Neural basis of social status hierarchy across species.

PubMed

Chiao, Joan Y

2010-12-01

Social status hierarchy is a ubiquitous principle of social organization across the animal kingdom. Recent findings in social neuroscience reveal distinct neural networks associated with the recognition and experience of social hierarchy in humans, as well as modulation of these networks by personality and culture. Additionally, allelic variation in the serotonin transporter gene is associated with prevalence of social hierarchy across species and cultures, suggesting the importance of the study of genetic factors underlying social hierarchy. Future studies are needed to determine how genetic and environmental factors shape neural systems involved in the production and maintenance of social hierarchy across ontogeny and phylogeny. Copyright © 2010 Elsevier Ltd. All rights reserved.

Diversification rates and species richness across the Tree of Life

PubMed Central

Scholl, Joshua P.

2016-01-01

Species richness varies dramatically among clades across the Tree of Life, by over a million-fold in some cases (e.g. placozoans versus arthropods). Two major explanations for differences in richness among clades are the clade-age hypothesis (i.e. species-rich clades are older) and the diversification-rate hypothesis (i.e. species-rich clades diversify more rapidly, where diversification rate is the net balance of speciation and extinction over time). Here, we examine patterns of variation in diversification rates across the Tree of Life. We address how rates vary across higher taxa, whether rates within higher taxa are related to the subclades within them, and how diversification rates of clades are related to their species richness. We find substantial variation in diversification rates, with rates in plants nearly twice as high as in animals, and rates in some eukaryotes approximately 10-fold faster than prokaryotes. Rates for each kingdom-level clade are then significantly related to the subclades within them. Although caution is needed when interpreting relationships between diversification rates and richness, a positive relationship between the two is not inevitable. We find that variation in diversification rates seems to explain most variation in richness among clades across the Tree of Life, in contrast to the conclusions of previous studies. PMID:27605507

Spatial-temporal population dynamics across species range: From centre to margin

USGS Publications Warehouse

Guo, Q.; Taper, M.; Schoenberger, M.; Brandle, J.

2005-01-01

Understanding the boundaries of species' ranges and the variations in population dynamics from the centre to margin of a species' range is critical. This study simulated spatial-temporal patterns of birth and death rates and migration across a species' range in different seasons. Our results demonstrated the importance of dispersal and migration in altering birth and death rates, balancing source and sink habitats, and governing expansion or contraction of species' ranges in changing environments. We also showed that the multiple equilibria of metapopulations across a species' range could be easily broken following climatic changes or physical disturbances either local or regional. Although we refer to our models as describing the population dynamics across whole species' range, they should also apply to small-scale habitats (metapopulations) in which species abundance follows a humped pattern or to any ecosystem or landscape where strong central-marginal (C-M) environmental gradients exist. Conservation of both central and marginal populations would therefore be equally important considerations in making management decisions.

Spatial-temporal population dynamics across species range: from center to margin

USGS Publications Warehouse

Guo, Q.; Taper, M.L.; Schoenberger, M.; Brandl, J.

2005-01-01

Understanding the boundaries of species' ranges and the variations in population dynamics from the centre to margin of a species' range is critical. This study simulated spatial-temporal patterns of birth and death rates and migration across a species' range in different seasons. Our results demonstrated the importance of dispersal and migration in altering birth and death rates, balancing source and sink habitats, and governing expansion or contraction of species' ranges in changing environments. We also showed that the multiple equilibria of metapopulations across a species' range could be easily broken following climatic changes or physical disturbances either or local or regional. Although we refer to our models as describing the population dynamics across whole species' range, they should also apply to small-scale habitats (metapopulations) in which species abundance follows a humped pattern or to any ecosystem or landscape where strong central-marginal (C-M) environmental gradients exist. Conservation of both central and marginal populations would therefore be equally important considerations in making management decisions.

Comparing Patterns of Natural Selection across Species Using Selective Signatures

PubMed Central

Shapiro, B. Jesse; Alm, Eric J

2008-01-01

Comparing gene expression profiles over many different conditions has led to insights that were not obvious from single experiments. In the same way, comparing patterns of natural selection across a set of ecologically distinct species may extend what can be learned from individual genome-wide surveys. Toward this end, we show how variation in protein evolutionary rates, after correcting for genome-wide effects such as mutation rate and demographic factors, can be used to estimate the level and types of natural selection acting on genes across different species. We identify unusually rapidly and slowly evolving genes, relative to empirically derived genome-wide and gene family-specific background rates for 744 core protein families in 30 γ-proteobacterial species. We describe the pattern of fast or slow evolution across species as the “selective signature” of a gene. Selective signatures represent a profile of selection across species that is predictive of gene function: pairs of genes with correlated selective signatures are more likely to share the same cellular function, and genes in the same pathway can evolve in concert. For example, glycolysis and phenylalanine metabolism genes evolve rapidly in Idiomarina loihiensis, mirroring an ecological shift in carbon source from sugars to amino acids. In a broader context, our results suggest that the genomic landscape is organized into functional modules even at the level of natural selection, and thus it may be easier than expected to understand the complex evolutionary pressures on a cell. PMID:18266472

Investigating Differences across Host Species and Scales to Explain the Distribution of the Amphibian Pathogen Batrachochytrium dendrobatidis

PubMed Central

Peterson, Anna C.; McKenzie, Valerie J.

2014-01-01

Many pathogens infect more than one host species, and clarifying how these different hosts contribute to pathogen dynamics can facilitate the management of pathogens and can lend insight into the functioning of pathogens in ecosystems. In this study, we investigated a suite of native and non-native amphibian hosts of the pathogen Batrachochytrium dendrobatidis (Bd) across multiple scales to identify potential mechanisms that may drive infection patterns in the Colorado study system. Specifically, we aimed to determine if: 1) amphibian populations vary in Bd infection across the landscape, 2) amphibian community composition predicts infection (e.g., does the presence or abundance of any particular species influence infection in others?), 3) amphibian species vary in their ability to produce infectious zoospores in a laboratory infection, 4) heterogeneity in host ability observed in the laboratory scales to predict patterns of Bd prevalence in the landscape. We found that non-native North American bullfrogs (Lithobates catesbeianus) are widespread and have the highest prevalence of Bd infection relative to the other native species in the landscape. Additionally, infection in some native species appears to be related to the density of sympatric L. catesbeianus populations. At the smaller host scale, we found that L. catesbeianus produces more of the infective zoospore stage relative to some native species, but that this zoospore output does not scale to predict infection in sympatric wild populations of native species. Rather, landscape level infection relates most strongly to density of hosts at a wetland as well as abiotic factors. While non-native L. catesbeianus have high levels of Bd infection in the Colorado Front Range system, we also identified Bd infection in a number of native amphibian populations allopatric with L. catesbeianus, suggesting that multiple host species are important contributors to the dynamics of the Bd pathogen in this landscape. PMID

Diversification rates and species richness across the Tree of Life.

PubMed

Scholl, Joshua P; Wiens, John J

2016-09-14

Species richness varies dramatically among clades across the Tree of Life, by over a million-fold in some cases (e.g. placozoans versus arthropods). Two major explanations for differences in richness among clades are the clade-age hypothesis (i.e. species-rich clades are older) and the diversification-rate hypothesis (i.e. species-rich clades diversify more rapidly, where diversification rate is the net balance of speciation and extinction over time). Here, we examine patterns of variation in diversification rates across the Tree of Life. We address how rates vary across higher taxa, whether rates within higher taxa are related to the subclades within them, and how diversification rates of clades are related to their species richness. We find substantial variation in diversification rates, with rates in plants nearly twice as high as in animals, and rates in some eukaryotes approximately 10-fold faster than prokaryotes. Rates for each kingdom-level clade are then significantly related to the subclades within them. Although caution is needed when interpreting relationships between diversification rates and richness, a positive relationship between the two is not inevitable. We find that variation in diversification rates seems to explain most variation in richness among clades across the Tree of Life, in contrast to the conclusions of previous studies. © 2016 The Author(s).

Transferability of retrotransposon primers derived from Persimmon (Diospyros kaki Thunb.) across other plant species.

PubMed

Du, X Y; Hu, Q N; Zhang, Q L; Wang, Y B; Luo, Z R

2013-06-06

Retrotransposon-based molecular markers are powerful molecular tools. However, these markers are not readily available due to the difficulty in obtaining species-specific retrotransposon primers. Although recent techniques enabling the rapid isolation of retrotransposon sequences have facilitated primer development, this process nonetheless remains time-consuming and costly. Therefore, research into the transferability of retrotransposon primers developed from one plant species onto others would be of great value. The present study investigated the transferability of retrotransposon primers derived from 'Luotian-tianshi' persimmon (Diospyros kaki Thunb.) across other fruit crops, as well as within the genus using inter-retrotransposon amplified polymorphism molecular marker. Fourteen of the 26 retrotransposon primers tested (53.85%) produced robust and reproducible amplification products across all fruit crops tested, indicating their applicability across plant species. Four of the 13 fruit crops showed the best transferability performances: persimmon, grape, citrus, and peach. Furthermore, similarity coefficients and UPGMA clustering indicated that these primers could further offer a potential tool for germplasm differentiation, parentage identification, genetic diversity assessment, classification, and phylogenetic studies across a variety of plant species. Transferability was further confirmed by examining published primers derived from Rosaceae, Gramineae, and Solanaceae. This study is one of the few currently available studies concerning the transferability of retrotransposon primers across plant species in general, and is the first successful study of the transferability of retrotransposon primers derived from persimmon. The primers presented here will help reduce costs for future retrotransposon primer development and therefore contribute to the popularization of retrotransposon molecular markers.

Nesting behaviour influences species-specific gas exchange across avian eggshells.

PubMed

Portugal, Steven J; Maurer, Golo; Thomas, Gavin H; Hauber, Mark E; Grim, Tomáš; Cassey, Phillip

2014-09-15

Carefully controlled gas exchange across the eggshell is essential for the development of the avian embryo. Water vapour conductance (G(H2O)) across the shell, typically measured as mass loss during incubation, has been demonstrated to optimally ensure the healthy development of the embryo while avoiding desiccation. Accordingly, eggs exposed to sub-optimal gas exchange have reduced hatching success. We tested the association between eggshell G(H2O) and putative life-history correlates of adult birds, ecological nest parameters and physical characteristics of the egg itself to investigate how variation in G(H2O) has evolved to maintain optimal water loss across a diverse set of nest environments. We measured gas exchange through eggshell fragments in 151 British breeding bird species and fitted phylogenetically controlled, general linear models to test the relationship between G(H2O) and potential predictor parameters of each species. Of our 17 life-history traits, only two were retained in the final model: wet-incubating parent and nest type. Eggs of species where the parent habitually returned to the nest with wet plumage had significantly higher G(H2O) than those of parents that returned to the nest with dry plumage. Eggs of species nesting in ground burrows, cliffs and arboreal cups had significantly higher G(H2O) than those of species nesting on the ground in open nests or cups, in tree cavities and in shallow arboreal nests. Phylogenetic signal (measured as Pagel's λ) was intermediate in magnitude, suggesting that differences observed in the G(H2O) are dependent upon a combination of shared ancestry and species-specific life history and ecological traits. Although these data are correlational by nature, they are consistent with the hypothesis that parents constrained to return to the nest with wet plumage will increase the humidity of the nest environment, and the eggs of these species have evolved a higher G(H2O) to overcome this constraint and still

Mammal responses to the human footprint vary across species and stressors.

PubMed

Toews, Mary; Juanes, Francis; Burton, A Cole

2018-07-01

A rapidly expanding human footprint - comprised of anthropogenic land-use change and infrastructure - is profoundly affecting wildlife distributions worldwide. Cumulative effects management (CEM) is a regional approach that seeks to manage combined effects of the human footprint on biodiversity across large spatial scales. Challenges to implementing this approach include a lack of ecological data at large spatial scales, the high cost of monitoring multiple indicators, and the need to manage multiple footprints across industries. To inform development of effective CEM, we used large mammals as indicators to address the following questions: a) do species respond more strongly to individual footprint features or to cumulative effects (combined area of all footprint types, measured as total footprint), b) which features elicit the strongest responses across species, and c) are the direction of responses to footprint consistent? We used data from 12 years of snowtrack surveys (2001-2013) in the boreal forest of Alberta, coupled with regional footprint and landcover data, to develop generalized linear mixed-effects models relating the relative abundance of five boreal mammals [gray wolf (Canis lupus), Canada lynx (Lynx canadensis), coyote (Canis latrans), white-tailed deer (Odocoileus virginianus) and moose (Alces alces)] to individual and cumulative effects of the human footprint. We found that across species the strongest responses were to agriculture, roads, and young cutblocks (<10 years), suggesting these as potential priority stressors to address within CEM. Most species also responded to total footprint, indicating that in the absence of detailed information on individual features, this coarse measure can serve as an index of cumulative effects. There was high variability in direction and magnitude of responses across species, indicating that community-level responses are likely and should be considered within CEM planning. Copyright © 2018 Elsevier Ltd. All

Multi-Scale Approach for Predicting Fish Species Distributions across Coral Reef Seascapes

PubMed Central

Pittman, Simon J.; Brown, Kerry A.

2011-01-01

Two of the major limitations to effective management of coral reef ecosystems are a lack of information on the spatial distribution of marine species and a paucity of data on the interacting environmental variables that drive distributional patterns. Advances in marine remote sensing, together with the novel integration of landscape ecology and advanced niche modelling techniques provide an unprecedented opportunity to reliably model and map marine species distributions across many kilometres of coral reef ecosystems. We developed a multi-scale approach using three-dimensional seafloor morphology and across-shelf location to predict spatial distributions for five common Caribbean fish species. Seascape topography was quantified from high resolution bathymetry at five spatial scales (5–300 m radii) surrounding fish survey sites. Model performance and map accuracy was assessed for two high performing machine-learning algorithms: Boosted Regression Trees (BRT) and Maximum Entropy Species Distribution Modelling (MaxEnt). The three most important predictors were geographical location across the shelf, followed by a measure of topographic complexity. Predictor contribution differed among species, yet rarely changed across spatial scales. BRT provided ‘outstanding’ model predictions (AUC = >0.9) for three of five fish species. MaxEnt provided ‘outstanding’ model predictions for two of five species, with the remaining three models considered ‘excellent’ (AUC = 0.8–0.9). In contrast, MaxEnt spatial predictions were markedly more accurate (92% map accuracy) than BRT (68% map accuracy). We demonstrate that reliable spatial predictions for a range of key fish species can be achieved by modelling the interaction between the geographical location across the shelf and the topographic heterogeneity of seafloor structure. This multi-scale, analytic approach is an important new cost-effective tool to accurately delineate essential fish habitat and support

Multi-scale approach for predicting fish species distributions across coral reef seascapes.

PubMed

Pittman, Simon J; Brown, Kerry A

2011-01-01

Two of the major limitations to effective management of coral reef ecosystems are a lack of information on the spatial distribution of marine species and a paucity of data on the interacting environmental variables that drive distributional patterns. Advances in marine remote sensing, together with the novel integration of landscape ecology and advanced niche modelling techniques provide an unprecedented opportunity to reliably model and map marine species distributions across many kilometres of coral reef ecosystems. We developed a multi-scale approach using three-dimensional seafloor morphology and across-shelf location to predict spatial distributions for five common Caribbean fish species. Seascape topography was quantified from high resolution bathymetry at five spatial scales (5-300 m radii) surrounding fish survey sites. Model performance and map accuracy was assessed for two high performing machine-learning algorithms: Boosted Regression Trees (BRT) and Maximum Entropy Species Distribution Modelling (MaxEnt). The three most important predictors were geographical location across the shelf, followed by a measure of topographic complexity. Predictor contribution differed among species, yet rarely changed across spatial scales. BRT provided 'outstanding' model predictions (AUC = >0.9) for three of five fish species. MaxEnt provided 'outstanding' model predictions for two of five species, with the remaining three models considered 'excellent' (AUC = 0.8-0.9). In contrast, MaxEnt spatial predictions were markedly more accurate (92% map accuracy) than BRT (68% map accuracy). We demonstrate that reliable spatial predictions for a range of key fish species can be achieved by modelling the interaction between the geographical location across the shelf and the topographic heterogeneity of seafloor structure. This multi-scale, analytic approach is an important new cost-effective tool to accurately delineate essential fish habitat and support conservation

Survey of thrips species infesting cotton across the southern U.S. cotton belt

USDA-ARS?s Scientific Manuscript database

A survey investigating the composition of adult thrips species and the effect of preventive, at-plant insecticides on this composition was conducted at multiple locations across the upland U.S. Cotton Belt in 2009 and 2010. Small-plot experiments included insecticide seed treatments containing imid...

High intra-specific variation in avian body condition responses to climate limits generalisation across species

PubMed Central

van der Jeugd, Henk P.; van de Pol, Martijn

2018-01-01

It is generally assumed that populations of a species will have similar responses to climate change, and thereby that a single value of sensitivity will reflect species-specific responses. However, this assumption is rarely systematically tested. High intraspecific variation will have consequences for identifying species- or population-level traits that can predict differences in sensitivity, which in turn can affect the reliability of projections of future climate change impacts. We investigate avian body condition responses to changes in six climatic variables and how consistent and generalisable these responses are both across and within species, using 21 years of data from 46 common passerines across 80 Dutch sites. We show that body condition decreases with warmer spring/early summer temperatures and increases with higher humidity, but other climate variables do not show consistent trends across species. In the future, body condition is projected to decrease by 2050, mainly driven by temperature effects. Strikingly, populations of the same species generally responded just as differently as populations of different species implying that a single species signal is not meaningful. Consequently, species-level traits did not explain interspecific differences in sensitivities, rather population-level traits were more important. The absence of a clear species signal in body condition responses implies that generalisation and identifying species for conservation prioritisation is problematic, which sharply contrasts conclusions of previous studies on the climate sensitivity of phenology. PMID:29466460

Selective sweeps in the homoploid hybrid species Helianthus deserticola: evolution in concert across populations and across origins

PubMed Central

GROSS, BRIANA L.; TURNER, KATHRYN G.; RIESEBERG, LOREN H.

2008-01-01

The evolution of different populations within a species in response to selective pressures can potentially happen in three different ways. It can occur in parallel, where similar changes occur independently in each population in response to selection; in concert, where the spread of an adaptive mutation across a species’ range results in a single allele fixing in each population; or populations can diverge in response to local selective pressures. We explored these possibilities in populations of the homoploid hybrid species Helianthus deserticola relative to its parental species Helianthus annuus and Helianthus petiolaris using an analysis of variation in 96 expressed sequence tag-based microsatellites. A total of nine loci showed evidence consistent with recent selection at either the species or population level, although two of these genes were discarded because the apparent sweep did not occur relative to the parent from which the locus was derived. Between one and five loci showed a putative sweep across the entire species range with the same microsatellite allele fixed in each population. This pattern is consistent with evolution in concert despite geographical isolation and potential independent origins of the populations. Only one population of H. deserticola showed candidate sweeps that were unique compared to the rest of the species, and this population has also potentially experienced recent admixture with the parental species. PMID:18092993

SeqAPASS: Sequence alignment to predict across-species ...

EPA Pesticide Factsheets

Efforts to shift the toxicity testing paradigm from whole organism studies to those focused on the initiation of toxicity and relevant pathways have led to increased utilization of in vitro and in silico methods. Hence the emergence of high through-put screening (HTS) programs, such as U.S. EPA ToxCast, and application of the adverse outcome pathway (AOP) framework for identifying and defining biological key events triggered upon perturbation of molecular initiating events and leading to adverse outcomes occuring at a level of organization relevant for risk assessment [1]. With these recent initiatives to harness the power of “the pathway” in describing and evaluating toxicity comes the need to extrapolate data beyond the model species. Sequence alignment to predict across-species susceptibilty (SeqAPASS) is a web-based tool that allows the user to begin to understand how broadly HTS data or AOP constructs may plausibly be extrapolated across species, while describing the relative intrinsic susceptibiltiy of different taxa to chemicals with known modes of action (e.g., pharmaceuticals and pesticides). The tool rapidly and strategically assesses available molecular target information to describe protein sequence similarity at the primary amino acid sequence, conserved domain, and individual amino acid residue levels. This in silico approach to species extrapolation was designed to automate and streamline the relatively complex and time-consuming process of co

Mosquito Species (Diptera: Culicidae) Persistence and Synchrony Across an Urban Altitudinal Gradient.

PubMed

Chaves, Luis Fernando

2017-03-01

Patterns of mosquito spatial persistence and temporal presence, as well as synchrony, i.e., the degree of concerted fluctuations in abundance, have been scarcely studied at finely grained spatial scales and over altitudinal gradients. Here, we present a spatial persistence, temporal presence, and synchrony analysis of four common mosquito species across the altitudinal gradient of Mt. Konpira in Nagasaki, Japan. We found that Aedes albopictus (Skuse) was more frequently found at the mountain base. In contrast, Aedes japonicus (Theobald) and Aedes flavopictus Yamada were common higher in the mountain, while Armigeres subalbatus (Coquillet) was uniformly present across the mountain, yet less frequently than the other species during the studied period. Our analysis showed that these spatial heterogeneities were associated with differences in landscape and microclimatic elements of Mt. Konpira. Temporally we found that presence across sampling locations was mainly synchronous across the four species and positively associated with rainfall and temperature. With the exception of Ae albopictus, where no significant synchrony was observed, mosquito species mainly showed flat synchrony profiles in Mt. Konpira when looking at the geographic (2-D) distance between their sampling locations. By contrast, when synchrony was studied across altitude, it was observed that Ae. flavopictus tracked the temperature synchrony pattern, decreasing its synchrony with the separation in altitude between sampling locations. Finally, our results suggest that differences in mosquito species persistence, temporal presence, and synchrony might be useful to understand the entomological risk of vector-borne disease transmission in urban landscapes. © 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.

Scaling behavior of sleep-wake transitions across species

NASA Astrophysics Data System (ADS)

Lo, Chung-Chuan; Chou, Thomas; Ivanov, Plamen Ch.; Penzel, Thomas; Mochizuki, Takatoshi; Scammell, Thomas; Saper, Clifford B.; Stanley, H. Eugene

2003-03-01

Uncovering the mechanisms controlling sleep is a fascinating scientific challenge. It can be viewed as transitions of states of a very complex system, the brain. We study the time dynamics of short awakenings during sleep for three species: humans, rats and mice. We find, for all three species, that wake durations follow a power-law distribution, and sleep durations follow exponential distributions. Surprisingly, all three species have the same power-law exponent for the distribution of wake durations, but the exponential time scale of the distributions of sleep durations varies across species. We suggest that the dynamics of short awakenings are related to species-independent fluctuations of the system, while the dynamics of sleep is related to system-dependent mechanisms which change with species.

Sequence Alignment to Predict Across Species Susceptibility (SeqAPASS) Version 3.0 User Guide

EPA Science Inventory

User Guide to describe the complete functionality of the Sequence Alignment to Predict Across Species Susceptibility (SeqAPASS) Version 3.0 online tool. The US Environmental Protection Agency Sequence Alignment to Predict Across Species Susceptibility tool (SeqAPASS; https://seqa...

Nematode distributions as spatial null models for macroinvertebrate species richness across environmental gradients: A case from mountain lakes.

PubMed

de Mendoza, Guillermo; Traunspurger, Walter; Palomo, Alejandro; Catalan, Jordi

2017-05-01

Nematode species are widely tolerant of environmental conditions and disperse passively. Therefore, the species richness distribution in this group might largely depend on the topological distribution of the habitats and main aerial and aquatic dispersal pathways connecting them. If so, the nematode species richness distributions may serve as null models for evaluating that of other groups more affected by environmental gradients. We investigated this hypothesis in lakes across an altitudinal gradient in the Pyrenees. We compared the altitudinal distribution, environmental tolerance, and species richness, of nematodes with that of three other invertebrate groups collected during the same sampling: oligochaetes, chironomids, and nonchironomid insects. We tested the altitudinal bias in distributions with t -tests and the significance of narrow-ranging altitudinal distributions with randomizations. We compared results between groups with Fisher's exact tests. We then explored the influence of environmental factors on species assemblages in all groups with redundancy analysis (RDA), using 28 environmental variables. And, finally, we analyzed species richness patterns across altitude with simple linear and quadratic regressions. Nematode species were rarely biased from random distributions (5% of species) in contrast with other groups (35%, 47%, and 50%, respectively). The altitudinal bias most often shifted toward low altitudes (85% of biased species). Nematodes showed a lower portion of narrow-ranging species than any other group, and differed significantly from nonchironomid insects (10% and 43%, respectively). Environmental variables barely explained nematode assemblages (RDA adjusted R 2  = 0.02), in contrast with other groups (0.13, 0.19 and 0.24). Despite these substantial differences in the response to environmental factors, species richness across altitude was unimodal, peaking at mid elevations, in all groups. This similarity indicates that the spatial

Advancement of tree species across ecotonal borders into non-forested ecosystems

NASA Astrophysics Data System (ADS)

Hanberry, Brice B.; Hansen, Mark H.

2015-10-01

Woody species are increasing in density, causing transition to more densely wooded vegetation states, and encroaching across ecotonal borders into non-forested ecosystems. We examined USDA Forest Service Forest Inventory and Analysis data to identify tree species that have expanded longitudinally in range, particularly into the central United States. We analyzed compositional differences within ecological regions (i.e., subsections) in eastern and western ranges of species using repeated measures ANOVA. We considered differences in outer ranges to indicate range expansion or contraction. We also estimated the shift in forest area and basal area relative to the center of the US and compared change in deciduous forest land cover. Out of 80 candidate species, 22 species expanded to the west, seven species expanded to the east, and five species expanded in both directions. During the survey interval, eastern tree species advanced into the predominantly non-forested ecosystems of central United States. Eastern cottonwood, eastern hophornbeam, eastern redbud, honeylocust, Osage-orange, pecan, red mulberry, and Shumard oak represent some of the species that are advancing eastern forest boundaries across forest-grassland ecotones into the central United States. Forest land has shifted towards the center of the continent, as has the center of mean tree basal area, and a simple comparison of deciduous cover change also displayed forest advancement into the central United States from eastern forests. The expanding species may spread along riparian migration corridors that provide protection from drought. Humans use the advancing tree species for windbreaks, fencerows, and ornamental landscaping, while wildlife spread fruit seeds, which results in unintentional assisted migration, or translocation, to drier sites across the region.

Supporting read-across using biological data.

PubMed

Zhu, Hao; Bouhifd, Mounir; Donley, Elizabeth; Egnash, Laura; Kleinstreuer, Nicole; Kroese, E Dinant; Liu, Zhichao; Luechtefeld, Thomas; Palmer, Jessica; Pamies, David; Shen, Jie; Strauss, Volker; Wu, Shengde; Hartung, Thomas

2016-01-01

Read-across, i.e. filling toxicological data gaps by relating to similar chemicals, for which test data are available, is usually done based on chemical similarity. Besides structure and physico-chemical properties, however, biological similarity based on biological data adds extra strength to this process. In the context of developing Good Read-Across Practice guidance, a number of case studies were evaluated to demonstrate the use of biological data to enrich read-across. In the simplest case, chemically similar substances also show similar test results in relevant in vitro assays. This is a well-established method for the read-across of e.g. genotoxicity assays. Larger datasets of biological and toxicological properties of hundreds and thousands of substances become increasingly available enabling big data approaches in read-across studies. Several case studies using various big data sources are described in this paper. An example is given for the US EPA's ToxCast dataset allowing read-across for high quality uterotrophic assays for estrogenic endocrine disruption. Similarly, an example for REACH registration data enhancing read-across for acute toxicity studies is given. A different approach is taken using omics data to establish biological similarity: Examples are given for stem cell models in vitro and short-term repeated dose studies in rats in vivo to support read-across and category formation. These preliminary biological data-driven read-across studies highlight the road to the new generation of read-across approaches that can be applied in chemical safety assessment.

Global hotspots and correlates of alien species richness across taxonomic groups

USGS Publications Warehouse

Dawson, Wayne; Moser, Dietmar; van Kleunen, Mark; Kreft, Holger; Pergl, Jan; Pysek, Petr; Weigelt, Patrick; Winter, Marten; Lenzner, Bernd; Blackburn, Tim M.; Dyer, Ellie; Cassey, Phillip; Scrivens, Sally-Louise; Economo, Evan P.; Guenard, Benoit; Capinha, Cesar; Seebens, Hanno; Garcia-Diaz, Pablo; Nentwig, Wolfgang; Garcia-Berthou, Emili; Casal, Christine; Mandrak, Nicholas E.; Fuller, Pam; Meyer, Carsten; Essl, Franz

2017-01-01

Human-mediated transport beyond biogeographic barriers has led to the introduction and establishment of alien species in new regions worldwide. However, we lack a global picture of established alien species richness for multiple taxonomic groups. Here, we assess global patterns and potential drivers of established alien species richness across eight taxonomic groups (amphibians, ants, birds, freshwater fishes, mammals, vascular plants, reptiles and spiders) for 186 islands and 423 mainland regions. Hotspots of established alien species richness are predominantly island and coastal mainland regions. Regions with greater gross domestic product per capita, human population density, and area have higher established alien richness, with strongest effects emerging for islands. Ants and reptiles, birds and mammals, and vascular plants and spiders form pairs of taxonomic groups with the highest spatial congruence in established alien richness, but drivers explaining richness differ between the taxa in each pair. Across all taxonomic groups, our results highlight the need to prioritize prevention of further alien species introductions to island and coastal mainland regions globally.

Drought resilience across ecologically dominant species: An experiment-model integration approach

NASA Astrophysics Data System (ADS)

Felton, A. J.; Warren, J.; Ricciuto, D. M.; Smith, M. D.

2017-12-01

Poorly understood are the mechanisms contributing to variability in ecosystem recovery following drought. Grasslands of the central U.S. are ecologically and economically important ecosystems, yet are also highly sensitive to drought. Although characteristics of these ecosystems change across gradients of temperature and precipitation, a consistent feature among these systems is the presence of highly abundant, dominant grass species that control biomass production. As a result, the incorporation of these species' traits into terrestrial biosphere models may constrain predictions amid increases in climatic variability. Here we report the results of a modeling-experiment (MODEX) research approach. We investigated the physiological, morphological and growth responses of the dominant grass species from each of the four major grasslands of the central U.S. (ranging from tallgrass prairie to desert grassland) following severe drought. Despite significant differences in baseline values, full recovery in leaf physiological function was evident across species, of which was consistently driven by the production of new leaves. Further, recovery in whole-plant carbon uptake tended to be driven by shifts in allocation from belowground to aboveground structures. However, there was clear variability among species in the magnitude of this dynamic as well as the relative allocation to stem versus leaf production. As a result, all species harbored the physiological capacity to recover from drought, yet we posit that variability in the recovery of whole-plant carbon uptake to be more strongly driven by variability in the sensitivity of species' morphology to soil moisture increases. The next step of this project will be to incorporate these and other existing data on these species and ecosystems into the community land model in an effort to test the sensitivity of this model to these data.

Spatial-temporal population dynamics across species range: from centre to margin

Treesearch

Qinfeng Guo; Mark Taper; Michele Schoenberger; J. Brandle

2005-01-01

Understanding the boundaries of species'rangs and the variations in population dynamics from the centre to margin of a species' range is critical. This study simulated spatial-tamporal patterns of birth and death rates and migration across a species' range in different seasons. Our results demonstrated the importance of dispersal and migration in...

Synchrony in small mammal community dynamics across a forested landscape

Treesearch

Ryan B. Stephens; Daniel J. Hocking; Mariko Yamasaki; Rebecca J. Rowe

2016-01-01

Long- term studies at local scales indicate that fluctuations in abundance among trophically similar species are often temporally synchronized. Complementary studies on synchrony across larger spatial extents are less common, as are studies that investigate the subsequent impacts on community dynamics across the landscape. We investigate the impact of species...

Neurocognitive Aging and the Hippocampus Across Species

PubMed Central

Leal, Stephanie L; Yassa, Michael A.

2016-01-01

There is extensive evidence that aging is associated with impairments in episodic memory. Many of these changes have been ascribed to neurobiological alterations to the hippocampal network and its input pathways. A cross-species consensus is beginning to emerge suggesting that subtle synaptic and functional changes within this network may underlie the majority of age-related memory impairments. In this review, we survey convergent data from animal and human studies that have contributed significantly to our understanding of the brain-behavior relationships in this network, particularly in the aging brain. We utilize a cognitive as well as a neurobiological perspective, and synthesize data across approaches and species to reach a more detailed understanding of age-related alterations in hippocampal memory function. PMID:26607684

Interactions between micro- and macroparasites predict microparasite species richness across primates.

PubMed

Nunn, Charles L; Brezine, Carrie; Jolles, Anna E; Ezenwa, Vanessa O

2014-04-01

Most wild animals face concurrent challenges by multiple infectious organisms, and immunological responses triggered by some parasites may increase susceptibility to other infectious agents. Immune-mediated interactions among parasites have been investigated among individuals in a population, but less is known about broader comparative patterns. We investigated the "macro-micro facilitation hypothesis" that higher helminth prevalence in a host species provides greater opportunities for intracellular parasites to invade, resulting in higher richness of intracellular microparasites. We obtained data on average helminth prevalence for 70 primate hosts, along with data on richness of intra- and extracellular infectious organisms. Using Bayesian phylogenetic methods, we found that primate species with higher overall helminth prevalence harbored more species of intracellular microparasites, while the positive association between helminth prevalence and extracellular microparasite species richness was weaker. The relationships held after controlling for potentially confounding variables, but associations were not found in focused tests of prevalence for six genera of well-studied helminths. The magnitude of support and effect sizes for overall helminth prevalence on intracellular microparasite species richness was similar to support for other well recognized ecological and life-history drivers of parasite species richness. Our findings therefore suggest that intrahost parasite interactions are as important as some ecological characteristics of hosts in accounting for parasite richness across host species.

A framework for studying emotions across species.

PubMed

Anderson, David J; Adolphs, Ralph

2014-03-27

Since the 19th century, there has been disagreement over the fundamental question of whether "emotions" are cause or consequence of their associated behaviors. This question of causation is most directly addressable in genetically tractable model organisms, including invertebrates such as Drosophila. Yet there is ongoing debate about whether such species even have "emotions," as emotions are typically defined with reference to human behavior and neuroanatomy. Here, we argue that emotional behaviors are a class of behaviors that express internal emotion states. These emotion states exhibit certain general functional and adaptive properties that apply across any specific human emotions like fear or anger, as well as across phylogeny. These general properties, which can be thought of as "emotion primitives," can be modeled and studied in evolutionarily distant model organisms, allowing functional dissection of their mechanistic bases and tests of their causal relationships to behavior. More generally, our approach not only aims at better integration of such studies in model organisms with studies of emotion in humans, but also suggests a revision of how emotion should be operationalized within psychology and psychiatry. Copyright © 2014 Elsevier Inc. All rights reserved.

Similar variation in carbon storage between deciduous and evergreen treeline species across elevational gradients

PubMed Central

Fajardo, Alex; Piper, Frida I.; Hoch, Günter

2013-01-01

Background and Aims The most plausible explanation for treeline formation so far is provided by the growth limitation hypothesis (GLH), which proposes that carbon sinks are more restricted by low temperatures than by carbon sources. Evidence supporting the GLH has been strong in evergreen, but less and weaker in deciduous treeline species. Here a test is made of the GLH in deciduous–evergreen mixed species forests across elevational gradients, with the hypothesis that deciduous treeline species show a different carbon storage trend from that shown by evergreen species across elevations. Methods Tree growth and concentrations of non-structural carbohydrates (NSCs) in foliage, branch sapwood and stem sapwood tissues were measured at four elevations in six deciduous–evergreen treeline ecotones (including treeline) in the southern Andes of Chile (40°S, Nothofagus pumilio and Nothofagus betuloides; 46°S, Nothofagus pumilio and Pinus sylvestris) and in the Swiss Alps (46°N, Larix decidua and Pinus cembra). Key Results Tree growth (basal area increment) decreased with elevation for all species. Regardless of foliar habit, NSCs did not deplete across elevations, indicating no shortage of carbon storage in any of the investigated tissues. Rather, NSCs increased significantly with elevation in leaves (P < 0·001) and branch sapwood (P = 0·012) tissues. Deciduous species showed significantly higher NSCs than evergreens for all tissues; on average, the former had 11 % (leaves), 158 % (branch) and 103 % (sapwood) significantly (P < 0·001) higher NSCs than the latter. Finally, deciduous species had higher NSC (particularly starch) increases with elevation than evergreens for stem sapwood, but the opposite was true for leaves and branch sapwood. Conclusions Considering the observed decrease in tree growth and increase in NSCs with elevation, it is concluded that both deciduous and evergreen treeline species are sink limited when faced with decreasing temperatures

Similar variation in carbon storage between deciduous and evergreen treeline species across elevational gradients.

PubMed

Fajardo, Alex; Piper, Frida I; Hoch, Günter

2013-08-01

The most plausible explanation for treeline formation so far is provided by the growth limitation hypothesis (GLH), which proposes that carbon sinks are more restricted by low temperatures than by carbon sources. Evidence supporting the GLH has been strong in evergreen, but less and weaker in deciduous treeline species. Here a test is made of the GLH in deciduous-evergreen mixed species forests across elevational gradients, with the hypothesis that deciduous treeline species show a different carbon storage trend from that shown by evergreen species across elevations. Tree growth and concentrations of non-structural carbohydrates (NSCs) in foliage, branch sapwood and stem sapwood tissues were measured at four elevations in six deciduous-evergreen treeline ecotones (including treeline) in the southern Andes of Chile (40°S, Nothofagus pumilio and Nothofagus betuloides; 46°S, Nothofagus pumilio and Pinus sylvestris) and in the Swiss Alps (46°N, Larix decidua and Pinus cembra). Tree growth (basal area increment) decreased with elevation for all species. Regardless of foliar habit, NSCs did not deplete across elevations, indicating no shortage of carbon storage in any of the investigated tissues. Rather, NSCs increased significantly with elevation in leaves (P < 0·001) and branch sapwood (P = 0·012) tissues. Deciduous species showed significantly higher NSCs than evergreens for all tissues; on average, the former had 11 % (leaves), 158 % (branch) and 103 % (sapwood) significantly (P < 0·001) higher NSCs than the latter. Finally, deciduous species had higher NSC (particularly starch) increases with elevation than evergreens for stem sapwood, but the opposite was true for leaves and branch sapwood. Considering the observed decrease in tree growth and increase in NSCs with elevation, it is concluded that both deciduous and evergreen treeline species are sink limited when faced with decreasing temperatures. Despite the overall higher requirements of deciduous tree

Analyzing the responses of species assemblages to climate change across the Great Basin, USA.

NASA Astrophysics Data System (ADS)

Henareh Khalyani, A.; Falkowski, M. J.; Crookston, N.; Yousef, F.

2016-12-01

The potential impacts of climate change on the future distribution of tree species in not well understood. Climate driven changes in tree species distribution could cause significant changes in realized species niches, potentially resulting in the loss of ecotonal species as well as the formation on novel assemblages of overlapping tree species. In an effort to gain a better understating of how the geographic distribution of tree species may respond to climate change, we model the potential future distribution of 50 different tree species across 70 million ha in the Great Basin, USA. This is achieved by leveraging a species realized niche model based on non-parametric analysis of species occurrences across climatic, topographic, and edaphic variables. Spatially explicit, high spatial resolution (30 m) climate variables (e.g., precipitation, and minimum, maximum, and mean temperature) and associated climate indices were generated on an annual basis between 1981-2010 by integrating climate station data with digital elevation data (Shuttle Radar Topographic Mission (SRTM) data) in a thin plate spline interpolation algorithm (ANUSPLIN). Bioclimate models of species niches in in the cotemporary period and three following 30 year periods were then generated by integrating the climate variables, soil data, and CMIP 5 general circulation model projections. Our results suggest that local scale contemporary variations in species realized niches across space are influenced by edaphic and topographic variables as well as climatic variables. The local variability in soil properties and topographic variability across space also affect the species responses to climate change through time and potential formation of species assemblages in future. The results presented here in will aid in the development of adaptive forest management techniques aimed at mitigating negative impacts of climate change on forest composition, structure, and function.

Drivers of Non-Native Aquatic Species Invasions across the ...

EPA Pesticide Factsheets

Background/Question/Methods Mapping the geographic distribution of non-native aquatic species is a critically important precursor to understanding the anthropogenic and environmental factors that drive freshwater biological invasions. Such efforts are often limited to local scales and/or to a single taxa, missing the opportunity to observe and understand the drivers of macroscale invasion patterns at sub-continental or continental scales. Here we map the distribution of exotic freshwater species richness across the continental United States using publicly accessible species occurrence data (e.g GBIF) and investigate the role of human activity in driving macroscale patterns of aquatic invasion. Using a dasymetric model of human population density and a spatially explicit model of recreational freshwater fishing demand, we analyzed the effect of these metrics of human influence on non-native aquatic species richness at the watershed scale, while controlling for spatial and sampling bias. We also assessed the effects that a temporal mismatch between occurrence data (collected since 1815) and cross-sectional predictors (developed using 2010 data) may have on model fit. Results/Conclusions Our results indicated that non-native aquatic species richness exhibits a highly patchy distribution, with hotspots in the Northeast, Great Lakes, Florida, and human population centers on the Pacific coast. These richness patterns are correlated with population density, but are m

Predicting Achievable Fundamental Frequency Ranges in Vocalization Across Species

PubMed Central

Titze, Ingo; Riede, Tobias; Mau, Ted

2016-01-01

Vocal folds are used as sound sources in various species, but it is unknown how vocal fold morphologies are optimized for different acoustic objectives. Here we identify two main variables affecting range of vocal fold vibration frequency, namely vocal fold elongation and tissue fiber stress. A simple vibrating string model is used to predict fundamental frequency ranges across species of different vocal fold sizes. While average fundamental frequency is predominantly determined by vocal fold length (larynx size), range of fundamental frequency is facilitated by (1) laryngeal muscles that control elongation and by (2) nonlinearity in tissue fiber tension. One adaptation that would increase fundamental frequency range is greater freedom in joint rotation or gliding of two cartilages (thyroid and cricoid), so that vocal fold length change is maximized. Alternatively, tissue layers can develop to bear a disproportionate fiber tension (i.e., a ligament with high density collagen fibers), increasing the fundamental frequency range and thereby vocal versatility. The range of fundamental frequency across species is thus not simply one-dimensional, but can be conceptualized as the dependent variable in a multi-dimensional morphospace. In humans, this could allow for variations that could be clinically important for voice therapy and vocal fold repair. Alternative solutions could also have importance in vocal training for singing and other highly-skilled vocalizations. PMID:27309543

Episodic death across species of desert shrubs.

PubMed

Miriti, Maria N; Rodríguez-Buriticá, Susana; Wright, S Joseph; Howe, Henry F

2007-01-01

Extreme events shape population and community trajectories. We report episodic mortality across common species of thousands of long-lived perennials individually tagged and monitored for 20 years in the Colorado Desert of California following severe regional drought. Demographic records from 1984 to 2004 show 15 years of virtual stasis in populations of adult shrubs and cacti, punctuated by a 55-100% die-off of six of the seven most common perennial species. In this episode, adults that experienced reduced growth in a lesser drought during 1984-1989 failed to survive the drought of 2002. The significance of this event is potentially profound because population dynamics of long-lived plants can be far more strongly affected by deaths of adults, which in deserts potentially live for centuries, than by seedling births or deaths. Differential mortality and rates of recovery during and after extreme climatic events quite likely determine the species composition of plant and associated animal communities for at least decades. The die-off recorded in this closely monitored community provides a unique window into the mechanics of this process of species decline and replacement.

Systematically evaluating read-across prediction and ...

EPA Pesticide Factsheets

Read-across is a popular data gap filling technique within category and analogue approaches for regulatory purposes. Acceptance of read-across remains an ongoing challenge with several efforts underway for identifying and addressing uncertainties. Here we demonstrate an algorithmic, automated approach to evaluate the utility of using in vitro bioactivity data (“bioactivity descriptors”, from EPA’s ToxCast program) in conjunction with chemical descriptor information to derive local validity domains (specific sets of nearest neighbors) to facilitate read-across for a number of in vivo repeated dose toxicity study types. Over 3400 different chemical structure descriptors were generated for a set of 976 chemicals and supplemented with the outcomes from 821 in vitro assays. The read-across prediction for a given chemical was based on the similarity weighted endpoint outcomes of its nearest neighbors. The approach enabled a performance baseline for read-across predictions of specific study outcomes to be established. Bioactivity descriptors were often found to be more predictive of in vivo toxicity outcomes than chemical descriptors or a combination of both. The approach shows promise as part of a screening assessment in the absence of prior knowledge. Future work will investigate to what extent encoding expert knowledge leads to an improvement in read-across prediction. Read-across is a popular data gap filling technique within category and analogue approaches

Seed dormancy responses to temperature relate to Nothofagus species distribution and determine temporal patterns of germination across altitudes in Patagonia.

PubMed

Arana, María V; Gonzalez-Polo, Marina; Martinez-Meier, Alejandro; Gallo, Leonardo A; Benech-Arnold, Roberto L; Sánchez, Rodolfo A; Batlla, Diego

2016-01-01

Seeds integrate environmental cues that modulate their dormancy and germination. Although many mechanisms have been identified in laboratory experiments, their contribution to germination dynamics in existing communities and their involvement in defining species habitats remain elusive. By coupling mathematical models with ecological data we investigated the contribution of seed temperature responses to the dynamics of germination of three Nothofagus species that are sharply distributed across different altitudes in the Patagonian Andes. Seed responsiveness to temperature of the three Nothofagus species was linked to the thermal characteristics of their preferred ecological niche. In their natural distribution range, there was overlap in the timing of germination of the species, which was restricted to mid-spring. By contrast, outside their species distribution range, germination was temporally uncoupled with altitude. This phenomenon was described mathematically by the interplay between interspecific differences in seed population thermal parameters and the range in soil thermic environments across different altitudes. The observed interspecific variations in seed responsiveness to temperature and its environmental regulation, constitute a major determinant of the dynamics of Nothofagus germination across elevations. This phenomenon likely contributes to the maintenance of patterns of species abundance across altitude by placing germinated seeds in a favorable environment for plant growth. © 2015 The Authors. New Phytologist © 2015 New Phytologist Trust.

Progress Towards an Interdisciplinary Science of Plant Phenology: Building Predictions Across Space, Time and Species Diversity

NASA Technical Reports Server (NTRS)

Wolkovich, Elizabeth M.; Cook, Benjamin I.; Davies, T. Jonathan

2013-01-01

Climate change has brought renewed interest in the study of plant phenology - the timing of life history events. Data on shifting phenologies with warming have accumulated rapidly, yet research has been comparatively slow to explain the diversity of phenological responses observed across latitudes, growing seasons and species. Here, we outline recent efforts to synthesize perspectives on plant phenology across the fields of ecology, climate science and evolution. We highlight three major axes that vary among these disciplines: relative focus on abiotic versus biotic drivers of phenology, on plastic versus genetic drivers of intraspecific variation, and on cross-species versus autecological approaches. Recent interdisciplinary efforts, building on data covering diverse species and climate space, have found a greater role of temperature in controlling phenology at higher latitudes and for early-flowering species in temperate systems. These efforts have also made progress in understanding the tremendous diversity of responses across species by incorporating evolutionary relatedness, and linking phenological flexibility to invasions and plant performance. Future research with a focus on data collection in areas outside the temperate mid-latitudes and across species' ranges, alongside better integration of how risk and investment shape plant phenology, offers promise for further progress.

Relationship of a lichen species diversity indicator to environmental factors across the coterminous United States

Treesearch

Susan Will-Wolf; Mark J. Ambrose; Randall S. Morin

2011-01-01

We have investigated relationships between one simple indicator of lichen species diversity and environmental variables in forests across the coterminous United States. We want to know whether this indicator can help quantify the influence that factors such as climate and air quality have on lichen biodiversity at large scales and whether it will be useful in...

Understanding Kidney Disease: Toward the Integration of Regulatory Networks Across Species

PubMed Central

Ju, Wenjun; Brosius, Frank C.

2010-01-01

Animal models have long been useful in investigating both normal and abnormal human physiology. Systems biology provides a relatively new set of approaches to identify similarities and differences between animal models and humans that may lead to a more comprehensive understanding of human kidney pathophysiology. In this review, we briefly describe how genome-wide analyses of mouse models have helped elucidate features of human kidney diseases, discuss strategies to achieve effective network integration, and summarize currently available web-based tools that may facilitate integration of data across species. The rapid progress in systems biology and orthology, as well as the advent of web-based tools to facilitate these processes, now make it possible to take advantage of knowledge from distant animal species in targeted identification of regulatory networks that may have clinical relevance for human kidney diseases. PMID:21044762

Shifts in Aboveground Biomass Allocation Patterns of Dominant Shrub Species across a Strong Environmental Gradient

PubMed Central

Kumordzi, Bright B.; Gundale, Michael J.; Nilsson, Marie-Charlotte; Wardle, David A.

2016-01-01

Most plant biomass allocation studies have focused on allocation to shoots versus roots, and little is known about drivers of allocation for aboveground plant organs. We explored the drivers of within-and between-species variation of aboveground biomass allocation across a strong environmental resource gradient, i.e., a long-term chronosequence of 30 forested islands in northern Sweden across which soil fertility and plant productivity declines while light availability increases. For each of the three coexisting dominant understory dwarf shrub species on each island, we estimated the fraction of the total aboveground biomass produced year of sampling that was allocated to sexual reproduction (i.e., fruits), leaves and stems for each of two growing seasons, to determine how biomass allocation responded to the chronosequence at both the within-species and whole community levels. Against expectations, within-species allocation to fruits was least on less fertile islands, and allocation to leaves at the whole community level was greatest on intermediate islands. Consistent with expectations, different coexisting species showed contrasting allocation patterns, with the species that was best adapted for more fertile conditions allocating the most to vegetative organs, and with its allocation pattern showing the strongest response to the gradient. Our study suggests that co-existing dominant plant species can display highly contrasting biomass allocations to different aboveground organs within and across species in response to limiting environmental resources within the same plant community. Such knowledge is important for understanding how community assembly, trait spectra, and ecological processes driven by the plant community vary across environmental gradients and among contrasting ecosystems. PMID:27270445

Native Environment Modulates Leaf Size and Response to Simulated Foliar Shade across Wild Tomato Species

PubMed Central

Filiault, Daniele L.; Kumar, Ravi; Jiménez-Gómez, José M.; Schrager, Amanda V.; Park, Daniel S.; Peng, Jie; Sinha, Neelima R.; Maloof, Julin N.

2012-01-01

The laminae of leaves optimize photosynthetic rates by serving as a platform for both light capture and gas exchange, while minimizing water losses associated with thermoregulation and transpiration. Many have speculated that plants maximize photosynthetic output and minimize associated costs through leaf size, complexity, and shape, but a unifying theory linking the plethora of observed leaf forms with the environment remains elusive. Additionally, the leaf itself is a plastic structure, responsive to its surroundings, further complicating the relationship. Despite extensive knowledge of the genetic mechanisms underlying angiosperm leaf development, little is known about how phenotypic plasticity and selective pressures converge to create the diversity of leaf shapes and sizes across lineages. Here, we use wild tomato accessions, collected from locales with diverse levels of foliar shade, temperature, and precipitation, as a model to assay the extent of shade avoidance in leaf traits and the degree to which these leaf traits correlate with environmental factors. We find that leaf size is correlated with measures of foliar shade across the wild tomato species sampled and that leaf size and serration correlate in a species-dependent fashion with temperature and precipitation. We use far-red induced changes in leaf length as a proxy measure of the shade avoidance response, and find that shade avoidance in leaves negatively correlates with the level of foliar shade recorded at the point of origin of an accession. The direction and magnitude of these correlations varies across the leaf series, suggesting that heterochronic and/or ontogenic programs are a mechanism by which selective pressures can alter leaf size and form. This study highlights the value of wild tomato accessions for studies of both morphological and light-regulated development of compound leaves, and promises to be useful in the future identification of genes regulating potentially adaptive plastic

Adaptive Introgression across Species Boundaries in Heliconius Butterflies

PubMed Central

Pardo-Diaz, Carolina; Salazar, Camilo; Baxter, Simon W.; Merot, Claire; Figueiredo-Ready, Wilsea; Joron, Mathieu; McMillan, W. Owen; Jiggins, Chris D.

2012-01-01

It is widely documented that hybridisation occurs between many closely related species, but the importance of introgression in adaptive evolution remains unclear, especially in animals. Here, we have examined the role of introgressive hybridisation in transferring adaptations between mimetic Heliconius butterflies, taking advantage of the recent identification of a gene regulating red wing patterns in this genus. By sequencing regions both linked and unlinked to the red colour locus, we found a region that displays an almost perfect genotype by phenotype association across four species, H. melpomene, H. cydno, H. timareta, and H. heurippa. This particular segment is located 70 kb downstream of the red colour specification gene optix, and coalescent analysis indicates repeated introgression of adaptive alleles from H. melpomene into the H. cydno species clade. Our analytical methods complement recent genome scale data for the same region and suggest adaptive introgression has a crucial role in generating adaptive wing colour diversity in this group of butterflies. PMID:22737081

Adaptive introgression across species boundaries in Heliconius butterflies.

PubMed

Pardo-Diaz, Carolina; Salazar, Camilo; Baxter, Simon W; Merot, Claire; Figueiredo-Ready, Wilsea; Joron, Mathieu; McMillan, W Owen; Jiggins, Chris D

2012-01-01

It is widely documented that hybridisation occurs between many closely related species, but the importance of introgression in adaptive evolution remains unclear, especially in animals. Here, we have examined the role of introgressive hybridisation in transferring adaptations between mimetic Heliconius butterflies, taking advantage of the recent identification of a gene regulating red wing patterns in this genus. By sequencing regions both linked and unlinked to the red colour locus, we found a region that displays an almost perfect genotype by phenotype association across four species, H. melpomene, H. cydno, H. timareta, and H. heurippa. This particular segment is located 70 kb downstream of the red colour specification gene optix, and coalescent analysis indicates repeated introgression of adaptive alleles from H. melpomene into the H. cydno species clade. Our analytical methods complement recent genome scale data for the same region and suggest adaptive introgression has a crucial role in generating adaptive wing colour diversity in this group of butterflies.

Culture, morality and individual differences: comparability and incomparability across species.

PubMed

Saucier, Gerard

2018-04-19

Major routes to identifying individual differences (in diverse species) include studies of behaviour patterns as represented in language and neurophysiology. But results from these approaches appear not to converge on some major dimensions. Identifying dimensions of human variation least applicable to non-human species may help to partition human-specific individual differences of recent evolutionary origin from those shared across species. Human culture includes learned, enforced social-norm systems that are symbolically reinforced and referenced in displays signalling adherence. At a key juncture in human evolution bullying aggression and deception-based cheating apparently became censured in the language of a moral community, enabling mutual observation coordinated in gossip, associated with external sanctions. That still-conserved cultural paradigm moralistically regulates selfish advantage-taking, with shared semantics and explicit rules. Ethics and moral codes remain critical and universal components of human culture and have a stronger imprint in language than most aspects of the currently popular Big-Five taxonomy, a model that sets out five major lines of individual-differences variation in human personality. In other species (e.g. chimpanzees), human observers might see apparent individual differences in morality-relevant traits, but not because the animals have human-analogue sanctioning systems. Removing the moral dimension of personality and other human-specific manifestations (e.g. religion) may aid in identifying those other bases of individual differences more ubiquitous across species.This article is part of the theme issue 'Diverse perspectives on diversity: multi-disciplinary approaches to taxonomies of individual differences'. © 2018 The Author(s).

The evolutionary history of bears is characterized by gene flow across species

PubMed Central

Kumar, Vikas; Lammers, Fritjof; Bidon, Tobias; Pfenninger, Markus; Kolter, Lydia; Nilsson, Maria A.; Janke, Axel

2017-01-01

Bears are iconic mammals with a complex evolutionary history. Natural bear hybrids and studies of few nuclear genes indicate that gene flow among bears may be more common than expected and not limited to polar and brown bears. Here we present a genome analysis of the bear family with representatives of all living species. Phylogenomic analyses of 869 mega base pairs divided into 18,621 genome fragments yielded a well-resolved coalescent species tree despite signals for extensive gene flow across species. However, genome analyses using different statistical methods show that gene flow is not limited to closely related species pairs. Strong ancestral gene flow between the Asiatic black bear and the ancestor to polar, brown and American black bear explains uncertainties in reconstructing the bear phylogeny. Gene flow across the bear clade may be mediated by intermediate species such as the geographically wide-spread brown bears leading to large amounts of phylogenetic conflict. Genome-scale analyses lead to a more complete understanding of complex evolutionary processes. Evidence for extensive inter-specific gene flow, found also in other animal species, necessitates shifting the attention from speciation processes achieving genome-wide reproductive isolation to the selective processes that maintain species divergence in the face of gene flow. PMID:28422140

The evolutionary history of bears is characterized by gene flow across species.

PubMed

Kumar, Vikas; Lammers, Fritjof; Bidon, Tobias; Pfenninger, Markus; Kolter, Lydia; Nilsson, Maria A; Janke, Axel

2017-04-19

Bears are iconic mammals with a complex evolutionary history. Natural bear hybrids and studies of few nuclear genes indicate that gene flow among bears may be more common than expected and not limited to polar and brown bears. Here we present a genome analysis of the bear family with representatives of all living species. Phylogenomic analyses of 869 mega base pairs divided into 18,621 genome fragments yielded a well-resolved coalescent species tree despite signals for extensive gene flow across species. However, genome analyses using different statistical methods show that gene flow is not limited to closely related species pairs. Strong ancestral gene flow between the Asiatic black bear and the ancestor to polar, brown and American black bear explains uncertainties in reconstructing the bear phylogeny. Gene flow across the bear clade may be mediated by intermediate species such as the geographically wide-spread brown bears leading to large amounts of phylogenetic conflict. Genome-scale analyses lead to a more complete understanding of complex evolutionary processes. Evidence for extensive inter-specific gene flow, found also in other animal species, necessitates shifting the attention from speciation processes achieving genome-wide reproductive isolation to the selective processes that maintain species divergence in the face of gene flow.

SeqAPASS (Sequence Alignment to Predict Across Species Susceptibility) software and documentation

EPA Science Inventory

SeqAPASS is a software application facilitates rapid and streamlined, yet transparent, comparisons of the similarity of toxicologically-significant molecular targets across species. The present application facilitates analysis of primary amino acid sequence similarity (including ...

Estimation of avian population sizes and species richness across a boreal landscape in Alaska

USGS Publications Warehouse

Handel, Colleen M.; Swanson, S.A.; Nigro, Debora A.; Matsuoka, S.M.

2009-01-01

We studied the distribution of birds breeding within five ecological landforms in Yukon-Charley Rivers National Preserve, a 10,194-km2 roadless conservation unit on the Alaska-Canada border in the boreal forest zone. Passerines dominated the avifauna numerically, comprising 97% of individuals surveyed but less than half of the 115 species recorded in the Preserve. We used distance-sampling and discrete-removal models to estimate detection probabilities, densities, and population sizes across the Preserve for 23 species of migrant passerines and five species of resident passerines. Yellow-rumped Warblers (Dendroica coronata) and Dark-eyed Juncos (Junco hyemalis) were the most abundant species, together accounting for 41% of the migrant passerine populations estimated. White-winged Crossbills (Loxia leucoptera), Boreal Chickadees (Poecile hudsonica), and Gray Jays (Perisoreus canadensis) were the most abundant residents. Species richness was greatest in the Floodplain/Terrace landform flanking the Yukon River but densities were highest in the Subalpine landform. Species composition was related to past glacial history and current physiography of the region and differed notably from other areas of the northwestern boreal forest. Point-transect surveys, augmented with auxiliary observations, were well suited to sampling the largely passerine avifauna across this rugged landscape and could be used across the boreal forest region to monitor changes in northern bird distribution and abundance. ?? 2009 The Wilson Ornithological Society.

Building Scientific Confidence in Read-Across: Progress in using HT Data to inform Read-Across Performance (Toxicology Forum)

EPA Science Inventory

Presentation at the 41st Annual Winter Meeting of The Toxicology Forum - From Assay to Assessment: Incorporating High Throughput Strategies into Health and Safety Evaluations on Building Scientific Confidence in Read-Across: Progress in using HT Data to inform Read-Across Perfor...

Seasonal fecundity and costs to λ are more strongly affected by direct than indirect predation effects across species

USGS Publications Warehouse

LaManna, Joseph A.; Martin, Thomas E.

2017-01-01

Increased perceived predation risk can cause behavioral and physiological responses to reduce direct predation mortality, but these responses can also cause demographic costs through reduced reproductive output. Such indirect costs of predation risk have received increased attention in recent years, but the relative importance of direct vs. indirect predation costs to population growth (λ) across species remains unclear. We measured direct nest predation rates as well as indirect benefits (i.e., reduced predation rates) and costs (i.e., decreased reproductive output) arising from parental responses to perceived offspring predation risk for 10 songbird species breeding along natural gradients in nest predation risk. We show that reductions in seasonal fecundity from behavioral responses to perceived predation risk represent significant demographic costs for six of the 10 species. However, demographic costs from these indirect predation effects on seasonal fecundity comprised only 12% of cumulative predation costs averaged across species. In contrast, costs from direct predation mortality comprised 88% of cumulative predation costs averaged across species. Demographic costs from direct offspring predation were relatively more important for species with higher within-season residual-reproductive value (i.e., multiple-brooded species) than for species with lower residual-reproductive value (i.e., single-brooded species). Costs from indirect predation effects were significant across single- but not multiple-brooded species. Ultimately, demographic costs from behavioral responses to offspring predation risk differed among species as a function of their life-history strategies. Yet direct predation mortality generally wielded a stronger influence than indirect effects on seasonal fecundity and projected λ across species.

Clade age and species richness are decoupled across the eukaryotic tree of life.

PubMed

Rabosky, Daniel L; Slater, Graham J; Alfaro, Michael E

2012-08-01

Explaining the dramatic variation in species richness across the tree of life remains a key challenge in evolutionary biology. At the largest phylogenetic scales, the extreme heterogeneity in species richness observed among different groups of organisms is almost certainly a function of many complex and interdependent factors. However, the most fundamental expectation in macroevolutionary studies is simply that species richness in extant clades should be correlated with clade age: all things being equal, older clades will have had more time for diversity to accumulate than younger clades. Here, we test the relationship between stem clade age and species richness across 1,397 major clades of multicellular eukaryotes that collectively account for more than 1.2 million described species. We find no evidence that clade age predicts species richness at this scale. We demonstrate that this decoupling of age and richness is unlikely to result from variation in net diversification rates among clades. At the largest phylogenetic scales, contemporary patterns of species richness are inconsistent with unbounded diversity increase through time. These results imply that a fundamentally different interpretative paradigm may be needed in the study of phylogenetic diversity patterns in many groups of organisms.

Species richness of motile cryptofauna across a gradient of reef framework erosion

NASA Astrophysics Data System (ADS)

Enochs, I. C.; Manzello, D. P.

2012-09-01

Coral reef ecosystems contain exceptionally high concentrations of marine biodiversity, potentially encompassing millions of species. Similar to tropical rainforests and their insects, the majority of reef animal species are small and cryptic, living in the cracks and crevices of structural taxa (trees and corals). Although the cryptofauna make up the majority of a reef's metazoan biodiversity, we know little about their basic ecology. We sampled motile cryptofaunal communities from both live corals and dead carbonate reef framework across a gradient of increasing erosion on a reef in Pacific Panamá. A total of 289 Operational Taxonomic Units (OTUs) from six phyla were identified. We used species-accumulation models fitted to individual- and sample-based rarefaction curves, as well as seven nonparametric richness estimators to estimate species richness among the different framework types. All procedures predicted the same trends in species richness across the differing framework types. Estimated species richness was higher in dead framework (261-370 OTUs) than in live coral substrates (112-219 OTUs). Surprisingly, richness increased as framework structure was eroded: coral rubble contained the greatest number of species (227-320 OTUs) and the lowest estimated richness of 47-115 OTUs was found in the zone where the reef framework had the greatest vertical relief. This contradicts the paradigm that abundant live coral indicates the apex of reef diversity.

Seed size and its rate of evolution correlate with species diversification across angiosperms

PubMed Central

Miller, Eleanor F.; Papadopulos, Alexander S. T.; Tanentzap, Andrew J.

2017-01-01

Species diversity varies greatly across the different taxonomic groups that comprise the Tree of Life (ToL). This imbalance is particularly conspicuous within angiosperms, but is largely unexplained. Seed mass is one trait that may help clarify why some lineages diversify more than others because it confers adaptation to different environments, which can subsequently influence speciation and extinction. The rate at which seed mass changes across the angiosperm phylogeny may also be linked to diversification by increasing reproductive isolation and allowing access to novel ecological niches. However, the magnitude and direction of the association between seed mass and diversification has not been assessed across the angiosperm phylogeny. Here, we show that absolute seed size and the rate of change in seed size are both associated with variation in diversification rates. Based on the largest available angiosperm phylogenetic tree, we found that smaller-seeded plants had higher rates of diversification, possibly due to improved colonisation potential. The rate of phenotypic change in seed size was also strongly positively correlated with speciation rates, providing rare, large-scale evidence that rapid morphological change is associated with species divergence. Our study now reveals that variation in morphological traits and, importantly, the rate at which they evolve can contribute to explaining the extremely uneven distribution of diversity across the ToL. PMID:28723902

Integrating single-cell transcriptomic data across different conditions, technologies, and species.

PubMed

Butler, Andrew; Hoffman, Paul; Smibert, Peter; Papalexi, Efthymia; Satija, Rahul

2018-06-01

Computational single-cell RNA-seq (scRNA-seq) methods have been successfully applied to experiments representing a single condition, technology, or species to discover and define cellular phenotypes. However, identifying subpopulations of cells that are present across multiple data sets remains challenging. Here, we introduce an analytical strategy for integrating scRNA-seq data sets based on common sources of variation, enabling the identification of shared populations across data sets and downstream comparative analysis. We apply this approach, implemented in our R toolkit Seurat (http://satijalab.org/seurat/), to align scRNA-seq data sets of peripheral blood mononuclear cells under resting and stimulated conditions, hematopoietic progenitors sequenced using two profiling technologies, and pancreatic cell 'atlases' generated from human and mouse islets. In each case, we learn distinct or transitional cell states jointly across data sets, while boosting statistical power through integrated analysis. Our approach facilitates general comparisons of scRNA-seq data sets, potentially deepening our understanding of how distinct cell states respond to perturbation, disease, and evolution.

SeqAPASS v3.0 for Extrapolation of Toxicity Knowledge Across Species

EPA Science Inventory

The U.S. Environmental Protection Agency Sequence Alignment to Predict Across Species Susceptibility (SeqAPASS; https://seqapass.epa.gov/seqapass/) tool was initially released to the public in 2016, providing a novel means to begin to address challenges in extrapolating toxicity ...

Use of ToxPrint chemotypes for exploring chemical feature enrichments across the ToxCast chemical-assay landscape

EPA Science Inventory

EPA’s ToxCast chemical library spans diverse chemical use-types, functionalities, structures and features potentially relevant to toxicity and environmental exposure. However, this structural diversity, along with assay noise and low average hit rates across the varied ToxCast h...

Differential paralog divergence modulates genome evolution across yeast species

PubMed Central

Lynch, Bryony; Huang, Mei; Alcantara, Erica; DeSevo, Christopher G.; Pai, Dave A.; Hoang, Margaret L.

2017-01-01

Evolutionary outcomes depend not only on the selective forces acting upon a species, but also on the genetic background. However, large timescales and uncertain historical selection pressures can make it difficult to discern such important background differences between species. Experimental evolution is one tool to compare evolutionary potential of known genotypes in a controlled environment. Here we utilized a highly reproducible evolutionary adaptation in Saccharomyces cerevisiae to investigate whether experimental evolution of other yeast species would select for similar adaptive mutations. We evolved populations of S. cerevisiae, S. paradoxus, S. mikatae, S. uvarum, and interspecific hybrids between S. uvarum and S. cerevisiae for ~200–500 generations in sulfate-limited continuous culture. Wild-type S. cerevisiae cultures invariably amplify the high affinity sulfate transporter gene, SUL1. However, while amplification of the SUL1 locus was detected in S. paradoxus and S. mikatae populations, S. uvarum cultures instead selected for amplification of the paralog, SUL2. We measured the relative fitness of strains bearing deletions and amplifications of both SUL genes from different species, confirming that, converse to S. cerevisiae, S. uvarum SUL2 contributes more to fitness in sulfate limitation than S. uvarum SUL1. By measuring the fitness and gene expression of chimeric promoter-ORF constructs, we were able to delineate the cause of this differential fitness effect primarily to the promoter of S. uvarum SUL1. Our data show evidence of differential sub-functionalization among the sulfate transporters across Saccharomyces species through recent changes in noncoding sequence. Furthermore, these results show a clear example of how such background differences due to paralog divergence can drive changes in genome evolution. PMID:28196070

Neo-sex chromosome inheritance across species in Silene hybrids.

PubMed

Weingartner, L A; Delph, L F

2014-07-01

Neo-sex chromosomes, which form through the major restructuring of ancestral sex chromosome systems, have evolved in various taxa. Such restructuring often consists of the fusion of an autosome to an existing sex chromosome, resulting in novel sex chromosome formations (e.g. X1X2Y or XY1Y2.). Comparative studies are often made between restructured sex chromosome systems of closely related species, and here we evaluate the consequences of variable sex chromosome systems to hybrids. If neo-sex chromosomes are improperly inherited across species, this could lead to aberrant development and reproductive isolation. In this study, we examine the fate of neo-sex chromosomes in hybrids of the flowering plants Silene diclinis and Silene latifolia. Silene diclinis has a neo-sex chromosome system (XY1Y2) that is thought to have evolved from an ancestral XY system that is still present in S. latifolia. These species do not hybridize naturally, and improper sex chromosome inheritance could contribute to reproductive isolation. We investigated whether this major restructuring of sex chromosomes prevents their proper inheritance in a variety of hybrid crosses, including some F2 - and later-generation hybrids, with sex chromosome-linked, species-specific, polymorphic markers and chromosome squashes. We discovered that despite the differences in sex chromosomes that exist between these two species, proper segregation had occurred in hybrids that made it to flowering, including later-generation hybrids, indicating that neo-sex chromosome formation alone does not result in complete reproductive isolation between these two species. Additionally, hybrids with aberrant sex expression (e.g. neuter, hermaphrodite) also inherited the restructured sex chromosomes properly, highlighting that issues with sexual development in hybrids can be caused by intrinsic genetic incompatibility rather than improper sex chromosome inheritance. © 2014 The Authors. Journal of Evolutionary Biology © 2014

Sequence Alignment to Predict Across Species Susceptibility (SeqAPASS): A web-based tool for addressing the challenges of cross-species extrapolation of chemical toxicity

EPA Science Inventory

Conservation of a molecular target across species can be used as a line-of-evidence to predict the likelihood of chemical susceptibility. The web-based Sequence Alignment to Predict Across Species Susceptibility (SeqAPASS) tool was developed to simplify, streamline, and quantitat...

Oxytocin receptor dynamics in the brain across development and species.

PubMed

Vaidyanathan, Radhika; Hammock, Elizabeth A D

2017-02-01

Oxytocin (OXT) signaling through the OXT receptor plays a significant role in a variety of physiological processes throughout the lifespan. OXT's effects depend on the tissue distribution of the receptor. This tissue specificity is dynamic and changes across development, and also varies with sex, experience, and species. The purpose of this review is to highlight these themes with examples from several life stages and several species. Important knowledge gaps will also be emphasized. Understanding the effective sites of action for OXT via its receptor will help refine hypotheses about the roles of this important neuropeptide in the experience-dependent development and expression of species-typical social behavior. © 2016 Wiley Periodicals, Inc. Develop Neurobiol 77: 143-157, 2017. © 2016 Wiley Periodicals, Inc.

Genome-Wide Distribution, Organisation and Functional Characterization of Disease Resistance and Defence Response Genes across Rice Species

PubMed Central

Singh, Sangeeta; Chand, Suresh; Singh, N. K.; Sharma, Tilak Raj

2015-01-01

The resistance (R) genes and defense response (DR) genes have become very important resources for the development of disease resistant cultivars. In the present investigation, genome-wide identification, expression, phylogenetic and synteny analysis was done for R and DR-genes across three species of rice viz: Oryza sativa ssp indica cv 93-11, Oryza sativa ssp japonica and wild rice species, Oryza brachyantha. We used the in silico approach to identify and map 786 R -genes and 167 DR-genes, 672 R-genes and 142 DR-genes, 251 R-genes and 86 DR-genes in the japonica, indica and O. brachyanth a genomes, respectively. Our analysis showed that 60.5% and 55.6% of the R-genes are tandemly repeated within clusters and distributed over all the rice chromosomes in indica and japonica genomes, respectively. The phylogenetic analysis along with motif distribution shows high degree of conservation of R- and DR-genes in clusters. In silico expression analysis of R-genes and DR-genes showed more than 85% were expressed genes showing corresponding EST matches in the databases. This study gave special emphasis on mechanisms of gene evolution and duplication for R and DR genes across species. Analysis of paralogs across rice species indicated 17% and 4.38% R-genes, 29% and 11.63% DR-genes duplication in indica and Oryza brachyantha, as compared to 20% and 26% duplication of R-genes and DR-genes in japonica respectively. We found that during the course of duplication only 9.5% of R- and DR-genes changed their function and rest of the genes have maintained their identity. Syntenic relationship across three genomes inferred that more orthology is shared between indica and japonica genomes as compared to brachyantha genome. Genome wide identification of R-genes and DR-genes in the rice genome will help in allele mining and functional validation of these genes, and to understand molecular mechanism of disease resistance and their evolution in rice and related species. PMID:25902056

Single Species Dinoflagellate Cyst Carbon Isotope Ecology across the Paleocene-Eocene Thermal Maximum

NASA Astrophysics Data System (ADS)

Sluijs, A.; Roij, L. V.; Frieling, J.; Laks, J.; Reichart, G. J.

2017-12-01

We present the first ever species-specific records of fossil dinoflagellate cyst stable carbon isotope ratios (δ13C). These records across a Paleocene-Eocene Thermal Maximum section in New Jersey were established using a novel coupled laser ablation - isotope ratio mass spectrometer setup. The overall good correspondence with carbonate δ13C records across the characteristic PETM carbon isotope excursion indicates that the δ13C of dissolved inorganic carbon exerts a major control on dinocysts δ13C. Pronounced and consistent differences between species, however, reflect the differential physiological response to changing seawater carbonate chemistry following PETM carbon injection. Moreover, they reflect different habitats or life cycle processes, notably related to bloom intensity. Intriguingly, decreased inter-specimen variability during the PETM in a species that also drops in abundance suggests a more limited niche, either in time (seasonal) or space. This opens a new approach for ecological and evolutionary reconstructions based on organic microfossils.

Comparing BMD‐derived genotoxic potency estimations across variants of the transgenic rodent gene mutation assay

PubMed Central

Johnson, George E.; Battaion, Hannah L.; Slob, Wout; Gollapudi, B.

2017-01-01

There is growing interest in quantitative analysis of in vivo genetic toxicity dose‐response data, and use of point‐of‐departure (PoD) metrics such as the benchmark dose (BMD) for human health risk assessment (HHRA). Currently, multiple transgenic rodent (TGR) assay variants, employing different rodent strains and reporter transgenes, are used for the assessment of chemically‐induced genotoxic effects in vivo. However, regulatory issues arise when different PoD values (e.g., lower BMD confidence intervals or BMDLs) are obtained for the same compound across different TGR assay variants. This study therefore employed the BMD approach to examine the ability of different TGR variants to yield comparable genotoxic potency estimates. Review of over 2000 dose‐response datasets identified suitably‐matched dose‐response data for three compounds (ethyl methanesulfonate or EMS, N‐ethyl‐N‐nitrosourea or ENU, and dimethylnitrosamine or DMN) across four commonly‐used murine TGR variants (Muta™Mouse lacZ, Muta™Mouse cII, gpt delta and BigBlue® lacI). Dose‐response analyses provided no conclusive evidence that TGR variant choice significantly influences the derived genotoxic potency estimate. This conclusion was reliant upon taking into account the importance of comparing BMD confidence intervals as opposed to directly comparing PoD values (e.g., comparing BMDLs). Comparisons with earlier works suggested that with respect to potency determination, tissue choice is potentially more important than choice of TGR assay variant. Scoring multiple tissues selected on the basis of supporting toxicokinetic information is therefore recommended. Finally, we used typical within‐group variances to estimate preliminary endpoint‐specific benchmark response (BMR) values across several TGR variants/tissues. We discuss why such values are required for routine use of genetic toxicity PoDs for HHRA. Environ. Mol. Mutagen. 58:632–643, 2017. © 2017 Her Majesty the

NSF Workshop Report: Discovering General Principles of Nervous System Organization by Comparing Brain Maps across Species

PubMed Central

Striedter, Georg F.; Belgard, T. Grant; Chen, Chun-Chun; Davis, Fred P.; Finlay, Barbara L.; Güntürkün, Onur; Hale, Melina E.; Harris, Julie A.; Hecht, Erin E.; Hof, Patrick R.; Hofmann, Hans A.; Holland, Linda Z.; Iwaniuk, Andrew N.; Jarvis, Erich D.; Karten, Harvey J.; Katz, Paul S.; Kristan, William B.; Macagno, Eduardo R.; Mitra, Partha P.; Moroz, Leonid L.; Preuss, Todd M.; Ragsdale, Clifton W.; Sherwood, Chet C.; Stevens, Charles F.; Stüttgen, Maik C.; Tsumoto, Tadaharu; Wilczynski, Walter

2014-01-01

Efforts to understand nervous system structure and function have received new impetus from the federal Brain Research through Advancing Innovative Neurotechnologies (BRAIN) Initiative. Comparative analyses can contribute to this effort by leading to the discovery of general principles of neural circuit design, information processing, and gene-structure-function relationships that are not apparent from studies on single species. We here propose to extend the comparative approach to nervous system ‘maps’ comprising molecular, anatomical, and physiological data. This research will identify which neural features are likely to generalize across species, and which are unlikely to be broadly conserved. It will also suggest causal relationships between genes, development, adult anatomy, physiology, and, ultimately, behavior. These causal hypotheses can then be tested experimentally. Finally, insights from comparative research can inspire and guide technological development. To promote this research agenda, we recommend that teams of investigators coalesce around specific research questions and select a set of ‘reference species’ to anchor their comparative analyses. These reference species should be chosen not just for practical advantages, but also with regard for their phylogenetic position, behavioral repertoire, well-annotated genome, or other strategic reasons. We envision that the nervous systems of these reference species will be mapped in more detail than those of other species. The collected data may range from the molecular to the behavioral, depending on the research question. To integrate across levels of analysis and across species, standards for data collection, annotation, archiving, and distribution must be developed and respected. To that end, it will help to form networks or consortia of researchers and centers for science, technology, and education that focus on organized data collection, distribution, and training. These activities could be

Unimodal Latitudinal Pattern of Land-Snail Species Richness across Northern Eurasian Lowlands

PubMed Central

Horsák, Michal; Chytrý, Milan

2014-01-01

Large-scale patterns of species richness and their causes are still poorly understood for most terrestrial invertebrates, although invertebrates can add important insights into the mechanisms that generate regional and global biodiversity patterns. Here we explore the general plausibility of the climate-based “water-energy dynamics” hypothesis using the latitudinal pattern of land-snail species richness across extensive topographically homogeneous lowlands of northern Eurasia. We established a 1480-km long latitudinal transect across the Western Siberian Plain (Russia) from the Russia-Kazakhstan border (54.5°N) to the Arctic Ocean (67.5°N), crossing eight latitudinal vegetation zones: steppe, forest-steppe, subtaiga, southern, middle and northern taiga, forest-tundra, and tundra. We sampled snails in forests and open habitats each half-degree of latitude and used generalized linear models to relate snail species richness to climatic variables and soil calcium content measured in situ. Contrary to the classical prediction of latitudinal biodiversity decrease, we found a striking unimodal pattern of snail species richness peaking in the subtaiga and southern-taiga zones between 57 and 59°N. The main south-to-north interchange of the two principal diversity constraints, i.e. drought stress vs. cold stress, explained most of the variance in the latitudinal diversity pattern. Water balance, calculated as annual precipitation minus potential evapotranspiration, was a single variable that could explain 81.7% of the variance in species richness. Our data suggest that the “water-energy dynamics” hypothesis can apply not only at the global scale but also at subcontinental scales of higher latitudes, as water availability was found to be the primary limiting factor also in this extratropical region with summer-warm and dry climate. A narrow zone with a sharp south-to-north switch in the two main diversity constraints seems to constitute the dominant and general

A tree of life based on ninety-eight expressed genes conserved across diverse eukaryotic species

PubMed Central

Jayaswal, Pawan Kumar; Dogra, Vivek; Shanker, Asheesh; Sharma, Tilak Raj

2017-01-01

Rapid advances in DNA sequencing technologies have resulted in the accumulation of large data sets in the public domain, facilitating comparative studies to provide novel insights into the evolution of life. Phylogenetic studies across the eukaryotic taxa have been reported but on the basis of a limited number of genes. Here we present a genome-wide analysis across different plant, fungal, protist, and animal species, with reference to the 36,002 expressed genes of the rice genome. Our analysis revealed 9831 genes unique to rice and 98 genes conserved across all 49 eukaryotic species analysed. The 98 genes conserved across diverse eukaryotes mostly exhibited binding and catalytic activities and shared common sequence motifs; and hence appeared to have a common origin. The 98 conserved genes belonged to 22 functional gene families including 26S protease, actin, ADP–ribosylation factor, ATP synthase, casein kinase, DEAD-box protein, DnaK, elongation factor 2, glyceraldehyde 3-phosphate, phosphatase 2A, ras-related protein, Ser/Thr protein phosphatase family protein, tubulin, ubiquitin and others. The consensus Bayesian eukaryotic tree of life developed in this study demonstrated widely separated clades of plants, fungi, and animals. Musa acuminata provided an evolutionary link between monocotyledons and dicotyledons, and Salpingoeca rosetta provided an evolutionary link between fungi and animals, which indicating that protozoan species are close relatives of fungi and animals. The divergence times for 1176 species pairs were estimated accurately by integrating fossil information with synonymous substitution rates in the comprehensive set of 98 genes. The present study provides valuable insight into the evolution of eukaryotes. PMID:28922368

Drosophila embryogenesis scales uniformly across temperature in developmentally diverse species.

PubMed

Kuntz, Steven G; Eisen, Michael B

2014-04-01

Temperature affects both the timing and outcome of animal development, but the detailed effects of temperature on the progress of early development have been poorly characterized. To determine the impact of temperature on the order and timing of events during Drosophila melanogaster embryogenesis, we used time-lapse imaging to track the progress of embryos from shortly after egg laying through hatching at seven precisely maintained temperatures between 17.5 °C and 32.5 °C. We employed a combination of automated and manual annotation to determine when 36 milestones occurred in each embryo. D. melanogaster embryogenesis takes [Formula: see text]33 hours at 17.5 °C, and accelerates with increasing temperature to a low of 16 hours at 27.5 °C, above which embryogenesis slows slightly. Remarkably, while the total time of embryogenesis varies over two fold, the relative timing of events from cellularization through hatching is constant across temperatures. To further explore the relationship between temperature and embryogenesis, we expanded our analysis to cover ten additional Drosophila species of varying climatic origins. Six of these species, like D. melanogaster, are of tropical origin, and embryogenesis time at different temperatures was similar for them all. D. mojavensis, a sub-tropical fly, develops slower than the tropical species at lower temperatures, while D. virilis, a temperate fly, exhibits slower development at all temperatures. The alpine sister species D. persimilis and D. pseudoobscura develop as rapidly as tropical flies at cooler temperatures, but exhibit diminished acceleration above 22.5 °C and have drastically slowed development by 30 °C. Despite ranging from 13 hours for D. erecta at 30 °C to 46 hours for D. virilis at 17.5 °C, the relative timing of events from cellularization through hatching is constant across all species and temperatures examined here, suggesting the existence of a previously unrecognized timer controlling the

Does enemy damage vary across the range of exotic plant species? Evidence from two coastal dune plant species in eastern Australia.

PubMed

Tabassum, Samiya; Leishman, Michelle R

2018-02-01

Release from natural enemies is often cited as a key factor for understanding the success of invasive plant species in novel environments. However, with time invasive species will accumulate native enemies in their invaded range, with factors such as spread distance from the site of introduction, climate and leaf-level traits potentially affecting enemy acquisition rates. However, the influence of such factors is difficult to assess without examining enemy attack across the entire species' range. We tested the significance of factors associated with range expansion (distance from source population and maximum population density), climatic variables (annual temperature and rainfall) and leaf-level traits [specific leaf area (SLA) and foliar nitrogen concentration] in explaining variation in enemy damage across multiple populations of two coastal invasive plants (Gladiolus gueinzii Kunze and Hydrocotyle bonariensis Lam.) along their entire introduced distribution in eastern Australia. We found that for H. bonariensis, amount of foliar damage increased with distance from source population. In contrast, for G. gueinzii, probability and amount of foliar damage decreased with decreasing temperature and increasing rainfall, respectively. Our results show that patterns of enemy attack across species' ranges are complex and cannot be generalised between species or even range edges.

Chlamydia Infection Across Host Species Boundaries Promotes Distinct Sets of Transcribed Anti-Apoptotic Factors

PubMed Central

Messinger, Joshua E.; Nelton, Emmalin; Feeney, Colleen; Gondek, David C.

2015-01-01

Chlamydiae, obligate intracellular bacteria, cause significant human and veterinary associated diseases. Having emerged an estimated 700-million years ago, these bacteria have twice adapted to humans as a host species, causing sexually transmitted infection (C. trachomatis) and respiratory associated disease (C. pneumoniae). The principle mechanism of host cell defense against these intracellular bacteria is the induction of cell death via apoptosis. However, in the “arms race” of co-evolution, Chlamydiae have developed mechanisms to promote cell viability and inhibit cell death. Herein we examine the impact of Chlamydiae infection across multiple host species on transcription of anti-apoptotic genes. We found mostly distinct patterns of gene expression (Mcl1 and cIAPs) elicited by each pathogen-host pair indicating Chlamydiae infection across host species boundaries does not induce a universally shared host response. Understanding species specific host-pathogen interactions is paramount to deciphering how potential pathogens become emerging diseases. PMID:26779446

Demographic Responses To Climate Manipulations Across a Species Range

NASA Astrophysics Data System (ADS)

Oldfather, M. F.

2016-12-01

Species biogeographic responses to climate change will occur through the local extinction and establishment of populations. The overall performance of populations across a species range is shaped by the idiosyncratic sensitivities of demographic rates to the changing climate conditions. Heterogeneous topography partially decouples temperature and soil moisture presenting an opportunity to disentangle demographic sensitivity to multiple local climate variables and refine range shift predictions in response to complex climate change. Since 2013, I have monitored 16 populations of a long-lived alpine plant, Ivesia lycopodioides var. scandularis (Rosaceae) across the entirety of its altitudinal range in the arid White Mountains, CA (3350 - 4420m). I quantified microclimatic soil moisture and temperature, and the demographic rates of over 4,000 individuals. Demographic rates exhibited sensitivity to accumulated degree-days (ex. reproduction), soil volumetric water content (ex. germination), or the interaction between these climate variables (ex. survival). These observations motivated an experimental test of the relationship between demography and local climate with manipulations of increased summertime temperature and precipitation in nine populations. All demographic rates were sensitive to the climate manipulations and the magnitude of the demographic response depended on the population's location within the range. However, the modeled population growth rate was only minimally affected by the manipulations in most populations. The inverse responses of many of the demographic rates may allow populations to demographically buffer against the climate manipulations. However, in one low elevation edge population the negative effect of heating on survival overwhelmed the positive effect on germination, indicating that the capacity of populations to demographically buffer may have a limit.

A sensitive new fluorescence assay for measuring proton transport across liposomal membranes.

PubMed

Orosz, D E; Garlid, K D

1993-04-01

6-Methoxy-N-(3-sulfopropyl)-quinolinium (SPQ) is a fluorophore that is collisionally quenched by halide anions and is widely used to measure chloride ion transport across cellular and liposomal membranes. We report a new finding that SPQ fluorescence is also quenched by the zwitterionic hydrogen ion buffers introduced by Good et al. [(1966) Biochemistry 5, 467-477]. Although buffer quenching interferes with chloride ion measurements using SPQ, it can be turned to good advantage for measurements of proton flux. The basis for this application is that, for most buffers, the anion quenches and the zwitterion does not. Accordingly, buffer quenching of SPQ can be used to assay proton transport across liposomal membranes. We describe application of the technique to liposomes in which proton transport was mediated by ionophores and by the purified, reconstituted uncoupling protein of brown adipose tissue mitochondria. Because SPQ detects changes in buffer anion concentration, it can be used to measure changes in total acidity, which is the parameter desired when measuring net proton transport. Furthermore, this technique can be used to measure proton transport under conditions in which pH changes are minimized with buffers, and, consequently, effects of pH on proton transport can be dissociated from the transport itself.

Modeling leaf phenology variation by groupings of species within and across ecosystems in northern Alaska

NASA Astrophysics Data System (ADS)

Euskirchen, E. S.; Carman, T. B.; McGuire, A. D.

2012-12-01

The phenology of arctic ecosystems is driven primarily by abiotic forces, with temperature acting as the main determinant of growing season onset and leaf budburst and in the spring. However, while the plant species in arctic ecosystems require differing amounts of accumulated heat for leaf-out, dynamic vegetation models simulated over a regional to global scale typically assume some average leaf-out for all of the species within an ecosystem. Here, we make use of air temperature records and observational data of spring leaf phenology collected across dominant groupings of species (dwarf birch shrubs, willow shrubs, other deciduous shrubs, grasses, sedges, and forbs) in arctic and ecotonal boreal ecosystems in Alaska. We then parameterize a dynamic vegetation model based on these data for four types of tundra ecosystems (heath tundra, shrub tundra, wet sedge tundra, and tussock tundra), as well as ecotonal boreal white spruce forest. This implementation improves the timing of the onset of carbon uptake in the spring, permitting a more accurate assessment of the contribution of each grouping of species to ecosystem performance. Furthermore, this implementation provides a more nuanced perspective on light competition among species and across ecosystems. For example, in the shrub tundra, the sedges and grasses leaf-out before the shade-inducing willow and dwarf birch, thereby providing the sedges and grasses time to accumulate biomass before shading effects arise. Also in the shrub tundra, the forbs leaf-out last, and are therefore, more prone to shading impacts by the taller willow and dwarf birch shrubs. However, in the wet sedge and heath tundra ecosystems, the forbs leaf-out before the shrubs, and are therefore less prone to shading impacts early in the growing season. These findings indicate the importance of leaf phenology data collection by species and across the various ecosystem types within the highly heterogeneous Arctic landscape. These findings also

Complementarity in nutrient foraging strategies of absorptive fine roots and arbuscular mycorrhizal fungi across 14 coexisting subtropical tree species.

PubMed

Liu, Bitao; Li, Hongbo; Zhu, Biao; Koide, Roger T; Eissenstat, David M; Guo, Dali

2015-10-01

In most cases, both roots and mycorrhizal fungi are needed for plant nutrient foraging. Frequently, the colonization of roots by arbuscular mycorrhizal (AM) fungi seems to be greater in species with thick and sparsely branched roots than in species with thin and densely branched roots. Yet, whether a complementarity exists between roots and mycorrhizal fungi across these two types of root system remains unclear. We measured traits related to nutrient foraging (root morphology, architecture and proliferation, AM colonization and extramatrical hyphal length) across 14 coexisting AM subtropical tree species following root pruning and nutrient addition treatments. After root pruning, species with thinner roots showed more root growth, but lower mycorrhizal colonization, than species with thicker roots. Under multi-nutrient (NPK) addition, root growth increased, but mycorrhizal colonization decreased significantly, whereas no significant changes were found under nitrogen or phosphate additions. Moreover, root length proliferation was mainly achieved by altering root architecture, but not root morphology. Thin-root species seem to forage nutrients mainly via roots, whereas thick-root species rely more on mycorrhizal fungi. In addition, the reliance on mycorrhizal fungi was reduced by nutrient additions across all species. These findings highlight complementary strategies for nutrient foraging across coexisting species with contrasting root traits. © 2015 The Authors. New Phytologist © 2015 New Phytologist Trust.

An Evolutionary Landscape of A-to-I RNA Editome across Metazoan Species

PubMed Central

Hung, Li-Yuan; Chen, Yen-Ju; Mai, Te-Lun; Chen, Chia-Ying; Yang, Min-Yu; Chiang, Tai-Wei; Wang, Yi-Da

2018-01-01

Abstract Adenosine-to-inosine (A-to-I) editing is widespread across the kingdom Metazoa. However, for the lack of comprehensive analysis in nonmodel animals, the evolutionary history of A-to-I editing remains largely unexplored. Here, we detect high-confidence editing sites using clustering and conservation strategies based on RNA sequencing data alone, without using single-nucleotide polymorphism information or genome sequencing data from the same sample. We thereby unveil the first evolutionary landscape of A-to-I editing maps across 20 metazoan species (from worm to human), providing unprecedented evidence on how the editing mechanism gradually expands its territory and increases its influence along the history of evolution. Our result revealed that highly clustered and conserved editing sites tended to have a higher editing level and a higher magnitude of the ADAR motif. The ratio of the frequencies of nonsynonymous editing to that of synonymous editing remarkably increased with increasing the conservation level of A-to-I editing. These results thus suggest potentially functional benefit of highly clustered and conserved editing sites. In addition, spatiotemporal dynamics analyses reveal a conserved enrichment of editing and ADAR expression in the central nervous system throughout more than 300 Myr of divergent evolution in complex animals and the comparability of editing patterns between invertebrates and between vertebrates during development. This study provides evolutionary and dynamic aspects of A-to-I editome across metazoan species, expanding this important but understudied class of nongenomically encoded events for comprehensive characterization. PMID:29294013

The extended Price equation quantifies species selection on mammalian body size across the Palaeocene/Eocene Thermal Maximum.

PubMed

Rankin, Brian D; Fox, Jeremy W; Barrón-Ortiz, Christian R; Chew, Amy E; Holroyd, Patricia A; Ludtke, Joshua A; Yang, Xingkai; Theodor, Jessica M

2015-08-07

Species selection, covariation of species' traits with their net diversification rates, is an important component of macroevolution. Most studies have relied on indirect evidence for its operation and have not quantified its strength relative to other macroevolutionary forces. We use an extension of the Price equation to quantify the mechanisms of body size macroevolution in mammals from the latest Palaeocene and earliest Eocene of the Bighorn and Clarks Fork Basins of Wyoming. Dwarfing of mammalian taxa across the Palaeocene/Eocene Thermal Maximum (PETM), an intense, brief warming event that occurred at approximately 56 Ma, has been suggested to reflect anagenetic change and the immigration of small bodied-mammals, but might also be attributable to species selection. Using previously reconstructed ancestor-descendant relationships, we partitioned change in mean mammalian body size into three distinct mechanisms: species selection operating on resident mammals, anagenetic change within resident mammalian lineages and change due to immigrants. The remarkable decrease in mean body size across the warming event occurred through anagenetic change and immigration. Species selection also was strong across the PETM but, intriguingly, favoured larger-bodied species, implying some unknown mechanism(s) by which warming events affect macroevolution. © 2015 The Author(s).

High spatial resolution spectral unmixing for mapping ash species across a complex urban environment

Treesearch

Jennifer Pontius; Ryan P. Hanavan; Richard A. Hallett; Bruce D. Cook; Lawrence A. Corp

2017-01-01

Ash (Fraxinus L.) species are currently threatened by the emerald ash borer (EAB; Agrilus planipennis Fairmaire) across a growing area in the eastern US. Accurate mapping of ash species is required to monitor the host resource, predict EAB spread and better understand the short- and long-term effects of EAB on the ash resource...

Determining the Effect of Natural Selection on Linked Neutral Divergence across Species.

PubMed

Phung, Tanya N; Huber, Christian D; Lohmueller, Kirk E

2016-08-01

A major goal in evolutionary biology is to understand how natural selection has shaped patterns of genetic variation across genomes. Studies in a variety of species have shown that neutral genetic diversity (intra-species differences) has been reduced at sites linked to those under direct selection. However, the effect of linked selection on neutral sequence divergence (inter-species differences) remains ambiguous. While empirical studies have reported correlations between divergence and recombination, which is interpreted as evidence for natural selection reducing linked neutral divergence, theory argues otherwise, especially for species that have diverged long ago. Here we address these outstanding issues by examining whether natural selection can affect divergence between both closely and distantly related species. We show that neutral divergence between closely related species (e.g. human-primate) is negatively correlated with functional content and positively correlated with human recombination rate. We also find that neutral divergence between distantly related species (e.g. human-rodent) is negatively correlated with functional content and positively correlated with estimates of background selection from primates. These patterns persist after accounting for the confounding factors of hypermutable CpG sites, GC content, and biased gene conversion. Coalescent models indicate that even when the contribution of ancestral polymorphism to divergence is small, background selection in the ancestral population can still explain a large proportion of the variance in divergence across the genome, generating the observed correlations. Our findings reveal that, contrary to previous intuition, natural selection can indirectly affect linked neutral divergence between both closely and distantly related species. Though we cannot formally exclude the possibility that the direct effects of purifying selection drive some of these patterns, such a scenario would be possible only

Determining the Effect of Natural Selection on Linked Neutral Divergence across Species

PubMed Central

Phung, Tanya N.; Lohmueller, Kirk E.

2016-01-01

A major goal in evolutionary biology is to understand how natural selection has shaped patterns of genetic variation across genomes. Studies in a variety of species have shown that neutral genetic diversity (intra-species differences) has been reduced at sites linked to those under direct selection. However, the effect of linked selection on neutral sequence divergence (inter-species differences) remains ambiguous. While empirical studies have reported correlations between divergence and recombination, which is interpreted as evidence for natural selection reducing linked neutral divergence, theory argues otherwise, especially for species that have diverged long ago. Here we address these outstanding issues by examining whether natural selection can affect divergence between both closely and distantly related species. We show that neutral divergence between closely related species (e.g. human-primate) is negatively correlated with functional content and positively correlated with human recombination rate. We also find that neutral divergence between distantly related species (e.g. human-rodent) is negatively correlated with functional content and positively correlated with estimates of background selection from primates. These patterns persist after accounting for the confounding factors of hypermutable CpG sites, GC content, and biased gene conversion. Coalescent models indicate that even when the contribution of ancestral polymorphism to divergence is small, background selection in the ancestral population can still explain a large proportion of the variance in divergence across the genome, generating the observed correlations. Our findings reveal that, contrary to previous intuition, natural selection can indirectly affect linked neutral divergence between both closely and distantly related species. Though we cannot formally exclude the possibility that the direct effects of purifying selection drive some of these patterns, such a scenario would be possible only

Recent Changes in Tree Species Abundance: Patterns, Trends, and Drivers Across Northeastern US Forests

NASA Astrophysics Data System (ADS)

Gudex-Cross, D.; Pontius, J.; Adams, A.

2017-12-01

Monitoring trends in the abundance and distribution of tree species is essential to understanding potential impacts of climate change on forested ecosystems. Related studies to date have largely focused on modeling distributional shifts according to future climate scenarios or used field inventory data to examine compositional changes across broader landscapes. Here, we leverage a novel remote sensing technique that utilizes field data, multitemporal Landsat imagery, and spectral unmixing to model regional changes in the abundance (percent basal area) of key northeastern US species over a 30-year period (1985-2015). We examine patterns in how species abundance has changed, as well as their relationship with climate, landscape, and soil characteristics using spatial regression models. Results show significant declines in overall abundance for sugar maple ( 8.6% 30-yr loss), eastern hemlock ( 7.8% 30-yr loss), balsam fir ( 5.0% 30-yr loss), and red spruce ( 3.8% total 30-yr loss). Species that saw significant increasing abundance include American beech ( 7.0% 30-yr gain) and red maple ( 2.5% 30-yr gain). However, these changes were not consistent across the landscape. For example, red spruce is increasing at upper elevations with concurrent losses in balsam fir and birch species. Similarly, sugar maple decreases are concentrated at lower elevations, likely due to increases in American beech. Various abiotic factors were significantly associated with changes in species composition including landscape position (e.g. longitude, elevation, and heat load index) and ecologically-relevant climate variables (e.g. growing season precipitation and annual temperature range). Interestingly, there was a stronger relationship in abundance changes across longitudes, rather than latitudes or elevations as predicted in modeled species migration scenarios.These results indicate that the dominant composition of northeastern forests is changing in ways that run counter to accepted

A comparison of auditory brainstem responses across diving bird species

PubMed Central

Crowell, Sara E.; Wells-Berlin, Alicia M.; Carr, Catherine E.; Olsen, Glenn H.; Therrien, Ronald E.; Yannuzzi, Sally E.; Ketten, Darlene R.

2015-01-01

There is little biological data available for diving birds because many live in hard-to-study, remote habitats. Only one species of diving bird, the black-footed penguin (Spheniscus demersus), has been studied in respect to auditory capabilities (Wever et al. 1969). We therefore measured in-air auditory threshold in ten species of diving birds, using the auditory brainstem response (ABR). The average audiogram obtained for each species followed the U-shape typical of birds and many other animals. All species tested shared a common region of greatest sensitivity, from 1000 to 3000 Hz, although audiograms differed significantly across species. Thresholds of all duck species tested were more similar to each other than to the two non-duck species tested. The red-throated loon (Gavia stellata) and northern gannet (Morus bassanus) exhibited the highest thresholds while the lowest thresholds belonged to the duck species, specifically the lesser scaup (Aythya affinis) and ruddy duck (Oxyura jamaicensis). Vocalization parameters were also measured for each species, and showed that with the exception of the common eider (Somateria mollisima), the peak frequency, i.e. frequency at the greatest intensity, of all species’ vocalizations measured here fell between 1000 and 3000 Hz, matching the bandwidth of the most sensitive hearing range. PMID:26156644

Are trait-scaling relationships invariant across contrasting elevations in the widely distributed treeline species Nothofagus pumilio?

PubMed

Fajardo, Alex

2016-05-01

The study of scaling examines the relative dimensions of diverse organismal traits. Understanding whether global scaling patterns are paralleled within species is key to identify causal factors of universal scaling. I examined whether the foliage-stem (Corner's rules), the leaf size-number, and the leaf mass-leaf area scaling relationships remained invariant and isometric with elevation in a wide-distributed treeline species in the southern Chilean Andes. Mean leaf area, leaf mass, leafing intensity, and twig cross-sectional area were determined for 1-2 twigs of 8-15 Nothofagus pumilio individuals across four elevations (including treeline elevation) and four locations (from central Chile at 36°S to Tierra del Fuego at 54°S). Mixed effects models were fitted to test whether the interaction term between traits and elevation was nonsignificant (invariant). The leaf-twig cross-sectional area and the leaf mass-leaf area scaling relationships were isometric (slope = 1) and remained invariant with elevation, whereas the leaf size-number (i.e., leafing intensity) scaling was allometric (slope ≠ -1) and showed no variation with elevation. Leaf area and leaf number were consistently negatively correlated across elevation. The scaling relationships examined in the current study parallel those seen across species. It is plausible that the explanation of intraspecific scaling relationships, as trait combinations favored by natural selection, is the same as those invoked to explain across species patterns. Thus, it is very likely that the global interspecific Corner's rules and other leaf-leaf scaling relationships emerge as the aggregate of largely parallel intraspecific patterns. © 2016 Botanical Society of America.

20180311 - Use of ToxPrint chemotypes for exploring chemical feature enrichments across the ToxCast chemical-assay landscape (SOT)

EPA Science Inventory

EPA’s ToxCast chemical library spans diverse chemical use-types, functionalities, structures and features potentially relevant to toxicity and environmental exposure. However, this structural diversity, along with assay noise and low average hit rates across the varied Tox...

Discriminating plant species across California's diverse ecosystems using airborne VSWIR and TIR imagery

NASA Astrophysics Data System (ADS)

Meerdink, S.; Roberts, D. A.; Roth, K. L.

2015-12-01

Accurate knowledge of the spatial distribution of plant species is required for many research and management agendas that track ecosystem health. Because of this, there is continuous development of research focused on remotely-sensed species classifications for many diverse ecosystems. While plant species have been mapped using airborne imaging spectroscopy, the geographic extent has been limited due to data availability and spectrally similar species continue to be difficult to separate. The proposed Hyperspectral Infrared Imager (HyspIRI) space-borne mission, which includes a visible near infrared/shortwave infrared (VSWIR) imaging spectrometer and thermal infrared (TIR) multi-spectral imager, would present an opportunity to improve species discrimination over a much broader scale. Here we evaluate: 1) the capability of VSWIR and/or TIR spectra to discriminate plant species; 2) the accuracy of species classifications within an ecosystem; and 3) the potential for discriminating among species across a range of ecosystems. Simulated HyspIRI imagery was acquired in spring/summer of 2013 spanning from Santa Barbara to Bakersfield, CA with the Airborne Visible/Infrared Imaging Spectrometer (AVIRIS) and the MODIS/ASTER Airborne Simulator (MASTER) instruments. Three spectral libraries were created from these images: AVIRIS (224 bands from 0.4 - 2.5 µm), MASTER (8 bands from 7.5 - 12 µm), and AVIRIS + MASTER. We used canonical discriminant analysis (CDA) as a dimension reduction technique and then classified plant species using linear discriminant analysis (LDA). Our results show the inclusion of TIR spectra improved species discrimination, but only for plant species with emissivities departing from that of a gray body. Ecosystems with species that have high spectral contrast had higher classification accuracies. Mapping plant species across all ecosystems resulted in a classification with lower accuracies than a single ecosystem due to the complex nature of

Roads to ruin: conservation threats to a sentinel species across an urban gradient.

PubMed

Feist, Blake E; Buhle, Eric R; Baldwin, David H; Spromberg, Julann A; Damm, Steven E; Davis, Jay W; Scholz, Nathaniel L

2017-12-01

Urbanization poses a global challenge to species conservation. This is primarily understood in terms of physical habitat loss, as agricultural and forested lands are replaced with urban infrastructure. However, aquatic habitats are also chemically degraded by urban development, often in the form of toxic stormwater runoff. Here we assess threats of urbanization to coho salmon throughout developed areas of the Puget Sound Basin in Washington, USA. Puget Sound coho are a sentinel species for freshwater communities and also a species of concern under the U.S. Endangered Species Act. Previous studies have demonstrated that stormwater runoff is unusually lethal to adult coho that return to spawn each year in urban watersheds. To further explore the relationship between land use and recurrent coho die-offs, we measured mortality rates in field surveys of 51 spawning sites across an urban gradient. We then used spatial analyses to measure landscape attributes (land use and land cover, human population density, roadways, traffic intensity, etc.) and climatic variables (annual summer and fall precipitation) associated with each site. Structural equation modeling revealed a latent urbanization gradient that was associated with road density and traffic intensity, among other variables, and positively related to coho mortality. Across years within sites, mortality increased with summer and fall precipitation, but the effect of rainfall was strongest in the least developed areas and was essentially neutral in the most urbanized streams. We used the best-supported structural equation model to generate a predictive mortality risk map for the entire Puget Sound Basin. This map indicates an ongoing and widespread loss of spawners across much of the Puget Sound population segment, particularly within the major regional north-south corridor for transportation and development. Our findings identify current and future urbanization-related threats to wild coho, and show where green

Data gaps in anthropogenically driven local-scale species richness change studies across the Earth's terrestrial biomes.

PubMed

Murphy, Grace E P; Romanuk, Tamara N

2016-05-01

There have been numerous attempts to synthesize the results of local-scale biodiversity change studies, yet several geographic data gaps exist. These data gaps have hindered ecologist's ability to make strong conclusions about how local-scale species richness is changing around the globe. Research on four of the major drivers of global change is unevenly distributed across the Earth's biomes. Here, we use a dataset of 638 anthropogenically driven species richness change studies to identify where data gaps exist across the Earth's terrestrial biomes based on land area, future change in drivers, and the impact of drivers on biodiversity, and make recommendations for where future studies should focus their efforts. Across all drivers of change, the temperate broadleaf and mixed forests and the tropical moist broadleaf forests are the best studied. The biome-driver combinations we have identified as most critical in terms of where local-scale species richness change studies are lacking include the following: land-use change studies in tropical and temperate coniferous forests, species invasion and nutrient addition studies in the boreal forest, and warming studies in the boreal forest and tropics. Gaining more information on the local-scale effects of the specific human drivers of change in these biomes will allow for better predictions of how human activity impacts species richness around the globe.

Across species-pool aggregation alters grassland productivity and diversity.

PubMed

McKenna, Thomas P; Yurkonis, Kathryn A

2016-08-01

Plant performance is determined by the balance of intra- and interspecific neighbors within an individual's zone of influence. If individuals interact over smaller scales than the scales at which communities are measured, then altering neighborhood interactions may fundamentally affect community responses. These interactions can be altered by changing the number (species richness), abundances (species evenness), and positions (species pattern) of the resident plant species, and we aimed to test whether aggregating species at planting would alter effects of species richness and evenness on biomass production at a common scale of observation in grasslands. We varied plant species richness (2, 4, or 8 species and monocultures), evenness (0.64, 0.8, or 1.0), and pattern (planted randomly or aggregated in groups of four individuals) within 1 × 1 m plots established with transplants from a pool of 16 tallgrass prairie species and assessed plot-scale biomass production and diversity over the first three growing seasons. As expected, more species-rich plots produced more biomass by the end of the third growing season, an effect associated with a shift from selection to complementarity effects over time. Aggregating conspecifics at a 0.25-m scale marginally reduced biomass production across all treatments and increased diversity in the most even plots, but did not alter biodiversity effects or richness-productivity relationships. Results support the hypothesis that fine-scale species aggregation affects diversity by promoting species coexistence in this system. However, results indicate that inherent changes in species neighborhood relationships along grassland diversity gradients may only minimally affect community (meter) - scale responses among similarly designed biodiversity-ecosystem function studies. Given that species varied in their responses to local aggregation, it may be possible to use such species-specific results to spatially design larger-scale grassland

A comparison of auditory brainstem responses across diving bird species

USGS Publications Warehouse

Crowell, Sara E.; Berlin, Alicia; Carr, Catherine E.; Olsen, Glenn H.; Therrien, Ronald E.; Yannuzzi, Sally E.; Ketten, Darlene R.

2015-01-01

There is little biological data available for diving birds because many live in hard-to-study, remote habitats. Only one species of diving bird, the black-footed penguin (Spheniscus demersus), has been studied in respect to auditory capabilities (Wever et al., Proc Natl Acad Sci USA 63:676–680, 1969). We, therefore, measured in-air auditory threshold in ten species of diving birds, using the auditory brainstem response (ABR). The average audiogram obtained for each species followed the U-shape typical of birds and many other animals. All species tested shared a common region of the greatest sensitivity, from 1000 to 3000 Hz, although audiograms differed significantly across species. Thresholds of all duck species tested were more similar to each other than to the two non-duck species tested. The red-throated loon (Gavia stellata) and northern gannet (Morus bassanus) exhibited the highest thresholds while the lowest thresholds belonged to the duck species, specifically the lesser scaup (Aythya affinis) and ruddy duck (Oxyura jamaicensis). Vocalization parameters were also measured for each species, and showed that with the exception of the common eider (Somateria mollisima), the peak frequency, i.e., frequency at the greatest intensity, of all species' vocalizations measured here fell between 1000 and 3000 Hz, matching the bandwidth of the most sensitive hearing range.

Shrubs as ecosystem engineers across an environmental gradient: effects on species richness and exotic plant invasion.

PubMed

Kleinhesselink, Andrew R; Magnoli, Susan M; Cushman, J Hall

2014-08-01

Ecosystem-engineering plants modify the physical environment and can increase species diversity and exotic species invasion. At the individual level, the effects of ecosystem engineers on other plants often become more positive in stressful environments. In this study, we investigated whether the community-level effects of ecosystem engineers also become stronger in more stressful environments. Using comparative and experimental approaches, we assessed the ability of a native shrub (Ericameria ericoides) to act as an ecosystem engineer across a stress gradient in a coastal dune in northern California, USA. We found increased coarse organic matter and lower wind speeds within shrub patches. Growth of a dominant invasive grass (Bromus diandrus) was facilitated both by aboveground shrub biomass and by growing in soil taken from shrub patches. Experimental removal of shrubs negatively affected species most associated with shrubs and positively affected species most often found outside of shrubs. Counter to the stress-gradient hypothesis, the effects of shrubs on the physical environment and individual plant growth did not increase across the established stress gradient at this site. At the community level, shrub patches increased beta diversity, and contained greater rarified richness and exotic plant cover than shrub-free patches. Shrub effects on rarified richness increased with environmental stress, but effects on exotic cover and beta diversity did not. Our study provides evidence for the community-level effects of shrubs as ecosystem engineers in this system, but shows that these effects do not necessarily become stronger in more stressful environments.

Meta-analysis reveals that hydraulic traits explain cross-species patterns of drought-induced tree mortality across the globe.

PubMed

Anderegg, William R L; Klein, Tamir; Bartlett, Megan; Sack, Lawren; Pellegrini, Adam F A; Choat, Brendan; Jansen, Steven

2016-05-03

Drought-induced tree mortality has been observed globally and is expected to increase under climate change scenarios, with large potential consequences for the terrestrial carbon sink. Predicting mortality across species is crucial for assessing the effects of climate extremes on forest community biodiversity, composition, and carbon sequestration. However, the physiological traits associated with elevated risk of mortality in diverse ecosystems remain unknown, although these traits could greatly improve understanding and prediction of tree mortality in forests. We performed a meta-analysis on species' mortality rates across 475 species from 33 studies around the globe to assess which traits determine a species' mortality risk. We found that species-specific mortality anomalies from community mortality rate in a given drought were associated with plant hydraulic traits. Across all species, mortality was best predicted by a low hydraulic safety margin-the difference between typical minimum xylem water potential and that causing xylem dysfunction-and xylem vulnerability to embolism. Angiosperms and gymnosperms experienced roughly equal mortality risks. Our results provide broad support for the hypothesis that hydraulic traits capture key mechanisms determining tree death and highlight that physiological traits can improve vegetation model prediction of tree mortality during climate extremes.

Preference assessments in the zoo: Keeper and staff predictions of enrichment preferences across species.

PubMed

Mehrkam, Lindsay R; Dorey, Nicole R

2015-01-01

Environmental enrichment is widely used in the management of zoo animals, and is an essential strategy for increasing the behavioral welfare of these populations. It may be difficult, however, to identify potentially effective enrichment strategies that are also cost-effective and readily available. An animal's preference for a potential enrichment item may be a reliable predictor of whether that individual will reliably interact with that item, and subsequently enable staff to evaluate the effects of that enrichment strategy. The aim of the present study was to assess the utility of preference assessments for identifying potential enrichment items across six different species--each representing a different taxonomic group. In addition, we evaluated the agreement between zoo personnel's predictions of animals' enrichment preferences and stimuli selected via a preference assessment. Five out of six species (nine out of 11 individuals) exhibited clear, systematic preferences for specific stimuli. Similarities in enrichment preferences were observed among all individuals of primates, whereas individuals within ungulate and avian species displayed individual differences in enrichment preferences. Overall, zoo personnel, regardless of experience level, were significantly more accurate at predicting least-preferred stimuli than most-preferred stimuli across species, and tended to make the same predictions for all individuals within a species. Preference assessments may therefore be a useful, efficient husbandry strategy for identifying viable enrichment items at both the individual and species levels. © 2015 Wiley Periodicals, Inc.

Development and validation of a LC-MS/MS assay for quantitation of plasma citrulline for application to animal models of the acute radiation syndrome across multiple species.

PubMed

Jones, Jace W; Tudor, Gregory; Bennett, Alexander; Farese, Ann M; Moroni, Maria; Booth, Catherine; MacVittie, Thomas J; Kane, Maureen A

2014-07-01

The potential risk of a radiological catastrophe highlights the need for identifying and validating potential biomarkers that accurately predict radiation-induced organ damage. A key target organ that is acutely sensitive to the effects of irradiation is the gastrointestinal (GI) tract, referred to as the GI acute radiation syndrome (GI-ARS). Recently, citrulline has been identified as a potential circulating biomarker for radiation-induced GI damage. Prior to biologically validating citrulline as a biomarker for radiation-induced GI injury, there is the important task of developing and validating a quantitation assay for citrulline detection within the radiation animal models used for biomarker validation. Herein, we describe the analytical development and validation of citrulline detection using a liquid chromatography tandem mass spectrometry assay that incorporates stable-label isotope internal standards. Analytical validation for specificity, linearity, lower limit of quantitation, accuracy, intra- and interday precision, extraction recovery, matrix effects, and stability was performed under sample collection and storage conditions according to the Guidance for Industry, Bioanalytical Methods Validation issued by the US Food and Drug Administration. In addition, the method was biologically validated using plasma from well-characterized mouse, minipig, and nonhuman primate GI-ARS models. The results demonstrated that circulating citrulline can be confidently quantified from plasma. Additionally, circulating citrulline displayed a time-dependent response for radiological doses covering GI-ARS across multiple species.

Assessments of sensory plasticity after spinal cord injury across species.

PubMed

Haefeli, Jenny; Huie, J Russell; Morioka, Kazuhito; Ferguson, Adam R

2017-06-23

Spinal cord injury (SCI) is a multifaceted phenomenon associated with alterations in both motor function and sensory function. A majority of patients with SCI report sensory disturbances, including not only loss of sensation, but in many cases enhanced abnormal sensation, dysesthesia and pain. Development of therapeutics to treat these abnormal sensory changes require common measurement tools that can enable cross-species translation from animal models to human patients. We review the current literature on translational nociception/pain measurement in SCI and discuss areas for further development. Although a number of tools exist for measuring both segmental and affective sensory changes, we conclude that there is a pressing need for better, integrative measurement of nociception/pain outcomes across species to enhance precise therapeutic innovation for sensory dysfunction in SCI. Copyright © 2016 Elsevier Ireland Ltd. All rights reserved.

Quantifying whole transcriptome size, a prerequisite for understanding transcriptome evolution across species: an example from a plant allopolyploid.

PubMed

Coate, Jeremy E; Doyle, Jeff J

2010-01-01

Evolutionary biologists are increasingly comparing gene expression patterns across species. Due to the way in which expression assays are normalized, such studies provide no direct information about expression per gene copy (dosage responses) or per cell and can give a misleading picture of genes that are differentially expressed. We describe an assay for estimating relative expression per cell. When used in conjunction with transcript profiling data, it is possible to compare the sizes of whole transcriptomes, which in turn makes it possible to compare expression per cell for each gene in the transcript profiling data set. We applied this approach, using quantitative reverse transcriptase-polymerase chain reaction and high throughput RNA sequencing, to a recently formed allopolyploid and showed that its leaf transcriptome was approximately 1.4-fold larger than either progenitor transcriptome (70% of the sum of the progenitor transcriptomes). In contrast, the allopolyploid genome is 94.3% as large as the sum of its progenitor genomes and retains > or =93.5% of the sum of its progenitor gene complements. Thus, "transcriptome downsizing" is greater than genome downsizing. Using this transcriptome size estimate, we inferred dosage responses for several thousand genes and showed that the majority exhibit partial dosage compensation. Homoeologue silencing is nonrandomly distributed across dosage responses, with genes showing extreme responses in either direction significantly more likely to have a silent homoeologue. This experimental approach will add value to transcript profiling experiments involving interspecies and interploidy comparisons by converting expression per transcriptome to expression per genome, eliminating the need for assumptions about transcriptome size.

Warming increases plant biomass and reduces diversity across continents, latitudes, and species migration scenarios in experimental wetland communities.

PubMed

Baldwin, Andrew H; Jensen, Kai; Schönfeldt, Marisa

2014-03-01

Atmospheric warming may influence plant productivity and diversity and induce poleward migration of species, altering communities across latitudes. Complicating the picture is that communities from different continents deviate in evolutionary histories, which may modify responses to warming and migration. We used experimental wetland plant communities grown from seed banks as model systems to determine whether effects of warming on biomass production and species richness are consistent across continents, latitudes, and migration scenarios. We collected soil samples from each of three tidal freshwater marshes in estuaries at three latitudes (north, middle, south) on the Atlantic coasts of Europe and North America. In one experiment, we exposed soil seed bank communities from each latitude and continent to ambient and elevated (+2.8 °C) temperatures in the greenhouse. In a second experiment, soil samples were mixed either within each estuary (limited migration) or among estuaries from different latitudes in each continent (complete migration). Seed bank communities of these migration scenarios were also exposed to ambient and elevated temperatures and contrasted with a no-migration treatment. In the first experiment, warming overall increased biomass (+16%) and decreased species richness (-14%) across latitudes in Europe and North America. Species richness and evenness of south-latitude communities were less affected by warming than those of middle and north latitudes. In the second experiment, warming also stimulated biomass and lowered species richness. In addition, complete migration led to increased species richness (+60% in North America, + 100% in Europe), but this higher diversity did not translate into increased biomass. Species responded idiosyncratically to warming, but Lythrum salicaria and Bidens sp. increased significantly in response to warming in both continents. These results reveal for the first time consistent impacts of warming on biomass and

Meaningful traits for grouping plant species across arid ecosystems.

PubMed

Bär Lamas, Marlene Ivonne; Carrera, A L; Bertiller, M B

2016-05-01

Grouping species may provide some degree of simplification to understand the ecological function of plants on key ecosystem processes. We asked whether groups of plant species based on morpho-chemical traits associated with plant persistence and stress/disturbance resistance reflect dominant plant growth forms in arid ecosystems. We selected twelve sites across an aridity gradient in northern Patagonia. At each site, we identified modal size plants of each dominant species and assessed specific leaf area (SLA), plant height, seed mass, N and soluble phenol concentration in green and senesced leaves at each plant. Plant species were grouped according with plant growth forms (perennial grasses, evergreen shrubs and deciduous shrubs) and plant morphological and/or chemical traits using cluster analysis. We calculated mean values of each plant trait for each species group and plant growth form. Plant growth forms significantly differed among them in most of the morpho-chemical traits. Evergreen shrubs were tall plants with the highest seed mass and soluble phenols in leaves, deciduous shrubs were also tall plants with high SLA and the highest N in leaves, and perennial grasses were short plants with high SLA and low concentration of N and soluble phenols in leaves. Grouping species by the combination of morpho-chemical traits yielded 4 groups in which species from one growth form prevailed. These species groups differed in soluble phenol concentration in senesced leaves and plant height. These traits were highly correlated. We concluded that (1) plant height is a relevant synthetic variable, (2) growth forms adequately summarize ecological strategies of species in arid ecosystems, and (3) the inclusion of plant morphological and chemical traits related to defenses against environmental stresses and herbivory enhanced the potential of species grouping, particularly within shrubby growth forms.

Evolutionary divergence of mitochondrial genomes in two Tetranychus species distributed across different climates.

PubMed

Sun, J-T; Jin, P-Y; Hoffmann, A A; Duan, X-Z; Dai, J; Hu, G; Xue, X-F; Hong, X-Y

2018-05-24

There is increasing evidence that mitochondrial genomes (mitogenomes) can be under selection, whereas the selective regimes shaping mitogenome evolution remain largely unclear. To test for mitochondrial genome evolution in relation to the climate adaptation, we explored mtDNA variation in two spider mite (Tetranychus) species, which distribute across different climates. We sequenced 26 complete mitogenomes of T. truncatus which occurs in both warm and cold regions, and 9 complete mitogenomes of T. pueraricola which is only restricted in warm regions. Patterns of evolution in the two species mitogenomes were compared through a series of d N /d S methods and physicochemical profiles of amino acid replacements. We found that (1) the mitogenomes of both species were under widespread purifying selection. (2) Elevated directional adaptive selection was observed in the T. truncatus mitogenome, perhaps linked to the cold climates adaptation of T. truncatus. (3) The strength of selection varied across genes, and diversifying positive selection detected on ND4 and ATP6 pointed to their crucial roles during adaptation to different climatic conditions. This study gained insight into the mitogenome evolution in relation to the climate adaptation. This article is protected by copyright. All rights reserved. © 2018 The Royal Entomological Society.

Incorporating latitudinal and central–marginal trends in assessing genetic variation across species ranges

Treesearch

Qinfeng Guo

2012-01-01

The genetic variation across a species’ range is an important factor in speciation and conservation, yet searching for general patterns and underlying causes remains challenging. While the majority of comparisons between central and marginal populations have revealed a general central–marginal (C-M) decline in genetic diversity, others show no clear pattern. Similarly...

Assessing the relative importance of environmental effects, carry-over effects and species differences in thermal stress resistance: a comparison of Drosophilids across field and laboratory generations.

PubMed

Schiffer, Michele; Hangartner, Sandra; Hoffmann, Ary A

2013-10-15

There is increasing interest in comparing species of related organisms for their susceptibility to thermal extremes in order to evaluate potential vulnerability to climate change. Comparisons are typically undertaken on individuals collected from the field with or without a period of acclimation. However, this approach does not allow the potential contributions of environmental and carry-over effects across generations to be separated from inherent species differences in susceptibility. To assess the importance of these different sources of variation, we here considered heat and cold resistance in Drosophilid species from tropical and temperate sites in the field and across two laboratory generations. Resistance in field-collected individuals tended to be lower when compared with F1 and F2 laboratory generations, and species differences in field flies were only weakly correlated to differences established under controlled rearing conditions, unlike in F1-F2 comparisons. This reflected large environmental effects on resistance associated with different sites and conditions experienced within sites. For the 8 h cold recovery assay there was no strong evidence of carry-over effects, whereas for the heat knockdown and 2 h cold recovery assays there was some evidence for such effects. However, for heat these were species specific in direction. Variance components for inherent species differences were substantial for resistance to heat and 8 h cold stress, but small for 2 h cold stress, though this may be a reflection of the species being considered in the comparisons. These findings highlight that inherent differences among species are difficult to characterise accurately without controlling for environmental sources of variation and carry-over effects. Moreover, they also emphasise the complex nature of carry-over effects that vary depending on the nature of stress traits and the species being evaluated.

Balance across contexts: importance of balanced need satisfaction across various life domains.

PubMed

Milyavskaya, Marina; Gingras, Isabelle; Mageau, Geneviève A; Koestner, Richard; Gagnon, Hugo; Fang, Jianqun; Boiché, Julie

2009-08-01

Self-determination theory posits that satisfaction of three basic psychological needs-autonomy, competence, and relatedness-are required for psychological well-being, and a recent study showed that the balance in the satisfaction of these three needs independently affects well-being. The present investigation builds on these findings by examining the balance of adolescents' need satisfaction across distinct life contexts. The results of three studies show that adolescents who experience a balance of need satisfaction across important life contexts, including at school, at home, with friends, and in part-time jobs, reported higher well-being and better school adjustment. This finding emerged consistently across four countries and across multiple measures of school adjustment, including teacher reports. Together, these results support previous research that highlights the importance of consistency for psychological functioning.

The positive relationships between plant coverage, species richness, and aboveground biomass are ubiquitous across plant growth forms in semi-steppe rangelands.

PubMed

Sanaei, Anvar; Ali, Arshad; Chahouki, Mohammad Ali Zare

2018-01-01

The positive relationships between biodiversity and aboveground biomass are important for biodiversity conservation and greater ecosystem functioning and services that humans depend on. However, the interaction effects of plant coverage and biodiversity on aboveground biomass across plant growth forms (shrubs, forbs and grasses) in natural rangelands are poorly studied. Here, we hypothesized that, while accounting for environmental factors and disturbance intensities, the positive relationships between plant coverage, biodiversity, and aboveground biomass are ubiquitous across plant growth forms in natural rangelands. We applied structural equation models (SEMs) using data from 735 quadrats across 35 study sites in semi-steppe rangelands in Iran. The combination of plant coverage and species richness rather than Shannon's diversity or species diversity (a latent variable of species richness and evenness) substantially enhance aboveground biomass across plant growth forms. In all selected SEMs, plant coverage had a strong positive direct effect on aboveground biomass (β = 0.72 for shrubs, 0.84 for forbs and 0.80 for grasses), followed by a positive effect of species richness (β = 0.26 for shrubs, 0.05 for forbs and 0.09 for grasses), and topographic factors. Disturbance intensity had a negative effect on plant coverage, whereas it had a variable effect on species richness across plant growth forms. Plant coverage had a strong positive total effect on aboveground biomass (β = 0.84 for shrubs, 0.88 for forbs, and 0.85 for grasses), followed by a positive effect of species richness, and a negative effect of disturbance intensity across plant growth forms. Our results shed light on the management of rangelands that is high plant coverage can significantly improve species richness and aboveground biomass across plant growth forms. We also found that high disturbance intensity due to heavy grazing has a strong negative effect on plant coverage rather than species

Climate Warming and Seasonal Precipitation Change Interact to Limit Species Distribution Shifts across Western North America

PubMed Central

Harsch, Melanie A.; HilleRisLambers, Janneke

2016-01-01

Using an extensive network of occurrence records for 293 plant species collected over the past 40 years across a climatically diverse geographic section of western North America, we find that plant species distributions were just as likely to shift upwards (i.e., towards higher elevations) as downward (i.e., towards lower elevations)–despite consistent warming across the study area. Although there was no clear directional response to climate warming across the entire study area, there was significant region- to region- variation in responses (i.e. from as many as 73% to as few as 32% of species shifting upward). To understand the factors that might be controlling region-specific distributional shifts of plant species, we explored the relationship between the direction of change in distribution limits and the nature of recent climate change. We found that the direction that distribution limits shifted was explained by an interaction between the rate of change in local summer temperatures and seasonal precipitation. Specifically, species were more likely to shift upward at their upper elevational limit when minimum temperatures increased and snowfall was unchanging or declined at slower rates (<0.5 mm/year). This suggests that both low temperature and water availability limit upward shifts at upper elevation limits. By contrast, species were more likely to shift upwards at their lower elevation limit when maximum temperatures increased, but also shifted upwards under conditions of cooling temperatures when precipitation decreased. This suggests increased water stress may drive upward shifts at lower elevation limits. Our results suggest that species’ elevational distribution shifts are not predictable by climate warming alone but depend on the interaction between seasonal temperature and precipitation change. PMID:27447834

Climate sensitivity across marine domains of life: limits to evolutionary adaptation shape species interactions.

PubMed

Storch, Daniela; Menzel, Lena; Frickenhaus, Stephan; Pörtner, Hans-O

2014-10-01

Organisms in all domains, Archaea, Bacteria, and Eukarya will respond to climate change with differential vulnerabilities resulting in shifts in species distribution, coexistence, and interactions. The identification of unifying principles of organism functioning across all domains would facilitate a cause and effect understanding of such changes and their implications for ecosystem shifts. For example, the functional specialization of all organisms in limited temperature ranges leads us to ask for unifying functional reasons. Organisms also specialize in either anoxic or various oxygen ranges, with animals and plants depending on high oxygen levels. Here, we identify thermal ranges, heat limits of growth, and critically low (hypoxic) oxygen concentrations as proxies of tolerance in a meta-analysis of data available for marine organisms, with special reference to domain-specific limits. For an explanation of the patterns and differences observed, we define and quantify a proxy for organismic complexity across species from all domains. Rising complexity causes heat (and hypoxia) tolerances to decrease from Archaea to Bacteria to uni- and then multicellular Eukarya. Within and across domains, taxon-specific tolerance limits likely reflect ultimate evolutionary limits of its species to acclimatization and adaptation. We hypothesize that rising taxon-specific complexities in structure and function constrain organisms to narrower environmental ranges. Low complexity as in Archaea and some Bacteria provide life options in extreme environments. In the warmest oceans, temperature maxima reach and will surpass the permanent limits to the existence of multicellular animals, plants and unicellular phytoplankter. Smaller, less complex unicellular Eukarya, Bacteria, and Archaea will thus benefit and predominate even more in a future, warmer, and hypoxic ocean. © 2014 John Wiley & Sons Ltd.

Effectiveness of PowerPoint-Based Lectures across Different Business Disciplines: An Investigation and Implications

ERIC Educational Resources Information Center

Burke, Lisa A.; James, Karen; Ahmadi, Mohammad

2009-01-01

The authors investigated business faculty members' degree of Power-Point (PPT) use across different functional areas in a business program and their use of specific PPT features. The authors also examined students' perceptions of PPT's effectiveness across different business courses (e.g., accounting, economics, management, business law,…

The Homogeneity of Optimal Sensor Placement Across Multiple Winged Insect Species

NASA Astrophysics Data System (ADS)

Jenkins, Abigail L.

Taking inspiration from biology, control algorithms can be implemented to imitate the naturally occurring control systems present in nature. This research is primarily concerned with insect flight and optimal wing sensor placement. Many winged insects with halteres are equipped with mechanoreceptors termed campaniform sensilla. Although the exact information these receptors provide to the insect's nervous system is unknown, it is thought to have the capability of measuring inertial rotation forces. During flight, when the wing bends, the information measured by the campaniform sensilla is received by the central nervous system, and provides the insect necessary data to control flight. This research compares three insect species - the hawkmoth Manduca sexta, the honeybee Apis mellifera, and the fruit fly Drosophila melanogaster. Using an observability-based sensor placement algorithm, the optimal sensor placement for these three species is determined. Simulations resolve if this optimal sensor placement corresponds to the insect's campaniform sensilla, as well as if placement is homogeneous across species.

Species distributions in response to individual soil nutrients and seasonal drought across a community of tropical trees

PubMed Central

Condit, Richard; Engelbrecht, Bettina M. J.; Pino, Delicia; Pérez, Rolando; Turner, Benjamin L.

2013-01-01

Tropical forest vegetation is shaped by climate and by soil, but understanding how the distributions of individual tree species respond to specific resources has been hindered by high diversity and consequent rarity. To study species over an entire community, we surveyed trees and measured soil chemistry across climatic and geological gradients in central Panama and then used a unique hierarchical model of species occurrence as a function of rainfall and soil chemistry to circumvent analytical difficulties posed by rare species. The results are a quantitative assessment of the responses of 550 tree species to eight environmental factors, providing a measure of the importance of each factor across the entire tree community. Dry-season intensity and soil phosphorus were the strongest predictors, each affecting the distribution of more than half of the species. Although we anticipated clear-cut responses to dry-season intensity, the finding that many species have pronounced associations with either high or low phosphorus reveals a previously unquantified role for this nutrient in limiting tropical tree distributions. The results provide the data necessary for understanding distributional limits of tree species and predicting future changes in forest composition. PMID:23440213

Species distributions in response to individual soil nutrients and seasonal drought across a community of tropical trees.

PubMed

Condit, Richard; Engelbrecht, Bettina M J; Pino, Delicia; Pérez, Rolando; Turner, Benjamin L

2013-03-26

Tropical forest vegetation is shaped by climate and by soil, but understanding how the distributions of individual tree species respond to specific resources has been hindered by high diversity and consequent rarity. To study species over an entire community, we surveyed trees and measured soil chemistry across climatic and geological gradients in central Panama and then used a unique hierarchical model of species occurrence as a function of rainfall and soil chemistry to circumvent analytical difficulties posed by rare species. The results are a quantitative assessment of the responses of 550 tree species to eight environmental factors, providing a measure of the importance of each factor across the entire tree community. Dry-season intensity and soil phosphorus were the strongest predictors, each affecting the distribution of more than half of the species. Although we anticipated clear-cut responses to dry-season intensity, the finding that many species have pronounced associations with either high or low phosphorus reveals a previously unquantified role for this nutrient in limiting tropical tree distributions. The results provide the data necessary for understanding distributional limits of tree species and predicting future changes in forest composition.

Climate Controls on Tree Growth Across Species and Sites in Northeastern Arizona

NASA Astrophysics Data System (ADS)

Schwan, M. R.; Guiterman, C. H.; Anchukaitis, K. J.

2016-12-01

Understanding how forests will respond to ongoing climate change is important for conservation and resource management. Conifer forests in the US Southwest are predicted to be particularly at risk from increased drought and higher temperatures projected to occur in the region. Tree-ring studies shed light on how trees respond to climate, but there remains considerable uncertainty as to which climate factors are most important, and which species are most at risk. Confounding climate and environmental factors, biological differences among species, and biogeography often complicate cross-species analysis. Here we present a multi-species, multivariate analysis of tree growth response to climate variability. We analyze data from three coexisting conifer tree species at two sites near Canyon de Chelly, Arizona. We use a high-resolution PRISM gridded climate dataset to determine the growth responses across species and sites to temperature and precipitation. We identify both common and differential responses in our data and use these to infer possible risks these forest communities may face under a changing climate.

PlaNet: Combined Sequence and Expression Comparisons across Plant Networks Derived from Seven Species[W][OA

PubMed Central

Mutwil, Marek; Klie, Sebastian; Tohge, Takayuki; Giorgi, Federico M.; Wilkins, Olivia; Campbell, Malcolm M.; Fernie, Alisdair R.; Usadel, Björn; Nikoloski, Zoran; Persson, Staffan

2011-01-01

The model organism Arabidopsis thaliana is readily used in basic research due to resource availability and relative speed of data acquisition. A major goal is to transfer acquired knowledge from Arabidopsis to crop species. However, the identification of functional equivalents of well-characterized Arabidopsis genes in other plants is a nontrivial task. It is well documented that transcriptionally coordinated genes tend to be functionally related and that such relationships may be conserved across different species and even kingdoms. To exploit such relationships, we constructed whole-genome coexpression networks for Arabidopsis and six important plant crop species. The interactive networks, clustered using the HCCA algorithm, are provided under the banner PlaNet (http://aranet.mpimp-golm.mpg.de). We implemented a comparative network algorithm that estimates similarities between network structures. Thus, the platform can be used to swiftly infer similar coexpressed network vicinities within and across species and can predict the identity of functional homologs. We exemplify this using the PSA-D and chalcone synthase-related gene networks. Finally, we assessed how ontology terms are transcriptionally connected in the seven species and provide the corresponding MapMan term coexpression networks. The data support the contention that this platform will considerably improve transfer of knowledge generated in Arabidopsis to valuable crop species. PMID:21441431

Environmental predictors of dispersal traits across a species' geographic range.

PubMed

LaRue, Elizabeth A; Holland, Jeffrey D; Emery, Nancy C

2018-05-30

Variation in habitat quality and quantity drive selection on dispersal traits in heterogeneous environments, but the extent to which environmental conditions predict geographic variation in dispersal is rarely evaluated. We assessed dispersal trait variation across the range of Cakile edentula var. lacustris, an annual herb that occupies beaches of the Great Lakes. Cakile edentula has dimorphic fruits that each contain one dispersive and one non-dispersive seed. Previous work showed that plant height, branching density, and dispersive fruit wing-loading can determine the distance that seeds disperse locally by wind, while pericarp thickness influences the distance they disperse by water. We tested if these traits vary predictably with latitude across the species' geographic range, and if variation in dispersal characteristics can be predicted by the quality and quantity of habitat available at a site. We observed that the dispersive fruits from northern and southern populations had thinner pericarps than those from the interior of the species' range, reflecting reduced long-distance dispersal by water at both range limits. Plants at the northern range limit were shorter with less dense branching and lower wing-loading than populations elsewhere in the range, suggesting that these populations have enhanced local wind dispersal. In contrast, southern populations exhibited traits with inconsistent effects on wind dispersal: plants tended to be short, which facilitates wind dispersal in C. edentula, but also had relatively higher branching density and distal segment wing-loading that reduce wind dispersal. Geographic variation in maternal plant height and branching density was partially explained by variation in habitat quality, which declined at the species' range limits. In addition, population differences in branching density, fruit wing-loading, and pericarp thickness were predicted by the abundance and distribution of beach habitat. Finally, a common garden

Divergent population structure and climate associations of a chromosomal inversion polymorphism across the Mimulus guttatus species complex

PubMed Central

Oneal, Elen; Lowry, David B.; Wright, Kevin M.; Zhu, Zhirui; Willis, John H.

2014-01-01

Chromosomal rearrangement polymorphisms are common and increasingly found to be associated with adaptive ecological divergence and speciation. Rearrangements, such as inversions, reduce recombination in heterozygous individuals and thus can protect favourable allelic combinations at linked loci, facilitating their spread in the presence of gene flow. Recently, we identified a chromosomal inversion polymorphism that contributes to ecological adaptation and reproductive isolation between annual and perennial ecotypes of the yellow monkeyflower, Mimulus guttatus. Here we evaluate the population genetic structure of this inverted region in comparison with the collinear regions of the genome across the M. guttatus species complex. We tested whether annual and perennial M. guttatus exhibit different patterns of divergence for loci in the inverted and noninverted regions of the genome. We then evaluated whether there are contrasting climate associations with these genomic regions through redundancy analysis. We found that the inversion exhibits broadly different patterns of divergence among annual and perennial M. guttatus and is associated with environmental variation across population accessions. This study is the first widespread population genetic survey of the diversity of the M. guttatus species complex. Our findings contribute to a greater understanding of morphological, ecological, and genetic evolutionary divergence across this highly diverse group of closely related ecotypes and species. Finally, understanding species relationships among M. guttatus sp. has hitherto been stymied by accumulated evidence of substantial gene flow among populations as well as designated species. Nevertheless, our results shed light on these relationships and provide insight into adaptation in life history traits within the complex. PMID:24796267

What determines species richness of parasitic organisms? A meta-analysis across animal, plant and fungal hosts.

PubMed

Kamiya, Tsukushi; O'Dwyer, Katie; Nakagawa, Shinichi; Poulin, Robert

2014-02-01

Although a small set of external factors account for much of the spatial variation in plant and animal diversity, the search continues for general drivers of variation in parasite species richness among host species. Qualitative reviews of existing evidence suggest idiosyncrasies and inconsistent predictive power for all proposed determinants of parasite richness. Here, we provide the first quantitative synthesis of the evidence using a meta-analysis of 62 original studies testing the relationship between parasite richness across animal, plant and fungal hosts, and each of its four most widely used presumed predictors: host body size, host geographical range size, host population density, and latitude. We uncover three universal predictors of parasite richness across host species, namely host body size, geographical range size and population density, applicable regardless of the taxa considered and independently of most aspects of study design. A proper match in the primary studies between the focal predictor and both the spatial scale of study and the level at which parasite species richness was quantified (i.e. within host populations or tallied across a host species' entire range) also affected the magnitude of effect sizes. By contrast, except for a couple of indicative trends in subsets of the full dataset, there was no strong evidence for an effect of latitude on parasite species richness; where found, this effect ran counter to the general latitude gradient in diversity, with parasite species richness tending to be higher further from the equator. Finally, the meta-analysis also revealed a negative relationship between the magnitude of effect sizes and the year of publication of original studies (i.e. a time-lag bias). This temporal bias may be due to the increasing use of phylogenetic correction in comparative analyses of parasite richness over time, as this correction yields more conservative effect sizes. Overall, these findings point to common underlying

Impact of Canopy Coupling on Canopy Average Stomatal Conductance Across Seven Tree Species in Northern Wisconsin

NASA Astrophysics Data System (ADS)

Ewers, B. E.; Mackay, D. S.; Samanta, S.; Ahl, D. E.; Burrows, S. S.; Gower, S. T.

2001-12-01

Land use changes over the last century in northern Wisconsin have resulted in a heterogeneous landscape composed of the following four main forest types: northern hardwoods, northern conifer, aspen/fir, and forested wetland. Based on sap flux measurements, aspen/fir has twice the canopy transpiration of northern hardwoods. In addition, daily transpiration was only explained by daily average vapor pressure deficit across the cover types. The objective of this study was to determine if canopy average stomatal conductance could be used to explain the species effects on tree transpiration. Our first hypothesis is that across all of the species, stomatal conductance will respond to vapor pressure deficit so as to maintain a minimum leaf water potential to prevent catostrophic cavitiation. The consequence of this hypothesis is that among species and individuals there is a proportionality between high stomatal conductance and the sensitivity of stomatal conductance to vapor pressure deficit. Our second hypothesis is that species that do not follow the proportionality deviate because the canopies are decoupled from the atmosphere. To test our two hypotheses we calculated canopy average stomatal conductance from sap flux measurements using an inversion of the Penman-Monteith equation. We estimated the canopy coupling using a leaf energy budget model that requires leaf transpiration and canopy aerodynamic conductance. We optimized the parameters of the aerodynamic conductance model using a Monte Carlo technique across six parameters. We determined the optimal model for each species by selecting parameter sets that resulted in the proportionality of our first hypothesis. We then tested the optimal energy budget models of each species by comparing leaf temperature and leaf width predicted by the models to measurements of each tree species. In red pine, sugar maple, and trembling aspen trees under high canopy coupling conditions, we found the hypothesized proportionality

Phenological response of sea turtles to environmental variation across a species' northern range.

PubMed

Mazaris, Antonios D; Kallimanis, Athanasios S; Pantis, John D; Hays, Graeme C

2013-01-22

Variations in environmental parameters (e.g. temperature) that form part of global climate change have been associated with shifts in the timing of seasonal events for a broad range of organisms. Most studies evaluating such phenological shifts of individual taxa have focused on a limited number of locations, making it difficult to assess how such shifts vary regionally across a species range. Here, by using 1445 records of the date of first nesting for loggerhead sea turtles (Caretta caretta) at different breeding sites, on different continents and in different years across a broad latitudinal range (25-39° 'N), we demonstrate that the gradient of the relationship between temperature and the date of first breeding is steeper at higher latitudes, i.e. the phenological responses to temperature appear strongest at the poleward range limit. These findings support the hypothesis that biological changes in response to climate change will be most acute at the poleward range limits and are in accordance with the predictions of MacArthur's hypothesis that poleward range limit for species range is environmentally limited. Our findings imply that the poleward populations of loggerheads are more sensitive to climate variations and thus they might display the impacts of climate change sooner and more prominently.

Phenological response of sea turtles to environmental variation across a species' northern range

PubMed Central

Mazaris, Antonios D.; Kallimanis, Athanasios S.; Pantis, John D.; Hays, Graeme C.

2013-01-01

Variations in environmental parameters (e.g. temperature) that form part of global climate change have been associated with shifts in the timing of seasonal events for a broad range of organisms. Most studies evaluating such phenological shifts of individual taxa have focused on a limited number of locations, making it difficult to assess how such shifts vary regionally across a species range. Here, by using 1445 records of the date of first nesting for loggerhead sea turtles (Caretta caretta) at different breeding sites, on different continents and in different years across a broad latitudinal range (25–39° ′N), we demonstrate that the gradient of the relationship between temperature and the date of first breeding is steeper at higher latitudes, i.e. the phenological responses to temperature appear strongest at the poleward range limit. These findings support the hypothesis that biological changes in response to climate change will be most acute at the poleward range limits and are in accordance with the predictions of MacArthur's hypothesis that poleward range limit for species range is environmentally limited. Our findings imply that the poleward populations of loggerheads are more sensitive to climate variations and thus they might display the impacts of climate change sooner and more prominently. PMID:23193130

The Number, Organization, and Size of Polymorphic Membrane Protein Coding Sequences as well as the Most Conserved Pmp Protein Differ within and across Chlamydia Species.

PubMed

Van Lent, Sarah; Creasy, Heather Huot; Myers, Garry S A; Vanrompay, Daisy

2016-01-01

Variation is a central trait of the polymorphic membrane protein (Pmp) family. The number of pmp coding sequences differs between Chlamydia species, but it is unknown whether the number of pmp coding sequences is constant within a Chlamydia species. The level of conservation of the Pmp proteins has previously only been determined for Chlamydia trachomatis. As different Pmp proteins might be indispensible for the pathogenesis of different Chlamydia species, this study investigated the conservation of Pmp proteins both within and across C. trachomatis,C. pneumoniae,C. abortus, and C. psittaci. The pmp coding sequences were annotated in 16 C. trachomatis, 6 C. pneumoniae, 2 C. abortus, and 16 C. psittaci genomes. The number and organization of polymorphic membrane coding sequences differed within and across the analyzed Chlamydia species. The length of coding sequences of pmpA,pmpB, and pmpH was conserved among all analyzed genomes, while the length of pmpE/F and pmpG, and remarkably also of the subtype pmpD, differed among the analyzed genomes. PmpD, PmpA, PmpH, and PmpA were the most conserved Pmp in C. trachomatis,C. pneumoniae,C. abortus, and C. psittaci, respectively. PmpB was the most conserved Pmp across the 4 analyzed Chlamydia species. © 2016 S. Karger AG, Basel.

Patterns and determinants of wood physical and mechanical properties across major tree species in China.

PubMed

Zhu, JiangLing; Shi, Yue; Fang, LeQi; Liu, XingE; Ji, ChengJun

2015-06-01

The physical and mechanical properties of wood affect the growth and development of trees, and also act as the main criteria when determining wood usage. Our understanding on patterns and controls of wood physical and mechanical properties could provide benefits for forestry management and bases for wood application and forest tree breeding. However, current studies on wood properties mainly focus on wood density and ignore other wood physical properties. In this study, we established a comprehensive database of wood physical properties across major tree species in China. Based on this database, we explored spatial patterns and driving factors of wood properties across major tree species in China. Our results showed that (i) compared with wood density, air-dried density, tangential shrinkage coefficient and resilience provide more accuracy and higher explanation power when used as the evaluation index of wood physical properties. (ii) Among life form, climatic and edaphic variables, life form is the dominant factor shaping spatial patterns of wood physical properties, climatic factors the next, and edaphic factors have the least effects, suggesting that the effects of climatic factors on spatial variations of wood properties are indirectly induced by their effects on species distribution.

Using Netbooks to Support Mobile Learners' Investigations across Activities and Places

ERIC Educational Resources Information Center

Gaved, Mark; Collins, Trevor; Mulholland, Paul; Kerawalla, Lucinda; Jones, Ann; Scanlon, Eileen; Littleton, Karen; Blake, Canan; Petrou, Marilena; Clough, Gill; Twiner, Alison

2010-01-01

We explore how small-format laptops ("netbooks") have been used within evidence-based investigations undertaken by secondary school students, to what extent these are suitable for effectively supporting learners across different locations and contexts, and their implications for open learning. Over the course of seven trials with 300…

Questioning Questions: Elementary Teachers' Adaptations of Investigation Questions Across the Inquiry Continuum

NASA Astrophysics Data System (ADS)

Biggers, Mandy

2018-02-01

Questioning is a central practice in science classrooms. However, not every question translates into a "good" science investigation. Questions that drive science investigations can be provided by many sources including the teacher, the curriculum, or the student. The variations in the source of investigation questions were explored in this study. A dataset of 120 elementary science classroom videos and associated lesson plans from 40 elementary teachers (K-5) across 21 elementary school campuses were scored on an instrument measuring the amount of teacher-direction or student-direction of the lessons' investigation questions. Results indicated that the investigation questions were overwhelmingly teacher directed in nature, with no opportunities for students to develop their own questions for investigation. This study has implications for researchers and practitioners alike, calling attention to the teacher-directed nature of investigation questions in existing science curriculum materials, and the need for teacher training in instructional strategies to adapt their existing curriculum materials across the continuum of teacher-directed and student-directed investigation questions. Teachers need strategies for adapting the teacher-directed questions provided in their existing curriculum materials in order to allow students the opportunity to engage in this essential scientific practice.

Cancer across the tree of life: cooperation and cheating in multicellularity

PubMed Central

Aktipis, C. Athena; Boddy, Amy M.; Jansen, Gunther; Hibner, Urszula; Hochberg, Michael E.; Maley, Carlo C.; Wilkinson, Gerald S.

2015-01-01

Multicellularity is characterized by cooperation among cells for the development, maintenance and reproduction of the multicellular organism. Cancer can be viewed as cheating within this cooperative multicellular system. Complex multicellularity, and the cooperation underlying it, has evolved independently multiple times. We review the existing literature on cancer and cancer-like phenomena across life, not only focusing on complex multicellularity but also reviewing cancer-like phenomena across the tree of life more broadly. We find that cancer is characterized by a breakdown of the central features of cooperation that characterize multicellularity, including cheating in proliferation inhibition, cell death, division of labour, resource allocation and extracellular environment maintenance (which we term the five foundations of multicellularity). Cheating on division of labour, exhibited by a lack of differentiation and disorganized cell masses, has been observed in all forms of multicellularity. This suggests that deregulation of differentiation is a fundamental and universal aspect of carcinogenesis that may be underappreciated in cancer biology. Understanding cancer as a breakdown of multicellular cooperation provides novel insights into cancer hallmarks and suggests a set of assays and biomarkers that can be applied across species and characterize the fundamental requirements for generating a cancer. PMID:26056363

Change Points in the Population Trends of Aerial-Insectivorous Birds in North America: Synchronized in Time across Species and Regions.

PubMed

Smith, Adam C; Hudson, Marie-Anne R; Downes, Constance M; Francis, Charles M

2015-01-01

North American populations of aerial insectivorous birds are in steep decline. Aerial insectivores (AI) are a group of bird species that feed almost exclusively on insects in flight, and include swallows, swifts, nightjars, and flycatchers. The causes of the declines are not well understood. Indeed, it is not clear when the declines began, or whether the declines are shared across all species in the group (e.g., caused by changes in flying insect populations) or specific to each species (e.g., caused by changes in species' breeding habitat). A recent study suggested that population trends of aerial insectivores changed for the worse in the 1980s. If there was such a change point in trends of the group, understanding its timing and geographic pattern could help identify potential causes of the decline. We used a hierarchical Bayesian, penalized regression spline, change point model to estimate group-level change points in the trends of 22 species of AI, across 153 geographic strata of North America. We found evidence for group-level change points in 85% of the strata. Change points for flycatchers (FC) were distinct from those for swallows, swifts and nightjars (SSN) across North America, except in the Northeast, where all AI shared the same group-level change points. During the 1980s, there was a negative change point across most of North America, in the trends of SSN. For FC, the group-level change points were more geographically variable, and in many regions there were two: a positive change point followed by a negative change point. This group-level synchrony in AI population trends is likely evidence of a response to a common environmental factor(s) with similar effects on many species across broad spatial extents. The timing and geographic patterns of the change points that we identify here should provide a spring-board for research into the causes behind aerial insectivore declines.

Robust Translation of γ-Secretase Modulator Pharmacology across Preclinical Species and Human Subjects

PubMed Central

Toyn, Jeremy H.; Boy, Kenneth M.; Raybon, Joseph; Meredith, Jere E.; Robertson, Alan S.; Guss, Valerie; Hoque, Nina; Sweeney, Francis; Zhuo, Xiaoliang; Clarke, Wendy; Snow, Kimberly; Denton, R. Rex; Zuev, Dmitry; Thompson, Lorin A.; Morrison, John; Grace, James; Berisha, Flora; Furlong, Michael; Wang, Jun-Sheng; Lentz, Kimberly A.; Padmanabha, Ramesh; Cook, Lynda; Wei, Cong; Drexler, Dieter M.; Macor, John E.; Albright, Charlie F.; Gasior, Maciej; Olson, Richard E.; Hong, Quan; Soares, Holly D.; AbuTarif, Malaz

2016-01-01

The amyloid-β peptide (Aβ)—in particular, the 42–amino acid form, Aβ1-42—is thought to play a key role in the pathogenesis of Alzheimer’s disease (AD). Thus, several therapeutic modalities aiming to inhibit Aβ synthesis or increase the clearance of Aβ have entered clinical trials, including γ-secretase inhibitors, anti-Aβ antibodies, and amyloid-β precursor protein cleaving enzyme inhibitors. A unique class of small molecules, γ-secretase modulators (GSMs), selectively reduce Aβ1-42 production, and may also decrease Aβ1-40 while simultaneously increasing one or more shorter Aβ peptides, such as Aβ1-38 and Aβ1-37. GSMs are particularly attractive because they do not alter the total amount of Aβ peptides produced by γ-secretase activity; they spare the processing of other γ-secretase substrates, such as Notch; and they do not cause accumulation of the potentially toxic processing intermediate, β-C-terminal fragment. This report describes the translation of pharmacological activity across species for two novel GSMs, (S)-7-(4-fluorophenyl)-N2-(3-methoxy-4-(3-methyl-1H-1,2,4-triazol-1-yl)phenyl)-N4-methyl-6,7-dihydro-5H-cyclopenta[d]pyrimidine-2,4-diamine (BMS-932481) and (S,Z)-17-(4-chloro-2-fluorophenyl)-34-(3-methyl-1H-1,2,4-triazol-1-yl)-16,17-dihydro-15H-4-oxa-2,9-diaza-1(2,4)-cyclopenta[d]pyrimidina-3(1,3)-benzenacyclononaphan-6-ene (BMS-986133). These GSMs are highly potent in vitro, exhibit dose- and time-dependent activity in vivo, and have consistent levels of pharmacological effect across rats, dogs, monkeys, and human subjects. In rats, the two GSMs exhibit similar pharmacokinetics/pharmacodynamics between the brain and cerebrospinal fluid. In all species, GSM treatment decreased Aβ1-42 and Aβ1-40 levels while increasing Aβ1-38 and Aβ1-37 by a corresponding amount. Thus, the GSM mechanism and central activity translate across preclinical species and humans, thereby validating this therapeutic modality for potential utility in AD

Effect of Lipophilicity and Drug Ionization on Permeation Across Porcine Sublingual Mucosa.

PubMed

Goswami, Tarun; Li, Xiaoling; Jasti, Bhaskara R

2017-01-01

Sublingual route is one of the oldest alternative routes studied for the administration of drugs. However, the effect of physical-chemical properties on drug permeation via this route has not been systemically investigated. The objective of this study was to determine the effect of two key physicochemical properties, lipophilicity and ionization, on the transport of drugs across porcine sublingual mucosa. A series of β-blockers were used to study the effect of lipophilicity on drug permeation across the sublingual mucosa, while nimesulide (pKa 6.5) was used as a model drug to study the effect of degree of ionization on sublingual mucosa permeation of ionized and unionized species. Permeation of β-blockers increased linearly with an increase in the lipophilicity for the range of compounds studied. The permeability of nimesulide across sublingual mucosa decreased with an increase of pH. The flux of ionized and unionized forms of nimesulide was determined to delineate the contribution of ionized and unionized species to the total flux. At low pH, the apparent flux was primarily contributed by unionized species; however, when the pH is increased beyond its pKa, the primary contributor to the apparent flux, nimesulide, is ionized species. The contribution of each species to the apparent flux was shown to be determined by the thermodynamic activity of ionized or unionized species. This study identified the roles of lipophilicity and thermodynamic activity in drug permeation across the sublingual mucosa. The findings can help guide the design of sublingual drug delivery systems with optimal pH and solubility.

Effects of Mothers' Education on Parenting: An Investigation across Three Generations

ERIC Educational Resources Information Center

Duckworth, Kathryn; Sabates, Ricardo

2005-01-01

The paper investigates the relationship between mother's education and her parenting using data from the child supplement of the 1958 National Child Development Study (NCDS). By considering data across generations, our dataset allows us to estimate the size of the bias in the relationship between education and parenting from failing to account for…

Permeability of rhynchophylline across human intestinal cell in vitro

PubMed Central

Ma, Bo; Wang, Jing; Sun, Jing; Li, Ming; Xu, Huibo; Sun, Guibo; Sun, Xiaobo

2014-01-01

Rhynchophylline (Rhy) is the major component of Uncaria species, which is used in Chinese traditional medicine for the treatment of central nervous system disorders. However, its oral bioavailability has not been known. This study aims to investigate the intestinal permeability and related mechanisms of Rhy using cultured human epithelial Caco-2 cells. The cytotoxicity of Rhy on Caco-2 cells was evaluated with MTT assay. The effect of Rhy on the integrity of Caco-2 cell monolayer was assayed with transepithelial electrical resistance. The permeability of Rhy across cell monolayer was assayed by measuring Rhy quantity in received side with HPLC. The effect of Rhy on the expression of P-glycoprotein and MDR1 was detected with Western blot and flow cytometry, respectively. In the concentration of Rhy, which did not produce toxicity on cell viability and integrity of Caco-2 cell monolayer, Rhy crossed the monolayer with velocity 2.76~5.57×10^-6 cm/sec and 10.68~15.66×10^-6 cm/sec from apical to basolateral side and from basolateral to apical side, respectively. The permeability of Rhy was increased by verapamil, a P-glycoprotein inhibitor, or rhodamine123, a P-glycoprotein substrate. Rhy revealed an induction effect on P-glycoprotein expression in Caco-2 cells. These results demonstrate the low permeability of Rhy in intro, and suggest that P-glycoprotein may underlie the mechanism. PMID:24966905

Phylogenetic Structure of Tree Species across Different Life Stages from Seedlings to Canopy Trees in a Subtropical Evergreen Broad-Leaved Forest.

PubMed

Jin, Yi; Qian, Hong; Yu, Mingjian

2015-01-01

Investigating patterns of phylogenetic structure across different life stages of tree species in forests is crucial to understanding forest community assembly, and investigating forest gap influence on the phylogenetic structure of forest regeneration is necessary for understanding forest community assembly. Here, we examine the phylogenetic structure of tree species across life stages from seedlings to canopy trees, as well as forest gap influence on the phylogenetic structure of forest regeneration in a forest of the subtropical region in China. We investigate changes in phylogenetic relatedness (measured as NRI) of tree species from seedlings, saplings, treelets to canopy trees; we compare the phylogenetic turnover (measured as βNRI) between canopy trees and seedlings in forest understory with that between canopy trees and seedlings in forest gaps. We found that phylogenetic relatedness generally increases from seedlings through saplings and treelets up to canopy trees, and that phylogenetic relatedness does not differ between seedlings in forest understory and those in forest gaps, but phylogenetic turnover between canopy trees and seedlings in forest understory is lower than that between canopy trees and seedlings in forest gaps. We conclude that tree species tend to be more closely related from seedling to canopy layers, and that forest gaps alter the seedling phylogenetic turnover of the studied forest. It is likely that the increasing trend of phylogenetic clustering as tree stem size increases observed in this subtropical forest is primarily driven by abiotic filtering processes, which select a set of closely related evergreen broad-leaved tree species whose regeneration has adapted to the closed canopy environments of the subtropical forest developed under the regional monsoon climate.

Phylogenetic Structure of Tree Species across Different Life Stages from Seedlings to Canopy Trees in a Subtropical Evergreen Broad-Leaved Forest

PubMed Central

Jin, Yi; Qian, Hong; Yu, Mingjian

2015-01-01

Investigating patterns of phylogenetic structure across different life stages of tree species in forests is crucial to understanding forest community assembly, and investigating forest gap influence on the phylogenetic structure of forest regeneration is necessary for understanding forest community assembly. Here, we examine the phylogenetic structure of tree species across life stages from seedlings to canopy trees, as well as forest gap influence on the phylogenetic structure of forest regeneration in a forest of the subtropical region in China. We investigate changes in phylogenetic relatedness (measured as NRI) of tree species from seedlings, saplings, treelets to canopy trees; we compare the phylogenetic turnover (measured as βNRI) between canopy trees and seedlings in forest understory with that between canopy trees and seedlings in forest gaps. We found that phylogenetic relatedness generally increases from seedlings through saplings and treelets up to canopy trees, and that phylogenetic relatedness does not differ between seedlings in forest understory and those in forest gaps, but phylogenetic turnover between canopy trees and seedlings in forest understory is lower than that between canopy trees and seedlings in forest gaps. We conclude that tree species tend to be more closely related from seedling to canopy layers, and that forest gaps alter the seedling phylogenetic turnover of the studied forest. It is likely that the increasing trend of phylogenetic clustering as tree stem size increases observed in this subtropical forest is primarily driven by abiotic filtering processes, which select a set of closely related evergreen broad-leaved tree species whose regeneration has adapted to the closed canopy environments of the subtropical forest developed under the regional monsoon climate. PMID:26098916

Biodiversity enhances ecosystem multifunctionality across trophic levels and habitats

PubMed Central

Lefcheck, Jonathan S.; Byrnes, Jarrett E. K.; Isbell, Forest; Gamfeldt, Lars; Griffin, John N.; Eisenhauer, Nico; Hensel, Marc J. S.; Hector, Andy; Cardinale, Bradley J.; Duffy, J. Emmett

2015-01-01

The importance of biodiversity for the integrated functioning of ecosystems remains unclear because most evidence comes from analyses of biodiversity's effect on individual functions. Here we show that the effects of biodiversity on ecosystem function become more important as more functions are considered. We present the first systematic investigation of biodiversity's effect on ecosystem multifunctionality across multiple taxa, trophic levels and habitats using a comprehensive database of 94 manipulations of species richness. We show that species-rich communities maintained multiple functions at higher levels than depauperate ones. These effects were stronger for herbivore biodiversity than for plant biodiversity, and were remarkably consistent across aquatic and terrestrial habitats. Despite observed tradeoffs, the overall effect of biodiversity on multifunctionality grew stronger as more functions were considered. These results indicate that prior research has underestimated the importance of biodiversity for ecosystem functioning by focusing on individual functions and taxonomic groups. PMID:25907115

Biodiversity enhances ecosystem multifunctionality across trophic levels and habitats.

PubMed

Lefcheck, Jonathan S; Byrnes, Jarrett E K; Isbell, Forest; Gamfeldt, Lars; Griffin, John N; Eisenhauer, Nico; Hensel, Marc J S; Hector, Andy; Cardinale, Bradley J; Duffy, J Emmett

2015-04-24

The importance of biodiversity for the integrated functioning of ecosystems remains unclear because most evidence comes from analyses of biodiversity's effect on individual functions. Here we show that the effects of biodiversity on ecosystem function become more important as more functions are considered. We present the first systematic investigation of biodiversity's effect on ecosystem multifunctionality across multiple taxa, trophic levels and habitats using a comprehensive database of 94 manipulations of species richness. We show that species-rich communities maintained multiple functions at higher levels than depauperate ones. These effects were stronger for herbivore biodiversity than for plant biodiversity, and were remarkably consistent across aquatic and terrestrial habitats. Despite observed tradeoffs, the overall effect of biodiversity on multifunctionality grew stronger as more functions were considered. These results indicate that prior research has underestimated the importance of biodiversity for ecosystem functioning by focusing on individual functions and taxonomic groups.

Comparative nucleotide diversity across North American and European populus species.

PubMed

Ismail, Mohamed; Soolanayakanahally, Raju Y; Ingvarsson, Pär K; Guy, Robert D; Jansson, Stefan; Silim, Salim N; El-Kassaby, Yousry A

2012-06-01

Nucleotide polymorphisms in two North American balsam poplars (Populus trichocarpa Torr. & Gray and P. balsamifera L.; section Tacamahaca), and one Eurasian aspen (P. tremula L.; section Populus) were compared using nine loci involved in defense, stress response, photoperiodism, freezing tolerance, and housekeeping. Nucleotide diversity varied among species and was highest for P. tremula (θ(w) = 0.005, π(T) = 0.007) as compared to P. balsamifera (θ(w) = 0.004, π(T) = 0.005) or P. trichocarpa (θ(w) = 0.002, π(T) = 0.003). Across species, the defense and the stress response loci accounted for the majority of the observed level of nucleotide diversity. In general, the studied loci did not deviate from neutral expectation either at the individual locus (non-significant normalized Fay and Wu's H) or at the multi-locus level (non-significant HKA test). Using molecular clock analysis, section Tacamahaca probably shared a common ancestor with section Populus approximately 4.5 million year ago. Divergence between the two closely related balsam poplars was about 0.8 million years ago, a pattern consistent with an isolation-with-migration (IM) model. As expected, P. tremula showed a five-fold higher substitution rate (2 × 10(-8) substitution/site/year) compared to the North American species (0.4 × 10(-8) substitution/site/year), probably reflecting its complex demographic history. Linkage disequilibrium (LD) varied among species with a more rapid decay in the North American species (<400 bp) in comparison to P. tremula (≫400 bp). The similarities in nucleotide diversity pattern and LD decay of the two balsam poplar species likely reflects the recent time of their divergence.

Across the City and across Grades: Investigating Energy Flow in the Boston Harbor Ecosystem

ERIC Educational Resources Information Center

Hashimoto-Martell, Erin; Clinchot, Michael; Daniels, Haven; Bennie, Fiona

2012-01-01

In the project described in this article, urban students from across grade levels, schools, and abilities were brought together by four science teachers to better understand an ecosystem of their local environment, the Boston Harbor. This project comprises two main field experiences to the Boston Harbor: the first one to a nearby beach, and the…

Conservation of transcription factor binding events predicts gene expression across species

PubMed Central

Hemberg, Martin; Kreiman, Gabriel

2011-01-01

Recent technological advances have made it possible to determine the genome-wide binding sites of transcription factors (TFs). Comparisons across species have suggested a relatively low degree of evolutionary conservation of experimentally defined TF binding events (TFBEs). Using binding data for six different TFs in hepatocytes and embryonic stem cells from human and mouse, we demonstrate that evolutionary conservation of TFBEs within orthologous proximal promoters is closely linked to function, defined as expression of the target genes. We show that (i) there is a significantly higher degree of conservation of TFBEs when the target gene is expressed in both species; (ii) there is increased conservation of binding events for groups of TFs compared to individual TFs; and (iii) conserved TFBEs have a greater impact on the expression of their target genes than non-conserved ones. These results link conservation of structural elements (TFBEs) to conservation of function (gene expression) and suggest a higher degree of functional conservation than implied by previous studies. PMID:21622661

Herbivory increases diversification across insect clades

PubMed Central

Wiens, John J.; Lapoint, Richard T.; Whiteman, Noah K.

2015-01-01

Insects contain more than half of all living species, but the causes of their remarkable diversity remain poorly understood. Many authors have suggested that herbivory has accelerated diversification in many insect clades. However, others have questioned the role of herbivory in insect diversification. Here, we test the relationships between herbivory and insect diversification across multiple scales. We find a strong, positive relationship between herbivory and diversification among insect orders. However, herbivory explains less variation in diversification within some orders (Diptera, Hemiptera) or shows no significant relationship with diversification in others (Coleoptera, Hymenoptera, Orthoptera). Thus, we support the overall importance of herbivory for insect diversification, but also show that its impacts can vary across scales and clades. In summary, our results illuminate the causes of species richness patterns in a group containing most living species, and show the importance of ecological impacts on diversification in explaining the diversity of life. PMID:26399434

Herbivory increases diversification across insect clades.

PubMed

Wiens, John J; Lapoint, Richard T; Whiteman, Noah K

2015-09-24

Insects contain more than half of all living species, but the causes of their remarkable diversity remain poorly understood. Many authors have suggested that herbivory has accelerated diversification in many insect clades. However, others have questioned the role of herbivory in insect diversification. Here, we test the relationships between herbivory and insect diversification across multiple scales. We find a strong, positive relationship between herbivory and diversification among insect orders. However, herbivory explains less variation in diversification within some orders (Diptera, Hemiptera) or shows no significant relationship with diversification in others (Coleoptera, Hymenoptera, Orthoptera). Thus, we support the overall importance of herbivory for insect diversification, but also show that its impacts can vary across scales and clades. In summary, our results illuminate the causes of species richness patterns in a group containing most living species, and show the importance of ecological impacts on diversification in explaining the diversity of life.

Stillbirth rates across three ape species in accredited American zoos.

PubMed

Saiyed, Sana T; Liubicich, Rebecca C; Fidino, Mason; Ross, Stephen R

2018-05-14

Stillbirths, or births of infants that died in the womb, represent a failure of the materno-feto-placental unit to maintain a suitable fetal environment. Typical studies of nonhuman primate (NHP) stillbirth patterns are primarily descriptive and focus on macaques (genus Macaca). Thus, less is known about other NHP species and rarer still are studies that examine possible biological factors that influence stillbirth rates across taxa. To examine possible contributors to stillbirths in great apes, we analyzed 36 years (1980-2016) of historical data documenting births of zoo-housed chimpanzees (Pan troglodytes, N = 391), western lowland gorillas (Gorilla gorilla gorilla, N = 491), and orangutans (Pongo spp, N = 307) in accredited zoological parks in the United States. The average number of births for each of the 446 mothers was 2.7, resulting in a total of 1,189 births with 143 stillbirths (12%). Stillbirths represented 12% of chimpanzee births, 13% of gorilla births, and 10% of orangutan births. We used generalized linear mixed-effects models to assess possible relationships between stillbirth likelihood and mother origin (wild- versus captive-born), age, and genus. Across taxa, older mothers were more likely to have a stillbirth (p = 0.004). While these results are likely influenced by both biological and management-related factors (e.g., selective captive breeding), they may be useful to population managers in evaluating pregnancy risks for great apes. Captive settings and archival studbook data such as these may provide a unique opportunity to further explore this topic. © 2018 Wiley Periodicals, Inc.

Change Points in the Population Trends of Aerial-Insectivorous Birds in North America: Synchronized in Time across Species and Regions

PubMed Central

Smith, Adam C.; Hudson, Marie-Anne R.; Downes, Constance M.; Francis, Charles M.

2015-01-01

North American populations of aerial insectivorous birds are in steep decline. Aerial insectivores (AI) are a group of bird species that feed almost exclusively on insects in flight, and include swallows, swifts, nightjars, and flycatchers. The causes of the declines are not well understood. Indeed, it is not clear when the declines began, or whether the declines are shared across all species in the group (e.g., caused by changes in flying insect populations) or specific to each species (e.g., caused by changes in species’ breeding habitat). A recent study suggested that population trends of aerial insectivores changed for the worse in the 1980s. If there was such a change point in trends of the group, understanding its timing and geographic pattern could help identify potential causes of the decline. We used a hierarchical Bayesian, penalized regression spline, change point model to estimate group-level change points in the trends of 22 species of AI, across 153 geographic strata of North America. We found evidence for group-level change points in 85% of the strata. Change points for flycatchers (FC) were distinct from those for swallows, swifts and nightjars (SSN) across North America, except in the Northeast, where all AI shared the same group-level change points. During the 1980s, there was a negative change point across most of North America, in the trends of SSN. For FC, the group-level change points were more geographically variable, and in many regions there were two: a positive change point followed by a negative change point. This group-level synchrony in AI population trends is likely evidence of a response to a common environmental factor(s) with similar effects on many species across broad spatial extents. The timing and geographic patterns of the change points that we identify here should provide a spring-board for research into the causes behind aerial insectivore declines. PMID:26147572

In silico site-directed mutagenesis informs species-specific predictions of chemical susceptibility derived from the Sequence Alignment to Predict Across Species Susceptibility (SeqAPASS) tool

EPA Science Inventory

The Sequence Alignment to Predict Across Species Susceptibility (SeqAPASS) tool was developed to address needs for rapid, cost effective methods of species extrapolation of chemical susceptibility. Specifically, the SeqAPASS tool compares the primary sequence (Level 1), functiona...

Invasive Congeners Differ in Successional Impacts across Space and Time

PubMed Central

David, Aaron S.; Zarnetske, Phoebe L.; Hacker, Sally D.; Ruggiero, Peter; Biel, Reuben G.; Seabloom, Eric W.

2015-01-01

Invasive species can alter the succession of ecological communities because they are often adapted to the disturbed conditions that initiate succession. The extent to which this occurs may depend on how widely they are distributed across environmental gradients and how long they persist over the course of succession. We focus on plant communities of the USA Pacific Northwest coastal dunes, where disturbance is characterized by changes in sediment supply, and the plant community is dominated by two introduced grasses – the long-established Ammophila arenaria and the currently invading A. breviligulata. Previous studies showed that A. breviligulata has replaced A. arenaria and reduced community diversity. We hypothesize that this is largely due to A. breviligulata occupying a wider distribution across spatial environmental gradients and persisting in later-successional habitat than A. arenaria. We used multi-decadal chronosequences and a resurvey study spanning 2 decades to characterize distributions of both species across space and time, and investigated how these distributions were associated with changes in the plant community. The invading A. breviligulata persisted longer and occupied a wider spatial distribution across the dune, and this corresponded with a reduction in plant species richness and native cover. Furthermore, backdunes previously dominated by A. arenaria switched to being dominated by A. breviligulata, forest, or developed land over a 23-yr period. Ammophila breviligulata likely invades by displacing A. arenaria, and reduces plant diversity by maintaining its dominance into later successional backdunes. Our results suggest distinct roles in succession, with A. arenaria playing a more classically facilitative role and A. breviligulata a more inhibitory role. Differential abilities of closely-related invasive species to persist through time and occupy heterogeneous environments allows for distinct impacts on communities during succession. PMID

QQS orphan gene regulates carbon and nitrogen partitioning across species via NF-YC interactions

PubMed Central

Li, Ling; Zheng, Wenguang; Zhu, Yanbing; Ye, Huaxun; Tang, Buyun; Arendsee, Zebulun W.; Jones, Dallas; Li, Ruoran; Ortiz, Diego; Zhao, Xuefeng; Du, Chuanlong; Nettleton, Dan; Scott, M. Paul; Salas-Fernandez, Maria G.; Yin, Yanhai; Wurtele, Eve Syrkin

2015-01-01

The allocation of carbon and nitrogen resources to the synthesis of plant proteins, carbohydrates, and lipids is complex and under the control of many genes; much remains to be understood about this process. QQS (Qua-Quine Starch; At3g30720), an orphan gene unique to Arabidopsis thaliana, regulates metabolic processes affecting carbon and nitrogen partitioning among proteins and carbohydrates, modulating leaf and seed composition in Arabidopsis and soybean. Here the universality of QQS function in modulating carbon and nitrogen allocation is exemplified by a series of transgenic experiments. We show that ectopic expression of QQS increases soybean protein independent of the genetic background and original protein content of the cultivar. Furthermore, transgenic QQS expression increases the protein content of maize, a C4 species (a species that uses 4-carbon photosynthesis), and rice, a protein-poor agronomic crop, both highly divergent from Arabidopsis. We determine that QQS protein binds to the transcriptional regulator AtNF-YC4 (Arabidopsis nuclear factor Y, subunit C4). Overexpression of AtNF-YC4 in Arabidopsis mimics the QQS-overexpression phenotype, increasing protein and decreasing starch levels. NF-YC, a component of the NF-Y complex, is conserved across eukaryotes. The NF-YC4 homologs of soybean, rice, and maize also bind to QQS, which provides an explanation of how QQS can act in species where it does not occur endogenously. These findings are, to our knowledge, the first insight into the mechanism of action of QQS in modulating carbon and nitrogen allocation across species. They have major implications for the emergence and function of orphan genes, and identify a nontransgenic strategy for modulating protein levels in crop species, a trait of great agronomic significance. PMID:26554020

QQS orphan gene regulates carbon and nitrogen partitioning across species via NF-YC interactions.

PubMed

Li, Ling; Zheng, Wenguang; Zhu, Yanbing; Ye, Huaxun; Tang, Buyun; Arendsee, Zebulun W; Jones, Dallas; Li, Ruoran; Ortiz, Diego; Zhao, Xuefeng; Du, Chuanlong; Nettleton, Dan; Scott, M Paul; Salas-Fernandez, Maria G; Yin, Yanhai; Wurtele, Eve Syrkin

2015-11-24

The allocation of carbon and nitrogen resources to the synthesis of plant proteins, carbohydrates, and lipids is complex and under the control of many genes; much remains to be understood about this process. QQS (Qua-Quine Starch; At3g30720), an orphan gene unique to Arabidopsis thaliana, regulates metabolic processes affecting carbon and nitrogen partitioning among proteins and carbohydrates, modulating leaf and seed composition in Arabidopsis and soybean. Here the universality of QQS function in modulating carbon and nitrogen allocation is exemplified by a series of transgenic experiments. We show that ectopic expression of QQS increases soybean protein independent of the genetic background and original protein content of the cultivar. Furthermore, transgenic QQS expression increases the protein content of maize, a C4 species (a species that uses 4-carbon photosynthesis), and rice, a protein-poor agronomic crop, both highly divergent from Arabidopsis. We determine that QQS protein binds to the transcriptional regulator AtNF-YC4 (Arabidopsis nuclear factor Y, subunit C4). Overexpression of AtNF-YC4 in Arabidopsis mimics the QQS-overexpression phenotype, increasing protein and decreasing starch levels. NF-YC, a component of the NF-Y complex, is conserved across eukaryotes. The NF-YC4 homologs of soybean, rice, and maize also bind to QQS, which provides an explanation of how QQS can act in species where it does not occur endogenously. These findings are, to our knowledge, the first insight into the mechanism of action of QQS in modulating carbon and nitrogen allocation across species. They have major implications for the emergence and function of orphan genes, and identify a nontransgenic strategy for modulating protein levels in crop species, a trait of great agronomic significance.

Vulnerabilities of ecosystems across U.S. National Parks to biome shifts, wildfire changes, and invasive species due to climate change

NASA Astrophysics Data System (ADS)

Gonzalez, P.; Eigenbrod, F.; Early, R.; Wang, F.; Notaro, M.; Williams, J. W.

2016-12-01

U.S. national parks conserve globally unique biodiversity. Yet, historical impacts of climate change and future vulnerabilities threaten species and ecosystems across this system of protected areas. Spatial analyses of historical climate and downscaled future climate projections show climate trends across the system. Spatial analyses of vegetation and wildfire (using a dynamic global vegetation model), habitat fragmentation (using remote sensing-derived land cover), and invasive species introduction and establishment show patterns of future vulnerability across the 50 U.S. states and 412 U.S. national parks. Results reveal high historical and projected temperature increases and precipitation changes, projected increases of wildfire across western U.S. national parks, high vulnerability to biome shifts and habitat fragmentation of up to one-third of National Park System area, and high vulnerability to invasive species of one-ninth of National Park System area. Ecosystems in the Sierra Nevada, Cascade Range, desert Southwest, and Laurentian Great Lakes are highly vulnerable to upslope and poleward shifts of the North America sequence of biomes: temperate shrubland - temperate broadleaf forest - temperate mixed forest - temperate conifer forest - subalpine and boreal forest - alpine and tundra. These areas include Grand Canyon, Mount Rainier, and Yosemite National Parks. The southwestern U.S., including Grand Canyon and Sequoia National Parks, is vulnerable to increases in wildfire. The eastern and midwestern U.S., including Great Smokey Mountains and Voyageurs National Parks, are highly vulnerable to invasive species. These results identify vulnerable areas and potential refugia to help prioritize areas for future natural resource management actions and biodiversity conservation in U.S. national parks.

Species Identity Supersedes the Dilution Effect Concerning Hantavirus Prevalence at Sites across Texas and México.

PubMed

Milholland, Matthew T; Castro-Arellano, Iván; Arellano, Elizabeth; Nava-García, Elizabeth; Rangel-Altamirano, Guadalupe; Gonzalez-Cozatl, Francisco X; Suzán, Gerardo; Schountz, Tony; González-Padrón, Shiara; Vigueras, Ana; Rubio, André V; Maikis, Troy J; Westrich, Bradford J; Martinez, Jose A; Esteve-Gassent, Maria D; Torres, Madison; Rodriguez-Ruiz, Erick R; Hahn, Dittmar; Lacher, Thomas E

2017-12-15

Recent models suggest a relationship exists between community diversity and pathogen prevalence, the proportion of individuals in a population that are infected by a pathogen, with most inferences tied to assemblage structure. Two contrasting outcomes of this relationship have been proposed: the "dilution effect" and the "amplification effect." Small mammal assemblage structure in disturbed habitats often differs from assemblages in sylvan environments, and hantavirus prevalence is often negatively correlated with habitats containing high species diversity via dilution effect dynamics. As species richness increases, prevalence of infection often is decreased. However, anthropogenic changes to sylvan landscapes have been shown to decrease species richness and/or increase phylogenetic similarities within assemblages. Between January 2011 and January 2016, we captured and tested 2406 individual small mammals for hantavirus antibodies at 20 sites across Texas and México and compared differences in hantavirus seroprevalence, species composition, and assemblage structure between sylvan and disturbed habitats. We found 313 small mammals positive for antibodies against hantaviruses, evincing an overall prevalence of 9.7% across all sites. In total, 40 species of small mammals were identified comprising 2 taxonomic orders (Rodentia and Eulipotyphla). By sampling both habitat types concurrently, we were able to make real-world inferences into the efficacy of dilution effect theory in terms of hantavirus ecology. Our hypothesis predicting greater species richness higher in sylvan habitats compared to disturbed areas was not supported, suggesting the characteristics of assemblage structure do not adhere to current conceptions of species richness negatively influencing prevalence via a dilution effect.

Logging impacts on avian species richness and composition differ across latitudes and foraging and breeding habitat preferences.

PubMed

LaManna, Joseph A; Martin, Thomas E

2017-08-01

Understanding the causes underlying changes in species diversity is a fundamental pursuit of ecology. Animal species richness and composition often change with decreased forest structural complexity associated with logging. Yet differences in latitude and forest type may strongly influence how species diversity responds to logging. We performed a meta-analysis of logging effects on local species richness and composition of birds across the world and assessed responses by different guilds (nesting strata, foraging strata, diet, and body size). This approach allowed identification of species attributes that might underlie responses to this anthropogenic disturbance. We only examined studies that allowed forests to regrow naturally following logging, and accounted for logging intensity, spatial extent, successional regrowth after logging, and the change in species composition expected due to random assembly from regional species pools. Selective logging in the tropics and clearcut logging in temperate latitudes caused loss of species from nearly all forest strata (ground to canopy), leading to substantial declines in species richness (up to 27% of species). Few species were lost or gained following any intensity of logging in lower-latitude temperate forests, but the relative abundances of these species changed substantially. Selective logging at higher-temperate latitudes generally replaced late-successional specialists with early-successional specialists, leading to no net changes in species richness but large changes in species composition. Removing less basal area during logging mitigated the loss of avian species from all forests and, in some cases, increased diversity in temperate forests. This meta-analysis provides insights into the important role of habitat specialization in determining differential responses of animal communities to logging across tropical and temperate latitudes. © 2016 Cambridge Philosophical Society.

Ontogeny of prosocial behavior across diverse societies.

PubMed

House, Bailey R; Silk, Joan B; Henrich, Joseph; Barrett, H Clark; Scelza, Brooke A; Boyette, Adam H; Hewlett, Barry S; McElreath, Richard; Laurence, Stephen

2013-09-03

Humans are an exceptionally cooperative species, but there is substantial variation in the extent of cooperation across societies. Understanding the sources of this variability may provide insights about the forces that sustain cooperation. We examined the ontogeny of prosocial behavior by studying 326 children 3-14 y of age and 120 adults from six societies (age distributions varied across societies). These six societies span a wide range of extant human variation in culture, geography, and subsistence strategies, including foragers, herders, horticulturalists, and urban dwellers across the Americas, Oceania, and Africa. When delivering benefits to others was personally costly, rates of prosocial behavior dropped across all six societies as children approached middle childhood and then rates of prosociality diverged as children tracked toward the behavior of adults in their own societies. When prosocial acts did not require personal sacrifice, prosocial responses increased steadily as children matured with little variation in behavior across societies. Our results are consistent with theories emphasizing the importance of acquired cultural norms in shaping costly forms of cooperation and creating cross-cultural diversity.

Ontogeny of prosocial behavior across diverse societies

PubMed Central

House, Bailey R.; Silk, Joan B.; Henrich, Joseph; Barrett, H. Clark; Scelza, Brooke A.; Boyette, Adam H.; Hewlett, Barry S.; McElreath, Richard; Laurence, Stephen

2013-01-01

Humans are an exceptionally cooperative species, but there is substantial variation in the extent of cooperation across societies. Understanding the sources of this variability may provide insights about the forces that sustain cooperation. We examined the ontogeny of prosocial behavior by studying 326 children 3–14 y of age and 120 adults from six societies (age distributions varied across societies). These six societies span a wide range of extant human variation in culture, geography, and subsistence strategies, including foragers, herders, horticulturalists, and urban dwellers across the Americas, Oceania, and Africa. When delivering benefits to others was personally costly, rates of prosocial behavior dropped across all six societies as children approached middle childhood and then rates of prosociality diverged as children tracked toward the behavior of adults in their own societies. When prosocial acts did not require personal sacrifice, prosocial responses increased steadily as children matured with little variation in behavior across societies. Our results are consistent with theories emphasizing the importance of acquired cultural norms in shaping costly forms of cooperation and creating cross-cultural diversity. PMID:23959869

Quantifying effects of biodiversity on ecosystem functioning across times and places†

PubMed Central

Isbell, Forest; Cowles, Jane; Dee, Laura E.; Loreau, Michel; Reich, Peter B.; Gonzalez, Andrew; Hector, Andy; Schmid, Bernhard

2018-01-01

Biodiversity loss decreases ecosystem functioning at the local scales at which species interact, but it remains unclear how biodiversity loss affects ecosystem functioning at the larger scales of space and time that are most relevant to biodiversity conservation and policy. Theory predicts that additional insurance effects of biodiversity on ecosystem functioning could emerge across time and space if species respond asynchronously to environmental variation and if species become increasingly dominant when and where they are most productive. Even if only a few dominant species maintain ecosystem functioning within a particular time and place, ecosystem functioning may be enhanced by many different species across many times and places (β-diversity). Here, we develop and apply a new approach to estimate these previously unquantified insurance effects of biodiversity on ecosystem functioning that arise due to species turnover across times and places. In a long-term (18-year) grassland plant diversity experiment, we find that total insurance effects are positive in sign and substantial in magnitude, amounting to 19% of the net biodiversity effect, mostly due to temporal insurance effects. Species loss can therefore reduce ecosystem functioning both locally and by eliminating species that would otherwise enhance ecosystem functioning across temporally fluctuating and spatially heterogeneous environments. PMID:29493062

Quantifying effects of biodiversity on ecosystem functioning across times and places.

PubMed

Isbell, Forest; Cowles, Jane; Dee, Laura E; Loreau, Michel; Reich, Peter B; Gonzalez, Andrew; Hector, Andy; Schmid, Bernhard

2018-06-01

Biodiversity loss decreases ecosystem functioning at the local scales at which species interact, but it remains unclear how biodiversity loss affects ecosystem functioning at the larger scales of space and time that are most relevant to biodiversity conservation and policy. Theory predicts that additional insurance effects of biodiversity on ecosystem functioning could emerge across time and space if species respond asynchronously to environmental variation and if species become increasingly dominant when and where they are most productive. Even if only a few dominant species maintain ecosystem functioning within a particular time and place, ecosystem functioning may be enhanced by many different species across many times and places (β-diversity). Here, we develop and apply a new approach to estimate these previously unquantified insurance effects of biodiversity on ecosystem functioning that arise due to species turnover across times and places. In a long-term (18-year) grassland plant diversity experiment, we find that total insurance effects are positive in sign and substantial in magnitude, amounting to 19% of the net biodiversity effect, mostly due to temporal insurance effects. Species loss can therefore reduce ecosystem functioning both locally and by eliminating species that would otherwise enhance ecosystem functioning across temporally fluctuating and spatially heterogeneous environments. © 2018 John Wiley & Sons Ltd/CNRS.

Molecular identification of python species: development and validation of a novel assay for forensic investigations.

PubMed

Ciavaglia, Sherryn A; Tobe, Shanan S; Donnellan, Stephen C; Henry, Julianne M; Linacre, Adrian M T

2015-05-01

Python snake species are often encountered in illegal activities and the question of species identity can be pertinent to such criminal investigations. Morphological identification of species of pythons can be confounded by many issues and molecular examination by DNA analysis can provide an alternative and objective means of identification. Our paper reports on the development and validation of a PCR primer pair that amplifies a segment of the mitochondrial cytochrome b gene that has been suggested previously as a good candidate locus for differentiating python species. We used this DNA region to perform species identification of pythons, even when the template DNA was of poor quality, as might be the case with forensic evidentiary items. Validation tests are presented to demonstrate the characteristics of the assay. Tests involved the cross-species amplification of this marker in non-target species, minimum amount of DNA template required, effects of degradation on product amplification and a blind trial to simulate a casework scenario that provided 100% correct identity. Our results demonstrate that this assay performs reliably and robustly on pythons and can be applied directly to forensic investigations where the presence of a species of python is in question. Copyright © 2014 Elsevier Ireland Ltd. All rights reserved.

Climate drives shifts in grass reproductive phenology across the western USA

USGS Publications Warehouse

Munson, Seth M.; Long, A. Lexine

2016-01-01

The capacity of grass species to alter their reproductive timing across space and through time can indicate their ability to cope with environmental variability and help predict their future performance under climate change.We determined the long-term (1895–2013) relationship between flowering times of grass species and climate in space and time using herbarium records across ecoregions of the western USA.There was widespread concordance of C3 grasses accelerating flowering time and general delays for C4 grasses with increasing mean annual temperature, with the largest changes for annuals and individuals occurring in more northerly, wetter ecoregions. Flowering time was delayed for most grass species with increasing mean annual precipitation across space, while phenology–precipitation relationships through time were more mixed.Our results suggest that the phenology of most grass species has the capacity to respond to increases in temperature and altered precipitation expected with climate change, but weak relationships for some species in time suggest that climate tracking via migration or adaptation may be required. Divergence in phenological responses among grass functional types, species, and ecoregions suggests that climate change will have unequal effects across the western USA.

The sunk cost effect across species: A review of persistence in a course of action due to prior investment.

PubMed

Magalhães, Paula; Geoffrey White, K

2016-05-01

The sunk cost effect is the bias or tendency to persist in a course of action due to prior investments of effort, money or time. At the time of the only review on the sunk cost effect across species (Arkes & Ayton, 1999), research with nonhuman animals had been ecological in its nature, and the findings about the effect of past investments on current choice were inconclusive. However, in the last decade a new line of experimental laboratory-based research has emerged with the promise of revolutionizing the way we approach the study of the sunk cost effect in nonhumans. In the present review we challenge Arkes and Ayton's conclusion that the sunk cost effect is exclusive to humans, and describe evidence for the sunk cost effect in nonhuman animals. By doing so, we also challenge the current explanations for the sunk cost effect in humans, as they are not applicable to nonhumans. We argue that a unified theory is called for, because different independent variables, in particular, investment amount, have the same influence on the sunk cost effect across species. Finally, we suggest possible psychological mechanisms shared across different species, contrast and depreciation, that could explain the sunk cost effect. © 2016 Society for the Experimental Analysis of Behavior.

Nuclear DNA microsatellites reveal genetic variation but a lack of phylogeographical structure in an endangered species, Fraxinus mandshurica, across North-east China.

PubMed

Hu, Li-Jiang; Uchiyama, Kentaro; Shen, Hai-Long; Saito, Yoko; Tsuda, Yoshiaki; Ide, Yuji

2008-08-01

The widely accepted paradigm that the modern genetic structure of plant species in the northern hemisphere has been largely determined by recolonization from refugia after the last glacial maximum fails to explain the presence of cold-tolerant species at intermediate latitudes. Another generally accepted paradigm is that mountain ridges act as important barriers causing genetic isolation of species, but this too has been challenged in recent studies. The aims of the work reported here were to determine the genetic diversity and distribution patterns of extant natural populations of an endangered cool temperate species, Faxinus mandshurica, and to examine whether these two paradigms are appropriate when applied to this species over a wide geographical scale. 1435 adult individuals were sampled from 30 natural populations across the main and central range of the species, covering major mountain ranges across North-east China (NEC). Genetic variation was estimated based on nine polymorphic nuclear microsatellite loci. Phylogeographical analyses were employed using various approaches, including Bayesian clustering, spatial analysis of molecular variance, Monmonier's algorithm, neighbor-joining trees, principal co-ordinate analysis and isolation by distance. Genetic diversity within populations was relatively high, and no significant recent bottlenecks were detected in any of the populations. A significant negative correlation between intra-population genetic diversity and latitude was identified. In contrast, genetic differentiation among all the populations examined was extremely low and no clear geographic genetic structure was identified, with the exception of one distinct population. The modern genetic structure in this species can be explained by extensive gene flow, an absence of mountains acting as barriers, and the presence of a wide refuge across NEC rather than multiple small refugia. Intra-population genetic variation along latitudes is probably associated

OrthoVenn: a web server for genome wide comparison and annotation of orthologous clusters across multiple species

USDA-ARS?s Scientific Manuscript database

Genome wide analysis of orthologous clusters is an important component of comparative genomics studies. Identifying the overlap among orthologous clusters can enable us to elucidate the function and evolution of proteins across multiple species. Here, we report a web platform named OrthoVenn that i...

Habitat type and dispersal mode underlie the capacity for plant migration across an intermittent seaway.

PubMed

Worth, J R P; Holland, B R; Beeton, N J; Schönfeld, B; Rossetto, M; Vaillancourt, R E; Jordan, G J

2017-10-17

Investigating species distributions across geographic barriers is a commonly utilized method in biogeography to help understand the functional traits that allow plants to disperse successfully. Here the biogeographic pattern analysis approach is extended by using chloroplast DNA whole-genome 'mining' to examine the functional traits that have impacted the dispersal of widespread temperate forest species across an intermittent seaway, the 200 km wide Bass Strait of south-eastern Australia. Multiple, co-distributed species of both dry and wet forests were sampled from five regions on either side of the Strait to obtain insights into past dispersal of these biomes via seed. Using a next-generation sequencing-based pool-seq method, the sharing of single nucleotide polymorphisms (SNPs) was estimated between all five regions in the chloroplast genome. A total of 3335 SNPs were detected in 20 species. SNP sharing patterns between regions provided evidence for significant seed-mediated gene flow across the study area, including across Bass Strait. A higher proportion of shared SNPs in dry forest species, especially those dispersed by birds, compared with wet forest species suggests that dry forest species have undergone greater seed-mediated gene flow across the study region during past climatic oscillations and sea level changes associated with the interglacial/glacial cycles. This finding is consistent with a greater propensity for long-distance dispersal for species of open habitats and proxy evidence that expansive areas of dry vegetation occurred during times of exposure of Bass Strait during glacials. Overall, this study provides novel genetic evidence that habitat type and its interaction with dispersal traits are major influences on dispersal of plants. © The Author 2017. Published by Oxford University Press on behalf of the Annals of Botany Company. All rights reserved. For Permissions, please email: journals.permissions@oup.com

Branch xylem density variations across the Amazon Basin

NASA Astrophysics Data System (ADS)

Patiño, S.; Lloyd, J.; Paiva, R.; Baker, T. R.; Quesada, C. A.; Mercado, L. M.; Schmerler, J.; Schwarz, M.; Santos, A. J. B.; Aguilar, A.; Czimczik, C. I.; Gallo, J.; Horna, V.; Hoyos, E. J.; Jimenez, E. M.; Palomino, W.; Peacock, J.; Peña-Cruz, A.; Sarmiento, C.; Sota, A.; Turriago, J. D.; Villanueva, B.; Vitzthum, P.; Alvarez, E.; Arroyo, L.; Baraloto, C.; Bonal, D.; Chave, J.; Costa, A. C. L.; Herrera, R.; Higuchi, N.; Killeen, T.; Leal, E.; Luizão, F.; Meir, P.; Monteagudo, A.; Neil, D.; Núñez-Vargas, P.; Peñuela, M. C.; Pitman, N.; Priante Filho, N.; Prieto, A.; Panfil, S. N.; Rudas, A.; Salomão, R.; Silva, N.; Silveira, M.; Soares Dealmeida, S.; Torres-Lezama, A.; Vásquez-Martínez, R.; Vieira, I.; Malhi, Y.; Phillips, O. L.

2009-04-01

Xylem density is a physical property of wood that varies between individuals, species and environments. It reflects the physiological strategies of trees that lead to growth, survival and reproduction. Measurements of branch xylem density, ρx, were made for 1653 trees representing 598 species, sampled from 87 sites across the Amazon basin. Measured values ranged from 218 kg m-3 for a Cordia sagotii (Boraginaceae) from Mountagne de Tortue, French Guiana to 1130 kg m-3 for an Aiouea sp. (Lauraceae) from Caxiuana, Central Pará, Brazil. Analysis of variance showed significant differences in average ρx across regions and sampled plots as well as significant differences between families, genera and species. A partitioning of the total variance in the dataset showed that species identity (family, genera and species) accounted for 33% with environment (geographic location and plot) accounting for an additional 26%; the remaining "residual" variance accounted for 41% of the total variance. Variations in plot means, were, however, not only accountable by differences in species composition because xylem density of the most widely distributed species in our dataset varied systematically from plot to plot. Thus, as well as having a genetic component, branch xylem density is a plastic trait that, for any given species, varies according to where the tree is growing in a predictable manner. Within the analysed taxa, exceptions to this general rule seem to be pioneer species belonging for example to the Urticaceae whose branch xylem density is more constrained than most species sampled in this study. These patterns of variation of branch xylem density across Amazonia suggest a large functional diversity amongst Amazonian trees which is not well understood.

Controlled comparison of species- and community-level models across novel climates and communities

PubMed Central

Maguire, Kaitlin C.; Blois, Jessica L.; Fitzpatrick, Matthew C.; Williams, John W.; Ferrier, Simon; Lorenz, David J.

2016-01-01

Species distribution models (SDMs) assume species exist in isolation and do not influence one another's distributions, thus potentially limiting their ability to predict biodiversity patterns. Community-level models (CLMs) capitalize on species co-occurrences to fit shared environmental responses of species and communities, and therefore may result in more robust and transferable models. Here, we conduct a controlled comparison of five paired SDMs and CLMs across changing climates, using palaeoclimatic simulations and fossil-pollen records of eastern North America for the past 21 000 years. Both SDMs and CLMs performed poorly when projected to time periods that are temporally distant and climatically dissimilar from those in which they were fit; however, CLMs generally outperformed SDMs in these instances, especially when models were fit with sparse calibration datasets. Additionally, CLMs did not over-fit training data, unlike SDMs. The expected emergence of novel climates presents a major forecasting challenge for all models, but CLMs may better rise to this challenge by borrowing information from co-occurring taxa. PMID:26962143

MDMA effects consistent across laboratories

PubMed Central

Kirkpatrick, Matthew G.; Baggott, Matthew J.; Mendelson, John E.; Galloway, Gantt P.; Liechti, Matthias E.; Hysek, Cédric M.; de Wit, Harriet

2014-01-01

Rationale Several laboratories have conducted placebo-controlled drug challenge studies with MDMA, providing a unique source of data to examine the reliability of the acute effects of the drug across subject samples and settings. We examined the subjective and physiological responses to the drug across three different laboratories, and investigated the influence of prior MDMA use. Methods Overall, 220 healthy volunteers with varying levels of previous MDMA experience participated in laboratory-based studies in which they received placebo or oral MDMA (1.5 mg/kg or 125 mg fixed dose) under double blind conditions. Cardiovascular and subjective effects were assessed before and repeatedly after drug administration. The studies were conducted independently by investigators in Basel, San Francisco and Chicago. Results Despite methodological differences between the studies and differences in the subjects' drug use histories, MDMA produced very similar cardiovascular and subjective effects across the sites. The participants' prior use of MDMA was inversely related to feeling `Any Drug Effect' only at sites testing more experienced users. Conclusions These data indicate that the pharmacological effects of MDMA are robust and highly reproducible across settings. There was also modest evidence for tolerance to the effects of MDMA in regular users. PMID:24633447

Phenotype diffusion and one health: A proposed framework for investigating the plurality of obesity epidemics across many species.

PubMed

Voss, J D; Goodson, M S; Leon, J C

2018-05-01

We propose the idea of "phenotype diffusion," which is a rapid convergence of an observed trait in some human and animal populations. The words phenotype and diffusion both imply observations independent of mechanism as phenotypes are observed traits with multiple possible genetic mechanisms and diffusion is an observed state of being widely distributed. Recognizing shared changes in phenotype in multiple species does not by itself reveal a particular mechanism such as a shared exposure, shared adaptive need, particular stochastic process or a transmission pathway. Instead, identifying phenotype diffusion suggests the mechanism should be explored to help illuminate the ways human and animal health are connected and new opportunities for optimizing these links. Using the plurality of obesity epidemics across multiple species as a prototype for shared changes in phenotype, the goal of this review was to explore eco-evolutionary theories that could inform further investigation. First, evolutionary changes described by hologenome evolution, pawnobe evolution, transposable element (TE) thrust and the drifty gene hypothesis will be discussed within the context of the selection asymmetries among human and animal populations. Secondly, the ecology of common source exposures (bovine milk, xenohormesis and "obesogens"), niche evolution and the hygiene hypothesis will be summarized. Finally, we synthesize these considerations. For example, many agricultural breeds have been aggressively selected for weight gain, microbiota (e.g., adenovirus 36, toxoplasmosis) associated with (or infecting) these breeds cause experimental weight gain in other animals, and these same microbes are associated with human obesity. We propose applications of phenotype diffusion could include zoonotic biosurveillance, biocontainment, antibiotic stewardship and environmental priorities. The One Health field is focused on the connections between the health of humans, animals and the environment, and so

Morphological variation of Pinus flexilis (Pinaceae), a bird-dispersed pine, across a range of elevations

Treesearch

Anna Schoettle; S. G. Rochelle

2000-01-01

Limber pine (Pinus flexilis James) grows across a wider range of elevations than any other tree species in the central Rockies, from ;1600 m at Pawnee Buttes to .3300 m at Rollins Pass. In this study we investigated two possible explanations for limber pine’s success across a broad range of elevations: (1) the sites on which it is found, although separated by...

Dual use research: investigation across multiple science disciplines.

PubMed

Oltmann, Shannon

2015-04-01

Most recent studies of dual use research have focused on the life sciences, although some researchers have suggested that dual use research occurs across many disciplines. This research is an initial investigation into the prevalence of dual use research in other scientific disciplines by surveying senior editors of scientific journals, drawn from Journal Citation Reports. The survey was emailed to 7,500 journal editors with a response rate of 10.1 %. Approximately 4.8 % of life science editors reported they had to consider whether to publish dual use research and 38.9 % said they decided to not publish the research in question. In disciplines other than the life sciences, 7.2 % of editors from other science disciplines reported that they had to consider whether to publish dual use research, and 48.4 % declined to publish it. The survey investigated relationships between dual use and the journal's source of funding and place of publication, but no relationships were found. Further research is needed to better understand the occurrence of dual use research in other science disciplines.

Pleistocene divergence across a mountain range and the influence of selection on mitogenome evolution in threatened Australian freshwater cod species.

PubMed

Harrisson, K; Pavlova, A; Gan, H M; Lee, Y P; Austin, C M; Sunnucks, P

2016-06-01

Climatic differences across a taxon's range may be associated with specific bioenergetic demands and may result in genetics-based metabolic adaptation, particularly in aquatic ectothermic organisms that rely on heat exchange with the environment to regulate key physiological processes. Extending down the east coast of Australia, the Great Dividing Range (GDR) has a strong influence on climate and the evolutionary history of freshwater fish species. Despite the GDR acting as a strong contemporary barrier to fish movement, many species, and species with shared ancestries, are found on both sides of the GDR, indicative of historical dispersal events. We sequenced complete mitogenomes from the four extant species of the freshwater cod genus Maccullochella, two of which occur on the semi-arid, inland side of the GDR, and two on the mesic coastal side. We constructed a dated phylogeny and explored the relative influences of purifying and positive selection in the evolution of mitogenome divergence among species. Results supported mid- to late-Pleistocene divergence of Maccullochella across the GDR (220-710 thousand years ago), bringing forward previously reported dates. Against a background of pervasive purifying selection, we detected potentially functionally relevant fixed amino acid differences across the GDR. Although many amino acid differences between inland and coastal species may have become fixed under relaxed purifying selection in coastal environments rather than positive selection, there was evidence of episodic positive selection acting on specific codons in the Mary River coastal lineage, which has consistently experienced the warmest and least extreme climate in the genus.

Pleistocene divergence across a mountain range and the influence of selection on mitogenome evolution in threatened Australian freshwater cod species

PubMed Central

Harrisson, K; Pavlova, A; Gan, H M; Lee, Y P; Austin, C M; Sunnucks, P

2016-01-01

Climatic differences across a taxon's range may be associated with specific bioenergetic demands and may result in genetics-based metabolic adaptation, particularly in aquatic ectothermic organisms that rely on heat exchange with the environment to regulate key physiological processes. Extending down the east coast of Australia, the Great Dividing Range (GDR) has a strong influence on climate and the evolutionary history of freshwater fish species. Despite the GDR acting as a strong contemporary barrier to fish movement, many species, and species with shared ancestries, are found on both sides of the GDR, indicative of historical dispersal events. We sequenced complete mitogenomes from the four extant species of the freshwater cod genus Maccullochella, two of which occur on the semi-arid, inland side of the GDR, and two on the mesic coastal side. We constructed a dated phylogeny and explored the relative influences of purifying and positive selection in the evolution of mitogenome divergence among species. Results supported mid- to late-Pleistocene divergence of Maccullochella across the GDR (220–710 thousand years ago), bringing forward previously reported dates. Against a background of pervasive purifying selection, we detected potentially functionally relevant fixed amino acid differences across the GDR. Although many amino acid differences between inland and coastal species may have become fixed under relaxed purifying selection in coastal environments rather than positive selection, there was evidence of episodic positive selection acting on specific codons in the Mary River coastal lineage, which has consistently experienced the warmest and least extreme climate in the genus. PMID:26883183

Root traits predict decomposition across a landscape-scale grazing experiment

PubMed Central

Smith, Stuart W; Woodin, Sarah J; Pakeman, Robin J; Johnson, David; van der Wal, René

2014-01-01

Root litter is the dominant soil carbon and nutrient input in many ecosystems, yet few studies have considered how root decomposition is regulated at the landscape scale and how this is mediated by land-use management practices. Large herbivores can potentially influence below-ground decomposition through changes in soil microclimate (temperature and moisture) and changes in plant species composition (root traits). To investigate such herbivore-induced changes, we quantified annual root decomposition of upland grassland species in situ across a landscape-scale livestock grazing experiment, in a common-garden experiment and in laboratory microcosms evaluating the influence of key root traits on decomposition. Livestock grazing increased soil temperatures, but this did not affect root decomposition. Grazing had no effect on soil moisture, but wetter soils retarded root decomposition. Species-specific decomposition rates were similar across all grazing treatments, and species differences were maintained in the common-garden experiment, suggesting an overriding importance of litter type. Supporting this, in microcosms, roots with lower specific root area (m2 g−1) or those with higher phosphorus concentrations decomposed faster. Our results suggest that large herbivores alter below-ground carbon and nitrogen dynamics more through their effects on plant species composition and associated root traits than through effects on the soil microclimate. PMID:24841886

Ecosystem engineering effects on species diversity across ecosystems: a meta-analysis.

PubMed

Romero, Gustavo Q; Gonçalves-Souza, Thiago; Vieira, Camila; Koricheva, Julia

2015-08-01

Ecosystem engineering is increasingly recognized as a relevant ecological driver of diversity and community composition. Although engineering impacts on the biota can vary from negative to positive, and from trivial to enormous, patterns and causes of variation in the magnitude of engineering effects across ecosystems and engineer types remain largely unknown. To elucidate the above patterns, we conducted a meta-analysis of 122 studies which explored effects of animal ecosystem engineers on species richness of other organisms in the community. The analysis revealed that the overall effect of ecosystem engineers on diversity is positive and corresponds to a 25% increase in species richness, indicating that ecosystem engineering is a facilitative process globally. Engineering effects were stronger in the tropics than at higher latitudes, likely because new or modified habitats provided by engineers in the tropics may help minimize competition and predation pressures on resident species. Within aquatic environments, engineering impacts were stronger in marine ecosystems (rocky shores) than in streams. In terrestrial ecosystems, engineers displayed stronger positive effects in arid environments (e.g. deserts). Ecosystem engineers that create new habitats or microhabitats had stronger effects than those that modify habitats or cause bioturbation. Invertebrate engineers and those with lower engineering persistence (<1 year) affected species richness more than vertebrate engineers which persisted for >1 year. Invertebrate species richness was particularly responsive to engineering impacts. This study is the first attempt to build an integrative framework of engineering effects on species diversity; it highlights the importance of considering latitude, habitat, engineering functional group, taxon and persistence of their effects in future theoretical and empirical studies. © 2014 The Authors. Biological Reviews © 2014 Cambridge Philosophical Society.

Ecological filtering and plant traits variation across quarry geomorphological surfaces: implication for restoration.

PubMed

Gilardelli, Federica; Sgorbati, Sergio; Armiraglio, Stefano; Citterio, Sandra; Gentili, Rodolfo

2015-05-01

Revegetation patterns after quarry abandonment have been widely studied from several ecological points of view, but a trait-based approach is still lacking. The aim of this study was to characterise the plant species assemblages and the associated functional traits filtered on different geomorphological surfaces in abandoned limestone quarry areas: artificial cliffs, embankments, and platforms. We then verified if species with certain traits were better able to overcome the dispersal and environmental filters necessary for establishment. To this aim, we analyzed 113 vegetation plots and collected data on 25 morphological, ecological, and dispersal traits to detect species adaptaions across these man-made environments. As a case study, we investigated the extraction basin of Botticino (Lombardy, Italy), the second largest in Italy. The results obtained by SIMPER and CCA analyses showed that rockiness, stoniness, slope, elevation, and time of surfaces are the main filters that varied across quarries and affected plant assemblages at the macro-scale level. Across the three geomorphological surfaces (meso-scale) of quarries, more specific abiotic filters selecting species were found. In turn, traits differentiation according to the three main geomorphological surfaces of quarry emphasized that further filters acting at the micro-scale imply differences in dispersal mechanisms and resource availability. This work highlighted the utility to study species assemblages and environmental filters to address quarry restoration according to the type of geomorphological surface. The investigation of some traits (chorological form, life forms, seed dispersal,s and plant height) can furnish some interesting indications for practice individuating further abiotic filters acting at the micro-scale.

Influence of elevation and site productivity on conifer distributions across Alaskan temperate rainforests

Treesearch

John P. Caouette; Ashley E. Steel; Paul E. Hennon; Pat G. Cunningham; Cathy A. Pohl; Barbara A. Schrader

2016-01-01

We investigated the influence of landscape factors on the distribution and life stage stability of coastal tree species near the northern limit of their ranges. Using data from 1465 forest inventory plots, we estimated probability of occurrence and basal area of six common conifer species across three broad latitudinal regions of coastal Alaska. By also comparing...

Integrating the pace-of-life syndrome across species, sexes and individuals: covariation of life history and personality under pesticide exposure.

PubMed

Debecker, Sara; Sanmartín-Villar, Iago; de Guinea-Luengo, Miguel; Cordero-Rivera, Adolfo; Stoks, Robby

2016-05-01

The pace-of-life syndrome (POLS) hypothesis integrates covariation of life-history traits along a fast-slow continuum and covariation of behavioural traits along a proactive-reactive personality continuum. Few studies have investigated these predicted life-history/personality associations among species and between sexes. Furthermore, whether and how contaminants interfere with POLS patterns remains unexplored. We tested for covariation patterns in life history and in behaviour, and for life-history/personality covariation among species, among individuals within species and between sexes. Moreover, we investigated whether pesticide exposure affects covariation between life history and behaviour and whether species and sexes with a faster POLS strategy have a higher sensitivity to pesticides. We reared larvae of four species of Ischnura damselflies in a common garden experiment with an insecticide treatment (chlorpyrifos absent/present) in the final instar. We measured four life-history traits (larval growth rate during the pesticide treatment, larval development time, adult mass and life span) and two behavioural traits (larval feeding activity and boldness, each before and after the pesticide treatment). At the individual level, life-history traits and behavioural traits aligned along a fast-slow and a proactive-reactive continuum, respectively. Species-specific differences in life history, with fast-lived species having a faster larval growth and development, a lower mass at emergence and a shorter life span, suggested that time constraints in the larval stage were predictably driving life-history evolution both in the larval stage and across metamorphosis in the adult stage. Across species, females were consistently more slow-lived than males, reflecting that a large body size and a long life span are generally more important for females. In contrast to the POLS hypothesis, there was only little evidence for the expected positive coupling between life

Plant response to nutrient availability across variable bedrock geologies

USGS Publications Warehouse

Castle, S.C.; Neff, J.C.

2009-01-01

We investigated the role of rock-derived mineral nutrient availability on the nutrient dynamics of overlying forest communities (Populus tremuloides and Picea engelmanni-Abies lasiocarpa v. arizonica) across three parent materials (andesite, limestone, and sandstone) in the southern Rocky Mountains of Colorado. Broad geochemical differences were observed between bedrock materials; however, bulk soil chemistries were remarkably similar between the three different sites. In contrast, soil nutrient pools were considerably different, particularly for P, Ca, and Mg concentrations. Despite variations in nutrient stocks and nutrient availability in soils, we observed relatively inflexible foliar concentrations and foliar stoichiometries for both deciduous and coniferous species. Foliar nutrient resorption (P and K) in the deciduous species followed patterns of nutrient content across substrate types, with higher resorption corresponding to lower bedrock concentrations. Work presented here indicates a complex plant response to available soil nutrients, wherein plant nutrient use compensates for variations in supply gradients and results in the maintenance of a narrow range in foliar stoichiometry. ?? 2008 Springer Science+Business Media, LLC.

OBLIQUE VIEW FROM ACROSS THE WEST, ACROSS THE STREET ...

Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

OBLIQUE VIEW FROM ACROSS THE WEST, ACROSS THE STREET - Camp H.M. Smith and Navy Public Works Center Manana Title VII (Capehart) Housing, U-Shaped Two-Bedroom Single-Family Type 6, Birch Circle, Elm Drive, Elm Circle, and Date Drive, Pearl City, Honolulu County, HI

Testing the Effectiveness of Environmental Variables to Explain European Terrestrial Vertebrate Species Richness across Biogeographical Scales

PubMed Central

Mouchet, Maud; Levers, Christian; Zupan, Laure; Kuemmerle, Tobias; Plutzar, Christoph; Erb, Karlheinz; Lavorel, Sandra; Thuiller, Wilfried; Haberl, Helmut

2015-01-01

We compared the effectiveness of environmental variables, and in particular of land-use indicators, to explain species richness patterns across taxonomic groups and biogeographical scales (i.e. overall pan-Europe and ecoregions within pan-Europe). Using boosted regression trees that handle non-linear relationships, we compared the relative influence (as a measure of effectiveness) of environmental variables related to climate, landscape (or habitat heterogeneity), land-use intensity or energy availability to explain European vertebrate species richness (birds, amphibians, and mammals) at the continental and ecoregion scales. We found that dominant land cover and actual evapotranspiration that relate to energy availability were the main correlates of vertebrate species richness over Europe. At the ecoregion scale, we identified four distinct groups of ecoregions where species richness was essentially associated to (i) seasonality of temperature, (ii) actual evapotranspiration and/or mean annual temperature, (iii) seasonality of precipitation, actual evapotranspiration and land cover) and (iv) and an even combination of the environmental variables. This typology of ecoregions remained valid for total vertebrate richness and the three vertebrate groups taken separately. Despite the overwhelming influence of land cover and actual evapotranspiration to explain vertebrate species richness patterns at European scale, the ranking of the main correlates of species richness varied between regions. Interestingly, landscape and land-use indicators did not stand out at the continental scale but their influence greatly increased in southern ecoregions, revealing the long-lasting human footprint on land-use–land-cover changes. Our study provides one of the first multi-scale descriptions of the variability in the ranking of correlates across several taxa. PMID:26161981

Multilayer networks reveal the spatial structure of seed-dispersal interactions across the Great Rift landscapes.

PubMed

Timóteo, Sérgio; Correia, Marta; Rodríguez-Echeverría, Susana; Freitas, Helena; Heleno, Ruben

2018-01-10

Species interaction networks are traditionally explored as discrete entities with well-defined spatial borders, an oversimplification likely impairing their applicability. Using a multilayer network approach, explicitly accounting for inter-habitat connectivity, we investigate the spatial structure of seed-dispersal networks across the Gorongosa National Park, Mozambique. We show that the overall seed-dispersal network is composed by spatially explicit communities of dispersers spanning across habitats, functionally linking the landscape mosaic. Inter-habitat connectivity determines spatial structure, which cannot be accurately described with standard monolayer approaches either splitting or merging habitats. Multilayer modularity cannot be predicted by null models randomizing either interactions within each habitat or those linking habitats; however, as habitat connectivity increases, random processes become more important for overall structure. The importance of dispersers for the overall network structure is captured by multilayer versatility but not by standard metrics. Highly versatile species disperse many plant species across multiple habitats, being critical to landscape functional cohesion.

Projected tree species redistribution under climate change: Implications for ecosystem vulnerability across protected areas in the eastern United States

Treesearch

Scott G. Zolkos; Patrick Jantz; Tina Cormier; Louis R. Iverson; Daniel W. McKenney; Scott J. Goetz

2015-01-01

The degree to which tree species will shift in response to climate change is uncertain yet critical to understand for assessing ecosystem vulnerability. We analyze results from recent studies that model potential tree species habitat across the eastern United States during the coming century. Our goals were to quantify and spatially analyze habitat projections and...

Logging impacts on avian species richness and composition differ across latitudes relative to foraging and breeding habitat preferences

USGS Publications Warehouse

LaManna, Joseph A.; Martin, Thomas E.

2017-01-01

Understanding the causes underlying changes in species diversity is a fundamental pursuit of ecology. Animal species richness and composition often change with decreased forest structural complexity associated with logging. Yet differences in latitude and forest type may strongly influence how species diversity responds to logging. We performed a meta-analysis of logging effects on local species richness and composition of birds across the world and assessed responses by different guilds (nesting strata, foraging strata, diet, and body size). This approach allowed identification of species attributes that might underlie responses to this anthropogenic disturbance. We only examined studies that allowed forests to regrow naturally following logging, and accounted for logging intensity, spatial extent, successional regrowth after logging, and the change in species composition expected due to random assembly from regional species pools. Selective logging in the tropics and clearcut logging in temperate latitudes caused loss of species from nearly all forest strata (ground to canopy), leading to substantial declines in species richness (up to 27% of species). Few species were lost or gained following any intensity of logging in lower-latitude temperate forests, but the relative abundances of these species changed substantially. Selective logging at higher-temperate latitudes generally replaced late-successional specialists with early-successional specialists, leading to no net changes in species richness but large changes in species composition. Removing less basal area during logging mitigated the loss of avian species from all forests and, in some cases, increased diversity in temperate forests. This meta-analysis provides insights into the important role of habitat specialization in determining differential responses of animal communities to logging across tropical and temperate latitudes.

Expression Atlas: gene and protein expression across multiple studies and organisms

PubMed Central

Tang, Y Amy; Bazant, Wojciech; Burke, Melissa; Fuentes, Alfonso Muñoz-Pomer; George, Nancy; Koskinen, Satu; Mohammed, Suhaib; Geniza, Matthew; Preece, Justin; Jarnuczak, Andrew F; Huber, Wolfgang; Stegle, Oliver; Brazma, Alvis; Petryszak, Robert

2018-01-01

Abstract Expression Atlas (http://www.ebi.ac.uk/gxa) is an added value database that provides information about gene and protein expression in different species and contexts, such as tissue, developmental stage, disease or cell type. The available public and controlled access data sets from different sources are curated and re-analysed using standardized, open source pipelines and made available for queries, download and visualization. As of August 2017, Expression Atlas holds data from 3,126 studies across 33 different species, including 731 from plants. Data from large-scale RNA sequencing studies including Blueprint, PCAWG, ENCODE, GTEx and HipSci can be visualized next to each other. In Expression Atlas, users can query genes or gene-sets of interest and explore their expression across or within species, tissues, developmental stages in a constitutive or differential context, representing the effects of diseases, conditions or experimental interventions. All processed data matrices are available for direct download in tab-delimited format or as R-data. In addition to the web interface, data sets can now be searched and downloaded through the Expression Atlas R package. Novel features and visualizations include the on-the-fly analysis of gene set overlaps and the option to view gene co-expression in experiments investigating constitutive gene expression across tissues or other conditions. PMID:29165655

Tree species diversity affects decomposition through modified micro-environmental conditions across European forests.

PubMed

Joly, François-Xavier; Milcu, Alexandru; Scherer-Lorenzen, Michael; Jean, Loreline-Katia; Bussotti, Filippo; Dawud, Seid Muhie; Müller, Sandra; Pollastrini, Martina; Raulund-Rasmussen, Karsten; Vesterdal, Lars; Hättenschwiler, Stephan

2017-05-01

Different tree species influence litter decomposition directly through species-specific litter traits, and indirectly through distinct modifications of the local decomposition environment. Whether these indirect effects on decomposition are influenced by tree species diversity is presently not clear. We addressed this question by studying the decomposition of two common substrates, cellulose paper and wood sticks, in a total of 209 forest stands of varying tree species diversity across six major forest types at the scale of Europe. Tree species richness showed a weak but positive correlation with the decomposition of cellulose but not with that of wood. Surprisingly, macroclimate had only a minor effect on cellulose decomposition and no effect on wood decomposition despite the wide range in climatic conditions among sites from Mediterranean to boreal forests. Instead, forest canopy density and stand-specific litter traits affected the decomposition of both substrates, with a particularly clear negative effect of the proportion of evergreen tree litter. Our study suggests that species richness and composition of tree canopies modify decomposition indirectly through changes in microenvironmental conditions. These canopy-induced differences in the local decomposition environment control decomposition to a greater extent than continental-scale differences in macroclimatic conditions. © 2017 The Authors. New Phytologist © 2017 New Phytologist Trust.

Biodiversity and body size are linked across metazoans

PubMed Central

McClain, Craig R.; Boyer, Alison G.

2009-01-01

Body size variation across the Metazoa is immense, encompassing 17 orders of magnitude in biovolume. Factors driving this extreme diversification in size and the consequences of size variation for biological processes remain poorly resolved. Species diversity is invoked as both a predictor and a result of size variation, and theory predicts a strong correlation between the two. However, evidence has been presented both supporting and contradicting such a relationship. Here, we use a new comprehensive dataset for maximum and minimum body sizes across all metazoan phyla to show that species diversity is strongly correlated with minimum size, maximum size and consequently intra-phylum variation. Similar patterns are also observed within birds and mammals. The observations point to several fundamental linkages between species diversification and body size variation through the evolution of animal life. PMID:19324730

Herbarium specimens show patterns of fruiting phenology in native and invasive plant species across New England.

PubMed

Gallinat, Amanda S; Russo, Luca; Melaas, Eli K; Willis, Charles G; Primack, Richard B

2018-01-01

Patterns of fruiting phenology in temperate ecosystems are poorly understood, despite the ecological importance of fruiting for animal nutrition and seed dispersal. Herbarium specimens represent an under-utilized resource for investigating geographical and climatic factors affecting fruiting times within species, patterns in fruiting times among species, and differences between native and non-native invasive species. We examined over 15,000 herbarium specimens, collected and housed across New England, and found 3159 specimens with ripe fruits, collected from 1849-2013. We examined patterns in fruiting phenology among 37 native and 18 invasive woody plant species common to New England. We compared fruiting dates between native and invasive species, and analyzed how fruiting phenology varies with temperature, space, and time. Spring temperature and year explained a small but significant amount of the variation in fruiting dates. Accounting for the moderate phylogenetic signal in fruiting phenology, invasive species fruited 26 days later on average than native species, with significantly greater standard deviations. Herbarium specimens can be used to detect patterns in fruiting times among species. However, the amount of intraspecific variation in fruiting times explained by temporal, geographic, and climatic predictors is small, due to a combination of low temporal resolution of fruiting specimens and the protracted nature of fruiting. Later fruiting times in invasive species, combined with delays in autumn bird migrations in New England, may increase the likelihood that migratory birds will consume and disperse invasive seeds in New England later into the year. © 2018 Botanical Society of America.

Modularity, pollination systems, and interaction turnover in plant-pollinator networks across space.

PubMed

Carstensen, Daniel W; Sabatino, Malena; Morellato, Leonor Patricia C

2016-05-01

Mutualistic interaction networks have been shown to be structurally conserved over space and time while pairwise interactions show high variability. In such networks, modularity is the division of species into compartments, or modules, where species within modules share more interactions with each other than they do with species from other modules. Such a modular structure is common in mutualistic networks and several evolutionary and ecological mechanisms have been proposed as underlying drivers. One prominent explanation is the existence of pollination syndromes where flowers tend to attract certain pollinators as determined by a set of traits. We investigate the modularity of seven community level plant-pollinator networks sampled in rupestrian grasslands, or campos rupestres, in SE Brazil. Defining pollination systems as corresponding groups of flower syndromes and pollinator functional groups, we test the two hypotheses that (1) interacting species from the same pollination system are more often assigned to the same module than interacting species from different pollination systems and; that (2) interactions between species from the same pollination system are more consistent across space than interactions between species from different pollination systems. Specifically we ask (1) whether networks are consistently modular across space; (2) whether interactions among species of the same pollination system occur more often inside modules, compared to interactions among species of different pollination systems, and finally; (3) whether the spatial variation in interaction identity, i.e., spatial interaction rewiring, is affected by trait complementarity among species as indicated by pollination systems. We confirm that networks are consistently modular across space and that interactions within pollination systems principally occur inside modules. Despite a strong tendency, we did not find a significant effect of pollination systems on the spatial consistency of

SERCA directs cell migration and branching across species and germ layers

PubMed Central

Lansdale, Nick; Navarro, Sonia; Truong, Thai V.; Bower, Dan J.; Featherstone, Neil C.; Connell, Marilyn G.; Al Alam, Denise; Frey, Mark R.; Trinh, Le A.; Fernandez, G. Esteban; Warburton, David; Fraser, Scott E.; Bennett, Daimark; Jesudason, Edwin C.

2017-01-01

ABSTRACT Branching morphogenesis underlies organogenesis in vertebrates and invertebrates, yet is incompletely understood. Here, we show that the sarco-endoplasmic reticulum Ca2+ reuptake pump (SERCA) directs budding across germ layers and species. Clonal knockdown demonstrated a cell-autonomous role for SERCA in Drosophila air sac budding. Live imaging of Drosophila tracheogenesis revealed elevated Ca2+ levels in migratory tip cells as they form branches. SERCA blockade abolished this Ca2+ differential, aborting both cell migration and new branching. Activating protein kinase C (PKC) rescued Ca2+ in tip cells and restored cell migration and branching. Likewise, inhibiting SERCA abolished mammalian epithelial budding, PKC activation rescued budding, while morphogens did not. Mesoderm (zebrafish angiogenesis) and ectoderm (Drosophila nervous system) behaved similarly, suggesting a conserved requirement for cell-autonomous Ca2+ signaling, established by SERCA, in iterative budding. PMID:28821490

Impact of prenatal stress on offspring glucocorticoid levels: A phylogenetic meta-analysis across 14 vertebrate species.

PubMed

Thayer, Zaneta M; Wilson, Meredith A; Kim, Andrew W; Jaeggi, Adrian V

2018-03-21

Prenatal exposure to maternal stress is commonly associated with variation in Hypothalamic Pituitary Adrenal (HPA)-axis functioning in offspring. However, the strength or consistency of this response has never been empirically evaluated across vertebrate species. Here we meta-analyzed 114 results from 39 studies across 14 vertebrate species using Bayesian phylogenetic mixed-effects models. We found a positive overall effect of prenatal stress on offspring glucocorticoids (d' = 0.43) though the 95% Highest Posterior Density Interval overlapped with 0 (-0.16-0.95). Meta-regressions of potential moderators highlighted that phylogeny and life history variables predicted relatively little variation in effect size. Experimental studies (d' = 0.64) produced stronger effects than observational ones (d' = -0.01), while prenatal stress affected glucocorticoid recovery following offspring stress exposure more strongly (d' = 0.75) than baseline levels (d' = 0.48) or glucocorticoid peak response (d' = 0.36). These findings are consistent with the argument that HPA-axis sensitivity to prenatal stress is evolutionarily ancient and occurs regardless of a species' overall life history strategy. These effects may therefore be especially important for mediating intra-specific life-history variation. In addition, these findings suggest that animal models of prenatal HPA-axis programming may be appropriate for studying similar effects in humans.

MethBank 3.0: a database of DNA methylomes across a variety of species.

PubMed

Li, Rujiao; Liang, Fang; Li, Mengwei; Zou, Dong; Sun, Shixiang; Zhao, Yongbing; Zhao, Wenming; Bao, Yiming; Xiao, Jingfa; Zhang, Zhang

2018-01-04

MethBank (http://bigd.big.ac.cn/methbank) is a database that integrates high-quality DNA methylomes across a variety of species and provides an interactive browser for visualization of methylation data. Here, we present an updated implementation of MethBank (version 3.0) by incorporating more DNA methylomes from multiple species and equipping with more enhanced functionalities for data annotation and more friendly web interfaces for data presentation, search and visualization. MethBank 3.0 features large-scale integration of high-quality methylomes, involving 34 consensus reference methylomes derived from a large number of human samples, 336 single-base resolution methylomes from different developmental stages and/or tissues of five plants, and 18 single-base resolution methylomes from gametes and early embryos at multiple stages of two animals. Additionally, it is enhanced by improving the functionalities for data annotation, which accordingly enables systematic identification of methylation sites closely associated with age, sites with constant methylation levels across different ages, differentially methylated promoters, age-specific differentially methylated cytosines/regions, and methylated CpG islands. Moreover, MethBank provides tools to estimate human methylation age online and to identify differentially methylated promoters, respectively. Taken together, MethBank is upgraded with significant improvements and advances over the previous version, which is of great help for deciphering DNA methylation regulatory mechanisms for epigenetic studies. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

Perceptual grouping across eccentricity.

PubMed

Tannazzo, Teresa; Kurylo, Daniel D; Bukhari, Farhan

2014-10-01

Across the visual field, progressive differences exist in neural processing as well as perceptual abilities. Expansion of stimulus scale across eccentricity compensates for some basic visual capacities, but not for high-order functions. It was hypothesized that as with many higher-order functions, perceptual grouping ability should decline across eccentricity. To test this prediction, psychophysical measurements of grouping were made across eccentricity. Participants indicated the dominant grouping of dot grids in which grouping was based upon luminance, motion, orientation, or proximity. Across trials, the organization of stimuli was systematically decreased until perceived grouping became ambiguous. For all stimulus features, grouping ability remained relatively stable until 40°, beyond which thresholds significantly elevated. The pattern of change across eccentricity varied across stimulus feature, in which stimulus scale, dot size, or stimulus size interacted with eccentricity effects. These results demonstrate that perceptual grouping of such stimuli is not reliant upon foveal viewing, and suggest that selection of dominant grouping patterns from ambiguous displays operates similarly across much of the visual field. Copyright © 2014 Elsevier Ltd. All rights reserved.

Phylogeography of the antilopine wallaroo (Macropus antilopinus) across tropical northern Australia.

PubMed

Wadley, Jessica J; Fordham, Damien A; Thomson, Vicki A; Ritchie, Euan G; Austin, Jeremy J

2016-11-01

. antilopinus revealed an unexpectedly complex evolutionary history involving multiple sympatric and parapatric mtDNA clades across northern Australia. These phylogeographic patterns highlight the importance of investigating genetic variation across distributions of species and integrating this information into biodiversity conservation.

Conservation conflicts across Africa.

PubMed

Balmford, A; Moore, J L; Brooks, T; Burgess, N; Hansen, L A; Williams, P; Rahbek, C

2001-03-30

There is increasing evidence that areas of outstanding conservation importance may coincide with dense human settlement or impact. We tested the generality of these findings using 1 degree-resolution data for sub-Saharan Africa. We find that human population density is positively correlated with species richness of birds, mammals, snakes, and amphibians. This association holds for widespread, narrowly endemic, and threatened species and looks set to persist in the face of foreseeable population growth. Our results contradict earlier expectations of low conflict based on the idea that species richness decreases and human impact increases with primary productivity. We find that across Africa, both variables instead exhibit unimodal relationships with productivity. Modifying priority-setting to take account of human density shows that, at this scale, conflicts between conservation and development are not easily avoided, because many densely inhabited grid cells contain species found nowhere else.

Species traits and environmental conditions govern the relationship between biodiversity effects across trophic levels

USGS Publications Warehouse

Spooner, D.E.; Vaughn, C.C.; Galbraith, H.S.

2012-01-01

Changing environments can have divergent effects on biodiversity-ecosystem function relationships at alternating trophic levels. Freshwater mussels fertilize stream foodwebs through nutrient excretion, and mussel species-specific excretion rates depend on environmental conditions. We asked how differences in mussel diversity in varying environments influence the dynamics between primary producers and consumers. We conducted field experiments manipulating mussel richness under summer (low flow, high temperature) and fall (moderate flow and temperature) conditions, measured nutrient limitation, algal biomass and grazing chironomid abundance, and analyzed the data with non-transgressive overyielding and tripartite biodiversity partitioning analyses. Algal biomass and chironomid abundance were best explained by trait-independent complementarity among mussel species, but the relationship between biodiversity effects across trophic levels (algae and grazers) depended on seasonal differences in mussel species' trait expression (nutrient excretion and activity level). Both species identity and overall diversity effects were related to the magnitude of nutrient limitation. Our results demonstrate that biodiversity of a resource-provisioning (nutrients and habitat) group of species influences foodweb dynamics and that understanding species traits and environmental context are important for interpreting biodiversity experiments. ?? 2011 Springer-Verlag.

Riding across the selection landscape: fitness consequences of annual variation in reproductive characteristics

PubMed Central

Tremblay, Raymond L.; Ackerman, James D.; Pérez, Maria-Eglée

2010-01-01

Evolutionary models estimating phenotypic selection in character size usually assume that the character is invariant across reproductive bouts. We show that variation in the size of reproductive traits may be large over multiple events and can influence fitness in organisms where these traits are produced anew each season. With data from populations of two orchid species, Caladenia valida and Tolumnia variegata, we used Bayesian statistics to investigate the effect on the distribution in fitness of individuals when the fitness landscape is not flat and when characters vary across reproductive bouts. Inconsistency in character size across reproductive periods within an individual increases the uncertainty of mean fitness and, consequently, the uncertainty in individual fitness. The trajectory of selection is likely to be muddled as a consequence of variation in morphology of individuals across reproductive bouts. The frequency and amplitude of such changes will certainly affect the dynamics between selection and genetic drift. PMID:20047875

Divergence with gene flow across a speciation continuum of Heliconius butterflies.

PubMed

Supple, Megan A; Papa, Riccardo; Hines, Heather M; McMillan, W Owen; Counterman, Brian A

2015-09-24

A key to understanding the origins of species is determining the evolutionary processes that drive the patterns of genomic divergence during speciation. New genomic technologies enable the study of high-resolution genomic patterns of divergence across natural speciation continua, where taxa pairs with different levels of reproductive isolation can be used as proxies for different stages of speciation. Empirical studies of these speciation continua can provide valuable insights into how genomes diverge during speciation. We examine variation across a handful of genomic regions in parapatric and allopatric populations of Heliconius butterflies with varying levels of reproductive isolation. Genome sequences were mapped to 2.2-Mb of the H. erato genome, including 1-Mb across the red color pattern locus and multiple regions unlinked to color pattern variation. Phylogenetic analyses reveal a speciation continuum of pairs of hybridizing races and incipient species in the Heliconius erato clade. Comparisons of hybridizing pairs of divergently colored races and incipient species reveal that genomic divergence increases with ecological and reproductive isolation, not only across the locus responsible for adaptive variation in red wing coloration, but also at genomic regions unlinked to color pattern. We observe high levels of divergence between the incipient species H. erato and H. himera, suggesting that divergence may accumulate early in the speciation process. Comparisons of genomic divergence between the incipient species and allopatric races suggest that limited gene flow cannot account for the observed high levels of divergence between the incipient species. Our results provide a reconstruction of the speciation continuum across the H. erato clade and provide insights into the processes that drive genomic divergence during speciation, establishing the H. erato clade as a powerful framework for the study of speciation.

Inference of biogeographical ancestry across central regions of Eurasia.

PubMed

Bulbul, O; Filoglu, G; Zorlu, T; Altuncul, H; Freire-Aradas, A; Söchtig, J; Ruiz, Y; Klintschar, M; Triki-Fendri, S; Rebai, A; Phillips, C; Lareu, M V; Carracedo, Á; Schneider, P M

2016-01-01

The inference of biogeographical ancestry (BGA) can provide useful information for forensic investigators when there are no suspects to be compared with DNA collected at the crime scene or when no DNA database matches exist. Although public databases are increasing in size and population scope, there is a lack of information regarding genetic variation in Eurasian populations, especially in central regions such as the Middle East. Inhabitants of these regions show a high degree of genetic admixture, characterized by an allele frequency cline running from NW Europe to East Asia. Although a proper differentiation has been established between the cline extremes of western Europe and South Asia, populations geographically located in between, i.e, Middle East and Mediterranean populations, require more detailed study in order to characterize their genetic background as well as to further understand their demographic histories. To initiate these studies, three ancestry informative SNP (AI-SNP) multiplex panels: the SNPforID 34-plex, Eurasiaplex and a novel 33-plex assay were used to describe the ancestry patterns of a total of 24 populations ranging across the longitudinal axis from NW Europe to East Asia. Different ancestry inference approaches, including STRUCTURE, PCA, DAPC and Snipper Bayes analysis, were applied to determine relationships among populations. The structure results show differentiation between continental groups and a NW to SE allele frequency cline running across Eurasian populations. This study adds useful population data that could be used as reference genotypes for future ancestry investigations in forensic cases. The 33-plex assay also includes pigmentation predictive SNPs, but this study primarily focused on Eurasian population differentiation using 33-plex and its combination with the other two AI-SNP sets.

Genomic and Resistance Gene Homolog Diversity of the Dominant Tallgrass Prairie Species across the U.S. Great Plains Precipitation Gradient

PubMed Central

Rouse, Matthew N.; Saleh, Amgad A.; Seck, Amadou; Keeler, Kathleen H.; Travers, Steven E.; Hulbert, Scot H.; Garrett, Karen A.

2011-01-01

Background Environmental variables such as moisture availability are often important in determining species prevalence and intraspecific diversity. The population genetic structure of dominant plant species in response to a cline of these variables has rarely been addressed. We evaluated the spatial genetic structure and diversity of Andropogon gerardii populations across the U.S. Great Plains precipitation gradient, ranging from approximately 48 cm/year to 105 cm/year. Methodology/Principal Findings Genomic diversity was evaluated with AFLP markers and diversity of a disease resistance gene homolog was evaluated by PCR-amplification and digestion with restriction enzymes. We determined the degree of spatial genetic structure using Mantel tests. Genomic and resistance gene homolog diversity were evaluated across prairies using Shannon's index and by averaging haplotype dissimilarity. Trends in diversity across prairies were determined using linear regression of diversity on average precipitation for each prairie. We identified significant spatial genetic structure, with genomic similarity decreasing as a function of distance between samples. However, our data indicated that genome-wide diversity did not vary consistently across the precipitation gradient. In contrast, we found that disease resistance gene homolog diversity was positively correlated with precipitation. Significance Prairie remnants differ in the genetic resources they maintain. Selection and evolution in this disease resistance homolog is environmentally dependent. Overall, we found that, though this environmental gradient may not predict genomic diversity, individual traits such as disease resistance genes may vary significantly. PMID:21532756

Larger testes are associated with a higher level of polyandry, but a smaller ejaculate volume, across bushcricket species (Tettigoniidae)

PubMed Central

Vahed, Karim; Parker, Darren J.; Gilbert, James D. J.

2011-01-01

While early models of ejaculate allocation predicted that both relative testes and ejaculate size should increase with sperm competition intensity across species, recent models predict that ejaculate size may actually decrease as testes size and sperm competition intensity increase, owing to the confounding effect of potential male mating rate. A recent study demonstrated that ejaculate volume decreased in relation to increased polyandry across bushcricket species, but testes mass was not measured. Here, we recorded testis mass for 21 bushcricket species, while ejaculate (ampulla) mass, nuptial gift mass, sperm number and polyandry data were largely obtained from the literature. Using phylogenetic-comparative analyses, we found that testis mass increased with the degree of polyandry, but decreased with increasing ejaculate mass. We found no significant relationship between testis mass and either sperm number or nuptial gift mass. While these results are consistent with recent models of ejaculate allocation, they could alternatively be driven by substances in the ejaculate that affect the degree of polyandry and/or by a trade-off between resources spent on testes mass versus non-sperm components of the ejaculate. PMID:21068028

High proportion of smaller ranged hummingbird species coincides with ecological specialization across the Americas

PubMed Central

Martín González, Ana M.; Maruyama, Pietro K.; Sandel, Brody; Vizentin-Bugoni, Jeferson; Schleuning, Matthias; Abrahamczyk, Stefan; Alarcón, Ruben; Araujo, Andréa C.; Araújo, Francielle P.; Mendes de Azevedo, Severino; Baquero, Andrea C.; Cotton, Peter A.; Ingversen, Tanja Toftemark; Kohler, Glauco; Lara, Carlos; Guedes Las-Casas, Flor Maria; Machado, Adriana O.; Machado, Caio Graco; Maglianesi, María Alejandra; Moura, Alan Cerqueira; Nogués-Bravo, David; Oliveira, Genilda M.; Oliveira, Paulo E.; Ornelas, Juan Francisco; Rodrigues, Licléia da Cruz; Rosero-Lasprilla, Liliana; Rui, Ana Maria; Sazima, Marlies; Timmermann, Allan; Varassin, Isabela Galarda; Wang, Zhiheng; Watts, Stella; Fjeldså, Jon; Svenning, Jens-Christian; Rahbek, Carsten; Dalsgaard, Bo

2016-01-01

Ecological communities that experience stable climate conditions have been speculated to preserve more specialized interspecific associations and have higher proportions of smaller ranged species (SRS). Thus, areas with disproportionally large numbers of SRS are expected to coincide geographically with a high degree of community-level ecological specialization, but this suggestion remains poorly supported with empirical evidence. Here, we analysed data for hummingbird resource specialization, range size, contemporary climate, and Late Quaternary climate stability for 46 hummingbird–plant mutualistic networks distributed across the Americas, representing 130 hummingbird species (ca 40% of all hummingbird species). We demonstrate a positive relationship between the proportion of SRS of hummingbirds and community-level specialization, i.e. the division of the floral niche among coexisting hummingbird species. This relationship remained strong even when accounting for climate, furthermore, the effect of SRS on specialization was far stronger than the effect of specialization on SRS, suggesting that climate largely influences specialization through species' range-size dynamics. Irrespective of the exact mechanism involved, our results indicate that communities consisting of higher proportions of SRS may be vulnerable to disturbance not only because of their small geographical ranges, but also because of their high degree of specialization. PMID:26842573

Mercury risk to avian piscivores across western United States and Canada

USGS Publications Warehouse

Jackson, Allyson K.; Evers, David C.; Eagles-Smith, Collin A.; Ackerman, Joshua T.; Willacker, James J.; Elliott, John E.; Lepak, Jesse M.; Vander Pol, Stacy S.; Bryan, Colleen E.

2016-01-01

The widespread distribution of mercury (Hg) threatens wildlife health, particularly piscivorous birds. Western North America is a diverse region that provides critical habitat to many piscivorous bird species, and also has a well-documented history of mercury contamination from legacy mining and atmospheric deposition. The diversity of landscapes in the west limits the distribution of avian piscivore species, complicating broad comparisons across the region. Mercury risk to avian piscivores was evaluated across the western United States and Canada using a suite of avian piscivore species representing a variety of foraging strategies that together occur broadly across the region. Prey fish Hg concentrations were size-adjusted to the preferred size class of the diet for each avian piscivore (Bald Eagle = 36 cm, Osprey = 30 cm, Common and Yellow-billed Loon = 15 cm, Western and Clark's Grebe = 6 cm, and Belted Kingfisher = 5 cm) across each species breeding range. Using a combination of field and lab-based studies on Hg effect in a variety of species, wet weight blood estimates were grouped into five relative risk categories including: background (< 0.5 μg/g), low (0.5–1 μg/g), moderate (1–2 μg/g), high (2–3 μg/g), and extra high (> 3 μg/g). These risk categories were used to estimate potential mercury risk to avian piscivores across the west at a 1 degree-by-1 degree grid cell resolution. Avian piscivores foraging on larger-sized fish generally were at a higher relative risk to Hg. Habitats with a relatively high risk included wetland complexes (e.g., prairie pothole in Saskatchewan), river deltas (e.g., San Francisco Bay, Puget Sound, Columbia River), and arid lands (Great Basin and central Arizona). These results indicate that more intensive avian piscivore sampling is needed across Western North America to generate a more robust assessment of exposure risk.

CLIMATE CHANGE. Climate change impacts on bumblebees converge across continents.

PubMed

Kerr, Jeremy T; Pindar, Alana; Galpern, Paul; Packer, Laurence; Potts, Simon G; Roberts, Stuart M; Rasmont, Pierre; Schweiger, Oliver; Colla, Sheila R; Richardson, Leif L; Wagner, David L; Gall, Lawrence F; Sikes, Derek S; Pantoja, Alberto

2015-07-10

For many species, geographical ranges are expanding toward the poles in response to climate change, while remaining stable along range edges nearest the equator. Using long-term observations across Europe and North America over 110 years, we tested for climate change-related range shifts in bumblebee species across the full extents of their latitudinal and thermal limits and movements along elevation gradients. We found cross-continentally consistent trends in failures to track warming through time at species' northern range limits, range losses from southern range limits, and shifts to higher elevations among southern species. These effects are independent of changing land uses or pesticide applications and underscore the need to test for climate impacts at both leading and trailing latitudinal and thermal limits for species. Copyright © 2015, American Association for the Advancement of Science.

Thermal Acclimation of Photosynthesis and Respiration Differ Across Mature Conifer Species in a Boreal Forest Peatland

NASA Astrophysics Data System (ADS)

Dusenge, M. E.; Stinziano, J. R.; Warren, J.; Ward, E. J.; Wullschleger, S.; Hanson, P. J.; Way, D.

2017-12-01

Boreal forests are often assumed to be temperature-limited, and warming is therefore expected to stimulate their carbon uptake. However, much of our information on the ability of boreal conifers to acclimate photosynthesis and respiration to rising temperatures comes from seedlings. We measured net CO2 assimilation rates (A) and dark respiration (R) at 25 °C (A25 and R25) and at prevailing growth temperatures (Ag and Rg) in mature Picea mariana (spruce) and Larix laricina (tamarack) exposed to ambient, +2.25, +4.5, +6.75 and +9 °C warming treatments in open top chambers in the field at the SPRUCE experiment (MN, USA). In spruce, A25 and Ag were similar across plots in May and June. In August, spruce in warmer treatments had higher A25, an effect that was offset by warmer leaf temperatures in the Ag data. In tamarack, A25 was stimulated by warming in both June and August, an effect that was mainly offset by higher leaf temperatures when Ag was assessed in June, while in August, Ag was still slightly higher in the warmest treatments (+6.75 and +9) compared to the ambient plots. In spruce, R25 was enhanced in warm-grown trees in May, but was similar across treatments in June and August, indicating little acclimation of R. Rg slightly increased with warming treatments across the season in spruce. In contrast, R in tamarack thermally acclimated, as R25 decreased with warming. But while this acclimation generated homeostatic Rg in June, Rg in August was still highest in the warmest treatments. Our work suggests that the capacity for thermal acclimation in both photosynthesis and respiration varies among boreal tree species, which may lead to shifts in the performance of these species as the climate warms.

Coral-associated bacterial diversity is conserved across two deep-sea Anthothela species

USGS Publications Warehouse

Lawler, Stephanie N.; Kellogg, Christina A.; France, Scott C; Clostio, Rachel W; Brooke, Sandra D.; Ross, Steve W.

2016-01-01

Cold-water corals, similar to tropical corals, contain diverse and complex microbial assemblages. These bacteria provide essential biological functions within coral holobionts, facilitating increased nutrient utilization and production of antimicrobial compounds. To date, few cold-water octocoral species have been analyzed to explore the diversity and abundance of their microbial associates. For this study, 23 samples of the family Anthothelidae were collected from Norfolk (n = 12) and Baltimore Canyons (n = 11) from the western Atlantic in August 2012 and May 2013. Genetic testing found that these samples comprised two Anthothela species (Anthothela grandiflora and Anthothela sp.) and Alcyonium grandiflorum. DNA was extracted and sequenced with primers targeting the V4-V5 variable region of the 16S rRNA gene using 454 pyrosequencing with GS FLX Titanium chemistry. Results demonstrated that the coral host was the primary driver of bacterial community composition. Al. grandiflorum, dominated by Alteromonadales and Pirellulales had much higher species richness, and a distinct bacterial community compared to Anthothela samples. Anthothela species (A. grandiflora and Anthothela sp.) had very similar bacterial communities, dominated by Oceanospirillales and Spirochaetes. Additional analysis of core-conserved bacteria at 90% sample coverage revealed genus level conservation across Anthothela samples. This core included unclassified Oceanospirillales, Kiloniellales, Campylobacterales, and genus Spirochaeta. Members of this core were previously recognized for their functional capabilities in nitrogen cycling and suggest the possibility of a nearly complete nitrogen cycle within Anthothela species. Overall, many of the bacterial associates identified in this study have the potential to contribute to the acquisition and cycling of nutrients within the coral holobiont.

Signatures of polygenic adaptation associated with climate across the range of a threatened fish species with high genetic connectivity.

PubMed

Harrisson, Katherine A; Amish, Stephen J; Pavlova, Alexandra; Narum, Shawn R; Telonis-Scott, Marina; Rourke, Meaghan L; Lyon, Jarod; Tonkin, Zeb; Gilligan, Dean M; Ingram, Brett A; Lintermans, Mark; Gan, Han Ming; Austin, Christopher M; Luikart, Gordon; Sunnucks, Paul

2017-11-01

Adaptive differences across species' ranges can have important implications for population persistence and conservation management decisions. Despite advances in genomic technologies, detecting adaptive variation in natural populations remains challenging. Key challenges in gene-environment association studies involve distinguishing the effects of drift from those of selection and identifying subtle signatures of polygenic adaptation. We used paired-end restriction site-associated DNA sequencing data (6,605 biallelic single nucleotide polymorphisms; SNPs) to examine population structure and test for signatures of adaptation across the geographic range of an iconic Australian endemic freshwater fish species, the Murray cod Maccullochella peelii. Two univariate gene-association methods identified 61 genomic regions associated with climate variation. We also tested for subtle signatures of polygenic adaptation using a multivariate method (redundancy analysis; RDA). The RDA analysis suggested that climate (temperature- and precipitation-related variables) and geography had similar magnitudes of effect in shaping the distribution of SNP genotypes across the sampled range of Murray cod. Although there was poor agreement among the candidate SNPs identified by the univariate methods, the top 5% of SNPs contributing to significant RDA axes included 67% of the SNPs identified by univariate methods. We discuss the potential implications of our findings for the management of Murray cod and other species generally, particularly in relation to informing conservation actions such as translocations to improve evolutionary resilience of natural populations. Our results highlight the value of using a combination of different approaches, including polygenic methods, when testing for signatures of adaptation in landscape genomic studies. © 2017 John Wiley & Sons Ltd.

Local brain connectivity across development in autism spectrum disorder: A cross-sectional investigation

PubMed Central

Dajani, Dina R.; Uddin, Lucina Q.

2015-01-01

Lay Abstract There is a general consensus that autism spectrum disorder (ASD) is accompanied by alterations in brain connectivity. Much of the neuroimaging work has focused on assessing long-range connectivity disruptions in ASD. However, evidence from both animal models and postmortem examination of the human brain suggests that local connections may also be disrupted in individuals with ASD. Here we investigated the development of local connectivity across three age cohorts of individuals with ASD and typically developing (TD) individuals. We find that in typical development, children exhibit high levels of local connectivity across the brain, while adolescents exhibit lower levels of local connectivity, similar to adult levels. On the other hand, children with ASD exhibit marginally lower local connectivity than TD children, and adolescents and adults with ASD exhibit levels of local connectivity comparable to that observed in neurotypical individuals. During all developmental stages -- childhood, adolescence, and adulthood -- individuals with ASD exhibited lower local connectivity in brain regions involved in sensory processing and higher local connectivity in brain regions involved in complex information processing. Further, higher local connectivity in ASD corresponded to more severe ASD symptomatology. Thus we demonstrate that local connectivity is disrupted in autism across development, with the most pronounced differences occurring in childhood. Scientific Abstract There is a general consensus that autism spectrum disorder (ASD) is accompanied by alterations in brain connectivity. Much of the neuroimaging work has focused on assessing long-range connectivity disruptions in ASD. However, evidence from both animal models and postmortem examination of the human brain suggests that local connections may also be disrupted in individuals with the disorder. Here we investigated how regional homogeneity (ReHo), a measure of similarity of a voxel’s timeseries to

Does size matter? An investigation of habitat use across a carnivore assemblage in the Serengeti, Tanzania

PubMed Central

Durant, Sarah M.; Craft, Meggan E.; Foley, Charles; Hampson, Katie; Lobora, Alex L.; Msuha, Maurus; Eblate, Ernest; Bukombe, John; Mchetto, John; Pettorelli, Nathalie

2012-01-01

Summary This study utilizes a unique data set covering over 19 000 georeferenced records of species presence collected between 1993 and 2008, to explore the distribution and habitat selectivity of an assemblage of 26 carnivore species in the Serengeti–Ngorongoro landscape in northern Tanzania. Two species, the large-spotted genet and the bushy-tailed mongoose, were documented for the first time within this landscape. Ecological Niche Factor Analysis (ENFA) was used to examine habitat selectivity for 18 of the 26 carnivore species for which there is sufficient data. Eleven ecogeographical variables (EGVs), such as altitude and habitat type, were used for these analyses. The ENFA demonstrated that species differed in their habitat selectivity, and supported the limited ecological information already available for these species, such as the golden jackals’ preference for grassland and the leopards’ preference for river valleys. Two aggregate scores, marginality and tolerance, are generated by the ENFA, and describe each species’ habitat selectivity in relation to the suite of EGVs. These scores were used to test the hypothesis that smaller species are expected to be more selective than larger species [Science, 1989, 243, 1145]. Two predictions were tested: Marginality should decrease with body mass; and tolerance should increase with body mass. Our study provided no evidence for either prediction. Our results not only support previous analyses of carnivore diet breadth, but also represent a novel approach to the investigation of habitat selection across species assemblages. Our method provides a powerful tool to explore similar questions in other systems and for other taxa. PMID:20646121

Polymorphic microsatellite markers for the endangered fish, the slender shiner Pseudopungtungia tenuicorpa and cross-species amplification across five related species.

PubMed

Kim, K S; Moon, S J; Han, S H; Kim, K Y; Bang, I C

2016-09-02

The slender shiner Pseudopungtungia tenuicorpa (Cypriniformes; Cyprinidae; Gobioninae) is an endangered freshwater fish species endemic to Korea. The current strategies for its conservation involve the study of population genetic characters and identification of management units. These strategies require suitable molecular markers to study genetic diversity and genetic structure. Here, we developed nine polymorphic microsatellite markers for P. tenuicorpa for the first time by applying an enrichment method from a size-selected genomic library. The developed microsatellite markers produced a total of 101 alleles (average 11.2). The observed and expected heterozygosities averaged 0.805 and 0.835, respectively. Among the nine identified markers, five markers showed successful amplification across five related Korean Gobioninae species. Thus, the microsatellite markers developed in this study will be useful to establish conservation strategies for both P. tenuicorpa and other related species.

Evolution of aging: individual life history trade-offs and population heterogeneity account for mortality patterns across species.

PubMed

Le Cunff, Y; Baudisch, A; Pakdaman, K

2014-08-01

A broad range of mortality patterns has been documented across species, some even including decreasing mortality over age. Whether there exist a common denominator to explain both similarities and differences in these mortality patterns remains an open question. The disposable soma theory, an evolutionary theory of aging, proposes that universal intracellular trade-offs between maintenance/lifespan and reproduction would drive aging across species. The disposable soma theory has provided numerous insights concerning aging processes in single individuals. Yet, which specific population mortality patterns it can lead to is still largely unexplored. In this article, we propose a model exploring the mortality patterns which emerge from an evolutionary process including only the disposable soma theory core principles. We adapt a well-known model of genomic evolution to show that mortality curves producing a kink or mid-life plateaus derive from a common minimal evolutionary framework. These mortality shapes qualitatively correspond to those of Drosophila melanogaster, Caenorhabditis elegans, medflies, yeasts and humans. Species evolved in silico especially differ in their population diversity of maintenance strategies, which itself emerges as an adaptation to the environment over generations. Based on this integrative framework, we also derive predictions and interpretations concerning the effects of diet changes and heat-shock treatments on mortality patterns. © 2014 The Authors. Journal of Evolutionary Biology © 2014 European Society For Evolutionary Biology.

Volitional components of consciousness vary across wakefulness, dreaming and lucid dreaming

PubMed Central

Dresler, Martin; Eibl, Leandra; Fischer, Christian F. J.; Wehrle, Renate; Spoormaker, Victor I.; Steiger, Axel; Czisch, Michael; Pawlowski, Marcel

2014-01-01

Consciousness is a multifaceted concept; its different aspects vary across species, vigilance states, or health conditions. While basal aspects of consciousness like perceptions and emotions are present in many states and species, higher-order aspects like reflective or volitional capabilities seem to be most pronounced in awake humans. Here we assess the experience of volition across different states of consciousness: 10 frequent lucid dreamers rated different aspects of volition according to the Volitional Components Questionnaire for phases of normal dreaming, lucid dreaming, and wakefulness. Overall, experienced volition was comparable for lucid dreaming and wakefulness, and rated significantly higher for both states compared to non-lucid dreaming. However, three subscales showed specific differences across states of consciousness: planning ability was most pronounced during wakefulness, intention enactment most pronounced during lucid dreaming, and self-determination most pronounced during both wakefulness and lucid dreaming. Our data confirm the multifaceted nature of consciousness: different higher-order aspects of consciousness are differentially expressed across different conscious states. PMID:24427149

Volitional components of consciousness vary across wakefulness, dreaming and lucid dreaming.

PubMed

Dresler, Martin; Eibl, Leandra; Fischer, Christian F J; Wehrle, Renate; Spoormaker, Victor I; Steiger, Axel; Czisch, Michael; Pawlowski, Marcel

2014-01-01

Consciousness is a multifaceted concept; its different aspects vary across species, vigilance states, or health conditions. While basal aspects of consciousness like perceptions and emotions are present in many states and species, higher-order aspects like reflective or volitional capabilities seem to be most pronounced in awake humans. Here we assess the experience of volition across different states of consciousness: 10 frequent lucid dreamers rated different aspects of volition according to the Volitional Components Questionnaire for phases of normal dreaming, lucid dreaming, and wakefulness. Overall, experienced volition was comparable for lucid dreaming and wakefulness, and rated significantly higher for both states compared to non-lucid dreaming. However, three subscales showed specific differences across states of consciousness: planning ability was most pronounced during wakefulness, intention enactment most pronounced during lucid dreaming, and self-determination most pronounced during both wakefulness and lucid dreaming. Our data confirm the multifaceted nature of consciousness: different higher-order aspects of consciousness are differentially expressed across different conscious states.

Cerebellar Abiotrophy Across Domestic Species.

PubMed

Scott, Erica Yuki; Woolard, Kevin Douglas; Finno, Carrie J; Murray, James D

2018-06-01

Cerebellar abiotrophy (CA) is a neurodegenerative disorder affecting the cerebellum and occurs in multiple species. Although CA is well researched in humans and mice, domestic species such as the dog, cat, sheep, cow, and horse receive little recognition. This may be due to few studies addressing the mechanism of CA in these species. However, valuable information can still be extracted from these cases. A review of the clinicohistologic phenotype of CA in these species and determining the various etiologies of CA may aid in determining conserved and required pathways necessary for proper cerebellar development and function. This review outlines research approaches of studies of CA in domestic species, compared to the approaches used in mice, with the objective of comparing CA in domestic species while identifying areas for further research efforts.

Examining shifts in Carabidae assemblages across a forest-agriculture ecotone.

PubMed

Leslie, T W; Biddinger, D J; Rohr, J R; Hulting, A G; Mortensen, D A; Fleischer, S J

2014-02-01

Northeastern U.S. farms are often situated adjacent to forestland due to the heterogeneous nature of the landscape. We investigated how forested areas influence Carabidae diversity within nearby crop fields by establishing transects of pitfall traps. Trapping extended across a forest-agriculture ecotone consisting of maize, an intermediate mowed grass margin, and a forest edge. Carabidae diversity was compared among the three habitats, and community and population dynamics were assessed along the transect. We used a principal response curve to examine and visualize community change across a spatial gradient. The highest levels of richness and evenness were observed in the forest community, and carabid assemblages shifted significantly across the ecotone, especially at the forest-grass interface. Despite strong ecotone effects, population distributions showed that some species were found in all three habitats and seemed to thrive at the ecotone. Based on similarity indices, carabid assemblages collected in maize adjacent to forest differed from carabid assemblages in maize not adjacent to forest. We conclude that forest carabid assemblages exhibit high degrees of dissimilarity with those found in agricultural fields and forested areas should thus be retained in agricultural landscapes to increase biodiversity at the landscape scale. However, ecotone species found at forest edges can still noticeably influence carabid community composition within neighboring agricultural fields. Further studies should determine how these shifts in carabid assemblages influence agroecosystem services in relation to ecosystem services observed in fields embedded in an agricultural matrix.

Intensive agriculture reduces soil biodiversity across Europe.

PubMed

Tsiafouli, Maria A; Thébault, Elisa; Sgardelis, Stefanos P; de Ruiter, Peter C; van der Putten, Wim H; Birkhofer, Klaus; Hemerik, Lia; de Vries, Franciska T; Bardgett, Richard D; Brady, Mark Vincent; Bjornlund, Lisa; Jørgensen, Helene Bracht; Christensen, Sören; Hertefeldt, Tina D'; Hotes, Stefan; Gera Hol, W H; Frouz, Jan; Liiri, Mira; Mortimer, Simon R; Setälä, Heikki; Tzanopoulos, Joseph; Uteseny, Karoline; Pižl, Václav; Stary, Josef; Wolters, Volkmar; Hedlund, Katarina

2015-02-01

Soil biodiversity plays a key role in regulating the processes that underpin the delivery of ecosystem goods and services in terrestrial ecosystems. Agricultural intensification is known to change the diversity of individual groups of soil biota, but less is known about how intensification affects biodiversity of the soil food web as a whole, and whether or not these effects may be generalized across regions. We examined biodiversity in soil food webs from grasslands, extensive, and intensive rotations in four agricultural regions across Europe: in Sweden, the UK, the Czech Republic and Greece. Effects of land-use intensity were quantified based on structure and diversity among functional groups in the soil food web, as well as on community-weighted mean body mass of soil fauna. We also elucidate land-use intensity effects on diversity of taxonomic units within taxonomic groups of soil fauna. We found that between regions soil food web diversity measures were variable, but that increasing land-use intensity caused highly consistent responses. In particular, land-use intensification reduced the complexity in the soil food webs, as well as the community-weighted mean body mass of soil fauna. In all regions across Europe, species richness of earthworms, Collembolans, and oribatid mites was negatively affected by increased land-use intensity. The taxonomic distinctness, which is a measure of taxonomic relatedness of species in a community that is independent of species richness, was also reduced by land-use intensification. We conclude that intensive agriculture reduces soil biodiversity, making soil food webs less diverse and composed of smaller bodied organisms. Land-use intensification results in fewer functional groups of soil biota with fewer and taxonomically more closely related species. We discuss how these changes in soil biodiversity due to land-use intensification may threaten the functioning of soil in agricultural production systems. © 2014 John Wiley

Longitudinal prevalence, oocyst shedding and molecular characterisation of Eimeria species in sheep across four states in Australia.

PubMed

Yang, Rongchang; Jacobson, Caroline; Gardner, Graham; Carmichael, Ian; Campbell, Angus J D; Ryan, Una

2014-10-01

The prevalence of Eimeria in sheep in Australia has not been well described, therefore a quantitative PCR (qPCR) was developed, validated and used to study the prevalence and oocyst concentration in lamb faecal samples at three sampling periods (weaning, post-weaning and pre-slaughter) from eight farms across South Australia, New South Wales, Victoria and Western Australia. A total of 3412 faecal samples were collected from approximately 1182 lambs across the 4 states and screened for the presence of Eimeria using this qPCR at the 18S ribosomal RNA (rRNA) locus. A subset of positives was typed by sequence analysis at the 18S locus. The overall prevalence was 18.1% (95% CI 16.8-19.3%) and of the 616 positives, 118 were successfully genotyped. The prevalence of Eimeria was highest in NSW and peaked at 70% during the post-weaning period. The range of oocyst shedding per gram of faeces (g(-1)) at weaning, post-weaning and pre-slaughter overall across all states was 23-2.1×10(7), 23-1.3×10(7) and 23-2.1×10(5), respectively. Median Eimeria shedding g(-1) was higher during post-weaning (1.1×10(3)) and pre-slaughter (1.1×10(3)) than during weaning (206). The following species were identified: Eimeria crandallis, Eimeria ahsata, Eimeria ovinoidalis, Eimeria weybridgensis and Eimeria cylindrica. Of these, E. crandallis and E. ovinoidalis, the most pathogenic species in sheep were responsible for 58.5% of infections typed. This highlights a need for further research to quantify the production impacts of Eimeria in sheep. Copyright © 2014 Elsevier Inc. All rights reserved.

Marital attitude trajectories across adolescence.

PubMed

Willoughby, Brian J

2010-11-01

The current study seeks to address the implicit assumption in the developmental literature that marital attitudes are static by investigating how various marital attitudes might change across adolescence. Longitudinal change for three marital attitudes in relation to family structure, educational aspirations, race and gender are examined. Utilizing a sample of 1,010 high school students (53% male; 76% white) recruited from a Midwestern metropolitan area, latent growth models were used to model marital attitude trajectories across adolescence. The sample was followed for 4 years from ages 14 until 18. Results revealed that adolescents placed a higher priority on marriage as they prepared to transition into young adulthood but that gender, race and educational aspirations all altered the degree in which marital attitudes changed across the time period of the study. Results highlight the importance of considering multiple constructs of marital attitudes and the need for more longitudinal work in this area of study.

Tree Nonstructural Carbohydrate Reserves Across Eastern US Temperate Forests

NASA Astrophysics Data System (ADS)

Mantooth, J.; Dietze, M.

2015-12-01

Understanding the roles, importance, and dynamics of tree non-structural carbohydrates (NSCs) is currently an active area of research. The question of how the relationships between NSCs, growth, and mortality can be used to develop more accurate projections of forest dynamics is central to this research. To begin to address this question, we have asked an even more fundamental question: How much are trees allocating carbon to storage, in the form of NSCs, versus new growth? Ecological theory predicts that there should be trade-offs between different plant life history strategies provided that there are the carbon mass-balance constraints to enforce these trade-offs. Current data on tree NSCs lack the spatial and taxonomic extent required to properly address this question. Therefore, we established a network of forest inventory plots at ten sites across the eastern US and measured growth in adult trees using increment cores and repeat measures of diameter at breast height (DBH). Increment cores were also used to measure sapwood NSCs. We hypothesized that across the eastern US, shade tolerant species, e.g. Sugar Maple (Acer saccharum) have the largest NSC reserves and that shade intolerant species have the lowest reserves. We also hypothesized that NSC reserves increase with temperature and precipitation, as with growth, and that within species NSC reserves increase with growth rate. Initial analyses of tree NSCs indicates that trees of intermediate shade tolerance, e.g. Red Oak (Quercus rubra) have the highest concentrations of sapwood NSCs, and among the highest growth rates. Across the entire study region, NSC concentrations are positively correlated with tree size and growth rate. Within species, NSC concentrations are also positively correlated with growth rate. Across functional groups healthy individuals have significantly higher sapwood NSC concentrations than visibly stressed individuals. There are also significantly lower NSC concentrations in sapwood of

Social learning across species: horses (Equus caballus) learn from humans by observation.

PubMed

Schuetz, Aurelia; Farmer, Kate; Krueger, Konstanze

2017-05-01

This study examines whether horses can learn by observing humans, given that they identify individual humans and orientate on the focus of human attention. We tested 24 horses aged between 3 and 12. Twelve horses were tested on whether they would learn to open a feeding apparatus by observing a familiar person. The other 12 were controls and received exactly the same experimental procedure, but without a demonstration of how to operate the apparatus. More horses from the group with demonstration (8/12) reached the learning criterion of opening the feeder twenty times consecutively than horses from the control group (2/12), and younger horses seemed to reach the criterion more quickly. Horses not reaching the learning criteria approached the human experimenters more often than those that did. The results demonstrate that horses learn socially across species, in this case from humans.

Investigating Attitudes toward Physical Education: Validation across Two Instruments

ERIC Educational Resources Information Center

Donovan, Corinne Baron; Mercier, Kevin; Phillips, Sharon R.

2015-01-01

The Centers for Disease Control have suggested that physical education plays a role in promoting healthy lifestyles. Prior research suggests a link between attitudes toward physical education and physical activity outside school. The current study provides additional evidence of construct validity through a validation across two instruments…

Trade-offs in seedling growth and survival within and across tropical forest microhabitats

PubMed Central

Inman-Narahari, Faith; Ostertag, Rebecca; Asner, Gregory P; Cordell, Susan; Hubbell, Stephen P; Sack, Lawren

2014-01-01

For niche differences to maintain coexistence of sympatric species, each species must grow and/or survive better than each of the others in at least one set of conditions (i.e., performance trade-offs). However, the extent of niche differentiation in tropical forests remains highly debated. We present the first test of performance trade-offs for wild seedlings in a tropical forest. We measured seedling relative growth rate (RGR) and survival of four common native woody species across 18 light, substrate, and topography microhabitats over 2.5 years within Hawaiian montane wet forest, an ideal location due to its low species diversity and strong species habitat associations. All six species pairs exhibited significant performance trade-offs across microhabitats and for RGR versus survival within microhabitats. We also found some evidence of performance equivalence, with species pairs having similar performance in 26% of comparisons across microhabitats. Across species, survival under low light was generally positively associated with RGR under high light. When averaged over all species, topography (slope, aspect, and elevation) explained most of the variation in RGR attributable to microhabitat variables (51–53%) followed by substrate type (35–37%) and light (11–12%). However, the relative effects of microhabitat differed among species and RGR metric (i.e., RGR for height, biomass, or leaf area). These findings indicate that performance trade-offs among species during regeneration are common in low-diversity tropical forest, although other mechanisms may better explain the coexistence of species with small performance differences. PMID:25614790

High proportion of smaller ranged hummingbird species coincides with ecological specialization across the Americas.

PubMed

Sonne, Jesper; Martín González, Ana M; Maruyama, Pietro K; Sandel, Brody; Vizentin-Bugoni, Jeferson; Schleuning, Matthias; Abrahamczyk, Stefan; Alarcón, Ruben; Araujo, Andréa C; Araújo, Francielle P; Mendes de Azevedo, Severino; Baquero, Andrea C; Cotton, Peter A; Ingversen, Tanja Toftemark; Kohler, Glauco; Lara, Carlos; Guedes Las-Casas, Flor Maria; Machado, Adriana O; Machado, Caio Graco; Maglianesi, María Alejandra; Moura, Alan Cerqueira; Nogués-Bravo, David; Oliveira, Genilda M; Oliveira, Paulo E; Ornelas, Juan Francisco; Rodrigues, Licléia da Cruz; Rosero-Lasprilla, Liliana; Rui, Ana Maria; Sazima, Marlies; Timmermann, Allan; Varassin, Isabela Galarda; Wang, Zhiheng; Watts, Stella; Fjeldså, Jon; Svenning, Jens-Christian; Rahbek, Carsten; Dalsgaard, Bo

2016-02-10

Ecological communities that experience stable climate conditions have been speculated to preserve more specialized interspecific associations and have higher proportions of smaller ranged species (SRS). Thus, areas with disproportionally large numbers of SRS are expected to coincide geographically with a high degree of community-level ecological specialization, but this suggestion remains poorly supported with empirical evidence. Here, we analysed data for hummingbird resource specialization, range size, contemporary climate, and Late Quaternary climate stability for 46 hummingbird-plant mutualistic networks distributed across the Americas, representing 130 hummingbird species (ca 40% of all hummingbird species). We demonstrate a positive relationship between the proportion of SRS of hummingbirds and community-level specialization, i.e. the division of the floral niche among coexisting hummingbird species. This relationship remained strong even when accounting for climate, furthermore, the effect of SRS on specialization was far stronger than the effect of specialization on SRS, suggesting that climate largely influences specialization through species' range-size dynamics. Irrespective of the exact mechanism involved, our results indicate that communities consisting of higher proportions of SRS may be vulnerable to disturbance not only because of their small geographical ranges, but also because of their high degree of specialization. © 2016 The Author(s).

Coral-Associated Bacterial Diversity Is Conserved across Two Deep-Sea Anthothela Species

PubMed Central

Lawler, Stephanie N.; Kellogg, Christina A.; France, Scott C.; Clostio, Rachel W.; Brooke, Sandra D.; Ross, Steve W.

2016-01-01

Cold-water corals, similar to tropical corals, contain diverse and complex microbial assemblages. These bacteria provide essential biological functions within coral holobionts, facilitating increased nutrient utilization and production of antimicrobial compounds. To date, few cold-water octocoral species have been analyzed to explore the diversity and abundance of their microbial associates. For this study, 23 samples of the family Anthothelidae were collected from Norfolk (n = 12) and Baltimore Canyons (n = 11) from the western Atlantic in August 2012 and May 2013. Genetic testing found that these samples comprised two Anthothela species (Anthothela grandiflora and Anthothela sp.) and Alcyonium grandiflorum. DNA was extracted and sequenced with primers targeting the V4–V5 variable region of the 16S rRNA gene using 454 pyrosequencing with GS FLX Titanium chemistry. Results demonstrated that the coral host was the primary driver of bacterial community composition. Al. grandiflorum, dominated by Alteromonadales and Pirellulales had much higher species richness, and a distinct bacterial community compared to Anthothela samples. Anthothela species (A. grandiflora and Anthothela sp.) had very similar bacterial communities, dominated by Oceanospirillales and Spirochaetes. Additional analysis of core-conserved bacteria at 90% sample coverage revealed genus level conservation across Anthothela samples. This core included unclassified Oceanospirillales, Kiloniellales, Campylobacterales, and genus Spirochaeta. Members of this core were previously recognized for their functional capabilities in nitrogen cycling and suggest the possibility of a nearly complete nitrogen cycle within Anthothela species. Overall, many of the bacterial associates identified in this study have the potential to contribute to the acquisition and cycling of nutrients within the coral holobiont. PMID:27092120

Human CRISP-3 binds serum alpha(1)B-glycoprotein across species.

PubMed

Udby, Lene; Johnsen, Anders H; Borregaard, Niels

2010-04-01

CRISP-3 was previously shown to be bound to alpha(1)B-glycoprotein (A1BG) in human serum/plasma. All mammalian sera are supposed to contain A1BG, although its presence in rodent sera is not well-documented. Since animal sera are often used to supplement buffers in experiments, in particular such that involve cell cultures, binding proteins present in sera might interfere in the experiments. We examined sera from five different animal species for CRISP-3 binding proteins using gel filtration and ligand blotting. We developed a rapid method for isolation of proteins that bind to human CRISP-3 and identified the isolated proteins by mass spectrometry and N-terminal sequencing. We identified A1BG as a CRISP-3 binding protein in sera from cow, horse and rabbit. CRISP-3 bound kininogen 1 in mouse serum, whereas rat serum showed no CRISP-3 binding activity. In equine serum, we furthermore detected a possible CRISP, already bound to A1BG. It seems to be a common mechanism that A1BGs bind CRISPs, also across species. Apart from the possible physiological implications hereof, complex binding of CRISPs by A1BG (and other proteins) may interfere with the detection and function of CRISPs, when these are studied in the presence of animal sera. Copyright 2009 Elsevier B.V. All rights reserved.

DNA barcoding unveils skate (Chondrichthyes: Rajidae) species diversity in 'ray' products sold across Ireland and the UK.

PubMed

Griffiths, Andrew Mark; Miller, Dana D; Egan, Aaron; Fox, Jennifer; Greenfield, Adam; Mariani, Stefano

2013-01-01

Skates are widely consumed across the globe, but many large species are subject to considerable concern regarding their conservation and management. Within Europe such issues have recently driven policy changes so that, for the first time, reports of skate landings now have to be made under species-specific names. Total allowable catches have also been established for many groups, which have been set to zero for a number of the most vulnerable species (e.g., Dipturus batis, Raja undulata and Rostoraja alba). Whilst accurate species identification has become an important issue for landings, the sale of skates is still usually made under a blanket term of "skate" or "ray". The matter of identifying species of skate is further complicated by their morphologically conservative nature and the fact that they are commercially valued for their wings. Thus, before sale their bodies are usually discarded (i.e., "winged") and often skinned, making morphological identification impossible. For the first time, DNA barcoding (of the mitochondrial COI gene) was applied to samples of skate wings from retail outlets across the British Isles, providing insight into which species are sold for consumption. A total of 98 wing samples were analysed, revealing that six species were sold; blonde ray (Raja brachyura), spotted ray (Raja montagui), thornback ray (Raja clavata), cuckoo ray (Leucoraja naevus) small-eyed ray (Raja microocellata) and shagreen ray (Leucoraja fullonica). Statistical testing demonstrated that there were significant differences in the species sold in the distinct retail groups which suggests complex drivers behind the patterns of sale in skates. The results also indicate that endangered species are not commonly being passed on to consumers. In addition, the practice of selling skate wings under ambiguous labels is highlighted as it makes it extremely difficult for consumers to exercise a right to avoid species of conservation concern. Interestingly, a single retailer

Cell culture-based profiling across mammals reveals DNA repair and metabolism as determinants of species longevity.

PubMed

Ma, Siming; Upneja, Akhil; Galecki, Andrzej; Tsai, Yi-Miau; Burant, Charles F; Raskind, Sasha; Zhang, Quanwei; Zhang, Zhengdong D; Seluanov, Andrei; Gorbunova, Vera; Clish, Clary B; Miller, Richard A; Gladyshev, Vadim N

2016-11-22

Mammalian lifespan differs by >100 fold, but the mechanisms associated with such longevity differences are not understood. Here, we conducted a study on primary skin fibroblasts isolated from 16 species of mammals and maintained under identical cell culture conditions. We developed a pipeline for obtaining species-specific ortholog sequences, profiled gene expression by RNA-seq and small molecules by metabolite profiling, and identified genes and metabolites correlating with species longevity. Cells from longer lived species up-regulated genes involved in DNA repair and glucose metabolism, down-regulated proteolysis and protein transport, and showed high levels of amino acids but low levels of lysophosphatidylcholine and lysophosphatidylethanolamine. The amino acid patterns were recapitulated by further analyses of primate and bird fibroblasts. The study suggests that fibroblast profiling captures differences in longevity across mammals at the level of global gene expression and metabolite levels and reveals pathways that define these differences.

Genetic diversity and species diversity of stream fishes covary across a land-use gradient.

PubMed

Blum, Michael J; Bagley, Mark J; Walters, David M; Jackson, Suzanne A; Daniel, F Bernard; Chaloud, Deborah J; Cade, Brian S

2012-01-01

Genetic diversity and species diversity are expected to covary according to area and isolation, but may not always covary with environmental heterogeneity. In this study, we examined how patterns of genetic and species diversity in stream fishes correspond to local and regional environmental conditions. To do so, we compared population size, genetic diversity and divergence in central stonerollers (Campostoma anomalum) to measures of species diversity and turnover in stream fish assemblages among similarly sized watersheds across an agriculture-forest land-use gradient in the Little Miami River basin (Ohio, USA). Significant correlations were found in many, but not all, pair-wise comparisons. Allelic richness and species richness were strongly correlated, for example, but diversity measures based on allele frequencies and assemblage structure were not. In-stream conditions related to agricultural land use were identified as significant predictors of genetic diversity and species diversity. Comparisons to population size indicate, however, that genetic diversity and species diversity are not necessarily independent and that variation also corresponds to watershed location and glaciation history in the drainage basin. Our findings demonstrate that genetic diversity and species diversity can covary in stream fish assemblages, and illustrate the potential importance of scaling observations to capture responses to hierarchical environmental variation. More comparisons according to life history variation could further improve understanding of conditions that give rise to parallel variation in genetic diversity and species diversity, which in turn could improve diagnosis of anthropogenic influences on aquatic ecosystems.

Genetic diversity and species diversity of stream fishes covary across a land-use gradient

USGS Publications Warehouse

Blum, M.J.; Bagley, M.J.; Walters, D.M.; Jackson, S.A.; Daniel, F.B.; Chaloud, D.J.; Cade, B.S.

2012-01-01

Genetic diversity and species diversity are expected to covary according to area and isolation, but may not always covary with environmental heterogeneity. In this study, we examined how patterns of genetic and species diversity in stream fishes correspond to local and regional environmental conditions. To do so, we compared population size, genetic diversity and divergence in central stonerollers (Campostoma anomalum) to measures of species diversity and turnover in stream fish assemblages among similarly sized watersheds across an agriculture-forest land-use gradient in the Little Miami River basin (Ohio, USA). Significant correlations were found in many, but not all, pair-wise comparisons. Allelic richness and species richness were strongly correlated, for example, but diversity measures based on allele frequencies and assemblage structure were not. In-stream conditions related to agricultural land use were identified as significant predictors of genetic diversity and species diversity. Comparisons to population size indicate, however, that genetic diversity and species diversity are not necessarily independent and that variation also corresponds to watershed location and glaciation history in the drainage basin. Our findings demonstrate that genetic diversity and species diversity can covary in stream fish assemblages, and illustrate the potential importance of scaling observations to capture responses to hierarchical environmental variation. More comparisons according to life history variation could further improve understanding of conditions that give rise to parallel variation in genetic diversity and species diversity, which in turn could improve diagnosis of anthropogenic influences on aquatic ecosystems. ?? 2011 Springer-Verlag.

Is it worth hyperaccumulating Ni on non-serpentine soils? Decomposition dynamics of mixed-species litters containing hyperaccumulated Ni across serpentine and non-serpentine environments.

PubMed

Adamidis, George C; Kazakou, Elena; Aloupi, Maria; Dimitrakopoulos, Panayiotis G

2016-06-01

Nickel (Ni)-hyperaccumulating species produce high-Ni litters and may potentially influence important ecosystem processes such as decomposition. Although litters resembling the natural community conditions are essential in order to predict decomposition dynamics, decomposition of mixed-species litters containing hyperaccumulated Ni has never been studied. This study aims to test the effect of different litter mixtures containing hyperaccumulated Ni on decomposition and Ni release across serpentine and non-serpentine soils. Three different litter mixtures were prepared based on the relative abundance of the dominant species in three serpentine soils in the island of Lesbos, Greece where the Ni-hyperaccumulator Alyssum lesbiacum is present. Each litter mixture decomposed on its original serpentine habitat and on an adjacent non-serpentine habitat, in order to investigate whether the decomposition rates differ across the contrasted soils. In order to make comparisons across litter mixtures and to investigate whether additive or non-additive patterns of mass loss occur, a control non-serpentine site was used. Mass loss and Ni release were measured after 90, 180 and 270 d of field exposure. The decomposition rates and Ni release had higher values on serpentine soils after all periods of field exposure. The recorded rapid release of hyperaccumulated Ni is positively related to the initial litter Ni concentration. No differences were found in the decomposition of the three different litter mixtures at the control non-serpentine site, while their patterns of mass loss were additive. Our results: (1) demonstrate the rapid decomposition of litters containing hyperaccumulated Ni on serpentine soils, indicating the presence of metal-tolerant decomposers; and (2) imply the selective decomposition of low-Ni parts of litters by the decomposers on non-serpentine soils. This study provides support for the elemental allelopathy hypothesis of hyperaccumulation, presenting the

Seeing the trees for the forest: Nitrogen deposition alters tree growth and survival across the northeastern U.S., responses vary by species.

NASA Astrophysics Data System (ADS)

Thomas, R. Q.; Canham, C. D.; Weathers, K. C.; Goodale, C. L.

2008-12-01

Assessments of regional forest carbon (C) balance have long speculated a role for atmospheric nitrogen (N) deposition. To date, however, evidence for an N effect has been restricted to plot-level fertilization and 15N experiments, biogeochemical modeling studies, and recent and controversial correlations between nitrogen deposition and C balance across 20 intensive C monitoring sites. These studies have yielded widely varying conclusions on the magnitude and even the direction of response (positive or negative effects on C storage). We assessed the effects of N deposition on forest growth and survival using forest inventory data from > 160,000 trees, spanning a 19-state region of the northeastern United States, and estimates of total (wet and plot-specific dry) inorganic N inputs (N deposition to the plots ranged from 3.2 to 11 kg N ha-1 y-1). The growth rates of 14 of the region's 24 most common tree species responded to N deposition. Nine species showed a monotonic increase in aboveground growth rates across the range of N deposition and some of these species experienced a doubling of growth rates. Four species showed humped-shaped responses. A single species, Pinus resinosa (red pine), showed a monotonic decline in growth across the range of deposition. Species responsiveness to N deposition increased with mean growth rate of the species. In the analysis of survival, 13 of the 24 species responded to N: eight species showed a monotonic decrease, 3 showed a monotonic increase and 1 showed a humped-shape response in survival. The stand-level analysis showed a distinctly humped-shaped relationship between N deposition and aboveground C increment, peaking at 6 kg N ha-1 yr-1, which can likely be explained by the distribution of species and their individual growth and mortality responses. Overall, our data suggest that moderate levels of N deposition have enhanced aboveground C accumulation in temperate forests of the northeastern U.S., but the shape and trajectory

Cophylogenetic signal is detectable in pollination interactions across ecological scales.

PubMed

Hutchinson, Matthew C; Cagua, Edgar Fernando; Stouffer, Daniel B

2017-10-01

That evolutionary history can influence the way that species interact is a basic tenet of evolutionary ecology. However, when the role of evolution in determining ecological interactions is investigated, focus typically centers on just one side of the interaction. A cophylogenetic signal, the congruence of evolutionary history across both sides of an ecological interaction, extends these previous explorations and provides a more complete picture of how evolutionary patterns influence the way species interact. To date, cophylogenetic signal has most typically been studied in interactions that occur between fine taxonomic clades that show high intimacy. In this study, we took an alternative approach and made an exhaustive assessment of cophylogeny in pollination interactions. To do so, we assessed the strength of cophylogenetic signal at four distinct scales of pollination interaction: (1) across plant-pollinator associations globally, (2) in local pollination communities, (3) within the modular structure of those communities, and (4) in individual modules. We did so using a globally distributed dataset comprised of 54 pollination networks, over 4000 species, and over 12,000 interactions. Within these data, we detected cophylogenetic signal at all four scales. Cophylogenetic signal was found at the level of plant-pollinator interactions on a global scale and in the majority of pollination communities. At the scale defined by the modular structure within those communities, however, we observed a much weaker cophylogenetic signal. Cophylogenetic signal was detectable in a significant proportion of individual modules and most typically when within-module phylogenetic diversity was low. In sum, the detection of cophylogenetic signal in pollination interactions across scales provides a new dimension to the story of how past evolution shapes extant pollinator-angiosperm interactions. © 2017 by the Ecological Society of America.

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

Winning the Future: An Investigation into the Creativity Capacity across the Levels of Education in Ireland

ERIC Educational Resources Information Center

Leahy, Keelin

2016-01-01

This research investigated the creativity capacity across the levels of education in Ireland, involving 702 participants. Creative capacity was investigated through a comparative analysis of creativity quotient (CQ). A divergent thinking task comprising the "how many uses" activity was assessed using the criteria for determining CQ;…

Environmental filtering structures tree functional traits combination and lineages across space in tropical tree assemblages.

PubMed

Asefa, Mengesha; Cao, Min; Zhang, Guocheng; Ci, Xiuqin; Li, Jie; Yang, Jie

2017-03-09

Environmental filtering consistently shapes the functional and phylogenetic structure of species across space within diverse forests. However, poor descriptions of community functional and lineage distributions across space hamper the accurate understanding of coexistence mechanisms. We combined environmental variables and geographic space to explore how traits and lineages are filtered by environmental factors using extended RLQ and fourth-corner analyses across different spatial scales. The dispersion patterns of traits and lineages were also examined in a 20-ha tropical rainforest dynamics plot in southwest China. We found that environmental filtering was detected across all spatial scales except the largest scale (100 × 100 m). Generally, the associations between functional traits and environmental variables were more or less consistent across spatial scales. Species with high resource acquisition-related traits were associated with the resource-rich part of the plot across the different spatial scales, whereas resource-conserving functional traits were distributed in limited-resource environments. Furthermore, we found phylogenetic and functional clustering at all spatial scales. Similar functional strategies were also detected among distantly related species, suggesting that phylogenetic distance is not necessarily a proxy for functional distance. In summary, environmental filtering considerably structured the trait and lineage assemblages in this species-rich tropical rainforest.

IS TREATMENT ADHERENCE CONSISTENT ACROSS TIME, ACROSS DIFFERENT TREATMENTS, AND ACROSS DIAGNOSES?

PubMed Central

Simon, Gregory E; Peterson, Do; Hubbard, Rebecca

2012-01-01

Objective Examine consistency of adherence across depression treatments and consistency of adherence between depression treatments and treatments for chronic medical illness. Methods For 25,456 health plan members beginning psychotherapy for depression between 2003 and 2008, health plan records were used to examine adherence to all episodes of psychotherapy, antidepressant medication, antihypertensive medication, and lipid-lowering medication. Results Within treatments, adherence to psychotherapy in one episode predicted approximately 20% greater likelihood of subsequent psychotherapy adherence (OR 2.20, 95% CI 1.83 to 2.64). Similarly, adherence to antidepressant medication in one episode predicted approximately 20% greater likelihood of subsequent antidepressant adherence (OR 1.99, 95% CI 1.74 to 2.28). Across treatments, adherence to antidepressant medication predicted approximately 10% greater likelihood of concurrent or subsequent adherence to psychotherapy (OR 1.52, 95% CI 1.42 to 1.63), a 4% greater likelihood of adherence to antihypertensive medication (OR 1.24, 95% CI 1.14 to 1.37) and a 3% greater likelihood of adherence to lipid-lowering medication (OR 1.16, 95% CI 1.03 to 1.32). Adherence to psychotherapy predicted a 2% greater likelihood of concurrent or subsequent adherence to antihypertensive medication (OR 1.11, 95% CI 1.04 to 1.19) and was not a significant predictor of adherence to lipid-lowering medication (OR 0.99, 95% CI 0.90 to 1.18). Conclusions Adherence is moderately consistent across episodes of depression treatment. Depression treatment adherence is a statistically significant, but relatively weak, predictor of adherence to antihypertensive or lipid-lowering medication. PMID:23141589

Measures of Dogs' Inhibitory Control Abilities Do Not Correlate across Tasks

PubMed Central

Brucks, Désirée; Marshall-Pescini, Sarah; Wallis, Lisa Jessica; Huber, Ludwig; Range, Friederike

2017-01-01

Inhibitory control, the ability to overcome prepotent but ineffective behaviors, has been studied extensively across species, revealing the involvement of this ability in many different aspects of life. While various different paradigms have been created in order to measure inhibitory control, only a limited number of studies have investigated whether such measurements indeed evaluate the same underlying mechanism, especially in non-human animals. In humans, inhibitory control is a complex construct composed of distinct behavioral processes rather than of a single unified measure. In the current study, we aimed to investigate the validity of inhibitory control paradigms in dogs. Sixty-seven dogs were tested in a battery consisting of frequently used inhibitory control tests. Additionally, dog owners were asked to complete an impulsivity questionnaire about their dog. No correlation of dogs' performance across tasks was found. In order to understand whether there are some underlying behavioral aspects explaining dogs' performance across tests, we performed principle component analyses. Results revealed that three components (persistency, compulsivity and decision speed) explained the variation across tasks. The questionnaire and dogs' individual characteristics (i.e., age and sex) provided only limited information for the derived components. Overall, results suggest that no unique measurement for inhibitory control exists in dogs, but tests rather measure different aspects of this ability. Considering the context-specificity of inhibitory control in dogs and most probably also in other non-human animals, extreme caution is needed when making conclusions about inhibitory control abilities based on a single test. PMID:28596749

Investigating the relationship between deforestation and changes in hydrology across the island of Hispaniola

NASA Astrophysics Data System (ADS)

Hakimdavar, R.

2013-05-01

Over recent decades, Haiti and the Dominican Republic have reported changes in reservoir water levels - while some areas have experienced increases others have seen decreasing trends, especially reservoirs located in the Dominican Republic - leading to, among other things, regional flooding and shortages in hydroelectricity output. We investigate whether extensive deforestation, particularly in the western part of Hispaniola - shared by the two nations - is driving these changes by affecting the regional water balance. Due to a lack of available spatiotemporal environmental data, remotely sensed vegetation and precipitation information is used along with estimated evapotranspiration rates to study regional hydro-climatologic fluctuations over three decades. Changes in vegetative cover, precipitation, and evapotranspiration across the island are investigated using 25 years of Normalized Difference Vegetation Index (NDVI) data, historical satellite and gauge precipitation records, and estimated surface temperature and solar radiation. NDVI values are derived from imagery obtained by NOAA's 8 km resolution AVHRR instrument. Monthly precipitation is collected from several different sources, including NASA and NOAA precipitation satellites, as well as local rain gauges. Evapotranspiration is estimated using an energy balance approach. Preliminary results indicate a general decrease in rainfall over the eastern part of the island during the past three decades, with little change observed across the western half. NDVI and precipitation anomalies across the island are not well correlated, suggesting that deforestation is likely not the cause of regional changes in precipitation. The results of this work hold potentially important implications for future land-use and water infrastructure planning for both nations.

Biological processes modulating longevity across primates: a phylogenetic genome-phenome analysis.

PubMed

Muntané, Gerard; Farré, Xavier; Antonio Rodríguez, Juan; Pegueroles, Cinta; Hughes, David A; de Magalhães, João Pedro; Gabaldón, Toni; Navarro, Arcadi

2018-05-21

Aging is a complex process affecting different species and individuals in different ways. Comparing genetic variation across species with their aging phenotypes will help understanding the molecular basis of aging and longevity. Although most studies on aging have so far focused on short-lived model organisms, recent comparisons of genomic, transcriptomic, and metabolomic data across lineages with different lifespans are unveiling molecular signatures associated with longevity. Here, we examine the relationship between genomic variation and maximum lifespan (MLS) across primate species. We used two different approaches. First, we searched for parallel amino acid mutations that co-occur with increases in longevity across the primate linage. Twenty-five such amino acid variants were identified, several of which have been previously reported by studies with different experimental setups and in different model organisms. The genes harboring these mutations are mainly enriched in functional categories such as Wound Healing, Blood Coagulation and Cardiovascular Disorders. We demonstrate that these pathways are highly enriched for pleiotropic effects, as predicted by the Antagonistic Pleiotropy (AP) theory of aging. A second approach was focused on changes in rates of protein evolution across the primate phylogeny. Using the Phylogenetic Generalized Least Squares (PGLS) we show that some genes exhibit strong correlations between their evolutionary rates and longevity-associated traits. These include genes in the Sphingosine 1-phosphate pathway, PI3K signaling and the Thrombin/protease-activated receptor pathway, among other cardiovascular processes. Together, these results shed light into human senescence patterns and underscore the power of comparative genomics to identify pathways related to aging and longevity.

Intra- and interspecific tree growth across a long altitudinal gradient in the Peruvian Andes.

PubMed

Rapp, Joshua M; Silman, Miles R; Clark, James S; Girardin, Cecile A J; Galiano, Darcy; Tito, Richard

2012-09-01

Tree growth response across environmental gradients is fundamental to understanding species distributional ecology and forest ecosystem ecology and to predict future ecosystem services. Cross-sectional patterns of ecosystem properties with respect to climatic gradients are often used to predict ecosystem responses to global change. Across sites in the tropics, primary productivity increases with temperature, suggesting that forest ecosystems will become more productive as temperature rises. However, this trend is confounded with a shift in species composition and so may not reflect the response of in situ forests to warming. In this study, we simultaneously studied tree diameter growth across the altitudinal ranges of species within a single genus across a geographically compact temperature gradient, to separate the direct effect of temperature on tree growth from that of species compositional turnover. Using a Bayesian state space modeling framework we combined data from repeated diameter censuses and dendrometer measurements from across a 1700-m altitudinal gradient collected over six years on over 2400 trees in Weinmannia, a dominant and widespread genus of cloud forest trees in the Andes. Within species, growth showed no consistent trend with altitude, but higher-elevation species had lower growth rates than lower-elevation species, suggesting that species turnover is largely responsible for the positive correlation between productivity and temperature in tropical forests. Our results may indicate a significant difference in how low- and high-latitude forests will respond to climate change, since temperate and boreal tree species are consistently observed to have a positive relationship between growth and temperature. If our results hold for other tropical species, a positive response in ecosystem productivity to increasing temperatures in the Andes will depend on the altitudinal migration of tree species. The rapid pace of climate change, and slow observed

Integrating across scales: Effectively applying science for the successful conservation of Atlantic salmon (Salmo salar)

USGS Publications Warehouse

Mather, M. E.; Parrish, D.L.; Folt, C.L.; DeGraaf, R.M.

1998-01-01

Atlantic salmon (Salmo salar) is an excellent species on which to focus synthetic, integrative investigations because it is an economically important species that captures the public imagination, is heavily impacted by humans, uses several ecosystems over its life, and is the subject of a large body of extant literature. The following 24 papers were solicited to provide the biological basis for effective and innovative approaches that biologists, managers, and social scientists can use to develop policies that sustain Atlantic salmon and related species. Together these papers highlight the need for and benefits of (a) synthesizing within populations, (b) choosing the appropriate scale, (c) comparing across populations using rigorous, focused, question-oriented methods, (d) integrating across disciplines, (e) incorporating the human perspective, (f) linking multiple ecosystems, and (g) applied problem solving. To show how Atlantic salmon can guide research and conservation efforts for other species in other systems, we review the justification for the supplement and summarize the defining concepts that emerge from the volume.

An Investigation of the Relationship Between Alcohol Use and Major Depressive Disorder Across Hispanic National Groups.

PubMed

Jetelina, Katelyn K; Reingle Gonzalez, Jennifer M; Vaeth, Patrice A C; Mills, Britain A; Caetano, Raul

2016-03-01

There has been consistent epidemiological evidence of the association between drinking, alcohol dependence, and depression. However, most of the research has ignored potential diversity across Hispanic national subgroups. This study examines the prevalence of depression and explores its association with volume of drinking, age at first drink, binge drinking, and alcohol dependence across Mexican American, Puerto Rican, Cuban, and South/Central American Hispanic national groups. Data from more than 19,000 Hispanic adults were obtained from the 2010 to 2012 National Survey on Drug Use and Health. Survey logistic regression methods were used to test for differences in the relationship between major depressive disorder (MDD) and alcohol consumption across national groups. The prevalence of MDD varied significantly across Hispanic national groups (χ(2)  = 67.06, p < 0.001). Puerto Ricans (14%) and Mexican Americans (9%) were most likely to have MDD. Mexican Americans had the highest prevalence of alcohol dependence, volume of consumption, and youngest age at first drink compared to Puerto Ricans, Cuban Americans, and Central/South Americans. Multivariate results suggest that the odds of alcohol dependence were nearly 4 times greater among Hispanics with MDD compared to Hispanics who did not meet the criteria for MDD. Hispanic national origin did not modify the association between MDD and alcohol use. Although significant differences in the prevalence rates of MDD and alcohol-use measures emerged across Hispanic national groups, there was no evidence that the relationships between these measures were different across Hispanic national groups. Further research should investigate the root causes of these variable MDD prevalence rates to inform detection and intervention efforts targeted toward specific national groups. Copyright © 2016 by the Research Society on Alcoholism.

Global priorities for conservation across multiple dimensions of mammalian diversity

PubMed Central

Graham, Catherine H.; Costa, Gabriel C.; Hedges, S. Blair; Penone, Caterina; Radeloff, Volker C.; Rondinini, Carlo; Davidson, Ana D.

2017-01-01

Conservation priorities that are based on species distribution, endemism, and vulnerability may underrepresent biologically unique species as well as their functional roles and evolutionary histories. To ensure that priorities are biologically comprehensive, multiple dimensions of diversity must be considered. Further, understanding how the different dimensions relate to one another spatially is important for conservation prioritization, but the relationship remains poorly understood. Here, we use spatial conservation planning to (i) identify and compare priority regions for global mammal conservation across three key dimensions of biodiversity—taxonomic, phylogenetic, and traits—and (ii) determine the overlap of these regions with the locations of threatened species and existing protected areas. We show that priority areas for mammal conservation exhibit low overlap across the three dimensions, highlighting the need for an integrative approach for biodiversity conservation. Additionally, currently protected areas poorly represent the three dimensions of mammalian biodiversity. We identify areas of high conservation priority among and across the dimensions that should receive special attention for expanding the global protected area network. These high-priority areas, combined with areas of high priority for other taxonomic groups and with social, economic, and political considerations, provide a biological foundation for future conservation planning efforts. PMID:28674013

Global priorities for conservation across multiple dimensions of mammalian diversity.

PubMed

Brum, Fernanda T; Graham, Catherine H; Costa, Gabriel C; Hedges, S Blair; Penone, Caterina; Radeloff, Volker C; Rondinini, Carlo; Loyola, Rafael; Davidson, Ana D

2017-07-18

Conservation priorities that are based on species distribution, endemism, and vulnerability may underrepresent biologically unique species as well as their functional roles and evolutionary histories. To ensure that priorities are biologically comprehensive, multiple dimensions of diversity must be considered. Further, understanding how the different dimensions relate to one another spatially is important for conservation prioritization, but the relationship remains poorly understood. Here, we use spatial conservation planning to ( i ) identify and compare priority regions for global mammal conservation across three key dimensions of biodiversity-taxonomic, phylogenetic, and traits-and ( ii ) determine the overlap of these regions with the locations of threatened species and existing protected areas. We show that priority areas for mammal conservation exhibit low overlap across the three dimensions, highlighting the need for an integrative approach for biodiversity conservation. Additionally, currently protected areas poorly represent the three dimensions of mammalian biodiversity. We identify areas of high conservation priority among and across the dimensions that should receive special attention for expanding the global protected area network. These high-priority areas, combined with areas of high priority for other taxonomic groups and with social, economic, and political considerations, provide a biological foundation for future conservation planning efforts.

Differential in surface elevation change across mangrove forests in the intertidal zone

NASA Astrophysics Data System (ADS)

Fu, Haifeng; Wang, Wenqing; Ma, Wei; Wang, Mao

2018-07-01

A better understanding of surface elevation changes in different mangrove forests would improve our predictions of sea-level rise impacts, not only upon mangrove species distributions in the intertidal zone, but also on the functioning of these wetlands. Here, a two-year (2015-2017) dataset derived from 18 RSET-MH (rod surface elevation table-marker horizon) stations at Dongzhaigang Bay, Hainan, China, was analyzed to investigate how surface elevation changes differed across mangrove species zones. The current SET data indicated a rather high rate (9.6 mm y-1, on average) of surface elevation gain that was mostly consistent with that (8.1 mm y-1, on average) inferred from either the 137Cs or 210Pb dating of sediment cores. In addition, these surface elevation changes were sensitive to elevation in the intertidal zone and differed significantly between the two study sites (Sanjiang and Houpai). Mangrove species inhabiting the lower intertidal zone tended to experience greater surface elevation change at Sanjiang, which agrees with the general view that sedimentation and elevation gains are driven by elevation in the intertidal zone (i.e., greater when positioned lower in the intertidal profile). However, at Houpai, both surface elevation change and surface accretion showed the opposite trend (i.e., greater when positioned higher in the intertidal profile). This study's results indicate that the pattern of surface elevation changes across the intertidal profile maybe inconsistent due to intricate biophysical controls. Therefore, instead of using a constant rate, models should presume a topography that evolves at differing rates of surface elevation change in different species zones across the intertidal profile when predicting the impacts of sea-level rise on mangrove distributions.

Substitution of synthetic chimpanzee androgen receptor for human androgen receptor in competitive binding and transcriptional activation assays for EDC screening

EPA Science Inventory

The potential effect of receptor-mediated endocrine modulators across species is of increasing concern. In attempts to address these concerns we are developing androgen and estrogen receptor binding assays using recombinant hormone receptors from a number of species across differ...

The evolution of highly variable immunity genes across a passerine bird radiation.

PubMed

O'Connor, E A; Strandh, M; Hasselquist, D; Nilsson, J-Å; Westerdahl, H

2016-02-01

To survive, individuals must be able to recognize and eliminate pathogens. The genes of the major histocompatibility complex (MHC) play an essential role in this process in vertebrates as their diversity affects the repertoire of pathogens that can be recognized by the immune system. Emerging evidence suggests that birds within the parvorder Passerida possess an exceptionally high number of MHC genes. However, this has yet to be directly investigated using a consistent framework, and the question of how this MHC diversity has evolved has not been addressed. We used next-generation sequencing to investigate how MHC class I gene copy number and sequence diversity varies across the Passerida radiation using twelve species chosen to represent the phylogenetic range of this group. Additionally, we performed phylogenetic analyses on this data to identify, for the first time, the evolutionary model that best describes how MHC class I gene diversity has evolved within Passerida. We found evidence of multiple MHC class I genes in every family tested, with an extremely broad range in gene copy number across Passerida. There was a strong phylogenetic signal in MHC gene copy number and diversity, and these traits appear to have evolved through a process of Brownian motion in the species studied, that is following the pattern of genetic drift or fluctuating selection, as opposed to towards a single optimal value or through evolutionary 'bursts'. By characterizing MHC class I gene diversity across Passerida in a systematic framework, this study provides a first step towards understanding this huge variation. © 2016 John Wiley & Sons Ltd.

Termite assemblages from oil palm agroecosystems across Riau Province, Sumatra, Indonesia

NASA Astrophysics Data System (ADS)

Saputra, Andi; Jalaludin, Nur-Atiqah; Hazmi, Izfa Riza; Rahim, Faszly

2016-11-01

Termite survey was conducted at six oil palm agroecosystem sites in Riau Province, Sumatra, Indonesia to document species richness across the sites. Six sites were surveyed by using continuous transect representing gradients of oil palm landuse across Indragiri Hulu to Bengkalis District since February 5th, 2015 until May 21st, 2015. Termites were sampled by modified transect protocols (100 m × 4 m × 10 cm). A total of 23 species belonging to two families and five subfamilies were collected. The termite assemblage was dominated by wood-feeding termites. The major family collected was Rhinotermitidae which included some pest species, such as Coptotermes curvignathus, C. sepangensis, C. kalshoveni, Schedorhinotermes malaccensis, S. medioobscurus, S. brevialatus, and S. javanicus.

Diversification in the Mexican horned lizard Phrynosoma orbiculare across a dynamic landscape.

PubMed

Bryson, Robert W; García-Vázquez, Uri Omar; Riddle, Brett R

2012-01-01

The widespread montane Mexican horned lizard Phrynosoma orbiculare (Squamata: Phrynosomatidae) represents an ideal species to investigate the relative impacts of Neogene vicariance and Quaternary climate change on lineage diversification across the Mexican highlands. We used mitochondrial DNA to examine the maternal history of P. orbiculare and estimate the timing and tempo of lineage diversification. Based on our results, we inferred 11 geographically structured, well supported mitochondrial lineages within this species, suggesting P. orbiculare represents a species complex. Six divergences between lineages likely occurred during the Late Miocene and Pliocene, and four splits probably happened during the Pleistocene. Diversification rate appeared relatively constant through time. Spatial and temporal divergences between lineages of P. orbiculare and co-distributed taxa suggest that a distinct period of uplifting of the Transvolcanic Belt around 7.5-3 million years ago broadly impacted diversification in taxa associated with this mountain range. To the north, several river drainages acting as filter barriers differentially subdivided co-distributed highland taxa through time. Diversification patterns observed in P. orbiculare provide additional insight into the mechanisms that impacted differentiation of highland taxa across the complex Mexican highlands. Copyright © 2011 Elsevier Inc. All rights reserved.

Photosynthetic capacity is negatively correlated with the concentration of leaf phenolic compounds across a range of different species

PubMed Central

Sumbele, Sally; Fotelli, Mariangela N.; Nikolopoulos, Dimosthenis; Tooulakou, Georgia; Liakoura, Vally; Liakopoulos, Georgios; Bresta, Panagiota; Dotsika, Elissavet; Adams, Mark A.; Karabourniotis, George

2012-01-01

Background and aims Phenolic compounds are the most commonly studied of all secondary metabolites because of their significant protective–defensive roles and their significant concentration in plant tissues. However, there has been little study on relationships between gas exchange parameters and the concentration of leaf phenolic compounds (total phenolics (TP) and condensed tannins (CT)) across a range of species. Therefore, we addressed the question: is there any correlation between photosynthetic capacity (Amax) and TP and CT across species from different ecosystems in different continents? Methodology A plethora of functional and structural parameters were measured in 49 plant species following different growth strategies from five sampling sites located in Greece and Australia. The relationships between several leaf traits were analysed by means of regression and principal component analysis. Principal results The results revealed a negative relationship between TP and CT and Amax among the different plant species, growth strategies and sampling sites, irrespective of expression (with respect to mass, area or nitrogen content). Principal component analysis showed that high concentrations of TP and CT are associated with thick, dense leaves with low nitrogen. This leaf type is characterized by low growth, Amax and transpiration rates, and is common in environments with low water and nutrient availability, high temperatures and high light intensities. Therefore, the high TP and CT in such leaves are compatible with the protective and defensive functions ascribed to them. Conclusions Our results indicate a functional integration between carbon gain and the concentration of leaf phenolic compounds that reflects the trade-off between growth and defence/protection demands, depending on the growth strategy adopted by each species. PMID:23050073

Photosynthetic capacity is negatively correlated with the concentration of leaf phenolic compounds across a range of different species.

PubMed

Sumbele, Sally; Fotelli, Mariangela N; Nikolopoulos, Dimosthenis; Tooulakou, Georgia; Liakoura, Vally; Liakopoulos, Georgios; Bresta, Panagiota; Dotsika, Elissavet; Adams, Mark A; Karabourniotis, George

2012-01-01

Phenolic compounds are the most commonly studied of all secondary metabolites because of their significant protective-defensive roles and their significant concentration in plant tissues. However, there has been little study on relationships between gas exchange parameters and the concentration of leaf phenolic compounds (total phenolics (TP) and condensed tannins (CT)) across a range of species. Therefore, we addressed the question: is there any correlation between photosynthetic capacity (A(max)) and TP and CT across species from different ecosystems in different continents? A plethora of functional and structural parameters were measured in 49 plant species following different growth strategies from five sampling sites located in Greece and Australia. The relationships between several leaf traits were analysed by means of regression and principal component analysis. The results revealed a negative relationship between TP and CT and A(max) among the different plant species, growth strategies and sampling sites, irrespective of expression (with respect to mass, area or nitrogen content). Principal component analysis showed that high concentrations of TP and CT are associated with thick, dense leaves with low nitrogen. This leaf type is characterized by low growth, A(max) and transpiration rates, and is common in environments with low water and nutrient availability, high temperatures and high light intensities. Therefore, the high TP and CT in such leaves are compatible with the protective and defensive functions ascribed to them. Our results indicate a functional integration between carbon gain and the concentration of leaf phenolic compounds that reflects the trade-off between growth and defence/protection demands, depending on the growth strategy adopted by each species.

Characterization of the nociceptin receptor (ORL-1) agonist, Ro64-6198, in tests of anxiety across multiple species.

PubMed

Varty, G B; Hyde, L A; Hodgson, R A; Lu, S X; McCool, M F; Kazdoba, T M; Del Vecchio, R A; Guthrie, D H; Pond, A J; Grzelak, M E; Xu, X; Korfmacher, W A; Tulshian, D; Parker, E M; Higgins, G A

2005-10-01

Previous studies have demonstrated behaviors indicative of anxiolysis in rats pretreated with the nociceptin receptor (opioid receptor like-1, ORL-1) agonist, Ro64-6198. The aim of this study was to examine the effects of Ro64-6198 in anxiety models across three species: rat, guinea pig, and mouse. In addition, the receptor specificity of Ro64-6198 was studied, using the ORL-1 receptor antagonist, J-113397, and ORL-1 receptor knockout (KO) mice. Finally, neurological studies examined potential side effects of Ro64-6198 in the rat and mouse. Ro64-6198 (3-10 mg/kg) increased punished responding in a rat conditioned lick suppression test similarly to chlordiazepoxide (6 mg/kg). This effect of Ro64-6198 was attenuated by J-113397 (10 mg/kg), but not the mu opioid antagonist, naltrexone (3 mg/kg). In addition, Ro64-6198 (1-3 mg/kg) reduced isolation-induced vocalizations in rat and guinea pig pups. Ro64-6198 (3 mg/kg) increased the proportion of punished responding in a mouse Geller-Seifter test in wild-type (WT) but not ORL-1 KO mice, whereas diazepam (1-5.6 mg/kg) was effective in both genotypes. In rats, Ro64-6198 reduced locomotor activity (LMA) and body temperature and impaired rotarod, beam walking, and fixed-ratio (FR) performance at doses of 10-30 mg/kg, i.e., three to ten times higher than an anxiolytic dose. In WT mice, Ro64-6198 (3-10 mg/kg) reduced LMA and rotarod performance, body temperature, and FR responding, but these same measures were unaffected in ORL-1 KO mice. Haloperidol (0.3-3 mg/kg) reduced these measures to a similar extent in both genotypes. These studies confirm the potent, ORL-1 receptor-mediated, anxiolytic-like effects of Ro64-6198, extending the findings across three species. Ro64-6198 has target-based side effects, although the magnitude of these effects varies across species.

Concordance between genetic and species diversity in coral reef fishes across the Pacific Ocean biodiversity gradient.

PubMed

Messmer, Vanessa; Jones, Geoffrey P; Munday, Philip L; Planes, Serge

2012-12-01

The relationship between genetic diversity and species diversity provides insights into biogeography and historic patterns of evolution and is critical for developing contemporary strategies for biodiversity conservation. Although concordant large-scale clines in genetic and species diversity have been described for terrestrial organisms, whether these parameters co-vary in marine species remains largely unknown. We examined patterns of genetic diversity for 11 coral reef fish species sampled at three locations across the Pacific Ocean species diversity gradient (Australia: ∼1600 species; New Caledonia: ∼1400 species; French Polynesia: ∼800 species). Combined genetic diversity for all 11 species paralleled the decline in species diversity from West to East, with French Polynesia exhibiting lowest total haplotype and nucleotide diversities. Haplotype diversity consistently declined toward French Polynesia in all and nucleotide diversity in the majority of species. The French Polynesian population of most species also exhibited significant genetic differentiation from populations in the West Pacific. A number of factors may have contributed to the general positive correlation between genetic and species diversity, including location and time of species origin, vicariance events, reduced gene flow with increasing isolation, and decreasing habitat area from West to East. However, isolation and habitat area, resulting in reduced population size, are likely to be the most influential. © 2012 The Author(s). Evolution© 2012 The Society for the Study of Evolution.

Identifying bioindicators across trait-taxon space for assessing water quality in marine environments.

PubMed

Xu, Guangjian; Zhong, Xiaoxiao; Al, Mamun Abdullah; Warren, Alan; Xu, Henglong

2018-06-01

The response units of protozoan communities, based on a community-weighted mean (CWM) dataset across trait-taxon space, were investigated in order to determine their utility as bioindicators of marine water quality. From a total of 17 functional categories of seven biological traits, three functional response units (FRUs) were identified at correlation levels of >0.75. FRUs 1 and 3 generally dominated the communities in more polluted areas during warm seasons, while FRU2 appeared to prefer less polluted waters and dominated the communities in spring and winter. Correlation analysis demonstrated that the CWM values of FRUs 1 and 3 were significantly positively correlated to the concentrations of chemical oxygen demand (COD), whereas those of FRU2 were negatively correlated to COD. Across taxon-function space, 16 species were identified as potential bioindicators of water quality. These results suggest that redundancy analysis across trait-taxon space is a useful tool for identifying indicators of environmental quality. Copyright © 2018 Elsevier Ltd. All rights reserved.

Evolutionary tradeoffs in cellular composition across diverse bacteria

PubMed Central

Kempes, Christopher P; Wang, Lawrence; Amend, Jan P; Doyle, John; Hoehler, Tori

2016-01-01

One of the most important classic and contemporary interests in biology is the connection between cellular composition and physiological function. Decades of research have allowed us to understand the detailed relationship between various cellular components and processes for individual species, and have uncovered common functionality across diverse species. However, there still remains the need for frameworks that can mechanistically predict the tradeoffs between cellular functions and elucidate and interpret average trends across species. Here we provide a comprehensive analysis of how cellular composition changes across the diversity of bacteria as connected with physiological function and metabolism, spanning five orders of magnitude in body size. We present an analysis of the trends with cell volume that covers shifts in genomic, protein, cellular envelope, RNA and ribosomal content. We show that trends in protein content are more complex than a simple proportionality with the overall genome size, and that the number of ribosomes is simply explained by cross-species shifts in biosynthesis requirements. Furthermore, we show that the largest and smallest bacteria are limited by physical space requirements. At the lower end of size, cell volume is dominated by DNA and protein content—the requirement for which predicts a lower limit on cell size that is in good agreement with the smallest observed bacteria. At the upper end of bacterial size, we have identified a point at which the number of ribosomes required for biosynthesis exceeds available cell volume. Between these limits we are able to discuss systematic and dramatic shifts in cellular composition. Much of our analysis is connected with the basic energetics of cells where we show that the scaling of metabolic rate is surprisingly superlinear with all cellular components. PMID:27046336

Food-Web Structure of Seagrass Communities across Different Spatial Scales and Human Impacts

PubMed Central

Coll, Marta; Schmidt, Allison; Romanuk, Tamara; Lotze, Heike K.

2011-01-01

Seagrass beds provide important habitat for a wide range of marine species but are threatened by multiple human impacts in coastal waters. Although seagrass communities have been well-studied in the field, a quantification of their food-web structure and functioning, and how these change across space and human impacts has been lacking. Motivated by extensive field surveys and literature information, we analyzed the structural features of food webs associated with Zostera marina across 16 study sites in 3 provinces in Atlantic Canada. Our goals were to (i) quantify differences in food-web structure across local and regional scales and human impacts, (ii) assess the robustness of seagrass webs to simulated species loss, and (iii) compare food-web structure in temperate Atlantic seagrass beds with those of other aquatic ecosystems. We constructed individual food webs for each study site and cumulative webs for each province and the entire region based on presence/absence of species, and calculated 16 structural properties for each web. Our results indicate that food-web structure was similar among low impact sites across regions. With increasing human impacts associated with eutrophication, however, food-web structure show evidence of degradation as indicated by fewer trophic groups, lower maximum trophic level of the highest top predator, fewer trophic links connecting top to basal species, higher fractions of herbivores and intermediate consumers, and higher number of prey per species. These structural changes translate into functional changes with impacted sites being less robust to simulated species loss. Temperate Atlantic seagrass webs are similar to a tropical seagrass web, yet differed from other aquatic webs, suggesting consistent food-web characteristics across seagrass ecosystems in different regions. Our study illustrates that food-web structure and functioning of seagrass habitats change with human impacts and that the spatial scale of food-web analysis

Food-web structure of seagrass communities across different spatial scales and human impacts.

PubMed

Coll, Marta; Schmidt, Allison; Romanuk, Tamara; Lotze, Heike K

2011-01-01

Seagrass beds provide important habitat for a wide range of marine species but are threatened by multiple human impacts in coastal waters. Although seagrass communities have been well-studied in the field, a quantification of their food-web structure and functioning, and how these change across space and human impacts has been lacking. Motivated by extensive field surveys and literature information, we analyzed the structural features of food webs associated with Zostera marina across 16 study sites in 3 provinces in Atlantic Canada. Our goals were to (i) quantify differences in food-web structure across local and regional scales and human impacts, (ii) assess the robustness of seagrass webs to simulated species loss, and (iii) compare food-web structure in temperate Atlantic seagrass beds with those of other aquatic ecosystems. We constructed individual food webs for each study site and cumulative webs for each province and the entire region based on presence/absence of species, and calculated 16 structural properties for each web. Our results indicate that food-web structure was similar among low impact sites across regions. With increasing human impacts associated with eutrophication, however, food-web structure show evidence of degradation as indicated by fewer trophic groups, lower maximum trophic level of the highest top predator, fewer trophic links connecting top to basal species, higher fractions of herbivores and intermediate consumers, and higher number of prey per species. These structural changes translate into functional changes with impacted sites being less robust to simulated species loss. Temperate Atlantic seagrass webs are similar to a tropical seagrass web, yet differed from other aquatic webs, suggesting consistent food-web characteristics across seagrass ecosystems in different regions. Our study illustrates that food-web structure and functioning of seagrass habitats change with human impacts and that the spatial scale of food-web analysis

Patterns of Genetic Variation across Altitude in Three Plant Species of Semi-Dry Grasslands

PubMed Central

Hahn, Thomas; Kettle, Chris J.; Ghazoul, Jaboury; Frei, Esther R.; Matter, Philippe; Pluess, Andrea R.

2012-01-01

Background Environmental gradients caused by altitudinal gradients may affect genetic variation within and among plant populations and inbreeding within populations. Populations in the upper range periphery of a species may be important source populations for range shifts to higher altitude in response to climate change. In this study we investigate patterns of population genetic variation at upper peripheral and lower more central altitudes in three common plant species of semi-dry grasslands in montane landscapes. Methodology/Principal Findings In Briza media, Trifolium montanum and Ranunculus bulbosus genetic diversity, inbreeding and genetic relatedness of individuals within populations and genetic differentiation among populations was characterized using AFLP markers. Populations were sampled in the Swiss Alps at 1800 (upper periphery of the study organisms) and at 1200 m a.s.l. Genetic diversity was not affected by altitude and only in B. media inbreeding was greater at higher altitudes. Genetic differentiation was slightly greater among populations at higher altitudes in B. media and individuals within populations were more related to each other compared to individuals in lower altitude populations. A similar but less strong pattern of differentiation and relatedness was observed in T. montanum, while in R. bulbosus there was no effect of altitude. Estimations of population size and isolation of populations were similar, both at higher and lower altitudes. Conclusions/Significance Our results suggest that altitude does not affect genetic diversity in the grassland species under study. Genetic differentiation of populations increased only slightly at higher elevation, probably due to extensive (historic) gene flow among altitudes. Potentially pre-adapted genes might therefore spread easily across altitudes. Our study indicates that populations at the upper periphery are not genetically depauperate or isolated and thus may be important source populations for

Urban Tree Species Show the Same Hydraulic Response to Vapor Pressure Deficit across Varying Tree Size and Environmental Conditions

PubMed Central

Chen, Lixin; Zhang, Zhiqiang; Ewers, Brent E.

2012-01-01

Background The functional convergence of tree transpiration has rarely been tested for tree species growing under urban conditions even though it is of significance to elucidate the relationship between functional convergence and species differences of urban trees for establishing sustainable urban forests in the context of forest water relations. Methodology/Principal Findings We measured sap flux of four urban tree species including Cedrus deodara, Zelkova schneideriana, Euonymus bungeanus and Metasequoia glyptostroboides in an urban park by using thermal dissipation probes (TDP). The concurrent microclimate conditions and soil moisture content were also measured. Our objectives were to examine 1) the influence of tree species and size on transpiration, and 2) the hydraulic control of urban trees under different environmental conditions over the transpiration in response to VPD as represented by canopy conductance. The results showed that the functional convergence between tree diameter at breast height (DBH) and tree canopy transpiration amount (E c) was not reliable to predict stand transpiration and there were species differences within same DBH class. Species differed in transpiration patterns to seasonal weather progression and soil water stress as a result of varied sensitivity to water availability. Species differences were also found in their potential maximum transpiration rate and reaction to light. However, a same theoretical hydraulic relationship between G c at VPD = 1 kPa (G cref) and the G c sensitivity to VPD (−dG c/dlnVPD) across studied species as well as under contrasting soil water and R s conditions in the urban area. Conclusions/Significance We concluded that urban trees show the same hydraulic regulation over response to VPD across varying tree size and environmental conditions and thus tree transpiration could be predicted with appropriate assessment of G cref. PMID:23118904

Urban tree species show the same hydraulic response to vapor pressure deficit across varying tree size and environmental conditions.

PubMed

Chen, Lixin; Zhang, Zhiqiang; Ewers, Brent E

2012-01-01

The functional convergence of tree transpiration has rarely been tested for tree species growing under urban conditions even though it is of significance to elucidate the relationship between functional convergence and species differences of urban trees for establishing sustainable urban forests in the context of forest water relations. We measured sap flux of four urban tree species including Cedrus deodara, Zelkova schneideriana, Euonymus bungeanus and Metasequoia glyptostroboides in an urban park by using thermal dissipation probes (TDP). The concurrent microclimate conditions and soil moisture content were also measured. Our objectives were to examine 1) the influence of tree species and size on transpiration, and 2) the hydraulic control of urban trees under different environmental conditions over the transpiration in response to VPD as represented by canopy conductance. The results showed that the functional convergence between tree diameter at breast height (DBH) and tree canopy transpiration amount (E(c)) was not reliable to predict stand transpiration and there were species differences within same DBH class. Species differed in transpiration patterns to seasonal weather progression and soil water stress as a result of varied sensitivity to water availability. Species differences were also found in their potential maximum transpiration rate and reaction to light. However, a same theoretical hydraulic relationship between G(c) at VPD = 1 kPa (G(cref)) and the G(c) sensitivity to VPD (-dG(c)/dlnVPD) across studied species as well as under contrasting soil water and R(s) conditions in the urban area. We concluded that urban trees show the same hydraulic regulation over response to VPD across varying tree size and environmental conditions and thus tree transpiration could be predicted with appropriate assessment of G(cref).

Signs of Pretense across Age and Scenario

ERIC Educational Resources Information Center

Lillard, Angeline; Nishida, Tracy; Massaro, Davide; Vaish, Amrisha; Ma, Lili; McRoberts, Gerald

2007-01-01

Participation in imagined worlds is a hallmark of the human species, and yet we know little about the context of its early emergence. The experiments reported here replicated and extended in 2 directions Lillard and Witherington's (2004) study of how mothers pretend to have snacks, across different ages of children (15- to 24-month-olds,…

Spatial distribution of tree species governs the spatio-temporal interaction of leaf area index and soil moisture across a forested landscape.

PubMed

Naithani, Kusum J; Baldwin, Doug C; Gaines, Katie P; Lin, Henry; Eissenstat, David M

2013-01-01

Quantifying coupled spatio-temporal dynamics of phenology and hydrology and understanding underlying processes is a fundamental challenge in ecohydrology. While variation in phenology and factors influencing it have attracted the attention of ecologists for a long time, the influence of biodiversity on coupled dynamics of phenology and hydrology across a landscape is largely untested. We measured leaf area index (L) and volumetric soil water content (θ) on a co-located spatial grid to characterize forest phenology and hydrology across a forested catchment in central Pennsylvania during 2010. We used hierarchical Bayesian modeling to quantify spatio-temporal patterns of L and θ. Our results suggest that the spatial distribution of tree species across the landscape created unique spatio-temporal patterns of L, which created patterns of water demand reflected in variable soil moisture across space and time. We found a lag of about 11 days between increase in L and decline in θ. Vegetation and soil moisture become increasingly homogenized and coupled from leaf-onset to maturity but heterogeneous and uncoupled from leaf maturity to senescence. Our results provide insight into spatio-temporal coupling between biodiversity and soil hydrology that is useful to enhance ecohydrological modeling in humid temperate forests.

DNA barcoding unveils skate (Chondrichthyes: Rajidae) species diversity in ‘ray’ products sold across Ireland and the UK

PubMed Central

Egan, Aaron; Fox, Jennifer; Greenfield, Adam; Mariani, Stefano

2013-01-01

Skates are widely consumed across the globe, but many large species are subject to considerable concern regarding their conservation and management. Within Europe such issues have recently driven policy changes so that, for the first time, reports of skate landings now have to be made under species-specific names. Total allowable catches have also been established for many groups, which have been set to zero for a number of the most vulnerable species (e.g., Dipturus batis, Raja undulata and Rostoraja alba). Whilst accurate species identification has become an important issue for landings, the sale of skates is still usually made under a blanket term of “skate” or “ray”. The matter of identifying species of skate is further complicated by their morphologically conservative nature and the fact that they are commercially valued for their wings. Thus, before sale their bodies are usually discarded (i.e., “winged”) and often skinned, making morphological identification impossible. For the first time, DNA barcoding (of the mitochondrial COI gene) was applied to samples of skate wings from retail outlets across the British Isles, providing insight into which species are sold for consumption. A total of 98 wing samples were analysed, revealing that six species were sold; blonde ray (Raja brachyura), spotted ray (Raja montagui), thornback ray (Raja clavata), cuckoo ray (Leucoraja naevus) small-eyed ray (Raja microocellata) and shagreen ray (Leucoraja fullonica). Statistical testing demonstrated that there were significant differences in the species sold in the distinct retail groups which suggests complex drivers behind the patterns of sale in skates. The results also indicate that endangered species are not commonly being passed on to consumers. In addition, the practice of selling skate wings under ambiguous labels is highlighted as it makes it extremely difficult for consumers to exercise a right to avoid species of conservation concern. Interestingly, a

Seedling root responses to soil moisture and the identification of a belowground trait spectrum across three growth forms.

PubMed

Larson, Julie E; Funk, Jennifer L

2016-05-01

Root trait variation and plasticity could be key factors differentiating plant performance under drought. However, water manipulation and root measurements are rarely coupled empirically across growth forms to identify whether belowground strategies are generalizable across species. We measured seedling root traits across three moisture levels in 18 Mediterranean forbs, grasses, and woody species. Drought increased the root mass fraction (RMF) and decreased the relative proportion of thin roots (indicated by increased root diameters and decreased specific root length (SRL)), rates of root elongation and growth, plant nitrogen uptake, and plant growth. Although responses varied across species, plasticity was not associated with growth form. Woody species differed from forbs and grasses in many traits, but herbaceous groups were similar. Across water treatments, trait correlations suggested a single spectrum of belowground trade-offs related to resource acquisition and plant growth. While effects of SRL and RMF on plant growth shifted with drought, root elongation rate consistently represented this spectrum. We demonstrate that general patterns of root morphology and plasticity are identifiable across diverse species. Root trait measurements should enhance our understanding of belowground strategy and performance across growth forms, but it will be critical to incorporate plasticity and additional aspects of root function into these efforts. © 2016 The Authors. New Phytologist © 2016 New Phytologist Trust.

New applications in EPA’s ECOTOX Knowledge System: Assimilating relative potencies of metals across chemical and biological species from literature-based toxicity effects data.

EPA Science Inventory

Toxicity of metals in field settings can vary widely among ionic chemical species and across biological receptors. Thus, a challenge often found in developing TRVs for the risk assessment of metals is identifying the most appropriate metal and biological species combinations for...

The phylogeography of Myotis bat-associated rabies viruses across Canada.

PubMed

Nadin-Davis, Susan; Alnabelseya, Noor; Knowles, M Kimberly

2017-05-01

As rabies in carnivores is increasingly controlled throughout much of the Americas, bats are emerging as a significant source of rabies virus infection of humans and domestic animals. Knowledge of the bat species that maintain rabies is a crucial first step in reducing this public health problem. In North America, several bat species are known to be rabies virus reservoirs but the role of bats of the Myotis genus has been unclear due to the scarcity of laboratory confirmed cases and the challenges encountered in species identification of poorly preserved diagnostic submissions by morphological traits alone. This study has employed a collection of rabid bat specimens collected across Canada over a 25 year period to clearly define the role of particular Myotis species as rabies virus reservoirs. The virus was characterised by partial genome sequencing and host genetic barcoding, used to confirm species assignment of specimens, proved crucial to the identification of certain bat species as disease reservoirs. Several variants were associated with Myotis species limited in their Canadian range to the westernmost province of British Columbia while others were harboured by Myotis species that circulate across much of eastern and central Canada. All of these Myotis-associated viral variants, except for one, clustered as a monophyletic MYCAN clade, which has emerged from a lineage more broadly distributed across North America; in contrast one distinct variant, associated with the long-legged bat in Canada, represents a relatively recent host jump from a big brown bat reservoir. Together with evidence from South America, these findings demonstrate that rabies virus has emerged in the Myotis genus independently on multiple occasions and highlights the potential for emergence of new viral-host associations within this genus.

The phylogeography of Myotis bat-associated rabies viruses across Canada

PubMed Central

Alnabelseya, Noor; Knowles, M. Kimberly

2017-01-01

As rabies in carnivores is increasingly controlled throughout much of the Americas, bats are emerging as a significant source of rabies virus infection of humans and domestic animals. Knowledge of the bat species that maintain rabies is a crucial first step in reducing this public health problem. In North America, several bat species are known to be rabies virus reservoirs but the role of bats of the Myotis genus has been unclear due to the scarcity of laboratory confirmed cases and the challenges encountered in species identification of poorly preserved diagnostic submissions by morphological traits alone. This study has employed a collection of rabid bat specimens collected across Canada over a 25 year period to clearly define the role of particular Myotis species as rabies virus reservoirs. The virus was characterised by partial genome sequencing and host genetic barcoding, used to confirm species assignment of specimens, proved crucial to the identification of certain bat species as disease reservoirs. Several variants were associated with Myotis species limited in their Canadian range to the westernmost province of British Columbia while others were harboured by Myotis species that circulate across much of eastern and central Canada. All of these Myotis-associated viral variants, except for one, clustered as a monophyletic MYCAN clade, which has emerged from a lineage more broadly distributed across North America; in contrast one distinct variant, associated with the long-legged bat in Canada, represents a relatively recent host jump from a big brown bat reservoir. Together with evidence from South America, these findings demonstrate that rabies virus has emerged in the Myotis genus independently on multiple occasions and highlights the potential for emergence of new viral-host associations within this genus. PMID:28542160

Climate change impacts on bumblebees converge across continents

USDA-ARS?s Scientific Manuscript database

For many species, geographical ranges are expanding toward the poles in response to climate change, while remaining stable along range edges nearest the equator. Using long term observations across Europe and North America over 110 years, we test for climate change-related range shifts in bumblebee ...

Diversity Promotes Temporal Stability across Levels of Ecosystem Organization in Experimental Grasslands

PubMed Central

Proulx, Raphaël; Wirth, Christian; Voigt, Winfried; Weigelt, Alexandra; Roscher, Christiane; Attinger, Sabine; Baade, Jussi; Barnard, Romain L.; Buchmann, Nina; Buscot, François; Eisenhauer, Nico; Fischer, Markus; Gleixner, Gerd; Halle, Stefan; Hildebrandt, Anke; Kowalski, Esther; Kuu, Annely; Lange, Markus; Milcu, Alex; Niklaus, Pascal A.; Oelmann, Yvonne; Rosenkranz, Stephan; Sabais, Alexander; Scherber, Christoph; Scherer-Lorenzen, Michael; Scheu, Stefan; Schulze, Ernst-Detlef; Schumacher, Jens; Schwichtenberg, Guido; Soussana, Jean-François; Temperton, Vicky M.; Weisser, Wolfgang W.; Wilcke, Wolfgang; Schmid, Bernhard

2010-01-01

The diversity–stability hypothesis states that current losses of biodiversity can impair the ability of an ecosystem to dampen the effect of environmental perturbations on its functioning. Using data from a long-term and comprehensive biodiversity experiment, we quantified the temporal stability of 42 variables characterizing twelve ecological functions in managed grassland plots varying in plant species richness. We demonstrate that diversity increases stability i) across trophic levels (producer, consumer), ii) at both the system (community, ecosystem) and the component levels (population, functional group, phylogenetic clade), and iii) primarily for aboveground rather than belowground processes. Temporal synchronization across studied variables was mostly unaffected with increasing species richness. This study provides the strongest empirical support so far that diversity promotes stability across different ecological functions and levels of ecosystem organization in grasslands. PMID:20967213

Diversity promotes temporal stability across levels of ecosystem organization in experimental grasslands.

PubMed

Proulx, Raphaël; Wirth, Christian; Voigt, Winfried; Weigelt, Alexandra; Roscher, Christiane; Attinger, Sabine; Baade, Jussi; Barnard, Romain L; Buchmann, Nina; Buscot, François; Eisenhauer, Nico; Fischer, Markus; Gleixner, Gerd; Halle, Stefan; Hildebrandt, Anke; Kowalski, Esther; Kuu, Annely; Lange, Markus; Milcu, Alex; Niklaus, Pascal A; Oelmann, Yvonne; Rosenkranz, Stephan; Sabais, Alexander; Scherber, Christoph; Scherer-Lorenzen, Michael; Scheu, Stefan; Schulze, Ernst-Detlef; Schumacher, Jens; Schwichtenberg, Guido; Soussana, Jean-François; Temperton, Vicky M; Weisser, Wolfgang W; Wilcke, Wolfgang; Schmid, Bernhard

2010-10-13

The diversity-stability hypothesis states that current losses of biodiversity can impair the ability of an ecosystem to dampen the effect of environmental perturbations on its functioning. Using data from a long-term and comprehensive biodiversity experiment, we quantified the temporal stability of 42 variables characterizing twelve ecological functions in managed grassland plots varying in plant species richness. We demonstrate that diversity increases stability i) across trophic levels (producer, consumer), ii) at both the system (community, ecosystem) and the component levels (population, functional group, phylogenetic clade), and iii) primarily for aboveground rather than belowground processes. Temporal synchronization across studied variables was mostly unaffected with increasing species richness. This study provides the strongest empirical support so far that diversity promotes stability across different ecological functions and levels of ecosystem organization in grasslands.

A cost minimisation and Bayesian inference model predicts startle reflex modulation across species.

PubMed

Bach, Dominik R

2015-04-07

In many species, rapid defensive reflexes are paramount to escaping acute danger. These reflexes are modulated by the state of the environment. This is exemplified in fear-potentiated startle, a more vigorous startle response during conditioned anticipation of an unrelated threatening event. Extant explanations of this phenomenon build on descriptive models of underlying psychological states, or neural processes. Yet, they fail to predict invigorated startle during reward anticipation and instructed attention, and do not explain why startle reflex modulation evolved. Here, we fill this lacuna by developing a normative cost minimisation model based on Bayesian optimality principles. This model predicts the observed pattern of startle modification by rewards, punishments, instructed attention, and several other states. Moreover, the mathematical formalism furnishes predictions that can be tested experimentally. Comparing the model with existing data suggests a specific neural implementation of the underlying computations which yields close approximations to the optimal solution under most circumstances. This analysis puts startle modification into the framework of Bayesian decision theory and predictive coding, and illustrates the importance of an adaptive perspective to interpret defensive behaviour across species. Copyright © 2015 The Author. Published by Elsevier Ltd.. All rights reserved.

ChloroMitoCU: Codon patterns across organelle genomes for functional genomics and evolutionary applications.

PubMed

Sablok, Gaurav; Chen, Ting-Wen; Lee, Chi-Ching; Yang, Chi; Gan, Ruei-Chi; Wegrzyn, Jill L; Porta, Nicola L; Nayak, Kinshuk C; Huang, Po-Jung; Varotto, Claudio; Tang, Petrus

2017-06-01

Organelle genomes are widely thought to have arisen from reduction events involving cyanobacterial and archaeal genomes, in the case of chloroplasts, or α-proteobacterial genomes, in the case of mitochondria. Heterogeneity in base composition and codon preference has long been the subject of investigation of topics ranging from phylogenetic distortion to the design of overexpression cassettes for transgenic expression. From the overexpression point of view, it is critical to systematically analyze the codon usage patterns of the organelle genomes. In light of the importance of codon usage patterns in the development of hyper-expression organelle transgenics, we present ChloroMitoCU, the first-ever curated, web-based reference catalog of the codon usage patterns in organelle genomes. ChloroMitoCU contains the pre-compiled codon usage patterns of 328 chloroplast genomes (29,960 CDS) and 3,502 mitochondrial genomes (49,066 CDS), enabling genome-wide exploration and comparative analysis of codon usage patterns across species. ChloroMitoCU allows the phylogenetic comparison of codon usage patterns across organelle genomes, the prediction of codon usage patterns based on user-submitted transcripts or assembled organelle genes, and comparative analysis with the pre-compiled patterns across species of interest. ChloroMitoCU can increase our understanding of the biased patterns of codon usage in organelle genomes across multiple clades. ChloroMitoCU can be accessed at: http://chloromitocu.cgu.edu.tw/. © The Author 2017. Published by Oxford University Press on behalf of Kazusa DNA Research Institute.

Malaria vector populations across ecological zones in Guinea Conakry and Mali, West Africa.

PubMed

Coulibaly, Boubacar; Kone, Raymond; Barry, Mamadou S; Emerson, Becky; Coulibaly, Mamadou B; Niare, Oumou; Beavogui, Abdoul H; Traore, Sekou F; Vernick, Kenneth D; Riehle, Michelle M

2016-04-08

Malaria remains a pervasive public health problem in sub-Saharan West Africa. Here mosquito vector populations were explored across four sites in Mali and the Republic of Guinea (Guinea Conakry). The study samples the major ecological zones of malaria-endemic regions in West Africa within a relatively small distance. Mosquito vectors were sampled from larval pools, adult indoor resting sites, and indoor and outdoor human-host seeking adults. Mosquitoes were collected at sites spanning 350 km that represented arid savannah, humid savannah, semi-forest and deep forest ecological zones, in areas where little was previously known about malaria vector populations. 1425 mosquito samples were analysed by molecular assays to determine species, genetic attributes, blood meal sources and Plasmodium infection status. Anopheles gambiae and Anopheles coluzzii were the major anophelines represented in all collections across the ecological zones, with A. coluzzii predominant in the arid savannah and A. gambiae in the more humid sites. The use of multiple collection methodologies across the sampling sites allows assessment of potential collection bias of the different methods. The L1014F kdr insecticide resistance mutation (kdr-w) is found at high frequency across all study sites. This mutation appears to have swept almost to fixation, from low frequencies 6 years earlier, despite the absence of widespread insecticide use for vector control. Rates of human feeding are very high across ecological zones, with only small fractions of animal derived blood meals in the arid and humid savannah. About 30 % of freshly blood-fed mosquitoes were positive for Plasmodium falciparum presence, while the rate of mosquitoes with established infections was an order of magnitude lower. The study represents detailed vector characterization from an understudied area in West Africa with endemic malaria transmission. The deep forest study site includes the epicenter of the 2014 Ebola virus epidemic

Cryptosporidium species and subtypes in animals inhabiting drinking water catchments in three states across Australia.

PubMed

Zahedi, Alireza; Monis, Paul; Gofton, Alexander W; Oskam, Charlotte L; Ball, Andrew; Bath, Andrew; Bartkow, Michael; Robertson, Ian; Ryan, Una

2018-05-01

As part of long-term monitoring of Cryptosporidium in water catchments serving Western Australia, New South Wales (Sydney) and Queensland, Australia, we characterised Cryptosporidium in a total of 5774 faecal samples from 17 known host species and 7 unknown bird samples, in 11 water catchment areas over a period of 30 months (July 2013 to December 2015). All samples were initially screened for Cryptosporidium spp. at the 18S rRNA locus using a quantitative PCR (qPCR). Positives samples were then typed by sequence analysis of an 825 bp fragment of the 18S gene and subtyped at the glycoprotein 60 (gp60) locus (832 bp). The overall prevalence of Cryptosporidium across the various hosts sampled was 18.3% (1054/5774; 95% CI, 17.3-19.3). Of these, 873 samples produced clean Sanger sequencing chromatograms, and the remaining 181 samples, which initially produced chromatograms suggesting the presence of multiple different sequences, were re-analysed by Next- Generation Sequencing (NGS) to resolve the presence of Cryptosporidium and the species composition of potential mixed infections. The overall prevalence of confirmed mixed infection was 1.7% (98/5774), and in the remaining 83 samples, NGS only detected one species of Cryptosporidium. Of the 17 Cryptosporidium species and four genotypes detected (Sanger sequencing combined with NGS), 13 are capable of infecting humans; C. parvum, C. hominis, C. ubiquitum, C. cuniculus, C. meleagridis, C. canis, C. felis, C. muris, C. suis, C. scrofarum, C. bovis, C. erinacei and C. fayeri. Oocyst numbers per gram of faeces (g -1 ) were also determined using qPCR, with medians varying from 6021-61,064 across the three states. The significant findings were the detection of C. hominis in cattle and kangaroo faeces and the high prevalence of C. parvum in cattle. In addition, two novel C. fayeri subtypes (IVaA11G3T1 and IVgA10G1T1R1) and one novel C. meleagridis subtype (IIIeA18G2R1) were identified. This is also the first report of

The pattern of expression of guanine nucleotide-binding protein β3 (GNB3) in the retina is conserved across vertebrate species

PubMed Central

Ritchey, Eric R.; Bongini, Rachel E.; Code, Kimberly A.; Zelinka, Christopher; Petersen-Jones, Simon; Fischer, Andy J.

2010-01-01

Guanine nucleotide-binding protein β3 (GNB3) is an isoform of the β subunit of the heterotrimeric G protein second messenger complex that is commonly associated with transmembrane receptors. The presence of GNB3 in photoreceptors, and possibly bipolar cells, has been confirmed in murine, bovine and primate retinas (Lee et al., 1992, Peng et al., 1992, Huang et al., 2003). Studies have indicated that a mutation in the GNB3 gene causes progressive retinopathy and globe enlargement (RGE) in chickens. The goals of this study were to 1) examine the expression pattern of GNB3 in wild-type and RGE mutant chickens, 2) characterize the types of bipolar cells that express GNB3 and 3) examine whether the expression of GNB3 in the retina is conserved across vertebrate species. We find that chickens homozygous for the RGE allele completely lack GNB3 protein. We find that the pattern of expression of GNB3 in the retina is highly conserved across vertebrate species, including teleost fish (Carassius auratus), frogs (Xenopus laevis), chickens (Gallus domesticus), mice (Mus musculata), guinea pigs (Cavia porcellus), dogs (Canis familiaris) and non-human primates (Macaca fasicularis). Regardless of the species, we find that GNB3 is expressed by Islet1-positive cone ON-bipolar cells and by cone photoreceptors. In some vertebrates, GNB3-immunoreactivity was observed in both rod and cone photoreceptors. A protein-protein alignment of GNB3 across different vertebrates, from fish to humans, indicates a high degree (>92%) of sequence conservation. Given that analogous types of retinal neurons express GNB3 in different species, we propose that the functions and the mechanisms that regulate the expression of GNB3 are highly conserved. PMID:20538044

Intraspecific trait variation and the leaf economics spectrum across resource gradients and levels of organization.

PubMed

Fajardo, Alex; Siefert, Andrew

2018-05-01

Understanding patterns of functional trait variation across environmental gradients offers an opportunity to increase inference in the mechanistic causes of plant community assembly. The leaf economics spectrum (LES) predicts global tradeoffs in leaf traits and trait-environment relationships, but few studies have examined whether these predictions hold across different levels of organization, particularly within species. Here, we asked (1) whether the main assumptions of the LES (expected trait relationships and shifts in trait values across resource gradients) hold at the intraspecific level, and (2) how within-species trait correlations scale up to interspecific or among-community levels. We worked with leaf traits of saplings of woody species growing across light and soil N and P availability gradients in temperate rainforests of southern Chile. We found that ITV accounted for a large proportion of community-level variation in leaf traits (e.g., LMA and leaf P) and played an important role in driving community-level shifts in leaf traits across environmental gradients. Additionally, intraspecific leaf trait relationships were generally consistent with interspecific and community-level trait relationships and with LES predictions-e.g., a strong negative intraspecific LMA-leaf N correlation-although, most trait relationships varied significantly among species, suggesting idiosyncrasies in the LES at the intraspecific level. © 2018 by the Ecological Society of America.

Secretive marsh aird species co-eccurrences and habitat associations across the midwest, USA

USGS Publications Warehouse

Bolenbaugh, Jason R.; Krementz, David G.; Lehnen, Sarah E.

2011-01-01

Because secretive marsh birds are difficult to detect, population status and habitat use for these birds are not well known. We conducted repeated surveys for secretive marsh birds across 264 sites in the Upper Mississippi River and Great Lakes Joint Venture region to estimate abundance, occupancy, and detection probabilities during the 2008 and 2009 breeding seasons. We identified species groups based on observed species co-occurrences. Two species, least bittern Ixobrychus exilis and American bittern Botaurus lentiginosus, co-occurred with other species less often than expected by chance, and two species groups, rails (Virginia rail Rallus limicola and sora Porzana carolina) and open-water birds (pied-billed grebe Podilymbus podiceps, common moorhen Gallinula chloropus, and American coot Fulica americana; coots were only surveyed in 2009), co-occurred more often than expected by chance. These groupings were consistent between years. We then estimated the relation of these species and groups to landscape and local site characteristics by using zero-inflated abundance models that accounted for incomplete detection. At the landscape level (5-km radius), the amount of emergent herbaceous wetland was positively associated with least bittern occupancy, whereas the amount of woody wetland was negatively associated with least bittern, rail, and open-water bird occupancy. At the local level, habitat variables that were associated with abundance were not consistent among groups or between years, with the exception that both least bitterns and open-water birds had a strong positive association between abundance and water-vegetation interspersion. Land managers interested in marsh bird management or conservation may want to consider focusing efforts on landscapes with high amounts of emergent herbaceous wetland and low amounts of woody wetland, and managing for high amounts of water-vegetation interspersion within the wetland.

In situ modeling of multimodal floral cues attracting wild pollinators across environments

PubMed Central

Dahlbom, Josefin; Ghosh, Suhrid; Olsson, Amadeus; Dyakova, Olga; Suresh, Shravanti Krishna

2017-01-01

With more than 80% of flowering plant species specialized for animal pollination, understanding how wild pollinators utilize resources across environments can encourage efficient planting and maintenance strategies to maximize pollination and establish resilience in the face of environmental change. A fundamental question is how generalist pollinators recognize “flower objects” in vastly different ecologies and environments. On one hand, pollinators could employ a specific set of floral cues regardless of environment. Alternatively, wild pollinators could recognize an exclusive signature of cues unique to each environment or flower species. Hoverflies, which are found across the globe, are one of the most ecologically important alternative pollinators after bees and bumblebees. Here, we have exploited their cosmopolitan status to understand how wild pollinator preferences change across different continents. Without employing any a priori assumptions concerning the floral cues, we measured, predicted, and finally artificially recreated multimodal cues from individual flowers visited by hoverflies in three different environments (hemiboreal, alpine, and tropical) using a field-based methodology. We found that although “flower signatures” were unique for each environment, some multimodal lures were ubiquitously attractive, despite not carrying any reward, or resembling real flowers. While it was unexpected that cue combinations found in real flowers were not necessary, the robustness of our lures across insect species and ecologies could reflect a general strategy of resource identification for generalist pollinators. Our results provide insights into how cosmopolitan pollinators such as hoverflies identify flowers and offer specific ecologically based cues and strategies for attracting pollinators across diverse environments. PMID:29180408

Leaf and root C-to-N ratios are poor predictors of soil microbial biomass C and respiration across 32 tree species.

PubMed

Ferlian, Olga; Wirth, Christian; Eisenhauer, Nico

2017-11-01

Soil microorganisms are the main primary decomposers of plant material and drive biogeochemical processes like carbon and nitrogen cycles. Hence, knowledge of their nutritional demands and limitations for activity and growth is of particular importance. However, potential effects of the stoichiometry of soil and plant species on soil microbial activity and carbon use efficiency are poorly understood. Soil properties and plant traits are assumed to drive microbial carbon and community structure. We investigated the associations between C and N concentrations of leaf, root, and soil as well as their ratios and soil microbial biomass C and activity (microbial basal respiration and specific respiratory quotient) across 32 young native angiosperm tree species at two locations in Central Germany. Correlations between C:N ratios of leaves, roots, and soil were positive but overall weak. Only regressions between root and leaf C:N ratios as well as between root and soil C:N ratios were significant at one site. Soil microbial properties differed significantly between the two sites and were significantly correlated with soil C:N ratio across sites. Soil C concentrations rather than N concentrations drove significant effects of soil C:N ratio on soil microbial properties. No significant correlations between soil microbial properties and leaf as well as root C:N ratios were found. We found weak correlations of C:N ratios between plant aboveground and belowground tissues. Furthermore, microorganisms were not affected by the stoichiometry of plant tissues in the investigated young trees. The results suggest that soil stoichiometry represents a consistent determinant of soil microbial biomass and respiration. Our study indicates that stoichiometric relationships among tree organs can be weak and poor predictors of soil microbial properties in young tree stands. Further research in controlled experimental settings with a wide range of tree species is needed to study the role of

Mesopelagic fishes across the tropical and equatorial Atlantic: Biogeographical and vertical patterns

NASA Astrophysics Data System (ADS)

Olivar, M. Pilar; Hulley, P. Alexander; Castellón, Arturo; Emelianov, Mikhail; López, Cristina; Tuset, Víctor M.; Contreras, Tabit; Molí, Balbina

2017-02-01

In this investigation we analysed the changes in fish species occurrences and relative abundances across the tropical and equatorial Atlantic, and their vertical distribution patterns in relation to the different environmental scenarios. The study covers a wide region encompassing different water masses, and marked differences in productivity, from an oligotrophic zone close to the Brazilian coast, to a very productive upwelling region close to the Northwest African upwelling. Fishes were collected with a medium-sized midwater trawl (Mesopelagos), complemented by hauls made with a macrozooplankton net (MOCNESS). Species richness in the region was higher than in subtropical, temperate and cold regions. The total number of species and their overall abundance was lower in the stations closer to the Brazilian coast. Abundant species across the entire region were the gonostomatids Cyclothone alba, Cyclothone acclinidens, Cyclothone pallida and Cyclothone pseudopallida, the myctophid Lampanyctus alatus, the sternoptychid Sternoptyx diaphana, and the phosichthyid Vinciguerria nimbaria. The occurrences and abundances of C. parapallida, Lampanyctus nobilis and Lepidophanes guentheri were related to zones where AAIW waters occupied the mesopelagic layers, while other species such as Cyclothone livida and Polyipnus polli increased their abundance when AAIW disappears from their living depths. The presence of Eastern North Atlantic Central Water (ENACW) was associated with the occurrence of several myctophids (Benthosema glaciale, Ceratoscopelus maderensis, Diaphus holti, Diaphus rafinesquii, Hygophum hygomii, Lampanyctus crocodilus, Myctophum punctatum, Symbolophorus veranyi), and the gonostomatid Cyclothone braueri. In spite of the important differences in hydrographic features across the tropical and equatorial Atlantic, all stations showed either the general night migration into the epipelagic layers carried out by myctophids, phosicthyids, and some stomiids, or the

The influence of vegetation height heterogeneity on forest and woodland bird species richness across the United States.

PubMed

Huang, Qiongyu; Swatantran, Anu; Dubayah, Ralph; Goetz, Scott J

2014-01-01

Avian diversity is under increasing pressures. It is thus critical to understand the ecological variables that contribute to large scale spatial distribution of avian species diversity. Traditionally, studies have relied primarily on two-dimensional habitat structure to model broad scale species richness. Vegetation vertical structure is increasingly used at local scales. However, the spatial arrangement of vegetation height has never been taken into consideration. Our goal was to examine the efficacies of three-dimensional forest structure, particularly the spatial heterogeneity of vegetation height in improving avian richness models across forested ecoregions in the U.S. We developed novel habitat metrics to characterize the spatial arrangement of vegetation height using the National Biomass and Carbon Dataset for the year 2000 (NBCD). The height-structured metrics were compared with other habitat metrics for statistical association with richness of three forest breeding bird guilds across Breeding Bird Survey (BBS) routes: a broadly grouped woodland guild, and two forest breeding guilds with preferences for forest edge and for interior forest. Parametric and non-parametric models were built to examine the improvement of predictability. Height-structured metrics had the strongest associations with species richness, yielding improved predictive ability for the woodland guild richness models (r(2) = ∼ 0.53 for the parametric models, 0.63 the non-parametric models) and the forest edge guild models (r(2) = ∼ 0.34 for the parametric models, 0.47 the non-parametric models). All but one of the linear models incorporating height-structured metrics showed significantly higher adjusted-r2 values than their counterparts without additional metrics. The interior forest guild richness showed a consistent low association with height-structured metrics. Our results suggest that height heterogeneity, beyond canopy height alone, supplements habitat characterization and

The Influence of Vegetation Height Heterogeneity on Forest and Woodland Bird Species Richness across the United States

PubMed Central

Huang, Qiongyu; Swatantran, Anu; Dubayah, Ralph; Goetz, Scott J.

2014-01-01

Avian diversity is under increasing pressures. It is thus critical to understand the ecological variables that contribute to large scale spatial distribution of avian species diversity. Traditionally, studies have relied primarily on two-dimensional habitat structure to model broad scale species richness. Vegetation vertical structure is increasingly used at local scales. However, the spatial arrangement of vegetation height has never been taken into consideration. Our goal was to examine the efficacies of three-dimensional forest structure, particularly the spatial heterogeneity of vegetation height in improving avian richness models across forested ecoregions in the U.S. We developed novel habitat metrics to characterize the spatial arrangement of vegetation height using the National Biomass and Carbon Dataset for the year 2000 (NBCD). The height-structured metrics were compared with other habitat metrics for statistical association with richness of three forest breeding bird guilds across Breeding Bird Survey (BBS) routes: a broadly grouped woodland guild, and two forest breeding guilds with preferences for forest edge and for interior forest. Parametric and non-parametric models were built to examine the improvement of predictability. Height-structured metrics had the strongest associations with species richness, yielding improved predictive ability for the woodland guild richness models (r2 = ∼0.53 for the parametric models, 0.63 the non-parametric models) and the forest edge guild models (r2 = ∼0.34 for the parametric models, 0.47 the non-parametric models). All but one of the linear models incorporating height-structured metrics showed significantly higher adjusted-r2 values than their counterparts without additional metrics. The interior forest guild richness showed a consistent low association with height-structured metrics. Our results suggest that height heterogeneity, beyond canopy height alone, supplements habitat characterization and

Dispersal assembly of rain forest tree communities across the Amazon basin

PubMed Central

Lavin, Mathew; Torke, Benjamin M.; Twyford, Alex D.; Kursar, Thomas A.; Coley, Phyllis D.; Drake, Camila; Hollands, Ruth; Pennington, R. Toby

2017-01-01

We investigate patterns of historical assembly of tree communities across Amazonia using a newly developed phylogeny for the species-rich neotropical tree genus Inga. We compare our results with those for three other ecologically important, diverse, and abundant Amazonian tree lineages, Swartzia, Protieae, and Guatteria. Our analyses using phylogenetic diversity metrics demonstrate a clear lack of geographic phylogenetic structure, and show that local communities of Inga and regional communities of all four lineages are assembled by dispersal across Amazonia. The importance of dispersal in the biogeography of Inga and other tree genera in Amazonian and Guianan rain forests suggests that speciation is not driven by vicariance, and that allopatric isolation following dispersal may be involved in the speciation process. A clear implication of these results is that over evolutionary timescales, the metacommunity for any local or regional tree community in the Amazon is the entire Amazon basin. PMID:28213498

Dispersal assembly of rain forest tree communities across the Amazon basin.

PubMed

Dexter, Kyle G; Lavin, Mathew; Torke, Benjamin M; Twyford, Alex D; Kursar, Thomas A; Coley, Phyllis D; Drake, Camila; Hollands, Ruth; Pennington, R Toby

2017-03-07

We investigate patterns of historical assembly of tree communities across Amazonia using a newly developed phylogeny for the species-rich neotropical tree genus Inga We compare our results with those for three other ecologically important, diverse, and abundant Amazonian tree lineages, Swartzia , Protieae, and Guatteria Our analyses using phylogenetic diversity metrics demonstrate a clear lack of geographic phylogenetic structure, and show that local communities of Inga and regional communities of all four lineages are assembled by dispersal across Amazonia. The importance of dispersal in the biogeography of Inga and other tree genera in Amazonian and Guianan rain forests suggests that speciation is not driven by vicariance, and that allopatric isolation following dispersal may be involved in the speciation process. A clear implication of these results is that over evolutionary timescales, the metacommunity for any local or regional tree community in the Amazon is the entire Amazon basin.

Conditional vulnerability of plant diversity to atmospheric nitrogen deposition across the United States

USGS Publications Warehouse

Simkin, Samuel M.; Allen, Edith B.; Bowman, William D.; Clark, Christopher M.; Belnap, Jayne; Brooks, Matthew L.; Cade, Brian S.; Collins, Scott L.; Geiser, Linda H.; Gilliam, Frank S.; Jovan, Sarah E.; Pardo, Linda H.; Schulz, Bethany K.; Stevens, Carly J.; Suding, Katharine N.; Throop, Heather L.; Waller, Donald M.

2016-01-01

Atmospheric nitrogen (N) deposition has been shown to decrease plant species richness along regional deposition gradients in Europe and in experimental manipulations. However, the general response of species richness to N deposition across different vegetation types, soil conditions, and climates remains largely unknown even though responses may be contingent on these environmental factors. We assessed the effect of N deposition on herbaceous richness for 15,136 forest, woodland, shrubland, and grassland sites across the continental United States, to address how edaphic and climatic conditions altered vulnerability to this stressor. In our dataset, with N deposition ranging from 1 to 19 kg N⋅ha−1⋅y−1, we found a unimodal relationship; richness increased at low deposition levels and decreased above 8.7 and 13.4 kg N⋅ha−1⋅y−1 in open and closed-canopy vegetation, respectively. N deposition exceeded critical loads for loss of plant species richness in 24% of 15,136 sites examined nationwide. There were negative relationships between species richness and N deposition in 36% of 44 community gradients. Vulnerability to N deposition was consistently higher in more acidic soils whereas the moderating roles of temperature and precipitation varied across scales. We demonstrate here that negative relationships between N deposition and species richness are common, albeit not universal, and that fine-scale processes can moderate vegetation responses to N deposition. Our results highlight the importance of contingent factors when estimating ecosystem vulnerability to N deposition and suggest that N deposition is affecting species richness in forested and nonforested systems across much of the continental United States.

Vertical gradients in species richness and community composition across the twilight zone in the North Pacific Subtropical Gyre.

PubMed

Sommer, Stephanie A; Van Woudenberg, Lauren; Lenz, Petra H; Cepeda, Georgina; Goetze, Erica

2017-11-01

Although metazoan animals in the mesopelagic zone play critical roles in deep pelagic food webs and in the attenuation of carbon in midwaters, the diversity of these assemblages is not fully known. A metabarcoding survey of mesozooplankton diversity across the epipelagic, mesopelagic and upper bathypelagic zones (0-1500 m) in the North Pacific Subtropical Gyre revealed far higher estimates of species richness than expected given prior morphology-based studies in the region (4,024 OTUs, 10-fold increase), despite conservative bioinformatic processing. Operational taxonomic unit (OTU) richness of the full assemblage peaked at lower epipelagic-upper mesopelagic depths (100-300 m), with slight shoaling of maximal richness at night due to diel vertical migration, in contrast to expectations of a deep mesopelagic diversity maximum as reported for several plankton groups in early systematic and zoogeographic studies. Four distinct depth-stratified species assemblages were identified, with faunal transitions occurring at 100 m, 300 m and 500 m. Highest diversity occurred in the smallest zooplankton size fractions (0.2-0.5 mm), which had significantly lower % OTUs classified due to poor representation in reference databases, suggesting a deep reservoir of poorly understood diversity in the smallest metazoan animals. A diverse meroplankton assemblage also was detected (350 OTUs), including larvae of both shallow and deep living benthic species. Our results provide some of the first insights into the hidden diversity present in zooplankton assemblages in midwaters, and a molecular reappraisal of vertical gradients in species richness, depth distributions and community composition for the full zooplankton assemblage across the epipelagic, mesopelagic and upper bathypelagic zones. © 2017 The Authors. Molecular Ecology Published by John Wiley & Sons Ltd.

Identification and Validation of Reference Genes and Their Impact on Normalized Gene Expression Studies across Cultivated and Wild Cicer Species

PubMed Central

Reddy, Palakolanu Sudhakar; Sri Cindhuri, Katamreddy; Sivaji Ganesh, Adusumalli; Sharma, Kiran Kumar

2016-01-01

Quantitative Real-Time PCR (qPCR) is a preferred and reliable method for accurate quantification of gene expression to understand precise gene functions. A total of 25 candidate reference genes including traditional and new generation reference genes were selected and evaluated in a diverse set of chickpea samples. The samples used in this study included nine chickpea genotypes (Cicer spp.) comprising of cultivated and wild species, six abiotic stress treatments (drought, salinity, high vapor pressure deficit, abscisic acid, cold and heat shock), and five diverse tissues (leaf, root, flower, seedlings and seed). The geNorm, NormFinder and RefFinder algorithms used to identify stably expressed genes in four sample sets revealed stable expression of UCP and G6PD genes across genotypes, while TIP41 and CAC were highly stable under abiotic stress conditions. While PP2A and ABCT genes were ranked as best for different tissues, ABCT, UCP and CAC were most stable across all samples. This study demonstrated the usefulness of new generation reference genes for more accurate qPCR based gene expression quantification in cultivated as well as wild chickpea species. Validation of the best reference genes was carried out by studying their impact on normalization of aquaporin genes PIP1;4 and TIP3;1, in three contrasting chickpea genotypes under high vapor pressure deficit (VPD) treatment. The chickpea TIP3;1 gene got significantly up regulated under high VPD conditions with higher relative expression in the drought susceptible genotype, confirming the suitability of the selected reference genes for expression analysis. This is the first comprehensive study on the stability of the new generation reference genes for qPCR studies in chickpea across species, different tissues and abiotic stresses. PMID:26863232

Identification and Validation of Reference Genes and Their Impact on Normalized Gene Expression Studies across Cultivated and Wild Cicer Species.

PubMed

Reddy, Dumbala Srinivas; Bhatnagar-Mathur, Pooja; Reddy, Palakolanu Sudhakar; Sri Cindhuri, Katamreddy; Sivaji Ganesh, Adusumalli; Sharma, Kiran Kumar

2016-01-01

Quantitative Real-Time PCR (qPCR) is a preferred and reliable method for accurate quantification of gene expression to understand precise gene functions. A total of 25 candidate reference genes including traditional and new generation reference genes were selected and evaluated in a diverse set of chickpea samples. The samples used in this study included nine chickpea genotypes (Cicer spp.) comprising of cultivated and wild species, six abiotic stress treatments (drought, salinity, high vapor pressure deficit, abscisic acid, cold and heat shock), and five diverse tissues (leaf, root, flower, seedlings and seed). The geNorm, NormFinder and RefFinder algorithms used to identify stably expressed genes in four sample sets revealed stable expression of UCP and G6PD genes across genotypes, while TIP41 and CAC were highly stable under abiotic stress conditions. While PP2A and ABCT genes were ranked as best for different tissues, ABCT, UCP and CAC were most stable across all samples. This study demonstrated the usefulness of new generation reference genes for more accurate qPCR based gene expression quantification in cultivated as well as wild chickpea species. Validation of the best reference genes was carried out by studying their impact on normalization of aquaporin genes PIP1;4 and TIP3;1, in three contrasting chickpea genotypes under high vapor pressure deficit (VPD) treatment. The chickpea TIP3;1 gene got significantly up regulated under high VPD conditions with higher relative expression in the drought susceptible genotype, confirming the suitability of the selected reference genes for expression analysis. This is the first comprehensive study on the stability of the new generation reference genes for qPCR studies in chickpea across species, different tissues and abiotic stresses.

Crossing Over: Nanostructures that Move Electrons and Ions Across Cellular Membranes

DOE PAGES

Ajo-Franklin, C. M.; Noy, A.

2015-04-27

Critical biological processes such as energy generation and signal transduction are driven by the flow of electrons and ions across the membranes of living cells. As a result, there is substantial interest in creating nanostructured materials that control transport of these charged species across biomembranes. The recent advances in the synthesis of de novo and protein nanostructures for transmembrane ion and electron transport and the mechanistic understanding underlying this transport are described. Moreover, this body of work highlights the promise such nanostructures hold for directing transmembrane transport of charged species as well as challenges that must be overcome to realizemore » that potential.« less

Crossing Over: Nanostructures that Move Electrons and Ions across Cellular Membranes.

PubMed

Ajo-Franklin, Caroline M; Noy, Aleksandr

2015-10-14

Critical biological processes such as energy generation and signal transduction are driven by the flow of electrons and ions across the membranes of living cells. As a result, there is substantial interest in creating nanostructured materials that control transport of these charged species across biomembranes. Recent advances in the synthesis of de novo and protein nanostructures for transmembrane ion and electron transport and the mechanistic understanding underlying this transport are described. This body of work highlights the promise such nanostructures hold for directing transmembrane transport of charged species as well as challenges that must be overcome to realize that potential. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Local brain connectivity across development in autism spectrum disorder: A cross-sectional investigation.

PubMed

Dajani, Dina R; Uddin, Lucina Q

2016-01-01

There is a general consensus that autism spectrum disorder (ASD) is accompanied by alterations in brain connectivity. Much of the neuroimaging work has focused on assessing long-range connectivity disruptions in ASD. However, evidence from both animal models and postmortem examination of the human brain suggests that local connections may also be disrupted in individuals with the disorder. Here, we investigated how regional homogeneity (ReHo), a measure of similarity of a voxel's timeseries to its nearest neighbors, varies across age in individuals with ASD and typically developing (TD) individuals using a cross-sectional design. Resting-state fMRI data obtained from a publicly available database were analyzed to determine group differences in ReHo between three age cohorts: children, adolescents, and adults. In typical development, ReHo across the entire brain was higher in children than in adolescents and adults. In contrast, children with ASD exhibited marginally lower ReHo than TD children, while adolescents and adults with ASD exhibited similar levels of local connectivity as age-matched neurotypical individuals. During all developmental stages, individuals with ASD exhibited lower local connectivity in sensory processing brain regions and higher local connectivity in complex information processing regions. Further, higher local connectivity in ASD corresponded to more severe ASD symptomatology. These results demonstrate that local connectivity is disrupted in ASD across development, with the most pronounced differences occurring in childhood. Developmental changes in ReHo do not mirror findings from fMRI studies of long-range connectivity in ASD, pointing to a need for more nuanced accounts of brain connectivity alterations in the disorder. © 2015 International Society for Autism Research, Wiley Periodicals, Inc.

Soil propagule banks of ectomycorrhizal fungi share many common species along an elevation gradient.

PubMed

Miyamoto, Yumiko; Nara, Kazuhide

2016-04-01

We conducted bioassay experiments to investigate the soil propagule banks of ectomycorrhizal (EM) fungi in old-growth forests along an elevation gradient and compared the elevation pattern with the composition of EM fungi on existing roots in the field. In total, 150 soil cores were collected from three forests on Mt. Ishizuchi, western Japan, and subjected to bioassays using Pinus densiflora and Betula maximowicziana. Using molecular analyses, we recorded 23 EM fungal species in the assayed propagule banks. Eight species (34.8 %) were shared across the three sites, which ranged from a warm-temperate evergreen mixed forest to a subalpine conifer forest. The elevation pattern of the assayed propagule banks differed dramatically from that of EM fungi on existing roots along the same gradient, where only a small proportion of EM fungal species (3.5 %) were shared across sites. The EM fungal species found in the assayed propagule banks included many pioneer fungal species and composition differed significantly from that on existing roots. Furthermore, only 4 of 23 species were shared between the two host species, indicating a strong effect of bioassay host identity in determining the propagule banks of EM fungi. These results imply that the assayed propagule bank is less affected by climate compared to EM fungal communities on existing roots. The dominance of disturbance-dependent fungal species in the assayed propagule banks may result in higher ecosystem resilience to disturbance even in old-growth temperate forests.

Entomopathogenicity to Two Hemipteran Insects Is Common but Variable across Epiphytic Pseudomonas syringae Strains.

PubMed

Smee, Melanie R; Baltrus, David A; Hendry, Tory A

2017-01-01

Strains of the well-studied plant pathogen Pseudomonas syringae show large differences in their ability to colonize plants epiphytically and to inflict damage to hosts. Additionally, P. syringae can infect some sap-sucking insects and at least one P. syringae strain is highly virulent to insects, causing death to most individuals within as few as 4 days and growing to high population densities within insect hosts. The likelihood of agricultural pest insects coming into contact with transient populations of P. syringae while feeding on plants is high, yet the ecological implications of these interactions are currently not well understood as virulence has not been tested across a wide range of strains. To investigate virulence differences across strains we exposed the sweet potato whitefly, Bemisia tabaci , and the pea aphid, Acyrthosiphon pisum , both of which are cosmopolitan agricultural pests, to 12 P. syringae strains. We used oral inoculations with bacteria suspended in artificial diet in order to assay virulence while controlling for other variables such as differences in epiphytic growth ability. Generally, patterns of pathogenicity remain consistent across the two species of hemipteran insects, with bacterial strains from phylogroup II, or genomospecies 1, causing the highest rate of mortality with up to 86% of individuals dead after 72 h post infection. The rate of mortality is highly variable across strains, some significantly different from negative control treatments and others showing no discernable difference. Interestingly, one of the most pathogenic strains to both aphids and whiteflies (Cit7) is thought to be non-pathogenic on plants. We also found Cit7 to establish the highest epiphytic population after 48 h on fava beans. Between the nine P. syringae strains tested for epiphytic ability there is also much variation, but epiphytic ability was positively correlated with pathogenicity to insects, suggesting that the two traits may be linked and that

Light pollution is associated with earlier tree budburst across the United Kingdom.

PubMed

Ffrench-Constant, Richard H; Somers-Yeates, Robin; Bennie, Jonathan; Economou, Theodoros; Hodgson, David; Spalding, Adrian; McGregor, Peter K

2016-06-29

The ecological impact of night-time lighting is of concern because of its well-demonstrated effects on animal behaviour. However, the potential of light pollution to change plant phenology and its corresponding knock-on effects on associated herbivores are less clear. Here, we test if artificial lighting can advance the timing of budburst in trees. We took a UK-wide 13 year dataset of spatially referenced budburst data from four deciduous tree species and matched it with both satellite imagery of night-time lighting and average spring temperature. We find that budburst occurs up to 7.5 days earlier in brighter areas, with the relationship being more pronounced for later-budding species. Excluding large urban areas from the analysis showed an even more pronounced advance of budburst, confirming that the urban 'heat-island' effect is not the sole cause of earlier urban budburst. Similarly, the advance in budburst across all sites is too large to be explained by increases in temperature alone. This dramatic advance of budburst illustrates the need for further experimental investigation into the impact of artificial night-time lighting on plant phenology and subsequent species interactions. As light pollution is a growing global phenomenon, the findings of this study are likely to be applicable to a wide range of species interactions across the world. © 2016 The Authors.

Assessing cross species conservation of ToxCast Assay targets using Sequence Alignment to Predict Across Species Susceptibility (SeqAPASS)

EPA Science Inventory

US EPA’s ToxCast program has screened thousands of chemicals in hundreds of mammalian-based HTS assays for biological activity suggestive of potential toxic effects. These data are being used to prioritize toxicity testing to focus on chemicals likely to lead to adverse health ef...

Attention flexibly trades off across points in time.

PubMed

Denison, Rachel N; Heeger, David J; Carrasco, Marisa

2017-08-01

Sensory signals continuously enter the brain, raising the question of how perceptual systems handle this constant flow of input. Attention to an anticipated point in time can prioritize visual information at that time. However, how we voluntarily attend across time when there are successive task-relevant stimuli has been barely investigated. We developed a novel experimental protocol that allowed us to assess, for the first time, both the benefits and costs of voluntary temporal attention when perceiving a short sequence of two or three visual targets with predictable timing. We found that when humans directed attention to a cued point in time, their ability to perceive orientation was better at that time but also worse earlier and later. These perceptual tradeoffs across time are analogous to those found across space for spatial attention. We concluded that voluntary attention is limited, and selective, across time.

Preservation Benefits Geoscientific Investigations Across the Nation

NASA Astrophysics Data System (ADS)

Powers, L. A.; Latysh, N.

2017-12-01

Since 2005, the National Geological and Geophysical Data Preservation Program (NGGDPP) of the U.S. Geological Survey (USGS) has distributed financial grants to state geological surveys to preserve, archive, and make available valuable geoscientific samples and data to researchers and the public. States have cataloged and preserved materials that include geophysical logs, geotechnical reports, fragile historical documents, maps, geologic samples, and legacy aerial and field-investigation photographs. Approximately 3 million metadata records describing preserved data and artifacts are cataloged in the National Digital Catalog, a component of the USGS ScienceBase data management infrastructure. Providing a centralized domain in the National Digital Catalog for uniformly described records has enabled discovery of important geoscientific assets across the Nation. Scientific investigations continue to be informed by preserved materials and data. Tennessee Geological Survey's preserved collection of historical documents describing coal mining activities in the State was used to identify vulnerable areas overlying abandoned underground coal mines, which caused surface collapses and sinkholes in populated areas. Missouri Geological Survey's preserved collection of legacy field notebooks was used to identify thousands of abandoned mines, many of which have significant soil or groundwater lead contamination and are located in areas that now have residential development. The information enabled the evaluation of risk to human health, environment, and infrastructure and identification of needed remedial actions. Information in the field notebooks also assisted the Missouri Department of Transportation responding to highway collapses and assessing collapse potential in abandoned coal mining lands. Digitization of natural gamma ray logs allowed Minnesota Geological Survey staff to directly access well data in the field, accelerating the ability to address geoscientific questions

Writing across the Curriculum.

ERIC Educational Resources Information Center

Smith, Barbara Leigh, Ed.

1983-01-01

The writing across the curriculum movement is discussed in six articles. Barbara Leigh Smith's introductory article, "Writing Across the Curriculum: What's at Stake?" reviews the rationale for this movement, including the declining emphasis on writing in high schools and colleges. In the "Winds of Change: Thomas Kuhn and the…

Replication of honey bee-associated RNA viruses across multiple bee species in apple orchards of Georgia, Germany and Kyrgyzstan.

PubMed

Radzevičiūtė, Rita; Theodorou, Panagiotis; Husemann, Martin; Japoshvili, George; Kirkitadze, Giorgi; Zhusupbaeva, Aigul; Paxton, Robert J

2017-06-01

The essential ecosystem service of pollination is provided largely by insects, which are considered threatened by diverse biotic and abiotic global change pressures. RNA viruses are one such pressure, and have risen in prominence as a major threat for honey bees (Apis mellifera) and global apiculture, as well as a risk factor for other bee species through pathogen spill-over between managed honey bees and sympatric wild pollinator communities. Yet despite their potential role in global bee decline, the prevalence of honey bee-associated RNA viruses in wild bees is poorly known from both geographic and taxonomic perspectives. We screened members of pollinator communities (honey bees, bumble bees and other wild bees belonging to four families) collected from apple orchards in Georgia, Germany and Kyrgyzstan for six common honey bee-associated RNA virus complexes encompassing nine virus targets. The Deformed wing virus complex (DWV genotypes A and B) had the highest prevalence across all localities and host species and was the only virus complex found in wild bee species belonging to all four studied families. Based on amplification of negative-strand viral RNA, we found evidence for viral replication in wild bee species of DWV-A/DWV-B (hosts: Andrena haemorrhoa and several Bombus spp.) and Black queen cell virus (hosts: Anthophora plumipes, several Bombus spp., Osmia bicornis and Xylocopa spp.). Viral amplicon sequences revealed that DWV-A and DWV-B are regionally distinct but identical in two or more bee species at any one site, suggesting virus is shared amongst sympatric bee taxa. This study demonstrates that honey bee associated RNA viruses are geographically and taxonomically widespread, likely infective in wild bee species, and shared across bee taxa. Copyright © 2017 Elsevier Inc. All rights reserved.

Biochemical Activities of 320 ToxCast Chemicals Evaluated Across 239 Functional Targets

EPA Science Inventory

EPA’s ToxCast research program is profiling chemical bioactivity in order to generate predictive signatures of toxicity. The present study evaluated 320 chemicals across 239 biochemical assays. ToxCast phase I chemicals include 309 unique structures, most of which are pesticide ...

Genes Suggest Ancestral Colour Polymorphisms Are Shared across Morphologically Cryptic Species in Arctic Bumblebees

PubMed Central

Williams, Paul H.; Byvaltsev, Alexandr M.; Cederberg, Björn; Berezin, Mikhail V.; Ødegaard, Frode; Rasmussen, Claus; Richardson, Leif L.; Huang, Jiaxing; Sheffield, Cory S.; Williams, Suzanne T.

2015-01-01

Our grasp of biodiversity is fine-tuned through the process of revisionary taxonomy. If species do exist in nature and can be discovered with available techniques, then we expect these revisions to converge on broadly shared interpretations of species. But for the primarily arctic bumblebees of the subgenus Alpinobombus of the genus Bombus, revisions by some of the most experienced specialists are unusual for bumblebees in that they have all reached different conclusions on the number of species present. Recent revisions based on skeletal morphology have concluded that there are from four to six species, while variation in colour pattern of the hair raised questions as to whether at least seven species might be present. Even more species are supported if we accept the recent move away from viewing species as morphotypes to viewing them instead as evolutionarily independent lineages (EILs) using data from genes. EILs are recognised here in practice from the gene coalescents that provide direct evidence for their evolutionary independence. We show from fitting both general mixed Yule/coalescent (GMYC) models and Poisson-tree-process (PTP) models to data for the mitochondrial COI gene that there is support for nine species in the subgenus Alpinobombus. Examination of the more slowly evolving nuclear PEPCK gene shows further support for a previously unrecognised taxon as a new species in northwestern North America. The three pairs of the most morphologically similar sister species are separated allopatrically and prevented from interbreeding by oceans. We also find that most of the species show multiple shared colour patterns, giving the appearance of mimicry among parts of the different species. However, reconstructing ancestral colour-pattern states shows that speciation is likely to have cut across widespread ancestral polymorphisms, without or largely without convergence. In the particular case of Alpinobombus, morphological, colour-pattern, and genetic groups show

Genes Suggest Ancestral Colour Polymorphisms Are Shared across Morphologically Cryptic Species in Arctic Bumblebees.

PubMed

Williams, Paul H; Byvaltsev, Alexandr M; Cederberg, Björn; Berezin, Mikhail V; Ødegaard, Frode; Rasmussen, Claus; Richardson, Leif L; Huang, Jiaxing; Sheffield, Cory S; Williams, Suzanne T

2015-01-01

Our grasp of biodiversity is fine-tuned through the process of revisionary taxonomy. If species do exist in nature and can be discovered with available techniques, then we expect these revisions to converge on broadly shared interpretations of species. But for the primarily arctic bumblebees of the subgenus Alpinobombus of the genus Bombus, revisions by some of the most experienced specialists are unusual for bumblebees in that they have all reached different conclusions on the number of species present. Recent revisions based on skeletal morphology have concluded that there are from four to six species, while variation in colour pattern of the hair raised questions as to whether at least seven species might be present. Even more species are supported if we accept the recent move away from viewing species as morphotypes to viewing them instead as evolutionarily independent lineages (EILs) using data from genes. EILs are recognised here in practice from the gene coalescents that provide direct evidence for their evolutionary independence. We show from fitting both general mixed Yule/coalescent (GMYC) models and Poisson-tree-process (PTP) models to data for the mitochondrial COI gene that there is support for nine species in the subgenus Alpinobombus. Examination of the more slowly evolving nuclear PEPCK gene shows further support for a previously unrecognised taxon as a new species in northwestern North America. The three pairs of the most morphologically similar sister species are separated allopatrically and prevented from interbreeding by oceans. We also find that most of the species show multiple shared colour patterns, giving the appearance of mimicry among parts of the different species. However, reconstructing ancestral colour-pattern states shows that speciation is likely to have cut across widespread ancestral polymorphisms, without or largely without convergence. In the particular case of Alpinobombus, morphological, colour-pattern, and genetic groups show

A Quantitative Model of Motility Reveals Low-Dimensional Variation in Exploratory Behavior Across Multiple Nematode Species

NASA Astrophysics Data System (ADS)

Helms, Stephen; Avery, Leon; Stephens, Greg; Shimizu, Tom

2014-03-01

Animal behavior emerges from many layers of biological organization--from molecular signaling pathways and neuronal networks to mechanical outputs of muscles. In principle, the large number of interconnected variables at each of these layers could imply dynamics that are complex and hard to control or even tinker with. Yet, for organisms to survive in a competitive, ever-changing environment, behavior must readily adapt. We applied quantitative modeling to identify important aspects of behavior in chromadorean nematodes ranging from the lab strain C. elegans N2 to wild strains and distant species. We revealed subtle yet important features such as speed control and heavy-tailed directional changes. We found that the parameters describing this behavioral model varied among individuals and across species in a correlated way that is consistent with a trade-off between exploratory and exploitative behavior.

Beekeeping practices and geographic distance, not land use, drive gene flow across tropical bees.

PubMed

Jaffé, Rodolfo; Pope, Nathaniel; Acosta, André L; Alves, Denise A; Arias, Maria C; De la Rúa, Pilar; Francisco, Flávio O; Giannini, Tereza C; González-Chaves, Adrian; Imperatriz-Fonseca, Vera L; Tavares, Mara G; Jha, Shalene; Carvalheiro, Luísa G

2016-11-01

Across the globe, wild bees are threatened by ongoing natural habitat loss, risking the maintenance of plant biodiversity and agricultural production. Despite the ecological and economic importance of wild bees and the fact that several species are now managed for pollination services worldwide, little is known about how land use and beekeeping practices jointly influence gene flow. Using stingless bees as a model system, containing wild and managed species that are presumed to be particularly susceptible to habitat degradation, here we examine the main drivers of tropical bee gene flow. We employ a novel landscape genetic approach to analyse data from 135 populations of 17 stingless bee species distributed across diverse tropical biomes within the Americas. Our work has important methodological implications, as we illustrate how a maximum-likelihood approach can be applied in a meta-analysis framework to account for multiple factors, and weight estimates by sample size. In contrast to previously held beliefs, gene flow was not related to body size or deforestation, and isolation by geographic distance (IBD) was significantly affected by management, with managed species exhibiting a weaker IBD than wild ones. Our study thus reveals the critical importance of beekeeping practices in shaping the patterns of genetic differentiation across bee species. Additionally, our results show that many stingless bee species maintain high gene flow across heterogeneous landscapes. We suggest that future efforts to preserve wild tropical bees should focus on regulating beekeeping practices to maintain natural gene flow and enhancing pollinator-friendly habitats, prioritizing species showing a limited dispersal ability. © 2016 John Wiley & Sons Ltd.

Costs of fear: Behavioral and life-history responses to risk and their demographic consequences vary across species

USGS Publications Warehouse

LaManna, Joseph A.; Martin, Thomas E.

2016-01-01

Behavioural responses to reduce predation risk might cause demographic ‘costs of fear’. Costs differ among species, but a conceptual framework to understand this variation is lacking. We use a life-history framework to tie together diverse traits and life stages to better understand interspecific variation in responses and costs. We used natural and experimental variation in predation risk to test phenotypic responses and associated demographic costs for 10 songbird species. Responses such as increased parental attentiveness yielded reduced development time and created benefits such as reduced predation probability. Yet, responses to increased risk also created demographic costs by reducing offspring production in the absence of direct predation. This cost of fear varied widely across species, but predictably with the probability of repeat breeding. Use of a life-history framework can aid our understanding of potential demographic costs from predation, both from responses to perceived risk and from direct predation mortality.

Magical thinking decreases across adulthood.

PubMed

Brashier, Nadia M; Multhaup, Kristi S

2017-12-01

Magical thinking, or illogical causal reasoning such as superstitions, decreases across childhood, but almost no data speak to whether this developmental trajectory continues across the life span. In four experiments, magical thinking decreased across adulthood. This pattern replicated across two judgment domains and could not be explained by age-related differences in tolerance of ambiguity, domain-specific knowledge, or search for meaning. These data complement and extend findings that experience, accumulated over decades, guides older adults' judgments so that they match, or even exceed, young adults' performance. They also counter participants' expectations, and cultural sayings (e.g., "old wives' tales"), that suggest that older adults are especially superstitious. (PsycINFO Database Record (c) 2017 APA, all rights reserved).

A psychometric investigation of gender differences and common processes across Borderline and Antisocial Personality Disorders

PubMed Central

Chun, Seokjoon; Harris, Alexa; Carrion, Margely; Rojas, Elizabeth; Stark, Stephen; Lejuez, Carl; Lechner, William V.; Bornovalova, Marina A.

2016-01-01

The comorbidity between Borderline Personality Disorder (BPD) and Antisocial Personality Disorder (ASPD) is well-established, and the two disorders share many similarities. However, there are also differences across disorders: most notably, BPD is diagnosed more frequently in females and ASPD in males. We investigated if a) comorbidity between BPD and ASPD is attributable to two discrete disorders or the expression of common underlying processes, and b) if the model of comorbidity is true across sex. Using a clinical sample of 1400 drug users in residential substance abuse treatment, we tested three competing models to explore whether the comorbidity of ASPD and BPD should be represented by a single common factor, two correlated factors, or a bifactor structure involving a general and disorder-specific factors. Next, we tested whether our resulting model was meaningful by examining its relationship with criterion variables previously reported to be associated with BPD and ASPD. The bifactor model provided the best fit and was invariant across sex. Overall, the general factor of the bifactor model significantly accounted for a large percentage of the variance in criterion variables, whereas the BPD and AAB specific factors added little to the models. The association of the general and specific factor with all criterion variables was equal for males and females. Our results suggest common underlying vulnerability accounts for both the comorbidity between BPD and AAB (across sex), and this common vulnerability drives the association with other psychopathology and maladaptive behavior. This in turn has implications for diagnostic classification systems and treatment. General scientific summary This study found that, for both males and females, borderline and antisocial personality disorders show a large degree of overlap, and little uniqueness. The commonality between BPD and ASPD mainly accounted for associations with criterion variables. This suggests that BPD and

High Cryptic Diversity across the Global Range of the Migratory Planktonic Copepods Pleuromamma piseki and P. gracilis

PubMed Central

Halbert, Kristin M. K.; Goetze, Erica; Carlon, David B.

2013-01-01

Although holoplankton are ocean drifters and exhibit high dispersal potential, a number of studies on single species are finding highly divergent genetic clades. These cryptic species complexes are important to discover and describe, as identification of common marine species is fundamental to understanding ecosystem dynamics. Here we investigate the global diversity within Pleuromamma piseki and P. gracilis, two dominant members of the migratory zooplankton assemblage in subtropical and tropical waters worldwide. Using DNA sequence data from the mitochondrial gene cytochrome c oxidase subunit II (mtCOII) from 522 specimens collected across the Pacific, Atlantic and Indian Oceans, we discover twelve well-resolved genetically distinct clades in this species complex (Bayesian posterior probabilities >0.7; 6.3–17% genetic divergence between clades). The morphologically described species P. piseki and P. gracilis did not form monophyletic groups, rather they were distributed throughout the phylogeny and sometimes co-occurred within well-resolved clades: this result suggests that morphological characters currently used for taxonomic identification of P. gracilis and P. piseki may be inaccurate as indicators of species’ boundaries. Cryptic clades within the species complex ranged from being common to rare, and from cosmopolitan to highly restricted in distribution across the global ocean. These novel lineages appear to be ecologically divergent, with distinct biogeographic distributions across varied pelagic habitats. We hypothesize that these mtDNA lineages are distinct species and suggest that resolving their systematic status is important, given the ecological significance of the genus Pleuromamma in subtropical-tropical waters worldwide. PMID:24167556

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.

A Zebrafish Embryo Culture System Defines Factors that Promote Vertebrate Myogenesis across Species

PubMed Central

Ciarlo, Christie; Liu, Jingxia; Castiglioni, Alessandra; Price, Emily; Liu, Min; Barton, Elisabeth R.; Kahn, C. Ronald; Wagers, Amy J.; Zon, Leonard I.

2013-01-01

SUMMARY Ex vivo expansion of satellite cells and directed differentiation of pluripotent cells to mature skeletal muscle have proved difficult challenges for regenerative biology. Using a zebrafish embryo culture system with reporters of early and late skeletal muscle differentiation, we examined the influence of 2,400 chemicals on myogenesis and identified six that expanded muscle progenitors, including three GSK3β inhibitors, two calpain inhibitors and one adenylyl cyclase activator, forskolin. Forskolin also enhanced proliferation of mouse satellite cells in culture and maintained their ability to engraft muscle in vivo. A combination of bFGF, forskolin and the GSK3β inhibitor BIO induced skeletal muscle differentiation in human induced pluripotent stem cells (iPSCs) and produced engraftable myogenic progenitors that contributed to muscle repair in vivo. In summary, these studies reveal functionally conserved pathways regulating myogenesis across species and identify chemical compounds that expand mouse satellite cells and differentiate human iPSCs into engraftable muscle. PMID:24209627

Microbiome patterns across the gastrointestinal tract of the rabbitfish Siganus fuscescens.

PubMed

Nielsen, Shaun; Wilkes Walburn, Jackson; Vergés, Adriana; Thomas, Torsten; Egan, Suhelen

2017-01-01

Most of our knowledge regarding the biodiversity of gut microbes comes from terrestrial organisms or marine species of economic value, with less emphasis on ecologically important species. Here we investigate the bacterial composition associated with the gut of Siganus fuscescens , a rabbitfish that plays an important ecological role in coastal ecosystems by consuming seaweeds. Members of Firmicutes, Bacteroidetes and delta-Proteobacteria were among the dominant taxa across samples taken from the contents and the walls (sites) of the midgut and hindgut (location). Despite the high variability among individual fish, we observed statistically significant differences in beta-diversity between gut sites and gut locations. Some bacterial taxa low in abundance in the midgut content (e.g., Desulfovibrio ) were found in greater abundances on the midgut wall and within the hindgut, suggesting that the gut may select for specific groups of environmental and/or food-associated microorganisms. In contrast, some distinct taxa present in the midgut content (e.g., Synechococcus ) were noticeably reduced in the midgut wall and hindgut, and are thus likely to be representative of transient microbiota. This is the first assessment of the bacterial diversity associated with the gut of S. fuscescens and highlights the need to consider the variability across different gut locations and sites when analyzing fish gut microbiomes.

Allometric Scaling of the Active Hematopoietic Stem Cell Pool across Mammals

PubMed Central

Dingli, David; Pacheco, Jorge M.

2006-01-01

Background Many biological processes are characterized by allometric relations of the type Y = Y 0 Mb between an observable Y and body mass M, which pervade at multiple levels of organization. In what regards the hematopoietic stem cell pool, there is experimental evidence that the size of the hematopoietic stem cell pool is conserved in mammals. However, demands for blood cell formation vary across mammals and thus the size of the active stem cell compartment could vary across species. Methodology/Principle Findings Here we investigate the allometric scaling of the hematopoietic system in a large group of mammalian species using reticulocyte counts as a marker of the active stem cell pool. Our model predicts that the total number of active stem cells, in an adult mammal, scales with body mass with the exponent ¾. Conclusion/Significance The scaling predicted here provides an intuitive justification of the Hayflick hypothesis and supports the current view of a small active stem cell pool supported by a large, quiescent reserve. The present scaling shows excellent agreement with the available (indirect) data for smaller mammals. The small size of the active stem cell pool enhances the role of stochastic effects in the overall dynamics of the hematopoietic system. PMID:17183646

Four new bat species (Rhinolophus hildebrandtii complex) reflect Plio-Pleistocene divergence of dwarfs and giants across an Afromontane archipelago.

PubMed

Taylor, Peter J; Stoffberg, Samantha; Monadjem, Ara; Schoeman, Martinus Corrie; Bayliss, Julian; Cotterill, Fenton P D

2012-01-01

Gigantism and dwarfism evolve in vertebrates restricted to islands. We describe four new species in the Rhinolophus hildebrandtii species-complex of horseshoe bats, whose evolution has entailed adaptive shifts in body size. We postulate that vicissitudes of palaeoenvironments resulted in gigantism and dwarfism in habitat islands fragmented across eastern and southern Africa. Mitochondrial and nuclear DNA sequences recovered two clades of R. hildebrandtii senso lato which are paraphyletic with respect to a third lineage (R. eloquens). Lineages differ by 7.7 to 9.0% in cytochrome b sequences. Clade 1 includes R. hildebrandtii sensu stricto from the east African highlands and three additional vicariants that speciated across an Afromontane archipelago through the Plio-Pleistocene, extending from the Kenyan Highlands through the Eastern Arc, northern Mozambique and the Zambezi Escarpment to the eastern Great Escarpment of South Africa. Clade 2 comprises one species confined to lowland savanna habitats (Mozambique and Zimbabwe). A third clade comprises R. eloquens from East Africa. Speciation within Clade 1 is associated with fixed differences in echolocation call frequency, and cranial shape and size in populations isolated since the late Pliocene (ca 3.74 Mya). Relative to the intermediate-sized savanna population (Clade 2), these island-populations within Clade 1 are characterised by either gigantism (South African eastern Great Escarpment and Mts Mabu and Inago in Mozambique) or dwarfism (Lutope-Ngolangola Gorge, Zimbabwe and Soutpansberg Mountains, South Africa). Sympatry between divergent clades (Clade 1 and Clade 2) at Lutope-Ngolangola Gorge (NW Zimbabwe) is attributed to recent range expansions. We propose an "Allometric Speciation Hypothesis", which attributes the evolution of this species complex of bats to divergence in constant frequency (CF) sonar calls. The origin of species-specific peak frequencies (overall range = 32 to 46 kHz) represents the

Humans recognize emotional arousal in vocalizations across all classes of terrestrial vertebrates: evidence for acoustic universals.

PubMed

Filippi, Piera; Congdon, Jenna V; Hoang, John; Bowling, Daniel L; Reber, Stephan A; Pašukonis, Andrius; Hoeschele, Marisa; Ocklenburg, Sebastian; de Boer, Bart; Sturdy, Christopher B; Newen, Albert; Güntürkün, Onur

2017-07-26

Writing over a century ago, Darwin hypothesized that vocal expression of emotion dates back to our earliest terrestrial ancestors. If this hypothesis is true, we should expect to find cross-species acoustic universals in emotional vocalizations. Studies suggest that acoustic attributes of aroused vocalizations are shared across many mammalian species, and that humans can use these attributes to infer emotional content. But do these acoustic attributes extend to non-mammalian vertebrates? In this study, we asked human participants to judge the emotional content of vocalizations of nine vertebrate species representing three different biological classes-Amphibia, Reptilia (non-aves and aves) and Mammalia. We found that humans are able to identify higher levels of arousal in vocalizations across all species. This result was consistent across different language groups (English, German and Mandarin native speakers), suggesting that this ability is biologically rooted in humans. Our findings indicate that humans use multiple acoustic parameters to infer relative arousal in vocalizations for each species, but mainly rely on fundamental frequency and spectral centre of gravity to identify higher arousal vocalizations across species. These results suggest that fundamental mechanisms of vocal emotional expression are shared among vertebrates and could represent a homologous signalling system. © 2017 The Author(s).

A genetics-based approach confirms immune associations with life history across multiple populations of an aquatic vertebrate (Gasterosteus aculeatus).

PubMed

Whiting, James R; Magalhaes, Isabel S; Singkam, Abdul R; Robertson, Shaun; D'Agostino, Daniele; Bradley, Janette E; MacColl, Andrew D C

2018-06-20

Understanding how wild immune variation covaries with other traits can reveal how costs and trade-offs shape immune evolution in the wild. Divergent life history strategies may increase or alleviate immune costs, helping shape immune variation in a consistent, testable way. Contrasting hypotheses suggest that shorter life histories may alleviate costs by offsetting them against increased mortality; or increase the effect of costs if immune responses are traded off against development or reproduction. We investigated the evolutionary relationship between life history and immune responses within an island radiation of three-spined stickleback, with discrete populations of varying life histories and parasitism. We sampled two short-lived, two long-lived and an anadromous population using qPCR to quantify current immune profile and RAD-seq data to study the distribution of immune variants within our assay genes and across the genome. Short-lived populations exhibited significantly increased expression of all assay genes, which was accompanied by a strong association with population-level variation in local alleles and divergence in a gene that may be involved in complement pathways. In addition, divergence around the eda gene in anadromous fish is likely associated with increased inflammation. A wider analysis of 15 populations across the island revealed that immune genes across the genome show evidence of having diverged alongside life history strategies. Parasitism and reproductive investment were also important sources of variation for expression, highlighting the caution required when assaying immune responses in the wild. These results provide strong, gene-based support for current hypotheses linking life history and immune variation across multiple populations of a vertebrate model. This article is protected by copyright. All rights reserved. This article is protected by copyright. All rights reserved.

Controlling turbulent drag across electrolytes using electric fields.

PubMed

Ostilla-Mónico, Rodolfo; Lee, Alpha A

2017-07-01

Reversible in operando control of friction is an unsolved challenge that is crucial to industrial tribology. Recent studies show that at low sliding velocities, this control can be achieved by applying an electric field across electrolyte lubricants. However, the phenomenology at high sliding velocities is yet unknown. In this paper, we investigate the hydrodynamic friction across electrolytes under shear beyond the transition to turbulence. We develop a novel, highly parallelised numerical method for solving the coupled Navier-Stokes Poisson-Nernst-Planck equation. Our results show that turbulent drag cannot be controlled across dilute electrolytes using static electric fields alone. The limitations of the Poisson-Nernst-Planck formalism hint at ways in which turbulent drag could be controlled using electric fields.

Molecular evolution across the Asteraceae: micro- and macroevolutionary processes.

PubMed

Kane, Nolan C; Barker, Michael S; Zhan, Shing H; Rieseberg, Loren H

2011-12-01

The Asteraceae (Compositae) is a large family of over 20,000 wild, weedy, and domesticated species that comprise approximately 10% of all angiosperms, including annual and perennial herbs, shrubs and trees, and species on every continent except Antarctica. As a result, the Asteraceae provide a unique opportunity to understand the evolutionary genomics of lineage radiation and diversification at numerous phylogenetic scales. Using publicly available expressed sequence tags from 22 species representing four of the major Asteraceae lineages, we assessed neutral and nonneutral evolutionary processes across this diverse plant family. We used bioinformatic tools to identify candidate genes under selection in each species. Evolution at silent and coding sites were assessed for different Gene Ontology functional categories to compare rates of evolution over both short and long evolutionary timescales. Our results indicate that patterns of molecular change across the family are surprisingly consistent on a macroevolutionary timescale and much more so more than would be predicted from the analysis of one (or many) examples of microevolution. These analyses also point to particular classes of genes that may be crucial in shaping the radiation of this diverse plant family. Similar analyses of nuclear and chloroplast genes in six other plant families confirm that many of these patterns are common features of the plant kingdom.

Local environment rather than past climate determines community composition of mountain stream macroinvertebrates across Europe.

PubMed

Múrria, Cesc; Bonada, Núria; Vellend, Mark; Zamora-Muñoz, Carmen; Alba-Tercedor, Javier; Sainz-Cantero, Carmen Elisa; Garrido, Josefina; Acosta, Raul; El Alami, Majida; Barquín, Jose; Derka, Tomáš; Álvarez-Cabria, Mario; Sáinz-Bariain, Marta; Filipe, Ana F; Vogler, Alfried P

2017-11-01

Community assembly is determined by a combination of historical events and contemporary processes that are difficult to disentangle, but eco-evolutionary mechanisms may be uncovered by the joint analysis of species and genetic diversity across multiple sites. Mountain streams across Europe harbour highly diverse macroinvertebrate communities whose composition and turnover (replacement of taxa) among sites and regions remain poorly known. We studied whole-community biodiversity within and among six mountain regions along a latitudinal transect from Morocco to Scandinavia at three levels of taxonomic hierarchy: genus, species and haplotypes. Using DNA barcoding of four insect families (>3100 individuals, 118 species) across 62 streams, we found that measures of local and regional diversity and intraregional turnover generally declined slightly towards northern latitudes. However, at all hierarchical levels we found complete (haplotype) or high (species, genus) turnover among regions (and even among sites within regions), which counters the expectations of Pleistocene postglacial northward expansion from southern refugia. Species distributions were mostly correlated with environmental conditions, suggesting a strong role of lineage- or species-specific traits in determining local and latitudinal community composition, lineage diversification and phylogenetic community structure (e.g., loss of Coleoptera, but not Ephemeroptera, at northern sites). High intraspecific genetic structure within regions, even in northernmost sites, reflects species-specific dispersal and demographic histories and indicates postglacial migration from geographically scattered refugia, rather than from only southern areas. Overall, patterns were not strongly concordant across hierarchical levels, but consistent with the overriding influence of environmental factors determining community composition at the species and genus levels. © 2017 John Wiley & Sons Ltd.

Ecological consequences of invasion across the freshwater-marine transition in a warming world.

PubMed

Crespo, Daniel; Solan, Martin; Leston, Sara; Pardal, Miguel A; Dolbeth, Marina

2018-02-01

The freshwater-marine transition that characterizes an estuarine system can provide multiple entry options for invading species, yet the relative importance of this gradient in determining the functional contribution of invading species has received little attention. The ecological consequences of species invasion are routinely evaluated within a freshwater versus marine context, even though many invasive species can inhabit a wide range of salinities. We investigate the functional consequences of different sizes of Corbicula fluminea -an invasive species able to adapt to a wide range of temperatures and salinity-across the freshwater-marine transition in the presence versus absence of warming. Specifically, we characterize how C. fluminea affect fluid and particle transport, important processes in mediating nutrient cycling (NH 4 -N, NO 3 -N, PO 4 -P). Results showed that sediment particle reworking (bioturbation) tends to be influenced by size and to a lesser extent, temperature and salinity; nutrient concentrations are influenced by different interactions between all variables (salinity, temperature, and size class). Our findings demonstrate the highly context-dependent nature of the ecosystem consequences of invasion and highlight the potential for species to simultaneously occupy multiple components of an ecosystem. Recognizing of this aspect of invasibility is fundamental to management and conservation efforts, particularly as freshwater and marine systems tend to be compartmentalized rather than be treated as a contiguous unit. We conclude that more comprehensive appreciation of the distribution of invasive species across adjacent habitats and different seasons is urgently needed to allow the true extent of biological introductions, and their ecological consequences, to be fully realized.

Growth Trajectories of Task Value and Self-Efficacy across an Academic Semester

ERIC Educational Resources Information Center

Johnson, Marcus Lee; Edwards, Ordene V.; Dai, Ting

2014-01-01

Many scholars have argued that motivation is dynamic and malleable across time and contexts. In this article, we investigated changes in undergraduates' task value and self-efficacy across an academic semester. Sixty three undergraduate students completed the Motivated Strategies for Learning Questionnaire across five time points in their…

Fluctuating selection across years and phenotypic variation in food-deceptive orchids.

PubMed

Scopece, Giovanni; Juillet, Nicolas; Lexer, Christian; Cozzolino, Salvatore

2017-01-01

Nectarless flowers that deceive pollinators offer an opportunity to study asymmetric plant-insect interactions. Orchids are a widely used model for studying these interactions because they encompass several thousand species adopting deceptive pollination systems. High levels of intra-specific phenotypic variation have been reported in deceptive orchids, suggesting a reduced consistency of pollinator-mediated selection on their floral traits. Nevertheless, several studies report on widespread directional selection mediated by pollinators even in these deceptive orchids. In this study we test the hypothesis that the observed selection can fluctuate across years in strength and direction thus likely contributing to the phenotypic variability of this orchid group. We performed a three-year study estimating selection differentials and selection gradients for nine phenotypic traits involved in insect attraction in two Mediterranean orchid species, namely Orchis mascula and O. pauciflora , both relying on a well-described food-deceptive pollination strategy. We found weak directional selection and marginally significant selection gradients in the two investigated species with significant intra-specific differences in selection differentials across years. Our data do not link this variation with a specific environmental cause, but our results suggest that pollinator-mediated selection in food-deceptive orchids can change in strength and in direction over time. In perennial plants, such as orchids, different selection differentials in the same populations in different flowering seasons can contribute to the maintenance of phenotypic variation often reported in deceptive orchids.

Weak tradeoff between xylem safety and xylem-specific hydraulic efficiency across the world's woody plant species.

PubMed

Gleason, Sean M; Westoby, Mark; Jansen, Steven; Choat, Brendan; Hacke, Uwe G; Pratt, Robert B; Bhaskar, Radika; Brodribb, Tim J; Bucci, Sandra J; Cao, Kun-Fang; Cochard, Hervé; Delzon, Sylvain; Domec, Jean-Christophe; Fan, Ze-Xin; Feild, Taylor S; Jacobsen, Anna L; Johnson, Daniel M; Lens, Frederic; Maherali, Hafiz; Martínez-Vilalta, Jordi; Mayr, Stefan; McCulloh, Katherine A; Mencuccini, Maurizio; Mitchell, Patrick J; Morris, Hugh; Nardini, Andrea; Pittermann, Jarmila; Plavcová, Lenka; Schreiber, Stefan G; Sperry, John S; Wright, Ian J; Zanne, Amy E

2016-01-01

The evolution of lignified xylem allowed for the efficient transport of water under tension, but also exposed the vascular network to the risk of gas emboli and the spread of gas between xylem conduits, thus impeding sap transport to the leaves. A well-known hypothesis proposes that the safety of xylem (its ability to resist embolism formation and spread) should trade off against xylem efficiency (its capacity to transport water). We tested this safety-efficiency hypothesis in branch xylem across 335 angiosperm and 89 gymnosperm species. Safety was considered at three levels: the xylem water potentials where 12%, 50% and 88% of maximal conductivity are lost. Although correlations between safety and efficiency were weak (r(2)  < 0.086), no species had high efficiency and high safety, supporting the idea for a safety-efficiency tradeoff. However, many species had low efficiency and low safety. Species with low efficiency and low safety were weakly associated (r(2)  < 0.02 in most cases) with higher wood density, lower leaf- to sapwood-area and shorter stature. There appears to be no persuasive explanation for the considerable number of species with both low efficiency and low safety. These species represent a real challenge for understanding the evolution of xylem. No claim to US government works. New Phytologist © 2015 New Phytologist Trust.

Quantifying in situ phenotypic variability in the hydraulic properties of four tree species across their distribution range in Europe

PubMed Central

Sterck, F.; Torres-Ruiz, J. M.; Petit, G.; Cochard, H.; von Arx, G.; Lintunen, A.; Caldeira, M. C.; Capdeville, G.; Copini, P.; Gebauer, R.; Grönlund, L.; Hölttä, T.; Lobo-do-Vale, R.; Peltoniemi, M.; Stritih, A.; Urban, J.; Delzon, S.

2018-01-01

Many studies have reported that hydraulic properties vary considerably between tree species, but little is known about their intraspecific variation and, therefore, their capacity to adapt to a warmer and drier climate. Here, we quantify phenotypic divergence and clinal variation for embolism resistance, hydraulic conductivity and branch growth, in four tree species, two angiosperms (Betula pendula, Populus tremula) and two conifers (Picea abies, Pinus sylvestris), across their latitudinal distribution in Europe. Growth and hydraulic efficiency varied widely within species and between populations. The variability of embolism resistance was in general weaker than that of growth and hydraulic efficiency, and very low for all species but Populus tremula. In addition, no and weak support for a safety vs. efficiency trade-off was observed for the angiosperm and conifer species, respectively. The limited variability of embolism resistance observed here for all species except Populus tremula, suggests that forest populations will unlikely be able to adapt hydraulically to drier conditions through the evolution of embolism resistance. PMID:29715289

Performance Characteristics of qPCR Assays Targeting Human- and Ruminant-Associated Bacteroidetes for Microbial Source Tracking across Sixteen Countries on Six Continents

PubMed Central

2013-01-01

Numerous quantitative PCR assays for microbial fecal source tracking (MST) have been developed and evaluated in recent years. Widespread application has been hindered by a lack of knowledge regarding the geographical stability and hence applicability of such methods beyond the regional level. This study assessed the performance of five previously reported quantitative PCR assays targeting human-, cattle-, or ruminant-associated Bacteroidetes populations on 280 human and animal fecal samples from 16 countries across six continents. The tested cattle-associated markers were shown to be ruminant-associated. The quantitative distributions of marker concentrations in target and nontarget samples proved to be essential for the assessment of assay performance and were used to establish a new metric for quantitative source-specificity. In general, this study demonstrates that stable target populations required for marker-based MST occur around the globe. Ruminant-associated marker concentrations were strongly correlated with total intestinal Bacteroidetes populations and with each other, indicating that the detected ruminant-associated populations seem to be part of the intestinal core microbiome of ruminants worldwide. Consequently tested ruminant-targeted assays appear to be suitable quantitative MST tools beyond the regional level while the targeted human-associated populations seem to be less prevalent and stable, suggesting potential for improvements in human-targeted methods. PMID:23755882

Student and Parent IEP Collaboration: A Comparison across School Settings

ERIC Educational Resources Information Center

Williams-Diehm, Kendra L.; Brandes, Joyce A.; Chesnut, Pik Wah; Haring, Kathryn A.

2014-01-01

The purpose of this study was to determine if differences existed across rural, urban, and suburban environments when special education teachers reported perceived levels of student and parent involvement and participation during IEP meetings. The investigators surveyed special education teachers (N = 159) across a Southwest state and applied log…

Contextual Cueing Effects across the Lifespan

ERIC Educational Resources Information Center

Merrill, Edward C.; Conners, Frances A.; Roskos, Beverly; Klinger, Mark R.; Klinger, Laura Grofer

2013-01-01

The authors evaluated age-related variations in contextual cueing, which reflects the extent to which visuospatial regularities can facilitate search for a target. Previous research produced inconsistent results regarding contextual cueing effects in young children and in older adults, and no study has investigated the phenomenon across the life…

Apparent competition drives community-wide parasitism rates and changes in host abundance across ecosystem boundaries

PubMed Central

Frost, Carol M.; Peralta, Guadalupe; Rand, Tatyana A.; Didham, Raphael K.; Varsani, Arvind; Tylianakis, Jason M.

2016-01-01

Species have strong indirect effects on others, and predicting these effects is a central challenge in ecology. Prey species sharing an enemy (predator or parasitoid) can be linked by apparent competition, but it is unknown whether this process is strong enough to be a community-wide structuring mechanism that could be used to predict future states of diverse food webs. Whether species abundances are spatially coupled by enemy movement across different habitats is also untested. Here, using a field experiment, we show that predicted apparent competitive effects between species, mediated via shared parasitoids, can significantly explain future parasitism rates and herbivore abundances. These predictions are successful even across edges between natural and managed forests, following experimental reduction of herbivore densities by aerial spraying of insecticide over 20 hectares. This result shows that trophic indirect effects propagate across networks and habitats in important, predictable ways, with implications for landscape planning, invasion biology and biological control. PMID:27577948

The Monarch Initiative: an integrative data and analytic platform connecting phenotypes to genotypes across species

PubMed Central

Mungall, Christopher J.; McMurry, Julie A.; Köhler, Sebastian; Balhoff, James P.; Borromeo, Charles; Brush, Matthew; Carbon, Seth; Conlin, Tom; Dunn, Nathan; Engelstad, Mark; Foster, Erin; Gourdine, J.P.; Jacobsen, Julius O.B.; Keith, Dan; Laraway, Bryan; Lewis, Suzanna E.; NguyenXuan, Jeremy; Shefchek, Kent; Vasilevsky, Nicole; Yuan, Zhou; Washington, Nicole; Hochheiser, Harry; Groza, Tudor; Smedley, Damian; Robinson, Peter N.; Haendel, Melissa A.

2017-01-01

The correlation of phenotypic outcomes with genetic variation and environmental factors is a core pursuit in biology and biomedicine. Numerous challenges impede our progress: patient phenotypes may not match known diseases, candidate variants may be in genes that have not been characterized, model organisms may not recapitulate human or veterinary diseases, filling evolutionary gaps is difficult, and many resources must be queried to find potentially significant genotype–phenotype associations. Non-human organisms have proven instrumental in revealing biological mechanisms. Advanced informatics tools can identify phenotypically relevant disease models in research and diagnostic contexts. Large-scale integration of model organism and clinical research data can provide a breadth of knowledge not available from individual sources and can provide contextualization of data back to these sources. The Monarch Initiative (monarchinitiative.org) is a collaborative, open science effort that aims to semantically integrate genotype–phenotype data from many species and sources in order to support precision medicine, disease modeling, and mechanistic exploration. Our integrated knowledge graph, analytic tools, and web services enable diverse users to explore relationships between phenotypes and genotypes across species. PMID:27899636

Using Citizen Science Observations to Model Species Distributions Over Space, Through Time, and Across Scales

NASA Astrophysics Data System (ADS)

Kelling, S.

2017-12-01

The goal of Biodiversity research is to identify, explain, and predict why a species' distribution and abundance vary through time, space, and with features of the environment. Measuring these patterns and predicting their responses to change are not exercises in curiosity. Today, they are essential tasks for understanding the profound effects that humans have on earth's natural systems, and for developing science-based environmental policies. To gain insight about species' distribution patterns requires studying natural systems at appropriate scales, yet studies of ecological processes continue to be compromised by inadequate attention to scale issues. How spatial and temporal patterns in nature change with scale often reflects fundamental laws of physics, chemistry, or biology, and we can identify such basic, governing laws only by comparing patterns over a wide range of scales. This presentation will provide several examples that integrate bird observations made by volunteers, with NASA Earth Imagery using Big Data analysis techniques to analyze the temporal patterns of bird occurrence across scales—from hemisphere-wide views of bird distributions to the impact of powerful city lights on bird migration.

Preservice Teacher Mobile Investigation and Interpretation of Everyday Mathematics across Settings

ERIC Educational Resources Information Center

Kalir, Jeremiah

2016-01-01

This study reports upon design-based research that enacted mobile mathematics learning for preservice teachers across classroom, community, and online settings. The integration of mobile learning within mathematics teacher education is understudied, and it is necessary to better understand mobile technology affordances when locating disciplinary…

Oxygen isotope fractionations across individual leaf carbohydrates in grass and tree species.

PubMed

Lehmann, Marco M; Gamarra, Bruno; Kahmen, Ansgar; Siegwolf, Rolf T W; Saurer, Matthias

2017-08-01

Almost no δ 18 O data are available for leaf carbohydrates, leaving a gap in the understanding of the δ 18 O relationship between leaf water and cellulose. We measured δ 18 O values of bulk leaf water (δ 18 O LW ) and individual leaf carbohydrates (e.g. fructose, glucose and sucrose) in grass and tree species and δ 18 O of leaf cellulose in grasses. The grasses were grown under two relative humidity (rH) conditions. Sucrose was generally 18 O-enriched compared with hexoses across all species with an apparent biosynthetic fractionation factor (ε bio ) of more than 27‰ relative to δ 18 O LW , which might be explained by isotopic leaf water and sucrose synthesis gradients. δ 18 O LW and δ 18 O values of carbohydrates and cellulose in grasses were strongly related, indicating that the leaf water signal in carbohydrates was transferred to cellulose (ε bio  = 25.1‰). Interestingly, damping factor p ex p x , which reflects oxygen isotope exchange with less enriched water during cellulose synthesis, responded to rH conditions if modelled from δ 18 O LW but not if modelled directly from δ 18 O of individual carbohydrates. We conclude that δ 18 O LW is not always a good substitute for δ 18 O of synthesis water due to isotopic leaf water gradients. Thus, compound-specific δ 18 O analyses of individual carbohydrates are helpful to better constrain (post-)photosynthetic isotope fractionation processes in plants. © 2017 John Wiley & Sons Ltd.

Listening comprehension across the adult lifespan.

PubMed

Sommers, Mitchell S; Hale, Sandra; Myerson, Joel; Rose, Nathan; Tye-Murray, Nancy; Spehar, Brent

2011-01-01

Although age-related declines in perceiving spoken language are well established, the primary focus of research has been on perception of phonemes, words, and sentences. In contrast, relatively few investigations have been directed at establishing the effects of age on the comprehension of extended spoken passages. Moreover, most previous work has used extreme-group designs in which the performance of a group of young adults is contrasted with that of a group of older adults and little if any information is available regarding changes in listening comprehension across the adult lifespan. Accordingly, the goals of the current investigation were to determine whether there are age differences in listening comprehension across the adult lifespan and, if so, whether similar trajectories are observed for age-related changes in auditory sensitivity and listening comprehension. This study used a cross-sectional lifespan design in which approximately 60 individuals in each of 7 decades, from age 20 to 89 yr (a total of 433 participants), were tested on three different measures of listening comprehension. In addition, we obtained measures of auditory sensitivity from all participants. Changes in auditory sensitivity across the adult lifespan exhibited the progressive high-frequency loss typical of age-related hearing impairment. Performance on the listening comprehension measures, however, demonstrated a very different pattern, with scores on all measures remaining relatively stable until age 65 to 70 yr, after which significant declines were observed. Follow-up analyses indicated that this same general pattern was observed across three different types of passages (lectures, interviews, and narratives) and three different question types (information, integration, and inference). Multiple regression analyses indicated that low-frequency pure-tone average was the single largest contributor to age-related variance in listening comprehension for individuals older than 65 yr, but

Meal patterns across ten European countries - results from the European Prospective Investigation into Cancer and Nutrition (EPIC) calibration study.

PubMed

Huseinovic, E; Winkvist, A; Slimani, N; Park, M K; Freisling, H; Boeing, H; Buckland, G; Schwingshackl, L; Weiderpass, E; Rostgaard-Hansen, A L; Tjønneland, A; Affret, A; Boutron-Ruault, M C; Fagherazzi, G; Katzke, V; Kühn, T; Naska, A; Orfanos, P; Trichopoulou, A; Pala, V; Palli, D; Ricceri, F; Santucci de Magistris, M; Tumino, R; Engeset, D; Enget, T; Skeie, G; Barricarte, A; Bonet, C B; Chirlaque, M D; Amiano, P; Quirós, J R; Sánchez, M J; Dias, J A; Drake, I; Wennberg, M; Boer, Jma; Ocké, M C; Verschuren, Wmm; Lassale, C; Perez-Cornago, A; Riboli, E; Ward, H; Forslund, H Bertéus

2016-10-01

To characterize meal patterns across ten European countries participating in the European Prospective Investigation into Cancer and Nutrition (EPIC) calibration study. Cross-sectional study utilizing dietary data collected through a standardized 24 h diet recall during 1995-2000. Eleven predefined intake occasions across a 24 h period were assessed during the interview. In the present descriptive report, meal patterns were analysed in terms of daily number of intake occasions, the proportion reporting each intake occasion and the energy contributions from each intake occasion. Twenty-seven centres across ten European countries. Women (64 %) and men (36 %) aged 35-74 years (n 36 020). Pronounced differences in meal patterns emerged both across centres within the same country and across different countries, with a trend for fewer intake occasions per day in Mediterranean countries compared with central and northern Europe. Differences were also found for daily energy intake provided by lunch, with 38-43 % for women and 41-45 % for men within Mediterranean countries compared with 16-27 % for women and 20-26 % for men in central and northern European countries. Likewise, a south-north gradient was found for daily energy intake from snacks, with 13-20 % (women) and 10-17 % (men) in Mediterranean countries compared with 24-34 % (women) and 23-35 % (men) in central/northern Europe. We found distinct differences in meal patterns with marked diversity for intake frequency and lunch and snack consumption between Mediterranean and central/northern European countries. Monitoring of meal patterns across various cultures and populations could provide critical context to the research efforts to characterize relationships between dietary intake and health.

Epithelial cell pro-inflammatory cytokine response differs across dental plaque bacterial species.

PubMed

Stathopoulou, Panagiota G; Benakanakere, Manjunatha R; Galicia, Johnah C; Kinane, Denis F

2010-01-01

The dental plaque is comprised of numerous bacterial species, which may or may not be pathogenic. Human gingival epithelial cells (HGECs) respond to perturbation by various bacteria of the dental plaque by production of different levels of inflammatory cytokines, which is a putative reflection of their virulence. The aim of the current study was to determine responses in terms of interleukin (IL)-1beta, IL-6, IL-8 and IL-10 secretion induced by Porphyromonas gingivalis, Aggregatibacter actinomycetemcomitans, Fusobacterium nucleatum and Streptococcus gordonii in order to gauge their virulence potential. HGECs were challenged with the four bacterial species, live or heat killed, at various multiplicity of infections and the elicited IL-1beta, IL-6, IL-8 and IL-10 responses were assayed by enzyme-linked immunosorbent assay. Primary HGECs challenged with live P. gingivalis produced high levels of IL-1beta, while challenge with live A. actinomycetemcomitans gave high levels of IL-8. The opportunistic pathogen F. nucleatum induces the highest levels of pro-inflammatory cytokines, while the commensal S. gordonii is the least stimulatory. We conclude that various dental plaque biofilm bacteria induce different cytokine response profiles in primary HGECs that may reflect their individual virulence or commensal status.

Inter-Tributary Movements by Resident Salmonids across a Boreal Riverscape

PubMed Central

Bentley, Kale T.; Schindler, Daniel E.; Armstrong, Jonathan B.; Cline, Timothy J.; Brooks, Gabriel T.

2015-01-01

Stream-dwelling fishes inhabit river networks where resources are distributed heterogeneously across space and time. Current theory emphasizes that fishes often perform large-scale movements among habitat patches for reproduction and seeking refugia, but assumes that fish are relatively sedentary during growth phases of their life cycle. Using stationary passive integrated transponder (PIT)-tag antennas and snorkel surveys, we assessed the individual and population level movement patterns of two species of fish across a network of tributaries within the Wood River basin in southwestern Alaska where summer foraging opportunities vary substantially among streams, seasons, and years. Across two years, Arctic grayling (Thymallus arcticus) and rainbow trout (Oncorhynchus mykiss) exhibited kilometer-scale movements among streams during the summer growing season. Although we monitored movements at a small fraction of all tributaries used by grayling and rainbow trout, approximately 50% of individuals moved among two or more streams separated by at least 7 km within a single summer. Movements were concentrated in June and July, and subsided by early August. The decline in movements coincided with spawning by anadromous sockeye salmon, which offer a high-quality resource pulse of food to resident species. Inter-stream movements may represent prospecting behavior as individuals seek out the most profitable foraging opportunities that are patchily distributed across space and time. Our results highlight that large-scale movements may not only be necessary for individuals to fulfill their life-cycle, but also to exploit heterogeneously spaced trophic resources. Therefore, habitat fragmentation and homogenization may have strong, but currently undescribed, ecological effects on the access to critical food resources in stream-dwelling fish populations. PMID:26379237

Comparing Dislodgeable 2,4-D Residues across Athletic Field Turfgrass Species and Time

PubMed Central

Brosnan, James T.; Breeden, Gregory K.

2016-01-01

2,4-dimethylamine salt (2,4-D) is an herbicide commonly applied on athletic fields for broadleaf weed control that can dislodge from treated turfgrass. Dislodge potential is affected by numerous factors, including turfgrass canopy conditions. Building on previous research confirming herbicide-turfgrass dynamics can vary widely between species, field research was initiated in 2014 and 2015 in Raleigh, NC, USA to quantify dislodgeable 2,4-D residues from dormant hybrid bermudagrass (Cynodon dactylon L. x C. transvaalensis) and hybrid bermudagrass overseeded with perennial ryegrass (Lolium perenne L.), which are common athletic field playing surfaces in subtropical climates. Additionally, dislodgeable 2,4-D was compared at AM (7:00 eastern standard time) and PM (14:00) sample timings within a day. Samples collected from perennial ryegrass consistently resulted in greater 2,4-D dislodgment immediately after application (9.4 to 9.9% of applied) compared to dormant hybrid bermudagrass (2.3 to 2.9%), as well as at all AM compared to PM timings from 1 to 3 d after treatment (DAT; 0.4 to 6.3% compared to 0.1 to 0.8%). Dislodgeable 2,4-D did not differ across turfgrass species at PM sample collections, with ≤ 0.1% of the 2,4-D applied dislodged from 1 to 6 DAT, and 2,4-D detection did not occur at 12 and 24 DAT. In conclusion, dislodgeable 2,4-D from treated turfgrass can vary between species and over short time-scales within a day. This information should be taken into account in human exposure risk assessments, as well as by turfgrass managers and athletic field event coordinators to minimize 2,4-D exposure. PMID:27936174

COMPUTATIONAL INVESTIGATION OF CHEMICAL REACTIVITY IN RELATION TO BIOACTIVATION AND TOXICITY ACROSS CLASSES OF HALOORGANICS: BROMINATION VS. CHLORINATION

EPA Science Inventory

COMPUTATIONAL INVESTIGATION OF CHEMICAL REACTIVITY IN RELATION TO BIOACTIV A TION AND TOXICITY ACROSS CLASSES OF HALOORGANICS: BROMINATION VS. CHLORINATION.

Halogenation is a common feature of many classes of environmental contaminants, and often plays a crucial role in po...

Hydraulic adjustment of Scots pine across Europe.

PubMed

Martínez-Vilalta, J; Cochard, H; Mencuccini, M; Sterck, F; Herrero, A; Korhonen, J F J; Llorens, P; Nikinmaa, E; Nolè, A; Poyatos, R; Ripullone, F; Sass-Klaassen, U; Zweifel, R

2009-10-01

* The variability of branch-level hydraulic properties was assessed across 12 Scots pine populations covering a wide range of environmental conditions, including some of the southernmost populations of the species. The aims were to relate this variability to differences in climate, and to study the potential tradeoffs between traits. * Traits measured included wood density, radial growth, xylem anatomy, sapwood- and leaf-specific hydraulic conductivity (K(S) and K(L)), vulnerability to embolism, leaf-to-sapwood area ratio (A(L) : A(S)), needle carbon isotope discrimination (Delta13C) and nitrogen content, and specific leaf area. * Between-population variability was high for most of the hydraulic traits studied, but it was directly associated with climate dryness (defined as a combination of atmospheric moisture demand and availability) only for A(L) : A(S), K(L) and Delta13C. Shoot radial growth and A(L) : A(S) declined with stand development, which is consistent with a strategy to avoid exceedingly low water potentials as tree size increases. In addition, we did not find evidence at the intraspecific level of some associations between hydraulic traits that have been commonly reported across species. * The adjustment of Scots pine's hydraulic system to local climatic conditions occurred primarily through modifications of A(L) : A(S) and direct stomatal control, whereas intraspecific variation in vulnerability to embolism and leaf physiology appears to be limited.

Parallel Evolution of Copy-Number Variation across Continents in Drosophila melanogaster

PubMed Central

Schrider, Daniel R.; Hahn, Matthew W.; Begun, David J.

2016-01-01

Genetic differentiation across populations that is maintained in the presence of gene flow is a hallmark of spatially varying selection. In Drosophila melanogaster, the latitudinal clines across the eastern coasts of Australia and North America appear to be examples of this type of selection, with recent studies showing that a substantial portion of the D. melanogaster genome exhibits allele frequency differentiation with respect to latitude on both continents. As of yet there has been no genome-wide examination of differentiated copy-number variants (CNVs) in these geographic regions, despite their potential importance for phenotypic variation in Drosophila and other taxa. Here, we present an analysis of geographic variation in CNVs in D. melanogaster. We also present the first genomic analysis of geographic variation for copy-number variation in the sister species, D. simulans, in order to investigate patterns of parallel evolution in these close relatives. In D. melanogaster we find hundreds of CNVs, many of which show parallel patterns of geographic variation on both continents, lending support to the idea that they are influenced by spatially varying selection. These findings support the idea that polymorphic CNVs contribute to local adaptation in D. melanogaster. In contrast, we find very few CNVs in D. simulans that are geographically differentiated in parallel on both continents, consistent with earlier work suggesting that clinal patterns are weaker in this species. PMID:26809315

Temporal patterns in adult salmon migration timing across southeast Alaska

USGS Publications Warehouse

Kovach, Ryan P.; Ellison, Stephen; Pyare, Sanjay; Tallmon, David

2015-01-01

Pacific salmon migration timing can drive population productivity, ecosystem dynamics, and human harvest. Nevertheless, little is known about long-term variation in salmon migration timing for multiple species across broad regions. We used long-term data for five Pacific salmon species throughout rapidly warming southeast Alaska to describe long-term changes in salmon migration timing, interannual phenological synchrony, relationships between climatic variation and migratory timing, and to test whether long-term changes in migration timing are related to glaciation in headwater streams. Temporal changes in the median date of salmon migration timing varied widely across species. Most sockeye populations are migrating later over time (11 of 14), but pink, chum, and especially coho populations are migrating earlier than they did historically (16 of 19 combined). Temporal trends in duration and interannual variation in migration timing were highly variable across species and populations. The greatest temporal shifts in the median date of migration timing were correlated with decreases in the duration of migration timing, suggestive of a loss of phenotypic variation due to natural selection. Pairwise interannual correlations in migration timing varied widely but were generally positive, providing evidence for weak region-wide phenological synchrony. This synchrony is likely a function of climatic variation, as interannual variation in migration timing was related to climatic phenomenon operating at large- (Pacific decadal oscillation), moderate- (sea surface temperature), and local-scales (precipitation). Surprisingly, the presence or the absence of glaciers within a watershed was unrelated to long-term shifts in phenology. Overall, there was extensive heterogeneity in long-term patterns of migration timing throughout this climatically and geographically complex region, highlighting that future climatic change will likely have widely divergent impacts on salmon

Imprints from genetic drift and mutation imply relative divergence times across marine transition zones in a pan-European small pelagic fish (Sprattus sprattus).

PubMed

Limborg, M T; Hanel, R; Debes, P V; Ring, A K; André, C; Tsigenopoulos, C S; Bekkevold, D

2012-08-01

Geographic distributions of most temperate marine fishes are affected by postglacial recolonisation events, which have left complex genetic imprints on populations of marine species. This study investigated population structure and demographic history of European sprat (Sprattus sprattus L.) by combining inference from both mtDNA and microsatellite genetic markers throughout the species' distribution. We compared effects from genetic drift and mutation for both genetic markers in shaping genetic differentiation across four transition zones. Microsatellite markers revealed significant isolation by distance and a complex population structure across the species' distribution (overall θ(ST)=0.038, P<0.01). Across transition zones markers indicated larger effects of genetic drift over mutations in the northern distribution of sprat contrasting a stronger relative impact of mutation in the species' southern distribution in the Mediterranean region. These results were interpreted to reflect more recent divergence times between northern populations in accordance with previous findings. This study demonstrates the usefulness of comparing inference from different markers and estimators of divergence for phylogeographic and population genetic studies in species with weak genetic structure, as is the case in many marine species.

Investigating Coral Disease Spread Across the Hawaiian Archipelago

NASA Astrophysics Data System (ADS)

Sziklay, Jamie

Coral diseases negatively impact reef ecosystems and they are increasing worldwide; yet, we have a limited understanding of the factors that influence disease risk and transmission. My dissertation research investigated coral disease spread for several common coral diseases in the Hawaiian archipelago to understand how host-pathogenenvironment interactions vary across different spatial scales and how we can use that information to improve management strategies. At broad spatial scales, I developed forecasting models to predict outbreak risk based on depth, coral density and temperature anomalies from remotely sensed data (chapter 1). In this chapter, I determined that host density, total coral density, depth and winter temperature variation were important predictors of disease prevalence for several coral diseases. Expanding on the predictive models, I also found that colony size, wave energy, water quality, fish abundance and nearby human population size altered disease risk (chapter 2). Most of the model variation occurred at the scale of sites and coastline, indicating that local coral composition and water quality were key determinants of disease risk. At the reef scale, I investigated factors that influence disease transmission among individuals using a tissue loss disease outbreak in Kane'ohe Bay, O'ahu, Hawai'i as a case study (chapter 3). I determined that host size, proximity to infected neighbors and numbers of infected neighbors were associated with disease risk. Disease transmission events were very localized (within 15 m) and rates changed dramatically over the course of the outbreak: the transmission rate initially increased quickly during the outbreak and then decreased steadily until the outbreak ended. At the colony scale, I investigated disease progression between polyps within individual coral colonies using confocal microscopy (chapter 4). Here, I determined that fragmented florescent pigment distributions appeared adjacent to the disease front

Obesity Exposure Across the Lifespan on Ovarian Cancer Pathogenesis

DTIC Science & Technology

2015-08-01

exposure to the HFD or LFD, obese mice weighed significantly greater than lean mice (p=0.003, Table 1). There was no effect of HFD on non- fasted blood...AWARD NUMBER: W81XWH-13-1-0164 TITLE: Obesity Exposure Across the Lifespan on Ovarian Cancer Pathogenesis PRINCIPAL INVESTIGATOR: Victoria Bae...31 May 2015 4. TITLE AND SUBTITLE 5a. CONTRACT NUMBER Obesity Exposure Across the Lifespan on Ovarian Cancer Pathogenesis 5b. GRANT NUMBER

Listening to Learners: An Investigation into "Successful Learning" across CLIL Contexts

ERIC Educational Resources Information Center

Coyle, Do

2013-01-01

This study is part of longitudinal research undertaken in 11 secondary schools across two countries, based in Content and Language Integrated Learning (CLIL) classrooms with 12-15 year olds. The aim was to listen to learners, provide them with a "voice" to analyse their perceptions of "successful learning" and to undertake participatory research…

Epidemiology of asexuality induced by the endosymbiotic Wolbachia across phytophagous wasp species: host plant specialization matters.

PubMed

Boivin, T; Henri, H; Vavre, F; Gidoin, C; Veber, P; Candau, J-N; Magnoux, E; Roques, A; Auger-Rozenberg, M-A

2014-05-01

Among eukaryotes, sexual reproduction is by far the most predominant mode of reproduction. However, some systems maintaining sexuality appear particularly labile and raise intriguing questions on the evolutionary routes to asexuality. Thelytokous parthenogenesis is a form of spontaneous loss of sexuality leading to strong distortion of sex ratio towards females and resulting from mutation, hybridization or infection by bacterial endosymbionts. We investigated whether ecological specialization is a likely mechanism of spread of thelytoky within insect communities. Focusing on the highly specialized genus Megastigmus (Hymenoptera: Torymidae), we first performed a large literature survey to examine the distribution of thelytoky in these wasps across their respective obligate host plant families. Second, we tested for thelytoky caused by endosymbionts by screening in 15 arrhenotokous and 10 thelytokous species for Wolbachia, Cardinium, Arsenophonus and Rickettsia endosymbionts and by performing antibiotic treatments. Finally, we performed phylogenetic reconstructions using multilocus sequence typing (MLST) to examine the evolution of endosymbiont-mediated thelytoky in Megastigmus and its possible connections to host plant specialization. We demonstrate that thelytoky evolved from ancestral arrhenotoky through the horizontal transmission and the fixation of the parthenogenesis-inducing Wolbachia. We find that ecological specialization in Wolbachia's hosts was probably a critical driving force for Wolbachia infection and spread of thelytoky, but also a constraint. Our work further reinforces the hypothesis that community structure of insects is a major driver of the epidemiology of endosymbionts and that competitive interactions among closely related species may facilitate their horizontal transmission. © 2014 John Wiley & Sons Ltd.

Lack of population genetic structure and host specificity in the bat fly, Cyclopodia horsfieldi, across species of Pteropus bats in Southeast Asia

PubMed Central

2013-01-01

Background Population-level studies of parasites have the potential to elucidate patterns of host movement and cross-species interactions that are not evident from host genealogy alone. Bat flies are obligate and generally host-specific blood-feeding parasites of bats. Old-World flies in the family Nycteribiidae are entirely wingless and depend on their hosts for long-distance dispersal; their population genetics has been unstudied to date. Methods We collected a total of 125 bat flies from three Pteropus species (Pteropus vampyrus, P. hypomelanus, and P. lylei) from eight localities in Malaysia, Cambodia, and Vietnam. We identified specimens morphologically and then sequenced three mitochondrial DNA gene fragments (CoI, CoII, cytB; 1744 basepairs total) from a subset of 45 bat flies. We measured genetic diversity, molecular variance, and population genetic subdivision (FST), and used phylogenetic and haplotype network analyses to quantify parasite genetic structure across host species and localities. Results All flies were identified as Cyclopodia horsfieldi with the exception of two individuals of Eucampsipoda sundaica. Low levels of population genetic structure were detected between populations of Cyclopodia horsfieldi from across a wide geographic range (~1000 km), and tests for isolation by distance were rejected. AMOVA results support a lack of geographic and host-specific population structure, with molecular variance primarily partitioned within populations. Pairwise FST values from flies collected from island populations of Pteropus hypomelanus in East and West Peninsular Malaysia supported predictions based on previous studies of host genetic structure. Conclusions The lack of population genetic structure and morphological variation observed in Cyclopodia horsfieldi is most likely due to frequent contact between flying fox species and subsequent high levels of parasite gene flow. Specifically, we suggest that Pteropus vampyrus may facilitate movement of

Lack of population genetic structure and host specificity in the bat fly, Cyclopodia horsfieldi, across species of Pteropus bats in Southeast Asia.

PubMed

Olival, Kevin J; Dick, Carl W; Simmons, Nancy B; Morales, Juan Carlos; Melnick, Don J; Dittmar, Katharina; Perkins, Susan L; Daszak, Peter; Desalle, Rob

2013-08-08

Population-level studies of parasites have the potential to elucidate patterns of host movement and cross-species interactions that are not evident from host genealogy alone. Bat flies are obligate and generally host-specific blood-feeding parasites of bats. Old-World flies in the family Nycteribiidae are entirely wingless and depend on their hosts for long-distance dispersal; their population genetics has been unstudied to date. We collected a total of 125 bat flies from three Pteropus species (Pteropus vampyrus, P. hypomelanus, and P. lylei) from eight localities in Malaysia, Cambodia, and Vietnam. We identified specimens morphologically and then sequenced three mitochondrial DNA gene fragments (CoI, CoII, cytB; 1744 basepairs total) from a subset of 45 bat flies. We measured genetic diversity, molecular variance, and population genetic subdivision (FST), and used phylogenetic and haplotype network analyses to quantify parasite genetic structure across host species and localities. All flies were identified as Cyclopodia horsfieldi with the exception of two individuals of Eucampsipoda sundaica. Low levels of population genetic structure were detected between populations of Cyclopodia horsfieldi from across a wide geographic range (~1000 km), and tests for isolation by distance were rejected. AMOVA results support a lack of geographic and host-specific population structure, with molecular variance primarily partitioned within populations. Pairwise FST values from flies collected from island populations of Pteropus hypomelanus in East and West Peninsular Malaysia supported predictions based on previous studies of host genetic structure. The lack of population genetic structure and morphological variation observed in Cyclopodia horsfieldi is most likely due to frequent contact between flying fox species and subsequent high levels of parasite gene flow. Specifically, we suggest that Pteropus vampyrus may facilitate movement of bat flies between the three Pteropus

Four New Bat Species (Rhinolophus hildebrandtii Complex) Reflect Plio-Pleistocene Divergence of Dwarfs and Giants across an Afromontane Archipelago

PubMed Central

Taylor, Peter J.; Stoffberg, Samantha; Monadjem, Ara; Schoeman, Martinus Corrie; Bayliss, Julian; Cotterill, Fenton P. D.

2012-01-01

Gigantism and dwarfism evolve in vertebrates restricted to islands. We describe four new species in the Rhinolophus hildebrandtii species-complex of horseshoe bats, whose evolution has entailed adaptive shifts in body size. We postulate that vicissitudes of palaeoenvironments resulted in gigantism and dwarfism in habitat islands fragmented across eastern and southern Africa. Mitochondrial and nuclear DNA sequences recovered two clades of R. hildebrandtii senso lato which are paraphyletic with respect to a third lineage (R. eloquens). Lineages differ by 7.7 to 9.0% in cytochrome b sequences. Clade 1 includes R. hildebrandtii sensu stricto from the east African highlands and three additional vicariants that speciated across an Afromontane archipelago through the Plio-Pleistocene, extending from the Kenyan Highlands through the Eastern Arc, northern Mozambique and the Zambezi Escarpment to the eastern Great Escarpment of South Africa. Clade 2 comprises one species confined to lowland savanna habitats (Mozambique and Zimbabwe). A third clade comprises R. eloquens from East Africa. Speciation within Clade 1 is associated with fixed differences in echolocation call frequency, and cranial shape and size in populations isolated since the late Pliocene (ca 3.74 Mya). Relative to the intermediate-sized savanna population (Clade 2), these island-populations within Clade 1 are characterised by either gigantism (South African eastern Great Escarpment and Mts Mabu and Inago in Mozambique) or dwarfism (Lutope-Ngolangola Gorge, Zimbabwe and Soutpansberg Mountains, South Africa). Sympatry between divergent clades (Clade 1 and Clade 2) at Lutope-Ngolangola Gorge (NW Zimbabwe) is attributed to recent range expansions. We propose an “Allometric Speciation Hypothesis”, which attributes the evolution of this species complex of bats to divergence in constant frequency (CF) sonar calls. The origin of species-specific peak frequencies (overall range = 32 to 46 kHz) represents the

Incidental Sequence Learning across the Lifespan

ERIC Educational Resources Information Center

Weiermann, Brigitte; Meier, Beat

2012-01-01

The purpose of the present study was to investigate incidental sequence learning across the lifespan. We tested 50 children (aged 7-16), 50 young adults (aged 20-30), and 50 older adults (aged >65) with a sequence learning paradigm that involved both a task and a response sequence. After several blocks of practice, all age groups slowed down…

Family Life Satisfaction across Positional Roles, Family Development Categories and SES.

ERIC Educational Resources Information Center

Tiffany, Phyllis G.

Marital satisfaction across the life cycle differs for men and women. To investigate family life satisfaction across positional roles, developmental categories, and socioeconomic status (SES), 100 husbands and wives (families) were administered the Heimler Schedule of Social Functioning (SOSF), which relates social function and stressors (work,…

Workshop proceedings: challenges and opportunities in evaluating protein allergenicity across biotechnology industries.

PubMed

Stagg, Nicola J; Ghantous, Hanan N; Ladics, Gregory S; House, Robert V; Gendel, Steven M; Hastings, Kenneth L

2013-01-01

A workshop entitled "Challenges and Opportunities in Evaluating Protein Allergenicity across Biotechnology Industries" was held at the 51st Annual Meeting of the Society of Toxicology (SOT) in San Francisco, California. The workshop was sponsored by the Biotechnology Specialty Section of SOT and was designed to present the science-based approaches used in biotechnology industries to evaluate and regulate protein allergenicity. A panel of experts from industry and government highlighted the allergenicity testing requirements and research in the agricultural, pharmaceutical/biopharma, and vaccine biotechnology industries and addressed challenges and opportunities for advancing the science of protein allergenicity. The main learning from the workshop was that immunoglobulin E-mediated allergenicity of biotechnology-derived products is difficult to assess without human data. The approaches currently being used to evaluate potential for allergenicity across biotechnology industries are very different and range from bioinformatics, in vitro serology, in vivo animal testing, in vitro and in vivo functional assays, and "biosimilar" assessments (ie, biotherapeutic equivalents to innovator products). The challenge remains with regard to the different or lack of regulatory requirements for allergenicity testing across industries, but the novel approaches being used with bioinformatics and biosimilars may lead to opportunities in the future to collaborate across biotechnology industries.

Sponge bioerosion accelerated by ocean acidification across species and latitudes?

NASA Astrophysics Data System (ADS)

Wisshak, M.; Schönberg, C. H. L.; Form, A.; Freiwald, A.

2014-06-01

In many marine biogeographic realms, bioeroding sponges dominate the internal bioerosion of calcareous substrates such as mollusc beds and coral reef framework. They biochemically dissolve part of the carbonate and liberate so-called sponge chips, a process that is expected to be facilitated and accelerated in a more acidic environment inherent to the present global change. The bioerosion capacity of the demosponge Cliona celata Grant, 1826 in subfossil oyster shells was assessed via alkalinity anomaly technique based on 4 days of experimental exposure to three different levels of carbon dioxide partial pressure ( pCO2) at ambient temperature in the cold-temperate waters of Helgoland Island, North Sea. The rate of chemical bioerosion at present-day pCO2 was quantified with 0.08-0.1 kg m-2 year-1. Chemical bioerosion was positively correlated with increasing pCO2, with rates more than doubling at carbon dioxide levels predicted for the end of the twenty-first century, clearly confirming that C. celata bioerosion can be expected to be enhanced with progressing ocean acidification (OA). Together with previously published experimental evidence, the present results suggest that OA accelerates sponge bioerosion (1) across latitudes and biogeographic areas, (2) independent of sponge growth form, and (3) for species with or without photosymbionts alike. A general increase in sponge bioerosion with advancing OA can be expected to have a significant impact on global carbonate (re)cycling and may result in widespread negative effects, e.g. on the stability of wild and farmed shellfish populations, as well as calcareous framework builders in tropical and cold-water coral reef ecosystems.

A molecular survey of Eimeria in chickens across Australia.

PubMed

Godwin, Rosamond M; Morgan, Jess A T

2015-11-30

Coccidiosis is a costly enteric disease of chickens caused by protozoan parasites of the genus Eimeria. Disease diagnosis and management is complicated since there are multiple Eimeria species infecting chickens and mixed species infections are common. Current control measures are only partially effective and this, combined with concerns over vaccine efficacy and increasing drug resistance, demonstrates a need for improved coccidiosis diagnosis and control. Before improvements can be made, it is important to understand the species commonly infecting poultry flocks in both backyard and commercial enterprises. The aim of this project was to conduct a survey and assessment of poultry Eimeria across Australia using genetic markers, and create a collection of isolates for each Eimeria species. A total of 260 samples (faecal or caecal) was obtained, and survey results showed that Eimeria taxa were present in 98% of commercial and 81% of backyard flocks. The distribution of each Eimeria species was widespread across Australia, with representatives of all species being found in every state and territory, and the Eimeria species predominating in commercial flocks differed from those in backyard flocks. Three operational taxonomic units also occurred frequently in commercial flocks highlighting the need to understand the impact of these uncharacterised species on poultry production. As Eimeria infections were also frequent in backyard flocks, there is a potential for backyard flocks to act as reservoirs for disease, especially as the industry moves towards free range production systems. This Eimeria collection will be an important genetic resource which is the crucial first step in the development of more sophisticated diagnostic tools and the development of new live vaccines which ultimately will provide savings to the industry in terms of more efficient coccidiosis management. Crown Copyright © 2015. Published by Elsevier B.V. All rights reserved.

A swath across the great divide: Kelp forests across the Samalga Pass biogeographic break

USGS Publications Warehouse

Konar, Brenda H.; Edwards, Matthew S.; Bland, Aaron; Metzger, Jacob; Ravelo, Alexandra; Traiger, Sarah; Weitzman, Ben P.

2017-01-01

Biogeographic breaks are often described as locations where a large number of species reach their geographic range limits. Samalga Pass, in the eastern Aleutian Archipelago, is a known biogeographic break for the spatial distribution of several species of offshore-pelagic communities, including numerous species of cold-water corals, zooplankton, fish, marine mammals, and seabirds. However, it remains unclear whether Samalga Pass also serves as a biogeographic break for nearshore benthic communities. The occurrence of biogeographic breaks across multiple habitats has not often been described. In this study, we examined if the biogeographic break for offshore-pelagic communities applies to nearshore kelp forests. To examine whether Samalga Pass serves as a biogeographic break for kelp forest communities, this study compared abundance, biomass and percent bottom cover of species associated with kelp forests on either side of the pass. We observed marked differences in kelp forest community structure, with some species reaching their geographic range limits on the opposing sides of the pass. In particular, the habitat-forming kelp Nereocystis luetkeana, and the predatory sea stars Pycnopodia helianthoides and Orthasterias koehleri all occurred on the eastern side of Samalga Pass but were not observed west of the pass. In contrast, the sea star Leptasterias camtschatica dispar was observed only on the western side of the pass. We also observed differences in overall abundance and biomass of numerous associated fish, invertebrate and macroalgal species on opposing sides of the pass. We conclude that Samalga Pass is important biogeographic break for kelp forest communities in the Aleutian Archipelago and may demark the geographic range limits of several ecologically important species.

The Monarch Initiative: an integrative data and analytic platform connecting phenotypes to genotypes across species

DOE PAGES

Mungall, Christopher J.; McMurry, Julie A.; Köhler, Sebastian; ...

2016-11-29

The correlation of phenotypic outcomes with genetic variation and environmental factors is a core pursuit in biology and biomedicine. Numerous challenges impede our progress: patient phenotypes may not match known diseases, candidate variants may be in genes that have not been characterized, model organisms may not recapitulate human or veterinary diseases, filling evolutionary gaps is difficult, and many resources must be queried to find potentially significant genotype-phenotype associations. Nonhuman organisms have proven instrumental in revealing biological mechanisms. Advanced informatics tools can identify phenotypically relevant disease models in research and diagnostic contexts. Large-scale integration of model organism and clinical research datamore » can provide a breadth of knowledge not available from individual sources and can provide contextualization of data back to these sources. The Monarch Initiative (monarchinitiative.org) is a collaborative, open science effort that aims to semantically integrate genotype-phenotype data from many species and sources in order to support precision medicine, disease modeling, and mechanistic exploration. Our integrated knowledge graph, analytic tools, and web services enable diverse users to explore relationships between phenotypes and genotypes across species.« less

A climate-change adaptation framework to reduce continental-scale vulnerability across conservation reserves

Treesearch

D.R. Magness; J.M. Morton; F. Huettmann; F.S. Chapin; A.D. McGuire

2011-01-01

Rapid climate change, in conjunction with other anthropogenic drivers, has the potential to cause mass species extinction. To minimize this risk, conservation reserves need to be coordinated at multiple spatial scales because the climate envelopes of many species may shift rapidly across large geographic areas. In addition, novel species assemblages and ecological...

An improved high-throughput Nile red fluorescence assay for estimating intracellular lipids in a variety of yeast species

PubMed Central

Sitepu, I.R.; Ignatia, L.; Franz, A. K.; Wong, D. M.; Faulina, S.A.; Tsui, M.; Kanti, A.; Boundy-Mills, K.

2012-01-01

A rapid and inexpensive method for estimating lipid content of yeasts is needed for screening large numbers of yeasts samples. Nile red is a fluorescent lipophilic dye used for detection and quantification of intracellular lipid droplets in various biological system including algae, yeasts and filamentous fungi. However, a published assay for yeast is affected by variable diffusion across the cell membrane, and variation in the time required to reach maximal fluorescence emission. In this study, parameters that may influence the emission were varied to determine optimal assay conditions. An improved assay with a high-throughput capability was developed that includes the addition of dimethyl sulfoxide (DMSO) solvent to improve cell permeability, elimination of the washing step, the reduction of Nile red concentration, kinetic readings rather than single time-point reading, and utilization of a black 96-well microplate. The improved method was validated by comparison to gravimetric determination of lipid content of a broad variety of ascomycete and basidiomycete yeast species. PMID:22985718

Sibling Communication Functions across the Life-Span.

ERIC Educational Resources Information Center

Myers, Scott A.; Smith, Ronda L.; Sonnier, Michelle F.

An investigation examined whether perceived use of sibling functional communication skills differed across the life-span. Participants were recruited through university students enrolled in an introductory communication course at a southern university. All students received extra credit for recruiting two participants. Potential participants were…

Reading wild minds: A computational assay of Theory of Mind sophistication across seven primate species

PubMed Central

Devaine, Marie; San-Galli, Aurore; Trapanese, Cinzia; Bardino, Giulia; Hano, Christelle; Saint Jalme, Michel; Bouret, Sebastien

2017-01-01

Theory of Mind (ToM), i.e. the ability to understand others' mental states, endows humans with highly adaptive social skills such as teaching or deceiving. Candidate evolutionary explanations have been proposed for the unique sophistication of human ToM among primates. For example, the Machiavellian intelligence hypothesis states that the increasing complexity of social networks may have induced a demand for sophisticated ToM. This type of scenario ignores neurocognitive constraints that may eventually be crucial limiting factors for ToM evolution. In contradistinction, the cognitive scaffolding hypothesis asserts that a species' opportunity to develop sophisticated ToM is mostly determined by its general cognitive capacity (on which ToM is scaffolded). However, the actual relationships between ToM sophistication and either brain volume (a proxy for general cognitive capacity) or social group size (a proxy for social network complexity) are unclear. Here, we let 39 individuals sampled from seven non-human primate species (lemurs, macaques, mangabeys, orangutans, gorillas and chimpanzees) engage in simple dyadic games against artificial ToM players (via a familiar human caregiver). Using computational analyses of primates' choice sequences, we found that the probability of exhibiting a ToM-compatible learning style is mainly driven by species' brain volume (rather than by social group size). Moreover, primates' social cognitive sophistication culminates in a precursor form of ToM, which still falls short of human fully-developed ToM abilities. PMID:29112973

Reading wild minds: A computational assay of Theory of Mind sophistication across seven primate species.

PubMed

Devaine, Marie; San-Galli, Aurore; Trapanese, Cinzia; Bardino, Giulia; Hano, Christelle; Saint Jalme, Michel; Bouret, Sebastien; Masi, Shelly; Daunizeau, Jean

2017-11-01

Theory of Mind (ToM), i.e. the ability to understand others' mental states, endows humans with highly adaptive social skills such as teaching or deceiving. Candidate evolutionary explanations have been proposed for the unique sophistication of human ToM among primates. For example, the Machiavellian intelligence hypothesis states that the increasing complexity of social networks may have induced a demand for sophisticated ToM. This type of scenario ignores neurocognitive constraints that may eventually be crucial limiting factors for ToM evolution. In contradistinction, the cognitive scaffolding hypothesis asserts that a species' opportunity to develop sophisticated ToM is mostly determined by its general cognitive capacity (on which ToM is scaffolded). However, the actual relationships between ToM sophistication and either brain volume (a proxy for general cognitive capacity) or social group size (a proxy for social network complexity) are unclear. Here, we let 39 individuals sampled from seven non-human primate species (lemurs, macaques, mangabeys, orangutans, gorillas and chimpanzees) engage in simple dyadic games against artificial ToM players (via a familiar human caregiver). Using computational analyses of primates' choice sequences, we found that the probability of exhibiting a ToM-compatible learning style is mainly driven by species' brain volume (rather than by social group size). Moreover, primates' social cognitive sophistication culminates in a precursor form of ToM, which still falls short of human fully-developed ToM abilities.

Successful kidney transplantation across a positive complement-dependent cytotoxicity crossmatch by using C1q assay-directed, bortezomib-assisted desensitization

PubMed Central

Lee, Juhan; Park, Borae G.; Jeong, Hyang Sook; Park, Youn Hee; Kim, Sinyoung; Kim, Beom Seok; Kim, Hye Jin; Huh, Kyu Ha; Jeong, Hyeon Joo; Kim, Yu Seun

2017-01-01

Abstract Rationale: Human leukocyte antigen (HLA) is the major immunologic barrier in kidney transplantation (KT). Various desensitization protocols to overcome the HLA barrier have increased the opportunity for transplantation in sensitized patients. In addition, technological advances in solid-phase assays have permitted more comprehensive assessment of donor-specific antibodies. Although various desensitization therapies and immunologic techniques have been developed, the final transplantation decision is still based on the classic complement-dependent cytotoxicity (CDC) crossmatch (XM) technique. Some patients who fail to achieve negative XM have lost their transplant opportunities, even after receiving sufficient desensitization therapies. Patient concerns: A 57-year-old male with end-stage renal disease secondary to chronic glomerulonephritis was scheduled to have a second transplant from his son, but CDC XM was positive. Diagnoses: Initial CDC XM (Initial T-AHG 1:32) and flow-cytometry XM were positive. Anti-HLA-B59 donor specific antibody was detected by Luminex single antigen assay. Interventions: Herein, we report a successful case of KT across a positive CDC XM (T-AHG 1:8 at the time of transplantation) by using C1q assay-directed, bortezomib-assisted desensitization. After confirming a negative conversion in the C1q donor-specific antibody, we decided to perform KT accepting a positive AHG-CDC XM of 1:8 at the time of transplantation. Outcomes: The posttransplant course was uneventful and a protocol biopsy at 3 months showed no evidence of rejection. The patient had excellent graft function at 12 months posttransplant. Lessons: The results of XM test and solid-phase assay should be interpreted in the context of the individual patient. PMID:28953652

Comparative genomics and evolution of the HSP90 family of genes across all kingdoms of organisms.

PubMed

Chen, Bin; Zhong, Daibin; Monteiro, Antónia

2006-06-17

HSP90 proteins are essential molecular chaperones involved in signal transduction, cell cycle control, stress management, and folding, degradation, and transport of proteins. HSP90 proteins have been found in a variety of organisms suggesting that they are ancient and conserved. In this study we investigate the nuclear genomes of 32 species across all kingdoms of organisms, and all sequences available in GenBank, and address the diversity, evolution, gene structure, conservation and nomenclature of the HSP90 family of genes across all organisms. Twelve new genes and a new type HSP90C2 were identified. The chromosomal location, exon splicing, and prediction of whether they are functional copies were documented, as well as the amino acid length and molecular mass of their polypeptides. The conserved regions across all protein sequences, and signature sequences in each subfamily were determined, and a standardized nomenclature system for this gene family is presented. The proeukaryote HSP90 homologue, HTPG, exists in most Bacteria species but not in Archaea, and it evolved into three lineages (Groups A, B and C) via two gene duplication events. None of the organellar-localized HSP90s were derived from endosymbionts of early eukaryotes. Mitochondrial TRAP and endoplasmic reticulum HSP90B separately originated from the ancestors of HTPG Group A in Firmicutes-like organisms very early in the formation of the eukaryotic cell. TRAP is monophyletic and present in all Animalia and some Protista species, while HSP90B is paraphyletic and present in all eukaryotes with the exception of some Fungi species, which appear to have lost it. Both HSP90C (chloroplast HSP90C1 and location-undetermined SP90C2) and cytosolic HSP90A are monophyletic, and originated from HSP90B by independent gene duplications. HSP90C exists only in Plantae, and was duplicated into HSP90C1 and HSP90C2 isoforms in higher plants. HSP90A occurs across all eukaryotes, and duplicated into HSP90AA and HSP90AB in

Comparative genomics and evolution of the HSP90 family of genes across all kingdoms of organisms

PubMed Central

Chen, Bin; Zhong, Daibin; Monteiro, Antónia

2006-01-01

Background HSP90 proteins are essential molecular chaperones involved in signal transduction, cell cycle control, stress management, and folding, degradation, and transport of proteins. HSP90 proteins have been found in a variety of organisms suggesting that they are ancient and conserved. In this study we investigate the nuclear genomes of 32 species across all kingdoms of organisms, and all sequences available in GenBank, and address the diversity, evolution, gene structure, conservation and nomenclature of the HSP90 family of genes across all organisms. Results Twelve new genes and a new type HSP90C2 were identified. The chromosomal location, exon splicing, and prediction of whether they are functional copies were documented, as well as the amino acid length and molecular mass of their polypeptides. The conserved regions across all protein sequences, and signature sequences in each subfamily were determined, and a standardized nomenclature system for this gene family is presented. The proeukaryote HSP90 homologue, HTPG, exists in most Bacteria species but not in Archaea, and it evolved into three lineages (Groups A, B and C) via two gene duplication events. None of the organellar-localized HSP90s were derived from endosymbionts of early eukaryotes. Mitochondrial TRAP and endoplasmic reticulum HSP90B separately originated from the ancestors of HTPG Group A in Firmicutes-like organisms very early in the formation of the eukaryotic cell. TRAP is monophyletic and present in all Animalia and some Protista species, while HSP90B is paraphyletic and present in all eukaryotes with the exception of some Fungi species, which appear to have lost it. Both HSP90C (chloroplast HSP90C1 and location-undetermined SP90C2) and cytosolic HSP90A are monophyletic, and originated from HSP90B by independent gene duplications. HSP90C exists only in Plantae, and was duplicated into HSP90C1 and HSP90C2 isoforms in higher plants. HSP90A occurs across all eukaryotes, and duplicated into HSP

Groundlayer vegetation gradients across oak woodland canopy gaps

USGS Publications Warehouse

Pavlovic, N.B.; Grundel, R.; Sluis, W.

2006-01-01

Frequency of groundlayer plants was measured across oak woodland canopy gaps at three sites in northwest Indiana to examine how vegetation varied with gap size, direction along the gap edge, and microhabitat. Microhabitats were defined as under the canopy adjacent to the gap, along the gap edge, and within the gap. Gap-sites consisted of gaps plus adjacent tree canopy. Gaps were classified as small (16 ± 1 m2), medium (97 ± 8), and large (310 ± 32). Neither richness nor diversity differed among microhabitats, gap sizes, or edges. Similarity between microhabitats wthin a gap-site increased as the distance between plots decreased and as the difference in PAR decreased, the latter explaining twice the variation in percent dissimilarity compared to Mg concentration, A horizon depth, and litter cover. Diervilla lonicera, Frageria virginiana, Helianthus divaricatus, Polygonatum pubescens, Quercus velutina, Smilacena stellata, and Tradescantia ohiensis decreased, whileTephrosia virginiana and legumes increased in frequency, from canopy to gap, and C4 grasses peaked at the gap edge, independent of gap size. Additional species frequency varied across the microhabitat gradient within specific sites. Sorghastrum nutans was three times more frequent in gaps at large sites than elsewhere. The vegetation in medium-sized gap-sites was more variable than within small and large gap-sites, suggesting greater environmental heterogeneity at that scale. Within gap-sites, vegetation was more heterogeneous within edges and canopies than in gaps. Edges were more similar in composition to gaps than to canopy groundlayer within gap-sites. Few species varied significantly in frequency around the gap edge. The oak woodland groundlayer on sandy substrates can be characterized as a mosaic of forb dominated vegetation that varies across light gradients associated with canopy gaps, transitioning to islands of grassland vegetation when gaps exceed 160 m2.

Wave attenuation across a tidal marsh in San Francisco Bay

USGS Publications Warehouse

Foster-Martinez, Madeline R.; Lacy, Jessica; Ferner, Matthew C.; Variano, Evan A.

2018-01-01

Wave attenuation is a central process in the mechanics of a healthy salt marsh. Understanding how wave attenuation varies with vegetation and hydrodynamic conditions informs models of other marsh processes that are a function of wave energy (e.g. sediment transport) and allows for the incorporation of marshes into coastal protection plans. Here, we examine the evolution of wave height across a tidal salt marsh in San Francisco Bay. Instruments were deployed along a cross-shore transect, starting on the mudflat and crossing through zones dominated by Spartina foliosa and Salicornia pacifica. This dataset is the first to quantify wave attenuation for these vegetation species, which are abundant in the intertidal zone of California estuaries. Measurements were collected in the summer and winter to assess seasonal variation in wave attenuation. Calculated drag coefficients of S. foliosa and S. pacifica were similar, indicating equal amounts of vegetation would lead to similar energy dissipation; however, S. pacifica has much greater biomass close to the bed (<20 cm) and retains biomass throughout the year, and therefore, it causes more total attenuation. S. foliosa dies back in the winter, and waves often grow across this section of the marsh. For both vegetation types, attenuation was greatest for low water depths, when the vegetation was emergent. For both seasons, attenuation rates across S. pacifica were the highest and were greater than published attenuation rates across similar (Spartina alterniflora) salt marshes for the comparable depths. These results can inform designs for marsh restorations and management plans in San Francisco Bay and other estuaries containing these species.

Facilitating climate-change-induced range shifts across continental land-use barriers.

PubMed

Robillard, Cassandra M; Coristine, Laura E; Soares, Rosana N; Kerr, Jeremy T

2015-12-01

Climate changes impose requirements for many species to shift their ranges to remain within environmentally tolerable areas, but near-continuous regions of intense human land use stretching across continental extents diminish dispersal prospects for many species. We reviewed the impact of habitat loss and fragmentation on species' abilities to track changing climates and existing plans to facilitate species dispersal in response to climate change through regions of intensive land uses, drawing on examples from North America and elsewhere. We identified an emerging analytical framework that accounts for variation in species' dispersal capacities relative to both the pace of climate change and habitat availability. Habitat loss and fragmentation hinder climate change tracking, particularly for specialists, by impeding both propagule dispersal and population growth. This framework can be used to identify prospective modern-era climatic refugia, where the pace of climate change has been slower than surrounding areas, that are defined relative to individual species' needs. The framework also underscores the importance of identifying and managing dispersal pathways or corridors through semi-continental land use barriers that can benefit many species simultaneously. These emerging strategies to facilitate range shifts must account for uncertainties around population adaptation to local environmental conditions. Accounting for uncertainties in climate change and dispersal capabilities among species and expanding biological monitoring programs within an adaptive management paradigm are vital strategies that will improve species' capacities to track rapidly shifting climatic conditions across landscapes dominated by intensive human land use. © 2015 Society for Conservation Biology.

Zooxanthellae of the Montastraea annularis species complex: patterns of distribution of four taxa of Symbiodinium on different reefs and across depths.

PubMed

Toller, W W; Rowan, R; Knowlton, N

2001-12-01

Corals of the Montastraea annularis complex host several different dinoflagellates in the genus Symbiodinium. Here we address two questions arising from our previous studies of these associations on an offshore reef. First, do the same taxa and patterns of association (Symbiodinium A and B found in higher irradiance habitats than Symbiodinium C) occur on an inshore reef? Second, does M. franksi at the limits of its depth range host only Symbiodinium C, as it does at intermediate depths? In both surveys, a new Symbiodinium taxon and different patterns of distribution (assayed by analyses of small ribosomal subunit RNA genes [srDNA]) were observed. Inshore, a taxon we name Symbiodinium E predominated in higher irradiance habitats in M. franksi and its two sibling species; the only other zooxanthella observed was Symbiodinium C. Offshore, M. franksi mainly hosted Symbiodinium C, but hosted Symbiodinium A, B, C, and E in shallow water and Symbiodinium E and C in very deep water. Symbiodinium E may be stress-tolerant. Observed srDNA heterogeneity within samples of Symbiodinium B, C, and E is interpreted as variation across copies within this multigene family. Experimental bleaching of Symbiodinium C supported this interpretation. Thus sequences from natural samples should be interpreted cautiously.

Microbial immigration across the Mediterranean via airborne dust

PubMed Central

Rosselli, Riccardo; Fiamma, Maura; Deligios, Massimo; Pintus, Gabriella; Pellizzaro, Grazia; Canu, Annalisa; Duce, Pierpaolo; Squartini, Andrea; Muresu, Rosella; Cappuccinelli, Pietro

2015-01-01

Dust particles lifting and discharge from Africa to Europe is a recurring phenomenon linked to air circulation conditions. The possibility that microorganisms are conveyed across distances entails important consequences in terms of biosafety and pathogens spread. Using culture independent DNA-based analyses via next generation sequencing of the 16 S genes from the airborne metagenome, the atmospheric microbial community was characterized and the hypothesis was tested that shifts in species diversity could be recorded in relation to dust discharge. As sampling ground the island of Sardinia was chosen, being an ideal cornerstone within the Mediterranean and a crossroad of wind circulation amidst Europe and Africa. Samples were collected in two opposite coastal sites and in two different weather conditions comparing dust-conveying winds from Africa with a control situation with winds from Europe. A major conserved core microbiome was evidenced but increases in species richness and presence of specific taxa were nevertheless observed in relation to each wind regime. Taxa which can feature strains with clinical implications were also detected. The approach is reported as a recommended model monitoring procedure for early warning alerts in frameworks of biosafety against natural spread of clinical microbiota across countries as well as to prevent bacteriological warfare. PMID:26542754

Actions to Abate Critical Threats, Such as Encroachment and Invasive Species, Using GIS and Conservation Area Planning Across the Gulf Coastal Plain Ecosystem Partnership (GCPEP) Landscape, Phase 1

DTIC Science & Technology

2006-12-22

invasive species include cogongrass ( Imperata cylindrica ), Chinese tallowtree (Sapium sebiferum), Japanese climbing fern (Lygodium japonicum), Chinese...Species in bold letter were identified as the top invasives across the partnership. Plants Animals 10 Cogon Grass( Imperata cylindrica ) 10...problematic invasive species include cogongrass ( Imperata cylindrica ), Chinese tallowtree (Sapium sebiferum), Japanese climbing fern (Lygodium japonicum

Dynamic species classification of microorganisms across time, abiotic and biotic environments—A sliding window approach

PubMed Central

Griffiths, Jason I.; Fronhofer, Emanuel A.; Garnier, Aurélie; Seymour, Mathew; Altermatt, Florian; Petchey, Owen L.

2017-01-01

The development of video-based monitoring methods allows for rapid, dynamic and accurate monitoring of individuals or communities, compared to slower traditional methods, with far reaching ecological and evolutionary applications. Large amounts of data are generated using video-based methods, which can be effectively processed using machine learning (ML) algorithms into meaningful ecological information. ML uses user defined classes (e.g. species), derived from a subset (i.e. training data) of video-observed quantitative features (e.g. phenotypic variation), to infer classes in subsequent observations. However, phenotypic variation often changes due to environmental conditions, which may lead to poor classification, if environmentally induced variation in phenotypes is not accounted for. Here we describe a framework for classifying species under changing environmental conditions based on the random forest classification. A sliding window approach was developed that restricts temporal and environmentally conditions to improve the classification. We tested our approach by applying the classification framework to experimental data. The experiment used a set of six ciliate species to monitor changes in community structure and behavior over hundreds of generations, in dozens of species combinations and across a temperature gradient. Differences in biotic and abiotic conditions caused simplistic classification approaches to be unsuccessful. In contrast, the sliding window approach allowed classification to be highly successful, as phenotypic differences driven by environmental change, could be captured by the classifier. Importantly, classification using the random forest algorithm showed comparable success when validated against traditional, slower, manual identification. Our framework allows for reliable classification in dynamic environments, and may help to improve strategies for long-term monitoring of species in changing environments. Our classification pipeline

Language Switching across Modalities: Evidence from Bimodal Bilinguals

ERIC Educational Resources Information Center

Dias, Patricia; Villameriel, Saúl; Giezen, Marcel R.; Costello, Brendan; Carreiras, Manuel

2017-01-01

This study investigated whether language control during language production in bilinguals generalizes across modalities, and to what extent the language control system is shaped by competition for the same articulators. Using a cued language-switching paradigm, we investigated whether switch costs are observed when hearing signers switch between a…

Movements of Blue Sharks (Prionace glauca) across Their Life History

PubMed Central

Vandeperre, Frederic; Aires-da-Silva, Alexandre; Fontes, Jorge; Santos, Marco; Serrão Santos, Ricardo; Afonso, Pedro

2014-01-01

Spatial structuring and segregation by sex and size is considered to be an intrinsic attribute of shark populations. These spatial patterns remain poorly understood, particularly for oceanic species such as blue shark (Prionace glauca), despite its importance for the management and conservation of this highly migratory species. This study presents the results of a long-term electronic tagging experiment to investigate the migratory patterns of blue shark, to elucidate how these patterns change across its life history and to assess the existence of a nursery area in the central North Atlantic. Blue sharks belonging to different life stages (n = 34) were tracked for periods up to 952 days during which they moved extensively (up to an estimated 28.139 km), occupying large parts of the oceanic basin. Notwithstanding a large individual variability, there were pronounced differences in movements and space use across the species' life history. The study provides strong evidence for the existence of a discrete central North Atlantic nursery, where juveniles can reside for up to at least 2 years. In contrast with previously described nurseries of coastal and semi-pelagic sharks, this oceanic nursery is comparatively vast and open suggesting that shelter from predators is not its main function. Subsequently, male and female blue sharks spatially segregate. Females engage in seasonal latitudinal migrations until approaching maturity, when they undergo an ontogenic habitat shift towards tropical latitudes. In contrast, juvenile males generally expanded their range southward and apparently displayed a higher degree of behavioural polymorphism. These results provide important insights into the spatial ecology of pelagic sharks, with implications for the sustainable management of this heavily exploited shark, especially in the central North Atlantic where the presence of a nursery and the seasonal overlap and alternation of different life stages coincides with a high fishing

Movements of blue sharks (Prionace glauca) across their life history.

PubMed

Vandeperre, Frederic; Aires-da-Silva, Alexandre; Fontes, Jorge; Santos, Marco; Serrão Santos, Ricardo; Afonso, Pedro

2014-01-01

Spatial structuring and segregation by sex and size is considered to be an intrinsic attribute of shark populations. These spatial patterns remain poorly understood, particularly for oceanic species such as blue shark (Prionace glauca), despite its importance for the management and conservation of this highly migratory species. This study presents the results of a long-term electronic tagging experiment to investigate the migratory patterns of blue shark, to elucidate how these patterns change across its life history and to assess the existence of a nursery area in the central North Atlantic. Blue sharks belonging to different life stages (n = 34) were tracked for periods up to 952 days during which they moved extensively (up to an estimated 28.139 km), occupying large parts of the oceanic basin. Notwithstanding a large individual variability, there were pronounced differences in movements and space use across the species' life history. The study provides strong evidence for the existence of a discrete central North Atlantic nursery, where juveniles can reside for up to at least 2 years. In contrast with previously described nurseries of coastal and semi-pelagic sharks, this oceanic nursery is comparatively vast and open suggesting that shelter from predators is not its main function. Subsequently, male and female blue sharks spatially segregate. Females engage in seasonal latitudinal migrations until approaching maturity, when they undergo an ontogenic habitat shift towards tropical latitudes. In contrast, juvenile males generally expanded their range southward and apparently displayed a higher degree of behavioural polymorphism. These results provide important insights into the spatial ecology of pelagic sharks, with implications for the sustainable management of this heavily exploited shark, especially in the central North Atlantic where the presence of a nursery and the seasonal overlap and alternation of different life stages coincides with a high fishing

Regulation of Ion Gradients across Myocardial Ischemic Border Zones: A Biophysical Modelling Analysis

PubMed Central

Niederer, Steven

2013-01-01

The myocardial ischemic border zone is associated with the initiation and sustenance of arrhythmias. The profile of ionic concentrations across the border zone play a significant role in determining cellular electrophysiology and conductivity, yet their spatial-temporal evolution and regulation are not well understood. To investigate the changes in ion concentrations that regulate cellular electrophysiology, a mathematical model of ion movement in the intra and extracellular space in the presence of ionic, potential and material property heterogeneities was developed. The model simulates the spatial and temporal evolution of concentrations of potassium, sodium, chloride, calcium, hydrogen and bicarbonate ions and carbon dioxide across an ischemic border zone. Ischemia was simulated by sodium-potassium pump inhibition, potassium channel activation and respiratory and metabolic acidosis. The model predicted significant disparities in the width of the border zone for each ionic species, with intracellular sodium and extracellular potassium having discordant gradients, facilitating multiple gradients in cellular properties across the border zone. Extracellular potassium was found to have the largest border zone and this was attributed to the voltage dependence of the potassium channels. The model also predicted the efflux of from the ischemic region due to electrogenic drift and diffusion within the intra and extracellular space, respectively, which contributed to depletion in the ischemic region. PMID:23577101

Cheating Perceptions and Prevalence across Academic Settings

ERIC Educational Resources Information Center

Honz, Kelly; Kiewra, Kenneth A.; Yang, Ya-Shu

2010-01-01

This study investigated high school students' perceptions of cheating and its prevalence. Students were administered the Academic Honesty Survey to determine their perceptions and prevalence of cheating across three academic settings: tests, homework, and report writing. Overall, students had traditional perceptions of what constitutes cheating.…

Leaf Protein and Mineral Concentrations across the "Miracle Tree" Genus Moringa.

PubMed

Olson, Mark E; Sankaran, Renuka P; Fahey, Jed W; Grusak, Michael A; Odee, David; Nouman, Wasif

2016-01-01

The moringa tree Moringa oleifera is a fast-growing, drought-resistant tree cultivated across the lowland dry tropics worldwide for its nutritious leaves. Despite its nutritious reputation, there has been no systematic survey of the variation in leaf nutritional quality across M. oleifera grown worldwide, or of the other species of the genus. To guide informed use of moringa, we surveyed protein, macro-, and micro- nutrients across 67 common garden samples of 12 Moringa taxa, including 23 samples of M. oleifera. Moringa oleifera, M. concanensis, M. stenopetala, an M. concanensis X oleifera hybrid, and M. longituba were highest in protein, with M. ruspoliana having the highest calcium levels. A protein-dry leaf mass tradeoff may preclude certain breeding possibilities, e.g. maximally high protein with large leaflets. These findings identify clear priorities and limitations for improved moringa varieties with traits such as high protein, calcium, or ease of preparation.

The Development of Self-Regulation across Early Childhood

PubMed Central

Montroy, Janelle J.; Bowles, Ryan P.; Skibbe, Lori E.; McClelland, Megan M.; Morrison, Frederick J.

2016-01-01

The development of early childhood self-regulation is often considered an early life marker for later life successes. Yet little longitudinal research has evaluated whether there are different trajectories of self-regulation development across children. This study investigates the development of behavioral self-regulation between the ages of three and seven, with a direct focus on possible heterogeneity in the developmental trajectories, and a set of potential indicators that distinguish unique behavioral self-regulation trajectories. Across three diverse samples, 1,386 children were assessed on behavioral self-regulation from preschool through first grade. Results indicated that majority of children develop self-regulation rapidly during early childhood, and that children follow three distinct developmental patterns of growth. These three trajectories were distinguishable based on timing of rapid gains, as well as child gender, early language skills, and maternal education levels. Findings highlight early developmental differences in how self-regulation unfolds with implications for offering individualized support across children. PMID:27709999

Palaeo-precipitation is a major determinant of palm species richness patterns across Madagascar: a tropical biodiversity hotspot

PubMed Central

Rakotoarinivo, Mijoro; Blach-Overgaard, Anne; Baker, William J.; Dransfield, John; Moat, Justin; Svenning, Jens-Christian

2013-01-01

The distribution of rainforest in many regions across the Earth was strongly affected by Pleistocene ice ages. However, the extent to which these dynamics are still important for modern-day biodiversity patterns within tropical biodiversity hotspots has not been assessed. We employ a comprehensive dataset of Madagascan palms (Arecaceae) and climate reconstructions from the last glacial maximum (LGM; 21 000 years ago) to assess the relative role of modern environment and LGM climate in explaining geographical species richness patterns in this major tropical biodiversity hotspot. We found that palaeoclimate exerted a strong influence on palm species richness patterns, with richness peaking in areas with higher LGM precipitation relative to present-day even after controlling for modern environment, in particular in northeastern Madagascar, consistent with the persistence of tropical rainforest during the LGM primarily in this region. Our results provide evidence that diversity patterns in the World's most biodiverse regions may be shaped by long-term climate history as well as contemporary environment. PMID:23427173

There's no place like home: seedling mortality contributes to the habitat specialisation of tree species across Amazonia.

PubMed

Fortunel, Claire; Paine, C E Timothy; Fine, Paul V A; Mesones, Italo; Goret, Jean-Yves; Burban, Benoit; Cazal, Jocelyn; Baraloto, Christopher

2016-10-01

Understanding the mechanisms generating species distributions remains a challenge, especially in hyperdiverse tropical forests. We evaluated the role of rainfall variation, soil gradients and herbivory on seedling mortality, and how variation in seedling performance along these gradients contributes to habitat specialisation. In a 4-year experiment, replicated at the two extremes of the Amazon basin, we reciprocally transplanted 4638 tree seedlings of 41 habitat-specialist species from seven phylogenetic lineages among the three most important forest habitats of lowland Amazonia. Rainfall variation, flooding and soil gradients strongly influenced seedling mortality, whereas herbivory had negligible impact. Seedling mortality varied strongly among habitats, consistent with predictions for habitat specialists in most lineages. This suggests that seedling performance is a primary determinant of the habitat associations of adult trees across Amazonia. It further suggests that tree diversity, currently mostly harboured in terra firme forests, may be strongly impacted by the predicted climate changes in Amazonia. © 2016 John Wiley & Sons Ltd/CNRS.

Contextual Cueing Effects Across the Lifespan

PubMed Central

MERRILL, EDWARD C.; CONNERS, FRANCES A.; ROSKOS, BEVERLY; KLINGER, MARK R.; KLINGER, LAURA GROFER

2018-01-01

The authors evaluated age-related variations in contextual cueing, which reflects the extent to which visuospatial regularities can facilitate search for a target. Previous research produced inconsistent results regarding contextual cueing effects in young children and in older adults, and no study has investigated the phenomenon across the life span. Three groups (6, 20, and 70 years old) were compared. Participants located a designated target stimulus embedded in a context of distractor stimuli. During exposure, the location of the target could be predicted from the location of the distracters in each display. During test, these predictable displays were intermixed with new displays that did not predict the target location. Response times to locating predictable relative to unpredictable targets were compared. All groups exhibited facilitation effects greater than 0 (95% CIs [.02, .11], d = .4; [.01, .12], d = .4; and [.01, .10], d = .4, for the children, young adults, and older adults, respectively) indicating that contextual cueing is robust across a wide age range. The relative magnitude of contextual cueing effects was essentially identical across the age range tested, F(2, 103) = 1.71,ηρ2 = .02. The authors argue that a mechanism that uses environmental covariation is available to all age ranges, but the expression of the contextual cueing may depend on the way it is measured. PMID:23991612

The plant economics spectrum is structured by leaf habits and growth forms across subtropical species.

PubMed

Zhao, Yan-Tao; Ali, Arshad; Yan, En-Rong

2017-02-01

The plant economics spectrum that integrates the combination of leaf and wood syndromes provides a useful framework for the examination of species strategies at the whole-plant level. However, it remains unclear how species that differ in leaf habits and growth forms are integrated within the plant economics spectrum in subtropical forests. We measured five leaf and six wood traits across 58 subtropical plant species, which represented two leaf habits (evergreen vs deciduous) and two growth forms (tree vs shrub) in eastern China. Principal component analysis (PCA) was employed separately to construct the leaf (LES), wood (WES) and whole-plant (WPES) economics spectra. Leaf and wood traits are highly intra- and intercorrelated, thus defining not only the LES and WES, but also a WPES. Multi-trait variations in PCAs revealed that the traits which were representative of the acquisitive strategy, i.e., cheap tissue investment and rapid returns on that investment, were clustered at one end, while traits that represented the conservative strategy, i.e., expensive tissue investment and slower returns, were clustered at other end in each of the axes of the leaf and wood syndromes (PC1-axis) and the plant height strategy (PC2-axis). The local WPES, LES and WES were tightly correlated with each other. Evergreens shaped the conservative side, while deciduous species structured the acquisitive side of the WPES and LES. With respect to plant height strategies, trees formulated the acquisitive side and shrub species made up the conservative side of the WPES, LES and WES. In conclusion, our results suggested that the LES and WES were coordinated to a WPES for subtropical species. The finding of this local spectrum of plant form and function would be beneficial for modeling nutrient fluxes and species compositions in the changing climate, but also for understanding species strategies in an evolutionary context. © The Author 2016. Published by Oxford University Press. All rights

Multi-scale factors influencing the characteristics of avian communities in urban parks across Beijing during the breeding season

PubMed Central

Xie, Shilin; Lu, Fei; Cao, Lei; Zhou, Weiqi; Ouyang, Zhiyun

2016-01-01

Understanding the factors that influence the characteristics of avian communities using urban parks at both the patch and landscape level is important to focus management effort towards enhancing bird diversity. Here, we investigated this issue during the breeding season across urban parks in Beijing, China, using high-resolution satellite imagery. Fifty-two bird species were recorded across 29 parks. Analysis of residence type of birds showed that passengers were the most prevalent (37%), indicating that Beijing is a major node in the East Asian–Australasian Flyway. Park size was crucial for total species abundance, but foliage height diversity was the most important factor influencing avian species diversity. Thus, optimizing the configuration of vertical vegetation structure in certain park areas is critical for supporting avian communities in urban parks. Human visitation also showed negative impact on species diversity. At the landscape level, the percentage of artificial surface and largest patch index of woodland in the buffer region significantly affected total species richness, with insectivores and granivores being more sensitive to the landscape pattern of the buffer region. In conclusion, urban birds in Beijing are influenced by various multi-scale factors; however, these effects vary with different feeding types. PMID:27404279

Multi-scale factors influencing the characteristics of avian communities in urban parks across Beijing during the breeding season

NASA Astrophysics Data System (ADS)

Xie, Shilin; Lu, Fei; Cao, Lei; Zhou, Weiqi; Ouyang, Zhiyun

2016-07-01

Understanding the factors that influence the characteristics of avian communities using urban parks at both the patch and landscape level is important to focus management effort towards enhancing bird diversity. Here, we investigated this issue during the breeding season across urban parks in Beijing, China, using high-resolution satellite imagery. Fifty-two bird species were recorded across 29 parks. Analysis of residence type of birds showed that passengers were the most prevalent (37%), indicating that Beijing is a major node in the East Asian-Australasian Flyway. Park size was crucial for total species abundance, but foliage height diversity was the most important factor influencing avian species diversity. Thus, optimizing the configuration of vertical vegetation structure in certain park areas is critical for supporting avian communities in urban parks. Human visitation also showed negative impact on species diversity. At the landscape level, the percentage of artificial surface and largest patch index of woodland in the buffer region significantly affected total species richness, with insectivores and granivores being more sensitive to the landscape pattern of the buffer region. In conclusion, urban birds in Beijing are influenced by various multi-scale factors; however, these effects vary with different feeding types.

Multi-scale factors influencing the characteristics of avian communities in urban parks across Beijing during the breeding season.

PubMed

Xie, Shilin; Lu, Fei; Cao, Lei; Zhou, Weiqi; Ouyang, Zhiyun

2016-07-11

Understanding the factors that influence the characteristics of avian communities using urban parks at both the patch and landscape level is important to focus management effort towards enhancing bird diversity. Here, we investigated this issue during the breeding season across urban parks in Beijing, China, using high-resolution satellite imagery. Fifty-two bird species were recorded across 29 parks. Analysis of residence type of birds showed that passengers were the most prevalent (37%), indicating that Beijing is a major node in the East Asian-Australasian Flyway. Park size was crucial for total species abundance, but foliage height diversity was the most important factor influencing avian species diversity. Thus, optimizing the configuration of vertical vegetation structure in certain park areas is critical for supporting avian communities in urban parks. Human visitation also showed negative impact on species diversity. At the landscape level, the percentage of artificial surface and largest patch index of woodland in the buffer region significantly affected total species richness, with insectivores and granivores being more sensitive to the landscape pattern of the buffer region. In conclusion, urban birds in Beijing are influenced by various multi-scale factors; however, these effects vary with different feeding types.

Aging and response interference across sensory modalities.

PubMed

Guerreiro, Maria J S; Adam, Jos J; Van Gerven, Pascal W M

2014-06-01

Advancing age is associated with decrements in selective attention. It was recently hypothesized that age-related differences in selective attention depend on sensory modality. The goal of the present study was to investigate the role of sensory modality in age-related vulnerability to distraction, using a response interference task. To this end, 16 younger (mean age = 23.1 years) and 24 older (mean age = 65.3 years) adults performed four response interference tasks, involving all combinations of visual and auditory targets and distractors. The results showed that response interference effects differ across sensory modalities, but not across age groups. These results indicate that sensory modality plays an important role in vulnerability to distraction, but not in age-related distractibility by irrelevant spatial information.

HormoneBase, a population-level database of steroid hormone levels across vertebrates

PubMed Central

Vitousek, Maren N.; Johnson, Michele A.; Donald, Jeremy W.; Francis, Clinton D.; Fuxjager, Matthew J.; Goymann, Wolfgang; Hau, Michaela; Husak, Jerry F.; Kircher, Bonnie K.; Knapp, Rosemary; Martin, Lynn B.; Miller, Eliot T.; Schoenle, Laura A.; Uehling, Jennifer J.; Williams, Tony D.

2018-01-01

Hormones are central regulators of organismal function and flexibility that mediate a diversity of phenotypic traits from early development through senescence. Yet despite these important roles, basic questions about how and why hormone systems vary within and across species remain unanswered. Here we describe HormoneBase, a database of circulating steroid hormone levels and their variation across vertebrates. This database aims to provide all available data on the mean, variation, and range of plasma glucocorticoids (both baseline and stress-induced) and androgens in free-living and un-manipulated adult vertebrates. HormoneBase (www.HormoneBase.org) currently includes >6,580 entries from 476 species, reported in 648 publications from 1967 to 2015, and unpublished datasets. Entries are associated with data on the species and population, sex, year and month of study, geographic coordinates, life history stage, method and latency of hormone sampling, and analysis technique. This novel resource could be used for analyses of the function and evolution of hormone systems, and the relationships between hormonal variation and a variety of processes including phenotypic variation, fitness, and species distributions. PMID:29786693

Phylogeography and post-glacial recolonization in wolverines (Gulo gulo) from across their circumpolar distribution.

PubMed

Zigouris, Joanna; Schaefer, James A; Fortin, Clément; Kyle, Christopher J

2013-01-01

Interglacial-glacial cycles of the Quaternary are widely recognized in shaping phylogeographic structure. Patterns from cold adapted species can be especially informative - in particular, uncovering additional glacial refugia, identifying likely recolonization patterns, and increasing our understanding of species' responses to climate change. We investigated phylogenetic structure of the wolverine, a wide-ranging cold adapted carnivore, using a 318 bp of the mitochondrial DNA control region for 983 wolverines (n=209 this study, n=774 from GenBank) from across their full Holarctic distribution. Bayesian phylogenetic tree reconstruction and the distribution of observed pairwise haplotype differences (mismatch distribution) provided evidence of a single rapid population expansion across the wolverine's Holarctic range. Even though molecular evidence corroborated a single refugium, significant subdivisions of population genetic structure (0.01< ΦST <0.99, P<0.05) were detected. Pairwise ΦST estimates separated Scandinavia from Russia and Mongolia, and identified five main divisions within North America - the Central Arctic, a western region, an eastern region consisting of Ontario and Quebec/Labrador, Manitoba, and California. These data are in contrast to the nearly panmictic structure observed in northwestern North America using nuclear microsatellites, but largely support the nuclear DNA separation of contemporary Manitoba and Ontario wolverines from northern populations. Historic samples (c. 1900) from the functionally extirpated eastern population of Quebec/Labrador displayed genetic similarities to contemporary Ontario wolverines. To understand these divergence patterns, four hypotheses were tested using Approximate Bayesian Computation (ABC). The most supported hypothesis was a single Beringia incursion during the last glacial maximum that established the northwestern population, followed by a west-to-east colonization during the Holocene. This pattern is

Transport across the outer membrane porin of mycolic acid containing actinomycetales: Nocardia farcinica.

PubMed

Singh, Pratik Raj; Bajaj, Harsha; Benz, Roland; Winterhalter, Mathias; Mahendran, Kozhinjampara R

2015-02-01

The role of the outer-membrane channel from a mycolic acid containing Gram-positive bacteria Nocardia farcinica, which forms a hydrophilic pathway across the cell wall, was characterized. Single channel electrophysiology measurements and liposome swelling assays revealed the permeation of hydrophilic solutes including sugars, amino acids and antibiotics. The cation selective N. farcinica channel exhibited strong interaction with the positively charged antibiotics; amikacin and kanamycin, and surprisingly also with the negatively charged ertapenem. Voltage dependent kinetics of amikacin and kanamycin interactions were studied to distinguish binding from translocation. Moreover, the importance of charged residues inside the channel was investigated using mutational studies that revealed rate limiting interactions during the permeation. Copyright © 2014 Elsevier B.V. All rights reserved.

Does the Mid-Atlantic Ridge affect the distribution of abyssal benthic crustaceans across the Atlantic Ocean?

NASA Astrophysics Data System (ADS)

Bober, Simon; Brix, Saskia; Riehl, Torben; Schwentner, Martin; Brandt, Angelika

2018-02-01

A trans-Atlantic transect along the Vema Fracture Zone was sampled during the Vema-TRANSIT expedition in 2014/15. The aim of the cruise was to investigate whether the Mid-Atlantic Ridge (MAR) isolates the abyssal fauna of the western and eastern abyssal basins. Based on two genetic datasets of Macrostylidae and Desmosomatidae/Nannoniscidae studied by Riehl et al. and Brix et al. in this issue we found that most of the therein-delimitated species were found at only one side of the MAR. We analysed those species of Macrostylidae and Desmosomatidae that were sampled across the MAR and complemented these with one species of a third family: Munnopsidae. With these datasets we were further able to consider the effect of different niche adaptations: Macrostylidae are infaunal (burrowing), Munnopsidae are considered epifaunal with pronounced swimming capabilities and Desmosomatidae and Nannoniscidae are partly able to swim, but are not as well adapted to swimming as Munnopsidae. We concluded that the MAR seems to be a dispersal barrier for the non-swimming Macrostylidae as well as weakly-swimming Desmosomatidae and Nannoniscidae. However, four species of Macrostylidae and Desmosomatidae did cross the MAR, but evidence for regular unrestricted gene flow is still lacking. For the swimming Munnopsidae we were able to detect persistent gene flow across the MAR.

An Investigation of Measurement Invariance across Genders on the Overexcitability Questionnaire-Two

ERIC Educational Resources Information Center

Warne, Russell T.

2011-01-01

The Overexcitability Questionnaire-Two (OEQII) is a quantitative instrument for assessing overexcitabilities as they are described in Dabrowski's theory of positive disintegration. This article uses multigroup confirmatory factor analysis to examine the measurement invariance of OEQII scores across genders. Results indicate that raw OEQII scores…

Phenotypic plasticity to light and nutrient availability alters functional trait ranking across eight perennial grassland species.

PubMed

Siebenkäs, Alrun; Schumacher, Jens; Roscher, Christiane

2015-03-27

Functional traits are often used as species-specific mean trait values in comparative plant ecology or trait-based predictions of ecosystem processes, assuming that interspecific differences are greater than intraspecific trait variation and that trait-based ranking of species is consistent across environments. Although this assumption is increasingly challenged, there is a lack of knowledge regarding to what degree the extent of intraspecific trait variation in response to varying environmental conditions depends on the considered traits and the characteristics of the studied species to evaluate the consequences for trait-based species ranking. We studied functional traits of eight perennial grassland species classified into different functional groups (forbs vs. grasses) and varying in their inherent growth stature (tall vs. small) in a common garden experiment with different environments crossing three levels of nutrient availability and three levels of light availability over 4 months of treatment applications. Grasses and forbs differed in almost all above- and belowground traits, while trait differences related to growth stature were generally small. The traits showing the strongest responses to resource availability were similarly for grasses and forbs those associated with allocation and resource uptake. The strength of trait variation in response to varying resource availability differed among functional groups (grasses > forbs) and species of varying growth stature (small-statured > tall-statured species) in many aboveground traits, but only to a lower extent in belowground traits. These differential responses altered trait-based species ranking in many aboveground traits, such as specific leaf area, tissue nitrogen and carbon concentrations and above-belowground allocation (leaf area ratio and root : shoot ratio) at varying resource supply, while trait-based species ranking was more consistent in belowground traits. Our study shows that species grouping

Community turnover of wood-inhabiting fungi across hierarchical spatial scales.

PubMed

Abrego, Nerea; García-Baquero, Gonzalo; Halme, Panu; Ovaskainen, Otso; Salcedo, Isabel

2014-01-01

For efficient use of conservation resources it is important to determine how species diversity changes across spatial scales. In many poorly known species groups little is known about at which spatial scales the conservation efforts should be focused. Here we examined how the community turnover of wood-inhabiting fungi is realised at three hierarchical levels, and how much of community variation is explained by variation in resource composition and spatial proximity. The hierarchical study design consisted of management type (fixed factor), forest site (random factor, nested within management type) and study plots (randomly placed plots within each study site). To examine how species richness varied across the three hierarchical scales, randomized species accumulation curves and additive partitioning of species richness were applied. To analyse variation in wood-inhabiting species and dead wood composition at each scale, linear and Permanova modelling approaches were used. Wood-inhabiting fungal communities were dominated by rare and infrequent species. The similarity of fungal communities was higher within sites and within management categories than among sites or between the two management categories, and it decreased with increasing distance among the sampling plots and with decreasing similarity of dead wood resources. However, only a small part of community variation could be explained by these factors. The species present in managed forests were in a large extent a subset of those species present in natural forests. Our results suggest that in particular the protection of rare species requires a large total area. As managed forests have only little additional value complementing the diversity of natural forests, the conservation of natural forests is the key to ecologically effective conservation. As the dissimilarity of fungal communities increases with distance, the conserved natural forest sites should be broadly distributed in space, yet the individual

Community Turnover of Wood-Inhabiting Fungi across Hierarchical Spatial Scales

PubMed Central

Abrego, Nerea; García-Baquero, Gonzalo; Halme, Panu; Ovaskainen, Otso; Salcedo, Isabel

2014-01-01

For efficient use of conservation resources it is important to determine how species diversity changes across spatial scales. In many poorly known species groups little is known about at which spatial scales the conservation efforts should be focused. Here we examined how the community turnover of wood-inhabiting fungi is realised at three hierarchical levels, and how much of community variation is explained by variation in resource composition and spatial proximity. The hierarchical study design consisted of management type (fixed factor), forest site (random factor, nested within management type) and study plots (randomly placed plots within each study site). To examine how species richness varied across the three hierarchical scales, randomized species accumulation curves and additive partitioning of species richness were applied. To analyse variation in wood-inhabiting species and dead wood composition at each scale, linear and Permanova modelling approaches were used. Wood-inhabiting fungal communities were dominated by rare and infrequent species. The similarity of fungal communities was higher within sites and within management categories than among sites or between the two management categories, and it decreased with increasing distance among the sampling plots and with decreasing similarity of dead wood resources. However, only a small part of community variation could be explained by these factors. The species present in managed forests were in a large extent a subset of those species present in natural forests. Our results suggest that in particular the protection of rare species requires a large total area. As managed forests have only little additional value complementing the diversity of natural forests, the conservation of natural forests is the key to ecologically effective conservation. As the dissimilarity of fungal communities increases with distance, the conserved natural forest sites should be broadly distributed in space, yet the individual

Delivery of paclitaxel across cellular barriers using a dendrimer-based nanocarrier.

PubMed

Teow, Huey Minn; Zhou, Zhengyuan; Najlah, Mohammad; Yusof, Siti R; Abbott, N Joan; D'Emanuele, Antony

2013-01-30

The aim of this study was to investigate the ability of a third-generation (G3) polyamidoamine (PAMAM) dendrimer-based carrier to enhance the permeability of paclitaxel (pac) and to overcome cellular barriers. G3 dendrimers were surface modified with lauryl chains (L) and conjugated with paclitaxel (pac) via a glutaric anhydride (glu) linker, followed by labeling with FITC. Biological evaluation of the dendrimer and conjugates was conducted using the human colon adenocarcinoma cell line (Caco-2) and primary cultured porcine brain endothelial cells (PBECs). LDH assay was used to evaluate the cytotoxicity of the dendrimer and conjugates. Cytotoxicity studies showed that the conjugation of lauryl chains and paclitaxel on G3 dendrimer significantly (p<0.05) increased the cytotoxicity against both cell types. Permeability studies of dendrimer-drug conjugates demonstrated an increase in the apparent permeability coefficient (P(app)) in both apical to basolateral A→B and basolateral to apical B→A directions across both cell monolayers compared to unmodified G3 and free drug. The B→A P(app) of paclitaxel was significantly (p<0.05) higher than the A→B P(app), indicating active function of P-gp efflux transporter system in both cell models. L6-G3-glu-pac conjugate had approximately 12-fold greater permeability across both cell monolayers than that of paclitaxel alone. Copyright © 2012 Elsevier B.V. All rights reserved.

Conservatism of lizard thermal tolerances and body temperatures across evolutionary history and geography.

PubMed

Grigg, Joseph W; Buckley, Lauren B

2013-04-23

Species may exhibit similar thermal tolerances via either common ancestry or environmental filtering and local adaptation, if the species inhabit similar environments. We ask whether upper and lower thermal limits (critical thermal maxima and minima) and body temperatures are more strongly conserved across evolutionary history or geography for lizard populations distributed globally. We find that critical thermal maxima are highly conserved with location accounting for a higher proportion of the variation than phylogeny. Notably, thermal tolerance breadth is conserved across the phylogeny despite critical thermal minima showing little niche conservatism. Body temperatures observed during activity in the field show the greatest degree of conservatism, with phylogeny accounting for most of the variation. This suggests that propensities for thermoregulatory behaviour, which can buffer body temperatures from environmental variation, are similar within lineages. Phylogeny and geography constrain thermal tolerances similarly within continents, but variably within clades. Conservatism of thermal tolerances across lineages suggests that the potential for local adaptation to alleviate the impacts of climate change on lizards may be limited.

Evolutionarily conserved coding properties of auditory neurons across grasshopper species

PubMed Central

Neuhofer, Daniela; Wohlgemuth, Sandra; Stumpner, Andreas; Ronacher, Bernhard

2008-01-01

We investigated encoding properties of identified auditory interneurons in two not closely related grasshopper species (Acrididae). The neurons can be homologized on the basis of their similar morphologies and physiologies. As test stimuli, we used the species-specific stridulation signals of Chorthippus biguttulus, which evidently are not relevant for the other species, Locusta migratoria. We recorded spike trains produced in response to these signals from several neuron types at the first levels of the auditory pathway in both species. Using a spike train metric to quantify differences between neuronal responses, we found a high similarity in the responses of homologous neurons: interspecific differences between the responses of homologous neurons in the two species were not significantly larger than intraspecific differences (between several specimens of a neuron in one species). These results suggest that the elements of the thoracic auditory pathway have been strongly conserved during the evolutionary divergence of these species. According to the ‘efficient coding’ hypothesis, an adaptation of the thoracic auditory pathway to the specific needs of acoustic communication could be expected. We conclude that there must have been stabilizing selective forces at work that conserved coding characteristics and prevented such an adaptation. PMID:18505715

Hierarchical Genetic Analysis of German Cockroach (Blattella germanica) Populations from within Buildings to across Continents

PubMed Central

Vargo, Edward L.; Crissman, Jonathan R.; Booth, Warren; Santangelo, Richard G.; Mukha, Dmitry V.; Schal, Coby

2014-01-01

Understanding the population structure of species that disperse primarily by human transport is essential to predicting and controlling human-mediated spread of invasive species. The German cockroach (Blattella germanica) is a widespread urban invader that can actively disperse within buildings but is spread solely by human-mediated dispersal over longer distances; however, its population structure is poorly understood. Using microsatellite markers we investigated population structure at several spatial scales, from populations within single apartment buildings to populations from several cities across the U.S. and Eurasia. Both traditional measures of genetic differentiation and Bayesian clustering methods revealed increasing levels of genetic differentiation at greater geographic scales. Our results are consistent with active dispersal of cockroaches largely limited to movement within a building. Their low levels of genetic differentiation, yet limited active spread between buildings, suggests a greater likelihood of human-mediated dispersal at more local scales (within a city) than at larger spatial scales (within and between continents). About half the populations from across the U.S. clustered together with other U.S. populations, and isolation by distance was evident across the U.S. Levels of genetic differentiation among Eurasian cities were greater than those in the U.S. and greater than those between the U.S. and Eurasia, but no clear pattern of structure at the continent level was detected. MtDNA sequence variation was low and failed to reveal any geographical structure. The weak genetic structure detected here is likely due to a combination of historical admixture among populations and periodic population bottlenecks and founder events, but more extensive studies are needed to determine whether signatures of global movement may be present in this species. PMID:25020136

Macroecological and macroevolutionary patterns of leaf herbivory across vascular plants.

PubMed

Turcotte, Martin M; Davies, T Jonathan; Thomsen, Christina J M; Johnson, Marc T J

2014-07-22

The consumption of plants by animals underlies important evolutionary and ecological processes in nature. Arthropod herbivory evolved approximately 415 Ma and the ensuing coevolution between plants and herbivores is credited with generating much of the macroscopic diversity on the Earth. In contemporary ecosystems, herbivory provides the major conduit of energy from primary producers to consumers. Here, we show that when averaged across all major lineages of vascular plants, herbivores consume 5.3% of the leaf tissue produced annually by plants, whereas previous estimates are up to 3.8× higher. This result suggests that for many plant species, leaf herbivory may play a smaller role in energy and nutrient flow than currently thought. Comparative analyses of a diverse global sample of 1058 species across 2085 populations reveal that models of stabilizing selection best describe rates of leaf consumption, and that rates vary substantially within and among major plant lineages. A key determinant of this variation is plant growth form, where woody plant species experience 64% higher leaf herbivory than non-woody plants. Higher leaf herbivory in woody species supports a key prediction of the plant apparency theory. Our study provides insight into how a long history of coevolution has shaped the ecological and evolutionary relationships between plants and herbivores. © 2014 The Author(s) Published by the Royal Society. All rights reserved.

Modeling of the Dorsal Gradient across Species Reveals Interaction between Embryo Morphology and Toll Signaling Pathway during Evolution

PubMed Central

Koslen, Hannah R.; Chiel, Hillel J.; Mizutani, Claudia Mieko

2014-01-01

Morphogenetic gradients are essential to allocate cell fates in embryos of varying sizes within and across closely related species. We previously showed that the maternal NF-κB/Dorsal (Dl) gradient has acquired different shapes in Drosophila species, which result in unequally scaled germ layers along the dorso-ventral axis and the repositioning of the neuroectodermal borders. Here we combined experimentation and mathematical modeling to investigate which factors might have contributed to the fast evolutionary changes of this gradient. To this end, we modified a previously developed model that employs differential equations of the main biochemical interactions of the Toll (Tl) signaling pathway, which regulates Dl nuclear transport. The original model simulations fit well the D. melanogaster wild type, but not mutant conditions. To broaden the applicability of this model and probe evolutionary changes in gradient distributions, we adjusted a set of 19 independent parameters to reproduce three quantified experimental conditions (i.e. Dl levels lowered, nuclear size and density increased or decreased). We next searched for the most relevant parameters that reproduce the species-specific Dl gradients. We show that adjusting parameters relative to morphological traits (i.e. embryo diameter, nuclear size and density) alone is not sufficient to reproduce the species Dl gradients. Since components of the Tl pathway simulated by the model are fast-evolving, we next asked which parameters related to Tl would most effectively reproduce these gradients and identified a particular subset. A sensitivity analysis reveals the existence of nonlinear interactions between the two fast-evolving traits tested above, namely the embryonic morphological changes and Tl pathway components. Our modeling further suggests that distinct Dl gradient shapes observed in closely related melanogaster sub-group lineages may be caused by similar sequence modifications in Tl pathway components, which

Target-Specificity in Scorpions; Comparing Lethality of Scorpion Venoms across Arthropods and Vertebrates

PubMed Central

Vargas-Muñoz, Leidy J.

2017-01-01

Scorpions use their venom in defensive situations as well as for subduing prey. Since some species of scorpion use their venom more in defensive situations than others, this may have led to selection for differences in effectiveness in defensive situations. Here, we compared the LD50 of the venom of 10 species of scorpions on five different species of target organisms; two insects and three vertebrates. We found little correlation between the target species in the efficacy of the different scorpion venoms. Only the two insects showed a positive correlation, indicating that they responded similarly to the panel of scorpion venoms. We discuss the lack of positive correlation between the vertebrate target species in the light of their evolution and development. When comparing the responses of the target systems to individual scorpion venoms pairwise, we found that closely related scorpion species tend to elicit a similar response pattern across the target species. This was further reflected in a significant phylogenetic signal across the scorpion phylogeny for the LD50 in mice and in zebrafish. We also provide the first mouse LD50 value for Grosphus grandidieri. PMID:28976932

Target-Specificity in Scorpions; Comparing Lethality of Scorpion Venoms across Arthropods and Vertebrates.

PubMed

van der Meijden, Arie; Koch, Bjørn; van der Valk, Tom; Vargas-Muñoz, Leidy J; Estrada-Gómez, Sebastian

2017-10-04

Scorpions use their venom in defensive situations as well as for subduing prey. Since some species of scorpion use their venom more in defensive situations than others, this may have led to selection for differences in effectiveness in defensive situations. Here, we compared the LD 50 of the venom of 10 species of scorpions on five different species of target organisms; two insects and three vertebrates. We found little correlation between the target species in the efficacy of the different scorpion venoms. Only the two insects showed a positive correlation, indicating that they responded similarly to the panel of scorpion venoms. We discuss the lack of positive correlation between the vertebrate target species in the light of their evolution and development. When comparing the responses of the target systems to individual scorpion venoms pairwise, we found that closely related scorpion species tend to elicit a similar response pattern across the target species. This was further reflected in a significant phylogenetic signal across the scorpion phylogeny for the LD 50 in mice and in zebrafish. We also provide the first mouse LD 50 value for Grosphus grandidieri .