here we evaluate the role of dispersal frequency and local predation perturbations in affecting patterns of diversity and stability in pond plankton metacommunities. Pond metacommunities were composed of three mesocosm communities: one of the three communities maintained constant "press" predation from a selective predator, bluegill sunfish (Lepomis macrochirus); the second community maintained "press" conditions without predation; and the third community experienced recurrent "pulsed" predation from bluegill sunfish. The triads of pond communities were connected at either no, low (0.7%/d), or high (20%/d) planktonic dispersal. Richness and composition of zooplankton and stability of plankton biomass and ecosystem productivity were measured at local and regional spatial scales. Dispersal significantly affected diversity such that local and regional biotas at the low dispersal rate maintained the greatest number of species. The unimodal local dispersal-diversity relationship was predator-dependent, however, as selective press predation excluded species regardless of dispersal. Further, there was no effect of dispersal on beta diversity because predation generated local conditions that selected for distinct community assemblages. Spatial and temporal ecosystem stability responded to dispersal frequency but not predation. Low dispersal destabilized the spatial stability of producer biomass but stabilized temporal ecosystem productivity. The results indicate that selective predation can prevent species augmentation from mass effects but has no apparent influence on stability. Dispersal rates, in contrast, can have significant effects on both species diversity and ecosystem stability at multiple spatial scales in metacommunities.

Waiting in the wings: what can we learn about gene co-option from the diversification of butterfly wing patterns?

PubMed

Jiggins, Chris D; Wallbank, Richard W R; Hanly, Joseph J

2017-02-05

A major challenge is to understand how conserved gene regulatory networks control the wonderful diversity of form that we see among animals and plants. Butterfly wing patterns are an excellent example of this diversity. Butterfly wings form as imaginal discs in the caterpillar and are constructed by a gene regulatory network, much of which is conserved across the holometabolous insects. Recent work in Heliconius butterflies takes advantage of genomic approaches and offers insights into how the diversification of wing patterns is overlaid onto this conserved network. WntA is a patterning morphogen that alters spatial information in the wing. Optix is a transcription factor that acts later in development to paint specific wing regions red. Both of these loci fit the paradigm of conserved protein-coding loci with diverse regulatory elements and developmental roles that have taken on novel derived functions in patterning wings. These discoveries offer insights into the 'Nymphalid Ground Plan', which offers a unifying hypothesis for pattern formation across nymphalid butterflies. These loci also represent 'hotspots' for morphological change that have been targeted repeatedly during evolution. Both convergent and divergent evolution of a great diversity of patterns is controlled by complex alleles at just a few genes. We suggest that evolutionary change has become focused on one or a few genetic loci for two reasons. First, pre-existing complex cis-regulatory loci that already interact with potentially relevant transcription factors are more likely to acquire novel functions in wing patterning. Second, the shape of wing regulatory networks may constrain evolutionary change to one or a few loci. Overall, genomic approaches that have identified wing patterning loci in these butterflies offer broad insight into how gene regulatory networks evolve to produce diversity.This article is part of the themed issue 'Evo-devo in the genomics era, and the origins of morphological diversity'. © 2016 The Author(s).

Canopy-derived fuels drive patterns of in-fire energy release and understory plant mortality in a longleaf pine ( Pinus palustris ) sandhill in northwest Florida, USA

Treesearch

Joseph J. O' Brien; E. Louise Loudermilk; J. Kevin Hiers; Scott Pokswinski; Benjamin Hornsby; Andrew Hudak; Dexter Strother; Eric Rowell; Benjamin C. Bright

2016-01-01

Wildland fire radiant energy emission is one of the only measurements of combustion that can be made at high temporal and spatial resolutions. Furthermore, spatially and temporally explicit measurements are critical for making inferences about ecological fire effects. Although the correlation between fire frequency and plant biological diversity in frequently burned ...

Strategies Influencing Spatial Heterogeneity of Microbial Life in a Soil Lysimeter

NASA Astrophysics Data System (ADS)

Sengupta, A.; Neilson, J. W.; Meira, A.; Wang, Y.; Meza, M.; Chorover, J.; Maier, R. M.; Troch, P. A. A.

2016-12-01

Soil microorganisms are critical drivers of biogeochemical processes. These microbes, in conjunction with their physical and chemical environment, contribute to ecosystem functioning and services of the landscape, have a profound impact on soil formation, and are of particular importance in oligotrophic environments; ecosystems that are characterized by low biotic diversity due to extremely low nutrient levels. Here, we present a study of microbial heterogeneity in a soil lysimeter under incipient conditions. The key questions asked were: 1) what is the spatial heterogeneity of microbes over a new and evolving landscape with inherent oligotrophic conditions, and 2) can patterns in diversity translate to patterns in microbe-mediated weathering processes and soil formation? We hypothesized that stratification of environmental conditions, brought about by varying water potential, flow paths, and redox conditions, will drive the heterogeneity of microbial life in a sub-meter scale. A suite of traditional and current microbiological tools were employed to study community characteristics. These included isolation on R2A media, quantitative polymerase chain reactions targeted at 16S rRNA bacterial and archaeal genes, and 18S fungal genes, and iTAG phylogenetic gene amplification. Illumina Mi-Seq platform generated sequences were analyzed using various bioinformatics pipelines to identify community patterns, classify microbial metabolic functions, and identify variables affecting the community dynamics. Numerous phyla (Verrucomicrobia, Actinobacteria, Planctomycetes, Proteobacteria, and Euryarchaeota) were identified. The surface layer had distinctly different distribution of communities compared to the other layers. Metabolically heterogeneous groups were found with respect to depth, with metabolic functions further confirmed by predictive functional profiling of the microbial communities. Therefore, despite being highly oligotrophic, the system was rich in species and functional diversity. Alongside physical and chemical data, the patterns observed in spatial and functional heterogeneity of microbes under incipient conditions is unique, and allows us to predict strategies undertaken by these microbes to survive in, and influence their oligotrophic environments.

Seasonal and spatial patterns of microbial diversity along a trophic gradient in the interconnected lakes of the Osterseen Lake District, Bavaria

PubMed Central

Zwirglmaier, Katrin; Keiz, Katharina; Engel, Marion; Geist, Juergen; Raeder, Uta

2015-01-01

The Osterseen Lake District in Bavaria consists of 19 small interconnected lakes that exhibit a pronounced trophic gradient from eutrophic to oligotrophic. It therefore presents a unique model system to address ecological questions regarding niche adaptation and Baas Becking's long standing hypothesis of “everything is everywhere, but the environment selects.” Here, we present the first assessment of the microbial diversity in these lakes. We sampled the lakes in August and December and used 454 pyrosequencing of 16S rRNA amplicons to analyze the microbial diversity. The diversity patterns between lakes and seasons were compared and the bacterial community composition was correlated with key chemical and physical parameters. Distinct patterns of bacterial diversity only emerged at the level of individual OTUs (operational taxonomic units), but not at the level of the major bacterial phyla. This emphasizes the high functional and physiological diversity among bacterial species within a phylum and calls for analysis of biodiversity at the level of OTUs in order to understand fine-scale biogeography. We were able to identify a number of cosmopolitan OTUs as well as specialist OTUs that were restricted to certain lakes or seasons, suggesting adaptation to specific ecological niches. PMID:26579082

Postglacial recolonization in a cold climate specialist in western Europe: patterns of genetic diversity in the adder (Vipera berus) support the central-marginal hypothesis.

PubMed

Ursenbacher, Sylvain; Guillon, Michaël; Cubizolle, Hervé; Dupoué, Andréaz; Blouin-Demers, Gabriel; Lourdais, Olivier

2015-07-01

Understanding the impact of postglacial recolonization on genetic diversity is essential in explaining current patterns of genetic variation. The central-marginal hypothesis (CMH) predicts a reduction in genetic diversity from the core of the distribution to peripheral populations, as well as reduced connectivity between peripheral populations. While the CMH has received considerable empirical support, its broad applicability is still debated and alternative hypotheses predict different spatial patterns of genetic diversity. Using microsatellite markers, we analysed the genetic diversity of the adder (Vipera berus) in western Europe to reconstruct postglacial recolonization. Approximate Bayesian Computation (ABC) analyses suggested a postglacial recolonization from two routes: a western route from the Atlantic Coast up to Belgium and a central route from the Massif Central to the Alps. This cold-adapted species likely used two isolated glacial refugia in southern France, in permafrost-free areas during the last glacial maximum. Adder populations further from putative glacial refugia had lower genetic diversity and reduced connectivity; therefore, our results support the predictions of the CMH. Our study also illustrates the utility of highly variable nuclear markers, such as microsatellites, and ABC to test competing recolonization hypotheses. © 2015 John Wiley & Sons Ltd.

Factors influencing spatial pattern in tropical forest clearance and stand age: Implications for carbon storage and species diversity.

Treesearch

E. H. Helmer; Thomas J. Brandeis; Ariel E. Lugo; Todd Kennaway

2008-01-01

Little is known about the tropical forests that undergo clearing as urban/built-up and other developed lands spread. This study uses remote sensing-based maps of Puerto Rico, multinomial logit models and forest inventory data to explain patterns of forest age and the age of forests cleared for land development and assess their implications for forest carbon storage and...

Factors affecting plant diversity during post-fire recovery and succession of mediterranean-climate shrublands in California, USA

USGS Publications Warehouse

Keeley, J.E.; Fotheringham, C.J.; Baer-Keeley, M.

2005-01-01

Plant community diversity, measured as species richness, is typically highest in the early post-fire years in California shrublands. However, this generalization is overly simplistic and the present study demonstrates that diversity is determined by a complex of temporal and spatial effects. Ninety sites distributed across southern California were studied for 5 years after a series of fires. Characteristics of the disturbance event, in this case fire severity, can alter post-fire diversity, both decreasing and increasing diversity, depending on life form. Spatial variability in resource availability is an important factor explaining patterns of diversity, and there is a complex interaction between landscape features and life form. Temporal variability in resource availability affects diversity, and the diversity peak in the immediate post-fire year (or two) appears to be driven by factors different from subsequent diversity peaks. Early post-fire diversity is influenced by life-history specialization, illustrated by species that spend the bulk of their life cycle as a dormant seed bank, which is then triggered to germinate by fire. Resource fluctuations, precipitation in particular, may be associated with subsequent post-fire diversity peaks. These later peaks in diversity comprise a flora that is compositionally different from the immediate post-fire flora, and their presence may be due to mass effects from population expansion of local populations in adjacent burned areas. ?? 2005 Blackwell Publishing Ltd.

Nearly a decade-long repeatable seasonal diversity patterns of bacterioplankton communities in the eutrophic Lake Donghu (Wuhan, China)

DOE Office of Scientific and Technical Information (OSTI.GOV)

Yan, Qingyun; Stegen, James C.; Yu, Yuhe

Uncovering which environmental factors have the greatest influence on community diversity patterns and how ecological processes govern community turnover are key questions related to understanding community assembly mechanisms. Although we have good understanding of plant and animal community assembly, the mechanisms regulating diversity patterns of aquatic bacterial communities in lake ecosystems remains poorly understood. Here we present nearly a decade-long time-series study of bacterioplankton communities from the eutrophic Lake Donghu (Wuhan, China) using 16S rRNA gene amplicon sequencing. We found strong repeatable seasonal patterns for the overall community, common (detected in more than 50% samples) and dominant bacterial taxa (relativemore » abundance > 1%). Moreover, community composition tracked the seasonal temperature gradient, indicating that temperature is an important environmental factor controlling observed diversity patterns. Total phosphorus also contributed significantly to the seasonal shifts in bacterioplankton composition. However, any spatial pattern across the main lake areas was overwhelmed by temporal variability in this eutrophic lake system. Phylogenetic analysis further indicated that 75%-82% of community turnover was governed by homogeneous selection, suggesting that the bacterioplankton communities are mainly controlled by niche-based processes. However, dominant niches available within seasons might be occupied by similar combinations of bacterial taxa with modest dispersal rates throughout this lake system. This study gives us important insights into community assembly and seasonal turnover of lake bacterioplankton, it may be also useful to predict temporal patterns of other planktonic communities.« less

Demographic stability and high historical connectivity explain the diversity of a savanna tree species in the Quaternary

PubMed Central

Telles, Mariana P. C.; Chaves, Lázaro J.; Lima-Ribeiro, Matheus S.; Collevatti, Rosane G.

2017-01-01

Abstract Background and Aims Cyclic glaciations were frequent throughout the Quaternary and this affected species distribution and population differentiation worldwide. The present study reconstructed the demographic history and dispersal routes of Eugenia dysenterica lineages and investigated the effects of Quaternary climate change on its spatial pattern of genetic diversity. Methods A total of 333 individuals were sampled from 23 populations and analysed by sequencing four regions of the chloroplast DNA and the internal transcribed spacer of the nuclear DNA. The analyses were performed using a multi-model inference approach based on ecological niche modelling and statistical phylogeography. Key Results Coalescent simulation showed that population stability through time is the most likely scenario. The palaeodistribution dynamics predicted by the ecological niche models revealed that the species was potentially distributed across a large area, extending over Central-Western Brazil through the last glaciation. The lineages of E. dysenterica dispersed from Central Brazil towards populations at the northern, western and south-eastern regions. A historical refugium through time may have favoured lineage dispersal and the maintenance of genetic diversity. Conclusions The results suggest that the central region of the Cerrado biome is probably the centre of distribution of E. dysenterica and that the spatial pattern of its genetic diversity may be the outcome of population stability throughout the Quaternary. The lower genetic diversity in populations in the south-eastern Cerrado biome is probably due to local climatic instability during the Quaternary. PMID:28115317

Contagious Deposition of Seeds in Spider Monkeys' Sleeping Trees Limits Effective Seed Dispersal in Fragmented Landscapes

PubMed Central

González-Zamora, Arturo; Arroyo-Rodríguez, Víctor; Escobar, Federico; Rös, Matthias; Oyama, Ken; Ibarra-Manríquez, Guillermo; Stoner, Kathryn E.; Chapman, Colin A.

2014-01-01

The repeated use of sleeping sites by frugivorous vertebrates promotes the deposition and aggregation of copious amounts of seeds in these sites. This spatially contagious pattern of seed deposition has key implications for seed dispersal, particularly because such patterns can persist through recruitment. Assessing the seed rain patterns in sleeping sites thus represents a fundamental step in understanding the spatial structure and regeneration of plant assemblages. We evaluated the seed rain produced by spider monkeys (Ateles geoffroyi) in latrines located beneath 60 sleeping trees in two continuous forest sites (CFS) and three forest fragments (FF) in the Lacandona rainforest, Mexico. We tested for differences among latrines, among sites, and between forest conditions in the abundance, diversity (α-, β- and, γ-components) and evenness of seed assemblages. We recorded 45,919 seeds ≥5 mm (in length) from 68 species. The abundance of seeds was 1.7 times higher in FF than in CFS, particularly because of the dominance of a few plant species. As a consequence, community evenness tended to be lower within FF. β-diversity of common and dominant species was two times greater among FF than between CFS. Although mean α-diversity per latrine did not differ among sites, the greater β-diversity among latrines in CFS increased γ-diversity in these sites, particularly when considering common and dominant species. Our results support the hypothesis that fruit scarcity in FF can ‘force’ spider monkeys to deplete the available fruit patches more intensively than in CFS. This feeding strategy can limit the effectiveness of spider monkeys as seed dispersers in FF, because (i) it can limit the number of seed dispersers visiting such fruit patches; (ii) it increases seed dispersal limitation; and (iii) it can contribute to the floristic homogenization (i.e., reduced β-diversity among latrines) in fragmented landscapes. PMID:24586705

Relevant genetic differentiation among Brazilian populations of Anastrepha fraterculus (Diptera, Tephritidae)

PubMed Central

Manni, Mosè; Lima, Kátia Manuela; Guglielmino, Carmela Rosalba; Lanzavecchia, Silvia Beatriz; Juri, Marianela; Vera, Teresa; Cladera, Jorge; Scolari, Francesca; Gomulski, Ludvik; Bonizzoni, Mariangela; Gasperi, Giuliano; Silva, Janisete Gomes; Malacrida, Anna Rodolfa

2015-01-01

Abstract We used a population genetic approach to detect the presence of genetic diversity among six populations of Anastrepha fraterculus across Brazil. To this aim, we used Simple Sequence Repeat (SSR) markers, which may capture the presence of differentiative processes across the genome in distinct populations. Spatial analyses of molecular variance were used to identify groups of populations that are both genetically and geographically homogeneous while also being maximally differentiated from each other. The spatial analysis of genetic diversity indicates that the levels of diversity among the six populations vary significantly on an eco-geographical basis. Particularly, altitude seems to represent a differentiating adaptation, as the main genetic differentiation is detected between the two populations present at higher altitudes and the other four populations at sea level. The data, together with the outcomes from different cluster analyses, identify a genetic diversity pattern that overlaps with the distribution of the known morphotypes in the Brazilian area. PMID:26798258

Inference of tumor evolution during chemotherapy by computational modeling and in situ analysis of genetic and phenotypic cellular diversity.

PubMed

Almendro, Vanessa; Cheng, Yu-Kang; Randles, Amanda; Itzkovitz, Shalev; Marusyk, Andriy; Ametller, Elisabet; Gonzalez-Farre, Xavier; Muñoz, Montse; Russnes, Hege G; Helland, Aslaug; Rye, Inga H; Borresen-Dale, Anne-Lise; Maruyama, Reo; van Oudenaarden, Alexander; Dowsett, Mitchell; Jones, Robin L; Reis-Filho, Jorge; Gascon, Pere; Gönen, Mithat; Michor, Franziska; Polyak, Kornelia

2014-02-13

Cancer therapy exerts a strong selection pressure that shapes tumor evolution, yet our knowledge of how tumors change during treatment is limited. Here, we report the analysis of cellular heterogeneity for genetic and phenotypic features and their spatial distribution in breast tumors pre- and post-neoadjuvant chemotherapy. We found that intratumor genetic diversity was tumor-subtype specific, and it did not change during treatment in tumors with partial or no response. However, lower pretreatment genetic diversity was significantly associated with pathologic complete response. In contrast, phenotypic diversity was different between pre- and posttreatment samples. We also observed significant changes in the spatial distribution of cells with distinct genetic and phenotypic features. We used these experimental data to develop a stochastic computational model to infer tumor growth patterns and evolutionary dynamics. Our results highlight the importance of integrated analysis of genotypes and phenotypes of single cells in intact tissues to predict tumor evolution. Copyright © 2014 The Authors. Published by Elsevier Inc. All rights reserved.

Inference of tumor evolution during chemotherapy by computational modeling and in situ analysis of cellular diversity for genetic and phenotypic features

PubMed Central

Almendro, Vanessa; Cheng, Yu-Kang; Randles, Amanda; Itzkovitz, Shalev; Marusyk, Andriy; Ametller, Elisabet; Gonzalez-Farre, Xavier; Muñoz, Montse; Russnes, Hege G.; Helland, Åslaug; Rye, Inga H.; Borresen-Dale, Anne-Lise; Maruyama, Reo; van Oudenaarden, Alexander; Dowsett, Mitchell; Jones, Robin L.; Reis-Filho, Jorge; Gascon, Pere; Gönen, Mithat; Michor, Franziska; Polyak, Kornelia

2014-01-01

SUMMARY Cancer therapy exerts a strong selection pressure that shapes tumor evolution, yet our knowledge of how tumors change during treatment is limited. Here we report the analysis of cellular heterogeneity for genetic and phenotypic features and their spatial distribution in breast tumors pre- and post-neoadjuvant chemotherapy. We found that intratumor genetic diversity was tumor subtype-specific and it did not change during treatment in tumors with partial or no response. However, lower pre-treatment genetic diversity was significantly associated with complete pathologic response. In contrast, phenotypic diversity was different between pre- and post-treatment samples. We also observed significant changes in the spatial distribution of cells with distinct genetic and phenotypic features. We used these experimental data to develop a stochastic computational model to infer tumor growth patterns and evolutionary dynamics. Our results highlight the importance of integrated analysis of genotypes and phenotypes of single cells in intact tissues to predict tumor evolution. PMID:24462293

Spatial and temporal patterns of neutral and adaptive genetic variation in the endangered African wild dog (Lycaon pictus).

PubMed

Marsden, Clare D; Woodroffe, Rosie; Mills, Michael G L; McNutt, J Weldon; Creel, Scott; Groom, Rosemary; Emmanuel, Masenga; Cleaveland, Sarah; Kat, Pieter; Rasmussen, Gregory S A; Ginsberg, Joshua; Lines, Robin; André, Jean-Marc; Begg, Colleen; Wayne, Robert K; Mable, Barbara K

2012-03-01

Deciphering patterns of genetic variation within a species is essential for understanding population structure, local adaptation and differences in diversity between populations. Whilst neutrally evolving genetic markers can be used to elucidate demographic processes and genetic structure, they are not subject to selection and therefore are not informative about patterns of adaptive variation. As such, assessments of pertinent adaptive loci, such as the immunity genes of the major histocompatibility complex (MHC), are increasingly being incorporated into genetic studies. In this study, we combined neutral (microsatellite, mtDNA) and adaptive (MHC class II DLA-DRB1 locus) markers to elucidate the factors influencing patterns of genetic variation in the African wild dog (Lycaon pictus); an endangered canid that has suffered extensive declines in distribution and abundance. Our genetic analyses found all extant wild dog populations to be relatively small (N(e)  < 30). Furthermore, through coalescent modelling, we detected a genetic signature of a recent and substantial demographic decline, which correlates with human expansion, but contrasts with findings in some other African mammals. We found strong structuring of wild dog populations, indicating the negative influence of extensive habitat fragmentation and loss of gene flow between habitat patches. Across populations, we found that the spatial and temporal structure of microsatellite diversity and MHC diversity were correlated and strongly influenced by demographic stability and population size, indicating the effects of genetic drift in these small populations. Despite this correlation, we detected signatures of selection at the MHC, implying that selection has not been completely overwhelmed by genetic drift. © 2012 Blackwell Publishing Ltd.

Spatial scaling of bacterial community diversity at shallow hydrothermal vents: a global comparison

NASA Astrophysics Data System (ADS)

Pop Ristova, P.; Hassenrueck, C.; Molari, M.; Fink, A.; Bühring, S. I.

2016-02-01

Marine shallow hydrothermal vents are extreme environments, often characterized by discharge of fluids with e.g. high temperatures, low pH, and laden with elements toxic to higher organisms. They occur at continental margins around the world's oceans, but represent fragmented, isolated habitats of locally small areal coverage. Microorganisms contribute the main biomass at shallow hydrothermal vent ecosystems and build the basis of the food chain by autotrophic fixation of carbon both via chemosynthesis and photosynthesis, occurring simultaneously. Despite their importance and unique capacity to adapt to these extreme environments, little is known about the spatial scales on which the alpha- and beta-diversity of microbial communities vary at shallow vents, and how the geochemical habitat heterogeneity influences shallow vent biodiversity. Here for the first time we investigated the spatial scaling of microbial biodiversity patterns and their interconnectivity at geochemically diverse shallow vents on a global scale. This study presents data on the comparison of bacterial community structures on large (> 1000 km) and small (0.1 - 100 m) spatial scales as derived from ARISA and Illumina sequencing. Despite the fragmented global distribution of shallow hydrothermal vents, similarity of vent bacterial communities decreased with geographic distance, confirming the ubiquity of distance-decay relationship. Moreover, at all investigated vents, pH was the main factor locally structuring these communities, while temperature influenced both the alpha- and beta-diversity.

Assessment of variations in taxonomic diversity, forest structure, and aboveground biomass using remote sensing along an altitudinal gradient in tropical montane forest of Costa Rica

NASA Astrophysics Data System (ADS)

Robinson, C. M.; Saatchi, S. S.; Clark, D.; Fricker, G. A.; Wolf, J.; Gillespie, T. W.; Rovzar, C. M.; Andelman, S.

2012-12-01

This research sought to understand how alpha and beta diversity of plants vary and relate to the three-dimensional vegetation structure and aboveground biomass along environmental gradients in the tropical montane forests of Braulio Carrillo National Park in Costa Rica. There is growing evidence that ecosystem structure plays an important role in defining patterns of species diversity and along with abiotic factors (climate and edaphic) control the phenotypic and functional variations across landscapes. It is well documented that strong subdivisions at local and regional scales are found mainly on geologic or climate gradients. These general determinants of biodiversity are best demonstrated in regions with natural gradients such as tropical montane forests. Altitudinal gradients provide a landscape scale changes through variations in topography, climate, and edaphic conditions on which we tested several theoretical and biological hypotheses regarding drivers of biodiversity. The study was performed by using forest inventory and botanical data from nine 1-ha plots ranging from 100 m to 2800 m above sea level and remote sensing data from airborne lidar and radar sensors to quantify variations in forest structure. In this study we report on the effectiveness of relating patterns of tree taxonomic alpha diversity to three-dimensional structure of a tropical montane forest using lidar and radar observations of forest structure and biomass. We assessed alpha and beta diversity at the species, genus, and family levels utilizing datasets provided by the Terrestrial Ecology Assessment and Monitoring (TEAM) Network. Through the comparison to active remote sensing imagery, our results show that there is a strong relationship between forest 3D-structure, and alpha and beta diversity controlled by variations in abiotic factors along the altitudinal gradient. Using spatial analysis with the aid of remote sensing data, we find distinct patterns along the environmental gradients defining species turnover and changes in functional diversity. The study will provide novel approaches to use detailed spatial information from remote sensing data to study relations between functional and taxonomic dimensions of diversity.

A rich diversity of opercle bone shape among teleost fishes

PubMed Central

Small, Clayton M.; Knope, Matthew L.

2017-01-01

The opercle is a prominent craniofacial bone supporting the gill cover in all bony fish and has been the subject of morphological, developmental, and genetic investigation. We surveyed the shapes of this bone among 110 families spanning the teleost tree and examined its pattern of occupancy in a principal component-based morphospace. Contrasting with expectations from the literature that suggest the local morphospace would be only sparsely occupied, we find primarily dense, broad filling of the morphological landscape, indicating rich diversity. Phylomorphospace plots suggest that dynamic evolution underlies the observed spatial patterning. Evolutionary transits through the morphospaces are sometimes long, and occur in a variety of directions. The trajectories seem to represent both evolutionary divergences and convergences, the latter supported by convevol analysis. We suggest that that this pattern of occupancy reflects the various adaptations of different groups of fishes, seemingly paralleling their diverse marine and freshwater ecologies and life histories. Opercle shape evolution within the acanthomorphs, spiny ray-finned fishes, appears to have been especially dynamic. PMID:29281662

The evolution of the competition-dispersal trade-off affects α- and β-diversity in a heterogeneous metacommunity.

PubMed

Laroche, Fabien; Jarne, Philippe; Perrot, Thomas; Massol, Francois

2016-04-27

Difference in dispersal ability is a key driver of species coexistence in metacommunities. However, the available frameworks for interpreting species diversity patterns in natura often overlook trade-offs and evolutionary constraints associated with dispersal. Here, we build a metacommunity model accounting for dispersal evolution and a competition-dispersal trade-off. Depending on the distribution of carrying capacities among communities, species dispersal values are distributed either around a single strategy (evolutionarily stable strategy, ESS), or around distinct strategies (evolutionary branching, EB). We show that limited dispersal generates spatial aggregation of dispersal traits in ESS and EB scenarios, and that the competition-dispersal trade-off strengthens the pattern in the EB scenario. Importantly, individuals in larger (respectively (resp.) smaller) communities tend to harbour lower (resp. higher) dispersal, especially under the EB scenario. We explore how dispersal evolution affects species diversity patterns by comparing those from our model to the predictions of a neutral metacommunity model. The most marked difference is detected under EB, with distinctive values of both α- and β-diversity (e.g. the dissimilarity in species composition between small and large communities was significantly larger than neutral predictions). We conclude that, from an empirical perspective, jointly assessing community carrying capacity with species dispersal strategies should improve our understanding of diversity patterns in metacommunities. © 2016 The Author(s).

Quantitative characterization of the regressive ecological succession by fractal analysis of plant spatial patterns

USGS Publications Warehouse

Alados, C.L.; Pueyo, Y.; Giner, M.L.; Navarro, T.; Escos, J.; Barroso, F.; Cabezudo, B.; Emlen, J.M.

2003-01-01

We studied the effect of grazing on the degree of regression of successional vegetation dynamic in a semi-arid Mediterranean matorral. We quantified the spatial distribution patterns of the vegetation by fractal analyses, using the fractal information dimension and spatial autocorrelation measured by detrended fluctuation analyses (DFA). It is the first time that fractal analysis of plant spatial patterns has been used to characterize the regressive ecological succession. Plant spatial patterns were compared over a long-term grazing gradient (low, medium and heavy grazing pressure) and on ungrazed sites for two different plant communities: A middle dense matorral of Chamaerops and Periploca at Sabinar-Romeral and a middle dense matorral of Chamaerops, Rhamnus and Ulex at Requena-Montano. The two communities differed also in the microclimatic characteristics (sea oriented at the Sabinar-Romeral site and inland oriented at the Requena-Montano site). The information fractal dimension increased as we moved from a middle dense matorral to discontinuous and scattered matorral and, finally to the late regressive succession, at Stipa steppe stage. At this stage a drastic change in the fractal dimension revealed a change in the vegetation structure, accurately indicating end successional vegetation stages. Long-term correlation analysis (DFA) revealed that an increase in grazing pressure leads to unpredictability (randomness) in species distributions, a reduction in diversity, and an increase in cover of the regressive successional species, e.g. Stipa tenacissima L. These comparisons provide a quantitative characterization of the successional dynamic of plant spatial patterns in response to grazing perturbation gradient. ?? 2002 Elsevier Science B.V. All rights reserved.

Patterns of orchid bee species diversity and turnover among forested plateaus of central Amazonia

PubMed Central

Machado, Carolina de Barros; Galetti, Pedro Manoel; Oliveira, Marcio; Dirzo, Rodolfo; Fernandes, Geraldo Wilson

2017-01-01

The knowledge of spatial pattern and geographic beta-diversity is of great importance for biodiversity conservation and interpreting ecological information. Tropical forests, especially the Amazon Rainforest, are well known for their high species richness and low similarity in species composition between sites, both at local and regional scales. We aimed to determine the effect and relative importance of area, isolation and climate on species richness and turnover in orchid bee assemblages among plateaus in central Brazilian Amazonia. Variance partitioning techniques were applied to assess the relative effects of spatial and environmental variables on bee species richness, phylogeny and composition. We hypothesized that greater abundance and richness of orchid bees would be found on larger plateaus, with a set of core species occurring on all of them. We also hypothesized that smaller plateaus would possess lower phylogenetic diversity. We found 55 bee species distributed along the nine sampling sites (plateaus) with 17 of them being singletons. There was a significant decrease in species richness with decreasing size of plateaus, and a significant decrease in the similarity in species composition with greater distance and climatic variation among sampling sites. Phylogenetic diversity varied among the sampling sites but was directly related to species richness. Although not significantly related to plateau area, smaller or larger PDFaith were observed in the smallest and the largest plateaus, respectively. PMID:28410432

Spatial and temporal patterns of macrozoobenthic community inhabiting sediments under tropical fish farming

NASA Astrophysics Data System (ADS)

Aufa, Abdullah; Hadi, Mochamad; Purnomo Putro, Sapto

2018-05-01

Macrozoobenthic animals is one of biota that may be used to assess the impact of the activities. They inhabit sediment of water ecosystem and may respond vary at different spatiotemporal scales. The purpose of this study is to study spatial and temporal patterns of macrozoobenthic community under fish farming activities at coastal area of Tembelas Island, Kepulauan Riau Province, Indonesia. The macrozoobenthic assemblages were assessedat three sampling locations, i.e. policulture [IMTA], monoculture and reference sites. Each sampling location consisted of three stations with three replicates for each station. The data obtained were analyzed using PRIMER software V.6.1.5. to compare number of taxa (S), Shanon- Wiener diversity index (H’), and Pielou’s evenness index (e) and K-dominance cumulative curves between sites and times. The results showed that diversity index at fish farming locations (IMTA and monoculture) exhibited lower than those at reference site, between 1.58 – 2.19 and between 1.99-2.84, respectively. However, diversity at all locations were considered moderate diverse ecosystem. Meanwhile, Pielou’s evenness indexbetween locations and sampling time showed no majordifference, ranging between 0.96-0.98. Based on K-dominance curves, P3T2 station curve was positioned on the top among other curves, implying certain taxa has dominated the assemblages, i.e. Nassarius sp. (Gastropod).

Patterns of orchid bee species diversity and turnover among forested plateaus of central Amazonia.

PubMed

Antonini, Yasmine; Machado, Carolina de Barros; Galetti, Pedro Manoel; Oliveira, Marcio; Dirzo, Rodolfo; Fernandes, Geraldo Wilson

2017-01-01

The knowledge of spatial pattern and geographic beta-diversity is of great importance for biodiversity conservation and interpreting ecological information. Tropical forests, especially the Amazon Rainforest, are well known for their high species richness and low similarity in species composition between sites, both at local and regional scales. We aimed to determine the effect and relative importance of area, isolation and climate on species richness and turnover in orchid bee assemblages among plateaus in central Brazilian Amazonia. Variance partitioning techniques were applied to assess the relative effects of spatial and environmental variables on bee species richness, phylogeny and composition. We hypothesized that greater abundance and richness of orchid bees would be found on larger plateaus, with a set of core species occurring on all of them. We also hypothesized that smaller plateaus would possess lower phylogenetic diversity. We found 55 bee species distributed along the nine sampling sites (plateaus) with 17 of them being singletons. There was a significant decrease in species richness with decreasing size of plateaus, and a significant decrease in the similarity in species composition with greater distance and climatic variation among sampling sites. Phylogenetic diversity varied among the sampling sites but was directly related to species richness. Although not significantly related to plateau area, smaller or larger PDFaith were observed in the smallest and the largest plateaus, respectively.

Visualizing Zonation Patterns

ERIC Educational Resources Information Center

Baumgartner, Erin; Zabin, Chela J.

2006-01-01

The study of "zonation", the distribution of plants and animals into distinct spatial areas, is a great way to introduce students to basic ecological concepts. Students can conduct methodical, quantifying surveys of zones in areas as diverse as mudflats, beaches, forests, wetlands, and fields. Students collect data from these areas with field…

The Nonrandom Distribution of Interior Landforms for 100-km Diameter Craters on Mercury Suggests Regional Variations in Near-Surface Mechanical Properties

NASA Astrophysics Data System (ADS)

Herrick, R. R.

2018-05-01

There is great diversity of appearance in the interiors of 100-km diameter craters. The spatial distribution of interior landforms is clustered and nonrandom, but does not clearly correlate with Mercury's surface geology patterns.

Melanopsin-expressing retinal ganglion-cell photoreceptors: cellular diversity and role in pattern vision

PubMed Central

Ecker, Jennifer L.; Dumitrescu, Olivia N.; Wong, Kwoon Y.; Alam, Nazia M.; Chen, Shih-Kuo; LeGates, Tara; Renna, Jordan M.; Prusky, Glen T.; Berson, David M.; Hattar, Samer

2010-01-01

Using the photopigment melanopsin, intrinsically photosensitive retinal ganglion cells (ipRGCs) respond directly to light to drive circadian clock resetting and pupillary constriction. We now report that ipRGCs are more abundant and diverse than previously appreciated, project more widely within the brain, and can support spatial visual perception. A Cre-based melanopsin reporter mouse line revealed at least five subtypes of ipRGCs with distinct morphological and physiological characteristics. Collectively, these cells project beyond the known brain targets of ipRGCs to heavily innervate the superior colliculus and dorsal lateral geniculate nucleus, retinotopically-organized nuclei mediating object localization and discrimination. Mice lacking classical rod-cone photoreception, and thus entirely dependent on melanopsin for light detection, were able to discriminate grating stimuli from equiluminant gray, and had measurable visual acuity. Thus, non-classical retinal photoreception occurs within diverse cell types, and influences circuits and functions encompassing luminance as well as spatial information. PMID:20624591

[Dynamics of ecological landscape pattern and its affecting factors in desert-oasis in Fukang, Xinjiang].

PubMed

Liu, Xinchun; Zhang, Yuandong; Ren, Guangyao; Pan, Xiaoling; He, Qing

2004-07-01

The spatial pattern of ecological landscape during land utilization in Fukang is heavily influenced by natural difference and the scale of water and land resource development. Analyses on the spatial pattern based on different zones and indexes showed that from 1987 to 1998, the change of the spatial pattern of ecological landscape during land utilization in Fukang was mainly the increase of plantation area in pluvial fan and the decrease in alluvial plain. The case was on the contrary about badlands. The acreage of woodland decreased in lower mountains, uplands and alluvial plain, but no variety in alluvial plain. The acreage of grassland increased in lower mountains and uplands, while decreased in other fields. The acreage of town increased in each sample field, while that of water area remained uncharged. The landscape diversity and evenness was descending, the dominance was ascending in lower mountains and in pluvial fan, while it was reverse in alluvial plain. Accessorial fragmentation showed the increasing influence of human beings. The change of the spatial pattern of ecological landscape in Fukang focused on the acreage alteration of plantation and badlands in pluvial fan and alluvial plain. The key factor was the dynamic variation of water-salt in water and soil resource utilization. Terrain and land utilization were the key factors affecting water table, and the continuous changes of the water table worked on the spatial distribution of soil water-salt.

Multiscale patterns and drivers of arbuscular mycorrhizal fungal communities in the roots and root-associated soil of a wild perennial herb.

PubMed

Rasmussen, Pil U; Hugerth, Luisa W; Blanchet, F Guillaume; Andersson, Anders F; Lindahl, Björn D; Tack, Ayco J M

2018-03-24

Arbuscular mycorrhizal (AM) fungi form diverse communities and are known to influence above-ground community dynamics and biodiversity. However, the multiscale patterns and drivers of AM fungal composition and diversity are still poorly understood. We sequenced DNA markers from roots and root-associated soil from Plantago lanceolata plants collected across multiple spatial scales to allow comparison of AM fungal communities among neighbouring plants, plant subpopulations, nearby plant populations, and regions. We also measured soil nutrients, temperature, humidity, and community composition of neighbouring plants and nonAM root-associated fungi. AM fungal communities were already highly dissimilar among neighbouring plants (c. 30 cm apart), albeit with a high variation in the degree of similarity at this small spatial scale. AM fungal communities were increasingly, and more consistently, dissimilar at larger spatial scales. Spatial structure and environmental drivers explained a similar percentage of the variation, from 7% to 25%. A large fraction of the variation remained unexplained, which may be a result of unmeasured environmental variables, species interactions and stochastic processes. We conclude that AM fungal communities are highly variable among nearby plants. AM fungi may therefore play a major role in maintaining small-scale variation in community dynamics and biodiversity. © 2018 The Authors New Phytologist © 2018 New Phytologist Trust.

Universal scaling of the distribution of land in urban areas

NASA Astrophysics Data System (ADS)

Riascos, A. P.

2017-09-01

In this work, we explore the spatial structure of built zones and green areas in diverse western cities by analyzing the probability distribution of areas and a coefficient that characterize their respective shapes. From the analysis of diverse datasets describing land lots in urban areas, we found that the distribution of built-up areas and natural zones in cities obey inverse power laws with a similar scaling for the cities explored. On the other hand, by studying the distribution of shapes of lots in urban regions, we are able to detect global differences in the spatial structure of the distribution of land. Our findings introduce information about spatial patterns that emerge in the structure of urban settlements; this knowledge is useful for the understanding of urban growth, to improve existing models of cities, in the context of sustainability, in studies about human mobility in urban areas, among other applications.

Spatial patterns of phylogenetic diversity.

PubMed

Morlon, Hélène; Schwilk, Dylan W; Bryant, Jessica A; Marquet, Pablo A; Rebelo, Anthony G; Tauss, Catherine; Bohannan, Brendan J M; Green, Jessica L

2011-02-01

Ecologists and conservation biologists have historically used species-area and distance-decay relationships as tools to predict the spatial distribution of biodiversity and the impact of habitat loss on biodiversity. These tools treat each species as evolutionarily equivalent, yet the importance of species' evolutionary history in their ecology and conservation is becoming increasingly evident. Here, we provide theoretical predictions for phylogenetic analogues of the species-area and distance-decay relationships. We use a random model of community assembly and a spatially explicit flora dataset collected in four Mediterranean-type regions to provide theoretical predictions for the increase in phylogenetic diversity - the total phylogenetic branch-length separating a set of species - with increasing area and the decay in phylogenetic similarity with geographic separation. These developments may ultimately provide insights into the evolution and assembly of biological communities, and guide the selection of protected areas. © 2010 Blackwell Publishing Ltd/CNRS.

Bathymetric patterns in standing stock and diversity of deep-sea nematodes at the long-term ecological research observatory HAUSGARTEN (Fram Strait)

NASA Astrophysics Data System (ADS)

Grzelak, Katarzyna; Kotwicki, Lech; Hasemann, Christiane; Soltwedel, Thomas

2017-08-01

Bathymetric patterns in standing stocks and diversity are a major topic of investigation in deep-sea biology. From the literature, responses of metazoan meiofauna and nematodes to bathymetric gradients are well studied, with a general decrease in biomass and abundance with increasing water depth, while bathymetric diversity gradients often, although it is not a rule, show a unimodal pattern. Spatial distribution patterns of nematode communities along bathymetric gradients are coupled with surface-water processes and interacting physical and biological factors within the benthic system. We studied the nematode communities at the Long-Term Ecological Research (LTER) observatory HAUSGARTEN, located in the Fram Strait at the Marginal Ice Zone, with respect to their standing stocks as well as structural and functional diversity. We evaluated whether nematode density, biomass and diversity indices, such as H0, Hinf, EG(50), Θ- 1, are linked with environmental conditions along a bathymetric transect spanning from 1200 m to 5500 m water depth. Nematode abundance, biomass and diversity, as well as food availability from phytodetritus sedimentation (indicated by chloroplastic pigments in the sediments), were higher at the stations located at upper bathyal depths (1200-2000 m) and tended to decrease with increasing water depth. A faunal shift was found below 3500 m water depth, where genus composition and trophic structure changed significantly and structural diversity indices markedly decreased. A strong dominance of very few genera and its high turnover particularly at the abyssal stations (4000-5500 m) suggests that environmental conditions were rather unfavorable for most genera. Despite the high concentrations of sediment-bound chloroplastic pigments and elevated standing stocks found at the deepest station (5500 m), nematode genus diversity remained the lowest compared to all other stations. This study provides a further insight into the knowledge of deep-sea nematodes, their diversity patterns and a deeper understanding of the environmental factors shaping nematodes communities at bathyal and abyssal depths.

Speciation gradients and the distribution of biodiversity.

PubMed

Schluter, Dolph; Pennell, Matthew W

2017-05-31

Global patterns of biodiversity are influenced by spatial and environmental variations in the rate at which new species form. We relate variations in speciation rates to six key patterns of biodiversity worldwide, including the species-area relationship, latitudinal gradients in species and genetic diversity, and between-habitat differences in species richness. Although they sometimes mirror biodiversity patterns, recent rates of speciation, at the tip of the tree of life, are often highest where species richness is low. Speciation gradients therefore shape, but are also shaped by, biodiversity gradients and are often more useful for predicting future patterns of biodiversity than for interpreting the past.

Temporal species richness-biomass relationships along successional gradients

USGS Publications Warehouse

Guo, Q.

2003-01-01

Diversity-biomass relationships are frequently reported to be hump-shaped over space at a given time. However, it is not yet clear how diversity and biomass change simultaneously and how they are related to each other over time (e.g. in succession) at one locality. This study develops a temporal model based on the projected changes of various community variables in a generalized terrestrial environment after fire and uses post-fire succession data on Santa Monica Mountains of southern California and other published succession data to examine the temporal diversity-biomass relationships. The results indicate that in the early stages of succession, both diversity and biomass increase and a positive relationship appears, while in the late stages of succession, biomass continued to increase but diversity usually declines; thus a negative relationship may be observed. When the scales of measurement become sufficiently large so that the measured diversity and biomass cross various stages of succession, a 'hump-shaped' relationship can emerge. The diversity-biomass relationship appears to be concordant in space and time when appropriate scales are used. Formerly proposed explanations for spatial patterns may well apply to the temporal patterns (particularly colonization, facilitation and competitive exclusion).

Temporal species richness-biomass relationships along successional gradients

USGS Publications Warehouse

Guo, Q.

2003-01-01

Diversity-biomass relationships are frequently reported to be hump-shaped over space at a given time. However, it is not yet clear how diversity and biomass change simultaneously and how they are related to each other overtime (e.g. in succession) at one locality. This study develops a temporal model based on the projected changes of various community variables in a generalized terrestrial environment after fire and uses post-fire succession data on Santa Monica Mountains of southern California and other published succession data to examine the temporal diversity-biomass relationships. The results indicate that in the early stages of succession, both diversity and biomass increase and a positive relationship appears, while in the late stages of succession, biomass continued to increase but diversity usually declines; thus a negative relationship may be observed. When the scales of measurement become sufficiently large so that the measured diversity and biomass cross various stages of succession, a 'hump-shaped' relationship can emerge. The diversity-biomass relationship appears to be concordant in space and time when appropriate scales are used. Formerly proposed explanations for spatial patterns may well apply to the temporal patterns (particularly colonization, facilitation and competitive exclusion).

Spatial organization of hominin activities at Gesher Benot Ya'aqov, Israel.

PubMed

Alperson-Afil, Nira; Sharon, Gonen; Kislev, Mordechai; Melamed, Yoel; Zohar, Irit; Ashkenazi, Shosh; Rabinovich, Rivka; Biton, Rebecca; Werker, Ella; Hartman, Gideon; Feibel, Craig; Goren-Inbar, Naama

2009-12-18

The spatial designation of discrete areas for different activities reflects formalized conceptualization of a living space. The results of spatial analyses of a Middle Pleistocene Acheulian archaeological horizon (about 750,000 years ago) at Gesher Benot Ya'aqov, Israel, indicate that hominins differentiated their activities (stone knapping, tool use, floral and faunal processing and consumption) across space. These were organized in two main areas, including multiple activities around a hearth. The diversity of human activities and the distinctive patterning with which they are organized implies advanced organizational skills of the Gesher Benot Ya'aqov hominins.

Spatio-temporal distribution of stored-product inects around food processing and storage facilities

USDA-ARS?s Scientific Manuscript database

Grain storage and processing facilities consist of a landscape of indoor and outdoor habitats that can potentially support stored-product insect pests, and understanding patterns of species diversity and spatial distribution in the landscape surrounding structures can provide insight into how the ou...

Tidal wetland plant and algal assemblages in Oregon: spatial patterns of composition and vulnerability to climate change

EPA Science Inventory

Tidal wetlands support important ecosystem functions along the coast of the Pacific Northwest such as primary production and nutrient transformation. Sea-level rise (SLR) and elevated salinity due to climate change may affect the abundance, distribution, and diversity of plants a...

Adapting populations in space: clonal interference and genetic diversity

NASA Astrophysics Data System (ADS)

Weissman, Daniel; Barton, Nick

Most species inhabit ranges much larger than the scales over which individuals interact. How does this spatial structure interact with adaptive evolution? We consider a simple model of a spatially-extended, adapting population and show that, while clonal interference severely limits the adaptation of purely asexual populations, even rare recombination is enough to allow adaptation at rates approaching those of well-mixed populations. We also find that the genetic hitchhiking produced by the adaptive alleles sweeping through the population has strange effects on the patterns of genetic diversity. In large spatial ranges, even low rates of adaptation cause all individuals in the population to rapidly trace their ancestry back to individuals living in a small region in the center of the range. The probability of fixation of an allele is thus strongly dependent on the allele's spatial location, with alleles from the center favored. Surprisingly, these effects are seen genome-wide (instead of being localized to the regions of the genome undergoing the sweeps). The spatial concentration of ancestry produces a power-law dependence of relatedness on distance, so that even individuals sampled far apart are likely to be fairly closely related, masking the underlying spatial structure.

Universal predictability of mobility patterns in cities

PubMed Central

Yan, Xiao-Yong; Zhao, Chen; Fan, Ying; Di, Zengru; Wang, Wen-Xu

2014-01-01

Despite the long history of modelling human mobility, we continue to lack a highly accurate approach with low data requirements for predicting mobility patterns in cities. Here, we present a population-weighted opportunities model without any adjustable parameters to capture the underlying driving force accounting for human mobility patterns at the city scale. We use various mobility data collected from a number of cities with different characteristics to demonstrate the predictive power of our model. We find that insofar as the spatial distribution of population is available, our model offers universal prediction of mobility patterns in good agreement with real observations, including distance distribution, destination travel constraints and flux. By contrast, the models that succeed in modelling mobility patterns in countries are not applicable in cities, which suggests that there is a diversity of human mobility at different spatial scales. Our model has potential applications in many fields relevant to mobility behaviour in cities, without relying on previous mobility measurements. PMID:25232053

Spatial patterns of fasting and fed antropyloric pressure waves in humans.

PubMed Central

Sun, W M; Hebbard, G S; Malbert, C H; Jones, K L; Doran, S; Horowitz, M; Dent, J

1997-01-01

1. Gastric mechanics were investigated by categorizing the temporal and spatial patterning of pressure waves associated with individual gastric contractions. 2. In twelve healthy volunteers, intraluminal pressures were monitored from nine side hole recording points spaced at 1.5 cm intervals along the antrum, pylorus and duodenum. 3. Pressure wave sequences that occurred during phase II fasting contractions (n = 221) and after food (n = 778) were evaluated. 4. The most common pattern of pressure wave onset along the antrum was a variable combination of antegrade, synchronous and retrograde propagation between side hole pairs. This variable pattern accounted for 42% of sequences after food, and 34% during fasting (P < 0.05). Other common pressure wave sequence patterns were: purely antegrade-29% after food and 42% during fasting (P < 0.05); purely synchronous-23% fed and 17% fasting; and purely retrograde-6% fed and 8% fasting. The length of sequences was shorter after food (P < 0.05). Some sequences 'skipped' individual recording points. 5. The spatial patterning of gastric pressure wave sequences is diverse, and may explain the differing mechanical outcomes among individual gastric contractions. 6. Better understanding of gastric mechanics may be gained from temporally precise correlations of luminal flows and pressures and gastric wall motion during individual gastric contraction sequences. PMID:9306286

Heterogeneity of clonal patterns among patches of kudzu, Pueraria montana var. lobata, an invasive plant

PubMed Central

Kartzinel, Tyler R.; Hamrick, J. L.; Wang, Chongyun; Bowsher, Alan W.; Quigley, Bryan G. P.

2015-01-01

Background and Aims Viny species are among the most serious invasive plants, and better knowledge of how vines grow to dominate landscapes is needed. Patches may contain a single genotype (i.e. genet), a competitively dominant genet or many independent but interacting genets, yet the clonal structure of vining species is often not apparent. Molecular markers can discriminate among the genetic identities of entwined vines to reveal the number and spatial distribution of genets. This study investigated how genets are spatially distributed within and among discrete patches of the invasive vine kudzu, Pueraria montana var. lobata, in the United States. It was expected that ramets of genets would be spatially clustered within patches, and that an increase in the number of genets within a patch would be associated with a decrease in the average size of each genet. Methods Six discrete kudzu patches were sampled across 2 years, and 1257 samples were genotyped at 21 polymorphic allozyme loci. Variation in genotypic and genetic diversity among patches was quantified and patterns of genet interdigitation were analysed. Key Results Substantial genotypic and genetic variation occurred within and among patches. As few as ten overlapping genets spanned up to 68 m2 in one patch, while >90 % of samples were genetically unique in another patch. Genotypic diversity within patches increased as mean clone size decreased, although spatially widespread genets did not preclude interdigitation. Eight genets were shared across ≥2 patches, suggesting that vegetative dispersal can occur among patches. Conclusions Genetically unique kudzu vines are highly interdigitated. Multiple vegetative propagules have become established in spatially discrete patches, probably through the movement of highway construction or maintenance machinery. The results suggest that common methods for controlling invasive vines (e.g. mowing) may inadvertently increase genotypic diversity. Thus, understanding vine architecture and growth has practical implications. PMID:26229064

Synergy of VSWIR and LiDAR for Ecosystem Structure, Biomass, and Canopy Diversity

NASA Technical Reports Server (NTRS)

Cook, Bruce D.; Asner, Gregory P.

2010-01-01

This slide presentation reviews the use of Visible ShortWave InfraRed (VSWIR) Imaging Spectrometer and LiDAR to study ecosystem structure, biomass and canopy diversity. It is shown that the biophysical data from LiDAR and biochemical information from hyperspectral remote sensing provides complementary data for: (1) describing spatial patterns of vegetation and biodiversity, (2) characterizing relationships between ecosystem form and function, and (3) detecting natural and human induced change that affects the biogeochemical cycles.

Targeting climate diversity in conservation planning to build resilience to climate change

USGS Publications Warehouse

Heller, Nicole E.; Kreitler, Jason R.; Ackerly, David; Weiss, Stuart; Recinos, Amanda; Branciforte, Ryan; Flint, Lorraine E.; Flint, Alan L.; Micheli, Elisabeth

2015-01-01

Climate change is raising challenging concerns for systematic conservation planning. Are methods based on the current spatial patterns of biodiversity effective given long-term climate change? Some conservation scientists argue that planning should focus on protecting the abiotic diversity in the landscape, which drives patterns of biological diversity, rather than focusing on the distribution of focal species, which shift in response to climate change. Climate is one important abiotic driver of biodiversity patterns, as different climates host different biological communities and genetic pools. We propose conservation networks that capture the full range of climatic diversity in a region will improve the resilience of biotic communities to climate change compared to networks that do not. In this study we used historical and future hydro-climate projections from the high resolution Basin Characterization Model to explore the utility of directly targeting climatic diversity in planning. Using the spatial planning tool, Marxan, we designed conservation networks to capture the diversity of climate types, at the regional and sub-regional scale, and compared them to networks we designed to capture the diversity of vegetation types. By focusing on the Conservation Lands Network (CLN) of the San Francisco Bay Area as a real-world case study, we compared the potential resilience of networks by examining two factors: the range of climate space captured, and climatic stability to 18 future climates, reflecting different emission scenarios and global climate models. We found that the climate-based network planned at the sub-regional scale captured a greater range of climate space and showed higher climatic stability than the vegetation and regional based-networks. At the same time, differences among network scenarios are small relative to the variance in climate stability across global climate models. Across different projected futures, topographically heterogeneous areas consistently show greater climate stability than homogenous areas. The analysis suggests that utilizing high-resolution climate and hydrological data in conservation planning improves the likely resilience of biodiversity to climate change. We used these analyses to suggest new conservation priorities for the San Francisco Bay Area.

Waiting in the wings: what can we learn about gene co-option from the diversification of butterfly wing patterns?

PubMed Central

Wallbank, Richard W. R.; Hanly, Joseph J.

2017-01-01

A major challenge is to understand how conserved gene regulatory networks control the wonderful diversity of form that we see among animals and plants. Butterfly wing patterns are an excellent example of this diversity. Butterfly wings form as imaginal discs in the caterpillar and are constructed by a gene regulatory network, much of which is conserved across the holometabolous insects. Recent work in Heliconius butterflies takes advantage of genomic approaches and offers insights into how the diversification of wing patterns is overlaid onto this conserved network. WntA is a patterning morphogen that alters spatial information in the wing. Optix is a transcription factor that acts later in development to paint specific wing regions red. Both of these loci fit the paradigm of conserved protein-coding loci with diverse regulatory elements and developmental roles that have taken on novel derived functions in patterning wings. These discoveries offer insights into the ‘Nymphalid Ground Plan’, which offers a unifying hypothesis for pattern formation across nymphalid butterflies. These loci also represent ‘hotspots’ for morphological change that have been targeted repeatedly during evolution. Both convergent and divergent evolution of a great diversity of patterns is controlled by complex alleles at just a few genes. We suggest that evolutionary change has become focused on one or a few genetic loci for two reasons. First, pre-existing complex cis-regulatory loci that already interact with potentially relevant transcription factors are more likely to acquire novel functions in wing patterning. Second, the shape of wing regulatory networks may constrain evolutionary change to one or a few loci. Overall, genomic approaches that have identified wing patterning loci in these butterflies offer broad insight into how gene regulatory networks evolve to produce diversity. This article is part of the themed issue ‘Evo-devo in the genomics era, and the origins of morphological diversity’. PMID:27994126

Glyph guessing for ‘oo’ and ‘ee’: spatial frequency information in sound symbolic matching for ancient and unfamiliar scripts

PubMed Central

2017-01-01

In three experiments, we asked whether diverse scripts contain interpretable information about the speech sounds they represent. When presented with a pair of unfamiliar letters, adult readers correctly guess which is /i/ (the ‘ee’ sound in ‘feet’), and which is /u/ (the ‘oo’ sound in ‘shoe’) at rates higher than expected by chance, as shown in a large sample of Singaporean university students (Experiment 1) and replicated in a larger sample of international Internet users (Experiment 2). To uncover what properties of the letters contribute to different scripts' ‘guessability,’ we analysed the visual spatial frequencies in each letter (Experiment 3). We predicted that the lower spectral frequencies in the formants of the vowel /u/ would pattern with lower spatial frequencies in the corresponding letters. Instead, we found that across all spatial frequencies, the letter with more black/white cycles (i.e. more ink) was more likely to be guessed as /u/, and the larger the difference between the glyphs in a pair, the higher the script's guessability. We propose that diverse groups of humans across historical time and geographical space tend to employ similar iconic strategies for representing speech in visual form, and provide norms for letter pairs from 56 diverse scripts. PMID:28989784

Spatial genetic structuring of baobab (Adansonia digitata, Malvaceae) in the traditional agroforestry systems of West Africa.

PubMed

Kyndt, Tina; Assogbadjo, Achille E; Hardy, Olivier J; Glele Kakaï, Romain; Sinsin, Brice; Van Damme, Patrick; Gheysen, Godelieve

2009-05-01

This study evaluates the spatial genetic structure of baobab (Adansonia digitata) populations from West African agroforestry systems at different geographical scales using AFLP fingerprints. Eleven populations from four countries (Benin, Ghana, Burkina Faso, and Senegal) had comparable levels of genetic diversity, although the two populations in the extreme west (Senegal) had less diversity. Pairwise F(ST) ranged from 0.02 to 0.28 and increased with geographic distance, even at a regional scale. Gene pools detected by Bayesian clustering seem to be a byproduct of the isolation-by-distance pattern rather than representing actual discrete entities. The organization of genetic diversity appears to result essentially from spatially restricted gene flow, with some influences of human seed exchange. Despite the potential for relatively long-distance pollen and seed dispersal by bats within populations, statistically significant spatial genetic structuring within populations (SGS) was detected and gave a mean indirect estimate of neighborhood size of ca. 45. This study demonstrated that relatively high levels of genetic structuring are present in baobab at both large and within-population level, which was unexpected in regard to its dispersal by bats and the influence of human exchange of seeds. Implications of these results for the conservation of baobab populations are discussed.

Geomorphic controls of soil spatial complexity in a primeval mountain forest in the Czech Republic

NASA Astrophysics Data System (ADS)

Daněk, Pavel; Šamonil, Pavel; Phillips, Jonathan D.

2016-11-01

Soil diversity and complexity is influenced by a variety of factors, and much recent research has been focused on interpreting or modeling complexity based on soil-topography relationships, and effects of biogeomorphic processes. We aimed to (i) describe local soil diversity in one of the oldest forest reserves in Europe, (ii) employ existing graph theory concepts in pedocomplexity calculation and extend them by a novel approach based on hypothesis testing and an index measuring graph sequentiality (the extent to which soils have gradual vs. abrupt variations in underlying soil factors), and (iii) reveal the main sources of pedocomplexity, with a particular focus on geomorphic controls. A total of 954 soil profiles were described and classified to soil taxonomic units (STU) within a 46 ha area. We analyzed soil diversity using the Shannon index, and soil complexity using a novel graph theory approach. Pairwise tests of observed adjacencies, spectral radius and a newly proposed sequentiality index were used to describe and quantify the complexity of the spatial pattern of STUs. This was then decomposed into the contributions of three soil factor sequences (SFS), (i) degree of weathering and leaching processes, (ii) hydromorphology, and (iii) proportion of rock fragments. Six Reference Soil Groups and 37 second-level soil units were found. A significant portion of pedocomplexity occurred at distances shorter than the 22 m spacing of neighbouring soil profiles. The spectral radius (an index of complexity) of the pattern of soil spatial adjacency was 14.73, to which the individual SFS accounted for values of 2.0, 8.0 and 3.5, respectively. Significant sequentiality was found for degree of weathering and hydromorphology. Exceptional overall pedocomplexity was particularly caused by enormous spatial variability of soil wetness, representing a crucial soil factor sequence in the primeval forest. Moreover, the soil wetness gradient was partly spatially correlated with the gradient of soil weathering and leaching, suggesting synergistic influences of topography, climate, (hydro)geology and biomechanical and biochemical effects of individual trees. The pattern of stony soils, random in most respects, resulted probably from local geology and quaternary biogeomorphological processes. Thus, while geomorphology is the primary control over a very locally complex soil pattern, microtopography and local disturbances, mostly related to the effects of individual trees, are also critical. Considerable local pedodiversity seems to be an important component of the dynamics of old-growth mixed temperate mountain forests, with implications for decreasing pedodiversity in managed forests and deforested areas.

Measuring forest landscape patterns in the Cascade Range of Oregon, USA

NASA Technical Reports Server (NTRS)

Ripple, William J.; Bradshaw, G. A.; Spies, Thomas A.

1995-01-01

This paper describes the use of a set of spatial statistics to quantify the landscape pattern caused by the patchwork of clearcuts made over a 15-year period in the western Cascades of Oregon. Fifteen areas were selected at random to represent a diversity of landscape fragmentation patterns. Managed forest stands (patches) were digitized and analyzed to produce both tabular and mapped information describing patch size, shape, abundance and spacing, and matrix characteristics of a given area. In addition, a GIS fragmentation index was developed which was found to be sensitive to patch abundance and to the spatial distribution of patches. Use of the GIS-derived index provides an automated method of determining the level of forest fragmentation and can be used to facilitate spatial analysis of the landscape for later coordination with field and remotely sensed data. A comparison of the spatial statistics calculated for the two years indicates an increase in forest fragmentation as characterized by an increase in mean patch abundance and a decrease in interpatch distance, amount of interior natural forest habitat, and the GIS fragmentation index. Such statistics capable of quantifying patch shape and spatial distribution may prove important in the evaluation of the changing character of interior and edge habitats for wildlife.

Large-Scale Spatial Distribution Patterns of Gastropod Assemblages in Rocky Shores

PubMed Central

Miloslavich, Patricia; Cruz-Motta, Juan José; Klein, Eduardo; Iken, Katrin; Weinberger, Vanessa; Konar, Brenda; Trott, Tom; Pohle, Gerhard; Bigatti, Gregorio; Benedetti-Cecchi, Lisandro; Shirayama, Yoshihisa; Mead, Angela; Palomo, Gabriela; Ortiz, Manuel; Gobin, Judith; Sardi, Adriana; Díaz, Juan Manuel; Knowlton, Ann; Wong, Melisa; Peralta, Ana C.

2013-01-01

Gastropod assemblages from nearshore rocky habitats were studied over large spatial scales to (1) describe broad-scale patterns in assemblage composition, including patterns by feeding modes, (2) identify latitudinal pattern of biodiversity, i.e., richness and abundance of gastropods and/or regional hotspots, and (3) identify potential environmental and anthropogenic drivers of these assemblages. Gastropods were sampled from 45 sites distributed within 12 Large Marine Ecosystem regions (LME) following the NaGISA (Natural Geography in Shore Areas) standard protocol (www.nagisa.coml.org). A total of 393 gastropod taxa from 87 families were collected. Eight of these families (9.2%) appeared in four or more different LMEs. Among these, the Littorinidae was the most widely distributed (8 LMEs) followed by the Trochidae and the Columbellidae (6 LMEs). In all regions, assemblages were dominated by few species, the most diverse and abundant of which were herbivores. No latitudinal gradients were evident in relation to species richness or densities among sampling sites. Highest diversity was found in the Mediterranean and in the Gulf of Alaska, while highest densities were found at different latitudes and represented by few species within one genus (e.g. Afrolittorina in the Agulhas Current, Littorina in the Scotian Shelf, and Lacuna in the Gulf of Alaska). No significant correlation was found between species composition and environmental variables (r≤0.355, p>0.05). Contributing variables to this low correlation included invasive species, inorganic pollution, SST anomalies, and chlorophyll-a anomalies. Despite data limitations in this study which restrict conclusions in a global context, this work represents the first effort to sample gastropod biodiversity on rocky shores using a standardized protocol across a wide scale. Our results will generate more work to build global databases allowing for large-scale diversity comparisons of rocky intertidal assemblages. PMID:23967204

Restricted mating dispersal and strong breeding group structure in a mid-sized marsupial mammal (Petrogale penicillata).

PubMed

Hazlitt, S L; Sigg, D P; Eldridge, M D B; Goldizen, A W

2006-09-01

Ecological genetic studies have demonstrated that spatial patterns of mating dispersal, the dispersal of gametes through mating behaviour, can facilitate inbreeding avoidance and strongly influence the structure of populations, particularly in highly philopatric species. Elements of breeding group dynamics, such as strong structuring and sex-biased dispersal among groups, can also minimize inbreeding and positively influence levels of genetic diversity within populations. Rock-wallabies are highly philopatric mid-sized mammals whose strong dependence on rocky terrain has resulted in series of discreet, small colonies in the landscape. Populations show no signs of inbreeding and maintain high levels of genetic diversity despite strong patterns of limited gene flow within and among colonies. We used this species to investigate the importance of mating dispersal and breeding group structure to inbreeding avoidance within a 'small' population. We examined the spatial patterns of mating dispersal, the extent of kinship within breeding groups, and the degree of relatedness among brush-tailed rock-wallaby breeding pairs within a colony in southeast Queensland. Parentage data revealed remarkably restricted mating dispersal and strong breeding group structuring for a mid-sized mammal. Breeding groups showed significant levels of female kinship with evidence of male dispersal among groups. We found no evidence for inbreeding avoidance through mate choice; however, anecdotal data suggest the importance of life history traits to inbreeding avoidance between first-degree relatives. We suggest that the restricted pattern of mating dispersal and strong breeding group structuring facilitates inbreeding avoidance within colonies. These results provide insight into the population structure and maintenance of genetic diversity within colonies of the threatened brush-tailed rock-wallaby.

Integrating the effects of latitude and altitude on the spatial differentiation of plant community diversity in a mountainous ecosystem in China

PubMed Central

Xu, Manhou; Ma, Li; Jia, Yanyan; Liu, Min

2017-01-01

Varying patterns of plant community diversity along geographical gradients are a significant topic in biodiversity research. Here, to explore the integrated effects of latitude and altitude on the plant community diversity in a mountainous ecosystem, we set Guancen Mountain in the northern section, Guandi Mountain in the middle section, and Wulu Mountain in the southern section of the Lvliang Mountains as study areas, and the plant community diversity (basal diameter and height of tree and species diversity indices of shrub and herb) was measured horizontally at different latitude gradients and vertically at different altitude gradients in late July 2015. The results showed that (1) the trees were taller and wider at the middle latitude and higher altitude with a stronger spatial heterogeneity in the structures along the latitudinal and altitudinal gradients. The evergreen tree growth preceded that of the deciduous trees in the higher latitude and lower altitude regions, whereas the deciduous tree growth preceded that of the evergreen trees in the middle latitude and higher altitude regions. (2) Shrubs and herbs tended to grow well in the lower latitude and middle-lower altitude regions. The shrubs had a larger species diversity at lower latitude and lower altitude, but the species diversity of the herbs was not sensitive to the influences of the latitudinal and altitudinal gradients. With the latitude and altitude increasing, perennial herbs tended to grow well at higher latitude and higher altitude, while annual herbs tended to thrive at the middle latitude and lower altitude. In conclusion, environmental deviations caused by latitudinal and altitudinal gradients had great influences on the spatial distributions of the plant community diversity in the Lvliang Mountains. PMID:28323909

Integrating the effects of latitude and altitude on the spatial differentiation of plant community diversity in a mountainous ecosystem in China.

PubMed

Xu, Manhou; Ma, Li; Jia, Yanyan; Liu, Min

2017-01-01

Varying patterns of plant community diversity along geographical gradients are a significant topic in biodiversity research. Here, to explore the integrated effects of latitude and altitude on the plant community diversity in a mountainous ecosystem, we set Guancen Mountain in the northern section, Guandi Mountain in the middle section, and Wulu Mountain in the southern section of the Lvliang Mountains as study areas, and the plant community diversity (basal diameter and height of tree and species diversity indices of shrub and herb) was measured horizontally at different latitude gradients and vertically at different altitude gradients in late July 2015. The results showed that (1) the trees were taller and wider at the middle latitude and higher altitude with a stronger spatial heterogeneity in the structures along the latitudinal and altitudinal gradients. The evergreen tree growth preceded that of the deciduous trees in the higher latitude and lower altitude regions, whereas the deciduous tree growth preceded that of the evergreen trees in the middle latitude and higher altitude regions. (2) Shrubs and herbs tended to grow well in the lower latitude and middle-lower altitude regions. The shrubs had a larger species diversity at lower latitude and lower altitude, but the species diversity of the herbs was not sensitive to the influences of the latitudinal and altitudinal gradients. With the latitude and altitude increasing, perennial herbs tended to grow well at higher latitude and higher altitude, while annual herbs tended to thrive at the middle latitude and lower altitude. In conclusion, environmental deviations caused by latitudinal and altitudinal gradients had great influences on the spatial distributions of the plant community diversity in the Lvliang Mountains.

The roles of microclimatic diversity and of behavior in mediating the responses of ectotherms to climate change.

PubMed

Woods, H Arthur; Dillon, Michael E; Pincebourde, Sylvain

2015-12-01

We analyze the effects of changing patterns of thermal availability, in space and time, on the performance of small ectotherms. We approach this problem by breaking it into a series of smaller steps, focusing on: (1) how macroclimates interact with living and nonliving objects in the environment to produce a mosaic of thermal microclimates and (2) how mobile ectotherms filter those microclimates into realized body temperatures by moving around in them. Although the first step (generation of mosaics) is conceptually straightforward, there still exists no general framework for predicting spatial and temporal patterns of microclimatic variation. We organize potential variation along three axes-the nature of the objects producing the microclimates (abiotic versus biotic), how microclimates translate macroclimatic variation (amplify versus buffer), and the temporal and spatial scales over which microclimatic conditions vary (long versus short). From this organization, we propose several general rules about patterns of microclimatic diversity. To examine the second step (behavioral sampling of locally available microclimates), we construct a set of models that simulate ectotherms moving on a thermal landscape according to simple sets of diffusion-based rules. The models explore the effects of both changes in body size (which affect the time scale over which organisms integrate operative body temperatures) and increases in the mean and variance of temperature on the thermal landscape. Collectively, the models indicate that both simple behavioral rules and interactions between body size and spatial patterns of thermal variation can profoundly affect the distribution of realized body temperatures experienced by ectotherms. These analyses emphasize the rich set of problems still to solve before arriving at a general, predictive theory of the biological consequences of climate change. Copyright © 2014 Elsevier Ltd. All rights reserved.

Over 150 years of long-term fertilization alters spatial scaling of microbial biodiversity

DOE PAGES

Liang, Yuting; Wu, Liyou; Clark, Ian M.; ...

2015-04-07

Spatial scaling is a critical issue in ecology, but how anthropogenic activities like fertilization affect spatial scaling is poorly understood, especially for microbial communities. Here, we determined the effects of long-term fertilization on the spatial scaling of microbial functional diversity and its relationships to plant diversity in the 150-year-old Park Grass Experiment, the oldest continuous grassland experiment in the world. Nested samples were taken from plots with contrasting inorganic fertilization regimes, and community DNAs were analyzed using the GeoChip-based functional gene array. The slopes of microbial gene-area relationships (GARs) and plant species-area relationships (SARs) were estimated in a plot receivingmore » nitrogen (N), phosphorus (P), and potassium (K) and a control plot without fertilization. Our results indicated that long-term inorganic fertilization significantly increased both microbial GARs and plant SARs. Microbial spatial turnover rates (i.e., z values) were less than 0.1 and were significantly higher in the fertilized plot (0.0583) than in the control plot (0.0449) (P < 0.0001). The z values also varied significantly with different functional genes involved in carbon (C), N, P, and sulfur (S) cycling and with various phylogenetic groups (archaea, bacteria, and fungi). Similarly, the plant SARs increased significantly (P < 0.0001), from 0.225 in the control plot to 0.419 in the fertilized plot. Soil fertilization, plant diversity, and spatial distance had roughly equal contributions in shaping the microbial functional community structure, while soil geochemical variables contributed less. These results indicated that long-term agricultural practice could alter the spatial scaling of microbial biodiversity. Determining the spatial scaling of microbial biodiversity and its response to human activities is important but challenging in microbial ecology. Most studies to date are based on different sites that may not be truly comparable or on short-term perturbations, and hence, the results observed could represent transient responses. This study examined the spatial patterns of microbial communities in response to different fertilization regimes at the Rothamsted Research Experimental Station, which has become an invaluable resource for ecologists, environmentalists, and soil scientists. The current study is the first showing that long-term fertilization has dramatic impacts on the spatial scaling of microbial communities. By identifying the spatial patterns in response to long-term fertilization and their underlying mechanisms, this study makes fundamental contributions to predictive understanding of microbial biogeography.« less

Over 150 years of long-term fertilization alters spatial scaling of microbial biodiversity

DOE Office of Scientific and Technical Information (OSTI.GOV)

Liang, Yuting; Wu, Liyou; Clark, Ian M.

Spatial scaling is a critical issue in ecology, but how anthropogenic activities like fertilization affect spatial scaling is poorly understood, especially for microbial communities. Here, we determined the effects of long-term fertilization on the spatial scaling of microbial functional diversity and its relationships to plant diversity in the 150-year-old Park Grass Experiment, the oldest continuous grassland experiment in the world. Nested samples were taken from plots with contrasting inorganic fertilization regimes, and community DNAs were analyzed using the GeoChip-based functional gene array. The slopes of microbial gene-area relationships (GARs) and plant species-area relationships (SARs) were estimated in a plot receivingmore » nitrogen (N), phosphorus (P), and potassium (K) and a control plot without fertilization. Our results indicated that long-term inorganic fertilization significantly increased both microbial GARs and plant SARs. Microbial spatial turnover rates (i.e., z values) were less than 0.1 and were significantly higher in the fertilized plot (0.0583) than in the control plot (0.0449) (P < 0.0001). The z values also varied significantly with different functional genes involved in carbon (C), N, P, and sulfur (S) cycling and with various phylogenetic groups (archaea, bacteria, and fungi). Similarly, the plant SARs increased significantly (P < 0.0001), from 0.225 in the control plot to 0.419 in the fertilized plot. Soil fertilization, plant diversity, and spatial distance had roughly equal contributions in shaping the microbial functional community structure, while soil geochemical variables contributed less. These results indicated that long-term agricultural practice could alter the spatial scaling of microbial biodiversity. Determining the spatial scaling of microbial biodiversity and its response to human activities is important but challenging in microbial ecology. Most studies to date are based on different sites that may not be truly comparable or on short-term perturbations, and hence, the results observed could represent transient responses. This study examined the spatial patterns of microbial communities in response to different fertilization regimes at the Rothamsted Research Experimental Station, which has become an invaluable resource for ecologists, environmentalists, and soil scientists. The current study is the first showing that long-term fertilization has dramatic impacts on the spatial scaling of microbial communities. By identifying the spatial patterns in response to long-term fertilization and their underlying mechanisms, this study makes fundamental contributions to predictive understanding of microbial biogeography.« less

Global trophic ecology of yellowfin, bigeye, and albacore tunas: Understanding predation on micronekton communities at ocean-basin scales

NASA Astrophysics Data System (ADS)

Duffy, Leanne M.; Kuhnert, Petra M.; Pethybridge, Heidi R.; Young, Jock W.; Olson, Robert J.; Logan, John M.; Goñi, Nicolas; Romanov, Evgeny; Allain, Valerie; Staudinger, Michelle D.; Abecassis, Melanie; Choy, C. Anela; Hobday, Alistair J.; Simier, Monique; Galván-Magaña, Felipe; Potier, Michel; Ménard, Frederic

2017-06-01

Predator-prey interactions for three commercially valuable tuna species: yellowfin (Thunnus albacares), bigeye (T. obesus), and albacore (T. alalunga), collected over a 40-year period from the Pacific, Indian, and Atlantic Oceans, were used to quantitatively assess broad, macro-scale trophic patterns in pelagic ecosystems. Analysis of over 14,000 tuna stomachs, using a modified classification tree approach, revealed for the first time the global expanse of pelagic predatory fish diet and global patterns of micronekton diversity. Ommastrephid squids were consistently one of the top prey groups by weight across all tuna species and in most ocean bodies. Interspecific differences in prey were apparent, with epipelagic scombrid and mesopelagic paralepidid fishes globally important for yellowfin and bigeye tunas, respectively, while vertically-migrating euphausiid crustaceans were important for albacore tuna in the Atlantic and Pacific Oceans. Diet diversity showed global and regional patterns among tuna species. In the central and western Pacific Ocean, characterized by low productivity, a high diversity of micronekton prey was detected while low prey diversity was evident in highly productive coastal waters where upwelling occurs. Spatial patterns of diet diversity were most variable in yellowfin and bigeye tunas while a latitudinal diversity gradient was observed with lower diversity in temperate regions for albacore tuna. Sea-surface temperature was a reasonable predictor of the diets of yellowfin and bigeye tunas, whereas chlorophyll-a was the best environmental predictor of albacore diet. These results suggest that the ongoing expansion of warmer, less productive waters in the world's oceans may alter foraging opportunities for tunas due to regional changes in prey abundances and compositions.

Disentangling how landscape spatial and temporal heterogeneity affects Savanna birds.

PubMed

Price, Bronwyn; McAlpine, Clive A; Kutt, Alex S; Ward, Doug; Phinn, Stuart R; Ludwig, John A

2013-01-01

In highly seasonal tropical environments, temporal changes in habitat and resources are a significant determinant of the spatial distribution of species. This study disentangles the effects of spatial and mid to long-term temporal heterogeneity in habitat on the diversity and abundance of savanna birds by testing four competing conceptual models of varying complexity. Focussing on sites in northeast Australia over a 20 year time period, we used ground cover and foliage projected cover surfaces derived from a time series of Landsat Thematic Mapper imagery, rainfall data and site-level vegetation surveys to derive measures of habitat structure at local (1-100 ha) and landscape (100-1000s ha) scales. We used generalised linear models and an information theoretic approach to test the independent effects of spatial and temporal influences on savanna bird diversity and the abundance of eight species with different life-history behaviours. Of four competing models defining influences on assemblages of savanna birds, the most parsimonious included temporal and spatial variability in vegetation cover and site-scale vegetation structure, suggesting savanna bird species respond to spatial and temporal habitat heterogeneity at both the broader landscape scale and at the fine-scale. The relative weight, strength and direction of the explanatory variables changed with each of the eight species, reflecting their different ecology and behavioural traits. This study demonstrates that variations in the spatial pattern of savanna vegetation over periods of 10 to 20 years at the local and landscape scale strongly affect bird diversity and abundance. Thus, it is essential to monitor and manage both spatial and temporal variability in avian habitat to achieve long-term biodiversity outcomes.

Disentangling How Landscape Spatial and Temporal Heterogeneity Affects Savanna Birds

PubMed Central

Price, Bronwyn; McAlpine, Clive A.; Kutt, Alex S.; Ward, Doug; Phinn, Stuart R.; Ludwig, John A.

2013-01-01

In highly seasonal tropical environments, temporal changes in habitat and resources are a significant determinant of the spatial distribution of species. This study disentangles the effects of spatial and mid to long-term temporal heterogeneity in habitat on the diversity and abundance of savanna birds by testing four competing conceptual models of varying complexity. Focussing on sites in northeast Australia over a 20 year time period, we used ground cover and foliage projected cover surfaces derived from a time series of Landsat Thematic Mapper imagery, rainfall data and site-level vegetation surveys to derive measures of habitat structure at local (1–100 ha) and landscape (100–1000s ha) scales. We used generalised linear models and an information theoretic approach to test the independent effects of spatial and temporal influences on savanna bird diversity and the abundance of eight species with different life-history behaviours. Of four competing models defining influences on assemblages of savanna birds, the most parsimonious included temporal and spatial variability in vegetation cover and site-scale vegetation structure, suggesting savanna bird species respond to spatial and temporal habitat heterogeneity at both the broader landscape scale and at the fine-scale. The relative weight, strength and direction of the explanatory variables changed with each of the eight species, reflecting their different ecology and behavioural traits. This study demonstrates that variations in the spatial pattern of savanna vegetation over periods of 10 to 20 years at the local and landscape scale strongly affect bird diversity and abundance. Thus, it is essential to monitor and manage both spatial and temporal variability in avian habitat to achieve long-term biodiversity outcomes. PMID:24066138

Trajectories of Ethnoracial Diversity in American Communities, 1980–2010*

PubMed Central

Hall, Matthew; Tach, Laura; Lee, Barrett A.

2017-01-01

The ethnoracial makeup of the U.S. population has undergone transformative change during recent decades, with the non-Hispanic white share of the population shrinking while the minority shares expand. Yet this trend toward greater racial diversity is not universal throughout the nation. Here we propose a framework of segmented change, which incorporates both spatial assimilation and ethnic stratification theories, to better understand variation in patterns of diversification across American communities. Our research applies growth mixture models to decennial census data on places for the 1980–2010 period, finding that trajectories of ethnoracial diversity are much more uneven than popularly claimed. Moreover, types of diversity change are stratified by initial racial composition. While places with mostly-white populations in 1980 underwent extensive diversification, places with larger shares of Hispanics and (especially) blacks in 1980 exhibited less uniform movement toward diversity and were more likely to remain racially homogeneous. Analysis of the underlying group-specific pathways of change indicates that the diversification of white communities was driven largely by Hispanic growth; when areas with a black presence did diversify, it occurred via contracting white populations. These racially conditioned and locally variable patterns emphasize the segmented nature of diversity change in American society. PMID:29398737

Landscape-Scale Controls on Aboveground Forest Carbon Stocks on the Osa Peninsula, Costa Rica

PubMed Central

Taylor, Philip; Asner, Gregory; Dahlin, Kyla; Anderson, Christopher; Knapp, David; Martin, Roberta; Mascaro, Joseph; Chazdon, Robin; Cole, Rebecca; Wanek, Wolfgang; Hofhansl, Florian; Malavassi, Edgar; Vilchez-Alvarado, Braulio; Townsend, Alan

2015-01-01

Tropical forests store large amounts of carbon in tree biomass, although the environmental controls on forest carbon stocks remain poorly resolved. Emerging airborne remote sensing techniques offer a powerful approach to understand how aboveground carbon density (ACD) varies across tropical landscapes. In this study, we evaluate the accuracy of the Carnegie Airborne Observatory (CAO) Light Detection and Ranging (LiDAR) system to detect top-of-canopy tree height (TCH) and ACD across the Osa Peninsula, Costa Rica. LiDAR and field-estimated TCH and ACD were highly correlated across a wide range of forest ages and types. Top-of-canopy height (TCH) reached 67 m, and ACD surpassed 225 Mg C ha-1, indicating both that airborne CAO LiDAR-based estimates of ACD are accurate in tall, high-biomass forests and that the Osa Peninsula harbors some of the most carbon-rich forests in the Neotropics. We also examined the relative influence of lithologic, topoedaphic and climatic factors on regional patterns in ACD, which are known to influence ACD by regulating forest productivity and turnover. Analyses revealed a spatially nested set of factors controlling ACD patterns, with geologic variation explaining up to 16% of the mapped ACD variation at the regional scale, while local variation in topographic slope explained an additional 18%. Lithologic and topoedaphic factors also explained more ACD variation at 30-m than at 100-m spatial resolution, suggesting that environmental filtering depends on the spatial scale of terrain variation. Our result indicate that patterns in ACD are partially controlled by spatial variation in geologic history and geomorphic processes underpinning topographic diversity across landscapes. ACD also exhibited spatial autocorrelation, which may reflect biological processes that influence ACD, such as the assembly of species or phenotypes across the landscape, but additional research is needed to resolve how abiotic and biotic factors contribute to ACD variation across high biomass, high diversity tropical landscapes. PMID:26061884

Predicting plant species diversity in a longleaf pine landscape

Treesearch

L. Katherine Kirkman; P. Charles Goebel; Brian J. Palik; Larry T. West

2004-01-01

In this study, we used a hierarchical, multifactor ecological classification system to examine how spatial patterns of biodiversity develop in one of the most species-rich ecosystems in North America, the fire-maintained longleaf pine-wiregrass ecosystem and associated depressional wetlands and riparian forests. Our goal was to determine which landscape features are...

Conserving relics from ancient underground worlds: assessing the influence of cave and landscape features on obligate iron cave dwellers from the Eastern Amazon

PubMed Central

Prous, Xavier; Calux, Allan; Gastauer, Markus; Nicacio, Gilberto; Zampaulo, Robson; Souza-Filho, Pedro W.M.; Oliveira, Guilherme; Brandi, Iuri V.; Siqueira, José O.

2018-01-01

The degradation of subterranean habitats is believed to represent a serious threat for the conservation of obligate subterranean dwellers (troglobites), many of which are short-range endemics. However, while the factors influencing cave biodiversity remain largely unknown, the influence of the surrounding landscape and patterns of subterranean connectivity of terrestrial troglobitic communities have never been systematically assessed. Using spatial statistics to analyze the most comprehensive speleological database yet available for tropical caves, we first assess the influence of iron cave characteristics and the surrounding landscape on troglobitic communities from the Eastern Amazon. We then determine the spatial pattern of troglobitic community composition, species richness, phylogenetic diversity, and the occurrence of frequent troglobitic species, and finally quantify how different landscape features influence the connectivity between caves. Our results reveal the key importance of habitat amount, guano, water, lithology, geomorphology, and elevation in shaping iron cave troglobitic communities. While mining within 250 m from the caves influenced species composition, increasing agricultural land cover within 50 m from the caves reduced species richness and phylogenetic diversity. Troglobitic species composition, species richness, phylogenetic diversity, and the occurrence of frequent troglobites showed spatial autocorrelation for up to 40 km. Finally, our results suggest that the conservation of cave clusters should be prioritized, as geographic distance was the main factor determining connectivity between troglobitic communities. Overall, our work sheds important light onto one of the most overlooked terrestrial ecosystems, and highlights the need to shift conservation efforts from individual caves to subterranean habitats as a whole. PMID:29576987

Conserving relics from ancient underground worlds: assessing the influence of cave and landscape features on obligate iron cave dwellers from the Eastern Amazon.

PubMed

Jaffé, Rodolfo; Prous, Xavier; Calux, Allan; Gastauer, Markus; Nicacio, Gilberto; Zampaulo, Robson; Souza-Filho, Pedro W M; Oliveira, Guilherme; Brandi, Iuri V; Siqueira, José O

2018-01-01

The degradation of subterranean habitats is believed to represent a serious threat for the conservation of obligate subterranean dwellers (troglobites), many of which are short-range endemics. However, while the factors influencing cave biodiversity remain largely unknown, the influence of the surrounding landscape and patterns of subterranean connectivity of terrestrial troglobitic communities have never been systematically assessed. Using spatial statistics to analyze the most comprehensive speleological database yet available for tropical caves, we first assess the influence of iron cave characteristics and the surrounding landscape on troglobitic communities from the Eastern Amazon. We then determine the spatial pattern of troglobitic community composition, species richness, phylogenetic diversity, and the occurrence of frequent troglobitic species, and finally quantify how different landscape features influence the connectivity between caves. Our results reveal the key importance of habitat amount, guano, water, lithology, geomorphology, and elevation in shaping iron cave troglobitic communities. While mining within 250 m from the caves influenced species composition, increasing agricultural land cover within 50 m from the caves reduced species richness and phylogenetic diversity. Troglobitic species composition, species richness, phylogenetic diversity, and the occurrence of frequent troglobites showed spatial autocorrelation for up to 40 km. Finally, our results suggest that the conservation of cave clusters should be prioritized, as geographic distance was the main factor determining connectivity between troglobitic communities. Overall, our work sheds important light onto one of the most overlooked terrestrial ecosystems, and highlights the need to shift conservation efforts from individual caves to subterranean habitats as a whole.

Characterizing uncertainties in recent trends of global terrestrial net primary production through ensemble modeling

NASA Astrophysics Data System (ADS)

Wang, W.; Hashimoto, H.; Ganguly, S.; Votava, P.; Nemani, R. R.; Myneni, R. B.

2010-12-01

Large uncertainties exist in our understanding of the trends and variability in global net primary production (NPP) and its controls. This study attempts to address this question through a multi-model ensemble experiment. In particular, we drive ecosystem models including CASA, LPJ, Biome-BGC, TOPS-BGC, and BEAMS with a long-term climate dataset (i.e., CRU-NCEP) to estimate global NPP from 1901 to 2009 at a spatial resolution of 0.5 x 0.5 degree. We calculate the trends of simulated NPP during different time periods and test their sensitivities to climate variables of solar radiation, air temperature, precipitation, vapor pressure deficit (VPD), and atmospheric CO2 levels. The results indicate a large diversity among the simulated NPP trends over the past 50 years, ranging from nearly no trend to an increasing trend of ~0.1 PgC/yr. Spatial patterns of the NPP generally show positive trends in boreal forests, induced mainly by increasing temperatures in these regions; they also show negative trends in the tropics, although the spatial patterns are more diverse. These diverse trends result from different climatic sensitivities of NPP among the tested models. Depending the ecological processes (e.g., photosynthesis or respiration) a model emphasizes, it can be more or less responsive to changes in solar radiation, temperatures, water, or atmospheric CO2 levels. Overall, these results highlight the limit of current ecosystem models in simulating NPP, which cannot be easily observed. They suggest that the traditional single-model approach is not ideal for characterizing trends and variability in global carbon cycling.

Pollinator communities in strawberry crops - variation at multiple spatial scales.

PubMed

Ahrenfeldt, E J; Klatt, B K; Arildsen, J; Trandem, N; Andersson, G K S; Tscharntke, T; Smith, H G; Sigsgaard, L

2015-08-01

Predicting potential pollination services of wild bees in crops requires knowledge of their spatial distribution within fields. Field margins can serve as nesting and foraging habitats for wild bees and can be a source of pollinators. Regional differences in pollinator community composition may affect this spill-over of bees. We studied how regional and local differences affect the spatial distribution of wild bee species richness, activity-density and body size in crop fields. We sampled bees both from the field centre and at two different types of semi-natural field margins, grass strips and hedges, in 12 strawberry fields. The fields were distributed over four regions in Northern Europe, representing an almost 1100 km long north-south gradient. Even over this gradient, daytime temperatures during sampling did not differ significantly between regions and did therefore probably not impact bee activity. Bee species richness was higher in field margins compared with field centres independent of field size. However, there was no difference between centre and margin in body-size or activity-density. In contrast, bee activity-density increased towards the southern regions, whereas the mean body size increased towards the north. In conclusion, our study revealed a general pattern across European regions of bee diversity, but not activity-density, declining towards the field interior which suggests that the benefits of functional diversity of pollinators may be difficult to achieve through spill-over effects from margins to crop. We also identified dissimilar regional patterns in bee diversity and activity-density, which should be taken into account in conservation management.

Patchiness in a large floodplain river: Associations among hydrology, nutrients, and fish communities

USGS Publications Warehouse

DeJager, Nathan R.; Houser, Jeff N.

2016-01-01

Large floodplain rivers have internal structures shaped by directions and rates of water movement. In a previous study, we showed that spatial variation in local current velocities and degrees of hydrological exchange creates a patch-work mosaic of nitrogen and phosphorus concentrations and ratios in the Upper Mississippi River. Here, we used long-term fish and limnological data sets to test the hypothesis that fish communities differ between the previously identified patches defined by high or low nitrogen to phosphorus ratios (TN:TP) and to determine the extent to which select limnological covariates might explain those differences. Species considered as habitat generalists were common in both patch types but were at least 2 times as abundant in low TN:TP patches. Dominance by these species resulted in lower diversity in low TN:TP patches, whereas an increased relative abundance of a number of rheophilic (flow-dependent) species resulted in higher diversity and a more even species distribution in high TN:TP patches. Of the limnological variables considered, the strongest predictor of fish species assemblage and diversity was water flow velocity, indicating that spatial patterns in water-mediated connectivity may act as the main driver of both local nutrient concentrations and fish community composition in these reaches. The coupling among hydrology, biogeochemistry, and biodiversity in these river reaches suggests that landscape-scale restoration projects that manipulate hydrogeomorphic patterns may also modify the spatial mosaic of nutrients and fish communities. Published 2016. This article is a U.S. Government work and is in the public domain in the USA.

The interplay between human population dynamics and flooding in Bangladesh: a spatial analysis

NASA Astrophysics Data System (ADS)

di Baldassarre, G.; Yan, K.; Ferdous, MD. R.; Brandimarte, L.

2014-09-01

In Bangladesh, socio-economic and hydrological processes are both extremely dynamic and inter-related. Human population patterns are often explained as a response, or adaptation strategy, to physical events, e.g. flooding, salt-water intrusion, and erosion. Meanwhile, these physical processes are exacerbated, or mitigated, by diverse human interventions, e.g. river diversion, levees and polders. In this context, this paper describes an attempt to explore the complex interplay between floods and societies in Bangladeshi floodplains. In particular, we performed a spatially-distributed analysis of the interactions between the dynamics of human settlements and flood inundation patterns. To this end, we used flooding simulation results from inundation modelling, LISFLOOD-FP, as well as global datasets of population distribution data, such as the Gridded Population of the World (20 years, from 1990 to 2010) and HYDE datasets (310 years, from 1700 to 2010). The outcomes of this work highlight the behaviour of Bangladeshi floodplains as complex human-water systems and indicate the need to go beyond the traditional narratives based on one-way cause-effects, e.g. climate change leading to migrations.

β-Diversity of Functional Groups of Woody Plants in a Tropical Dry Forest in Yucatan

PubMed Central

López-Martínez, Jorge Omar; Sanaphre-Villanueva, Lucía; Dupuy, Juan Manuel; Hernández-Stefanoni, José Luis; Meave, Jorge Arturo; Gallardo-Cruz, José Alberto

2013-01-01

Two main theories have attempted to explain variation in plant species composition (β-diversity). Niche theory proposes that most of the variation is related to environment (environmental filtering), whereas neutral theory posits that dispersal limitation is the main driver of β-diversity. In this study, we first explored how α- and β-diversity of plant functional groups defined by growth form (trees, shrubs and lianas, which represent different strategies of resource partitioning), and dispersal syndrome (autochory, anemochory and zoochory, which represent differences in dispersal limitation) vary with successional age and topographic position in a tropical dry forest. Second, we examined the effects of environmental, spatial, and spatially-structured environmental factors on β-diversity of functional groups; we used the spatial structure of sampling sites as a proxy for dispersal limitation, and elevation, soil properties and forest stand age as indicators of environmental filtering. We recorded 200 species and 22,245 individuals in 276 plots; 120 species were trees, 41 shrubs and 39 lianas. We found that β-diversity was highest for shrubs, intermediate for lianas and lowest for trees, and was slightly higher for zoochorous than for autochorous and anemochorous species. All three dispersal syndromes, trees and shrubs varied in composition among vegetation classes (successional age and topographic position), whilst lianas did not. β-diversity was influenced mostly by proxies of environmental filtering, except for shrubs, for which the influence of dispersal limitation was more important. Stand age and topography significantly influenced α-diversity across functional groups, but showed a low influence on β-diversity –possibly due to the counterbalancing effect of resprouting on plant distribution and composition. Our results show that considering different plant functional groups reveals important differences in both α- and β-diversity patterns and correlates that are not apparent when focusing on overall woody plant diversity, and that have important implications for ecological theory and biodiversity conservation. PMID:24040014

[Spatial patterns in communities of aquatic macroinvertebrates of Argentinean Puna].

PubMed

Nieto, Carolina; Malizia, Agustina; Carilla, Julieta; Izquierdo, Andrea; Rodríguez, José; Cuello, Soledad; Zannier, Martín; Grau, H Ricardo

2016-06-01

Spatial patterns in communities of aquatic macroinvertebrates of Argentinean Puna. The macroinvertebrates are a vital component of freshwater ecosystems as they contribute to the process of organic matter while serving as food for other organisms such as fish and amphibians. Unfortunately, the knowledge of the aquatic diversity is poor in the high Andean systems (between 3 200 and 5 200 m.a.s.l. and rainfall below 300 mm per year), especially in the Argentinean peatbogs, a fact which has made difficult the interpretation of spatial patterns on a regional scale. The present study aimed to describe the composition of aquatic macroinvertebrates in seven peatbogs in the Argentinean Puna, and to analyze for the first time their spatial patterns. For this, we studied the relationship of these organisms with the environment, and obtained information about the surrounding vegetation and water physico-chemical characteristics. A total of 3 131 specimens of aquatic macroinvertebrates were collected, representing 25 taxa belonging to 22 families and 24 genera. In addition, 62 species of vascular plants were recorded, belonging to 20 families. The most abundant life form were the tufted grasses, followed by cushions. By using an NMDS (Non-Metrical Multidimensional Scaling) statistical analysis, the sampling sites were ordered in each peatbog as follows. The peatbogs located furthest West and South with higher water temperature were grouped on axis 1, whereas those with higher conductivity, whole water dissolved solids and salt concentration were grouped on axis 2. The water temperature was higher than air temperature at all times, and we found no association between temperature and altitude. The altitude had no correlation with the abundance of macroinvertebrates or with plant richness. Life forms such as scattered graminoids, trailing and prostrate herbs (in many cases they get into the channel) and aquatic plants were more abundant in peatbogs 4, 5 and 7 and they had a correlation with some macroinvertebrates belonging to functional trophic groups such as filter-collectors, collectors and scrapers. Finally, conductivity, whole dissolved solids and salt concentration had their highest value in peatbog 6, where Bivalvia (filter-collector) and Hyalella (collector) were also found. The results obtained attest that these macroinvertebrates displayed diversity and composition spatial patterns, the most important feature being their relationship with the surrounding vegetation, and to a lesser extent, with the physical and chemical traits of water in seven fertile lowlands in the Argentinean Puna.

Quantifying spatial scaling patterns and their local and regional correlates in headwater streams: Implications for resilience

USGS Publications Warehouse

Gothe, Emma; Sandin, Leonard; Allen, Craig R.; Angeler, David G.

2014-01-01

The distribution of functional traits within and across spatiotemporal scales has been used to quantify and infer the relative resilience across ecosystems. We use explicit spatial modeling to evaluate within- and cross-scale redundancy in headwater streams, an ecosystem type with a hierarchical and dendritic network structure. We assessed the cross-scale distribution of functional feeding groups of benthic invertebrates in Swedish headwater streams during two seasons. We evaluated functional metrics, i.e., Shannon diversity, richness, and evenness, and the degree of redundancy within and across modeled spatial scales for individual feeding groups. We also estimated the correlates of environmental versus spatial factors of both functional composition and the taxonomic composition of functional groups for each spatial scale identified. Measures of functional diversity and within-scale redundancy of functions were similar during both seasons, but both within- and cross-scale redundancy were low. This apparent low redundancy was partly attributable to a few dominant taxa explaining the spatial models. However, rare taxa with stochastic spatial distributions might provide additional information and should therefore be considered explicitly for complementing future resilience assessments. Otherwise, resilience may be underestimated. Finally, both environmental and spatial factors correlated with the scale-specific functional and taxonomic composition. This finding suggests that resilience in stream networks emerges as a function of not only local conditions but also regional factors such as habitat connectivity and invertebrate dispersal.

Microbial biogeography: putting microorganisms on the map.

PubMed

Martiny, Jennifer B Hughes; Bohannan, Brendan J M; Brown, James H; Colwell, Robert K; Fuhrman, Jed A; Green, Jessica L; Horner-Devine, M Claire; Kane, Matthew; Krumins, Jennifer Adams; Kuske, Cheryl R; Morin, Peter J; Naeem, Shahid; Ovreås, Lise; Reysenbach, Anna-Louise; Smith, Val H; Staley, James T

2006-02-01

We review the biogeography of microorganisms in light of the biogeography of macroorganisms. A large body of research supports the idea that free-living microbial taxa exhibit biogeographic patterns. Current evidence confirms that, as proposed by the Baas-Becking hypothesis, 'the environment selects' and is, in part, responsible for spatial variation in microbial diversity. However, recent studies also dispute the idea that 'everything is everywhere'. We also consider how the processes that generate and maintain biogeographic patterns in macroorganisms could operate in the microbial world.

Measuring spatial patterns in floodplains: A step towards understanding the complexity of floodplain ecosystems: Chapter 6

USGS Publications Warehouse

Scown, Murray W.; Thoms, Martin C.; DeJager, Nathan R.; Gilvear, David J.; Greenwood, Malcolm T.; Thoms, Martin C.; Wood, Paul J.

2016-01-01

Floodplains can be viewed as complex adaptive systems (Levin, 1998) because they are comprised of many different biophysical components, such as morphological features, soil groups and vegetation communities as well as being sites of key biogeochemical processing (Stanford et al., 2005). Interactions and feedbacks among the biophysical components often result in additional phenomena occuring over a range of scales, often in the absence of any controlling factors (sensu Hallet, 1990). This emergence of new biophysical features and rates of processing can lead to alternative stable states which feed back into floodplain adaptive cycles (cf. Hughes, 1997; Stanford et al., 2005). Interactions between different biophysical components, feedbacks, self emergence and scale are all key properties of complex adaptive systems (Levin, 1998; Phillips, 2003; Murray et al., 2014) and therefore will influence the manner in which we study and view spatial patterns. Measuring the spatial patterns of floodplain biophysical components is a prerequisite to examining and understanding these ecosystems as complex adaptive systems. Elucidating relationships between pattern and process, which are intrinsically linked within floodplains (Ward et al., 2002), is dependent upon an understanding of spatial pattern. This knowledge can help river scientists determine the major drivers, controllers and responses of floodplain structure and function, as well as the consequences of altering those drivers and controllers (Hughes and Cass, 1997; Whited et al., 2007). Interactions and feedbacks between physical, chemical and biological components of floodplain ecosystems create and maintain a structurally diverse and dynamic template (Stanford et al., 2005). This template influences subsequent interactions between components that consequently affect system trajectories within floodplains (sensu Bak et al., 1988). Constructing and evaluating models used to predict floodplain ecosystem responses to natural and anthropogenic disturbances therefore require quantification of spatial pattern (Asselman and Middelkoop, 1995; Walling and He, 1998). Quantifying these patterns also provides insights into the spatial and temporal domains of structuring processes as well as enabling the detection of self-emergent phenomena, environmental constraints or anthropogenic interference (Turner et al., 1990; Holling, 1992; De Jager and Rohweder, 2012). Thus, quantifying spatial pattern is an important building block on which to examine floodplains as complex adaptive systems (Levin, 1998). Approaches to measuring spatial pattern in floodplains must be cognisant of scale, self-emergent phenomena, spatial organisation, and location. Fundamental problems may arise when patterns observed at a site or transect scale are scaled-up to infer processes and patterns over entire floodplain surfaces (Wiens, 2002; Thorp et al., 2008). Likewise, patterns observed over the entire spatial extent of a landscape can mask important variation and detail at finer scales (Riitters et al., 2002). Indeed, different patterns often emerge at different scales (Turner et al., 1990) because of hierarchical structuring processes (O'Neill et al., 1991). Categorising data into discrete, homogeneous and predefined spatial units at a particular scale (e.g. polygons) creates issues and errors associated with scale and subjective classification (McGarigal et al., 2009; Cushman et al., 2010). These include, loss of information within classified ‘patches’, as well as the ability to detect the emergence of new features that do not fit the original classification scheme. Many of these issues arise because floodplains are highly heterogeneous and have complex spatial organizations (Carbonneau et al., 2012; Legleiter, 2013). As a result, the scale and location at which measurements are made can influence the observed spatial patterns; and patterns may not be scale independent or applicable in different geomorp

Indigenous and Invasive Fruit Fly Diversity along an Altitudinal Transect in Eastern Central Tanzania

PubMed Central

Geurts, Katrien; Mwatawala, Maulid; De Meyer, Marc

2012-01-01

The relative abundance of indigenous and invasive frugivorous fruit flies (Diptera: Tephritidae) was evaluated spatially and temporally along an altitudinal transect between 581–1650 m in the Uluguru Mountains near Morogoro, Tanzania. The polyphagous invasive fruit fly Bactrocera invadens Drew, Tsuruta, and White and the indigenous fruit fly Ceratitis rosa Karsch show a similar temporal pattern, but are largely separated spatially, with B. invadens being abundant at lower elevation and C. rosa predominant at higher elevation. The polyphagous indigenous C. cosyra (Walker) coincides with B. invadens but shows an inverse temporal pattern. The cucurbit feeders B. cucurbitae (Coquillett) and Dacus bivittatus (Bigot) show a similar temporal pattern, but the former is restricted to lower elevations. Host availability and climatic differences seem to be the determining factors to explain the differences in occurrence and abundance in time and space. PMID:22935017

Mistaking geography for biology: inferring processes from species distributions.

PubMed

Warren, Dan L; Cardillo, Marcel; Rosauer, Dan F; Bolnick, Daniel I

2014-10-01

Over the past few decades, there has been a rapid proliferation of statistical methods that infer evolutionary and ecological processes from data on species distributions. These methods have led to considerable new insights, but they often fail to account for the effects of historical biogeography on present-day species distributions. Because the geography of speciation can lead to patterns of spatial and temporal autocorrelation in the distributions of species within a clade, this can result in misleading inferences about the importance of deterministic processes in generating spatial patterns of biodiversity. In this opinion article, we discuss ways in which patterns of species distributions driven by historical biogeography are often interpreted as evidence of particular evolutionary or ecological processes. We focus on three areas that are especially prone to such misinterpretations: community phylogenetics, environmental niche modelling, and analyses of beta diversity (compositional turnover of biodiversity). Crown Copyright © 2014. Published by Elsevier Ltd. All rights reserved.

Ectomycorrhizal-dominated boreal and tropical forests have distinct fungal communities, but analogous spatial patterns across soil horizons.

PubMed

McGuire, Krista L; Allison, Steven D; Fierer, Noah; Treseder, Kathleen K

2013-01-01

Fungi regulate key nutrient cycling processes in many forest ecosystems, but their diversity and distribution within and across ecosystems are poorly understood. Here, we examine the spatial distribution of fungi across a boreal and tropical ecosystem, focusing on ectomycorrhizal fungi. We analyzed fungal community composition across litter (organic horizons) and underlying soil horizons (0-20 cm) using 454 pyrosequencing and clone library sequencing. In both forests, we found significant clustering of fungal communities by site and soil horizons with analogous patterns detected by both sequencing technologies. Free-living saprotrophic fungi dominated the recently-shed leaf litter and ectomycorrhizal fungi dominated the underlying soil horizons. This vertical pattern of fungal segregation has also been found in temperate and European boreal forests, suggesting that these results apply broadly to ectomycorrhizal-dominated systems, including tropical rain forests. Since ectomycorrhizal and free-living saprotrophic fungi have different influences on soil carbon and nitrogen dynamics, information on the spatial distribution of these functional groups will improve our understanding of forest nutrient cycling.

Spatial pattern in Antarctica: what can we learn from Antarctic bacterial isolates?

PubMed

Chong, Chun Wie; Goh, Yuh Shan; Convey, Peter; Pearce, David; Tan, Irene Kit Ping

2013-09-01

A range of small- to moderate-scale studies of patterns in bacterial biodiversity have been conducted in Antarctica over the last two decades, most suggesting strong correlations between the described bacterial communities and elements of local environmental heterogeneity. However, very few of these studies have advanced interpretations in terms of spatially associated patterns, despite increasing evidence of patterns in bacterial biogeography globally. This is likely to be a consequence of restricted sampling coverage, with most studies to date focusing only on a few localities within a specific Antarctic region. Clearly, there is now a need for synthesis over a much larger spatial to consolidate the available data. In this study, we collated Antarctic bacterial culture identities based on the 16S rRNA gene information available in the literature and the GenBank database (n > 2,000 sequences). In contrast to some recent evidence for a distinct Antarctic microbiome, our phylogenetic comparisons show that a majority (~75 %) of Antarctic bacterial isolates were highly similar (≥99 % sequence similarity) to those retrieved from tropical and temperate regions, suggesting widespread distribution of eurythermal mesophiles in Antarctic environments. However, across different Antarctic regions, the dominant bacterial genera exhibit some spatially distinct diversity patterns analogous to those recently proposed for Antarctic terrestrial macroorganisms. Taken together, our results highlight the threat of cross-regional homogenisation in Antarctic biodiversity, and the imperative to include microbiota within the framework of biosecurity measures for Antarctica.

Disentangling vegetation diversity from climate–energy and habitat heterogeneity for explaining animal geographic patterns

USGS Publications Warehouse

Jimenez-Alfaro, Borja; Chytry, Milan; Mucina, Ladislav; Grace, James B.; Rejmanek, Marcel

2016-01-01

Broad-scale animal diversity patterns have been traditionally explained by hypotheses focused on climate–energy and habitat heterogeneity, without considering the direct influence of vegetation structure and composition. However, integrating these factors when considering plant–animal correlates still poses a major challenge because plant communities are controlled by abiotic factors that may, at the same time, influence animal distributions. By testing whether the number and variation of plant community types in Europe explain country-level diversity in six animal groups, we propose a conceptual framework in which vegetation diversity represents a bridge between abiotic factors and animal diversity. We show that vegetation diversity explains variation in animal richness not accounted for by altitudinal range or potential evapotranspiration, being the best predictor for butterflies, beetles, and amphibians. Moreover, the dissimilarity of plant community types explains the highest proportion of variation in animal assemblages across the studied regions, an effect that outperforms the effect of climate and their shared contribution with pure spatial variation. Our results at the country level suggest that vegetation diversity, as estimated from broad-scale classifications of plant communities, may contribute to our understanding of animal richness and may be disentangled, at least to a degree, from climate–energy and abiotic habitat heterogeneity.

Understanding global patterns of mammalian functional and phylogenetic diversity

PubMed Central

Safi, Kamran; Cianciaruso, Marcus V.; Loyola, Rafael D.; Brito, Daniel; Armour-Marshall, Katrina; Diniz-Filho, José Alexandre F.

2011-01-01

Documenting and exploring the patterns of diversity of life on Earth has always been a central theme in biology. Species richness despite being the most commonly used measure of diversity in macroecological studies suffers from not considering the evolutionary and ecological differences among species. Phylogenetic diversity (PD) and functional diversity (FD) have been proposed as alternative measures to overcome this limitation. Although species richness, PD and FD are closely related, their relationships have never been investigated on a global scale. Comparing PD and FD with species richness corroborated the general assumptions of surrogacy of the different diversity measures. However, the analysis of the residual variance suggested that the mismatches between the diversity measures are influenced by environmental conditions. PD increased relative to species richness with increasing mean annual temperature, whereas FD decreased with decreasing seasonality relative to PD. We also show that the tropical areas are characterized by a FD deficit, a phenomenon, that suggests that in tropical areas more species can be packed into the ecological space. We discuss potential mechanisms that could have resulted in the gradient of spatial mismatch observed in the different biodiversity measures and draw parallels to local scale studies. We conclude that the use of multiple diversity measures on a global scale can help to elucidate the relative importance of historical and ecological processes shaping the present gradients in mammalian diversity. PMID:21807734

Emerging spatial patterns in Antarctic prokaryotes

PubMed Central

Chong, Chun-Wie; Pearce, David A.; Convey, Peter

2015-01-01

Recent advances in knowledge of patterns of biogeography in terrestrial eukaryotic organisms have led to a fundamental paradigm shift in understanding of the controls and history of life on land in Antarctica, and its interactions over the long term with the glaciological and geological processes that have shaped the continent. However, while it has long been recognized that the terrestrial ecosystems of Antarctica are dominated by microbes and their processes, knowledge of microbial diversity and distributions has lagged far behind that of the macroscopic eukaryote organisms. Increasing human contact with and activity in the continent is leading to risks of biological contamination and change in a region whose isolation has protected it for millions of years at least; these risks may be particularly acute for microbial communities which have, as yet, received scant recognition and attention. Even a matter apparently as straightforward as Protected Area designation in Antarctica requires robust biodiversity data which, in most parts of the continent, remain almost completely unavailable. A range of important contributing factors mean that it is now timely to reconsider the state of knowledge of Antarctic terrestrial prokaryotes. Rapid advances in molecular biological approaches are increasingly demonstrating that bacterial diversity in Antarctica may be far greater than previously thought, and that there is overlap in the environmental controls affecting both Antarctic prokaryotic and eukaryotic communities. Bacterial dispersal mechanisms and colonization patterns remain largely unaddressed, although evidence for regional evolutionary differentiation is rapidly accruing and, with this, there is increasing appreciation of patterns in regional bacterial biogeography in this large part of the globe. In this review, we set out to describe the state of knowledge of Antarctic prokaryote diversity patterns, drawing analogy with those of eukaryote groups where appropriate. Based on our synthesis, it is clear that spatial patterns of Antarctic prokaryotes can be unique at local scales, while the limited evidence available to date supports the group exhibiting overall regional biogeographical patterns similar to the eukaryotes. We further consider the applicability of the concept of “functional redundancy” for the Antarctic microbial community and highlight the requirements for proper consideration of their important and distinctive roles in Antarctic terrestrial ecosystems. PMID:26483777

Relationship between spatial and genetic distance in Agrobacterium spp. in 1 cubic centimeter of soil.

PubMed

Vogel, J; Normand, P; Thioulouse, J; Nesme, X; Grundmann, G L

2003-03-01

The spatial and genetic unit of bacterial population structure is the clone. Surprisingly, very little is known about the spread of a clone (spatial distance between clonally related bacteria) and the relationship between spatial distance and genetic distance, especially at very short scale (microhabitat scale), where cell division takes place. Agrobacterium spp. Biovar 1 was chosen because it is a soil bacterial taxon easy to isolate. A total of 865 microsamples 500 microm in diameter were sampled with spatial coordinates in 1 cm(3) of undisturbed soil. The 55 isolates obtained yielded 42 ribotypes, covering three genomic species based on amplified ribosomal DNA restriction analysis (ARDRA) of the intergenic spacer 16S-23S, seven of which contained two to six isolates. These clonemates (identical ARDRA patterns) could be found in the same microsample or 1 cm apart. The genetic diversity did not change with distance, indicating the same habitat variability across the cube. The mixing of ribotypes, as assessed by the spatial position of clonemates, corresponded to an overlapping of clones. Although the population probably was in a recession stage in the cube (10(3) agrobacteria g(-1)), a high genetic diversity was maintained. In two independent microsamples (500 microm in diameter) at the invasion stage, the average genetic diversity was at the same level as in the cube. Quantification of the microdiversity landscape will help to estimate the probability of encounter between bacteria under realistic natural conditions and to set appropriate sampling strategies for population genetic analysis.

Disentangling environmental correlates of vascular plant biodiversity in a Mediterranean hotspot.

PubMed

Molina-Venegas, Rafael; Aparicio, Abelardo; Pina, Francisco José; Valdés, Benito; Arroyo, Juan

2013-10-01

We determined the environmental correlates of vascular plant biodiversity in the Baetic-Rifan region, a plant biodiversity hotspot in the western Mediterranean. A catalog of the whole flora of Andalusia and northern Morocco, the region that includes most of the Baetic-Rifan complex, was compiled using recent comprehensive floristic catalogs. Hierarchical cluster analysis (HCA) and detrended correspondence analysis (DCA) of the different ecoregions of Andalusia and northern Morocco were conducted to determine their floristic affinities. Diversity patterns were studied further by focusing on regional endemic taxa. Endemic and nonendemic alpha diversities were regressed to several environmental variables. Finally, semi-partial regressions on distance matrices were conducted to extract the respective contributions of climatic, altitudinal, lithological, and geographical distance matrices to beta diversity in endemic and nonendemic taxa. We found that West Rifan plant assemblages had more similarities with Andalusian ecoregions than with other nearby northern Morocco ecoregions. The endemic alpha diversity was explained relatively well by the environmental variables related to summer drought and extreme temperature values. Of all the variables, geographical distance contributed by far the most to spatial turnover in species diversity in the Baetic-Rifan hotspot. In the Baetic range, elevation was the most significant driver of nonendemic species beta diversity, while lithology and elevation were the main drivers of endemic beta diversity. Despite the fact that Andalusia and northern Morocco are presently separated by the Atlantic Ocean and the Mediterranean Sea, the Baetic and Rifan mountain ranges have many floristic similarities - especially in their western ranges - due to past migration of species across the Strait of Gibraltar. Climatic variables could be shaping the spatial distribution of endemic species richness throughout the Baetic-Rifan hotspot. Determinants of spatial turnover in biodiversity in the Baetic-Rifan hotspot vary in importance between endemic and nonendemic species.

Reproductive phenology of coastal plain Atlantic forest vegetation: comparisons from seashore to foothills.

PubMed

Staggemeier, Vanessa Graziele; Morellato, Leonor Patrícia Cerdeira

2011-11-01

The diversity of tropical forest plant phenology has called the attention of researchers for a long time. We continue investigating the factors that drive phenological diversity on a wide scale, but we are unaware of the variation of plant reproductive phenology at a fine spatial scale despite the high spatial variation in species composition and abundance in tropical rainforests. We addressed fine scale variability by investigating the reproductive phenology of three contiguous vegetations across the Atlantic rainforest coastal plain in Southeastern Brazil. We asked whether the vegetations differed in composition and abundance of species, the microenvironmental conditions and the reproductive phenology, and how their phenology is related to regional and local microenvironmental factors. The study was conducted from September 2007 to August 2009 at three contiguous sites: (1) seashore dominated by scrub vegetation, (2) intermediary covered by restinga forest and (3) foothills covered by restinga pre-montane transitional forest. We conducted the microenvironmental, plant and phenological survey within 30 transects of 25 m × 4 m (10 per site). We detected significant differences in floristic, microenvironment and reproductive phenology among the three vegetations. The microenvironment determines the spatial diversity observed in the structure and composition of the flora, which in turn determines the distinctive flowering and fruiting peaks of each vegetation (phenological diversity). There was an exchange of species providing flowers and fruits across the vegetation complex. We conclude that plant reproductive patterns as described in most phenological studies (without concern about the microenvironmental variation) may conceal the fine scale temporal phenological diversity of highly diverse tropical vegetation. This phenological diversity should be taken into account when generating sensor-derived phenologies and when trying to understand tropical vegetation responses to environmental changes.

Selecting landscape metrics as indicators of spatial heterogeneity-A comparison among Greek landscapes

NASA Astrophysics Data System (ADS)

Plexida, Sofia G.; Sfougaris, Athanassios I.; Ispikoudis, Ioannis P.; Papanastasis, Vasilios P.

2014-02-01

This paper investigates the spatial heterogeneity of three landscapes along an altitudinal gradient and different human land use. The main aim was the identification of appropriate landscape indicators using different extents. ASTER image was used to create a land cover map consisting of three landscapes which differed in altitude and land use. A number of landscape metrics quantifying patch complexity, configuration, diversity and connectivity were derived from the thematic map at the landscape level. There were significant differences among the three landscapes regarding these four aspects of landscape heterogeneity. The analysis revealed a specific pattern of land use where lowlands are being increasingly utilized by humans (percentage of agricultural land = 65.84%) characterized by physical connectedness (high values of Patch Cohesion Index) and relatively simple geometries (low values of fractal dimension index). The landscape pattern of uplands was found to be highly diverse based upon the Shannon Diversity index. After selecting the scale (600 ha) where metrics values stabilized, it was shown that metrics were more correlated at the small scale of 60 ha. From the original 24 metrics, 14 individual metrics with high Spearman correlation coefficient and Variance Inflation Factor criterion were eliminated, leaving 10 representative metrics for subsequent analysis. Data reduction analysis showed that Patch Density, Area-Weighted Mean Fractal Dimension Index and Patch Cohesion Index are suitable to describe landscape patterns irrespective of the scale. A systematic screening of these metrics could enhance a deeper understanding of the results obtained by them and contribute to a sustainable landscape management of Mediterranean landscapes.

Interfaces of Malignant and Immunologic Clonal Dynamics in Ovarian Cancer.

PubMed

Zhang, Allen W; McPherson, Andrew; Milne, Katy; Kroeger, David R; Hamilton, Phineas T; Miranda, Alex; Funnell, Tyler; Little, Nicole; de Souza, Camila P E; Laan, Sonya; LeDoux, Stacey; Cochrane, Dawn R; Lim, Jamie L P; Yang, Winnie; Roth, Andrew; Smith, Maia A; Ho, Julie; Tse, Kane; Zeng, Thomas; Shlafman, Inna; Mayo, Michael R; Moore, Richard; Failmezger, Henrik; Heindl, Andreas; Wang, Yi Kan; Bashashati, Ali; Grewal, Diljot S; Brown, Scott D; Lai, Daniel; Wan, Adrian N C; Nielsen, Cydney B; Huebner, Curtis; Tessier-Cloutier, Basile; Anglesio, Michael S; Bouchard-Côté, Alexandre; Yuan, Yinyin; Wasserman, Wyeth W; Gilks, C Blake; Karnezis, Anthony N; Aparicio, Samuel; McAlpine, Jessica N; Huntsman, David G; Holt, Robert A; Nelson, Brad H; Shah, Sohrab P

2018-05-07

High-grade serous ovarian cancer (HGSC) exhibits extensive malignant clonal diversity with widespread but non-random patterns of disease dissemination. We investigated whether local immune microenvironment factors shape tumor progression properties at the interface of tumor-infiltrating lymphocytes (TILs) and cancer cells. Through multi-region study of 212 samples from 38 patients with whole-genome sequencing, immunohistochemistry, histologic image analysis, gene expression profiling, and T and B cell receptor sequencing, we identified three immunologic subtypes across samples and extensive within-patient diversity. Epithelial CD8+ TILs negatively associated with malignant diversity, reflecting immunological pruning of tumor clones inferred by neoantigen depletion, HLA I loss of heterozygosity, and spatial tracking between T cell and tumor clones. In addition, combinatorial prognostic effects of mutational processes and immune properties were observed, illuminating how specific genomic aberration types associate with immune response and impact survival. We conclude that within-patient spatial immune microenvironment variation shapes intraperitoneal malignant spread, provoking new evolutionary perspectives on HGSC clonal dispersion. Copyright © 2018 Elsevier Inc. All rights reserved.

A hierarchical perspective of plant diversity

USGS Publications Warehouse

Sarr, Daniel; Hibbs, D.E.; Huston, M.

2005-01-01

Predictive models of plant diversity have typically focused on either a landscapea??s capacity for richness (equilibrium models), or on the processes that regulate competitive exclusion, and thus allow species to coexist (nonequilibrium models). Here, we review the concepts and purposes of a hierarchical, multiscale model of the controls of plant diversity that incorporates the equilibrium model of climatic favorability at macroscales, nonequilibrium models of competition at microscales, and a mixed model emphasizing environmental heterogeneity at mesoscales. We evaluate the conceptual model using published data from three spatially nested datasets: (1) a macroscale analysis of ecoregions in the continental and western U.S.; (2) a mesoscale study in California; and (3) a microscale study in the Siskiyou Mountains of Oregon and California. At the macroscale (areas from 3889 km2 to 638,300 km2), climate (actual evaporation) was a strong predictor of tree diversity (R2 = 0.80), as predicted by the conceptual model, but area was a better predictor for vascular plant diversity overall (R2 = 0.38), which suggests different types of plants differ in their sensitivity to climatic controls. At mesoscales (areas from 1111 km2 to 15,833 km2 ), climate was still an important predictor of richness (R2 = 0.52), but, as expected, topographic heterogeneity explained an important share of the variance (R2 = 0.19), showed positive correlations with diversity of trees, shrubs, and annual and perennial herbs, and was the primary predictor of shrub and annual plant species richness. At microscales (0.1 ha plots), spatial patterns of diversity showed a clear unimodal pattern along a climatea??driven productivity gradient and a negative relationship with soil fertility. The strong decline in understory and total diversity at the most productive sites suggests that competitive controls, as predicted, can override climatic controls at this scale. We conclude that this hierarchical, multiscale model provides a sound basis to understand and analyze plant species diversity. Specifically, future research should employ the principles in this paper to explore climatic controls on species richness of different life forms, better quantify environmental heterogeneity in landscapes, and analyze how these largea??scale factors interact with local nonequilibrium dynamics to maintain plant diversity.

Effects of species' similarity and dominance on the functional and phylogenetic structure of a plant meta-community.

PubMed

Chalmandrier, L; Münkemüller, T; Lavergne, S; Thuiller, W

2015-01-01

Different assembly processes drive the spatial structure of meta-communities (beta-diversity). Recently, functional and phylogenetic diversities have been suggested as indicators of these assembly processes. Assuming that diversity is a good proxy for niche overlap, high beta-diversity along environmental gradients should be the result of environmental filtering while low beta-diversity should stem from competitive interactions. So far, studies trying to disentangle the relative importance of these assembly processes have provided mixed results. One reason for this may be that these studies often rely on a single measure of diversity and thus implicitly make a choice on how they account for species relative abundances and how species similarities are captured by functional traits or phylogeny. Here, we tested the effect of gradually scaling the importance of dominance (the weight given to dominant vs. rare species) and species similarity (the weight given to small vs. large similarities) on resulting beta-diversity patterns of an alpine plant meta-community. To this end, we combined recent extensions of the Hill numbers framework with Pagel's phylogenetic tree transformation approach. We included functional (based on the leaf-height-seed spectrum) and phylogenetic facets of beta-diversity in our analysis and explicitly accounted for effects of environmental and spatial covariates. We found that functional beta-diversity, was high when the same weight was given to dominant vs. rare species and to large vs. small species' similarities. In contrast, phylogenetic beta-diversity was low when greater weight was given to dominant species and small species' similarities. Those results suggested that different environments along the gradients filtered different species according to their functional traits, while, the same competitive lineages dominated communities across the gradients. Our results highlight that functional vs. phylogenetic facets, presence-absence vs. abundance structure and different weights of species' dissimilarity provide complementary and important information on the drivers of meta-community structure. By utilizing the full extent of information provided by the flexible frameworks of Hill numbers and Pagel's tree transformation, we propose a new approach to disentangle the patterns resulting from different assembly processes.

Variation in Orthologous Shell-Forming Proteins Contribute to Molluscan Shell Diversity

PubMed Central

Jackson, Daniel J.; Reim, Laurin; Randow, Clemens; Cerveau, Nicolas; Degnan, Bernard M.; Fleck, Claudia

2017-01-01

Abstract Despite the evolutionary success and ancient heritage of the molluscan shell, little is known about the molecular details of its formation, evolutionary origins, or the interactions between the material properties of the shell and its organic constituents. In contrast to this dearth of information, a growing collection of molluscan shell-forming proteomes and transcriptomes suggest they are comprised of both deeply conserved, and lineage specific elements. Analyses of these sequence data sets have suggested that mechanisms such as exon shuffling, gene co-option, and gene family expansion facilitated the rapid evolution of shell-forming proteomes and supported the diversification of this phylum specific structure. In order to further investigate and test these ideas we have examined the molecular features and spatial expression patterns of two shell-forming genes (Lustrin and ML1A2) and coupled these observations with materials properties measurements of shells from a group of closely related gastropods (abalone). We find that the prominent “GS” domain of Lustrin, a domain believed to confer elastomeric properties to the shell, varies significantly in length between the species we investigated. Furthermore, the spatial expression patterns of Lustrin and ML1A2 also vary significantly between species, suggesting that both protein architecture, and the regulation of spatial gene expression patterns, are important drivers of molluscan shell evolution. Variation in these molecular features might relate to certain materials properties of the shells of these species. These insights reveal an important and underappreciated source of variation within shell-forming proteomes that must contribute to the diversity of molluscan shell phenotypes. PMID:28961798

Stronger tests of mechanisms underlying geographic gradients of biodiversity: insights from the dimensionality of biodiversity.

PubMed

Stevens, Richard D; Tello, J Sebastián; Gavilanez, María Mercedes

2013-01-01

Inference involving diversity gradients typically is gathered by mechanistic tests involving single dimensions of biodiversity such as species richness. Nonetheless, because traits such as geographic range size, trophic status or phenotypic characteristics are tied to a particular species, mechanistic effects driving broad diversity patterns should manifest across numerous dimensions of biodiversity. We develop an approach of stronger inference based on numerous dimensions of biodiversity and apply it to evaluate one such putative mechanism: the mid-domain effect (MDE). Species composition of 10,000-km(2) grid cells was determined by overlaying geographic range maps of 133 noctilionoid bat taxa. We determined empirical diversity gradients in the Neotropics by calculating species richness and three indices each of phylogenetic, functional and phenetic diversity for each grid cell. We also created 1,000 simulated gradients of each examined metric of biodiversity based on a MDE model to estimate patterns expected if species distributions were randomly placed within the Neotropics. For each simulation run, we regressed the observed gradient onto the MDE-expected gradient. If a MDE drives empirical gradients, then coefficients of determination from such an analysis should be high, the intercept no different from zero and the slope no different than unity. Species richness gradients predicted by the MDE fit empirical patterns. The MDE produced strong spatially structured gradients of taxonomic, phylogenetic, functional and phenetic diversity. Nonetheless, expected values generated from the MDE for most dimensions of biodiversity exhibited poor fit to most empirical patterns. The MDE cannot account for most empirical patterns of biodiversity. Fuller understanding of latitudinal gradients will come from simultaneous examination of relative effects of random, environmental and historical mechanisms to better understand distribution and abundance of the current biota.

Stronger Tests of Mechanisms Underlying Geographic Gradients of Biodiversity: Insights from the Dimensionality of Biodiversity

PubMed Central

Stevens, Richard D.; Tello, J. Sebastián; Gavilanez, María Mercedes

2013-01-01

Inference involving diversity gradients typically is gathered by mechanistic tests involving single dimensions of biodiversity such as species richness. Nonetheless, because traits such as geographic range size, trophic status or phenotypic characteristics are tied to a particular species, mechanistic effects driving broad diversity patterns should manifest across numerous dimensions of biodiversity. We develop an approach of stronger inference based on numerous dimensions of biodiversity and apply it to evaluate one such putative mechanism: the mid-domain effect (MDE). Species composition of 10,000-km2 grid cells was determined by overlaying geographic range maps of 133 noctilionoid bat taxa. We determined empirical diversity gradients in the Neotropics by calculating species richness and three indices each of phylogenetic, functional and phenetic diversity for each grid cell. We also created 1,000 simulated gradients of each examined metric of biodiversity based on a MDE model to estimate patterns expected if species distributions were randomly placed within the Neotropics. For each simulation run, we regressed the observed gradient onto the MDE-expected gradient. If a MDE drives empirical gradients, then coefficients of determination from such an analysis should be high, the intercept no different from zero and the slope no different than unity. Species richness gradients predicted by the MDE fit empirical patterns. The MDE produced strong spatially structured gradients of taxonomic, phylogenetic, functional and phenetic diversity. Nonetheless, expected values generated from the MDE for most dimensions of biodiversity exhibited poor fit to most empirical patterns. The MDE cannot account for most empirical patterns of biodiversity. Fuller understanding of latitudinal gradients will come from simultaneous examination of relative effects of random, environmental and historical mechanisms to better understand distribution and abundance of the current biota. PMID:23451099

Assessing exotic plant species invasions and associated soil characteristics: A case study in eastern Rocky Mountain National Park, Colorado, USA, using the pixel nested plot design

USGS Publications Warehouse

Kalkhan, M.A.; Stafford, E.J.; Woodly, P.J.; Stohlgren, T.J.

2007-01-01

Rocky Mountain National Park (RMNP), Colorado, USA, contains a diversity of plant species. However, many exotic plant species have become established, potentially impacting the structure and function of native plant communities. Our goal was to quantify patterns of exotic plant species in relation to native plant species, soil characteristics, and other abiotic factors that may indicate or predict their establishment and success. Our research approach for field data collection was based on a field plot design called the pixel nested plot. The pixel nested plot provides a link to multi-phase and multi-scale spatial modeling-mapping techniques that can be used to estimate total species richness and patterns of plant diversity at finer landscape scales. Within the eastern region of RMNP, in an area of approximately 35,000 ha, we established a total of 60 pixel nested plots in 9 vegetation types. We used canonical correspondence analysis (CCA) and multiple linear regressions to quantify relationships between soil characteristics and native and exotic plant species richness and cover. We also used linear correlation, spatial autocorrelation and cross correlation statistics to test for the spatial patterns of variables of interest. CCA showed that exotic species were significantly (P < 0.05) associated with photosynthetically active radiation (r = 0.55), soil nitrogen (r = 0.58) and bare ground (r = -0.66). Pearson's correlation statistic showed significant linear relationships between exotic species, organic carbon, soil nitrogen, and bare ground. While spatial autocorrelations indicated that our 60 pixel nested plots were spatially independent, the cross correlation statistics indicated that exotic plant species were spatially associated with bare ground, in general, exotic plant species were most abundant in areas of high native species richness. This indicates that resource managers should focus on the protection of relatively rare native rich sites with little canopy cover, and fertile soils. Using the pixel nested plot approach for data collection can facilitate the ecological monitoring of these vulnerable areas at the landscape scale in a time- and cost-effective manner. ?? 2006 Elsevier B.V. All rights reserved.

Selective extinction drives taxonomic and functional alpha and beta diversities in island bird assemblages.

PubMed

Si, Xingfeng; Baselga, Andrés; Leprieur, Fabien; Song, Xiao; Ding, Ping

2016-03-01

Taxonomic diversity considers all species being equally different from each other and thus disregards species' different ecological functions. Exploring taxonomic and functional aspects of biodiversity simultaneously can better understand the processes of community assembly. We analysed taxonomic and functional alpha and beta diversities of breeding bird assemblages on land-bridge islands in the Thousand Island Lake, China. Given the high dispersal ability of most birds at this spatial scale (several kilometres), we predicted (i) selective extinction driving alpha and beta diversities after the creation of land-bridge islands of varying area and (ii) low taxonomic and functional beta diversities that were not correlated to spatial distance. Breeding birds were surveyed on 37 islands annually from 2007 to 2014. We decomposed beta diversity of breeding birds into spatial turnover and nestedness-resultant components, and related taxonomic and functional diversities to island area and isolation using power regression models (for alpha diversity) and multiple regression models on distance matrices (for beta diversity). We then ran simulations to assess the strength of the correlations between taxonomic and functional diversities. Results revealed that both taxonomic and functional alpha diversities increased with island area. The taxonomic nestedness-resultant and turnover components increased and decreased with difference in area, respectively, but functional counterparts did not. Isolation played a minor role in explaining alpha- and beta-diversity patterns. By partitioning beta diversity, we found low levels of overall taxonomic and functional beta diversities. The functional nestedness-resultant component dominated overall functional beta diversity, whereas taxonomic turnover was the dominant component for taxonomic beta diversity. The simulation showed that functional alpha and beta diversities were significantly correlated with taxonomic diversities, and the observed values of correlations were significantly different from null expectations of random extinction. Our assessment of island bird assemblages validated the predictions of no distance effects and low beta diversity due to pervasive dispersal events among islands and also suggested that selective extinction drives taxonomic and functional alpha and beta diversities. The contrasting turnover and nestedness-resultant components of taxonomic and functional beta diversities demonstrate the importance of considering the multifaceted nature of biodiversity when examining community assembly. © 2015 The Authors. Journal of Animal Ecology © 2015 British Ecological Society.

Divergent and nonuniform gene expression patterns in mouse brain

PubMed Central

Morris, John A.; Royall, Joshua J.; Bertagnolli, Darren; Boe, Andrew F.; Burnell, Josh J.; Byrnes, Emi J.; Copeland, Cathy; Desta, Tsega; Fischer, Shanna R.; Goldy, Jeff; Glattfelder, Katie J.; Kidney, Jolene M.; Lemon, Tracy; Orta, Geralyn J.; Parry, Sheana E.; Pathak, Sayan D.; Pearson, Owen C.; Reding, Melissa; Shapouri, Sheila; Smith, Kimberly A.; Soden, Chad; Solan, Beth M.; Weller, John; Takahashi, Joseph S.; Overly, Caroline C.; Lein, Ed S.; Hawrylycz, Michael J.; Hohmann, John G.; Jones, Allan R.

2010-01-01

Considerable progress has been made in understanding variations in gene sequence and expression level associated with phenotype, yet how genetic diversity translates into complex phenotypic differences remains poorly understood. Here, we examine the relationship between genetic background and spatial patterns of gene expression across seven strains of mice, providing the most extensive cellular-resolution comparative analysis of gene expression in the mammalian brain to date. Using comprehensive brainwide anatomic coverage (more than 200 brain regions), we applied in situ hybridization to analyze the spatial expression patterns of 49 genes encoding well-known pharmaceutical drug targets. Remarkably, over 50% of the genes examined showed interstrain expression variation. In addition, the variability was nonuniformly distributed across strain and neuroanatomic region, suggesting certain organizing principles. First, the degree of expression variance among strains mirrors genealogic relationships. Second, expression pattern differences were concentrated in higher-order brain regions such as the cortex and hippocampus. Divergence in gene expression patterns across the brain could contribute significantly to variations in behavior and responses to neuroactive drugs in laboratory mouse strains and may help to explain individual differences in human responsiveness to neuroactive drugs. PMID:20956311

Greater diversity of soil fungal communities and distinguishable seasonal variation in temperate deciduous forests compared with subtropical evergreen forests of eastern China.

PubMed

He, Jinhong; Tedersoo, Leho; Hu, Ang; Han, Conghai; He, Dan; Wei, Hui; Jiao, Min; Anslan, Sten; Nie, Yanxia; Jia, Yongxia; Zhang, Gengxin; Yu, Guirui; Liu, Shirong; Shen, Weijun

2017-07-01

Whether and how seasonality of environmental variables impacts the spatial variability of soil fungal communities remain poorly understood. We assessed soil fungal diversity and community composition of five Chinese zonal forests along a latitudinal gradient spanning 23°N to 42°N in three seasons to address these questions. We found that soil fungal diversity increased linearly or parabolically with latitude. The seasonal variations in fungal diversity were more distinguishable in three temperate deciduous forests than in two subtropical evergreen forests. Soil fungal diversity was mainly correlated with edaphic factors such as pH and nutrient contents. Both latitude and its interactions with season also imposed significant impacts on soil fungal community composition (FCC), but the effects of latitude were stronger than those of season. Vegetational properties such as plant diversity and forest age were the dominant factors affecting FCC in the subtropical evergreen forests while edaphic properties were the dominant ones in the temperate deciduous forests. Our results indicate that latitudinal variation patterns of soil fungal diversity and FCC may differ among seasons. The stronger effect of latitude relative to that of season suggests a more important influence by the spatial than temporal heterogeneity in shaping soil fungal communities across zonal forests. © FEMS 2017. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Anthropogenic disturbance homogenizes seagrass fish communities.

PubMed

Iacarella, Josephine C; Adamczyk, Emily; Bowen, Dan; Chalifour, Lia; Eger, Aaron; Heath, William; Helms, Sibylla; Hessing-Lewis, Margot; Hunt, Brian P V; MacInnis, Andrew; O'Connor, Mary I; Robinson, Clifford L K; Yakimishyn, Jennifer; Baum, Julia K

2018-05-01

Anthropogenic activities have led to the biotic homogenization of many ecological communities, yet in coastal systems this phenomenon remains understudied. In particular, activities that locally affect marine habitat-forming foundation species may perturb habitat and promote species with generalist, opportunistic traits, in turn affecting spatial patterns of biodiversity. Here, we quantified fish diversity in seagrass communities across 89 sites spanning 6° latitude along the Pacific coast of Canada, to test the hypothesis that anthropogenic disturbances homogenize (i.e., lower beta-diversity) assemblages within coastal ecosystems. We test for patterns of biotic homogenization at sites within different anthropogenic disturbance categories (low, medium, and high) at two spatial scales (within and across regions) using both abundance- and incidence-based beta-diversity metrics. Our models provide clear evidence that fish communities in high anthropogenic disturbance seagrass areas are homogenized relative to those in low disturbance areas. These results were consistent across within-region comparisons using abundance- and incidence-based measures of beta-diversity, and in across-region comparisons using incidence-based measures. Physical and biotic characteristics of seagrass meadows also influenced fish beta-diversity. Biotic habitat characteristics including seagrass biomass and shoot density were more differentiated among high disturbance sites, potentially indicative of a perturbed environment. Indicator species and trait analyses revealed fishes associated with low disturbance sites had characteristics including stenotopy, lower swimming ability, and egg guarding behavior. Our study is the first to show biotic homogenization of fishes across seagrass meadows within areas of relatively high human impact. These results support the importance of targeting conservation efforts in low anthropogenic disturbance areas across land- and seascapes, as well as managing anthropogenic impacts in high activity areas. © 2018 John Wiley & Sons Ltd.

Managed forest landscape structure and avian species richness in the southeastern US

Treesearch

Craig Loehle; T. Bently Wigley; Scott Rutzmoser; John A. Gerwin; Patrick D. Keyser; Richard A. Lancia; Christopher J. Reynolds; Ronald E. Thill; Robert Weih; Don White; Petra Bohall Wood

2005-01-01

Forest structural features at the stand scale (e.g., snags, stem density, species composition) and habitat attributes at larger spatial scales (e.g., landscape pattern, road density) can influence biological diversity and have been proposed as indicators in sustainable forestry programs. This study investigated relationships between such factors and total richness of...

An overview of the floristic richness and conservation of the arid regions of northern Mexico

Treesearch

Laura Arriaga; Elizabeth Moreno; Claudia Aguilar

2005-01-01

The arid and semiarid regions of Northern Mexico harbor diverse, highly endemic, and geographically complex ecosystems. These share topographic and biogeographic similarities that can be used as an analytical framework to assess biodiversity patterns. This study presents the current status of vascular plant inventories for Mexican Aridamerica. The spatial distribution...

Climate change and the future of freshwater fisheries

Treesearch

Daniel J. Isaak

2014-01-01

My first awareness of the importance that climate has for fish came during my summer field seasons as a Ph.D. student at the University of Wyoming. While conducting electrofishing surveys in the climatically diverse Salt River basin along the mountainous border between Wyoming and Idaho, I observed spatial patterns in species distributions and abundance that strongly...

Can a linguistic serial founder effect originating in Africa explain the worldwide phonemic cline?

PubMed Central

2016-01-01

It has been proposed that a serial founder effect could have caused the present observed pattern of global phonemic diversity. Here we present a model that simulates the human range expansion out of Africa and the subsequent spatial linguistic dynamics until today. It does not assume copying errors, Darwinian competition, reduced contrastive possibilities or any other specific linguistic mechanism. We show that the decrease of linguistic diversity with distance (from the presumed origin of the expansion) arises under three assumptions, previously introduced by other authors: (i) an accumulation rate for phonemes; (ii) small phonemic inventories for the languages spoken before the out-of-Africa dispersal; (iii) an increase in the phonemic accumulation rate with the number of speakers per unit area. Numerical simulations show that the predictions of the model agree with the observed decrease of linguistic diversity with increasing distance from the most likely origin of the out-of-Africa dispersal. Thus, the proposal that a serial founder effect could have caused the present observed pattern of global phonemic diversity is viable, if three strong assumptions are satisfied. PMID:27122180

Interaction of Soil Heavy Metal Pollution with Industrialisation and the Landscape Pattern in Taiyuan City, China

PubMed Central

Liu, Yong; Su, Chao; Zhang, Hong; Li, Xiaoting; Pei, Jingfei

2014-01-01

Many studies indicated that industrialization and urbanization caused serious soil heavy metal pollution from industrialized age. However, fewer previous studies have conducted a combined analysis of the landscape pattern, urbanization, industrialization, and heavy metal pollution. This paper was aimed at exploring the relationships of heavy metals in the soil (Pb, Cu, Ni, As, Cd, Cr, Hg, and Zn) with landscape pattern, industrialisation, urbanisation in Taiyuan city using multivariate analysis. The multivariate analysis included correlation analysis, analysis of variance (ANOVA), independent-sample T test, and principal component analysis (PCA). Geographic information system (GIS) was also applied to determine the spatial distribution of the heavy metals. The spatial distribution maps showed that the heavy metal pollution of the soil was more serious in the centre of the study area. The results of the multivariate analysis indicated that the correlations among heavy metals were significant, and industrialisation could significantly affect the concentrations of some heavy metals. Landscape diversity showed a significant negative correlation with the heavy metal concentrations. The PCA showed that a two-factor model for heavy metal pollution, industrialisation, and the landscape pattern could effectively demonstrate the relationships between these variables. The model explained 86.71% of the total variance of the data. Moreover, the first factor was mainly loaded with the comprehensive pollution index (P), and the second factor was primarily loaded with landscape diversity and dominance (H and D). An ordination of 80 samples could show the pollution pattern of all the samples. The results revealed that local industrialisation caused heavy metal pollution of the soil, but such pollution could respond negatively to the landscape pattern. The results of the study could provide a basis for agricultural, suburban, and urban planning. PMID:25251460

Interaction of soil heavy metal pollution with industrialisation and the landscape pattern in Taiyuan city, China.

PubMed

Liu, Yong; Su, Chao; Zhang, Hong; Li, Xiaoting; Pei, Jingfei

2014-01-01

Many studies indicated that industrialization and urbanization caused serious soil heavy metal pollution from industrialized age. However, fewer previous studies have conducted a combined analysis of the landscape pattern, urbanization, industrialization, and heavy metal pollution. This paper was aimed at exploring the relationships of heavy metals in the soil (Pb, Cu, Ni, As, Cd, Cr, Hg, and Zn) with landscape pattern, industrialisation, urbanisation in Taiyuan city using multivariate analysis. The multivariate analysis included correlation analysis, analysis of variance (ANOVA), independent-sample T test, and principal component analysis (PCA). Geographic information system (GIS) was also applied to determine the spatial distribution of the heavy metals. The spatial distribution maps showed that the heavy metal pollution of the soil was more serious in the centre of the study area. The results of the multivariate analysis indicated that the correlations among heavy metals were significant, and industrialisation could significantly affect the concentrations of some heavy metals. Landscape diversity showed a significant negative correlation with the heavy metal concentrations. The PCA showed that a two-factor model for heavy metal pollution, industrialisation, and the landscape pattern could effectively demonstrate the relationships between these variables. The model explained 86.71% of the total variance of the data. Moreover, the first factor was mainly loaded with the comprehensive pollution index (P), and the second factor was primarily loaded with landscape diversity and dominance (H and D). An ordination of 80 samples could show the pollution pattern of all the samples. The results revealed that local industrialisation caused heavy metal pollution of the soil, but such pollution could respond negatively to the landscape pattern. The results of the study could provide a basis for agricultural, suburban, and urban planning.

Contrasting spatial patterns in active-fire and fire-suppressed Mediterranean climate old-growth mixed conifer forests.

PubMed

Fry, Danny L; Stephens, Scott L; Collins, Brandon M; North, Malcolm P; Franco-Vizcaíno, Ernesto; Gill, Samantha J

2014-01-01

In Mediterranean environments in western North America, historic fire regimes in frequent-fire conifer forests are highly variable both temporally and spatially. This complexity influenced forest structure and spatial patterns, but some of this diversity has been lost due to anthropogenic disruption of ecosystem processes, including fire. Information from reference forest sites can help management efforts to restore forests conditions that may be more resilient to future changes in disturbance regimes and climate. In this study, we characterize tree spatial patterns using four-ha stem maps from four old-growth, Jeffrey pine-mixed conifer forests, two with active-fire regimes in northwestern Mexico and two that experienced fire exclusion in the southern Sierra Nevada. Most of the trees were in patches, averaging six to 11 trees per patch at 0.007 to 0.014 ha(-1), and occupied 27-46% of the study areas. Average canopy gap sizes (0.04 ha) covering 11-20% of the area were not significantly different among sites. The putative main effects of fire exclusion were higher densities of single trees in smaller size classes, larger proportion of trees (≥ 56%) in large patches (≥ 10 trees), and decreases in spatial complexity. While a homogenization of forest structure has been a typical result from fire exclusion, some similarities in patch, single tree, and gap attributes were maintained at these sites. These within-stand descriptions provide spatially relevant benchmarks from which to manage for structural heterogeneity in frequent-fire forest types.

Environmental correlates of plant diversity in Korean temperate forests

NASA Astrophysics Data System (ADS)

Černý, Tomáš; Doležal, Jiří; Janeček, Štěpán; Šrůtek, Miroslav; Valachovič, Milan; Petřík, Petr; Altman, Jan; Bartoš, Michael; Song, Jong-Suk

2013-02-01

Mountainous areas of the Korean Peninsula are among the biodiversity hotspots of the world's temperate forests. Understanding patterns in spatial distribution of their species richness requires explicit consideration of different environmental drivers and their effects on functionally differing components. In this study, we assess the impact of both geographical and soil variables on the fine-scale (400 m2) pattern of plant diversity using field data from six national parks, spanning a 1300 m altitudinal gradient. Species richness and the slopes of species-area curves were calculated separately for the tree, shrub and herb layer and used as response variables in regression tree analyses. A cluster analysis distinguished three dominant forest communities with specific patterns in the diversity-environment relationship. The most widespread middle-altitude oak forests had the highest tree richness but the lowest richness of herbaceous plants due to a dense bamboo understory. Total richness was positively associated with soil reaction and negatively associated with soluble phosphorus and solar radiation (site dryness). Tree richness was associated mainly with soil factors, although trees are frequently assumed to be controlled mainly by factors with large-scale impact. A U-shaped relationship was found between herbaceous plant richness and altitude, caused by a distribution pattern of dwarf bamboo in understory. No correlation between the degree of canopy openness and herb layer richness was detected. Slopes of the species-area curves indicated the various origins of forest communities. Variable diversity-environment responses in different layers and communities reinforce the necessity of context-dependent differentiation for the assessment of impacts of climate and land-use changes in these diverse but intensively exploited regions.

Parametric scaling from species to growth-form diversity: an interesting analogy with multifractal functions.

PubMed

Ricotta, Carlo; Pacini, Alessandra; Avena, Giancarlo

2002-01-01

We propose a measure of divergence from species to life-form diversity aimed at summarizing the ecological similarity among different plant communities without losing information on traditional taxonomic diversity. First, species and life-form relative abundances within a given plant community are determined. Next, using Rényi's generalized entropy, the diversity profiles of the analyzed community are computed both from species and life-form relative abundances. Finally, the speed of decrease from species to life-form diversity is obtained by combining the outcome of both profiles. Interestingly, the proposed measure shows some formal analogies with multifractal functions developed in statistical physics for the analysis of spatial patterns. As an application for demonstration, a small data set from a plant community sampled in the archaeological site of Paestum (southern Italy) is used.

Distribution of Escherichia coli in a coastal lagoon (Venice, Italy): Temporal patterns, genetic diversity and the role of tidal forcing.

PubMed

Perini, L; Quero, G M; García, E Serrano; Luna, G M

2015-12-15

Despite its worldwide importance as fecal indicator in aquatic systems, little is known about the diversity of Escherichia coli in the environment and the factors driving its spatial distribution. The city of Venice (Italy), lying at the forefront of a large European lagoon, is an ideal site to study the mechanisms driving the fate of fecal bacteria, due to the huge fluxes of tourists, the city's unique architecture (causing poor efficiency of sewages treatment), and the long branching network of canals crossing the city. We summarize the results of a multi-year investigation to study the temporal dynamics of E. coli around the city, describe the population structure (by assigning isolates to their phylogenetic group) and the genotypic diversity, and explore the role of environmental factors in determining its variability. E. coli abundance in water was highly variable, ranging from being undetectable up to 10(4) Colony Forming Units (CFU) per 100 ml. Abundance did not display significant relationships with the water physico-chemical variables. The analysis of the population structure showed the presence of all known phylogroups, including extra-intestinal and potentially pathogenic ones. The genotypic diversity was very high, as likely consequence of the heterogeneous input of fecal bacteria from the city, and showed site-specific patterns. Intensive sampling during the tidal fluctuations highlighted the prominent role of tides, rather than environmental variables, as source of spatial variation, with a more evident influence in water than sediments. These results, the first providing information on the genetic properties, spatial heterogeneity and influence of tides on E. coli populations around Venice, have implications to manage the fecal pollution, and the associated waterborne disease risks, in coastal cities lying in front of lagoons and semi-enclosed basins. Copyright © 2015 Elsevier Ltd. All rights reserved.

Exploring the relation between spatial configuration of buildings and remotely sensed temperatures

NASA Astrophysics Data System (ADS)

Myint, S. W.; Zheng, B.; Kaplan, S.; Huang, H.

2013-12-01

While the relationship between fractional cover of buildings and the UHI has been well studied, relationships of how spatial arrangements (e.g., clustered, dispersed) of buildings influence urban warming are not well understood. Since a diversity of spatial patterns can be observed under the same percentage of buildings cover, it is of great interest and importance to investigate the amount of variation in certain urban thermal feature such as surface temperature that is accounted for by the inclusion of spatial arrangement component. The various spatial arrangements of buildings cover can give rise to different urban thermal behaviors that may not be uncovered with the information of buildings fraction only, but can be captured to some extent using spatial analysis. The goal of this study is to examine how spatial arrangements of buildings influence and shape surface temperature in different urban settings. The study area selected is the Las-Vegas metropolitan area in Nevada, located in the Mojave Desert. An object-oriented approach was used to identify buildings using a Geoeye-1 image acquired on October 12, 2011. A spatial autocorrelation technique (i.e., Moran's I) that can measure spatial pattern (clustered, dispersed) was used to determine spatial configuration of buildings. A daytime temperature layer in degree Celsius, generated from Advanced Spaceborne Thermal Emission and Reflection Radiometer (ASTER) image, was integrated with Moran's I values of building cover and building fractions to achieve the goals set in the study. To avoid uncertainty and properly evaluate if spatial pattern of buildings has an impact on urban warming, the relation between Moran's I values and surface temperatures was observed at different levels according to their fractions (e.g., 0-0.1, 0.5-0.6, 0.9-1). There is a negative correlation exists between spatial pattern of buildings and surface temperatures implying that dispersed building arrangements elevate surface temperatures more severely than clustered buildings. This suggests that more clustered buildings have less impact on the urban heat island (UHI) effect. We conclude that having buildings as clustered as possible can be expected to protect the settlements from increased heat island effects, reduce pollution, and preserve the hydrological systems.

Intracultural diversity in a model of social dynamics

NASA Astrophysics Data System (ADS)

Parravano, A.; Rivera-Ramirez, H.; Cosenza, M. G.

2007-06-01

We study the consequences of introducing individual nonconformity in social interactions, based on Axelrod's model for the dissemination of culture. A constraint on the number of situations in which interaction may take place is introduced in order to lift the unavoidable homogeneity present in the final configurations arising in Axelrod's related models. The inclusion of this constraint leads to the occurrence of complex patterns of intracultural diversity whose statistical properties and spatial distribution are characterized by means of the concepts of cultural affinity and cultural cline. It is found that the relevant quantity that determines the properties of intracultural diversity is given by the fraction of cultural features that characterizes the cultural nonconformity of individuals.

A neutral theory for interpreting correlations between species and genetic diversity in communities.

PubMed

Laroche, Fabien; Jarne, Philippe; Lamy, Thomas; David, Patrice; Massol, Francois

2015-01-01

Spatial patterns of biological diversity have been extensively studied in ecology and population genetics, because they reflect the forces acting on biodiversity. A growing number of studies have found that genetic (within-species) and species diversity can be correlated in space (the so-called species-gene diversity correlation [SGDC]), which suggests that they are controlled by nonindependent processes. Positive SGDCs are generally assumed to arise from parallel responses of genetic and species diversity to variation in site size and connectivity. However, this argument implicitly assumes a neutral model that has yet to be developed. Here, we build such a model to predict SGDC in a metacommunity. We describe how SGDC emerges from competition within sites and variation in connectivity and carrying capacity among sites. We then introduce the formerly ignored mutation process, which affects genetic but not species diversity. When mutation rate is low, our model confirms that variation in the number of migrants among sites creates positive SGDCs. However, when considering high mutation rates, interactions between mutation, migration, and competition can produce negative SGDCs. Neutral processes thus do not always contribute positively to SGDCs. Our approach provides empirical guidelines for interpreting these novel patterns in natura with respect to evolutionary and ecological forces shaping metacommunities.

Environmental heterogeneity predicts species richness of freshwater mollusks in sub-Saharan Africa

NASA Astrophysics Data System (ADS)

Hauffe, T.; Schultheiß, R.; Van Bocxlaer, B.; Prömmel, K.; Albrecht, C.

2016-09-01

Species diversity and how it is structured on a continental scale is influenced by stochastic, ecological, and evolutionary driving forces, but hypotheses on determining factors have been mainly examined for terrestrial and marine organisms. The extant diversity of African freshwater mollusks is in general well assessed to facilitate conservation strategies and because of the medical importance of several taxa as intermediate hosts for tropical parasites. This historical accumulation of knowledge has, however, not resulted in substantial macroecological studies on the spatial distribution of freshwater mollusks. Here, we use continental distribution data and a recently developed method of random and cohesive allocation of species distribution ranges to test the relative importance of various factors in shaping species richness of Bivalvia and Gastropoda. We show that the mid-domain effect, that is, a hump-shaped richness gradient in a geographically bounded system despite the absence of environmental gradients, plays a minor role in determining species richness of freshwater mollusks in sub-Saharan Africa. The western branch of the East African Rift System was included as dispersal barrier in richness models, but these simulation results did not fit observed diversity patterns significantly better than models where this effect was not included, which suggests that the rift has played a more complex role in generating diversity patterns. Present-day precipitation and temperature explain richness patterns better than Eemian climatic condition. Therefore, the availability of water and energy for primary productivity during the past does not influence current species richness patterns much, and observed diversity patterns appear to be in equilibrium with contemporary climate. The availability of surface waters was the best predictor of bivalve and gastropod richness. Our data indicate that habitat diversity causes the observed species-area relationship, and hence, that environmental heterogeneity is a principal driver of freshwater mollusk richness on a continental scale.

Diversity patterns of selected Andean plant groups correspond to topography and habitat dynamics, not orogeny

PubMed Central

Mutke, Jens; Jacobs, Rana; Meyers, Katharina; Henning, Tilo; Weigend, Maximilian

2014-01-01

The tropical Andes are a hotspot of biodiversity, but detailed altitudinal and latitudinal distribution patterns of species are poorly understood. We compare the distribution and diversity patterns of four Andean plant groups on the basis of georeferenced specimen data: the genus Nasa (Loasaceae), the two South American sections of Ribes (sect. Parilla and sect. Andina, Grossulariaceae), and the American clade of Urtica (Urticaceae). In the tropical Andes, these often grow together, especially in (naturally or anthropogenically) disturbed or secondary vegetation at middle to upper elevations. The climatic niches of the tropical groups studied here are relatively similar in temperature and temperature seasonality, but do differ in moisture seasonality. The Amotape–Huancabamba Zone (AHZ) between 3 and 8° S shows a clear diversity peak of overall species richness as well as for narrowly endemic species across the groups studied. For Nasa, we also show a particular diversity of growth forms in the AHZ. This can be interpreted as proxy for a high diversity of ecological niches based on high spatial habitat heterogeneity in this zone. Latitudinal ranges are generally larger toward the margins of overall range of the group. Species number and number of endemic species of our taxa peak at elevations of 2,500–3,500 m in the tropical Andes. Altitudinal diversity patterns correspond well with the altitudinal distribution of slope inclination. We hypothesize that the likelihood and frequency of landslides at steeper slopes translate into temporal habitat heterogeneity. The frequency of landslides may be causally connected to diversification especially for the numerous early colonizing taxa, such as Urtica and annual species of Nasa. In contrast to earlier hypotheses, uplift history is not reflected in the pattern here retrieved, since the AHZ is the area of the most recent Andean uplift. Similarly, a barrier effect of the low-lying Huancabamba depression is not retrieved in our data. PMID:25346750

Spatially Explicit Models to Investigate Geographic Patterns in the Distribution of Forensic STRs: Application to the North-Eastern Mediterranean.

PubMed

Messina, Francesco; Finocchio, Andrea; Akar, Nejat; Loutradis, Aphrodite; Michalodimitrakis, Emmanuel I; Brdicka, Radim; Jodice, Carla; Novelletto, Andrea

2016-01-01

Human forensic STRs used for individual identification have been reported to have little power for inter-population analyses. Several methods have been developed which incorporate information on the spatial distribution of individuals to arrive at a description of the arrangement of diversity. We genotyped at 16 forensic STRs a large population sample obtained from many locations in Italy, Greece and Turkey, i.e. three countries crucial to the understanding of discontinuities at the European/Asian junction and the genetic legacy of ancient migrations, but seldom represented together in previous studies. Using spatial PCA on the full dataset, we detected patterns of population affinities in the area. Additionally, we devised objective criteria to reduce the overall complexity into reduced datasets. Independent spatially explicit methods applied to these latter datasets converged in showing that the extraction of information on long- to medium-range geographical trends and structuring from the overall diversity is possible. All analyses returned the picture of a background clinal variation, with regional discontinuities captured by each of the reduced datasets. Several aspects of our results are confirmed on external STR datasets and replicate those of genome-wide SNP typings. High levels of gene flow were inferred within the main continental areas by coalescent simulations. These results are promising from a microevolutionary perspective, in view of the fast pace at which forensic data are being accumulated for many locales. It is foreseeable that this will allow the exploitation of an invaluable genotypic resource, assembled for other (forensic) purposes, to clarify important aspects in the formation of local gene pools.

Woody Species Diversity in Forest Plantations in a Mountainous Region of Beijing, China: Effects of Sampling Scale and Species Selection

PubMed Central

Zhang, Yuxin; Zhang, Shuang; Ma, Keming; Fu, Bojie; Anand, Madhur

2014-01-01

The role of forest plantations in biodiversity conservation has gained more attention in recent years. However, most work on evaluating the diversity of forest plantations focuses only on one spatial scale; thus, we examined the effects of sampling scale on diversity in forest plantations. We designed a hierarchical sampling strategy to collect data on woody species diversity in planted pine (Pinus tabuliformis Carr.), planted larch (Larix principis-rupprechtii Mayr.), and natural secondary deciduous broadleaf forests in a mountainous region of Beijing, China. Additive diversity partition analysis showed that, compared to natural forests, the planted pine forests had a different woody species diversity partitioning pattern at multi-scales (except the Simpson diversity in the regeneration layer), while the larch plantations did not show multi-scale diversity partitioning patterns that were obviously different from those in the natural secondary broadleaf forest. Compare to the natural secondary broadleaf forests, the effects of planted pine forests on woody species diversity are dependent on the sampling scale and layers selected for analysis. Diversity in the planted larch forest, however, was not significantly different from that in the natural forest for all diversity components at all sampling levels. Our work demonstrated that the species selected for afforestation and the sampling scales selected for data analysis alter the conclusions on the levels of diversity supported by plantations. We suggest that a wide range of scales should be considered in the evaluation of the role of forest plantations on biodiversity conservation. PMID:25545860

Diversity and Distribution Patterns of Cetaceans in the Subtropical Southwestern Atlantic Outer Continental Shelf and Slope

PubMed Central

Di Tullio, Juliana Couto; Gandra, Tiago B. R.; Zerbini, Alexandre N.; Secchi, Eduardo R.

2016-01-01

Temporal and spatial patterns of cetacean diversity and distribution were investigated through eight ship-based surveys carried out during spring and autumn between 2009 and 2014 on the outer continental shelf (~150m) and slope (1500m) off southeastern and southern Brazil (~23°S to ~34°S). The survey area was divided into southeast and south areas according to their oceanographic characteristics. Twenty-one species were observed in 503 sightings. The overall number of species was similar between the two areas, though it was higher in the spring in the south area. Five species were dominant and diversity varied more seasonally than spatially. ANOVA and kernel analyses showed that overall cetacean densities were higher in spring compared to autumn. Physeter macrocephalus, the most frequent species, concentrated throughout the south area at depths over 1000m in both seasons. Despite the overlapped occurrence at a broader scale, small delphinids presented latitudinal and in-offshore gradients as well as seasonal variation in distribution patterns, which could indicate habitat partitioning between some species. Delphinus delphis was only recorded in the south and its density decreased in areas where the presence of Stenella frontalis increased, mainly beyond the 250m isobath. Densities of S. longirostris and S. attenuata increased in lower latitudes and beyond the shelf break. The large delphinids Tursiops truncatus and Globicephala melas formed mixed groups in many occasions and were observed along the study area around depths of 500m. Grampus griseus was twice as frequent in the south area and densities increased in waters deeper than 600m. As expected, densities of both small and large migratory whales were higher during spring, over the continental slope, in the southeast area. The results presented here provided strong evidence on the importance of the outer continental shelf and slope to a diverse community of cetaceans occurring in the subtropical Southwestern Atlantic. PMID:27243455

Diversity and Distribution Patterns of Cetaceans in the Subtropical Southwestern Atlantic Outer Continental Shelf and Slope.

PubMed

Di Tullio, Juliana Couto; Gandra, Tiago B R; Zerbini, Alexandre N; Secchi, Eduardo R

2016-01-01

Temporal and spatial patterns of cetacean diversity and distribution were investigated through eight ship-based surveys carried out during spring and autumn between 2009 and 2014 on the outer continental shelf (~150m) and slope (1500m) off southeastern and southern Brazil (~23°S to ~34°S). The survey area was divided into southeast and south areas according to their oceanographic characteristics. Twenty-one species were observed in 503 sightings. The overall number of species was similar between the two areas, though it was higher in the spring in the south area. Five species were dominant and diversity varied more seasonally than spatially. ANOVA and kernel analyses showed that overall cetacean densities were higher in spring compared to autumn. Physeter macrocephalus, the most frequent species, concentrated throughout the south area at depths over 1000m in both seasons. Despite the overlapped occurrence at a broader scale, small delphinids presented latitudinal and in-offshore gradients as well as seasonal variation in distribution patterns, which could indicate habitat partitioning between some species. Delphinus delphis was only recorded in the south and its density decreased in areas where the presence of Stenella frontalis increased, mainly beyond the 250m isobath. Densities of S. longirostris and S. attenuata increased in lower latitudes and beyond the shelf break. The large delphinids Tursiops truncatus and Globicephala melas formed mixed groups in many occasions and were observed along the study area around depths of 500m. Grampus griseus was twice as frequent in the south area and densities increased in waters deeper than 600m. As expected, densities of both small and large migratory whales were higher during spring, over the continental slope, in the southeast area. The results presented here provided strong evidence on the importance of the outer continental shelf and slope to a diverse community of cetaceans occurring in the subtropical Southwestern Atlantic.

Impacts of transportation routes on landscape diversity: a comparison of different route types and their combined effects.

PubMed

Su, Shiliang; Xiao, Rui; Li, Delong; Hu, Yi'na

2014-03-01

A comparison of different transportation route types and their combined effects on landscape diversity was conducted within Tiaoxi watershed (China) between 1994 and 2005. Buffer analysis and Mann-Kendall's test were used to quantify the relationships between distance from transportation routes (railway, highway, national, and provincial road) and a family of landscape diversity parameters (Simpson's diversity index, Simpson's evenness index, Shannon's diversity index, and Shannon's evenness index). One-way ANOVA was further applied to compare influences from different route types and their combined effects. Five other landscape metrics (patch density, edge density, area-weighted mean shape index, connectance index, and Euclidean nearest neighbor distance) were also calculated to analyze the associations between landscape diversity and landscape pattern characteristics. Results showed that transportation routes exerted significant impacts on landscape diversity. Impact from railway was comparable to that from highway and national road but was more significant than that from provincial road. The spatial influential range of railway and national road was wider than that of highway and provincial road. Combined effects of routes were nonlinear, and impacts from different route types were more complex than those from the same type. The four landscape diversity metrics were comparably effective at the buffer zone scale. In addition, landscape diversity can be alternatively used to indicate fragmentation, connectivity, and isolation at route buffer scale. This study demonstrates an applicable approach to quantitatively characterize the impacts from transportation routes on landscape patterns and has potential to facilitate route network planning.

High-fidelity large area nano-patterning of silicon with femtosecond light sheet

NASA Astrophysics Data System (ADS)

Sidhu, Mehra S.; Munjal, Pooja; Singh, Kamal P.

2018-01-01

We employ a femtosecond light sheet generated by a cylindrical lens to rapidly produce high-fidelity nano-structures over large area on silicon surface. The Fourier analysis of electron microscopy images of the laser-induced surface structures reveals sharp peaks indicating good homogeneity. We observed an emergence of second-order spatial periodicity on increasing the scan speed. Our reliable approach may rapidly nano-pattern curved solid surfaces and tiny objects for diverse potential applications in optical devices, structural coloring, plasmonic substrates and in high-harmonic generation.

Consistent patterns of variation in macrobenthic assemblages and environmental variables over multiple spatial scales using taxonomic and functional approaches.

PubMed

Veiga, Puri; Torres, Ana Catarina; Aneiros, Fernando; Sousa-Pinto, Isabel; Troncoso, Jesús S; Rubal, Marcos

2016-09-01

Spatial variability of environmental factors and macrobenthos, using species and functional groups, was examined over the same scales (100s of cm to >100 km) in intertidal sediments of two transitional water systems. The objectives were to test if functional groups were a good species surrogate and explore the relationship between environmental variables and macrobenthos. Environmental variables, diversity and the multivariate assemblage structure showed the highest variability at the scale of 10s of km. However, abundance was more variable at 10s of m. Consistent patterns were achieved using species and functional groups therefore, these may be a good species surrogate. Total carbon, salinity and silt/clay were the strongest correlated with macrobenthic assemblages. Results are valuable for design and interpretation of future monitoring programs including detection of anthropogenic disturbances in transitional systems and propose improvements in environmental variable sampling to refine the assessment of their relationship with biological data across spatial scales. Copyright © 2016 Elsevier Ltd. All rights reserved.

Surrogate taxa and fossils as reliable proxies of spatial biodiversity patterns in marine benthic communities.

PubMed

Tyler, Carrie L; Kowalewski, Michał

2017-03-15

Rigorous documentation of spatial heterogeneity (β-diversity) in present-day and preindustrial ecosystems is required to assess how marine communities respond to environmental and anthropogenic drivers. However, the overwhelming majority of contemporary and palaeontological assessments have centred on single higher taxa. To evaluate the validity of single taxa as community surrogates and palaeontological proxies, we compared macrobenthic communities and sympatric death assemblages at 52 localities in Onslow Bay (NC, USA). Compositional heterogeneity did not differ significantly across datasets based on live molluscs, live non-molluscs, and all live organisms. Death assemblages were less heterogeneous spatially, likely reflecting homogenization by time-averaging. Nevertheless, live and dead datasets were greater than 80% congruent in pairwise comparisons to the literature estimates of β-diversity in other marine ecosystems, yielded concordant bathymetric gradients, and produced nearly identical ordinations consistently delineating habitats. Congruent estimates from molluscs and non-molluscs suggest that single groups can serve as reliable community proxies. High spatial fidelity of death assemblages supports the emerging paradigm of Conservation Palaeobiology. Integrated analyses of ecological and palaeontological data based on surrogate taxa can quantify anthropogenic changes in marine ecosystems and advance our understanding of spatial and temporal aspects of biodiversity. © 2017 The Author(s).

Taxonomic and functional patterns of macrobenthic communities on a high-Arctic shelf: A case study from the Laptev Sea

NASA Astrophysics Data System (ADS)

Kokarev, V. N.; Vedenin, A. A.; Basin, A. B.; Azovsky, A. I.

2017-11-01

The studies of functional structure of high-Arctic Ecosystems are scarce. We used data on benthic macrofauna from 500-km latitudinal transect in the eastern Laptev Sea, from the Lena delta to the continental shelf break, to describe spatial patterns in species composition, taxonomic and functional structure in relation to environmental factors. Both taxonomy-based approach and Biological Trait analysis yielded similar results and showed general depth-related gradient in benthic diversity and composition. This congruence between taxonomical and functional dimensions of community organization suggests that the same environmental factors (primarily riverine input and regime of sedimentation) have similar effect on both community structure and functioning. BTA also revealed a distinct functional structure of stations situated at the Eastern Lena valley, with dominance of motile, burrowing sub-surface deposit-feeders and absence of sedentary tube-dwelling forms. The overall spatial distribution of benthic assemblages corresponds well to that described there in preceding decades, evidencing the long-term stability of bottom ecosystem. Strong linear relationship between species and traits diversity, however, indicates low functional redundancy, which potentially makes the ecosystem susceptible to a species loss or structural shifts.

Crop monoculture rather than agriculture reduces the spatial turnover of soil bacterial communities at a regional scale.

PubMed

Figuerola, Eva L M; Guerrero, Leandro D; Türkowsky, Dominique; Wall, Luis G; Erijman, Leonardo

2015-03-01

The goal of this study was to investigate the spatial turnover of soil bacterial communities in response to environmental changes introduced by the practices of soybean monoculture or crop rotations, relative to grassland soils. Amplicon sequencing of the 16S rRNA gene was used to analyse bacterial diversity in producer fields through three successive cropping cycles within one and a half years, across a regional scale of the Argentinean Pampas. Unlike local diversity, which was not significantly affected by land use type, agricultural management had a strong influence on β-diversity patterns. Distributions of pairwise distances between all soils samples under soybean monoculture had significantly lower β-diversity and narrower breadth compared with distributions of pairwise distances between soils managed with crop rotation. Interestingly, good agricultural practices had similar degree of β-diversity as natural grasslands. The higher phylogenetic relatedness of bacterial communities in soils under monoculture across the region was likely determined by the observed loss of endemic species, and affected mostly to phyla with low regional diversity, such as Acidobacteria, Verrucomicrobia and the candidates phyla SPAM and WS3. These results suggest that the implementation of good agricultural practices, including crop rotation, may be critical for the long-term conservation of soil biodiversity. © 2014 Society for Applied Microbiology and John Wiley & Sons Ltd.

Population structure and cultural geography of a folktale in Europe

PubMed Central

Ross, Robert M.; Greenhill, Simon J.; Atkinson, Quentin D.

2013-01-01

Despite a burgeoning science of cultural evolution, relatively little work has focused on the population structure of human cultural variation. By contrast, studies in human population genetics use a suite of tools to quantify and analyse spatial and temporal patterns of genetic variation within and between populations. Human genetic diversity can be explained largely as a result of migration and drift giving rise to gradual genetic clines, together with some discontinuities arising from geographical and cultural barriers to gene flow. Here, we adapt theory and methods from population genetics to quantify the influence of geography and ethnolinguistic boundaries on the distribution of 700 variants of a folktale in 31 European ethnolinguistic populations. We find that geographical distance and ethnolinguistic affiliation exert significant independent effects on folktale diversity and that variation between populations supports a clustering concordant with European geography. This pattern of geographical clines and clusters parallels the pattern of human genetic diversity in Europe, although the effects of geographical distance and ethnolinguistic boundaries are stronger for folktales than genes. Our findings highlight the importance of geography and population boundaries in models of human cultural variation and point to key similarities and differences between evolutionary processes operating on human genes and culture. PMID:23390109

Modeling vertebrate diversity in Oregon using satellite imagery

NASA Astrophysics Data System (ADS)

Cablk, Mary Elizabeth

Vertebrate diversity was modeled for the state of Oregon using a parametric approach to regression tree analysis. This exploratory data analysis effectively modeled the non-linear relationships between vertebrate richness and phenology, terrain, and climate. Phenology was derived from time-series NOAA-AVHRR satellite imagery for the year 1992 using two methods: principal component analysis and derivation of EROS data center greenness metrics. These two measures of spatial and temporal vegetation condition incorporated the critical temporal element in this analysis. The first three principal components were shown to contain spatial and temporal information about the landscape and discriminated phenologically distinct regions in Oregon. Principal components 2 and 3, 6 greenness metrics, elevation, slope, aspect, annual precipitation, and annual seasonal temperature difference were investigated as correlates to amphibians, birds, all vertebrates, reptiles, and mammals. Variation explained for each regression tree by taxa were: amphibians (91%), birds (67%), all vertebrates (66%), reptiles (57%), and mammals (55%). Spatial statistics were used to quantify the pattern of each taxa and assess validity of resulting predictions from regression tree models. Regression tree analysis was relatively robust against spatial autocorrelation in the response data and graphical results indicated models were well fit to the data.

[Distribution patterns of canopy and understory tree species at local scale in a Tierra Firme forest, the Colombian Amazonia].

PubMed

Barreto-Silva, Juan Sebastian; López, Dairon Cárdenas; Montoya, Alvaro Javier Duque

2014-03-01

The effect of environmental variation on the structure of tree communities in tropical forests is still under debate. There is evidence that in landscapes like Tierra Firme forest, where the environmental gradient decreases at a local level, the effect of soil on the distribution patterns of plant species is minimal, happens to be random or is due to biological processes. In contrast, in studies with different kinds of plants from tropical forests, a greater effect on floristic composition of varying soil and topography has been reported. To assess this, the current study was carried out in a permanent plot of ten hectares in the Amacayacu National Park, Colombian Amazonia. To run the analysis, floristic and environmental variations were obtained according to tree species abundance categories and growth forms. In order to quantify the role played by both environmental filtering and dispersal limitation, the variation of the spatial configuration was included. We used Detrended Correspondence Analysis and Canonical Correspondence Analysis, followed by a variation partitioning, to analyze the species distribution patterns. The spatial template was evaluated using the Principal Coordinates of Neighbor Matrix method. We recorded 14 074 individuals from 1 053 species and 80 families. The most abundant families were Myristicaceae, Moraceae, Meliaceae, Arecaceae and Lecythidaceae, coinciding with other studies from Northwest Amazonia. Beta diversity was relatively low within the plot. Soils were very poor, had high aluminum concentration and were predominantly clayey. The floristic differences explained along the ten hectares plot were mainly associated to biological processes, such as dispersal limitation. The largest proportion of community variation in our dataset was unexplained by either environmental or spatial data. In conclusion, these results support random processes as the major drivers of the spatial variation of tree species at a local scale on Tierra Firme forests of Amacayacu National Park, and suggest reserve's size as a key element to ensure the conservation of plant diversity at both regional and local levels.

Fish diversity in the Río de la Plata and adjacent waters: an overview of environmental influences on its spatial and temporal structure.

PubMed

Jaureguizar, A J; Solari, A; Cortés, F; Milessi, A C; Militelli, M I; Camiolo, M D; Luz Clara, M; García, M

2016-07-01

The fish diversity and the main environmental factors affecting the spatial distribution of species, life history stages and community structure in the Río de la Plata (RdP) and adjacent waters are reviewed and analysed, with emphasis on the functional guild classification. The functional guild classification indicated that most species in the RdP were marine stragglers, zoobenthivores and oviparous species, although the biomass was dominated by estuarine species. Salinity had a stronger influence than temperature on the spatial pattern for all life stages, shallower and fresher waters are the preferred habitats of neonates and juveniles. During the breeding season (spring-summer), adults showed an intrusion into the inner part of RdP or to its adjacent nearshore waters from the offshore waters for spawning or mating, respectively. Variations in river discharge and wind patterns greatly affected the spatial extent of estuarine water, which ultimately influenced the domain of the main life-history stages (juveniles or adults) for both marine and estuarine fishes, as well as species and fish assemblage composition. The strong environmental gradient restricts some species and life-history stages to a particular section and defines three main fish assemblage areas. The composition of the fish assemblage is indicative of the recruitment of freshwater and marine species to the estuary in opposite ways, determined by the vertical stratification. Seasonal changes in the species composition were related to migration as a result of salinity and temperature variations and reproductive migrations to spawning and mating areas. This overview reveals that the RdP is under environmental variations that are likely to produce modifications to fish distribution and abundance that affect its fisheries. This context plus fish stock declines and changes in exploitation patterns could amplify the magnitude of the variations in the fisheries resources availability and affect the sustainability of fishing communities. © 2016 The Fisheries Society of the British Isles.

Spatial and Temporal Variation of Archaeal, Bacterial and Fungal Communities in Agricultural Soils

PubMed Central

Pereira e Silva, Michele C.; Dias, Armando Cavalcante Franco; van Elsas, Jan Dirk; Salles, Joana Falcão

2012-01-01

Background Soil microbial communities are in constant change at many different temporal and spatial scales. However, the importance of these changes to the turnover of the soil microbial communities has been rarely studied simultaneously in space and time. Methodology/Principal Findings In this study, we explored the temporal and spatial responses of soil bacterial, archaeal and fungal β-diversities to abiotic parameters. Taking into account data from a 3-year sampling period, we analyzed the abundances and community structures of Archaea, Bacteria and Fungi along with key soil chemical parameters. We questioned how these abiotic variables influence the turnover of bacterial, archaeal and fungal communities and how they impact the long-term patterns of changes of the aforementioned soil communities. Interestingly, we found that the bacterial and fungal β-diversities are quite stable over time, whereas archaeal diversity showed significantly higher fluctuations. These fluctuations were reflected in temporal turnover caused by soil management through addition of N-fertilizers. Conclusions Our study showed that management practices applied to agricultural soils might not significantly affect the bacterial and fungal communities, but cause slow and long-term changes in the abundance and structure of the archaeal community. Moreover, the results suggest that, to different extents, abiotic and biotic factors determine the community assembly of archaeal, bacterial and fungal communities. PMID:23284712

Genetic analysis across different spatial scales reveals multiple dispersal mechanisms for the invasive hydrozoan Cordylophora in the Great Lakes.

PubMed

Darling, John A; Folino-Rorem, Nadine C

2009-12-01

Discerning patterns of post-establishment spread by invasive species is critically important for the design of effective management strategies and the development of appropriate theoretical models predicting spatial expansion of introduced populations. The globally invasive colonial hydrozoan Cordylophora produces propagules both sexually and vegetatively and is associated with multiple potential dispersal mechanisms, making it a promising system to investigate complex patterns of population structure generated throughout the course of rapid range expansion. Here, we explore genetic patterns associated with the spread of this taxon within the North American Great Lakes basin. We collected intensively from eight harbours in the Chicago area in order to conduct detailed investigation of local population expansion. In addition, we collected from Lakes Michigan, Erie, and Ontario, as well as Lake Cayuga in the Finger Lakes of upstate New York in order to assess genetic structure on a regional scale. Based on data from eight highly polymorphic microsatellite loci we examined the spatial extent of clonal genotypes, assessed levels of neutral genetic diversity, and explored patterns of migration and dispersal at multiple spatial scales through assessment of population level genetic differentiation (pairwise F(ST) and factorial correspondence analysis), Bayesian inference of population structure, and assignment tests on individual genotypes. Results of these analyses indicate that Cordylophora populations in this region spread predominantly through sexually produced propagules, and that while limited natural larval dispersal can drive expansion locally, regional expansion likely relies on anthropogenic dispersal vectors.

Habitat predictors of genetic diversity for two sympatric wetland-breeding amphibian species.

PubMed

McKee, Anna M; Maerz, John C; Smith, Lora L; Glenn, Travis C

2017-08-01

Population genetic diversity is widely accepted as important to the conservation and management of wildlife. However, habitat features may differentially affect evolutionary processes that facilitate population genetic diversity among sympatric species. We measured genetic diversity for two pond-breeding amphibian species (Dwarf salamanders, Eurycea quadridigitata ; and Southern Leopard frogs, Lithobates sphenocephalus ) to understand how habitat characteristics and spatial scale affect genetic diversity across a landscape. Samples were collected from wetlands on a longleaf pine reserve in Georgia. We genotyped microsatellite loci for both species to assess population structures and determine which habitat features were most closely associated with observed heterozygosity and rarefied allelic richness. Both species exhibited significant population genetic structure; however, structure in Southern Leopard frogs was driven primarily by one outlier site. Dwarf salamander allelic richness was greater at sites with less surrounding road area within 0.5 km and more wetland area within 1.0 and 2.5 km, and heterozygosity was greater at sites with more wetland area within 0.5 km. In contrast, neither measure of Southern Leopard frog genetic diversity was associated with any habitat features at any scale we evaluated. Genetic diversity in the Dwarf salamander was strongly associated with land cover variables up to 2.5 km away from breeding wetlands, and/or results suggest that minimizing roads in wetland buffers may be beneficial to the maintenance of population genetic diversity. This study suggests that patterns of genetic differentiation and genetic diversity have associations with different habitat features across different spatial scales for two syntopic pond-breeding amphibian species.

Understanding the genetic diversity, spatial genetic structure and mating system at the hierarchical levels of fruits and individuals of a continuous Theobroma cacao population from the Brazilian Amazon.

PubMed

Silva, C R S; Albuquerque, P S B; Ervedosa, F R; Mota, J W S; Figueira, A; Sebbenn, A M

2011-06-01

Understanding the mating patterns of populations of tree species is a key component of ex situ genetic conservation. In this study, we analysed the genetic diversity, spatial genetic structure (SGS) and mating system at the hierarchical levels of fruits and individuals as well as pollen dispersal patterns in a continuous population of Theobroma cacao in Pará State, Brazil. A total of 156 individuals in a 0.56 ha plot were mapped and genotyped for nine microsatellite loci. For the mating system analyses, 50 seeds were collected from nine seed trees by sampling five fruits per tree (10 seeds per fruit). Among the 156 individuals, 127 had unique multilocus genotypes, and the remaining were clones. The population was spatially aggregated; it demonstrated a significant SGS up to 15 m that could be attributed primarily to the presence of clones. However, the short seed dispersal distance also contributed to this pattern. Population matings occurred mainly via outcrossing, but selfing was observed in some seed trees, which indicated the presence of individual variation for self-incompatibility. The matings were also correlated, especially within (Ρ(p(m))=0.607) rather than among the fruits (Ρ(p(m))=0.099), which suggested that a small number of pollen donors fertilised each fruit. The paternity analysis suggested a high proportion of pollen migration (61.3%), although within the plot, most of the pollen dispersal encompassed short distances (28 m). The determination of these novel parameters provides the fundamental information required to establish long-term ex situ conservation strategies for this important tropical species.

Variation in Orthologous Shell-Forming Proteins Contribute to Molluscan Shell Diversity.

PubMed

Jackson, Daniel J; Reim, Laurin; Randow, Clemens; Cerveau, Nicolas; Degnan, Bernard M; Fleck, Claudia

2017-11-01

Despite the evolutionary success and ancient heritage of the molluscan shell, little is known about the molecular details of its formation, evolutionary origins, or the interactions between the material properties of the shell and its organic constituents. In contrast to this dearth of information, a growing collection of molluscan shell-forming proteomes and transcriptomes suggest they are comprised of both deeply conserved, and lineage specific elements. Analyses of these sequence data sets have suggested that mechanisms such as exon shuffling, gene co-option, and gene family expansion facilitated the rapid evolution of shell-forming proteomes and supported the diversification of this phylum specific structure. In order to further investigate and test these ideas we have examined the molecular features and spatial expression patterns of two shell-forming genes (Lustrin and ML1A2) and coupled these observations with materials properties measurements of shells from a group of closely related gastropods (abalone). We find that the prominent "GS" domain of Lustrin, a domain believed to confer elastomeric properties to the shell, varies significantly in length between the species we investigated. Furthermore, the spatial expression patterns of Lustrin and ML1A2 also vary significantly between species, suggesting that both protein architecture, and the regulation of spatial gene expression patterns, are important drivers of molluscan shell evolution. Variation in these molecular features might relate to certain materials properties of the shells of these species. These insights reveal an important and underappreciated source of variation within shell-forming proteomes that must contribute to the diversity of molluscan shell phenotypes. © The Author 2017. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

Understanding the genetic diversity, spatial genetic structure and mating system at the hierarchical levels of fruits and individuals of a continuous Theobroma cacao population from the Brazilian Amazon

PubMed Central

Silva, C R S; Albuquerque, P S B; Ervedosa, F R; Mota, J W S; Figueira, A; Sebbenn, A M

2011-01-01

Understanding the mating patterns of populations of tree species is a key component of ex situ genetic conservation. In this study, we analysed the genetic diversity, spatial genetic structure (SGS) and mating system at the hierarchical levels of fruits and individuals as well as pollen dispersal patterns in a continuous population of Theobroma cacao in Pará State, Brazil. A total of 156 individuals in a 0.56 ha plot were mapped and genotyped for nine microsatellite loci. For the mating system analyses, 50 seeds were collected from nine seed trees by sampling five fruits per tree (10 seeds per fruit). Among the 156 individuals, 127 had unique multilocus genotypes, and the remaining were clones. The population was spatially aggregated; it demonstrated a significant SGS up to 15 m that could be attributed primarily to the presence of clones. However, the short seed dispersal distance also contributed to this pattern. Population matings occurred mainly via outcrossing, but selfing was observed in some seed trees, which indicated the presence of individual variation for self-incompatibility. The matings were also correlated, especially within (r̂p(m)=0.607) rather than among the fruits (r̂p(m)=0.099), which suggested that a small number of pollen donors fertilised each fruit. The paternity analysis suggested a high proportion of pollen migration (61.3%), although within the plot, most of the pollen dispersal encompassed short distances (28 m). The determination of these novel parameters provides the fundamental information required to establish long-term ex situ conservation strategies for this important tropical species. PMID:21139632

[Dynamic evolution of wetland landscape spatial pattern in Nansi Lake, China].

PubMed

Chen, Zhi Cong; Xie, Xiao Ping; Bai, Mao Wei

2016-10-01

Based on Landsat images in 1987, 2002 and 2014 from Nansi Lake located in Shandong Province, landscape pattern index, dynamic index, landscape gradient and gridding model were used for analysis of the wetland distribution in the lake. The results showed that the landscape contagion index and aggregation index gradually decreased from 1987 to 2014, while the landscape diversity index and evenness index gradually increased. The distribution of landscape area was more uniform while its patterns trended to be fragmented. Human activities impacted Nansi wetland distribution and the disturbance presented an increasing trend. The total area of Nansi wetland gradually increased during the study period. The area of lake first decreased then increased, and the area reached the maximum in 2014. The area of the ponds along the riparian zone had increased gradually, but the increasing speed slowed down. The area of the rivers remained stable, while the area of the swamps decreased continually during the period. The change of landscape pattern of Nansi Lake wetland mainly resulted from agricultural activities, establishment of Nansi Lake Natural Reserve, and the South-to-North Water Diversion Project.

Diversity patterns and activity of uncultured marine heterotrophic flagellates unveiled with pyrosequencing

PubMed Central

Logares, Ramiro; Audic, Stephane; Santini, Sebastien; Pernice, Massimo C; de Vargas, Colomban; Massana, Ramon

2012-01-01

Flagellated heterotrophic microeukaryotes have key roles for the functioning of marine ecosystems as they channel large amounts of organic carbon to the upper trophic levels and control the population sizes of bacteria and archaea. Still, we know very little on the diversity patterns of most groups constituting this evolutionary heterogeneous assemblage. Here, we investigate 11 groups of uncultured flagellates known as MArine STramenopiles (MASTs). MASTs are ecologically very important and branch at the base of stramenopiles. We explored the diversity patterns of MASTs using pyrosequencing (18S rDNA) in coastal European waters. We found that MAST groups range from highly to lowly diversified. Pyrosequencing (hereafter ‘454') allowed us to approach to the limits of taxonomic diversity for all MAST groups, which varied in one order of magnitude (tens to hundreds) in terms of operational taxonomic units (98% similarity). We did not evidence large differences in activity, as indicated by ratios of DNA:RNA-reads. Most groups were strictly planktonic, although we found some groups that were active in sediments and even in anoxic waters. The proportion of reads per size fraction indicated that most groups were composed of very small cells (∼2–5 μm). In addition, phylogenetically different assemblages appeared to be present in different size fractions, depths and geographic zones. Thus, MAST diversity seems to be highly partitioned in spatial scales. Altogether, our results shed light on these ecologically very important but poorly known groups of uncultured marine flagellates. PMID:22534609

The effects of biome and spatial scale on the Co-occurrence patterns of a group of Namibian beetles

NASA Astrophysics Data System (ADS)

Pitzalis, Monica; Montalto, Francesca; Amore, Valentina; Luiselli, Luca; Bologna, Marco A.

2017-08-01

Co-occurrence patterns (studied by C-score, number of checkerboard units, number of species combinations, and V-ratio, and by an empirical Bayes approach developed by Gotelli and Ulrich, 2010) are crucial elements in order to understand assembly rules in ecological communities at both local and spatial scales. In order to explore general assembly rules and the effects of biome and spatial scale on such rules, here we studied a group of beetles (Coleoptera, Meloidae), using Namibia as a case of study. Data were gathered from 186 sampling sites, which allowed collection of 74 different species. We analyzed data at the level of (i) all sampled sites, (ii) all sites stratified by biome (Savannah, Succulent Karoo, Nama Karoo, Desert), and (iii) three randomly selected nested areas with three spatial scales each. Three competing algorithms were used for all analyses: (i) Fixed-Equiprobable, (ii) Fixed-Fixed, and (iii) Fixed-Proportional. In most of the null models we created, co-occurrence indicators revealed a non-random structure in meloid beetle assemblages at the global scale and at the scale of biomes, with species aggregation being much more important than species segregation in determining this non-randomness. At the level of biome, the same non-random organization was uncovered in assemblages from Savannah (where the aggregation pattern was particularly strong) and Succulent Karoo, but not in Desert and Nama Karoo. We conclude that species facilitation and similar niche in endemic species pairs may be particularly important as community drivers in our case of study. This pattern is also consistent with the evidence of a higher species diversity (normalized according to biome surface area) in the two former biomes. Historical patterns were perhaps also important for Succulent Karoo assemblages. Spatial scale had a reduced effect on patterning our data. This is consistent with the general homogeneity of environmental conditions over wide areas in Namibia.

Population genomic analysis suggests strong influence of river network on spatial distribution of genetic variation in invasive saltcedar across the southwestern United States

USGS Publications Warehouse

Lee, Soo-Rang; Jo, Yeong-Seok; Park, Chan-Ho; Friedman, Jonathan M.; Olson, Matthew S.

2018-01-01

Understanding the complex influences of landscape and anthropogenic elements that shape the population genetic structure of invasive species provides insight into patterns of colonization and spread. The application of landscape genomics techniques to these questions may offer detailed, previously undocumented insights into factors influencing species invasions. We investigated the spatial pattern of genetic variation and the influences of landscape factors on population similarity in an invasive riparian shrub, saltcedar (Tamarix L.) by analysing 1,997 genomewide SNP markers for 259 individuals from 25 populations collected throughout the southwestern United States. Our results revealed a broad-scale spatial genetic differentiation of saltcedar populations between the Colorado and Rio Grande river basins and identified potential barriers to population similarity along both river systems. River pathways most strongly contributed to population similarity. In contrast, low temperature and dams likely served as barriers to population similarity. We hypothesize that large-scale geographic patterns in genetic diversity resulted from a combination of early introductions from distinct populations, the subsequent influence of natural selection, dispersal barriers and founder effects during range expansion.

Additive diversity partitioning of fish in a Caribbean coral reef undergoing shift transition.

PubMed

Acosta-González, Gilberto; Rodríguez-Zaragoza, Fabián A; Hernández-Landa, Roberto C; Arias-González, Jesús E

2013-01-01

Shift transitions in dominance on coral reefs from hard coral cover to fleshy macroalgae are having negative effects on Caribbean coral reef communities. Data on spatiotemporal changes in biodiversity during these modifications are important for decision support for coral reef biodiversity protection. The main objective of this study is to detect the spatiotemporal patterns of coral reef fish diversity during this transition using additive diversity-partitioning analysis. We examined α, β and γ fish diversity from 2000 to 2010, during which time a shift transition occurred at Mahahual Reef, located in Quintana Roo, Mexico. Data on coral reef fish and benthic communities were obtained from 12 transects per geomorphological unit (GU) in two GUs (reef slope and terrace) over six years (2000, 2005, 2006, 2007, 2008, 2010). Spatial analysis within and between the GUs indicated that the γ-diversity was primarily related to higher β-diversity. Throughout the six study years, there were losses of α, β and γ-diversity associated spatially with the shallow (reef slope) and deeper (reef terrace) GUs and temporally with the transition in cover from mound corals to fleshy macroalgae and boulder corals. Despite a drastic reduction in the number of species over time, β-diversity continues to be the highest component of γ-diversity. The shift transition had a negative effect on α, β and γ-diversity, primarily by impacting rare species, leading a group of small and less vulnerable fish species to become common and an important group of rare species to become locally extinct. The maintenance of fish heterogeneity (β-diversity) over time may imply the abetment of vulnerability in the face of local and global changes.

Temporal and spatial variability in thalweg profiles of a gravel-bed river

USGS Publications Warehouse

Madej, Mary Ann

1999-01-01

This study used successive longitudinal thalweg profiles in gravel-bed rivers to monitor changes in bed topography following floods and associated large sediment inputs. Variations in channel bed elevations, distributions of residual water depths, percentage of channel length occupied by riffles, and a spatial autocorrelation coefficient (Moran's I) were used to quantify changes in morphological diversity and spatial structure in Redwood Creek basin, northwestern California. Bed topography in Redwood Creek and its major tributaries consists primarily of a series of pools and riffles. The size, frequency and spatial distribution of the pools and riffles have changed significantly during the past 20 years. Following large floods and high sediment input in Redwood Creek and its tributaries in 1975, variation in channel bed elevations was low and the percentage of the channel length occupied by riffles was high. Over the next 20 years, variation in bed elevations increased while the length of channel occupied by riffles decreased. An index [(standard deviation of residual water depth/bankfull depth) × 100] was developed to compare variations in bed elevation over a range of stream sizes, with a higher index being indicative of greater morphological diversity. Spatial autocorrelation in the bed elevation data was apparent at both fine and coarse scales in many of the thalweg profiles and the observed spatial pattern of bed elevations was found to be related to the dominant channel material and the time since disturbance. River reaches in which forced pools dominated, and in which large woody debris and bed particles could not be easily mobilized, exhibited a random distribution of bed elevations. In contrast, in reaches where alternate bars dominated, and both wood and gravel were readily transported, regularly spaced bed topography developed at a spacing that increased with time since disturbance. This pattern of regularly spaced bed features was reversed following a 12-year flood when bed elevations became more randomly arranged.

Spatial phylogenetics of the native California flora.

PubMed

Thornhill, Andrew H; Baldwin, Bruce G; Freyman, William A; Nosratinia, Sonia; Kling, Matthew M; Morueta-Holme, Naia; Madsen, Thomas P; Ackerly, David D; Mishler, Brent D

2017-10-26

California is a world floristic biodiversity hotspot where the terms neo- and paleo-endemism were first applied. Using spatial phylogenetics, it is now possible to evaluate biodiversity from an evolutionary standpoint, including discovering significant areas of neo- and paleo-endemism, by combining spatial information from museum collections and DNA-based phylogenies. Here we used a distributional dataset of 1.39 million herbarium specimens, a phylogeny of 1083 operational taxonomic units (OTUs) and 9 genes, and a spatial randomization test to identify regions of significant phylogenetic diversity, relative phylogenetic diversity, and phylogenetic endemism (PE), as well as to conduct a categorical analysis of neo- and paleo-endemism (CANAPE). We found (1) extensive phylogenetic clustering in the South Coast Ranges, southern Great Valley, and deserts of California; (2) significant concentrations of short branches in the Mojave and Great Basin Deserts and the South Coast Ranges and long branches in the northern Great Valley, Sierra Nevada foothills, and the northwestern and southwestern parts of the state; (3) significant concentrations of paleo-endemism in Northwestern California, the northern Great Valley, and western Sonoran Desert, and neo-endemism in the White-Inyo Range, northern Mojave Desert, and southern Channel Islands. Multiple analyses were run to observe the effects on significance patterns of using different phylogenetic tree topologies (uncalibrated trees versus time-calibrated ultrametric trees) and using different representations of OTU ranges (herbarium specimen locations versus species distribution models). These analyses showed that examining the geographic distributions of branch lengths in a statistical framework adds a new dimension to California floristics that, in comparison with climatic data, helps to illuminate causes of endemism. In particular, the concentration of significant PE in more arid regions of California extends previous ideas about aridity as an evolutionary stimulus. The patterns seen are largely robust to phylogenetic uncertainty and time calibration but are sensitive to the use of occurrence data versus modeled ranges, indicating that special attention toward improving geographic distributional data should be top priority in the future for advancing understanding of spatial patterns of biodiversity.

Characterization of spiraling patterns in spatial rock-paper-scissors games.

PubMed

Szczesny, Bartosz; Mobilia, Mauro; Rucklidge, Alastair M

2014-09-01

The spatiotemporal arrangement of interacting populations often influences the maintenance of species diversity and is a subject of intense research. Here, we study the spatiotemporal patterns arising from the cyclic competition between three species in two dimensions. Inspired by recent experiments, we consider a generic metapopulation model comprising "rock-paper-scissors" interactions via dominance removal and replacement, reproduction, mutations, pair exchange, and hopping of individuals. By combining analytical and numerical methods, we obtain the model's phase diagram near its Hopf bifurcation and quantitatively characterize the properties of the spiraling patterns arising in each phase. The phases characterizing the cyclic competition away from the Hopf bifurcation (at low mutation rate) are also investigated. Our analytical approach relies on the careful analysis of the properties of the complex Ginzburg-Landau equation derived through a controlled (perturbative) multiscale expansion around the model's Hopf bifurcation. Our results allow us to clarify when spatial "rock-paper-scissors" competition leads to stable spiral waves and under which circumstances they are influenced by nonlinear mobility.

Patterns, biases and prospects in the distribution and diversity of Neotropical snakes

PubMed Central

Sawaya, Ricardo J.; Zizka, Alexander; Laffan, Shawn; Faurby, Søren; Pyron, R. Alexander; Bérnils, Renato S.; Jansen, Martin; Passos, Paulo; Prudente, Ana L. C.; Cisneros‐Heredia, Diego F.; Braz, Henrique B.; Nogueira, Cristiano de C.; Antonelli, Alexandre; Meiri, Shai

2017-01-01

Abstract Motivation We generated a novel database of Neotropical snakes (one of the world's richest herpetofauna) combining the most comprehensive, manually compiled distribution dataset with publicly available data. We assess, for the first time, the diversity patterns for all Neotropical snakes as well as sampling density and sampling biases. Main types of variables contained We compiled three databases of species occurrences: a dataset downloaded from the Global Biodiversity Information Facility (GBIF), a verified dataset built through taxonomic work and specialized literature, and a combined dataset comprising a cleaned version of the GBIF dataset merged with the verified dataset. Spatial location and grain Neotropics, Behrmann projection equivalent to 1° × 1°. Time period Specimens housed in museums during the last 150 years. Major taxa studied Squamata: Serpentes. Software format Geographical information system (GIS). Results The combined dataset provides the most comprehensive distribution database for Neotropical snakes to date. It contains 147,515 records for 886 species across 12 families, representing 74% of all species of snakes, spanning 27 countries in the Americas. Species richness and phylogenetic diversity show overall similar patterns. Amazonia is the least sampled Neotropical region, whereas most well‐sampled sites are located near large universities and scientific collections. We provide a list and updated maps of geographical distribution of all snake species surveyed. Main conclusions The biodiversity metrics of Neotropical snakes reflect patterns previously documented for other vertebrates, suggesting that similar factors may determine the diversity of both ectothermic and endothermic animals. We suggest conservation strategies for high‐diversity areas and sampling efforts be directed towards Amazonia and poorly known species. PMID:29398972

Contrasting Spatial Patterns in Active-Fire and Fire-Suppressed Mediterranean Climate Old-Growth Mixed Conifer Forests

PubMed Central

Fry, Danny L.; Stephens, Scott L.; Collins, Brandon M.; North, Malcolm P.; Franco-Vizcaíno, Ernesto; Gill, Samantha J.

2014-01-01

In Mediterranean environments in western North America, historic fire regimes in frequent-fire conifer forests are highly variable both temporally and spatially. This complexity influenced forest structure and spatial patterns, but some of this diversity has been lost due to anthropogenic disruption of ecosystem processes, including fire. Information from reference forest sites can help management efforts to restore forests conditions that may be more resilient to future changes in disturbance regimes and climate. In this study, we characterize tree spatial patterns using four-ha stem maps from four old-growth, Jeffrey pine-mixed conifer forests, two with active-fire regimes in northwestern Mexico and two that experienced fire exclusion in the southern Sierra Nevada. Most of the trees were in patches, averaging six to 11 trees per patch at 0.007 to 0.014 ha−1, and occupied 27–46% of the study areas. Average canopy gap sizes (0.04 ha) covering 11–20% of the area were not significantly different among sites. The putative main effects of fire exclusion were higher densities of single trees in smaller size classes, larger proportion of trees (≥56%) in large patches (≥10 trees), and decreases in spatial complexity. While a homogenization of forest structure has been a typical result from fire exclusion, some similarities in patch, single tree, and gap attributes were maintained at these sites. These within-stand descriptions provide spatially relevant benchmarks from which to manage for structural heterogeneity in frequent-fire forest types. PMID:24586472

Distinct microbial communities in the active and permafrost layers on the Tibetan Plateau.

PubMed

Chen, Yong-Liang; Deng, Ye; Ding, Jin-Zhi; Hu, Hang-Wei; Xu, Tian-Le; Li, Fei; Yang, Gui-Biao; Yang, Yuan-He

2017-12-01

Permafrost represents an important understudied genetic resource. Soil microorganisms play important roles in regulating biogeochemical cycles and maintaining ecosystem function. However, our knowledge of patterns and drivers of permafrost microbial communities is limited over broad geographic scales. Using high-throughput Illumina sequencing, this study compared soil bacterial, archaeal and fungal communities between the active and permafrost layers on the Tibetan Plateau. Our results indicated that microbial alpha diversity was significantly higher in the active layer than in the permafrost layer with the exception of fungal Shannon-Wiener index and Simpson's diversity index, and microbial community structures were significantly different between the two layers. Our results also revealed that environmental factors such as soil fertility (soil organic carbon, dissolved organic carbon and total nitrogen contents) were the primary drivers of the beta diversity of bacterial, archaeal and fungal communities in the active layer. In contrast, environmental variables such as the mean annual precipitation and total phosphorus played dominant roles in driving the microbial beta diversity in the permafrost layer. Spatial distance was important for predicting the bacterial and archaeal beta diversity in both the active and permafrost layers, but not for fungal communities. Collectively, these results demonstrated different driving factors of microbial beta diversity between the active layer and permafrost layer, implying that the drivers of the microbial beta diversity observed in the active layer cannot be used to predict the biogeographic patterns of the microbial beta diversity in the permafrost layer. © 2017 John Wiley & Sons Ltd.

Disturbance Impacts on Thermal Hot Spots and Hot Moments at the Peatland-Atmosphere Interface

NASA Astrophysics Data System (ADS)

Leonard, R. M.; Kettridge, N.; Devito, K. J.; Petrone, R. M.; Mendoza, C. A.; Waddington, J. M.; Krause, S.

2018-01-01

Soil-surface temperature acts as a master variable driving nonlinear terrestrial ecohydrological, biogeochemical, and micrometeorological processes, inducing short-lived or spatially isolated extremes across heterogeneous landscape surfaces. However, subcanopy soil-surface temperatures have been, to date, characterized through isolated, spatially discrete measurements. Using spatially complex forested northern peatlands as an exemplar ecosystem, we explore the high-resolution spatiotemporal thermal behavior of this critical interface and its response to disturbances by using Fiber-Optic Distributed Temperature Sensing. Soil-surface thermal patterning was identified from 1.9 million temperature measurements under undisturbed, trees removed and vascular subcanopy removed conditions. Removing layers of the structurally diverse vegetation canopy not only increased mean temperatures but it shifted the spatial and temporal distribution, range, and longevity of thermal hot spots and hot moments. We argue that linking hot spots and/or hot moments with spatially variable ecosystem processes and feedbacks is key for predicting ecosystem function and resilience.

Competition of tolerant strategies in the spatial public goods game

NASA Astrophysics Data System (ADS)

Szolnoki, Attila; Perc, Matjaž

2016-08-01

Tolerance implies enduring trying circumstances with a fair and objective attitude. To determine whether evolutionary advantages might be stemming from diverse levels of tolerance in a population, we study a spatial public goods game, where in addition to cooperators, defectors, and loners, tolerant players are also present. Depending on the number of defectors within a group, a tolerant player can either cooperate in or abstain from a particular instance of the game. We show that the diversity of tolerance can give rise to synergistic effects, wherein players with a different threshold in terms of the tolerated number of defectors in a group compete most effectively against defection and default abstinence. Such synergistic associations can stabilise states of full cooperation where otherwise defection would dominate. We observe complex pattern formation that gives rise to an intricate phase diagram, where invisible yet stable strategy alliances require outmost care lest they are overlooked. Our results highlight the delicate importance of diversity and tolerance for the provisioning of public goods, and they reveal fascinating subtleties of the spatiotemporal dynamics that is due to the competition of subsystem solutions in structured populations.

DOE Office of Scientific and Technical Information (OSTI.GOV)

O'Brien, Sarah L.; Gibbons, Sean M.; Owens, Sarah M.

Soil microbial communities are essential for ecosystem function, but linking community composition to biogeochemical processes is challenging because of high microbial diversity and large spatial variability of most soil characteristics. We investigated soil bacterial community structure in a switchgrass stand planted on soil with a history of grassland vegetation at high spatial resolution to determine whether biogeographic trends occurred at the centimeter scale. Moreover, we tested whether such heterogeneity, if present, influenced community structure within or among ecosystems. Pronounced heterogeneity was observed at centimeter scales, with abrupt changes in relative abundance of phyla from sample to sample. At the ecosystemmore » scale (> 10 m), however, bacterial community composition and structure were subtly, but significantly, altered by fertilization, with higher alpha diversity in fertilized plots. Moreover, by comparing these data with data from 1772 soils from the Earth Microbiome Project, it was found that 20% diverse globally sourced soil samples, while grassland soils shared approximately 40% of their operational taxonomic units with the current study. By spanning several orders of magnitude, the analysis suggested that extreme patchiness characterized community structure at smaller scales but that coherent patterns emerged at larger length scales.« less

Are hotspots of evolutionary potential adequately protected in southern California?

USGS Publications Warehouse

Vandergast, A.G.; Bohonak, A.J.; Hathaway, S.A.; Boys, J.; Fisher, R.N.

2008-01-01

Reserves are often designed to protect rare habitats, or "typical" exemplars of ecoregions and geomorphic provinces. This approach focuses on current patterns of organismal and ecosystem-level biodiversity, but typically ignores the evolutionary processes that control the gain and loss of biodiversity at these and other levels (e.g., genetic, ecological). In order to include evolutionary processes in conservation planning efforts, their spatial components must first be identified and mapped. We describe a GIS-based approach for explicitly mapping patterns of genetic divergence and diversity for multiple species (a "multi-species genetic landscape"). Using this approach, we analyzed mitochondrial DNA datasets from 21 vertebrate and invertebrate species in southern California to identify areas with common phylogeographic breaks and high intrapopulation diversity. The result is an evolutionary framework for southern California within which patterns of genetic diversity can be analyzed in the context of historical processes, future evolutionary potential and current reserve design. Our multi-species genetic landscapes pinpoint six hotspots where interpopulation genetic divergence is consistently high, five evolutionary hotspots within which genetic connectivity is high, and three hotspots where intrapopulation genetic diversity is high. These 14 hotspots can be grouped into eight geographic areas, of which five largely are unprotected at this time. The multi-species genetic landscape approach may provide an avenue to readily incorporate measures of evolutionary process into GIS-based systematic conservation assessment and land-use planning.

Climate and soil texture influence patterns of forb species richness and composition in big sagebrush plant communities across their spatial extent in the western US

USGS Publications Warehouse

Pennington, Victoria E.; Palmquist, Kyle A.; Bradford, John B.; Lauenroth, William K.

2017-01-01

Article for outlet: Plant Ecology. Abstract: Big sagebrush (Artemisia tridentata Nutt.) plant communities are widespread non-forested drylands in western North American and similar to all shrub steppe ecosystems world-wide are composed of a shrub overstory layer and a forb and graminoid understory layer. Forbs account for the majority of plant species diversity in big sagebrush plant communities and are important for ecosystem function. Few studies have explored the geographic patterns of forb species richness and composition and their relationships with environmental variables in these communities. Our objectives were to examine the small and large-scale spatial patterns in forb species richness and composition and the influence of environmental variables. We sampled forb species richness and composition along transects at 15 field sites in Colorado, Idaho, Montana, Nevada, Oregon, Utah, and Wyoming, built species-area relationships to quantify differences in forb species richness at sites, and used Principal Components Analysis and nonmetric multidimensional scaling to identify relationships among environmental variables and forb species richness and composition. We found that species richness was most strongly correlated with soil texture, while species composition was most related to climate. The combination of climate and soil texture influences water availability, with important consequences for forb species richness and composition, which suggests climate-change induced modification of soil water availability may have important implications for plant species diversity in the future. Our paper is the first to our knowledge to examine forb biodiversity patterns in big sagebrush ecosystems in relation to environmental factors across the big sagebrush region.

Recent advancements in structured-illumination microscopy toward live-cell imaging.

PubMed

Hirano, Yasuhiro; Matsuda, Atsushi; Hiraoka, Yasushi

2015-08-01

Fluorescence microscopy allows us to observe fluorescently labeled molecules in diverse biological processes and organelle structures within living cells. However, the diffraction limit restricts its spatial resolution to about half of its wavelength, limiting the capability of biological observation at the molecular level. Structured-illumination microscopy (SIM), a type of super-resolution microscopy, doubles the spatial resolution in all three dimensions by illuminating the sample with a patterned excitation light, followed by computer reconstruction. SIM uses a relatively low illumination power compared with other methods of super-resolution microscopy and is easily available for multicolor imaging. SIM has great potential for meeting the requirements of live-cell imaging. Recent developments in diverse types of SIM have achieved higher spatial (∼50 nm lateral) and temporal (∼100 Hz) resolutions. Here, we review recent advancements in SIM and discuss its application in noninvasive live-cell imaging. © The Author 2015. Published by Oxford University Press on behalf of The Japanese Society of Microscopy. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

A spatial analysis of health-related resources in three diverse metropolitan areas

PubMed Central

Smiley, Melissa J.; Diez Roux, Ana V.; Brines, Shannon J.; Brown, Daniel G.; Evenson, Kelly R.; Rodriguez, Daniel A.

2010-01-01

Few studies have investigated the spatial clustering of multiple health-related resources. We constructed 0.5-mile kernel densities of resources for census areas in New York City, NY (n=819 block groups), Baltimore, MD (n=737), and Winston-Salem, NC (n=169). Three of the four resource densities (supermarkets/produce stores, retail areas, and recreational facilities) tended to be correlated with each other, whereas park density was less consistently and sometimes negatively correlated with the others. Blacks were more likely to live in block groups with multiple low resource densities. Spatial regression models showed that block groups with higher proportions of black residents tended to have lower supermarket/produce, retail, and recreational facility densities, although these associations did not always achieve statistical significance. A measure that combined local and neighboring block group racial composition was often a stronger predictor of resources than the local measure alone. Overall, our results from three diverse U.S. cities show that health-related resources are not randomly distributed across space and that disadvantage in multiple domains often clusters with residential racial patterning. PMID:20478737

Temporal and spatial distribution characteristics in the natural plague foci of Chinese Mongolian gerbils based on spatial autocorrelation.

PubMed

Du, Hai-Wen; Wang, Yong; Zhuang, Da-Fang; Jiang, Xiao-San

2017-08-07

The nest flea index of Meriones unguiculatus is a critical indicator for the prevention and control of plague, which can be used not only to detect the spatial and temporal distributions of Meriones unguiculatus, but also to reveal its cluster rule. This research detected the temporal and spatial distribution characteristics of the plague natural foci of Mongolian gerbils by body flea index from 2005 to 2014, in order to predict plague outbreaks. Global spatial autocorrelation was used to describe the entire spatial distribution pattern of the body flea index in the natural plague foci of typical Chinese Mongolian gerbils. Cluster and outlier analysis and hot spot analysis were also used to detect the intensity of clusters based on geographic information system methods. The quantity of M. unguiculatus nest fleas in the sentinel surveillance sites from 2005 to 2014 and host density data of the study area from 2005 to 2010 used in this study were provided by Chinese Center for Disease Control and Prevention. The epidemic focus regions of the Mongolian gerbils remain the same as the hot spot regions relating to the body flea index. High clustering areas possess a similar pattern as the distribution pattern of the body flea index indicating that the transmission risk of plague is relatively high. In terms of time series, the area of the epidemic focus gradually increased from 2005 to 2007, declined rapidly in 2008 and 2009, and then decreased slowly and began trending towards stability from 2009 to 2014. For the spatial change, the epidemic focus regions began moving northward from the southwest epidemic focus of the Mongolian gerbils from 2005 to 2007, and then moved from north to south in 2007 and 2008. The body flea index of Chinese gerbil foci reveals significant spatial and temporal aggregation characteristics through the employing of spatial autocorrelation. The diversity of temporary and spatial distribution is mainly affected by seasonal variation, the human activity and natural factors.

Spatial and Temporal Patterns of Throughfall Amounts and Solutes in a Tropical Montane Forest - Comparisons with Findings From Lowland Rain Forests

NASA Astrophysics Data System (ADS)

Zimmermann, A.

2007-05-01

The diverse tree species composition, irregular shaped tree crowns and a multi-layered forest structure affect the redistribution of rainfall in lower montane rain forests. In addition, abundant epiphyte biomass and associated canopy humus influence spatial patterns of throughfall. The spatial variability of throughfall amounts controls spatial patterns of solute concentrations and deposition. Moreover, the living and dead biomass interacts with the rainwater during the passage through the canopy and creates a chemical variability of its own. Since spatial and temporal patterns are intimately linked, the analysis of temporal solute concentration dynamics is an important step to understand the emerging spatial patterns. I hypothesized that: (1) the spatial variability of volumes and chemical composition of throughfall is particularly high compared with other forests because of the high biodiversity and epiphytism, (2) the temporal stability of the spatial pattern is high because of stable structures in the canopy (e.g. large epiphytes) that show only minor changes during the short term observation period, and (3) the element concentrations decrease with increasing rainfall because of exhausting element pools in the canopy. The study area at 1950 m above sea level is located in the south Ecuadorian Andes far away from anthropogenic emission sources and marine influences. Rain and throughfall were collected from August to October 2005 on an event and within-event basis for five precipitation periods and analyzed for pH, K, Na, Ca, Mg, NH4+, Cl-, NO3-, PO43-, TN, TP and TOC. Throughfall amounts and most of the solutes showed a high spatial variability, thereby the variability of H+, K, Ca, Mg, Cl- and NO3- exceeded those from a Brazilian tropical rain forest. The temporal persistence of the spatial patterns was high for throughfall amounts and varied depending on the solute. Highly persistent time stability patterns were detected for K, Mg and TOC concentrations. Time stability patterns of solute deposition were somewhat weaker than for concentrations for most of the solutes. Epiphytes strongly affected time stability patterns in that collectors situated below thick moss mats or arboreal bromeliads were in large part responsible for the extreme persistence with low throughfall amounts and high ion concentrations (H+ showed low concentrations). Rainfall solute concentrations were low compared with a variety of other tropical lowland and montane forest sites and showed a small temporal variability during the study period for both between and within-event dynamics, respectively. Throughfall solute concentrations were more within the range when compared with other sites and showed highly variable within-event dynamics. For most of the solutes, within-event concentrations did not reach low, constant concentrations in later event stages, rather concentrations fluctuated (e.g. Cl-) or increased (e.g. K and TOC). The within-event throughfall solute concentration dynamics in this lower montane rain forest contrast to recent observations from lowland tropical rain forests in Panama and Brazil. The observed within-event patterns are attributed (1) to the influence of epiphytes and associated canopy humus, and (2) to low rainfall intensities.

Holarctic phylogeography of the testate amoeba Hyalosphenia papilio (Amoebozoa: Arcellinida) reveals extensive genetic diversity explained more by environment than dispersal limitation.

PubMed

Heger, Thierry J; Mitchell, Edward A D; Leander, Brian S

2013-10-01

Although free-living protists play essential roles in aquatic and soil ecology, little is known about their diversity and phylogeography, especially in terrestrial ecosystems. We used mitochondrial cytochrome c oxidase subunit 1 (COI) gene sequences to investigate the genetic diversity and phylogeography of the testate amoeba morphospecies Hyalosphenia papilio in 42 Sphagnum (moss)-dominated peatlands in North America, Europe and Asia. Based on ≥1% sequence divergence threshold, our results from single-cell PCRs of 301 individuals revealed 12 different genetic lineages and both the general mixed Yule-coalescent (GMYC) model and the automatic barcode gap discovery (ABGD) methods largely support the hypothesis that these 12 H. papilio lineages correspond to evolutionary independent units (i.e. cryptic species). Our data also showed a high degree of genetic heterogeneity within different geographical regions. Furthermore, we used variation partitioning based on partial redundancy analyses (pRDA) to evaluate the contributions of climate and dispersal limitations on the distribution patterns of the different genetic lineages. The largest fraction of the variation in genetic lineage distribution was attributed to purely climatic factors (21%), followed by the joint effect of spatial and bioclimatic factors (13%), and a purely spatial effect (3%). Therefore, these data suggest that the distribution patterns of H. papilio genetic lineages in the Northern Hemisphere are more influenced by climatic conditions than by dispersal limitations. © 2013 John Wiley & Sons Ltd.

Multiple diseases impact survival of pine species planted in red spine stands harvested in spatially variable retention patterns

Treesearch

M.E. Ostry; M.J. Moore; C.C. Kern; R.C. Venette; B.J. Palik

2012-01-01

Increasing the diversity of species and structure of red pine (Pinus resinosa) is often a management goal in stands simplified by practices such as fire suppression and plantation management in many areas of the Great Lakes Region. One approach to diversification is to convert predominantly even-aged, pure red pine stands to multi-cohort, mixed-...

The Biodiversity of the Mediterranean Sea: Estimates, Patterns, and Threats

PubMed Central

Coll, Marta; Piroddi, Chiara; Steenbeek, Jeroen; Kaschner, Kristin; Ben Rais Lasram, Frida; Aguzzi, Jacopo; Ballesteros, Enric; Bianchi, Carlo Nike; Corbera, Jordi; Dailianis, Thanos; Danovaro, Roberto; Estrada, Marta; Froglia, Carlo; Galil, Bella S.; Gasol, Josep M.; Gertwagen, Ruthy; Gil, João; Guilhaumon, François; Kesner-Reyes, Kathleen; Kitsos, Miltiadis-Spyridon; Koukouras, Athanasios; Lampadariou, Nikolaos; Laxamana, Elijah; López-Fé de la Cuadra, Carlos M.; Lotze, Heike K.; Martin, Daniel; Mouillot, David; Oro, Daniel; Raicevich, Saša; Rius-Barile, Josephine; Saiz-Salinas, Jose Ignacio; San Vicente, Carles; Somot, Samuel; Templado, José; Turon, Xavier; Vafidis, Dimitris; Villanueva, Roger; Voultsiadou, Eleni

2010-01-01

The Mediterranean Sea is a marine biodiversity hot spot. Here we combined an extensive literature analysis with expert opinions to update publicly available estimates of major taxa in this marine ecosystem and to revise and update several species lists. We also assessed overall spatial and temporal patterns of species diversity and identified major changes and threats. Our results listed approximately 17,000 marine species occurring in the Mediterranean Sea. However, our estimates of marine diversity are still incomplete as yet—undescribed species will be added in the future. Diversity for microbes is substantially underestimated, and the deep-sea areas and portions of the southern and eastern region are still poorly known. In addition, the invasion of alien species is a crucial factor that will continue to change the biodiversity of the Mediterranean, mainly in its eastern basin that can spread rapidly northwards and westwards due to the warming of the Mediterranean Sea. Spatial patterns showed a general decrease in biodiversity from northwestern to southeastern regions following a gradient of production, with some exceptions and caution due to gaps in our knowledge of the biota along the southern and eastern rims. Biodiversity was also generally higher in coastal areas and continental shelves, and decreases with depth. Temporal trends indicated that overexploitation and habitat loss have been the main human drivers of historical changes in biodiversity. At present, habitat loss and degradation, followed by fishing impacts, pollution, climate change, eutrophication, and the establishment of alien species are the most important threats and affect the greatest number of taxonomic groups. All these impacts are expected to grow in importance in the future, especially climate change and habitat degradation. The spatial identification of hot spots highlighted the ecological importance of most of the western Mediterranean shelves (and in particular, the Strait of Gibraltar and the adjacent Alboran Sea), western African coast, the Adriatic, and the Aegean Sea, which show high concentrations of endangered, threatened, or vulnerable species. The Levantine Basin, severely impacted by the invasion of species, is endangered as well. This abstract has been translated to other languages (File S1). PMID:20689844

The biodiversity of the Mediterranean Sea: estimates, patterns, and threats.

PubMed

Coll, Marta; Piroddi, Chiara; Steenbeek, Jeroen; Kaschner, Kristin; Ben Rais Lasram, Frida; Aguzzi, Jacopo; Ballesteros, Enric; Bianchi, Carlo Nike; Corbera, Jordi; Dailianis, Thanos; Danovaro, Roberto; Estrada, Marta; Froglia, Carlo; Galil, Bella S; Gasol, Josep M; Gertwagen, Ruthy; Gil, João; Guilhaumon, François; Kesner-Reyes, Kathleen; Kitsos, Miltiadis-Spyridon; Koukouras, Athanasios; Lampadariou, Nikolaos; Laxamana, Elijah; López-Fé de la Cuadra, Carlos M; Lotze, Heike K; Martin, Daniel; Mouillot, David; Oro, Daniel; Raicevich, Sasa; Rius-Barile, Josephine; Saiz-Salinas, Jose Ignacio; San Vicente, Carles; Somot, Samuel; Templado, José; Turon, Xavier; Vafidis, Dimitris; Villanueva, Roger; Voultsiadou, Eleni

2010-08-02

The Mediterranean Sea is a marine biodiversity hot spot. Here we combined an extensive literature analysis with expert opinions to update publicly available estimates of major taxa in this marine ecosystem and to revise and update several species lists. We also assessed overall spatial and temporal patterns of species diversity and identified major changes and threats. Our results listed approximately 17,000 marine species occurring in the Mediterranean Sea. However, our estimates of marine diversity are still incomplete as yet-undescribed species will be added in the future. Diversity for microbes is substantially underestimated, and the deep-sea areas and portions of the southern and eastern region are still poorly known. In addition, the invasion of alien species is a crucial factor that will continue to change the biodiversity of the Mediterranean, mainly in its eastern basin that can spread rapidly northwards and westwards due to the warming of the Mediterranean Sea. Spatial patterns showed a general decrease in biodiversity from northwestern to southeastern regions following a gradient of production, with some exceptions and caution due to gaps in our knowledge of the biota along the southern and eastern rims. Biodiversity was also generally higher in coastal areas and continental shelves, and decreases with depth. Temporal trends indicated that overexploitation and habitat loss have been the main human drivers of historical changes in biodiversity. At present, habitat loss and degradation, followed by fishing impacts, pollution, climate change, eutrophication, and the establishment of alien species are the most important threats and affect the greatest number of taxonomic groups. All these impacts are expected to grow in importance in the future, especially climate change and habitat degradation. The spatial identification of hot spots highlighted the ecological importance of most of the western Mediterranean shelves (and in particular, the Strait of Gibraltar and the adjacent Alboran Sea), western African coast, the Adriatic, and the Aegean Sea, which show high concentrations of endangered, threatened, or vulnerable species. The Levantine Basin, severely impacted by the invasion of species, is endangered as well. This abstract has been translated to other languages (File S1).

Diversity of herbaceous plants and bacterial communities regulates soil resistome across forest biomes.

PubMed

Hu, Hang-Wei; Wang, Jun-Tao; Singh, Brajesh K; Liu, Yu-Rong; Chen, Yong-Liang; Zhang, Yu-Jing; He, Ji-Zheng

2018-04-24

Antibiotic resistance is ancient and prevalent in natural ecosystems and evolved long before the utilization of synthetic antibiotics started, but factors influencing the large-scale distribution patterns of natural antibiotic resistance genes (ARGs) remain largely unknown. Here, a large-scale investigation over 4000 km was performed to profile soil ARGs, plant communities and bacterial communities from 300 quadrats across five forest biomes with minimal human impact. We detected diverse and abundant ARGs in forests, including over 160 genes conferring resistance to eight major categories of antibiotics. The diversity of ARGs was strongly and positively correlated with the diversity of bacteria, herbaceous plants and mobile genetic elements (MGEs). The ARG composition was strongly correlated with the taxonomic structure of bacteria and herbs. Consistent with this strong correlation, structural equation modelling demonstrated that the positive effects of bacterial and herb communities on ARG patterns were maintained even when simultaneously accounting for multiple drivers (climate, spatial predictors and edaphic factors). These findings suggest a paradigm that the interactions between aboveground and belowground communities shape the large-scale distribution of soil resistomes, providing new knowledge for tackling the emerging environmental antibiotic resistance. © 2018 Society for Applied Microbiology and John Wiley & Sons Ltd.

Polychaete richness and abundance enhanced in anthropogenically modified estuaries despite high concentrations of toxic contaminants.

PubMed

Dafforn, Katherine A; Kelaher, Brendan P; Simpson, Stuart L; Coleman, Melinda A; Hutchings, Pat A; Clark, Graeme F; Knott, Nathan A; Doblin, Martina A; Johnston, Emma L

2013-01-01

Ecological communities are increasingly exposed to multiple chemical and physical stressors, but distinguishing anthropogenic impacts from other environmental drivers remains challenging. Rarely are multiple stressors investigated in replicated studies over large spatial scales (>1000 kms) or supported with manipulations that are necessary to interpret ecological patterns. We measured the composition of sediment infaunal communities in relation to anthropogenic and natural stressors at multiple sites within seven estuaries. We observed increases in the richness and abundance of polychaete worms in heavily modified estuaries with severe metal contamination, but no changes in the diversity or abundance of other taxa. Estuaries in which toxic contaminants were elevated also showed evidence of organic enrichment. We hypothesised that the observed response of polychaetes was not a 'positive' response to toxic contamination or a reduction in biotic competition, but due to high levels of nutrients in heavily modified estuaries driving productivity in the water column and enriching the sediment over large spatial scales. We deployed defaunated field-collected sediments from the surveyed estuaries in a small scale experiment, but observed no effects of sediment characteristics (toxic or enriching). Furthermore, invertebrate recruitment instead reflected the low diversity and abundance observed during field surveys of this relatively 'pristine' estuary. This suggests that differences observed in the survey are not a direct consequence of sediment characteristics (even severe metal contamination) but are related to parameters that covary with estuary modification such as enhanced productivity from nutrient inputs and the diversity of the local species pool. This has implications for the interpretation of diversity measures in large-scale monitoring studies in which the observed patterns may be strongly influenced by many factors that covary with anthropogenic modification.

Polychaete Richness and Abundance Enhanced in Anthropogenically Modified Estuaries Despite High Concentrations of Toxic Contaminants

PubMed Central

Dafforn, Katherine A.; Kelaher, Brendan P.; Simpson, Stuart L.; Coleman, Melinda A.; Hutchings, Pat A.; Clark, Graeme F.; Knott, Nathan A.; Doblin, Martina A.; Johnston, Emma L.

2013-01-01

Ecological communities are increasingly exposed to multiple chemical and physical stressors, but distinguishing anthropogenic impacts from other environmental drivers remains challenging. Rarely are multiple stressors investigated in replicated studies over large spatial scales (>1000 kms) or supported with manipulations that are necessary to interpret ecological patterns. We measured the composition of sediment infaunal communities in relation to anthropogenic and natural stressors at multiple sites within seven estuaries. We observed increases in the richness and abundance of polychaete worms in heavily modified estuaries with severe metal contamination, but no changes in the diversity or abundance of other taxa. Estuaries in which toxic contaminants were elevated also showed evidence of organic enrichment. We hypothesised that the observed response of polychaetes was not a ‘positive’ response to toxic contamination or a reduction in biotic competition, but due to high levels of nutrients in heavily modified estuaries driving productivity in the water column and enriching the sediment over large spatial scales. We deployed defaunated field-collected sediments from the surveyed estuaries in a small scale experiment, but observed no effects of sediment characteristics (toxic or enriching). Furthermore, invertebrate recruitment instead reflected the low diversity and abundance observed during field surveys of this relatively ‘pristine’ estuary. This suggests that differences observed in the survey are not a direct consequence of sediment characteristics (even severe metal contamination) but are related to parameters that covary with estuary modification such as enhanced productivity from nutrient inputs and the diversity of the local species pool. This has implications for the interpretation of diversity measures in large-scale monitoring studies in which the observed patterns may be strongly influenced by many factors that covary with anthropogenic modification. PMID:24098816

Spatial structure in the diet of imperial eagles Aquila heliaca in Kazakhstan

USGS Publications Warehouse

Katzner, T.E.; Bragin, E.A.; Knick, S.T.; Smith, A.T.

2006-01-01

We evaluated the relationship between spatial variability in prey and food habits of eastern imperial eagles Aquila heliaca at a 90,000 ha national nature reserve in north-central Kazakhstan. Eagle diet varied greatly within the population and the spatial structure of eagle diet within the population varied according to the scale of measurement. Patterns in dietary response were inconsistent with expectations if either ontogenetic imprinting or competition determined diet choice, but they met expectations if functional response determined diet. Eagles nesting near a high-density prey resource used that resource almost exclusively. In contrast, in locations with no single high-density prey species, eagles' diet was more diverse. Our results demonstrate that spatial structuring of diet of vertebrate predators can provide important insight into the mechanisms that drive dietary decisions. ?? OIKOS.

Disturbance Is an Important Driver of Clonal Richness in Tropical Seagrasses

PubMed Central

McMahon, Kathryn M.; Evans, Richard D.; van Dijk, Kor-jent; Hernawan, Udhi; Kendrick, Gary A.; Lavery, Paul S.; Lowe, Ryan; Puotinen, Marji; Waycott, Michelle

2017-01-01

Clonality is common in many aquatic plant species, including seagrasses, where populations are maintained through a combination of asexual and sexual reproduction. One common measure used to describe the clonal structure of populations is clonal richness. Clonal richness is strongly dependent on the biological characteristics of the species, and how these interact with the environment but can also reflect evolutionary scale processes especially at the edge of species ranges. However, little is known about the spatial patterns and drivers of clonal richness in tropical seagrasses. This study assessed the spatial patterns of clonal richness in meadows of three tropical seagrass species, Thalassia hemprichii, Halodule uninervis, and Halophila ovalis, spanning a range of life-history strategies and spatial scales (2.5–4,711 km) in Indonesia and NW Australia. We further investigated the drivers of clonal richness using general additive mixed models for two of the species, H. uninervis and H. ovalis, over 8° latitude. No significant patterns were observed in clonal richness with latitude, yet disturbance combined with sea surface temperature strongly predicted spatial patterns of clonal richness. Sites with a high probability of cyclone disturbance had low clonal richness, whereas an intermediate probability of cyclone disturbance and the presence of dugong grazing combined with higher sea surface temperatures resulted in higher levels of clonal richness. We propose potential mechanisms for these patterns related to the recruitment and mortality rates of individuals as well as reproductive effort. Under a changing climate, increased severity of tropical cyclones and the decline in populations of mega-grazers have the potential to reduce clonal richness leading to less genetically diverse populations. PMID:29259609

Spatially Explicit Models to Investigate Geographic Patterns in the Distribution of Forensic STRs: Application to the North-Eastern Mediterranean

PubMed Central

Messina, Francesco; Finocchio, Andrea; Akar, Nejat; Loutradis, Aphrodite; Michalodimitrakis, Emmanuel I.; Brdicka, Radim; Jodice, Carla

2016-01-01

Human forensic STRs used for individual identification have been reported to have little power for inter-population analyses. Several methods have been developed which incorporate information on the spatial distribution of individuals to arrive at a description of the arrangement of diversity. We genotyped at 16 forensic STRs a large population sample obtained from many locations in Italy, Greece and Turkey, i.e. three countries crucial to the understanding of discontinuities at the European/Asian junction and the genetic legacy of ancient migrations, but seldom represented together in previous studies. Using spatial PCA on the full dataset, we detected patterns of population affinities in the area. Additionally, we devised objective criteria to reduce the overall complexity into reduced datasets. Independent spatially explicit methods applied to these latter datasets converged in showing that the extraction of information on long- to medium-range geographical trends and structuring from the overall diversity is possible. All analyses returned the picture of a background clinal variation, with regional discontinuities captured by each of the reduced datasets. Several aspects of our results are confirmed on external STR datasets and replicate those of genome-wide SNP typings. High levels of gene flow were inferred within the main continental areas by coalescent simulations. These results are promising from a microevolutionary perspective, in view of the fast pace at which forensic data are being accumulated for many locales. It is foreseeable that this will allow the exploitation of an invaluable genotypic resource, assembled for other (forensic) purposes, to clarify important aspects in the formation of local gene pools. PMID:27898725

Contrasting patterns of connectivity among endemic and widespread fire coral species ( Millepora spp.) in the tropical Southwestern Atlantic

NASA Astrophysics Data System (ADS)

de Souza, Júlia N.; Nunes, Flávia L. D.; Zilberberg, Carla; Sanchez, Juan A.; Migotto, Alvaro E.; Hoeksema, Bert W.; Serrano, Xaymara M.; Baker, Andrew C.; Lindner, Alberto

2017-09-01

Fire corals are the only branching corals in the South Atlantic and provide an important ecological role as habitat-builders in the region. With three endemic species ( Millepora brazilensis, M. nitida and M. laboreli) and one amphi-Atlantic species ( M. alcicornis), fire coral diversity in the Brazilian Province rivals that of the Caribbean Province. Phylogenetic relationships and patterns of population genetic structure and diversity were investigated in all four fire coral species occurring in the Brazilian Province to understand patterns of speciation and biogeography in the genus. A total of 273 colonies from the four species were collected from 17 locations spanning their geographic ranges. Sequences from the 16S ribosomal DNA (rDNA) were used to evaluate phylogenetic relationships. Patterns in genetic diversity and connectivity were inferred by measures of molecular diversity, analyses of molecular variance, pairwise differentiation, and by spatial analyses of molecular variance. Morphometrics of the endemic species M. braziliensis and M. nitida were evaluated by discriminant function analysis; macro-morphological characters were not sufficient to distinguish the two species. Genetic analyses showed that, although they are closely related, each species forms a well-supported clade. Furthermore, the endemic species characterized a distinct biogeographic barrier: M. braziliensis is restricted to the north of the São Francisco River, whereas M. nitida occurs only to the south. Millepora laboreli is restricted to a single location and has low genetic diversity. In contrast, the amphi-Atlantic species M. alcicornis shows high genetic connectivity within the Brazilian Province, and within the Caribbean Province (including Bermuda), despite low levels of gene flow between these populations and across the tropical Atlantic. These patterns reflect the importance of the Amazon-Orinoco Plume and the Mid-Atlantic Barrier as biogeographic barriers, and suggest that, while M. alcicornis is capable of long-distance dispersal, the three endemics have restricted ranges and more limited dispersal capabilities.

Estimating spatially distributed soil texture using time series of thermal remote sensing - a case study in central Europe

NASA Astrophysics Data System (ADS)

Müller, Benjamin; Bernhardt, Matthias; Jackisch, Conrad; Schulz, Karsten

2016-09-01

For understanding water and solute transport processes, knowledge about the respective hydraulic properties is necessary. Commonly, hydraulic parameters are estimated via pedo-transfer functions using soil texture data to avoid cost-intensive measurements of hydraulic parameters in the laboratory. Therefore, current soil texture information is only available at a coarse spatial resolution of 250 to 1000 m. Here, a method is presented to derive high-resolution (15 m) spatial topsoil texture patterns for the meso-scale Attert catchment (Luxembourg, 288 km2) from 28 images of ASTER (advanced spaceborne thermal emission and reflection radiometer) thermal remote sensing. A principle component analysis of the images reveals the most dominant thermal patterns (principle components, PCs) that are related to 212 fractional soil texture samples. Within a multiple linear regression framework, distributed soil texture information is estimated and related uncertainties are assessed. An overall root mean squared error (RMSE) of 12.7 percentage points (pp) lies well within and even below the range of recent studies on soil texture estimation, while requiring sparser sample setups and a less diverse set of basic spatial input. This approach will improve the generation of spatially distributed topsoil maps, particularly for hydrologic modeling purposes, and will expand the usage of thermal remote sensing products.

Spatial-Temporal Variations of Chlorophyll-a in the Adjacent Sea Area of the Yangtze River Estuary Influenced by Yangtze River Discharge.

PubMed

Wang, Ying; Jiang, Hong; Jin, Jiaxin; Zhang, Xiuying; Lu, Xuehe; Wang, Yueqi

2015-05-20

Carrying abundant nutrition, terrigenous freshwater has a great impact on the spatial and temporal heterogeneity of phytoplankton in coastal waters. The present study analyzed the spatial-temporal variations of Chlorophyll-a (Chl-a) concentration under the influence of discharge from the Yangtze River, based on remotely sensed Chl-a concentrations. The study area was initially zoned to quantitatively investigate the spatial variation patterns of Chl-a. Then, the temporal variation of Chl-a in each zone was simulated by a sinusoidal curve model. The results showed that in the inshore waters, the terrigenous discharge was the predominant driving force determining the pattern of Chl-a, which brings the risk of red tide disasters; while in the open sea areas, Chl-a was mainly affected by meteorological factors. Furthermore, a diversity of spatial and temporal variations of Chl-a existed based on the degree of influences from discharge. The diluted water extended from inshore to the east of Jeju Island. This process affected the Chl-a concentration flowing through the area, and had a potential impact on the marine environment. The Chl-a from September to November showed an obvious response to the discharge from July to September with a lag of 1 to 2 months.

Spatial-Temporal Variations of Chlorophyll-a in the Adjacent Sea Area of the Yangtze River Estuary Influenced by Yangtze River Discharge

PubMed Central

Wang, Ying; Jiang, Hong; Jin, Jiaxin; Zhang, Xiuying; Lu, Xuehe; Wang, Yueqi

2015-01-01

Carrying abundant nutrition, terrigenous freshwater has a great impact on the spatial and temporal heterogeneity of phytoplankton in coastal waters. The present study analyzed the spatial-temporal variations of Chlorophyll-a (Chl-a) concentration under the influence of discharge from the Yangtze River, based on remotely sensed Chl-a concentrations. The study area was initially zoned to quantitatively investigate the spatial variation patterns of Chl-a. Then, the temporal variation of Chl-a in each zone was simulated by a sinusoidal curve model. The results showed that in the inshore waters, the terrigenous discharge was the predominant driving force determining the pattern of Chl-a, which brings the risk of red tide disasters; while in the open sea areas, Chl-a was mainly affected by meteorological factors. Furthermore, a diversity of spatial and temporal variations of Chl-a existed based on the degree of influences from discharge. The diluted water extended from inshore to the east of Jeju Island. This process affected the Chl-a concentration flowing through the area, and had a potential impact on the marine environment. The Chl-a from September to November showed an obvious response to the discharge from July to September with a lag of 1 to 2 months. PMID:26006121

Population genetics of sporophytic self-incompatibility in Senecio squalidus L. (Asteraceae) II: a spatial autocorrelation approach to determining mating behaviour in the presence of low S allele diversity.

PubMed

Brennan, A C; Harris, S A; Hiscock, S J

2003-11-01

We recently estimated that as few as six S alleles represent the extent of S locus diversity in a British population of the self-incompatible (SI) coloniser Senecio squalidus (Oxford Ragwort). Despite the predicted constraints to mating imposed by such a low number of S alleles, S. squalidus maintains a strong sporophytic self-incompatibility (SSI) system and there is no evidence for a breakdown of SSI or any obvious negative reproductive consequences for this highly successful coloniser. The present paper assesses mating behaviour in an Oxford S. squalidus population through observations of its effect on spatial patterns of genetic diversity and thus the extent to which it is responsible for ameliorating the potentially detrimental reproductive consequences of low S allele diversity in British S. squalidus. A spatial autocorrelation (SA) treatment of S locus and allozyme polymorphism data for four loci indicates that mating events regularly occur at all the distance classes examined from 60 to 480 m throughout the entire sample population. Less SA is observed for S locus data than for allozyme data in accordance with the hypothesis that SSI and low diversity at the S locus are driving these large-scale mating events. The limited population structure at small distances of 60 m and less observed for SA analysis of the Me-2 locus and by F-statistics for all the allozyme data, is evidence of some local relatedness due to limited seed and pollen dispersal in S. squalidus. However, the overall impression of mating dynamics in this S. squalidus population is that of ample potential mating opportunities with many individuals at large population scales, indicating that reproductive success is not seriously affected by few S alleles available for mating interactions.

beta-diversity and species accumulation in antarctic coastal benthos: influence of habitat, distance and productivity on ecological connectivity.

PubMed

Thrush, Simon F; Hewitt, Judi E; Cummings, Vonda J; Norkko, Alf; Chiantore, Mariachiara

2010-07-30

High Antarctic coastal marine environments are comparatively pristine with strong environmental gradients, which make them important places to investigate biodiversity relationships. Defining how different environmental features contribute to shifts in beta-diversity is especially important as these shifts reflect both spatio-temporal variations in species richness and the degree of ecological separation between local and regional species pools. We used complementary techniques (species accumulation models, multivariate variance partitioning and generalized linear models) to assess how the roles of productivity, bio-physical habitat heterogeneity and connectivity change with spatial scales from metres to 100's of km. Our results demonstrated that the relative importance of specific processes influencing species accumulation and beta-diversity changed with increasing spatial scale, and that patterns were never driven by only one factor. Bio-physical habitat heterogeneity had a strong influence on beta-diversity at scales <290 km, while the effects of productivity were low and significant only at scales >40 km. Our analysis supports the emphasis on the analysis of diversity relationships across multiple spatial scales and highlights the unequal connectivity of individual sites to the regional species pool. This has important implications for resilience to habitat loss and community homogenisation, especially for Antarctic benthic communities where rates of recovery from disturbance are slow, there is a high ratio of poor-dispersing and brooding species, and high biogenic habitat heterogeneity and spatio-temporal variability in primary production make the system vulnerable to disturbance. Consequently, large areas need to be included within marine protected areas for effective management and conservation of these special ecosystems in the face of increasing anthropogenic disturbance.

Biomarker patterns in present-day vegetation: consistency and variation - A study on plaggen soils

NASA Astrophysics Data System (ADS)

Kirkels, Frédérique; Jansen, Boris; Kalbitz, Karsten

2013-04-01

Biomarker patterns in present-day vegetation are commonly used as proxies to reconstruct paleo-vegetation composition, land use history and to elucidate carbon cycling. Plaggen soils are formed by diverse vegetational inputs during century-long plaggen (i.e. sod) application associated with plaggen-agriculture on poor soils in north-western Europe. This resulted in remarkably stable organic matter. Plant source identification by biomarkers could provide insight in yet unknown stabilization mechanisms and the fate of organic matter upon ongoing land use change. The current rationale behind biomarker-based source identification is that patterns observed in present-day vegetation are generally representative with little random variation. However, our knowledge on variability and consistency of biomarker patterns is yet scarce. Therefore, to assess the applicability of biomarkers for source identification in plaggen soils, we analyzed published n-alkane and n-alcohol patterns of species and their various parts which contribute(d) input to plaggen soils. We considered shrubs, trees and grass species and evaluated rescaled patterns (i.e. relative abundances in chain-length range C17-36), odd-over-even predominance (OEP) and predominant n-alkanes. In addition, we explicitly looked into potential sources of systematic variation, e.g. spatial variation (climate, site conditions), temporal variation (seasonality, ontogeny) and laboratory methodology (extraction technique: washing/shaking, Soxhlet/ASE, saponification). We found meaningful clustering of n-alkanes C27, C29, C31 and C33, allowing for clear distinction of input by shrubs, trees and grasses to plaggen soils. Combination of these homologues with complete n-alkane patterns (C17-36) and OEP enabled further differentiation, while n-alcohols patterns were less distinct. Current limitation is the lack of extended and diverse quantitative records on biomarker patterns, especially for n-alcohols, non-leaf and belowground tissues, which hindered full statistical analysis. On species level we also recognized outliers and spreading. Systematic variation was indicated among tree species according to spatial conditions and by ontogeny. Yet, observed effects were ambiguous for other variation sources. This study highlights clear opportunities for application of biomarker patterns for source identification and elucidation of stabilization processes in (plaggen) soils. At the same time, application is challenged by systematic variation. Further research is key to quantify controls, magnitude and potential correction factors for such systematic variation. This would validate the use of n-alkane and n-alcohol patterns across broad spatial and temporal scales or identify boundaries wherein their consistency is ensured. Likely, these challenges apply to vegetation in a broad perspective, transcending plaggen vegetation, as assessment and application of present-day vegetation patterns is emerging.

Spatiotemporal Analysis of Microbiological Contamination in New York State Produce Fields following Extensive Flooding from Hurricane Irene, August 2011.

PubMed

Bergholz, Peter W; Strawn, Laura K; Ryan, Gina T; Warchocki, Steven; Wiedmann, Martin

2016-03-01

Although flooding introduces microbiological, chemical, and physical hazards onto croplands, few data are available on the spatial extent, patterns, and development of contamination over time postflooding. To address this paucity of information, we conducted a spatially explicit study of Escherichia coli and Salmonella contamination prevalence and genetic diversity in produce fields after the catastrophic flooding that occurred in New England during 2011. Although no significant differences were detected between the two participating farms, both random forest and logistic regression revealed changes in the spatial pattern of E. coli contamination in drag swab samples over time. Analyses also indicated that E. coli detection was associated with changes in farm management to remediate the land after flooding. In particular, E. coli was widespread in drag swab samples at 21 days postflooding, but the spatial pattern changed by 238 days postflooding such that E. coli was then most prevalent in close proximity to surface water features. The combined results of several population genetics analyses indicated that over time postflooding E. coli populations on the farms (i) changed in composition and (ii) declined overall. Salmonella was primarily detected in surface water features, but some Salmonella strains were isolated from soil and drag swab samples at 21 and 44 days postflooding. Although postflood contamination and land management responses should always be evaluated in the context of each unique farm landscape, our results provide quantitative data on the general patterns of contamination after flooding and support the practice of establishing buffer zones between flood-contaminated cropland and harvestable crops in produce fields.

Landscapes of facilitation: how self-organized patchiness of aquatic macrophytes promotes diversity in streams.

PubMed

Cornacchia, Loreta; van de Koppel, Johan; van der Wal, Daphne; Wharton, Geraldene; Puijalon, Sara; Bouma, Tjeerd J

2018-04-01

Spatial heterogeneity plays a crucial role in the coexistence of species. Despite recognition of the importance of self-organization in creating environmental heterogeneity in otherwise uniform landscapes, the effects of such self-organized pattern formation in promoting coexistence through facilitation are still unknown. In this study, we investigated the effects of pattern formation on species interactions and community spatial structure in ecosystems with limited underlying environmental heterogeneity, using self-organized patchiness of the aquatic macrophyte Callitriche platycarpa in streams as a model system. Our theoretical model predicted that pattern formation in aquatic vegetation - due to feedback interactions between plant growth, water flow and sedimentation processes - could promote species coexistence, by creating heterogeneous flow conditions inside and around the plant patches. The spatial plant patterns predicted by our model agreed with field observations at the reach scale in naturally vegetated rivers, where we found a significant spatial aggregation of two macrophyte species around C. platycarpa. Field transplantation experiments showed that C. platycarpa had a positive effect on the growth of both beneficiary species, and the intensity of this facilitative effect was correlated with the heterogeneous hydrodynamic conditions created within and around C. platycarpa patches. Our results emphasize the importance of self-organized patchiness in promoting species coexistence by creating a landscape of facilitation, where new niches and facilitative effects arise in different locations. Understanding the interplay between competition and facilitation is therefore essential for successful management of biodiversity in many ecosystems. © 2018 The Authors Ecology published by Wiley Periodicals, Inc. on behalf of Ecological Society of America.

Neutrality and Robustness in Evo-Devo: Emergence of Lateral Inhibition

PubMed Central

Munteanu, Andreea; Solé, Ricard V.

2008-01-01

Embryonic development is defined by the hierarchical dynamical process that translates genetic information (genotype) into a spatial gene expression pattern (phenotype) providing the positional information for the correct unfolding of the organism. The nature and evolutionary implications of genotype–phenotype mapping still remain key topics in evolutionary developmental biology (evo-devo). We have explored here issues of neutrality, robustness, and diversity in evo-devo by means of a simple model of gene regulatory networks. The small size of the system allowed an exhaustive analysis of the entire fitness landscape and the extent of its neutrality. This analysis shows that evolution leads to a class of robust genetic networks with an expression pattern characteristic of lateral inhibition. This class is a repertoire of distinct implementations of this key developmental process, the diversity of which provides valuable clues about its underlying causal principles. PMID:19023404

Late Cenozoic onset of the latitudinal diversity gradient of North American mammals

NASA Astrophysics Data System (ADS)

Marcot, Jonathan D.; Fox, David L.; Niebuhr, Spencer R.

2016-06-01

The decline of species richness from equator to pole, or latitudinal diversity gradient (LDG), is nearly universal among clades of living organisms, yet whether it was such a pervasive pattern in the geologic past remains uncertain. Here, we calculate the strength of the LDG for terrestrial mammals in North America over the past 65 My, using 27,903 fossil occurrences of Cenozoic terrestrial mammals from western North America downloaded from the Paleobiology Database. Accounting for temporal and spatial variation in sampling, the LDG was substantially weaker than it is today for most of the Cenozoic and the robust modern LDG of North American mammals evolved only over the last 4 My. The strength of the LDG correlates negatively with global temperature, suggesting a role of global climate patterns in the establishment and maintenance of the LDG for North American mammals.

The Upper Mississippi River floodscape: spatial patterns of flood inundation and associated plant community distributions

USGS Publications Warehouse

DeJager, Nathan R.; Rohweder, Jason J.; Yin, Yao; Hoy, Erin E.

2016-01-01

Questions How is the distribution of different plant communities associated with patterns of flood inundation across a large floodplain landscape? Location Thirty-eight thousand nine hundred and seventy hectare of floodplain, spanning 320 km of the Upper Mississippi River (UMR). Methods High-resolution elevation data (Lidar) and 30 yr of daily river stage data were integrated to produce a ‘floodscape’ map of growing season flood inundation duration. The distributions of 16 different remotely sensed plant communities were quantified along the gradient of flood duration. Results Models fitted to the cumulative frequency of occurrence of different vegetation types as a function of flood duration showed that most types exist along a continuum of flood-related occurrence. The diversity of community types was greatest at high elevations (0–10 d of flooding), where both upland and lowland community types were found, as well as at very low elevations (70–180 d of flooding), where a variety of lowland herbaceous communities were found. Intermediate elevations (20–60 d of flooding) tended to be dominated by floodplain forest and had the lowest diversity of community types. Conclusions Although variation in flood inundation is often considered to be the main driver of spatial patterns in floodplain plant communities, few studies have quantified flood–vegetation relationships at broad scales. Our results can be used to identify targets for restoration of historical hydrological regimes or better anticipate hydro-ecological effects of climate change at broad scales.

[Correlative analysis of the diversity patterns of regional surface water, NDVI and thermal environment].

PubMed

Duan, Jin-Long; Zhang, Xue-Lei

2012-10-01

Taking Zhengzhou City, the capital of Henan Province in Central China, as the study area, and by using the theories and methodologies of diversity, a discreteness evaluation on the regional surface water, normalized difference vegetation index (NDVI), and land surface temperature (LST) distribution was conducted in a 2 km x 2 km grid scale. Both the NDVI and the LST were divided into 4 levels, their spatial distribution diversity indices were calculated, and their connections were explored. The results showed that it was of operability and practical significance to use the theories and methodologies of diversity in the discreteness evaluation of the spatial distribution of regional thermal environment. There was a higher overlap of location between the distributions of surface water and the lowest temperature region, and the high vegetation coverage was often accompanied by low land surface temperature. In 1988-2009, the discreteness of the surface water distribution in the City had an obvious decreasing trend. The discreteness of the surface water distribution had a close correlation with the discreteness of the temperature region distribution, while the discreteness of the NDVI classification distribution had a more complicated correlation with the discreteness of the temperature region distribution. Therefore, more environmental factors were needed to be included for a better evaluation.

Patterns of benthic bacterial diversity in coastal areas contaminated by heavy metals, polycyclic aromatic hydrocarbons (PAHs) and polychlorinated biphenyls (PCBs)

PubMed Central

Quero, Grazia Marina; Cassin, Daniele; Botter, Margherita; Perini, Laura; Luna, Gian Marco

2015-01-01

Prokaryotes in coastal sediments are fundamental players in the ecosystem functioning and regulate processes relevant in the global biogeochemical cycles. Nevertheless, knowledge on benthic microbial diversity patterns across spatial scales, or as function to anthropogenic influence, is still limited. We investigated the microbial diversity in two of the most chemically polluted sites along the coast of Italy. One site is the Po River Prodelta (Northern Adriatic Sea), which receives contaminant discharge from one of the largest rivers in Europe. The other site, the Mar Piccolo of Taranto (Ionian Sea), is a chronically polluted area due to steel production plants, oil refineries, and intense maritime traffic. We collected sediments from 30 stations along gradients of contamination, and studied prokaryotic diversity using Illumina sequencing of amplicons of a 16S rDNA gene fragment. The main sediment variables and the concentration of eleven metals, polychlorinated biphenyls (PCBs) and polycyclic aromatic hydrocarbons (PAHs) were measured. Chemical analyses confirmed the high contamination in both sites, with concentrations of PCBs particularly high and often exceeding the sediment guidelines. The analysis of more than 3 millions 16S rDNA sequences showed that richness decreased with higher contamination levels. Multivariate analyses showed that contaminants significantly shaped community composition. Assemblages differed significantly between the two sites, but showed wide within-site variations related with spatial gradients in the chemical contamination, and the presence of a core set of OTUs shared by the two geographically distant sites. A larger importance of PCB-degrading taxa was observed in the Mar Piccolo, suggesting their potential selection in this historically polluted site. Our results indicate that sediment contamination by multiple contaminants significantly alter benthic prokaryotic diversity in coastal areas, and suggests considering the potential contribution of the resident microbes to contaminant bioremediation actions. PMID:26528247

Structure and spatial patterns of macrobenthic community in Tai Lake, a large shallow lake, China

USGS Publications Warehouse

Di Li,; Erickson, Richard A.; Song Tang,; Xuwen Li,; Niu, Zhichun; Xia Wang,; Hongling Liu,; Hongxia Yu,

2016-01-01

Tai Lake (Chinese: Taihu), the third-largest freshwater lake in China, suffers from harmful cyanobacteria blooms that are caused by economic development and population growth near the lake. Several studies have focused on phytoplankton in Tai Lake after a drinking water crisis in 2007; however, these studies primarily focused on microcystin bioaccumulation and toxicity to individual species without examining the effects of microcystin on macrobenthic community diversity. In this study, we conducted a survey of the lake to examine the effects of microcystine and other pollutants on marcobenthic community diversity. A totally of forty-nine species of macroinvertebrates were found in Tai Lake. Limnodrilus hoffmeisteri and Corbicula fluminea were the most abundant species. Cluster-analysis and one-way analysis of similarity (ANOSIM) identified three significantly different macrobenthic communities among the sample sites. More specifically, sites in the eastern bays, where aquatic macrophytes were abundant, had the highest diversity of macrobenthic communities, which were dominated by Bellamya aeruginosa, Bellamya purificata, L. hoffmeisteri, and Alocinma longicornis. Sites in Zhushan Bay contained relatively diverse communities, mainly composed of L. hoffmeisteri, C. fluminea, L. claparederanus, R. sinicus, and Cythura sp. Sites in the western region, Meiliang Bay and Wuli Bay had the lowest diversity, mainly composed ofL. hoffmeisteri, C. fluminea, Branchiura sowerbyi, and Rhyacodrilus sinicus. In addition, the relationships between macrobenthic metrics (Shannon–Wiener, Margalef, and Pielou) and environmental variables showed that community structure and spatial patterns of macrobenthos in Tai Lake were significantly influenced by chemical oxygen demand (CODCr), biochemical oxygen demand (BOD5), lead (Pb), and microcystin-LR (L for leucine and R for arginine). Our findings provide critical information that could help managers and policymakers assess and modify ecological restoration practices.

Evolutionary history of the angiosperm flora of China.

PubMed

Lu, Li-Min; Mao, Ling-Feng; Yang, Tuo; Ye, Jian-Fei; Liu, Bing; Li, Hong-Lei; Sun, Miao; Miller, Joseph T; Mathews, Sarah; Hu, Hai-Hua; Niu, Yan-Ting; Peng, Dan-Xiao; Chen, You-Hua; Smith, Stephen A; Chen, Min; Xiang, Kun-Li; Le, Chi-Toan; Dang, Viet-Cuong; Lu, An-Ming; Soltis, Pamela S; Soltis, Douglas E; Li, Jian-Hua; Chen, Zhi-Duan

2018-02-08

High species diversity may result from recent rapid speciation in a 'cradle' and/or the gradual accumulation and preservation of species over time in a 'museum'. China harbours nearly 10% of angiosperm species worldwide and has long been considered as both a museum, owing to the presence of many species with hypothesized ancient origins, and a cradle, as many lineages have originated as recent topographic changes and climatic shifts-such as the formation of the Qinghai-Tibetan Plateau and the development of the monsoon-provided new habitats that promoted remarkable radiation. However, no detailed phylogenetic study has addressed when and how the major components of the Chinese angiosperm flora assembled to form the present-day vegetation. Here we investigate the spatio-temporal divergence patterns of the Chinese flora using a dated phylogeny of 92% of the angiosperm genera for the region, a nearly complete species-level tree comprising 26,978 species and detailed spatial distribution data. We found that 66% of the angiosperm genera in China did not originate until early in the Miocene epoch (23 million years ago (Mya)). The flora of eastern China bears a signature of older divergence (mean divergence times of 22.04-25.39 Mya), phylogenetic overdispersion (spatial co-occurrence of distant relatives) and higher phylogenetic diversity. In western China, the flora shows more recent divergence (mean divergence times of 15.29-18.86 Mya), pronounced phylogenetic clustering (co-occurrence of close relatives) and lower phylogenetic diversity. Analyses of species-level phylogenetic diversity using simulated branch lengths yielded results similar to genus-level patterns. Our analyses indicate that eastern China represents a floristic museum, and western China an evolutionary cradle, for herbaceous genera; eastern China has served as both a museum and a cradle for woody genera. These results identify areas of high species richness and phylogenetic diversity, and provide a foundation on which to build conservation efforts in China.

Evolutionary history of the angiosperm flora of China

NASA Astrophysics Data System (ADS)

Lu, Li-Min; Mao, Ling-Feng; Yang, Tuo; Ye, Jian-Fei; Liu, Bing; Li, Hong-Lei; Sun, Miao; Miller, Joseph T.; Mathews, Sarah; Hu, Hai-Hua; Niu, Yan-Ting; Peng, Dan-Xiao; Chen, You-Hua; Smith, Stephen A.; Chen, Min; Xiang, Kun-Li; Le, Chi-Toan; Dang, Viet-Cuong; Lu, An-Ming; Soltis, Pamela S.; Soltis, Douglas E.; Li, Jian-Hua; Chen, Zhi-Duan

2018-02-01

High species diversity may result from recent rapid speciation in a ‘cradle’ and/or the gradual accumulation and preservation of species over time in a ‘museum’. China harbours nearly 10% of angiosperm species worldwide and has long been considered as both a museum, owing to the presence of many species with hypothesized ancient origins, and a cradle, as many lineages have originated as recent topographic changes and climatic shifts—such as the formation of the Qinghai-Tibetan Plateau and the development of the monsoon—provided new habitats that promoted remarkable radiation. However, no detailed phylogenetic study has addressed when and how the major components of the Chinese angiosperm flora assembled to form the present-day vegetation. Here we investigate the spatio-temporal divergence patterns of the Chinese flora using a dated phylogeny of 92% of the angiosperm genera for the region, a nearly complete species-level tree comprising 26,978 species and detailed spatial distribution data. We found that 66% of the angiosperm genera in China did not originate until early in the Miocene epoch (23 million years ago (Mya)). The flora of eastern China bears a signature of older divergence (mean divergence times of 22.04-25.39 Mya), phylogenetic overdispersion (spatial co-occurrence of distant relatives) and higher phylogenetic diversity. In western China, the flora shows more recent divergence (mean divergence times of 15.29-18.86 Mya), pronounced phylogenetic clustering (co-occurrence of close relatives) and lower phylogenetic diversity. Analyses of species-level phylogenetic diversity using simulated branch lengths yielded results similar to genus-level patterns. Our analyses indicate that eastern China represents a floristic museum, and western China an evolutionary cradle, for herbaceous genera; eastern China has served as both a museum and a cradle for woody genera. These results identify areas of high species richness and phylogenetic diversity, and provide a foundation on which to build conservation efforts in China.

Uniform functional structure across spatial scales in an intertidal benthic assemblage.

PubMed

Barnes, R S K; Hamylton, Sarah

2015-05-01

To investigate the causes of the remarkable similarity of emergent assemblage properties that has been demonstrated across disparate intertidal seagrass sites and assemblages, this study examined whether their emergent functional-group metrics are scale related by testing the null hypothesis that functional diversity and the suite of dominant functional groups in seagrass-associated macrofauna are robust structural features of such assemblages and do not vary spatially across nested scales within a 0.4 ha area. This was carried out via a lattice of 64 spatially referenced stations. Although densities of individual components were patchily dispersed across the locality, rank orders of importance of the 14 functional groups present, their overall functional diversity and evenness, and the proportions of the total individuals contained within each showed, in contrast, statistically significant spatial uniformity, even at areal scales <2 m(2). Analysis of the proportional importance of the functional groups in their geospatial context also revealed weaker than expected levels of spatial autocorrelation, and then only at the smaller scales and amongst the most dominant groups, and only a small number of negative correlations occurred between the proportional importances of the individual groups. In effect, such patterning was a surface veneer overlying remarkable stability of assemblage functional composition across all spatial scales. Although assemblage species composition is known to be homogeneous in some soft-sediment marine systems over equivalent scales, this combination of patchy individual components yet basically constant functional-group structure seems as yet unreported. Copyright © 2015 Elsevier Ltd. All rights reserved.

Plate tectonics drive tropical reef biodiversity dynamics

PubMed Central

Leprieur, Fabien; Descombes, Patrice; Gaboriau, Théo; Cowman, Peter F.; Parravicini, Valeriano; Kulbicki, Michel; Melián, Carlos J.; de Santana, Charles N.; Heine, Christian; Mouillot, David; Bellwood, David R.; Pellissier, Loïc

2016-01-01

The Cretaceous breakup of Gondwana strongly modified the global distribution of shallow tropical seas reshaping the geographic configuration of marine basins. However, the links between tropical reef availability, plate tectonic processes and marine biodiversity distribution patterns are still unknown. Here, we show that a spatial diversification model constrained by absolute plate motions for the past 140 million years predicts the emergence and movement of diversity hotspots on tropical reefs. The spatial dynamics of tropical reefs explains marine fauna diversification in the Tethyan Ocean during the Cretaceous and early Cenozoic, and identifies an eastward movement of ancestral marine lineages towards the Indo-Australian Archipelago in the Miocene. A mechanistic model based only on habitat-driven diversification and dispersal yields realistic predictions of current biodiversity patterns for both corals and fishes. As in terrestrial systems, we demonstrate that plate tectonics played a major role in driving tropical marine shallow reef biodiversity dynamics. PMID:27151103

Plate tectonics drive tropical reef biodiversity dynamics.

PubMed

Leprieur, Fabien; Descombes, Patrice; Gaboriau, Théo; Cowman, Peter F; Parravicini, Valeriano; Kulbicki, Michel; Melián, Carlos J; de Santana, Charles N; Heine, Christian; Mouillot, David; Bellwood, David R; Pellissier, Loïc

2016-05-06

The Cretaceous breakup of Gondwana strongly modified the global distribution of shallow tropical seas reshaping the geographic configuration of marine basins. However, the links between tropical reef availability, plate tectonic processes and marine biodiversity distribution patterns are still unknown. Here, we show that a spatial diversification model constrained by absolute plate motions for the past 140 million years predicts the emergence and movement of diversity hotspots on tropical reefs. The spatial dynamics of tropical reefs explains marine fauna diversification in the Tethyan Ocean during the Cretaceous and early Cenozoic, and identifies an eastward movement of ancestral marine lineages towards the Indo-Australian Archipelago in the Miocene. A mechanistic model based only on habitat-driven diversification and dispersal yields realistic predictions of current biodiversity patterns for both corals and fishes. As in terrestrial systems, we demonstrate that plate tectonics played a major role in driving tropical marine shallow reef biodiversity dynamics.

The spatial organization of intra-tumour heterogeneity and evolutionary trajectories of metastases in hepatocellular carcinoma

NASA Astrophysics Data System (ADS)

Zhai, Weiwei; Lim, Tony Kiat-Hon; Zhang, Tong; Phang, Su-Ting; Tiang, Zenia; Guan, Peiyong; Ng, Ming-Hwee; Lim, Jia Qi; Yao, Fei; Li, Zheng; Ng, Poh Yong; Yan, Jie; Goh, Brian K.; Chung, Alexander Yaw-Fui; Choo, Su-Pin; Khor, Chiea Chuen; Soon, Wendy Wei-Jia; Sung, Ken Wing-Kin; Foo, Roger Sik-Yin; Chow, Pierce Kah-Hoe

2017-02-01

Hepatocellular carcinoma (HCC) has one of the poorest survival rates among cancers. Using multi-regional sampling of nine resected HCC with different aetiologies, here we construct phylogenetic relationships of these sectors, showing diverse levels of genetic sharing, spanning early to late diversification. Unlike the variegated pattern found in colorectal cancers, a large proportion of HCC display a clear isolation-by-distance pattern where spatially closer sectors are genetically more similar. Two resected intra-hepatic metastases showed genetic divergence occurring before and after primary tumour diversification, respectively. Metastatic tumours had much higher variability than their primary tumours, suggesting that intra-hepatic metastasis is accompanied by rapid diversification at the distant location. The presence of co-existing mutations offers the possibility of drug repositioning for HCC treatment. Taken together, these insights into intra-tumour heterogeneity allow for a comprehensive understanding of the evolutionary trajectories of HCC and suggest novel avenues for personalized therapy.

Analysis of spatial patterns informs community assembly and sampling requirements for Collembola in forest soils

NASA Astrophysics Data System (ADS)

Dirilgen, Tara; Juceviča, Edite; Melecis, Viesturs; Querner, Pascal; Bolger, Thomas

2018-01-01

The relative importance of niche separation, non-equilibrial and neutral models of community assembly has been a theme in community ecology for many decades with none appearing to be applicable under all circumstances. In this study, Collembola species abundances were recorded over eleven consecutive years in a spatially explicit grid and used to examine (i) whether observed beta diversity differed from that expected under conditions of neutrality, (ii) whether sampling points differed in their relative contributions to overall beta diversity, and (iii) the number of samples required to provide comparable estimates of species richness across three forest sites. Neutrality could not be rejected for 26 of the forest by year combinations. However, there is a trend toward greater structure in the oldest forest, where beta diversity was greater than predicted by neutrality on five of the eleven sampling dates. The lack of difference in individual- and sample-based rarefaction curves also suggests randomness in the system at this particular scale of investigation. It seems that Collembola communities are not spatially aggregated and assembly is driven primarily by neutral processes particularly in the younger two sites. Whether this finding is due to small sample size or unaccounted for environmental variables cannot be determined. Variability between dates and sites illustrates the potential of drawing incorrect conclusions if data are collected at a single site and a single point in time.

Temporal and spatial variation of fish assemblages in Dianshan Lake, Shanghai, China

NASA Astrophysics Data System (ADS)

Hu, Zhongjun; Wang, Siqing; Wu, Hao; Chen, Qingjiang; Ruan, Renliang; Chen, Liqiao; Liu, Qigen

2014-07-01

Using multi-mesh gillnets and trawls, the fish communities in Dianshan Lake at 6 stations from Oct. 2009 to Jul. 2010 were investigated seasonally to reveal the biodiversity and its spatial and temporal distribution patterns. The long-term changes in their structural characteristics were then analyzed to identify the main influencing factors and several measures for lake restoration were put forward. Thirty six species, belonging to 9 family and 30 genera, were collected, amongst which, the order Cypriniformes accounted for 61.1% of the total species number. In terms of importance value, Cypriniformes was the predominant group, Coilia nasus the dominant species, while Cyprinus carpio and Rhinogobius giurinus were the subdominant taxa. The community types did not differ among stations, but between seasons. There were no significant differences between seasons and among stations in species diversity, but richness differed both spatially and seasonally. Along with the process of eutrophication and the drastic reduction of the area colonized by macrophytes from 1959 to 2009-2010, the fish diversity declined markedly, and species numbers of herbivores and piscivores declined proportionately more than those of invertivores, omnivores, and planktivores. The decline of potamophilus and river-lake migratory fish was more marked than those of sedentary, river-sea migratory, and estuarine fishes. Eutrophication concomitant with sharp reduction of macrophyte area and overfishing may be the main reasons for the decline in fish diversity in Dianshan Lake.

Exploring spatial patterns of vulnerability for diverse biodiversity descriptors in regional conservation planning.

PubMed

Vimal, Ruppert; Pluvinet, Pascal; Sacca, Céline; Mazagol, Pierre-Olivier; Etlicher, Bernard; Thompson, John D

2012-03-01

In this study, we developed a multi-criteria assessment of spatial variability of the vulnerability of three different biodiversity descriptors: sites of high conservation interest by virtue of the presence of rare or remarkable species, extensive areas of high ecological integrity, and landscape diversity in grid cells across an entire region. We assessed vulnerability in relation to (a) direct threats in and around sites to a distance of 2 km associated with intensive agriculture, building and road infrastructure and (b) indirect effects of human population density on a wider scale (50 km). The different combinations of biodiversity and threat indicators allowed us to set differential priorities for biodiversity conservation and assess their spatial variation. For example, with this method we identified sites and grid cells which combined high biodiversity with either high threat values or low threat values for the three different biodiversity indicators. In these two classes the priorities for conservation planning will be different, reduce threat values in the former and restrain any increase in the latter. We also identified low priority sites (low biodiversity with either high or low threats). This procedure thus allows for the integration of a spatial ranking of vulnerability into priority setting for regional conservation planning. Copyright © 2011 Elsevier Ltd. All rights reserved.

Diversity, distribution and spatial structure of the cold-water coral fauna of the Azores (NE Atlantic)

NASA Astrophysics Data System (ADS)

Braga-Henriques, A.; Porteiro, F. M.; Ribeiro, P. A.; de Matos, V.; Sampaio, Í.; Ocaña, O.; Santos, R. S.

2013-06-01

Cold-water corals are widely considered as important structural components of benthic habitats, potentially enhancing local abundance in a variety of fish and invertebrate species. Yet, current knowledge of the taxonomic diversity and distribution patterns of these vulnerable, slow-growing organisms is scarce and fragmented, limiting the effectiveness of spatial management and conservation measures. We have conducted an exhaustive compilation of records of alcyonaceans, antipatharians, scleractinians and stylasterids available through present day to assess the diversity, distribution and spatial structure of coral assemblages in the Azores exclusive economic zone (EEZ). The resulting database comprises 2501 entries concerning historical oceanographic expeditions and other published sources, as well as unpublished data from bottom longline by-catch. Our taxonomic inventory appears to be fairly complete for the explored habitats, accounting for 164 species (79 alcyonaceans, 58 scleractinians, 18 antipatharians and 9 stylasterids), nine of which were documented for the first time. The Azores EEZ harbours a mixed coral fauna with several zoogeographic origins, showing the closest affinity with the Lusitanian-Mediterranean region. Very few apparent endemics were found (14%), and only in part supported by consistent sampling. Coral diversity is particularly high between 300 and 900 m depths, in areas recognized as traditional fishing grounds or exploitable fish habitat within the 100-mile limit of the EEZ. The composition of coral assemblages shows significant geographical structure among longitudinal sections of the study area at comparable depths (100-1500 m). There is no evidence of a possible role of the Mid-Atlantic Ridge or latitudinal effects underlying this pattern, which suggests that it may instead reflect assemblage variability among features. Stronger changes in species composition were found along the bathymetric gradient. Notwithstanding the mix of partially overlapping steno- and eurybathic species that characterize the vertical distribution of corals, there is a distinct transition from shallow (100-600 m) to intermediate (600-1000 m) depths. The analysis presented here constitutes a valuable contribution for efficient conservation policies of coral-associated vulnerable marine ecosystems and their sustainable use as fishing areas.

Diversity, distribution and spatial structure of the cold-water coral fauna of the Azores (NE Atlantic)

NASA Astrophysics Data System (ADS)

Braga-Henriques, A.; Porteiro, F. M.; Ribeiro, P. A.; de Matos, V.; Sampaio, Í.; Ocaña, O.; Santos, R. S.

2013-01-01

Cold-water corals are widely considered as important structural components of benthic habitats, potentially enhancing local abundance in a variety of fish and invertebrate species. Yet, current knowledge of the taxonomic diversity and distribution patterns of these vulnerable, slow-growing organisms is scarce and fragmented, limiting the effectiveness of spatial management and conservation measures. We have conducted an exhaustive compilation of records of alcyonaceans, antipatharians, scleractinians and stylasterids available until the present day to assess the diversity, distribution, and spatial structure of coral assemblages in the Azores Exclusive Economic Zone (EEZ). The resulting database comprises 2501 entries concerning historical oceanographic expeditions and other published sources, as well as recent data from longline bycatch. Our taxonomic inventory appears to be fairly complete for the explored habitats, accounting for 164 species (79 alcyonaceans, 58 scleractinians, 18 antipatharians and 9 stylasterids), nine of which were new records. The Azores EEZ harbours a mixed coral fauna with several zoogeographic origins, showing the closest affinity with the Lusitanian-Mediterranean region. Very few apparent endemics were found (14%), and only in part supported by consistent sampling. Coral diversity is particularly high between 300 and 900 m depths, in areas recognized as traditional fishing grounds or exploitable fish habitat within the 100-mile limit of the EEZ. The composition of coral assemblages shows significant geographical structure among longitudinal sections of the study area at comparable depths (100-1500 m). There is no evidence of a possible role of the Mid-Atlantic Ridge or latitudinal effects underlying this pattern, which suggests that it may instead reflect assemblage variability among features. Stronger changes in species composition were found along the bathymetric gradient. Notwithstanding the mix of partially overlapping steno- and eurybathic species that characterize the vertical distribution of corals, there is a distinct transition from shallow (100-600 m) to intermediate (600-1000 m) depths.The analysis here presented constitutes a~valuable contribution for efficient conservation policies of coral-associated vulnerable marine ecosystems and their sustainable use as fishing areas.

A combinatorial code for pattern formation in Drosophila oogenesis.

PubMed

Yakoby, Nir; Bristow, Christopher A; Gong, Danielle; Schafer, Xenia; Lembong, Jessica; Zartman, Jeremiah J; Halfon, Marc S; Schüpbach, Trudi; Shvartsman, Stanislav Y

2008-11-01

Two-dimensional patterning of the follicular epithelium in Drosophila oogenesis is required for the formation of three-dimensional eggshell structures. Our analysis of a large number of published gene expression patterns in the follicle cells suggests that they follow a simple combinatorial code based on six spatial building blocks and the operations of union, difference, intersection, and addition. The building blocks are related to the distribution of inductive signals, provided by the highly conserved epidermal growth factor receptor and bone morphogenetic protein signaling pathways. We demonstrate the validity of the code by testing it against a set of patterns obtained in a large-scale transcriptional profiling experiment. Using the proposed code, we distinguish 36 distinct patterns for 81 genes expressed in the follicular epithelium and characterize their joint dynamics over four stages of oogenesis. The proposed combinatorial framework allows systematic analysis of the diversity and dynamics of two-dimensional transcriptional patterns and guides future studies of gene regulation.

Assessment of post-fire forest structural diversity using neighborhood parameter in the Sierra Madre Oriental, Mexico

Treesearch

Diana Yemilet Avila Flores; Marco Aurelio González Tagle; Javier Jiménez Pérez; Oscar Aguirre Calderón; Eduardo Treviño Garza

2013-01-01

The objective of this research was to characterize the spatial structure patterns of a Pinus hartwegii forest in the Sierra Madre Oriental, affected by a fire in 1998. Sampling was stratified by fire severity. A total of three fire severity classes (low, medium and high) were defined. Three sample plots of 40m x 40m were established for each...

Spatiotemporal patterns of phytoplankton composition and abundance in the Maryland Coastal Bays: The influence of freshwater discharge and anthropogenic activities

NASA Astrophysics Data System (ADS)

Oseji, Ozuem F.; Chigbu, Paulinus; Oghenekaro, Efeturi; Waguespack, Yan; Chen, Nianhong

2018-07-01

The spatial and temporal variations in phytoplankton abundance and community structure in the northern and southern parts of the Maryland Coastal Bays (MCBs) that differ in anthropogenic activities and hydrological characteristics were studied in 2012 and 2013 using photosynthetic pigments as biomarkers. Phytoplankton pigment biomass and diversity were generally higher in the northern bays that receive high nutrient input from St. Martin River, than in the southern bays where nutrient levels were comparatively low. Sites close to the mouths of tributaries in northern and southern bays had higher nutrient levels, which favored the development of dinoflagellates, and nano- and picophytoplankton, than sites closer to the inlets. The microplankton dominated the phytoplankton community in spring (>90%) and decreased in relative abundance into fall (<60%) whereas nanoplankton peaked in summer or fall. Picoplankton relative abundance increased from late spring (<10%, March 2012 & 2013) to summer (40%, July 2012 and August 2013) and was correlated positively with NH4+ and negatively with salinity. The observed spatial and seasonal patterns of phytoplankton relative abundance and diversity are likely due to changes in nutrient concentrations and ratios, driven by variations in freshwater discharge, and selective grazing of phytoplankton. Water quality management in the MCBs should continue to focus on reducing nutrient inputs into the bays.

Vertical stratification of the foliar fungal community in the world's tallest trees.

PubMed

Harrison, Joshua G; Forister, Matthew L; Parchman, Thomas L; Koch, George W

2016-12-01

The aboveground tissues of plants host numerous, ecologically important fungi, yet patterns in the spatial distribution of these fungi remain little known. Forest canopies in particular are vast reservoirs of fungal diversity, but intracrown variation in fungal communities has rarely been explored. Knowledge of how fungi are distributed throughout tree crowns will contribute to our understanding of interactions between fungi and their host trees and is a first step toward investigating drivers of community assembly for plant-associated fungi. Here we describe spatial patterns in fungal diversity within crowns of the world's tallest trees, coast redwoods (Sequoia sempervirens). We took a culture-independent approach, using the Illumina MiSeq platform, to characterize the fungal assemblage at multiple heights within the crown across the geographical range of the coast redwood. Within each tree surveyed, we uncovered evidence for vertical stratification in the fungal community; different portions of the tree crown harbored different assemblages of fungi. We also report between-tree variation in the fungal community within redwoods. Our results suggest the potential for vertical stratification of fungal communities in the crowns of other tall tree species and should prompt future study of the factors giving rise to this stratification. © 2016 Botanical Society of America.

Soil Landscape Pattern Changes in Response to Rural Anthropogenic Activity across Tiaoxi Watershed, China

PubMed Central

Xiao, Rui; Jiang, Diwei; Christakos, George; Fei, Xufeng; Wu, Jiaping

2016-01-01

Soil sealing (loss of soil resources due to extensive land covering for the purpose of house building, road construction etc.) and subsequent soil landscape pattern changes constitute typical environmental problems in many places worldwide. Previous studies concentrated on soil sealing in urbanized regions, whereas rural areas have not been given sufficient attention. Accordingly, this paper studies soil landscape pattern dynamics (i.e., landscape pattern changes in response to rural anthropogenic activities) in the Tiaoxi watershed (Zhejiang province, eastern China), in which surface sealing is by far the predominant component of human forcing with respect to environmental change. A novel approach of quantifying the impacts of rural anthropogenic activities on soil resources is presented. Specifically, quantitative relationships were derived between five soil landscape pattern metrics (patch density, edge density, shape index, Shannon’s diversity index and aggregation index) and three rural anthropogenic activity indicators (anthropogenic activity intensity, distance to towns, and distance to roads) at two landscape block scales (3 and 5 km) between 1985 and 2010. The results showed that the Tiaoxi watershed experienced extensive rural settlement expansion and high rates of soil sealing. Soil landscapes became more fragmented, more irregular, more isolated, and less diverse. Relationships between soil landscape pattern changes and rural anthropogenic activities differed with the scale (spatial and temporal) and variable considered. In particular, the anthropogenic activity intensity was found to be the most important indicator explaining social development intensity, whereas the other two proximity indicators had a significant impact at certain temporal interval. In combination with scale effects, spatial dependency (correlation) was shown to play a key role that should be carefully taken into consideration in any relevant environmental study. Overall, the findings of this work suggest that soil sealing can be a critical human forcing issue with considerable consequences deserving serious attention by the experts, the public and the government alike. PMID:27832167

Soil Landscape Pattern Changes in Response to Rural Anthropogenic Activity across Tiaoxi Watershed, China.

PubMed

Xiao, Rui; Jiang, Diwei; Christakos, George; Fei, Xufeng; Wu, Jiaping

2016-01-01

Soil sealing (loss of soil resources due to extensive land covering for the purpose of house building, road construction etc.) and subsequent soil landscape pattern changes constitute typical environmental problems in many places worldwide. Previous studies concentrated on soil sealing in urbanized regions, whereas rural areas have not been given sufficient attention. Accordingly, this paper studies soil landscape pattern dynamics (i.e., landscape pattern changes in response to rural anthropogenic activities) in the Tiaoxi watershed (Zhejiang province, eastern China), in which surface sealing is by far the predominant component of human forcing with respect to environmental change. A novel approach of quantifying the impacts of rural anthropogenic activities on soil resources is presented. Specifically, quantitative relationships were derived between five soil landscape pattern metrics (patch density, edge density, shape index, Shannon's diversity index and aggregation index) and three rural anthropogenic activity indicators (anthropogenic activity intensity, distance to towns, and distance to roads) at two landscape block scales (3 and 5 km) between 1985 and 2010. The results showed that the Tiaoxi watershed experienced extensive rural settlement expansion and high rates of soil sealing. Soil landscapes became more fragmented, more irregular, more isolated, and less diverse. Relationships between soil landscape pattern changes and rural anthropogenic activities differed with the scale (spatial and temporal) and variable considered. In particular, the anthropogenic activity intensity was found to be the most important indicator explaining social development intensity, whereas the other two proximity indicators had a significant impact at certain temporal interval. In combination with scale effects, spatial dependency (correlation) was shown to play a key role that should be carefully taken into consideration in any relevant environmental study. Overall, the findings of this work suggest that soil sealing can be a critical human forcing issue with considerable consequences deserving serious attention by the experts, the public and the government alike.

Recombination, Pairing, and Synapsis of Homologs during Meiosis

PubMed Central

Zickler, Denise; Kleckner, Nancy

2015-01-01

Recombination is a prominent feature of meiosis in which it plays an important role in increasing genetic diversity during inheritance. Additionally, in most organisms, recombination also plays mechanical roles in chromosomal processes, most notably to mediate pairing of homologous chromosomes during prophase and, ultimately, to ensure regular segregation of homologous chromosomes when they separate at the first meiotic division. Recombinational interactions are also subject to important spatial patterning at both early and late stages. Recombination-mediated processes occur in physical and functional linkage with meiotic axial chromosome structure, with interplay in both directions, before, during, and after formation and dissolution of the synaptonemal complex (SC), a highly conserved meiosis-specific structure that links homolog axes along their lengths. These diverse processes also are integrated with recombination-independent interactions between homologous chromosomes, nonhomology-based chromosome couplings/clusterings, and diverse types of chromosome movement. This review provides an overview of these diverse processes and their interrelationships. PMID:25986558

The scale dependence of optical diversity in a prairie ecosystem

NASA Astrophysics Data System (ADS)

Gamon, J. A.; Wang, R.; Stilwell, A.; Zygielbaum, A. I.; Cavender-Bares, J.; Townsend, P. A.

2015-12-01

Biodiversity loss, one of the most crucial challenges of our time, endangers ecosystem services that maintain human wellbeing. Traditional methods of measuring biodiversity require extensive and costly field sampling by biologists with extensive experience in species identification. Remote sensing can be used for such assessment based upon patterns of optical variation. This provides efficient and cost-effective means to determine ecosystem diversity at different scales and over large areas. Sampling scale has been described as a "fundamental conceptual problem" in ecology, and is an important practical consideration in both remote sensing and traditional biodiversity studies. On the one hand, with decreasing spatial and spectral resolution, the differences among different optical types may become weak or even disappear. Alternately, high spatial and/or spectral resolution may introduce redundant or contradictory information. For example, at high resolution, the variation within optical types (e.g., between leaves on a single plant canopy) may add complexity unrelated to specie richness. We studied the scale-dependence of optical diversity in a prairie ecosystem at Cedar Creek Ecosystem Science Reserve, Minnesota, USA using a variety of spectrometers from several platforms on the ground and in the air. Using the coefficient of variation (CV) of spectra as an indicator of optical diversity, we found that high richness plots generally have a higher coefficient of variation. High resolution imaging spectrometer data (1 mm pixels) showed the highest sensitivity to richness level. With decreasing spatial resolution, the difference in CV between richness levels decreased, but remained significant. These findings can be used to guide airborne studies of biodiversity and develop more effective large-scale biodiversity sampling methods.

Species associations structured by environment and land-use history promote beta-diversity in a temperate forest.

PubMed

Murphy, Stephen J; Audino, Livia D; Whitacre, James; Eck, Jenalle L; Wenzel, John W; Queenborough, Simon A; Comita, Liza S

2015-03-01

Patterns of diversity and community composition in forests are controlled by a combination of environmental factors, historical events, and stochastic or neutral mechanisms. Each of these processes has been linked to forest community assembly, but their combined contributions to alpha and beta-diversity in forests has not been well explored. Here we use variance partitioning to analyze approximately 40,000 individual trees of 49 species, collected within 137 ha of sampling area spread across a 900-ha temperate deciduous forest reserve in Pennsylvania to ask (1) To what extent is site-to-site variation in species richness and community composition of a temperate forest explained by measured environmental gradients and by spatial descriptors (used here to estimate dispersal-assembly or unmeasured, spatially structured processes)? (2) How does the incorporation of land-use history information increase the importance attributed to deterministic community assembly? and (3) How do the distributions and abundances of individual species within the community correlate with these factors? Environmental variables (i.e., topography, soils, and distance to stream), spatial descriptors (i.e., spatial eigenvectors derived from Cartesian coordinates), and land-use history variables (i.e., land-use type and intensity, forest age, and distance to road), explained about half of the variation in both species richness and community composition. Spatial descriptors explained the most variation, followed by measured environmental variables and then by land- use history. Individual species revealed variable responses to each of these sets of predictor variables. Several species were associated with stream habitats, and others were strictly delimited across opposing north- and south-facing slopes. Several species were also associated with areas that experienced recent (i.e., <100 years) human land-use impacts. These results indicate that deterministic factors, including environmental and land-use history variables, are important drivers of community response. The large amount of "unexplained" variation seen here (about 50%) is commonly observed in other such studies attempting to explain distribution and abundance patterns of plant communities. Determining whether such large fractions of unaccounted for variation are caused by a lack of sufficient data, or are an indication of stochastic features of forest communities globally, will remain an important challenge for ecologists in the future.

Ecological Drivers of Biogeographic Patterns of Soil Archaeal Community

PubMed Central

Zheng, Yuan-Ming; Cao, Peng; Fu, Bojie; Hughes, Jane M.; He, Ji-Zheng

2013-01-01

Knowledge about the biogeography of organisms has long been a focus in ecological research, including the mechanisms that generate and maintain diversity. In this study, we targeted a microbial group relatively underrepresented in the microbial biogeographic literature, the soil Archaea. We surveyed the archaeal abundance and community composition using real-time quantitative PCR and T-RFLP approaches for 105 soil samples from 2 habitat types to identify the archaeal distribution patterns and factors driving these patterns. Results showed that the soil archaeal community was affected by spatial and environmental variables, and 79% and 51% of the community variation was explained in the non-flooded soil (NS) and flooded soil (FS) habitat, respectively, showing its possible biogeographic distribution. The diversity patterns of soil Archaea across the landscape were influenced by a combination of stochastic and deterministic processes. The contribution from neutral processes was higher than that from deterministic processes associated with environmental variables. The variables pH, sample depth and longitude played key roles in determining the archaeal distribution in the NS habitat, while sampling depth, longitude and NH4 +-N were most important in the FS habitat. Overall, there might be similar ecological drivers in the soil archaeal community as in macroorganism communities. PMID:23717418

Multispecies coexistence of trees in tropical forests: spatial signals of topographic niche differentiation increase with environmental heterogeneity.

PubMed

Brown, C; Burslem, D F R P; Illian, J B; Bao, L; Brockelman, W; Cao, M; Chang, L W; Dattaraja, H S; Davies, S; Gunatilleke, C V S; Gunatilleke, I A U N; Huang, J; Kassim, A R; Lafrankie, J V; Lian, J; Lin, L; Ma, K; Mi, X; Nathalang, A; Noor, S; Ong, P; Sukumar, R; Su, S H; Sun, I F; Suresh, H S; Tan, S; Thompson, J; Uriarte, M; Valencia, R; Yap, S L; Ye, W; Law, R

2013-08-07

Neutral and niche theories give contrasting explanations for the maintenance of tropical tree species diversity. Both have some empirical support, but methods to disentangle their effects have not yet been developed. We applied a statistical measure of spatial structure to data from 14 large tropical forest plots to test a prediction of niche theory that is incompatible with neutral theory: that species in heterogeneous environments should separate out in space according to their niche preferences. We chose plots across a range of topographic heterogeneity, and tested whether pairwise spatial associations among species were more variable in more heterogeneous sites. We found strong support for this prediction, based on a strong positive relationship between variance in the spatial structure of species pairs and topographic heterogeneity across sites. We interpret this pattern as evidence of pervasive niche differentiation, which increases in importance with increasing environmental heterogeneity.

Clonality, genetic diversity and support for the diversifying selection hypothesis in natural populations of a flower-living yeast.

PubMed

Herrera, C M; Pozo, M I; Bazaga, P

2011-11-01

Vast amounts of effort have been devoted to investigate patterns of genetic diversity and structuring in plants and animals, but similar information is scarce for organisms of other kingdoms. The study of the genetic structure of natural populations of wild yeasts can provide insights into the ecological and genetic correlates of clonality, and into the generality of recent hypotheses postulating that microbial populations lack the potential for genetic divergence and allopatric speciation. Ninety-one isolates of the flower-living yeast Metschnikowia gruessii from southeastern Spain were DNA fingerprinted using amplified fragment length polymorphism (AFLP) markers. Genetic diversity and structuring was investigated with band-based methods and model- and nonmodel-based clustering. Linkage disequilibrium tests were used to assess reproduction mode. Microsite-dependent, diversifying selection was tested by comparing genetic characteristics of isolates from bumble bee vectors and different floral microsites. AFLP polymorphism (91%) and genotypic diversity were very high. Genetic diversity was spatially structured, as shown by amova (Φ(st)  = 0.155) and clustering. The null hypothesis of random mating was rejected, clonality seeming the prevailing reproductive mode in the populations studied. Genetic diversity of isolates declined from bumble bee mouthparts to floral microsites, and frequency of five AFLP markers varied significantly across floral microsites, thus supporting the hypothesis of diversifying selection on clonal lineages. Wild populations of clonal fungal microbes can exhibit levels of genetic diversity and spatial structuring that are not singularly different from those shown by sexually reproducing plants or animals. Microsite-dependent, divergent selection can maintain high local and regional genetic diversity in microbial populations despite extensive clonality. © 2011 Blackwell Publishing Ltd.

Constancy despite variability: Local and regional macrofaunal diversity in intertidal seagrass beds

NASA Astrophysics Data System (ADS)

Boyé, Aurélien; Legendre, Pierre; Grall, Jacques; Gauthier, Olivier

2017-12-01

The importance of seagrass habitat for the diversity of benthic fauna has been extensively studied worldwide. Most of the information available is, however, about α diversity while little consideration has been given to β diversity. To fill the knowledge gaps regarding the variability of epifaunal and infaunal seagrass assemblages at large spatial and temporal scales, we scrutinized an extensive dataset covering five years of monitoring of eight intertidal Zostera marina meadows around Brittany (France). High species richness arose at the regional scale from the combination of high local diversity of the meadows and substantial among-meadows β diversity. Epifauna and infauna appeared as distinct self-communities as they displayed different spatial and temporal patterns and varied in their responses to local hydrological conditions. Infauna had higher total β diversity than epifauna due to a tighter link to the great variability of local environmental conditions in the region. Both exhibited substantial variations in species composition and community structure with variations of dominant species that were accompanied by extensive change in numerous rare species. The dominant epifaunal species were all grazers. Changes in species composition were induced mostly by species replacement and rarely by richness differences between meadows. Indeed, species richness remained within a narrow range for all seagrass beds, suggesting a potential carrying capacity for species richness of the meadows. Overall, all meadows contributed equally to the regional turnover of seagrass macrofauna, emphasizing high variability and complementarity among beds at the regional scale. The implications of this substantial within-seagrass variability for the functioning of benthic ecosystems at broad scale and for conservation purposes in habitat mosaics warrant further investigations but our results clearly advocate taking into account within-habitat variation when evaluating the diversity of benthic habitats and the potential effect of habitat loss.

Population genetic structure and direct observations reveal sex-reversed patterns of dispersal in a cooperative bird.

PubMed

Harrison, Xavier A; York, Jennifer E; Young, Andrew J

2014-12-01

Sex-biased dispersal is pervasive and has diverse evolutionary implications, but the fundamental drivers of dispersal sex biases remain unresolved. This is due in part to limited diversity within taxonomic groups in the direction of dispersal sex biases, which leaves hypothesis testing critically dependent upon identifying rare reversals of taxonomic norms. Here, we use a combination of observational and genetic data to demonstrate a rare reversal of the avian sex bias in dispersal in the cooperatively breeding white-browed sparrow weaver (Plocepasser mahali). Direct observations revealed that (i) natal philopatry was rare, with both sexes typically dispersing locally to breed, and (ii), unusually for birds, males bred at significantly greater distances from their natal group than females. Population genetic analyses confirmed these patterns, as (i) corrected Assignment index (AIc), FST tests and isolation-by-distance metrics were all indicative of longer dispersal distances among males than females, and (ii) spatial autocorrelation analysis indicated stronger within-group genetic structure among females than males. Examining the spatial scale of extra-group mating highlighted that the resulting 'sperm dispersal' could have acted in concert with individual dispersal to generate these genetic patterns, but gamete dispersal alone cannot account entirely for the sex differences in genetic structure observed. That leading hypotheses for the evolution of dispersal sex biases cannot readily account for these sex-reversed patterns of dispersal in white-browed sparrow weavers highlights the continued need for attention to alternative explanations for this enigmatic phenomenon. We highlight the potential importance of sex differences in the distances over which dispersal opportunities can be detected. © 2014 The Authors. Molecular Ecology Published by John Wiley & Sons Ltd.

Challenges of pedodiversity in soil science

NASA Astrophysics Data System (ADS)

Toomanian, N.; Esfandiarpoor, I.

2010-12-01

Soil diversity is not a completely new concept in soil science. It has been discussed from early times but it was not challenged this much broad. Ibañez with introducing the pedodiversity opened a new conceptual window to ease the induction of the soils complexity, spatial and temporal evolution and distribution. Pedodiversity now attracts more attention and goes to open new windows in soil science. Pedodiversity faces now with different challenges, which could be critical in its way on. Do the current soil diversity indices conceptually define all aspects of soil variability, or do we need to bind them with other characteristics like taxonomic distances? How is the soil individualism defined within the context of spatial variability and soil continuum? How are pedocomplexity, connectance, pedodiversity and soil spatial structure related? Can the changes of soil diversity be accounted as the rate of soil development? Can a range of pedodiversity index be a scale for soil series definition? Initial and some of current pedodiversity studies were/are focused on the concepts and measurement of pedodiversity and soil complexity indices of soilscape compared with the biological diversity and complexity. However, for the pedogenetic studies, the most important issues are the evolutionary concerns out of this approach compared with the other biotic systems. The new contexts, which should be more undertaken in future studies are: functional diversity, temporal diversity, study of soil and landform extinction and preservation. The last question could be: how pedodiversity could be changed under different understanding levels? A case study has been carried out in Charmahal and Bakhtiary province, Iran. Its objectives are the following: comparing the pedodiversity indices combined with and without taxonomic distances within tow replication of a geomorphic surface (Pi 111). What the pedodiversity says here? Did the unique calcification process which rules the soil formation here result in endemism or soil zonality? Do different pedodiversity indices correlate with the soil patterns?

Species-richness patterns of the living collections of the world's botanic gardens: a matter of socio-economics?

PubMed

Golding, Janice; Güsewell, Sabine; Kreft, Holger; Kuzevanov, Victor Y; Lehvävirta, Susanna; Parmentier, Ingrid; Pautasso, Marco

2010-05-01

The botanic gardens of the world are now unmatched ex situ collections of plant biodiversity. They mirror two biogeographical patterns (positive diversity-area and diversity-age relationships) but differ from nature with a positive latitudinal gradient in their richness. Whether these relationships can be explained by socio-economic factors is unknown. Species and taxa richness of a comprehensive sample of botanic gardens were analysed as a function of key ecological and socio-economic factors using (a) multivariate models controlling for spatial autocorrelation and (b) structural equation modelling. The number of plant species in botanic gardens increases with town human population size and country Gross Domestic Product (GDP) per person. The country flora richness is not related to the species richness of botanic gardens. Botanic gardens in more populous towns tend to have a larger area and can thus host richer living collections. Botanic gardens in richer countries have more species, and this explains the positive latitudinal gradient in botanic gardens' species richness. Socio-economic factors contribute to shaping patterns in the species richness of the living collections of the world's botanic gardens.

Coalescent Times and Patterns of Genetic Diversity in Species with Facultative Sex: Effects of Gene Conversion, Population Structure, and Heterogeneity

PubMed Central

Hartfield, Matthew; Wright, Stephen I.; Agrawal, Aneil F.

2016-01-01

Many diploid organisms undergo facultative sexual reproduction. However, little is currently known concerning the distribution of neutral genetic variation among facultative sexual organisms except in very simple cases. Understanding this distribution is important when making inferences about rates of sexual reproduction, effective population size, and demographic history. Here we extend coalescent theory in diploids with facultative sex to consider gene conversion, selfing, population subdivision, and temporal and spatial heterogeneity in rates of sex. In addition to analytical results for two-sample coalescent times, we outline a coalescent algorithm that accommodates the complexities arising from partial sex; this algorithm can be used to generate multisample coalescent distributions. A key result is that when sex is rare, gene conversion becomes a significant force in reducing diversity within individuals. This can reduce genomic signatures of infrequent sex (i.e., elevated within-individual allelic sequence divergence) or entirely reverse the predicted patterns. These models offer improved methods for assessing null patterns of molecular variation in facultative sexual organisms. PMID:26584902

Coalescent Times and Patterns of Genetic Diversity in Species with Facultative Sex: Effects of Gene Conversion, Population Structure, and Heterogeneity.

PubMed

Hartfield, Matthew; Wright, Stephen I; Agrawal, Aneil F

2016-01-01

Many diploid organisms undergo facultative sexual reproduction. However, little is currently known concerning the distribution of neutral genetic variation among facultative sexual organisms except in very simple cases. Understanding this distribution is important when making inferences about rates of sexual reproduction, effective population size, and demographic history. Here we extend coalescent theory in diploids with facultative sex to consider gene conversion, selfing, population subdivision, and temporal and spatial heterogeneity in rates of sex. In addition to analytical results for two-sample coalescent times, we outline a coalescent algorithm that accommodates the complexities arising from partial sex; this algorithm can be used to generate multisample coalescent distributions. A key result is that when sex is rare, gene conversion becomes a significant force in reducing diversity within individuals. This can reduce genomic signatures of infrequent sex (i.e., elevated within-individual allelic sequence divergence) or entirely reverse the predicted patterns. These models offer improved methods for assessing null patterns of molecular variation in facultative sexual organisms. Copyright © 2016 by the Genetics Society of America.

Programming Cells for Dynamic Assembly of Inorganic Nano-Objects with Spatiotemporal Control.

PubMed

Wang, Xinyu; Pu, Jiahua; An, Bolin; Li, Yingfeng; Shang, Yuequn; Ning, Zhijun; Liu, Yi; Ba, Fang; Zhang, Jiaming; Zhong, Chao

2018-04-01

Programming living cells to organize inorganic nano-objects (NOs) in a spatiotemporally precise fashion would advance new techniques for creating ordered ensembles of NOs and new bio-abiotic hybrid materials with emerging functionalities. Bacterial cells often grow in cellular communities called biofilms. Here, a strategy is reported for programming dynamic biofilm formation for the synchronized assembly of discrete NOs or hetero-nanostructures on diverse interfaces in a dynamic, scalable, and hierarchical fashion. By engineering Escherichia coli to sense blue light and respond by producing biofilm curli fibers, biofilm formation is spatially controlled and the patterned NOs' assembly is simultaneously achieved. Diverse and complex fluorescent quantum dot patterns with a minimum patterning resolution of 100 µm are demonstrated. By temporally controlling the sequential addition of NOs into the culture, multilayered heterostructured thin films are fabricated through autonomous layer-by-layer assembly. It is demonstrated that biologically dynamic self-assembly can be used to advance a new repertoire of nanotechnologies and materials with increasing complexity that would be otherwise challenging to produce. © 2018 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Does seasonality drive spatial patterns in demography? Variation in survival in African reed warblers Acrocephalus baeticatus across southern Africa does not reflect global patterns

PubMed Central

Jansen, Dorine YM; Abadi, Fitsum; Harebottle, Doug; Altwegg, Res

2014-01-01

Among birds, northern temperate species generally have larger clutches, shorter development periods and lower adult survival than similarly-sized southern and tropical species. Even though this global pattern is well accepted, the driving mechanism is still not fully understood. The main theories are founded on the differing environmental seasonality of these zones (higher seasonality in the North). These patterns arise in cross-species comparisons, but we hypothesized that the same patterns should arise among populations within a species if different types of seasonality select for different life histories. Few studies have examined this. We estimated survival of an azonal habitat specialist, the African reed warbler, across the environmentally diverse African subcontinent, and related survival to latitude and to the seasonality of the different environments of their breeding habitats. Data (1998–2010) collected through a public ringing scheme were analyzed with hierarchical capture-mark-recapture models to determine resident adult survival and its spatial variance across sixteen vegetation units spread across four biomes. The models were defined as state-space multi-state models to account for transience and implemented in a Bayesian framework. We did not find a latitudinal trend in survival or a clear link between seasonality and survival. Spatial variation in survival was substantial across the sixteen sites (spatial standard deviation of the logit mean survival: 0.70, 95% credible interval (CRI): 0.33–1.27). Mean site survival ranged from 0.49 (95% CRI: 0.18–0.80) to 0.83 (95% CRI: 0.62–0.97) with an overall mean of 0.67 (95% CRI: 0.47–0.85). A hierarchical modeling approach enabled us to estimate spatial variation in survival of the African reed warbler across the African subcontinent from sparse data. Although we could not confirm the global pattern of higher survival in less seasonal environments, our findings from a poorly studied region contribute to the study of life-history strategies. PMID:24772268

Vast underestimation of Madagascar's biodiversity evidenced by an integrative amphibian inventory

PubMed Central

Vieites, David R.; Wollenberg, Katharina C.; Andreone, Franco; Köhler, Jörn; Glaw, Frank; Vences, Miguel

2009-01-01

Amphibians are in decline worldwide. However, their patterns of diversity, especially in the tropics, are not well understood, mainly because of incomplete information on taxonomy and distribution. We assess morphological, bioacoustic, and genetic variation of Madagascar's amphibians, one of the first near-complete taxon samplings from a biodiversity hotspot. Based on DNA sequences of 2,850 specimens sampled from over 170 localities, our analyses reveal an extreme proportion of amphibian diversity, projecting an almost 2-fold increase in species numbers from the currently described 244 species to a minimum of 373 and up to 465. This diversity is widespread geographically and across most major phylogenetic lineages except in a few previously well-studied genera, and is not restricted to morphologically cryptic clades. We classify the genealogical lineages in confirmed and unconfirmed candidate species or deeply divergent conspecific lineages based on concordance of genetic divergences with other characters. This integrative approach may be widely applicable to improve estimates of organismal diversity. Our results suggest that in Madagascar the spatial pattern of amphibian richness and endemism must be revisited, and current habitat destruction may be affecting more species than previously thought, in amphibians as well as in other animal groups. This case study suggests that worldwide tropical amphibian diversity is probably underestimated at an unprecedented level and stresses the need for integrated taxonomic surveys as a basis for prioritizing conservation efforts within biodiversity hotspots. PMID:19416818

Vast underestimation of Madagascar's biodiversity evidenced by an integrative amphibian inventory.

PubMed

Vieites, David R; Wollenberg, Katharina C; Andreone, Franco; Köhler, Jörn; Glaw, Frank; Vences, Miguel

2009-05-19

Amphibians are in decline worldwide. However, their patterns of diversity, especially in the tropics, are not well understood, mainly because of incomplete information on taxonomy and distribution. We assess morphological, bioacoustic, and genetic variation of Madagascar's amphibians, one of the first near-complete taxon samplings from a biodiversity hotspot. Based on DNA sequences of 2,850 specimens sampled from over 170 localities, our analyses reveal an extreme proportion of amphibian diversity, projecting an almost 2-fold increase in species numbers from the currently described 244 species to a minimum of 373 and up to 465. This diversity is widespread geographically and across most major phylogenetic lineages except in a few previously well-studied genera, and is not restricted to morphologically cryptic clades. We classify the genealogical lineages in confirmed and unconfirmed candidate species or deeply divergent conspecific lineages based on concordance of genetic divergences with other characters. This integrative approach may be widely applicable to improve estimates of organismal diversity. Our results suggest that in Madagascar the spatial pattern of amphibian richness and endemism must be revisited, and current habitat destruction may be affecting more species than previously thought, in amphibians as well as in other animal groups. This case study suggests that worldwide tropical amphibian diversity is probably underestimated at an unprecedented level and stresses the need for integrated taxonomic surveys as a basis for prioritizing conservation efforts within biodiversity hotspots.

Selecting for extinction: nonrandom disease-associated extinction homogenizes amphibian biotas.

PubMed

Smith, Kevin G; Lips, Karen R; Chase, Jonathan M

2009-10-01

Studying the patterns in which local extinctions occur is critical to understanding how extinctions affect biodiversity at local, regional and global spatial scales. To understand the importance of patterns of extinction at a regional spatial scale, we use data from extirpations associated with a widespread pathogenic agent of amphibian decline, Batrachochytrium dendrobatidis (Bd) as a model system. We apply novel null model analyses to these data to determine whether recent extirpations associated with Bd have resulted in selective extinction and homogenization of diverse tropical American amphibian biotas. We find that Bd-associated extinctions in this region were nonrandom and disproportionately, but not exclusively, affected low-occupancy and endemic species, resulting in homogenization of the remnant amphibian fauna. The pattern of extirpations also resulted in phylogenetic homogenization at the family level and ecological homogenization of reproductive mode and habitat association. Additionally, many more species were extirpated from the region than would be expected if extirpations occurred randomly. Our results indicate that amphibian declines in this region are an extinction filter, reducing regional amphibian biodiversity to highly similar relict assemblages and ultimately causing amplified biodiversity loss at regional and global scales.

Isolation by environment.

PubMed

Wang, Ian J; Bradburd, Gideon S

2014-12-01

The interactions between organisms and their environments can shape distributions of spatial genetic variation, resulting in patterns of isolation by environment (IBE) in which genetic and environmental distances are positively correlated, independent of geographic distance. IBE represents one of the most important patterns that results from the ways in which landscape heterogeneity influences gene flow and population connectivity, but it has only recently been examined in studies of ecological and landscape genetics. Nevertheless, the study of IBE presents valuable opportunities to investigate how spatial heterogeneity in ecological processes, agents of selection and environmental variables contributes to genetic divergence in nature. New and increasingly sophisticated studies of IBE in natural systems are poised to make significant contributions to our understanding of the role of ecology in genetic divergence and of modes of differentiation both within and between species. Here, we describe the underlying ecological processes that can generate patterns of IBE, examine its implications for a wide variety of disciplines and outline several areas of future research that can answer pressing questions about the ecological basis of genetic diversity. © 2014 John Wiley & Sons Ltd.

Floral resource availability from groundcover promotes bee abundance in coffee agroecosystems.

PubMed

Fisher, Kaleigh; Gonthier, David J; Ennis, Katherine K; Perfecto, Ivette

2017-09-01

Patterns of bee abundance and diversity across different spatial scales have received thorough research consideration. However, the impact of short- and long-term temporal resource availability on biodiversity has been less explored. This is highly relevant in tropical agricultural systems for pollinators, as many foraging periods of pollinators extend beyond flowering of any single crop species. In this study, we sought to understand how bee communities in tropical agroecosystems changed between seasons, and if short- and long-term floral resource availability influenced their diversity and abundance. We used a threshold analysis approach in order to explore this relationship at two time scales. This study took place in a region dominated by coffee agroecosystems in Southern Mexico. This was an ideal system because the landscape offers a range of coffee management regimes that maintain heterogeneity in floral resource availability spatially and temporally. We found that the bee community varies significantly between seasons. There were higher abundances of native social, solitary and managed honey bees during the dry season when coffee flowers. Additionally, we found that floral resources from groundcover, but not trees, were associated with bee abundance. Further, the temporal scale of the availability of these resources is important, whereby short-term floral resource availability appears particularly important in maintaining high bee abundance at sites with lower seasonal complementarity. We argue that in addition to spatial resource heterogeneity, temporal resource heterogeneity is critical in explaining bee community patterns, and should thus be considered to promote pollinator conservation. © 2017 by the Ecological Society of America.

Spatial pattern formation of microbes at the soil microscale affect soil C and N turnover in an individual-based microbial community model

NASA Astrophysics Data System (ADS)

Kaiser, Christina; Evans, Sarah; Dieckmann, Ulf; Widder, Stefanie

2016-04-01

At the μm-scale, soil is a highly structured and complex environment, both in physical as well as in biological terms, characterized by non-linear interactions between microbes, substrates and minerals. As known from mathematics and theoretical ecology, spatial structure significantly affects the system's behaviour by enabling synergistic dynamics, facilitating diversity, and leading to emergent phenomena such as self-organisation and self-regulation. Such phenomena, however, are rarely considered when investigating mechanisms of microbial soil organic matter turnover. Soil organic matter is the largest terrestrial reservoir for organic carbon (C) and nitrogen (N) and plays a pivotal role in global biogeochemical cycles. Still, the underlying mechanisms of microbial soil organic matter buildup and turnover remain elusive. We explored mechanisms of microbial soil organic matter turnover using an individual-based, stoichiometrically and spatially explicit computer model, which simulates the microbial de-composer system at the soil microscale (i.e. on a grid of 100 x 100 soil microsites). Soil organic matter dynamics in our model emerge as the result of interactions among individual microbes with certain functional traits (f.e. enzyme production rates, growth rates, cell stoichiometry) at the microscale. By degrading complex substrates, and releasing labile substances microbes in our model continusly shape their environment, which in turn feeds back to spatiotemporal dynamics of the microbial community. In order to test the effect of microbial functional traits and organic matter input rate on soil organic matter turnover and C and N storage, we ran the model into steady state using continuous inputs of fresh organic material. Surprisingly, certain parameter settings that induce resource limitation of microbes lead to regular spatial pattern formation (f.e. moving spiral waves) of microbes and substrate at the μm-scale at steady-state. The occurrence of these pattern can be explained by the Turing mechanism. These pattern formation had strong consequences for process rates, as well as for C and N storage in the soil at the steady state: Scenarios that exhibited pattern formation were generally associated with higher C storage at steady state compared to those without pattern formation (i.e. at non-limiting conditions for microbes). Moreover, pattern formation lead to a spatial decoupling of C and N turnover processes, and to a spatial decoupling of microbial N mineralization and N immobilization. Taken together, our theoretical analysis shows that self-organisation may be a feature of the soil decomposer system, with consequences for process rates of microbial C and N turnover. Pattern formation through spatial self-organization, which has been observed on larger spatial scales in other resource-limited communities (e.g., vegetation patterns in arid or wetland eco-systems), may also occur at the soil microscale, leaving its mark on the soil's storage capacity for C and N.

Evaluating simulated functional trait patterns and quantifying modelled trait diversity effects on simulated ecosystem fluxes

NASA Astrophysics Data System (ADS)

Pavlick, R.; Schimel, D.

2014-12-01

Dynamic Global Vegetation Models (DGVMs) typically employ only a small set of Plant Functional Types (PFTs) to represent the vast diversity of observed vegetation forms and functioning. There is growing evidence, however, that this abstraction may not adequately represent the observed variation in plant functional traits, which is thought to play an important role for many ecosystem functions and for ecosystem resilience to environmental change. The geographic distribution of PFTs in these models is also often based on empirical relationships between present-day climate and vegetation patterns. Projections of future climate change, however, point toward the possibility of novel regional climates, which could lead to no-analog vegetation compositions incompatible with the PFT paradigm. Here, we present results from the Jena Diversity-DGVM (JeDi-DGVM), a novel traits-based vegetation model, which simulates a large number of hypothetical plant growth strategies constrained by functional tradeoffs, thereby allowing for a more flexible temporal and spatial representation of the terrestrial biosphere. First, we compare simulated present-day geographical patterns of functional traits with empirical trait observations (in-situ and from airborne imaging spectroscopy). The observed trait patterns are then used to improve the tradeoff parameterizations of JeDi-DGVM. Finally, focusing primarily on the simulated leaf traits, we run the model with various amounts of trait diversity. We quantify the effects of these modeled biodiversity manipulations on simulated ecosystem fluxes and stocks for both present-day conditions and transient climate change scenarios. The simulation results reveal that the coarse treatment of plant functional traits by current PFT-based vegetation models may contribute substantial uncertainty regarding carbon-climate feedbacks. Further development of trait-based models and further investment in global in-situ and spectroscopic plant trait observations are needed.

Diversity and Spatiotemporal Distribution of Larval Odonate Assemblages in Temperate Neotropical Farm Ponds

PubMed Central

Pires, Mateus Marques; Kotzian, Carla Bender; Spies, Marcia Regina

2014-01-01

Abstract Farm ponds help maintain diversity in altered landscapes. However, studies on the features that drive this type of property in the Neotropics are still lacking, especially for the insect fauna. We analyzed the spatial and temporal distribution of odonate larval assemblages in farm ponds. Odonates were sampled monthly at four farm ponds from March 2008 to February 2009 in a temperate montane region of southern Brazil. A small number of genera were frequent and accounted for most of the dominant fauna. The dominant genera composition differed among ponds. Local spatial drivers such as area, hydroperiod, and margin vegetation structure likely explain these results more than spatial predictors due to the small size of the study area. Circular analysis detected seasonal effect on assemblage abundance but not on richness. Seasonality in abundance was related to the life cycles of a few dominant genera. This result was explained by temperature and not rainfall due to the temperate climate of the region studied. The persistence of dominant genera and the sparse occurrence of many taxa over time probably led to a lack in a seasonal pattern in assemblage richness. PMID:25527585

Reproductive isolation and patterns of genetic differentiation in a cryptic butterfly species complex

PubMed Central

Dincâ, V; Wiklund, C; Lukhtanov, V A; Kodandaramaiah, U; Norén, K; Dapporto, L; Wahlberg, N; Vila, R; Friberg, M

2013-01-01

Molecular studies of natural populations are often designed to detect and categorize hidden layers of cryptic diversity, and an emerging pattern suggests that cryptic species are more common and more widely distributed than previously thought. However, these studies are often decoupled from ecological and behavioural studies of species divergence. Thus, the mechanisms by which the cryptic diversity is distributed and maintained across large spatial scales are often unknown. In 1988, it was discovered that the common Eurasian Wood White butterfly consisted of two species (Leptidea sinapis and Leptidea reali), and the pair became an emerging model for the study of speciation and chromosomal evolution. In 2011, the existence of a third cryptic species (Leptidea juvernica) was proposed. This unexpected discovery raises questions about the mechanisms preventing gene flow and about the potential existence of additional species hidden in the complex. Here, we compare patterns of genetic divergence across western Eurasia in an extensive data set of mitochondrial and nuclear DNA sequences with behavioural data on inter- and intraspecific reproductive isolation in courtship experiments. We show that three species exist in accordance with both the phylogenetic and biological species concepts and that additional hidden diversity is unlikely to occur in Europe. The Leptidea species are now the best studied cryptic complex of butterflies in Europe and a promising model system for understanding the formation of cryptic species and the roles of local processes, colonization patterns and heterospecific interactions for ecological and evolutionary divergence. PMID:23909947

Use of multiple functional traits of protozoa for bioassessment of marine pollution.

PubMed

Zhong, Xiaoxiao; Xu, Guangjian; Xu, Henglong

2017-06-30

Ecological parameters based on multiply functional traits have many advantages for monitoring programs by reducing "signal to noise" ratios of observed species data. To identify potential indicators for bioassessment of marine pollution in function space, the functional patterns of protozoan communities and relationships with environmental changes were studied in coastal waters of the Yellow Sea during a 1-year period. The results showed that: (1) the spatial variability in functional trait distributions of the protozoa was significantly associated with changes in environmental variables, especially chemical oxygen demand (COD) and nutrients on spatial scale; (2) the functional traits, especially food resources and feeding type, were significantly correlated with COD and nutrients; and (3) the functional diversity indices were generally related to nutrients or COD. Based on the results, we suggest that the functional traits and diversity indices of protozoan communities may be used as more effective indicators for bioassessment of marine pollution. Copyright © 2017 Elsevier Ltd. All rights reserved.

Use of ecoacoustics to determine biodiversity patterns across ecological gradients.

PubMed

Grant, Paul B C; Samways, Michael J

2016-12-01

The variety of local animal sounds characterizes a landscape. We used ecoacoustics to noninvasively assess the species richness of various biotopes typical of an ecofriendly forest plantation with diverse ecological gradients and both nonnative and indigenous vegetation. The reference area was an adjacent large World Heritage Site protected area (PA). All sites were in a global biodiversity hotspot. Our results showed how taxa segregated into various biotopes. We identified 65 singing species, including birds, frogs, crickets, and katydids. Large, natural, protected grassland sites in the PA had the highest mean acoustic diversity (14.1 species/site). Areas covered in nonnative timber or grass species were devoid of acoustic species. Sites grazed by native and domestic megaherbivores were fairly rich (5.1) in acoustic species but none were unique to this habitat type, where acoustic diversity was greater than in intensively managed grassland sites (0.04). Natural vegetation patches inside the plantation mosaic supported high mean acoustic diversity (indigenous forests 7.6, grasslands 8.0, wetlands 9.1), which increased as plant heterogeneity and patch size increased. Indigenous forest patches within the plantation mosaic contained a highly characteristic acoustic species assemblage, emphasizing their complementary contribution to local biodiversity. Overall, acoustic signals determined spatial biodiversity patterns and can be a useful tool for guiding conservation. © 2016 Society for Conservation Biology.

Global linkages between teleconnection patterns and the terrestrial biosphere

NASA Astrophysics Data System (ADS)

Dahlin, Kyla M.; Ault, Toby R.

2018-07-01

Interannual variability in the global carbon cycle is largely due to variations in carbon uptake by terrestrial ecosystems, yet linkages between climate variability and variability in the terrestrial carbon cycle are not well understood at the global scale. Using a 30-year satellite record of semi-monthly leaf area index (LAI), we show that four modes of climate variability - El Niño/Southern Oscillation, the North Atlantic Oscillation, the Atlantic Meridional Mode, and the Indian Ocean Dipole Mode - strongly impact interannual vegetation growth patterns, with 68% of the land surface impacted by at least one of these teleconnection patterns, yet the spatial distribution of these impacts is heterogeneous. Considering the patterns' impacts by biome, none has an exclusively positive or negative relationship with LAI. Our findings imply that future changes in the frequency and/or magnitude of teleconnection patterns will lead to diverse changes to the terrestrial biosphere and the global carbon cycle.

Polariton Pattern Formation and Photon Statistics of the Associated Emission

NASA Astrophysics Data System (ADS)

Whittaker, C. E.; Dzurnak, B.; Egorov, O. A.; Buonaiuto, G.; Walker, P. M.; Cancellieri, E.; Whittaker, D. M.; Clarke, E.; Gavrilov, S. S.; Skolnick, M. S.; Krizhanovskii, D. N.

2017-07-01

We report on the formation of a diverse family of transverse spatial polygon patterns in a microcavity polariton fluid under coherent driving by a blue-detuned pump. Patterns emerge spontaneously as a result of energy-degenerate polariton-polariton scattering from the pump state to interfering high-order vortex and antivortex modes, breaking azimuthal symmetry. The interplay between a multimode parametric instability and intrinsic optical bistability leads to a sharp spike in the value of second-order coherence g(2 )(0 ) of the emitted light, which we attribute to the strongly superlinear kinetics of the underlying scattering processes driving the formation of patterns. We show numerically by means of a linear stability analysis how the growth of parametric instabilities in our system can lead to spontaneous symmetry breaking, predicting the formation and competition of different pattern states in good agreement with experimental observations.

Genetic diversity pattern of microeukaryotic communities and its relationship with the environment based on PCR-DGGE and T-RFLP techniques in Dongshan Bay, southeast China

NASA Astrophysics Data System (ADS)

Zhang, Wenjing; Mo, Yuanyuan; Yang, Jun; Zhou, Jing; Lin, Yuanshao; Isabwe, Alain; Zhang, Jian; Gao, Xiu; Yu, Zheng

2018-07-01

Microeukaryotes play important roles in aquatic ecosystems, and could act as drivers of the biological nutrient cycling processes. However, compared with prokaryotic ones, little is known about the genetic diversity pattern of their community, and the environmental factors affecting their ecological pattern, especially in marine ecosystems. In this study, we used denaturing gradient gel electrophoresis (DGGE) and terminal restriction fragment length polymorphism (T-RFLP) to explore the genetic diversity structure of microeukaryotic communities in Dongshan Bay, southeast China. Our results revealed that microeukaryotic diversity ranged from 31 to 48 phylotypes (on average, 42) using the DGGE approach, while from 22 to 38 phylotypes (on average, 30) based on T-RFLP method, and the Shannon-Wiener diversity (DGGE-based) was relatively higher, suggesting that DGGE displayed a slightly higher resolution than T-RFLP. Surprisingly, the DGGE showed significant horizontal difference among microeukaryotic communities, but was similar with T-RFLP analysis that had no significant influence on microeukaryotic diversity at vertical scale. Further, redundancy analysis (RDA) indicated that the DGGE-based microeukaryotic communities distribution was significantly correlated with three environmental factors (Chl-a, TP and salinity), whereas microeukaryotic community revealed by T-RFLP was affected by four environmental factors namely salinity, temperature, depth and NOX-N. Compared with RDA, BIO-ENV analysis showed that heterotrophic bacteria and NOX-N were important environmental variable influencing microeukaryotic communities in both methods. These differences may be attributed to the noisy effects caused by the relatively large number of environmental variables. Generally speaking, despite differences in beta-diversity ordination for both DGGE and T-RFLP methods, there exists some consistency in the results of both techniques in terms of microeukaryotes responses to the environmental variables. These results suggested that environmental parameters had a great effect on spatial distribution of microeukaryotic community and contributed to marine ecosystem health to be further evaluated.

Ancient Urban Ecology Reconstructed from Archaeozoological Remains of Small Mammals in the Near East

PubMed Central

Weissbrod, Lior; Malkinson, Dan; Cucchi, Thomas; Gadot, Yuval; Finkelstein, Israel; Bar-Oz, Guy

2014-01-01

Modern rapidly expanding cities generate intricate patterns of species diversity owing to immense complexity in urban spatial structure and current growth trajectories. We propose to identify and uncouple the drivers that give rise to these patterns by looking at the effect of urbanism on species diversity over a previously unexplored long temporal frame that covers early developments in urbanism. To provide this historical perspective we analyzed archaeozoological remains of small mammals from ancient urban and rural sites in the Near East from the 2nd to the 1st millennium BCE, and compared them to observations from modern urban areas. Our data show that ancient urban assemblages consistently comprised two main taxa (Mus musculus domesticus and Crocidura sp.), whereas assemblages of contemporaneous rural sites were significantly richer. Low species diversity also characterizes high-density core areas of modern cities, suggesting that similar ecological drivers have continued to operate in urban areas despite the vast growth in their size and population densities, as well as in the complexity of their technologies and social organization. Research in urban ecology has tended to emphasize the relatively high species diversity observed in low-density areas located on the outskirts of cities, where open and vegetated patches are abundant. The fact that over several millennia urban evolution did not significantly alter species diversity suggests that low diversity is an attribute of densely-populated settlements. The possibility that high diversity in peripheral urban areas arose only recently as a short-term phenomenon in urban ecology merits further research based on long-term data. PMID:24622726

Ancient urban ecology reconstructed from archaeozoological remains of small mammals in the Near East.

PubMed

Weissbrod, Lior; Malkinson, Dan; Cucchi, Thomas; Gadot, Yuval; Finkelstein, Israel; Bar-Oz, Guy

2014-01-01

Modern rapidly expanding cities generate intricate patterns of species diversity owing to immense complexity in urban spatial structure and current growth trajectories. We propose to identify and uncouple the drivers that give rise to these patterns by looking at the effect of urbanism on species diversity over a previously unexplored long temporal frame that covers early developments in urbanism. To provide this historical perspective we analyzed archaeozoological remains of small mammals from ancient urban and rural sites in the Near East from the 2nd to the 1st millennium BCE, and compared them to observations from modern urban areas. Our data show that ancient urban assemblages consistently comprised two main taxa (Mus musculus domesticus and Crocidura sp.), whereas assemblages of contemporaneous rural sites were significantly richer. Low species diversity also characterizes high-density core areas of modern cities, suggesting that similar ecological drivers have continued to operate in urban areas despite the vast growth in their size and population densities, as well as in the complexity of their technologies and social organization. Research in urban ecology has tended to emphasize the relatively high species diversity observed in low-density areas located on the outskirts of cities, where open and vegetated patches are abundant. The fact that over several millennia urban evolution did not significantly alter species diversity suggests that low diversity is an attribute of densely-populated settlements. The possibility that high diversity in peripheral urban areas arose only recently as a short-term phenomenon in urban ecology merits further research based on long-term data.

River network architecture, genetic effective size and distributional patterns predict differences in genetic structure across species in a dryland stream fish community.

PubMed

Pilger, Tyler J; Gido, Keith B; Propst, David L; Whitney, James E; Turner, Thomas F

2017-05-01

Dendritic ecological network (DEN) architecture can be a strong predictor of spatial genetic patterns in theoretical and simulation studies. Yet, interspecific differences in dispersal capabilities and distribution within the network may equally affect species' genetic structuring. We characterized patterns of genetic variation from up to ten microsatellite loci for nine numerically dominant members of the upper Gila River fish community, New Mexico, USA. Using comparative landscape genetics, we evaluated the role of network architecture for structuring populations within species (pairwise F ST ) while explicitly accounting for intraspecific demographic influences on effective population size (N e ). Five species exhibited patterns of connectivity and/or genetic diversity gradients that were predicted by network structure. These species were generally considered to be small-bodied or habitat specialists. Spatial variation of N e was a strong predictor of pairwise F ST for two species, suggesting patterns of connectivity may also be influenced by genetic drift independent of network properties. Finally, two study species exhibited genetic patterns that were unexplained by network properties and appeared to be related to nonequilibrium processes. Properties of DENs shape community-wide genetic structure but effects are modified by intrinsic traits and nonequilibrium processes. Further theoretical development of the DEN framework should account for such cases. © 2017 John Wiley & Sons Ltd.

Patterns of fish diversity and assemblage structure and water quality in the longest Asian tropical river (Mekong)

NASA Astrophysics Data System (ADS)

Chea, R.; Lek, S.; Grenouillet, G.

2016-12-01

Although the Mekong River is one of the world's 35 biodiversity hotspots, the large-scale patterns of fish diversity and assemblage structure remain poorly addressed. The present study aimed to investigate the spatial variability of water quality in the Lower Mekong Basin and the fish distribution patterns in the Lower Mekong River (LMR) and to identify their environmental determinants. Daily fish catch data at 38 sites distributed along the LMR were related to 15 physicochemical and 19 climatic variables. As a result, four different clusters were defined according to the similarity in assemblage composition and 80 indicator species were identified. While fish species richness was highest in the Mekong delta and lowest in the upper part of the LMR, the diversity index was highest in the middle part of the LMR and lowest in the delta. We found that fish assemblages changed along the environmental gradients and that the main drivers affecting the fish assemblage structure were the seasonal variation of temperature, precipitation, dissolved oxygen, pH, and total phosphorus. Specifically, upstream assemblages were characterized by cyprinids and Pangasius catfish, well suited to low temperature, high dissolved oxygen and high pH. Fish assemblages in the delta were dominated by perch-like fish and clupeids, more tolerant to high temperatures, and high levels of nutrients (nitrates and total phosphorus) and salinity. Overall, the patterns were consistent between seasons. Our study contributes to establishing the first holistic fish community study in the LMR. Overall of the LMR water quality, we found that the water in the mainstream was less polluted than its tributaries; eutrophication and salinity could be key factors affecting water quality in LMR. Moreover, the seasonal variation of water quality seemed to be less marked than spatial variation occurring along the longitudinal gradient of Mekong River. Significant degradations were mainly associated with human disturbance and particularly apparent in sites distributed along the man-made canals in Vietnam delta where population growth and agricultural development are intensive.

Spatial genetic structure reflects extensive clonality, low genotypic diversity and habitat fragmentation in Grevillea renwickiana (Proteaceae), a rare, sterile shrub from south-eastern Australia

PubMed Central

James, Elizabeth A.; McDougall, Keith L.

2014-01-01

Background and Aims The association of clonality, polyploidy and reduced fecundity has been identified as an extinction risk for clonal plants. Compromised sexual reproduction limits both their ability to adapt to new conditions and their capacity to disperse to more favourable environments. Grevillea renwickiana is a prostrate, putatively sterile shrub reliant on asexual reproduction. Dispersal is most likely limited by the rate of clonal expansion via rhizomes. The nine localized populations constituting this species provide an opportunity to examine the extent of clonality and spatial genotypic diversity to evaluate its evolutionary prospects. Methods Ten microsatellite loci were used to compare genetic and genotypic diversity across all sites with more intensive sampling at four locations (n = 185). The spatial distribution of genotypes and chloroplast DNA haplotypes based on the trnQ–rps16 intergenic spacer region were compared. Chromosome counts provided a basis for examining genetic profiles inconsistent with diploidy. Key Results Microsatellite analysis identified 46 multilocus genotypes (MLGs) in eight multilocus clonal lineages (MLLs). MLLs are not shared among sites, with two exceptions. Spatial autocorrelation was significant to 1·6 km. Genotypic richness ranged from 0 to 0·33. Somatic mutation is likely to contribute to minor variation between MLGs within clonal lineages. The eight chloroplast haplotypes identified were correlated with eight MLLs defined by ordination and generally restricted to single populations. Triploidy is the most likely reason for tri-allelic patterns. Conclusions Grevillea renwickiana comprises few genetic individuals. Sterility has most likely been induced by triploidy. Extensive lateral suckering in long-lived sterile clones facilitates the accumulation of somatic mutations, which contribute to the measured genetic diversity. Genetic conservation value may not be a function of population size. Despite facing evolutionary stagnation, sterile clonal species can play a vital role in mitigating ecological instability as floras respond to rapid environmental change. PMID:24737718

Speciation has a spatial scale that depends on levels of gene flow.

PubMed

Kisel, Yael; Barraclough, Timothy G

2010-03-01

Area is generally assumed to affect speciation rates, but work on the spatial context of speciation has focused mostly on patterns of range overlap between emerging species rather than on questions of geographical scale. A variety of geographical theories of speciation predict that the probability of speciation occurring within a given region should (1) increase with the size of the region and (2) increase as the spatial extent of intraspecific gene flow becomes smaller. Using a survey of speciation events on isolated oceanic islands for a broad range of taxa, we find evidence for both predictions. The probability of in situ speciation scales with island area in bats, carnivorous mammals, birds, flowering plants, lizards, butterflies and moths, and snails. Ferns are an exception to these findings, but they exhibit high frequencies of polyploid and hybrid speciation, which are expected to be scale independent. Furthermore, the minimum island size for speciation correlates across groups with the strength of intraspecific gene flow, as is estimated from a meta-analysis of published population genetic studies. These results indicate a general geographical model of speciation rates that are dependent on both area and gene flow. The spatial scale of population divergence is an important but neglected determinant of broad-scale diversity patterns.

The Link between Microbial Diversity and Nitrogen Cycling in Marine Sediments Is Modulated by Macrofaunal Bioturbation

PubMed Central

Yazdani Foshtomi, Maryam; Braeckman, Ulrike; Derycke, Sofie; Sapp, Melanie; Van Gansbeke, Dirk; Sabbe, Koen; Willems, Anne; Vincx, Magda; Vanaverbeke, Jan

2015-01-01

Objectives The marine benthic nitrogen cycle is affected by both the presence and activity of macrofauna and the diversity of N-cycling microbes. However, integrated research simultaneously investigating macrofauna, microbes and N-cycling is lacking. We investigated spatio-temporal patterns in microbial community composition and diversity, macrofaunal abundance and their sediment reworking activity, and N-cycling in seven subtidal stations in the Southern North Sea. Spatio-Temporal Patterns of the Microbial Communities Our results indicated that bacteria (total and β-AOB) showed more spatio-temporal variation than archaea (total and AOA) as sedimentation of organic matter and the subsequent changes in the environment had a stronger impact on their community composition and diversity indices in our study area. However, spatio-temporal patterns of total bacterial and β-AOB communities were different and related to the availability of ammonium for the autotrophic β-AOB. Highest bacterial richness and diversity were observed in June at the timing of the phytoplankton bloom deposition, while richness of β-AOB as well as AOA peaked in September. Total archaeal community showed no temporal variation in diversity indices. Macrofauna, Microbes and the Benthic N-Cycle Distance based linear models revealed that, independent from the effect of grain size and the quality and quantity of sediment organic matter, nitrification and N-mineralization were affected by respectively the diversity of metabolically active β-AOB and AOA, and the total bacteria, near the sediment-water interface. Separate models demonstrated a significant and independent effect of macrofaunal activities on community composition and richness of total bacteria, and diversity indices of metabolically active AOA. Diversity of β-AOB was significantly affected by macrofaunal abundance. Our results support the link between microbial biodiversity and ecosystem functioning in marine sediments, and provided broad correlative support for the hypothesis that this relationship is modulated by macrofaunal activity. We hypothesized that the latter effect can be explained by their bioturbating and bio-irrigating activities, increasing the spatial complexity of the biogeochemical environment. PMID:26102286

Spatial Co-Occurrence and Activity Patterns of Mesocarnivores in the Temperate Forests of Southwest China.

PubMed

Bu, Hongliang; Wang, Fang; McShea, William J; Lu, Zhi; Wang, Dajun; Li, Sheng

2016-01-01

Understanding the interactions between species and their coexistence mechanisms will help explain biodiversity maintenance and enable managers to make sound conservation decisions. Mesocarnivores are abundant and diverse mid-sized carnivores and can have profound impacts on the function, structure and dynamics of ecosystem after the extirpation of apex predators in many ecosystems. The moist temperate forests of Southwest China harbor a diverse community of mesocarnivores in the absence of apex predators. Sympatric species tend to partition limited resources along time, diet and space to facilitate coexistence. We determined the spatial and temporal patterns for five species of mesocarnivores. We used detection histories from a large camera-trap dataset collected from 2004-2015 with an extensive effort of 23,313 camera-days from 495 camera locations. The five mesocarnivore species included masked palm civet Paguma larvata, leopard cat Prionailurus bengalensis, hog badger Arctonyx collaris, yellow-throated marten Martes flavigula, and Siberian weasel Mustela sibirica. Only the masked palm civet and hog badger tended to avoid each other; while for other pairs of species, they occurred independently of each other, or no clear pattern observed. With regard to seasonal activity, yellow-throated marten was most active in winter, opposite the pattern observed for masked palm civet, leopard cat and hog badger. For diel activity, masked palm civet, leopard cat and hog badger were primarily nocturnal and crepuscular; yellow-throated marten was diurnal, and Siberian weasel had no clear pattern for most of the year (March to November), but was nocturnal in the winter (December to February). The seasonal shift of the Siberian weasel may be due to the high diet overlap among species in winter. Our results provided new facts and insights into this unique community of mesocarnivores of southwest China, and will facilitate future studies on the mechanism determining coexistence of animal species within complex system.

Isolation by distance and vicariance drive genetic structure of a coral reef fish in the Pacific Ocean.

PubMed

Planes, S; Fauvelot, C

2002-02-01

We studied the genetic diversity of a coral reef fish species to investigate the origin of the differentiation. A total of 727 Acanthurus triostegus collected from 15 locations throughout the Pacific were analyzed for 20 polymorphic loci. The genetic structure showed limited internal disequilibrium within each population; 3.7% of the loci showed significant Hardy-Weinberg disequilibrium, mostly associated with Adh*, and we subsequently removed this locus from further analysis of geographic pattern. The genetic structure of A. triostegus throughout the tropical Pacific Ocean revealed a strong geographic pattern. Overall, there was significant population differentiation (multilocus F(ST) = 0.199), which was geographically structured according to bootstraps of neighbor-joining analysis on Nei's unbiased genetic distances and AMOVA analysis. The genetic structure revealed five geographic groups in the Pacific Ocean: western Pacific (Guam, Philippines, Palau, and Great Barrier Reef); central Pacific (Solomons, New Caledonia, and Fiji); and three groups made up of the eastern populations, namely Hawaiian Archipelago (north), Marquesas (equatorial), and southern French Polynesia (south) that incorporates Clipperton Island located in the northeastern Pacific. In addition, heterozygosity values were found to be geographically structured with higher values grouped within Polynesian and Clipperton populations, which exhibited lower population size. Finally, the genetic differentiation (F(ST)) was significantly correlated with geographic distance when populations from the Hawaiian and Marquesas archipelagos were separated from all the other locations. These results show that patterns of differentiation vary within the same species according to the spatial scale, with one group probably issued from vicariance, whereas the other followed a pattern of isolation by distance. The geographic pattern for A. triostegus emphasizes the diversity of the evolutionary processes that lead to the present genetic structure with some being more influential in certain areas or according to a particular spatial scale.

Genetic diversity is related to climatic variation and vulnerability in threatened bull trout

USGS Publications Warehouse

Kovach, Ryan; Muhlfeld, Clint C.; Wade, Alisa A.; Hand, Brian K.; Whited, Diane C.; DeHaan, Patrick W.; Al-Chokhachy, Robert K.; Luikart, Gordon

2015-01-01

Understanding how climatic variation influences ecological and evolutionary processes is crucial for informed conservation decision-making. Nevertheless, few studies have measured how climatic variation influences genetic diversity within populations or how genetic diversity is distributed across space relative to future climatic stress. Here, we tested whether patterns of genetic diversity (allelic richness) were related to climatic variation and habitat features in 130 bull trout (Salvelinus confluentus) populations from 24 watersheds (i.e., ~4–7th order river subbasins) across the Columbia River Basin, USA. We then determined whether bull trout genetic diversity was related to climate vulnerability at the watershed scale, which we quantified on the basis of exposure to future climatic conditions (projected scenarios for the 2040s) and existing habitat complexity. We found a strong gradient in genetic diversity in bull trout populations across the Columbia River Basin, where populations located in the most upstream headwater areas had the greatest genetic diversity. After accounting for spatial patterns with linear mixed models, allelic richness in bull trout populations was positively related to habitat patch size and complexity, and negatively related to maximum summer temperature and the frequency of winter flooding. These relationships strongly suggest that climatic variation influences evolutionary processes in this threatened species and that genetic diversity will likely decrease due to future climate change. Vulnerability at a watershed scale was negatively correlated with average genetic diversity (r = −0.77;P < 0.001); watersheds containing populations with lower average genetic diversity generally had the lowest habitat complexity, warmest stream temperatures, and greatest frequency of winter flooding. Together, these findings have important conservation implications for bull trout and other imperiled species. Genetic diversity is already depressed where climatic vulnerability is highest; it will likely erode further in the very places where diversity may be most needed for future persistence.

Landscape patterns in rainforest phylogenetic signal: isolated islands of refugia or structured continental distributions?

PubMed

Kooyman, Robert M; Rossetto, Maurizio; Sauquet, Hervé; Laffan, Shawn W

2013-01-01

Identify patterns of change in species distributions, diversity, concentrations of evolutionary history, and assembly of Australian rainforests. We used the distribution records of all known rainforest woody species in Australia across their full continental extent. These were analysed using measures of species richness, phylogenetic diversity (PD), phylogenetic endemism (PE) and phylogenetic structure (net relatedness index; NRI). Phylogenetic structure was assessed using both continental and regional species pools. To test the influence of growth-form, freestanding and climbing plants were analysed independently, and in combination. Species richness decreased along two generally orthogonal continental axes, corresponding with wet to seasonally dry and tropical to temperate habitats. The PE analyses identified four main areas of substantially restricted phylogenetic diversity, including parts of Cape York, Wet Tropics, Border Ranges, and Tasmania. The continental pool NRI results showed evenness (species less related than expected by chance) in groups of grid cells in coastally aligned areas of species rich tropical and sub-tropical rainforest, and in low diversity moist forest areas in the south-east of the Great Dividing Range and in Tasmania. Monsoon and drier vine forests, and moist forests inland from upland refugia showed phylogenetic clustering, reflecting lower diversity and more relatedness. Signals for evenness in Tasmania and clustering in northern monsoon forests weakened in analyses using regional species pools. For climbing plants, values for NRI by grid cell showed strong spatial structuring, with high diversity and PE concentrated in moist tropical and subtropical regions. Concentrations of rainforest evolutionary history (phylo-diversity) were patchily distributed within a continuum of species distributions. Contrasting with previous concepts of rainforest community distribution, our findings of continuous distributions and continental connectivity have significant implications for interpreting rainforest evolutionary history and current day ecological processes, and for managing rainforest diversity in changing circumstances.

Genetic and Morphometric Divergence of an Invasive Bird: The Introduced House Sparrow (Passer domesticus) in Brazil

PubMed Central

Lima, Marcos R.; Macedo, Regina H. F.; Martins, Thaís L. F.; Schrey, Aaron W.; Martin, Lynn B.; Bensch, Staffan

2012-01-01

Introduced species are interesting systems for the study of contemporary evolution in new environments because of their spatial and temporal scales. For this study we had three aims: (i) to determine how genetic diversity and genetic differentiation of introduced populations of the house sparrow (Passer domesticus) in Brazil varies with range expansion, (ii) to determine how genetic diversity and differentiation in Brazil compares to ancestral European populations; and (iii) to determine whether selection or genetic drift has been more influential on phenotypic divergence. We used six microsatellite markers to genotype six populations from Brazil and four populations from Europe. We found slightly reduced levels of genetic diversity in Brazilian compared to native European populations. However, among introduced populations of Brazil, we found no association between genetic diversity and time since introduction. Moreover, overall genetic differentiation among introduced populations was low indicating that the expansion took place from large populations in which genetic drift effects would likely have been weak. We found significant phenotypic divergence among sites in Brazil. Given the absence of a spatial genetic pattern, divergent selection and not genetic drift seems to be the main force behind most of the phenotypic divergence encountered. Unravelling whether microevolution (e.g., allele frequency change), phenotypic plasticity, or both mediated phenotypic divergence is challenging and will require experimental work (e.g., common garden experiments or breeding programs). PMID:23285283

Genetic structure and seed-mediated dispersal rates of an endangered shrub in a fragmented landscape: a case study for Juniperus communis in northwestern Europe

PubMed Central

2011-01-01

Background Population extinction risk in a fragmented landscape is related to the differential ability of the species to spread its genes across the landscape. The impact of landscape fragmentation on plant population dynamics will therefore vary across different spatial scales. We quantified successful seed-mediated dispersal of the dioecious shrub Juniperus communis in a fragmented landscape across northwestern Europe by using amplified fragment length polymorphism (AFLP) markers. Furthermore we investigated the genetic diversity and structure on two spatial scales: across northwestern Europe and across Flanders (northern Belgium). We also studied whether seed viability and populations size were correlated with genetic diversity. Results Unexpectedly, estimated seed-mediated dispersal rates were quite high and ranged between 3% and 14%. No population differentiation and no spatial genetic structure were detected on the local, Flemish scale. A significant low to moderate genetic differentiation between populations was detected at the regional, northwest European scale (PhiPT = 0.10). In general, geographically nearby populations were also genetically related. High levels of within-population genetic diversity were detected but no correlation was found between any genetic diversity parameter and population size or seed viability. Conclusions In northwestern Europe, landscape fragmentation has lead to a weak isolation-by-distance pattern but not to genetic impoverishment of common juniper. Substantial rates of successful migration by seed-mediated gene flow indicate a high dispersal ability which could enable Juniperus communis to naturally colonize suitable habitats. However, it is not clear whether the observed levels of migration will suffice to counterbalance the effects of genetic drift in small populations on the long run. PMID:21859457

Genetic structure and seed-mediated dispersal rates of an endangered shrub in a fragmented landscape: a case study for Juniperus communis in northwestern Europe.

PubMed

Vanden-Broeck, An; Gruwez, Robert; Cox, Karen; Adriaenssens, Sandy; Michalczyk, Inga M; Verheyen, Kris

2011-08-22

Population extinction risk in a fragmented landscape is related to the differential ability of the species to spread its genes across the landscape. The impact of landscape fragmentation on plant population dynamics will therefore vary across different spatial scales. We quantified successful seed-mediated dispersal of the dioecious shrub Juniperus communis in a fragmented landscape across northwestern Europe by using amplified fragment length polymorphism (AFLP) markers. Furthermore we investigated the genetic diversity and structure on two spatial scales: across northwestern Europe and across Flanders (northern Belgium). We also studied whether seed viability and populations size were correlated with genetic diversity. Unexpectedly, estimated seed-mediated dispersal rates were quite high and ranged between 3% and 14%. No population differentiation and no spatial genetic structure were detected on the local, Flemish scale. A significant low to moderate genetic differentiation between populations was detected at the regional, northwest European scale (PhiPT = 0.10). In general, geographically nearby populations were also genetically related. High levels of within-population genetic diversity were detected but no correlation was found between any genetic diversity parameter and population size or seed viability. In northwestern Europe, landscape fragmentation has lead to a weak isolation-by-distance pattern but not to genetic impoverishment of common juniper. Substantial rates of successful migration by seed-mediated gene flow indicate a high dispersal ability which could enable Juniperus communis to naturally colonize suitable habitats. However, it is not clear whether the observed levels of migration will suffice to counterbalance the effects of genetic drift in small populations on the long run.

Spatial patterns of species richness in New World coral snakes and the metabolic theory of ecology

NASA Astrophysics Data System (ADS)

Terribile, Levi Carina; Diniz-Filho, José Alexandre Felizola

2009-03-01

The metabolic theory of ecology (MTE) has attracted great interest because it proposes an explanation for species diversity gradients based on temperature-metabolism relationships of organisms. Here we analyse the spatial richness pattern of 73 coral snake species from the New World in the context of MTE. We first analysed the association between ln-transformed richness and environmental variables, including the inverse transformation of annual temperature (1/ kT). We used eigenvector-based spatial filtering to remove the residual spatial autocorrelation in the data and geographically weighted regression to account for non-stationarity in data. In a model I regression (OLS), the observed slope between ln-richness and 1/ kT was -0.626 ( r2 = 0.413), but a model II regression generated a much steeper slope (-0.975). When we added additional environmental correlates and the spatial filters in the OLS model, the R2 increased to 0.863 and the partial regression coefficient of 1/ kT was -0.676. The GWR detected highly significant non-stationarity, in data, and the median of local slopes of ln-richness against 1/ kT was -0.38. Our results expose several problems regarding the assumptions needed to test MTE: although the slope of OLS fell within that predicted by the theory and the dataset complied with the assumption of temperature-independence of average body size, the fact that coral snakes consist of a restricted taxonomic group and the non-stationarity of slopes across geographical space makes MTE invalid to explain richness in this case. Also, it is clear that other ecological and historical factors are important drivers of species richness patterns and must be taken into account both in theoretical modeling and data analysis.

Neutral processes contribute to patterns of spatial variation for flower colour in the Mediterranean Iris lutescens (Iridaceae)

PubMed Central

Wang, Hui; Talavera, María; Min, Ya; Flaven, Elodie; Imbert, Eric

2016-01-01

Background and Aims Flower colour polymorphism in plants has been used as a classic model for understanding the importance of neutral processes vs. natural selection in population differentiation. However, current explanations for the maintenance of flower colour polymorphism mainly rely on balancing selection, while neutral processes have seldom been championed. Iris lutescens (Iridaceae) is a widespread species in the northern Mediterranean basin, which shows a stable and striking purple–yellow flower colour polymorphism. To evaluate the roles of neutral processes in the spatial variation for flower colour in this species, patterns of neutral genetic variation across its distribution range were quantified, and phenotypic differentiation was compared with neutral genetic differentiation. Methods Genetic diversity levels and population genetic structure were investigated through the genotyping of a collection of 1120 individuals in 41 populations ranging from Spain to France, using a set of eight newly developed microsatellite markers. In addition, phenotypic differentiation for flower colour was also quantified by counting colour morph frequency in each population, and measuring the reflectance spectra of sampled individuals. Key Results Populations in Spain present a sharp colour transition from solely purple to solely yellow. The results provide evidence that genetic drift through limited gene flow is important in the evolution of monomorphic populations. In contrast, most populations in France are polymorphic with both phenotypes, and the colour frequencies vary geographically without any spatial gradients observed. A pattern of isolation by distance is detected in France, and gene flow between adjacent populations seems to be an important factor maintaining populations polymorphic. Conclusions Overall, neutral processes contribute to patterns of spatial variation for flower colour in I. lutescens, but it cannot be excluded that natural selection is also operating. An interaction between neutral processes and natural selection is suggested to explain the spatial variation for flower colour in I. lutescens. PMID:27084922

Neutral processes contribute to patterns of spatial variation for flower colour in the Mediterranean Iris lutescens (Iridaceae).

PubMed

Wang, Hui; Talavera, María; Min, Ya; Flaven, Elodie; Imbert, Eric

2016-05-01

Flower colour polymorphism in plants has been used as a classic model for understanding the importance of neutral processes vs. natural selection in population differentiation. However, current explanations for the maintenance of flower colour polymorphism mainly rely on balancing selection, while neutral processes have seldom been championed. Iris lutescens (Iridaceae) is a widespread species in the northern Mediterranean basin, which shows a stable and striking purple-yellow flower colour polymorphism. To evaluate the roles of neutral processes in the spatial variation for flower colour in this species, patterns of neutral genetic variation across its distribution range were quantified, and phenotypic differentiation was compared with neutral genetic differentiation. Genetic diversity levels and population genetic structure were investigated through the genotyping of a collection of 1120 individuals in 41 populations ranging from Spain to France, using a set of eight newly developed microsatellite markers. In addition, phenotypic differentiation for flower colour was also quantified by counting colour morph frequency in each population, and measuring the reflectance spectra of sampled individuals. Populations in Spain present a sharp colour transition from solely purple to solely yellow. The results provide evidence that genetic drift through limited gene flow is important in the evolution of monomorphic populations. In contrast, most populations in France are polymorphic with both phenotypes, and the colour frequencies vary geographically without any spatial gradients observed. A pattern of isolation by distance is detected in France, and gene flow between adjacent populations seems to be an important factor maintaining populations polymorphic. Overall, neutral processes contribute to patterns of spatial variation for flower colour in I. lutescens, but it cannot be excluded that natural selection is also operating. An interaction between neutral processes and natural selection is suggested to explain the spatial variation for flower colour in I. lutescens. © The Author 2016. Published by Oxford University Press on behalf of the Annals of Botany Company. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

Morphological Constraints on Cerebellar Granule Cell Combinatorial Diversity.

PubMed

Gilmer, Jesse I; Person, Abigail L

2017-12-13

Combinatorial expansion by the cerebellar granule cell layer (GCL) is fundamental to theories of cerebellar contributions to motor control and learning. Granule cells (GrCs) sample approximately four mossy fiber inputs and are thought to form a combinatorial code useful for pattern separation and learning. We constructed a spatially realistic model of the cerebellar GCL and examined how GCL architecture contributes to GrC combinatorial diversity. We found that GrC combinatorial diversity saturates quickly as mossy fiber input diversity increases, and that this saturation is in part a consequence of short dendrites, which limit access to diverse inputs and favor dense sampling of local inputs. This local sampling also produced GrCs that were combinatorially redundant, even when input diversity was extremely high. In addition, we found that mossy fiber clustering, which is a common anatomical pattern, also led to increased redundancy of GrC input combinations. We related this redundancy to hypothesized roles of temporal expansion of GrC information encoding in service of learned timing, and we show that GCL architecture produces GrC populations that support both temporal and combinatorial expansion. Finally, we used novel anatomical measurements from mice of either sex to inform modeling of sparse and filopodia-bearing mossy fibers, finding that these circuit features uniquely contribute to enhancing GrC diversification and redundancy. Our results complement information theoretic studies of granule layer structure and provide insight into the contributions of granule layer anatomical features to afferent mixing. SIGNIFICANCE STATEMENT Cerebellar granule cells are among the simplest neurons, with tiny somata and, on average, just four dendrites. These characteristics, along with their dense organization, inspired influential theoretical work on the granule cell layer as a combinatorial expander, where each granule cell represents a unique combination of inputs. Despite the centrality of these theories to cerebellar physiology, the degree of expansion supported by anatomically realistic patterns of inputs is unknown. Using modeling and anatomy, we show that realistic input patterns constrain combinatorial diversity by producing redundant combinations, which nevertheless could support temporal diversification of like combinations, suitable for learned timing. Our study suggests a neural substrate for producing high levels of both combinatorial and temporal diversity in the granule cell layer. Copyright © 2017 the authors 0270-6474/17/3712153-14$15.00/0.

Individual-Based Model of Microbial Life on Hydrated Rough Soil Surfaces

PubMed Central

Kim, Minsu; Or, Dani

2016-01-01

Microbial life in soil is perceived as one of the most interesting ecological systems, with microbial communities exhibiting remarkable adaptability to vast dynamic environmental conditions. At the same time, it is a notoriously challenging system to understand due to its complexity including physical, chemical, and biological factors in synchrony. This study presents a spatially-resolved model of microbial dynamics on idealised rough soil surfaces represented as patches with different (roughness) properties that preserve the salient hydration physics of real surfaces. Cell level microbial interactions are considered within an individual-based formulation including dispersion and various forms of trophic dependencies (competition, mutualism). The model provides new insights into mechanisms affecting microbial community dynamics and gives rise to spontaneous formation of microbial community spatial patterns. The framework is capable of representing many interacting species and provides diversity metrics reflecting surface conditions and their evolution over time. A key feature of the model is its spatial scalability that permits representation of microbial processes from cell-level (micro-metric scales) to soil representative volumes at sub-metre scales. Several illustrative examples of microbial trophic interactions and population dynamics highlight the potential of the proposed modelling framework to quantitatively study soil microbial processes. The model is highly applicable in a wide range spanning from quantifying spatial organisation of multiple species under various hydration conditions to predicting microbial diversity residing in different soils. PMID:26807803

Influence of landscape structure on reef fish assemblages

USGS Publications Warehouse

Grober-Dunsmore, R.; Frazer, T.K.; Beets, J.P.; Lindberg, W.J.; Zwick, P.; Funicelli, N.A.

2008-01-01

Management of tropical marine environments calls for interdisciplinary studies and innovative methodologies that consider processes occurring over broad spatial scales. We investigated relationships between landscape structure and reef fish assemblage structure in the US Virgin Islands. Measures of landscape structure were transformed into a reduced set of composite indices using principal component analyses (PCA) to synthesize data on the spatial patterning of the landscape structure of the study reefs. However, composite indices (e.g., habitat diversity) were not particularly informative for predicting reef fish assemblage structure. Rather, relationships were interpreted more easily when functional groups of fishes were related to individual habitat features. In particular, multiple reef fish parameters were strongly associated with reef context. Fishes responded to benthic habitat structure at multiple spatial scales, with various groups of fishes each correlated to a unique suite of variables. Accordingly, future experiments should be designed to test functional relationships based on the ecology of the organisms of interest. Our study demonstrates that landscape-scale habitat features influence reef fish communities, illustrating promise in applying a landscape ecology approach to better understand factors that structure coral reef ecosystems. Furthermore, our findings may prove useful in design of spatially-based conservation approaches such as marine protected areas (MPAs), because landscape-scale metrics may serve as proxies for areas with high species diversity and abundance within the coral reef landscape. ?? 2007 Springer Science+Business Media B.V.

Predicting the impacts of Mississippi River diversions and sea-level rise on spatial patterns of eastern oyster growth rate and production

USGS Publications Warehouse

Wang, Hongqing; Chen, Qin; La Peyre, Megan K.; Hu, Kelin; La Peyre, Jerome F.

2017-01-01

There remains much debate regarding the perceived tradeoffs of using freshwater and sediment diversions for coastal restoration in terms of balancing the need for wetland restoration versus preserving eastern oyster (Crassostrea virginica) production. Further complicating the issue, climate change-induced sea-level rise (SLR) and land subsidence are also expected to affect estuarine water quality. In this study, we developed a process-based numerical modeling system that couples hydrodynamic, water quality, and oyster population dynamics. We selected Breton Sound Estuary (BSE) (∼2740 km2) in the eastern Mississippi River Deltaic Plain since it is home to several of the largest public oyster seed grounds and private leases for the Gulf coast. The coupled oyster population model was calibrated and validated against field observed oyster growth data. We predicted the responses of oyster population in BSE to small- (142 m3 s−1) and large-scale (7080 m3 s−1) river diversions at the Caernarvon Freshwater Diversion structure planned in the 2012 Coastal Master Plan (Louisiana) under low (0.38 m) and high (1.44 m) relative sea-level rise (RSLR = eustatic SLR + subsidence) compared to a baseline condition (Year 2009). Model results showed that the large-scale diversion had a stronger negative impact on oyster population dynamics via freshening of the entire estuary, resulting in reduced oyster growth rate and production than RSLR. Under the large-scale diversion, areas with optimal oyster growth rates (>15 mg ash-free dry weight (AFDW) oyster−1 wk−1) and production (>500 g AFDW m−2 yr−1) would shift seaward to the southeastern edge of the estuary, turning the estuary into a very low oyster production system. RSLR however played a greater role than the small-scale diversion on the magnitude and spatial pattern of oyster growth rate and production. RSLR would result in an overall estuary-wide decrease in oyster growth rate and production as a consequence of decreased salinities in the middle and lower estuary because rising sea level likely causes increased stage and overbank flow downstream along the lower Mississippi River.

Effects of climate change on ecological disturbance in the Northern Rockies Region [Chapter 8

USGS Publications Warehouse

Loehman, Rachel A.; Bentz, Barbara J.; DeNitto, Gregg A.; Keane, Robert E.; Manning, Mary E.; Duncan, Jacob P.; Egan, Joel M.; Jackson, Marcus B.; Kegley, Sandra; Lockman, I. Blakey; Pearson, Dean E.; Powell, James A.; Shelly, Steve; Steed, Brytten E.; Zambino, Paul J.

2018-01-01

This chapter describes the ecology of important disturbance regimes in the Forest Service, U.S. Department of Agriculture (USFS) Northern Region and the Greater Yellowstone Area, hereafter called the Northern Rockies region, and potential shifts in these regimes as a consequence of observed and projected climate change. The term disturbance regime describes the general temporal and spatial characteristics of a disturbance agent - insect, disease, fire, weather, even human activity - and the effects of that agent on the landscape (table 8.1). More specifically, a disturbance regime is the cumulative effect of multiple disturbance events over space and time (Keane 2013). Disturbances disrupt an ecosystem, community, or population structure and change elements of the biological environment, physical environment, or both (White and Pickett 1985). The resulting shifting mosaic of diverse ecological patterns and structures in turn affects future patterns of disturbance, in a reciprocal, linked relationship that shapes the fundamental character of landscapes and ecosystems. Disturbance creates and maintains biological diversity in the form of shifting, heterogeneous mosaics of diverse communities and habitats across a landscape (McKinney and Drake 1998), and biodiversity is generally highest when disturbance is neither too rare nor too frequent on the landscape (Grime 1973).

Diversity, competition, extinction: the ecophysics of language change.

PubMed

Solé, Ricard V; Corominas-Murtra, Bernat; Fortuny, Jordi

2010-12-06

As indicated early by Charles Darwin, languages behave and change very much like living species. They display high diversity, differentiate in space and time, emerge and disappear. A large body of literature has explored the role of information exchanges and communicative constraints in groups of agents under selective scenarios. These models have been very helpful in providing a rationale on how complex forms of communication emerge under evolutionary pressures. However, other patterns of large-scale organization can be described using mathematical methods ignoring communicative traits. These approaches consider shorter time scales and have been developed by exploiting both theoretical ecology and statistical physics methods. The models are reviewed here and include extinction, invasion, origination, spatial organization, coexistence and diversity as key concepts and are very simple in their defining rules. Such simplicity is used in order to catch the most fundamental laws of organization and those universal ingredients responsible for qualitative traits. The similarities between observed and predicted patterns indicate that an ecological theory of language is emerging, supporting (on a quantitative basis) its ecological nature, although key differences are also present. Here, we critically review some recent advances and outline their implications and limitations as well as highlight problems for future research.

Diversity, competition, extinction: the ecophysics of language change

PubMed Central

Solé, Ricard V.; Corominas-Murtra, Bernat; Fortuny, Jordi

2010-01-01

As indicated early by Charles Darwin, languages behave and change very much like living species. They display high diversity, differentiate in space and time, emerge and disappear. A large body of literature has explored the role of information exchanges and communicative constraints in groups of agents under selective scenarios. These models have been very helpful in providing a rationale on how complex forms of communication emerge under evolutionary pressures. However, other patterns of large-scale organization can be described using mathematical methods ignoring communicative traits. These approaches consider shorter time scales and have been developed by exploiting both theoretical ecology and statistical physics methods. The models are reviewed here and include extinction, invasion, origination, spatial organization, coexistence and diversity as key concepts and are very simple in their defining rules. Such simplicity is used in order to catch the most fundamental laws of organization and those universal ingredients responsible for qualitative traits. The similarities between observed and predicted patterns indicate that an ecological theory of language is emerging, supporting (on a quantitative basis) its ecological nature, although key differences are also present. Here, we critically review some recent advances and outline their implications and limitations as well as highlight problems for future research. PMID:20591847

Biogeographical characterization of Saccharomyces cerevisiae wine yeast by molecular methods

PubMed Central

Tofalo, Rosanna; Perpetuini, Giorgia; Schirone, Maria; Fasoli, Giuseppe; Aguzzi, Irene; Corsetti, Aldo; Suzzi, Giovanna

2013-01-01

Biogeography is the descriptive and explanatory study of spatial patterns and processes involved in the distribution of biodiversity. Without biogeography, it would be difficult to study the diversity of microorganisms because there would be no way to visualize patterns in variation. Saccharomyces cerevisiae, “the wine yeast,” is the most important species involved in alcoholic fermentation, and in vineyard ecosystems, it follows the principle of “everything is everywhere.” Agricultural practices such as farming (organic versus conventional) and floor management systems have selected different populations within this species that are phylogenetically distinct. In fact, recent ecological and geographic studies highlighted that unique strains are associated with particular grape varieties in specific geographical locations. These studies also highlighted that significant diversity and regional character, or ‘terroir,’ have been introduced into the winemaking process via this association. This diversity of wild strains preserves typicity, the high quality, and the unique flavor of wines. Recently, different molecular methods were developed to study population dynamics of S. cerevisiae strains in both vineyards and wineries. In this review, we will provide an update on the current molecular methods used to reveal the geographical distribution of S. cerevisiae wine yeast. PMID:23805132

[Spatial distribution and scale effect of species diversity of secondary forests in montane region of eastern Liaoning Province, China.

PubMed

Deng, Li Ping; Bai, Xue Jiao; Qin, Sheng Jin; Wei, Ya Wei; Zhou, Yong Bin; Li, Lu Lu; Niu, Sha Sha; Han, Mei Na

2016-07-01

With secondary forest in the montane region of eastern Liaoning Province as research object, this paper analyzed the spatial distribution and scale effect of Gleason richness index, Simpson dominance index, Shannon diversity index and Pielou evenness index in a 4 hm 2 plot. The results showed that spatial distributions of the four diversity indices showed higher spatial heterogeneity. Variance of the four diversity indices varied with increasing scale. Coefficients of variation of the four diversity indices decreased with increasing scale. The four diversity indices of the tree layer were higher than those of the shrub layer, and the variation tendency varied with increasing scale. The results indicated that sampling scale should be taken into account when studying species diversity in the montane region of eastern Liaoning Province.

Resource shifts in Malagasy dung beetles: contrasting processes revealed by dissimilar spatial genetic patterns

PubMed Central

Hanski, Ilkka; Wirta, Helena; Nyman, Toshka; Rahagalala, Pierre

2008-01-01

The endemic dung beetle subtribe Helictopleurina has 65 species mostly in wet forests in eastern Madagascar. There are no extant native ungulates in Madagascar, but three Helictopleurus species have shifted to the introduced cattle dung in open habitats in the past 1500 years. Helictopleurus neoamplicollis and Helictopleurus marsyas exhibit very limited cytochrome oxidase subunit 1 haplotype diversity and a single haplotype is present across Madagascar, suggesting that these species shifted to cattle dung in a small region followed by rapid range expansion. In contrast, patterns of molecular diversity in Helictopleurus quadripunctatus indicate a gradual diet shift across most of southern Madagascar, consistent with somewhat broader diet in this species. The three cattle dung-using Helictopleurus species have significantly greater geographical ranges than the forest-dwelling species, apparently because the shift to the currently very abundant new resource relaxed interspecific competition that hinders range expansion in the forest species. Ecology Letters (2008) 11: 1208–1215 PMID:18778273

Phylogeography of the finless porpoise (genus Neophocaena): testing the stepwise divergence hypothesis in the northwestern Pacific.

PubMed

Lin, Wenzhi; Frère, Céline H; Karczmarski, Leszek; Xia, Jia; Gui, Duan; Wu, Yuping

2014-10-10

We used 344 mitochondrial control region (717 bp) sequences from the finless porpoise (genus Neophocaena) from the northwestern Pacific to investigate the extent and manner in which past climatic oscillations may have shaped patterns of genetic diversity for this marine mammal. Both SplitsTree and Analysis of Molecular Variance (AMOVA) revealed the presence of a deep divergence among N. phocaenoides in subtropical waters compared with N. asiaeorientalis in temperate waters. Results from Migrate-n indicated that migration increased along the continent during the early Pleistocene period. Migration increased, although to a lesser extent than that during the Pleistocene, along the marginal shelf in the Yellow/Bohai Sea during the Last Glacial Maximum (LGM) due to a shortening coastline. Our results suggest that the current patterns of genetic diversity of Neophocaena vary at a hierarchy on a temporal and spatial scale, and phylogeographic history should be taken into account when examining species population structure and taxonomy.

Microglial brain region-dependent diversity and selective regional sensitivities to ageing

PubMed Central

Grabert, Kathleen; Michoel, Tom; Karavolos, Michail H; Clohisey, Sara; Baillie, J Kenneth; Stevens, Mark P; Freeman, Tom C; Summers, Kim M; McColl, Barry W

2015-01-01

Microglia play critical roles in neural development, homeostasis and neuroinflammation and are increasingly implicated in age-related neurological dysfunction. Neurodegeneration often occurs in disease-specific spatially-restricted patterns, the origins of which are unknown. We performed the first genome-wide analysis of microglia from discrete brain regions across the adult lifespan of the mouse and reveal that microglia have distinct region-dependent transcriptional identities and age in a regionally variable manner. In the young adult brain, differences in bioenergetic and immunoregulatory pathways were the major sources of heterogeneity and suggested that cerebellar and hippocampal microglia exist in a more immune vigilant state. Immune function correlated with regional transcriptional patterns. Augmentation of the distinct cerebellar immunophenotype and a contrasting loss in distinction of the hippocampal phenotype among forebrain regions were key features during ageing. Microglial diversity may enable regionally localised homeostatic functions but could also underlie region-specific sensitivities to microglial dysregulation and involvement in age-related neurodegeneration. PMID:26780511

Spartina alterniflora genotype influences facilitation and suppression of high marsh species colonizing an early successional salt marsh

USGS Publications Warehouse

Proffitt, C.E.; Chiasson, R.L.; Owens, A.B.; Edwards, K.R.; Travis, S.E.

2005-01-01

1. Genetically based phenotypic and ecotypic variation in a dominant plant species can influence ecological functions and patterns of recruitment by other species in plant communities. However, the nature and degree of importance of genotypic differences is poorly understood in most systems. 2. The dominant salt marsh species, Spartina alterniflora, is known to induce facultative and competitive effects in different plant species, and the outcomes of interactions can be affected by nutrients and flooding stress. Clonal genotypes, which maintained their different plant architecture phenotypes throughout 31 months of a field experiment, underwent considerable genet-specific senescence in their centres over the last 12 months. 3. Different clonal genotypes and different locations (robust edges vs. senescent centres) permitted significantly different levels of light penetration of the canopy (14.8-77.6%), thus establishing spatial heterogeneity for this important environmental factor. 4. S. alterniflora clonal genotype influenced the degree of suppression of the previously dominant Salicornia bigelovii as well as facilitation of recruitment and growth by other plant species. Aster subulatus and Atriplex, patula performed better in Spartina clone centres, and experienced reduced growth in Salicornia-dominated areas. 5. Four other high marsh species (Borrichia frutescens, Aster tenuifolius, Iva frutescens and Limonium carolinianum) colonized only into Spartina clones but not into the Salicornia-dominated area. 6. These results suggest that differences in clone size, centre senescence, stem density, height, total stem length and biomass in different genotypes of a dominant marsh plant species can influence recruitment and growth of other plant species. The spatial pattern of habitat heterogeneity is, at least in part, dependent on the genotypic diversity, and possibly the genetic diversity, of such foundation species. 7. We hypothesize that as genotypic diversity increases in populations of a dominant plant species like S. alterniflora, the number and diversity of interactions with other species will increase as well. ?? 2005 British Ecological Society.

Spatial patterns of aquatic habitat richness in the Upper Mississippi River floodplain, USA

USGS Publications Warehouse

De Jager, Nathan R.; Rohweder, Jason J.

2012-01-01

Interactions among hydrology and geomorphology create shifting mosaics of aquatic habitat patches in large river floodplains (e.g., main and side channels, floodplain lakes, and shallow backwater areas) and the connectivity among these habitat patches underpins high levels of biotic diversity and productivity. However, the diversity and connectivity among the habitats of most floodplain rivers have been negatively impacted by hydrologic and structural modifications that support commercial navigation and control flooding. We therefore tested the hypothesis that the rate of increase in patch richness (# of types) with increasing scale reflects anthropogenic modifications to habitat diversity and connectivity in a large floodplain river, the Upper Mississippi River (UMR). To do this, we calculated the number of aquatic habitat patch types within neighborhoods surrounding each of the ≈19 million 5-m aquatic pixels of the UMR for multiple neighborhood sizes (1–100 ha). For all of the 87 river-reach focal areas we examined, changes in habitat richness (R) with increasing neighborhood length (L, # pixels) were characterized by a fractal-like power function R = Lz (R2 > 0.92 (P z) measures the rate of increase in habitat richness with neighborhood size and is related to a fractal dimension. Variation in z reflected fundamental changes to spatial patterns of aquatic habitat richness in this river system. With only a few exceptions, z exceeded the river-wide average of 0.18 in focal areas where side channels, contiguous floodplain lakes, and contiguous shallow-water areas exceeded 5%, 5%, and 10% of the floodplain respectively. In contrast, z was always less than 0.18 for focal areas where impounded water exceeded 40% of floodplain area. Our results suggest that rehabilitation efforts that target areas with <5% of the floodplain in side channels, <5% in floodplain lakes, and/or <10% in shallow-water areas could improve habitat diversity across multiple scales in the UMR.

Moving GIS Research Indoors: Spatiotemporal Analysis of Agricultural Animals

PubMed Central

Daigle, Courtney L.; Banerjee, Debasmit; Montgomery, Robert A.; Biswas, Subir; Siegford, Janice M.

2014-01-01

A proof of concept applying wildlife ecology techniques to animal welfare science in intensive agricultural environments was conducted using non-cage laying hens. Studies of wildlife ecology regularly use Geographic Information Systems (GIS) to assess wild animal movement and behavior within environments with relatively unlimited space and finite resources. However, rather than depicting landscapes, a GIS could be developed in animal production environments to provide insight into animal behavior as an indicator of animal welfare. We developed a GIS-based approach for studying agricultural animal behavior in an environment with finite space and unlimited resources. Concurrent data from wireless body-worn location tracking sensor and video-recording systems, which depicted spatially-explicit behavior of hens (135 hens/room) in two identical indoor enclosures, were collected. The spatial configuration of specific hen behaviors, variation in home range patterns, and variation in home range overlap show that individual hens respond to the same environment differently. Such information could catalyze management practice adjustments (e.g., modifying feeder design and/or location). Genetically-similar hens exhibited diverse behavioral and spatial patterns via a proof of concept approach enabling detailed examinations of individual non-cage laying hen behavior and welfare. PMID:25098421

The spatial organization of intra-tumour heterogeneity and evolutionary trajectories of metastases in hepatocellular carcinoma

PubMed Central

Zhai, Weiwei; Lim, Tony Kiat-Hon; Zhang, Tong; Phang, Su-Ting; Tiang, Zenia; Guan, Peiyong; Ng, Ming-Hwee; Lim, Jia Qi; Yao, Fei; Li, Zheng; Ng, Poh Yong; Yan, Jie; Goh, Brian K.; Chung, Alexander Yaw-Fui; Choo, Su-Pin; Khor, Chiea Chuen; Soon, Wendy Wei-Jia; Sung, Ken Wing-Kin; Foo, Roger Sik-Yin; Chow, Pierce Kah-Hoe

2017-01-01

Hepatocellular carcinoma (HCC) has one of the poorest survival rates among cancers. Using multi-regional sampling of nine resected HCC with different aetiologies, here we construct phylogenetic relationships of these sectors, showing diverse levels of genetic sharing, spanning early to late diversification. Unlike the variegated pattern found in colorectal cancers, a large proportion of HCC display a clear isolation-by-distance pattern where spatially closer sectors are genetically more similar. Two resected intra-hepatic metastases showed genetic divergence occurring before and after primary tumour diversification, respectively. Metastatic tumours had much higher variability than their primary tumours, suggesting that intra-hepatic metastasis is accompanied by rapid diversification at the distant location. The presence of co-existing mutations offers the possibility of drug repositioning for HCC treatment. Taken together, these insights into intra-tumour heterogeneity allow for a comprehensive understanding of the evolutionary trajectories of HCC and suggest novel avenues for personalized therapy. PMID:28240289

Relationship between structure of macrobenthic assemblages and environmental variables in shallow sublittoral soft bottoms.

PubMed

Veiga, Puri; Redondo, Waldo; Sousa-Pinto, Isabel; Rubal, Marcos

2017-08-01

We establish baseline knowledge of abundance, diversity and multivariate structure of macrobenthos from shallow sublitoral soft bottoms in the North Portuguese coast and elucidate main environmental factors that shape their spatial patterns. In this area distribution of soft bottoms is patchy, surrounded by boulders and rocky substrates. This particular landscape and the lack of significant anthropogenic disturbances are values for the conservation of this habitat. Sediment and physicochemical properties of the water column were studied to provide models for each studied macrobenthic variable. Our models highlighted that most of variation (59%-72%) in macrobenthic spatial patterns was explained by the studied environmental variables. Sedimentary variables were more relevant that those of the water column. Therefore, disturbances affecting sedimentary environment could cause dramatic changes in macrobenthic assemblages because of the limited availability of soft bottoms in the area. In this way, results are useful to adopt right management and conservation strategies. Copyright © 2017 Elsevier Ltd. All rights reserved.

Inference of tumor evolution during chemotherapy by computational modeling and in situ analysis of genetic and phenotypic cellular diversity

DOE PAGES

Almendro, Vanessa; Cheng, Yu -Kang; Randles, Amanda; ...

2014-02-01

Cancer therapy exerts a strong selection pressure that shapes tumor evolution, yet our knowledge of how tumors change during treatment is limited. Here, we report the analysis of cellular heterogeneity for genetic and phenotypic features and their spatial distribution in breast tumors pre- and post-neoadjuvant chemotherapy. We found that intratumor genetic diversity was tumor-subtype specific, and it did not change during treatment in tumors with partial or no response. However, lower pretreatment genetic diversity was significantly associated with pathologic complete response. In contrast, phenotypic diversity was different between pre- and post-treatment samples. We also observed significant changes in the spatialmore » distribution of cells with distinct genetic and phenotypic features. We used these experimental data to develop a stochastic computational model to infer tumor growth patterns and evolutionary dynamics. Our results highlight the importance of integrated analysis of genotypes and phenotypes of single cells in intact tissues to predict tumor evolution.« less

Changing bacterial profile of Sundarbans, the world heritage mangrove: impact of anthropogenic interventions.

PubMed

Chakraborty, Arpita; Bera, Amit; Mukherjee, Arghya; Basak, Pijush; Khan, Imroze; Mondal, Arindam; Roy, Arunava; Bhattacharyya, Anish; SenGupta, Sohan; Roy, Debojyoti; Nag, Sudip; Ghosh, Abhrajyoti; Chattopadhyay, Dhrubajyoti; Bhattacharyya, Maitree

2015-04-01

Mangrove microbial communities and their associated activities have profound impact on biogeochemical cycles. Although microbial composition and structure are known to be influenced by biotic and abiotic factors in the mangrove sediments, finding direct correlations between them remains a challenge. In this study we have explored sediment bacterial diversity of the Sundarbans, a world heritage site using a culture-independent molecular approach. Bacterial diversity was analyzed from three different locations with a history of exposure to differential anthropogenic activities. 16S rRNA gene libraries were constructed and partial sequencing of the clones was performed to identify the microbial strains. We identified bacterial strains known to be involved in a variety of biodegradation/biotransformation processes including hydrocarbon degradation, and heavy metal resistance. Canonical Correspondence Analysis of the environmental and exploratory datasets revealed correlations between the ecological indices associated with pollutant levels and bacterial diversity across the sites. Our results indicate that sites with similar exposure of anthropogenic intervention reflect similar patterns of microbial diversity besides spatial commonalities.

Assessing the extent and diversity of riparian ecosystems in Sonora, Mexico

USGS Publications Warehouse

Scott, M.L.; Nagler, P.L.; Glenn, E.P.; Valdes-Casillas, C.; Erker, J.A.; Reynolds, E.W.; Shafroth, P.B.; Gomez-Limon, E.; Jones, C.L.

2009-01-01

Conservation of forested riparian ecosystems is of international concern. Relatively little is known of the structure, composition, diversity, and extent of riparian ecosystems in Mexico. We used high- and low-resolution satellite imagery from 2000 to 2006, and ground-based sampling in 2006, to assess the spatial pattern, extent, and woody plant composition of riparian forests across a range of spatial scales for the state of Sonora, Mexico. For all 3rd and higher order streams, river bottomlands with riparian forests occupied a total area of 2,301 km2. Where forested bottomlands remained, on average, 34% of the area had been converted to agriculture while 39% remained forested. We estimated that the total area of riparian forest along the principal streams was 897 km2. Including fencerow trees, the total forested riparian area was 944 km2, or 0.5% of the total land area of Sonora. Ground-based sampling of woody riparian vegetation consisted of 92, 50 m radius circular plots. About 79 woody plant species were noted. The most important tree species, based on cover and frequency, were willow species Salix spp. (primarily S. goodingii and S. bonplandiana), mesquite species Prosopis spp. (primarily P. velutina), and Fremont cottonwood Populus fremontii. Woody riparian taxa at the reach scale showed a trend of increasing diversity from north to south within Sonora. Species richness was greatest in the willow-bald cypress Taxodium distichum var. mexicanum-Mexican cottonwood P. mexicana subsp. dimorphia ecosystem. The non-native tamarisk Tamarix spp. was rare, occurring at just three study reaches. Relatively natural stream flow patterns and fluvial disturbance regimes likely limit its establishment and spread. ?? 2008 Springer Science + Business Media BV.

Population genetic structure, genetic diversity, and natural history of the South American species of Nothofagus subgenus Lophozonia (Nothofagaceae) inferred from nuclear microsatellite data

PubMed Central

Vergara, Rodrigo; Gitzendanner, Matthew A; Soltis, Douglas E; Soltis, Pamela S

2014-01-01

The effect of glaciation on the levels and patterns of genetic variation has been well studied in the Northern Hemisphere. However, although glaciation has undoubtedly shaped the genetic structure of plants in the Southern Hemisphere, fewer studies have characterized the effect, and almost none of them using microsatellites. Particularly, complex patterns of genetic structure might be expected in areas such as the Andes, where both latitudinal and altitudinal glacial advance and retreat have molded modern plant communities. We therefore studied the population genetics of three closely related, hybridizing species of Nothofagus (N. obliqua, N. alpina, and N. glauca, all of subgenus Lophozonia; Nothofagaceae) from Chile. To estimate population genetic parameters and infer the influence of the last ice age on the spatial and genetic distribution of these species, we examined and analyzed genetic variability at seven polymorphic microsatellite DNA loci in 640 individuals from 40 populations covering most of the ranges of these species in Chile. Populations showed no significant inbreeding and exhibited relatively high levels of genetic diversity (HE = 0.502–0.662) and slight, but significant, genetic structure (RST = 8.7–16.0%). However, in N. obliqua, the small amount of genetic structure was spatially organized into three well-defined latitudinal groups. Our data may also suggest some introgression of N. alpina genes into N. obliqua in the northern populations. These results allowed us to reconstruct the influence of the last ice age on the genetic structure of these species, suggesting several centers of genetic diversity for N. obliqua and N. alpina, in agreement with the multiple refugia hypothesis. PMID:25360279

Biogeography and Change among Regional Coral Communities across the Western Indian Ocean

PubMed Central

McClanahan, Timothy R.; Ateweberhan, Mebrahtu; Darling, Emily S.; Graham, Nicholas A. J.; Muthiga, Nyawira A.

2014-01-01

Coral reefs are biodiverse ecosystems structured by abiotic and biotic factors operating across many spatial scales. Regional-scale interactions between climate change, biogeography and fisheries management remain poorly understood. Here, we evaluated large-scale patterns of coral communities in the western Indian Ocean after a major coral bleaching event in 1998. We surveyed 291 coral reef sites in 11 countries and over 30° of latitude between 2004 and 2011 to evaluate variations in coral communities post 1998 across gradients in latitude, mainland-island geography and fisheries management. We used linear mixed-effect hierarchical models to assess total coral cover, the abundance of four major coral families (acroporids, faviids, pocilloporids and poritiids), coral genus richness and diversity, and the bleaching susceptibility of the coral communities. We found strong latitudinal and geographic gradients in coral community structure and composition that supports the presence of a high coral cover and diversity area that harbours temperature-sensitive taxa in the northern Mozambique Channel between Tanzania, northern Mozambique and northern Madagascar. Coral communities in the more northern latitudes of Kenya, Seychelles and the Maldives were generally composed of fewer bleaching-tolerant coral taxa and with reduced richness and diversity. There was also evidence for continued declines in the abundance of temperature-sensitive taxa and community change after 2004. While there are limitations of our regional dataset in terms of spatial and temporal replication, these patterns suggest that large-scale interactions between biogeographic factors and strong temperature anomalies influence coral communities while smaller-scale factors, such as the effect of fisheries closures, were weak. The northern Mozambique Channel, while not immune to temperature disturbances, shows continued signs of resistance to climate disturbances and remains a priority for future regional conservation and management actions. PMID:24718371

Biogeography and change among regional coral communities across the Western Indian Ocean.

PubMed

McClanahan, Timothy R; Ateweberhan, Mebrahtu; Darling, Emily S; Graham, Nicholas A J; Muthiga, Nyawira A

2014-01-01

Coral reefs are biodiverse ecosystems structured by abiotic and biotic factors operating across many spatial scales. Regional-scale interactions between climate change, biogeography and fisheries management remain poorly understood. Here, we evaluated large-scale patterns of coral communities in the western Indian Ocean after a major coral bleaching event in 1998. We surveyed 291 coral reef sites in 11 countries and over 30° of latitude between 2004 and 2011 to evaluate variations in coral communities post 1998 across gradients in latitude, mainland-island geography and fisheries management. We used linear mixed-effect hierarchical models to assess total coral cover, the abundance of four major coral families (acroporids, faviids, pocilloporids and poritiids), coral genus richness and diversity, and the bleaching susceptibility of the coral communities. We found strong latitudinal and geographic gradients in coral community structure and composition that supports the presence of a high coral cover and diversity area that harbours temperature-sensitive taxa in the northern Mozambique Channel between Tanzania, northern Mozambique and northern Madagascar. Coral communities in the more northern latitudes of Kenya, Seychelles and the Maldives were generally composed of fewer bleaching-tolerant coral taxa and with reduced richness and diversity. There was also evidence for continued declines in the abundance of temperature-sensitive taxa and community change after 2004. While there are limitations of our regional dataset in terms of spatial and temporal replication, these patterns suggest that large-scale interactions between biogeographic factors and strong temperature anomalies influence coral communities while smaller-scale factors, such as the effect of fisheries closures, were weak. The northern Mozambique Channel, while not immune to temperature disturbances, shows continued signs of resistance to climate disturbances and remains a priority for future regional conservation and management actions.

Diversity among macroalgae-consuming fishes on coral reefs: a transcontinental comparison.

PubMed

Vergés, Adriana; Bennett, Scott; Bellwood, David R

2012-01-01

Despite high diversity and abundance of nominally herbivorous fishes on coral reefs, recent studies indicate that only a small subset of taxa are capable of removing dominant macroalgae once these become established. This limited functional redundancy highlights the potential vulnerability of coral reefs to disturbance and stresses the need to assess the functional role of individual species of herbivores. However, our knowledge of species-specific patterns in macroalgal consumption is limited geographically, and there is a need to determine the extent to which patterns observed in specific reefs can be generalised at larger spatial scales. In this study, video cameras were used to quantify rates of macroalgae consumption by fishes in two coral reefs located at a similar latitude in opposite sides of Australia: the Keppel Islands in the Great Barrier Reef (eastern coast) and Ningaloo Reef (western coast). The community of nominally herbivorous fish was also characterised in both systems to determine whether potential differences in the species observed feeding on macroalgae were related to spatial dissimilarities in herbivore community composition. The total number of species observed biting on the dominant brown alga Sargassum myriocystum differed dramatically among the two systems, with 23 species feeding in Ningaloo, compared with just 8 in the Keppel Islands. Strong differences were also found in the species composition and total biomass of nominally herbivorous fish, which was an order of magnitude higher in Ningaloo. However, despite such marked differences in the diversity, biomass, and community composition of resident herbivorous fishes, Sargassum consumption was dominated by only four species in both systems, with Naso unicornis and Kyphosus vaigiensis consistently emerging as dominant feeders of macroalgae.

Distribution, abundance, diversity and habitat associations of fishes across a bioregion experiencing rapid coastal development

NASA Astrophysics Data System (ADS)

McLean, Dianne L.; Langlois, Tim J.; Newman, Stephen J.; Holmes, Thomas H.; Birt, Matthew J.; Bornt, Katrina R.; Bond, Todd; Collins, Danielle L.; Evans, Scott N.; Travers, Michael J.; Wakefield, Corey B.; Babcock, Russ C.; Fisher, Rebecca

2016-09-01

Knowledge of the factors that influence spatial patterns in fish abundance, distribution and diversity are essential for informing fisheries and conservation management. The present study was conducted in the nearshore Pilbara bioregion of north-western Australia where the dynamic marine environment is characterised by large embayments, numerous islands and islets, coexisting with globally significant petrochemical and mineral industries. Within Western Australia, this nearshore bioregion has high biodiversity and is considered to play an essential role in the recruitment of species of commercial importance. To better inform future investigations into both ecological processes and planning scenarios for management, a rapid assessment of the distribution, abundance and associations with nearshore habitats of fishes across the region was conducted. Baited remote underwater stereo-video systems (stereo-BRUVs) were used to simultaneously sample the fish assemblage and habitat composition. Generalised additive mixed models (GAMMs) were used to determine whether the abundance of fishes were related to habitat and a range of environmental variables (visibility, depth, distance to 30 m and 200 m depth isobars, boat ramps and the nearest large embayment (Exmouth Gulf). A diverse fish assemblage comprising 343 species from 58 families was recorded. The abundance and distribution patterns of fishery-target species and of the five most common and abundant species and families were linked positively with areas of high relief, hard coral cover, reef and macroalgae and negatively with the distance to the nearest oceanic waters (200 m depth isobar). This study provides information that can contribute to future marine spatial planning scenarios for management of the Pilbara using a unique, analytical approach that has broad application in biogeography.

Patterns in micronekton diversity across the North Pacific Subtropical Gyre observed from the diet of longnose lancetfish (Alepisaurus ferox)

NASA Astrophysics Data System (ADS)

Portner, Elan J.; Polovina, Jeffrey J.; Choy, C. Anela

2017-07-01

We examined the diet of a common midwater predator, the longnose lancetfish (Alepisaurus ferox, n=1371), with respect to fork length, season, and capture location within the North Pacific Subtropical Gyre (NPSG). While A. ferox fed diversely across 97 prey families, approximately 70% of its diet by wet weight consisted of seven prey families (fishes: Sternoptychidae, Anoplogastridae, Omosudidae, Alepisauridae; hyperiid amphipods: Phrosinidae; octopods: Amphitretidae; polychaetes: Alciopidae). Altogether, these micronekton prey families constitute a poorly known forage community distinct from those exploited by other pelagic predators and poorly sampled by conventional methods. We demonstrate ontogenetic variation in diet between two size classes of A. ferox (<97 cm fork length=;small;, ≥97 cm fork length=;large;). Large A. ferox consumed more fish and octopods, fewer crustaceans, and were more cannibalistic than small A. ferox. Ontogenetic shifts in vertical foraging habitat were observed as the consumption of larger and more mesopelagic prey with increasing fork length. Spatial and seasonal variation in the diet of A. ferox is consistent with expected patterns of variation in prey distribution with respect to oceanographic features of the NPSG. Within both size classes, the diets of specimens collected from the oligotrophic core of the NPSG were more diverse than those collected near the boundaries of the gyre and appeared to track seasonal variation in the position of the northern boundary of the gyre. Our data suggest seasonal and spatial variability in the composition of midwater forage communities exploited by A. ferox across the NPSG, and demonstrate that sustained monitoring of diet could provide valuable insights into long-term changes in these understudied communities.