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Sample records for abundant tree species

  1. Geographical Range and Local Abundance of Tree Species in China

    PubMed Central

    Ren, Haibao; Condit, Richard; Chen, Bin; Mi, Xiangcheng; Cao, Min; Ye, Wanhui; Hao, Zhanqing; Ma, Keping

    2013-01-01

    Most studies on the geographical distribution of species have utilized a few well-known taxa in Europe and North America, with little research in China and its wide range of climate and forest types. We assembled large datasets to quantify the geographic ranges of tree species in China and to test several biogeographic hypotheses: 1) whether locally abundant species tend to be geographically widespread; 2) whether species are more abundant towards their range-centers; and 3) how abundances are correlated between sites. Local abundances of 651 species were derived from four tree plots of 20–25 ha where all individuals ≥1 cm in stem diameter were mapped and identified taxonomically. Range sizes of these species across China were then estimated from over 460,000 geo-referenced records; a Bayesian approach was used, allowing careful measures of error of each range estimate. The log-transformed range sizes had a bell-shaped distribution with a median of 703,000 km2, and >90% of 651 species had ranges >105 km2. There was no relationship between local abundance and range size, and no evidence for species being more abundant towards their range-centers. Finally, species’ abundances were positively correlated between sites. The widespread nature of most tree species in China suggests few are vulnerable to global extinction, and there is no indication of the double-peril that would result if rare species also had narrow ranges. PMID:24130772

  2. Why abundant tropical tree species are phylogenetically old.

    PubMed

    Wang, Shaopeng; Chen, Anping; Fang, Jingyun; Pacala, Stephen W

    2013-10-01

    Neutral models of species diversity predict patterns of abundance for communities in which all individuals are ecologically equivalent. These models were originally developed for Panamanian trees and successfully reproduce observed distributions of abundance. Neutral models also make macroevolutionary predictions that have rarely been evaluated or tested. Here we show that neutral models predict a humped or flat relationship between species age and population size. In contrast, ages and abundances of tree species in the Panamanian Canal watershed are found to be positively correlated, which falsifies the models. Speciation rates vary among phylogenetic lineages and are partially heritable from mother to daughter species. Variable speciation rates in an otherwise neutral model lead to a demographic advantage for species with low speciation rate. This demographic advantage results in a positive correlation between species age and abundance, as found in the Panamanian tropical forest community. PMID:24043767

  3. Tree species composition affects the abundance of rowan (Sorbus aucuparia L.) in urban forests in Finland.

    PubMed

    Hamberg, Leena; Lehvävirta, Susanna; Kotze, D Johan; Heikkinen, Juha

    2015-03-15

    Recent studies have shown a considerable increase in the abundance of rowan (Sorbus aucuparia) saplings in urban forests in Finland, yet the reasons for this increase are not well understood. Here we investigated whether canopy cover or tree species composition, i.e., the basal areas of different tree species in Norway spruce dominated urban forests, affects the abundances of rowan seedlings, saplings and trees. Altogether 24 urban forest patches were investigated. We sampled the number of rowan and other saplings, and calculated the basal areas of trees. We showed that rowan abundance was affected by tree species composition. The basal area of rowan trees (≥ 5 cm in diameter at breast height, dbh) decreased with increasing basal area of Norway spruce, while the cover of rowan seedlings increased with an increase in Norway spruce basal area. However, a decrease in the abundance of birch (Betula pendula) and an increase in the broad-leaved tree group (Acer platanoides, Alnus glutinosa, Alnus incana, Amelanchier spicata, Prunus padus, Quercus robur, Rhamnus frangula and Salix caprea) coincided with a decreasing number of rowans. Furthermore, rowan saplings were scarce in the vicinity of mature rowan trees. Although it seems that tree species composition has an effect on rowan, the relationship between rowan saplings and mature trees is complex, and therefore we conclude that regulating tree species composition is not an easy way to keep rowan thickets under control in urban forests in Finland. PMID:25588119

  4. Regional-scale directional changes in abundance of tree species along a temperature gradient in Japan.

    PubMed

    Suzuki, Satoshi N; Ishihara, Masae I; Hidaka, Amane

    2015-09-01

    Climate changes are assumed to shift the ranges of tree species and forest biomes. Such range shifts result from changes in abundances of tree species or functional types. Owing to global warming, the abundance of a tree species or functional type is expected to increase near the colder edge of its range and decrease near the warmer edge. This study examined directional changes in abundance and demographic parameters of forest trees along a temperature gradient, as well as a successional gradient, in Japan. Changes in the relative abundance of each of four functional types (evergreen broad-leaved, deciduous broad-leaved, evergreen temperate conifer, and evergreen boreal conifer) and the demography of each species (recruitment rate, mortality, and population growth rate) were analyzed in 39 permanent forest plots across the Japanese archipelago. Directional changes in the relative abundance of functional types were detected along the temperature gradient. Relative abundance of evergreen broad-leaved trees increased near their colder range boundaries, especially in secondary forests, coinciding with the decrease in deciduous broad-leaved trees. Similarly, relative abundance of deciduous broad-leaved trees increased near their colder range boundaries, coinciding with the decrease in boreal conifers. These functional-type-level changes were mainly due to higher recruitment rates and partly to the lower mortality of individual species at colder sites. This is the first report to show that tree species abundances in temperate forests are changing directionally along a temperature gradient, which might be due to current or past climate changes as well as recovery from past disturbances. PMID:25712048

  5. The effect of soil-borne pathogens depends on the abundance of host tree species

    PubMed Central

    Liu, Yu; Fang, Suqin; Chesson, Peter; He, Fangliang

    2015-01-01

    The overarching issue for understanding biodiversity maintenance is how fitness advantages accrue to a species as it becomes rare, as this is the defining feature of stable coexistence mechanisms. Without these fitness advantages, average fitness differences between species will lead to exclusion. However, empirical evidence is lacking, especially for forests, due to the difficulty of manipulating density on a large-enough scale. Here we took advantage of naturally occurring contrasts in abundance between sites of a subtropical tree species, Ormosia glaberrima, to demonstrate how low-density fitness advantages accrue by the Janzen–Connell mechanism. The results showed that soil pathogens suppressed seedling recruitment of O. glaberrima when it is abundant but had little effect on the seedlings when it is at low density due to the lack of pathogens. The difference in seedling survival between abundant and low-density sites demonstrates strong dependence of pathogenic effect on the abundance of host species. PMID:26632594

  6. The effect of soil-borne pathogens depends on the abundance of host tree species.

    PubMed

    Liu, Yu; Fang, Suqin; Chesson, Peter; He, Fangliang

    2015-01-01

    The overarching issue for understanding biodiversity maintenance is how fitness advantages accrue to a species as it becomes rare, as this is the defining feature of stable coexistence mechanisms. Without these fitness advantages, average fitness differences between species will lead to exclusion. However, empirical evidence is lacking, especially for forests, due to the difficulty of manipulating density on a large-enough scale. Here we took advantage of naturally occurring contrasts in abundance between sites of a subtropical tree species, Ormosia glaberrima, to demonstrate how low-density fitness advantages accrue by the Janzen-Connell mechanism. The results showed that soil pathogens suppressed seedling recruitment of O. glaberrima when it is abundant but had little effect on the seedlings when it is at low density due to the lack of pathogens. The difference in seedling survival between abundant and low-density sites demonstrates strong dependence of pathogenic effect on the abundance of host species. PMID:26632594

  7. Restinga forests of the Brazilian coast: richness and abundance of tree species on different soils.

    PubMed

    Magnago, Luiz F S; Martins, Sebastião V; Schaefer, Carlos E G R; Neri, Andreza V

    2012-09-01

    The aim of this study was to determine changes in composition, abundance and richness of species along a forest gradient with varying soils and flood regimes. The forests are located on the left bank of the lower Jucu River, in Jacarenema Natural Municipal Park, Espírito Santo. A survey of shrub/tree species was done in 80 plots, 5x25 m, equally distributed among the forests studied. We included in the sampling all individuals with >3.2 cm diameter at breast height (1.30 m). Soil samples were collected from the surface layer (0-10 cm) in each plot for chemical and physical analysis. The results indicate that a significant pedological gradient occurs, which is influenced by varying seasonal groundwater levels. Restinga forest formations showed significant differences in species richness, except for Non-flooded Forest and Non-flooded Forest Transition. The Canonical Correlation Analysis (CCA) showed that some species are distributed along the gradient under the combined influence of drainage, nutrient concentration and physical characteristics of the soil. Regarding the variables tested, flooding seems to be a more limiting factor for the establishment of plant species in Restinga forests than basic soil fertility attributes. PMID:22886165

  8. Where to nest? Ecological determinants of chimpanzee nest abundance and distribution at the habitat and tree species scale.

    PubMed

    Carvalho, Joana S; Meyer, Christoph F J; Vicente, Luis; Marques, Tiago A

    2015-02-01

    Conversion of forests to anthropogenic land-uses increasingly subjects chimpanzee populations to habitat changes and concomitant alterations in the plant resources available to them for nesting and feeding. Based on nest count surveys conducted during the dry season, we investigated nest tree species selection and the effect of vegetation attributes on nest abundance of the western chimpanzee, Pan troglodytes verus, at Lagoas de Cufada Natural Park (LCNP), Guinea-Bissau, a forest-savannah mosaic widely disturbed by humans. Further, we assessed patterns of nest height distribution to determine support for the anti-predator hypothesis. A zero-altered generalized linear mixed model showed that nest abundance was negatively related to floristic diversity (exponential form of the Shannon index) and positively with the availability of smaller-sized trees, reflecting characteristics of dense-canopy forest. A positive correlation between nest abundance and floristic richness (number of plant species) and composition indicated that species-rich open habitats are also important in nest site selection. Restricting this analysis to feeding trees, nest abundance was again positively associated with the availability of smaller-sized trees, further supporting the preference for nesting in food tree species from dense forest. Nest tree species selection was non-random, and oil palms were used at a much lower proportion (10%) than previously reported from other study sites in forest-savannah mosaics. While this study suggests that human disturbance may underlie the exclusive arboreal nesting at LCNP, better quantitative data are needed to determine to what extent the construction of elevated nests is in fact a response to predators able to climb trees. Given the importance of LCNP as refuge for Pan t. verus our findings can improve conservation decisions for the management of this important umbrella species as well as its remaining suitable habitats. PMID:25224379

  9. Associations between regional moisture gradient, tree species dominance, and downed wood abundance

    NASA Astrophysics Data System (ADS)

    Johnson, A. C.; Mills, J.

    2007-12-01

    Downed wood functions as a source of nurse logs, physical structure in streams, food, and carbon. Because downed wood is important in upland and aquatic habitats, an understanding of wood recruitment along a continuum from wet to dry landscapes is critical for both preservation of biodiversity and restoration of natural ecosystem structure and function. We assessed downed wood in public and private forests of Washington and Oregon by using a subset of the Forest Inventory and Analysis (FIA) database including 15,842 sampled conditions. Multivariate regression trees, ANOVA, and t-tests were used to discern environmental conditions most closely associated with abundance of woody debris. Of the 16 parameters included in the analysis, rainfall, forest ownership, number of damaged standing trees, and forest elevation were most indicative of woody debris abundance. The Hemlock/spruce Group, including hemlock, spruce, cedar, and white pine, most associated with wetter soils, had significantly more downed wood than 12 other forest groups. The Ponderosa Pine Group, indicative of drier sites with higher fire frequencies, included ponderosa pine, sugar pine, and incense cedar, and had significantly less downed wood volume. Overall, the amount of woody debris in either the Spruce/hemlock Group or the Ponderosa Pine Group did not change significantly as tree age increased from 5 to 350 years. Plots within the Hemlock/spruce with greater standing tree volume also had significantly greater downed wood volume. In contrast, greater downed wood volume was not associated with greater standing tree volume in the Ponderosa Pine Group. Knowledge of linkages among environmental variables and stand characteristics are useful in development of regional forest models aimed at understanding the effects of climate change and disturbance on forest succession.

  10. Macroscale intraspecific variation and environmental heterogeneity: analysis of cold and warm zone abundance, mortality, and regeneration distributions of four eastern US tree species.

    PubMed

    Prasad, Anantha M

    2015-11-01

    I test for macroscale intraspecific variation of abundance, mortality, and regeneration of four eastern US tree species (Tsuga canadensis,Betula lenta,Liriodendron tulipifera, and Quercus prinus) by splitting them into three climatic zones based on plant hardiness zones (PHZs). The primary goals of the analysis are to assess the differences in environmental heterogeneity and demographic responses among climatic zones, map regional species groups based on decision tree rules, and evaluate univariate and multivariate patterns of species demography with respect to environmental variables. I use the Forest Inventory Analysis (FIA) data to derive abundance, mortality, and regeneration indices and split the range into three climatic zones based on USDA PHZs: (1) cold adapted, leading region; (2) middle, well-adapted region; and (3) warm adapted, trailing region. I employ decision tree ensemble methods to assess the importance of environmental predictors on the abundance of the species between the cold and warm zones and map zonal variations in species groups. Multivariate regression trees are used to simultaneously explore abundance, mortality, and regeneration in tandem to assess species vulnerability. Analyses point to the relative importance of climate in the warm adapted, trailing zone (especially moisture) compared to the cold adapted, leading zone. Higher mortality and lower regeneration patterns in the warm trailing zone point to its vulnerability to growing season temperature and precipitation changes that could figure more prominently in the future. This study highlights the need to account for intraspecific variation of demography in order to understand environmental heterogeneity and differential adaptation. It provides a methodology for assessing the vulnerability of tree species by delineating climatic zones based on easily available PHZ data, and FIA derived abundance, mortality, and regeneration indices as a proxy for overall growth and fitness. Based on

  11. Thysanoptera (Thrips) Within Citrus Orchards in Florida: Species Distribution, Relative and Seasonal Abundance Within Trees, and Species on Vines and Ground Cover Plants

    PubMed Central

    Childers, Carl C.; Nakahara, Sueo

    2006-01-01

    crops in Florida. The five most abundant thrips species collected within citrus tree canopies were: A. fasciapennis, F. bispinosa, C. orchidii, K. flavipes, and D. trifasciatus. In comparison, the following five thrips species were most abundant on vines or ground cover plants: F. bispinosa, H. gowdeyi, F. cephalica, M. abdominalis, and F. gossypiana. Fifty-eight species of vines or ground cover plants in 26 families were infested with one or more of 27 species of thrips. PMID:20233100

  12. Variation in leaf litter production and resorption of nutrients in abundant tree species in Nyungwe tropical montane rainforest in Rwanda

    NASA Astrophysics Data System (ADS)

    Nyirambangutse, Brigitte; Mirindi Dusenge, Eric; Nsabimana, Donat; Bizuru, Elias; Pleijel, Håkan; Uddling, Johan; Wallin, Göran

    2014-05-01

    African tropical rainforests play many roles from local to global scale as providers of resources and ecosystem services. Although covering 30% of the global rainforest, only few studies aiming to better understand the storage and fluxes of carbon and nutrients in these forests have been conducted. To answer questions related to these issues, we have established 15 permanent 0.5 ha plots where we compare carbon and nutrient fluxes of primary and secondary forest tree communities in a tropical montane forest in central Africa. The studies are conducted in Nyungwe montane tropical rain forest gazetted as a National Park to protect its extensive floral and faunal diversity covering an area of 970 km2. Nyungwe is located in Southwest Rwanda (2o17'-2o50'S, 29o07'-29o26A'E). The forest is ranging between 1600-2950 m.a.s.l. and is one of the most biologically important rainforest in Albertine Rift region in terms of Biodiversity. Nyungwe consists of a mixture of primary and secondary forest communities supporting a richness of plant and animal life. More than 260 species of trees and shrubs have been found in Nyungwe, including species endemic to the Albertine Rift. The forest has a climate with a mean annual temperature of 15.5oC and annual rainfall of ca 1850 mm yr-1, with July and August being the only months when rainfall drops. A part of this study is focusing on the dynamics of nutrients through leaf turnover. This turnover of leaves is regulated to maximize the carbon gain through canopy photosynthesis and resource-use efficiency of the plant. It is known that about half of leaf nitrogen is invested in photosynthetic apparatus and that there normally is a strong correlation between the photosynthetic capacity and leaf nitrogen per unit area. Hence leaf nitrogen is an important factor for canopy photosynthesis. However, leaves are produced, senesce and fall. Some nitrogen in the leaf is lost when leaves senesce but other is resorbed. The resorption of nitrogen

  13. Species integrity in trees.

    PubMed

    Ortiz-Barrientos, Daniel; Baack, Eric J

    2014-09-01

    From California sequoia, to Australian eucalyptus, to the outstanding diversity of Amazonian forests, trees are fundamental to many processes in ecology and evolution. Trees define the communities that they inhabit, are host to a multiplicity of other organisms and can determine the ecological dynamics of other plants and animals. Trees are also at the heart of major patterns of biodiversity such as the latitudinal gradient of species diversity and thus are important systems for studying the origin of new plant species. Although the role of trees in community assembly and ecological succession is partially understood, the origin of tree diversity remains largely opaque. For instance, the relative importance of differing habitats and phenologies as barriers to hybridization between closely related species is still largely uncharacterized in trees. Consequently, we know very little about the origin of trees species and their integrity. Similarly, studies on the interplay between speciation and tree community assembly are in their infancy and so are studies on how processes like forest maturation modifies the context in which reproductive isolation evolves. In this issue of Molecular Ecology, Lindtke et al. (2014) and Lagache et al. (2014) overcome some traditional difficulties in studying mating systems and sexual isolation in the iconic oaks and poplars, providing novel insights about the integrity of tree species and on how ecology leads to variation in selection on reproductive isolation over time and space. PMID:25155715

  14. Eupalopsellidae and Stigmaeidae (Acari: Prostigmata) within citrus orchards in Florida: species distribution, relative and seasonal abundance within trees, associated vines, and ground cover plants.

    PubMed

    Childers, Carl C; Ueckermann, Eduard A

    2014-10-01

    Seven citrus orchards on reduced- to no-pesticide spray programs were sampled for predacious mites in the families Eupalopsellidae and Stigmaeidae (Acari: Prostigmata) in central and south central Florida. Inner and outer canopy leaves, fruit, twigs, and trunk scrapings were sampled monthly between August 1994 and January 1996. Open flowers were sampled in March from five of the sites. Two species of eupalopsellid mites (Exothorhis caudata Summers and Saniosulus harteni (van-Dis and Ueckermann)) were identified from 252 specimens collected within citrus tree canopies within the seven citrus orchards of which 249 were E. caudata. Only two E. caudata were collected from ground cover plants within five of the seven orchards. Eight species of Stigmaeidae were identified from 5,637 specimens: Agistemus floridanus Gonzalez, A. terminalis Gonzalez, Eustigmaeus arcuata (Chandhri), E. sp. near arcuata, E. segnis (Koch), Mediostigmaeus citri (Rakha and McCoy), Stigmaeus seminudus Wood, and Zetzellia languida Gonzalez were collected from within citrus tree canopies from seven orchard sites. Agistemus floridanus was the only species in either family that was abundant with 5,483 collected from within citrus tree canopies compared with only 39 from vine or ground cover plants. A total of 431 samples from one or more of 82 vines and ground cover plants were sampled monthly between September 1994 and January 1996 in five of these orchards and one or more eupalopsellids or stigmaeids were collected from 19 of these plants. Richardia brasiliensis (Meg.) Gomez had nine A. floridanus from 5 of 25 samples collected from this plant. Solanum sp. had five A. floridanus from three samples taken. Both eupalopsellid and stigmaeid species numbers represented <1 % of the total numbers of phytoseiid species taken from the same plants. The two remaining orchards were on full herbicide programs and ground cover plants were absent. Agistemus floridanus was more abundant in the citrus orchards

  15. Phytoseiidae (Acari: Mesostigmata) within citrus orchards in Florida: species distribution, relative and seasonal abundance within trees, associated vines and ground cover plants.

    PubMed

    Childers, Carl C; Denmark, Harold A

    2011-08-01

    Seven citrus orchards on reduced- to no-pesticide spray programs were sampled for predacious mites in the family Phytoseiidae (Acari: Mesostigmata) in central and south central Florida. Inner and outer canopy leaves, open flowers, fruit, twigs, and trunk scrapings were sampled monthly between September 1994 and January 1996. Vines and ground cover plants were sampled monthly between September 1994 and January 1996 in five of these orchards. The two remaining orchards were on full herbicide programs and ground cover plants were absent. Thirty-three species of phytoseiid mites were identified from 35,405 specimens collected within citrus tree canopies within the seven citrus orchards, and 8,779 specimens from vines and ground cover plants within five of the seven orchards. The six most abundant phytoseiid species found within citrus tree canopies were: Euseius mesembrinus (Dean) (20,948), Typhlodromalus peregrinus (Muma) (8,628), Iphiseiodes quadripilis (Banks) (2,632), Typhlodromips dentilis (De Leon) (592), Typhlodromina subtropica Muma and Denmark (519), and Galendromus helveolus (Chant) (315). The six most abundant species found on vines or ground cover plants were: T. peregrinus (6,608), E. mesembrinus (788), T. dentilis (451), I. quadripilis (203), T. subtropica (90), and Proprioseiopsis asetus (Chant) (48). The remaining phytoseiids included: Amblyseius aerialis (Muma), A. herbicolus (Chant), A. largoensis (Chant), A. multidentatus (Chant), A. sp. near multidentatus, A. obtusus (Koch), Chelaseius vicinus (Muma), Euseius hibisci Chant, Galendromus gratus (Chant), Metaseiulus mcgregori (Chant), Neoseiulus mumai (Denmark), N. vagus (Denmark), Phytoscutus sexpilis (Muma), Phytoseiulus macropilis (Banks), Proprioseiopsis detritus (Muma), P. dorsatus (Muma), P. macrosetae (Banks), P. rotundus (Muma), P. solens (De Leon), Typhlodromips deleoni (Muma), T. dillus (De Leon), T. dimidiatus (De Leon), T. mastus Denmark and Muma, T. simplicissimus (De Leon), and T. sp

  16. Urban Warming Drives Insect Pest Abundance on Street Trees

    PubMed Central

    Meineke, Emily K.; Dunn, Robert R.; Sexton, Joseph O.; Frank, Steven D.

    2013-01-01

    Cities profoundly alter biological communities, favoring some species over others, though the mechanisms that govern these changes are largely unknown. Herbivorous arthropod pests are often more abundant in urban than in rural areas, and urban outbreaks have been attributed to reduced control by predators and parasitoids and to increased susceptibility of stressed urban plants. These hypotheses, however, leave many outbreaks unexplained and fail to predict variation in pest abundance within cities. Here we show that the abundance of a common insect pest is positively related to temperature even when controlling for other habitat characteristics. The scale insect Parthenolecanium quercifex was 13 times more abundant on willow oak trees in the hottest parts of Raleigh, NC, in the southeastern United States, than in cooler areas, though parasitism rates were similar. We further separated the effects of heat from those of natural enemies and plant quality in a greenhouse reciprocal transplant experiment. P. quercifex collected from hot urban trees became more abundant in hot greenhouses than in cool greenhouses, whereas the abundance of P. quercifex collected from cooler urban trees remained low in hot and cool greenhouses. Parthenolecanium quercifex living in urban hot spots succeed with warming, and they do so because some demes have either acclimatized or adapted to high temperatures. Our results provide the first evidence that heat can be a key driver of insect pest outbreaks on urban trees. Since urban warming is similar in magnitude to global warming predicted in the next 50 years, pest abundance on city trees may foreshadow widespread outbreaks as natural forests also grow warmer. PMID:23544087

  17. Urban warming drives insect pest abundance on street trees.

    PubMed

    Meineke, Emily K; Dunn, Robert R; Sexton, Joseph O; Frank, Steven D

    2013-01-01

    Cities profoundly alter biological communities, favoring some species over others, though the mechanisms that govern these changes are largely unknown. Herbivorous arthropod pests are often more abundant in urban than in rural areas, and urban outbreaks have been attributed to reduced control by predators and parasitoids and to increased susceptibility of stressed urban plants. These hypotheses, however, leave many outbreaks unexplained and fail to predict variation in pest abundance within cities. Here we show that the abundance of a common insect pest is positively related to temperature even when controlling for other habitat characteristics. The scale insect Parthenolecanium quercifex was 13 times more abundant on willow oak trees in the hottest parts of Raleigh, NC, in the southeastern United States, than in cooler areas, though parasitism rates were similar. We further separated the effects of heat from those of natural enemies and plant quality in a greenhouse reciprocal transplant experiment. P. quercifex collected from hot urban trees became more abundant in hot greenhouses than in cool greenhouses, whereas the abundance of P. quercifex collected from cooler urban trees remained low in hot and cool greenhouses. Parthenolecanium quercifex living in urban hot spots succeed with warming, and they do so because some demes have either acclimatized or adapted to high temperatures. Our results provide the first evidence that heat can be a key driver of insect pest outbreaks on urban trees. Since urban warming is similar in magnitude to global warming predicted in the next 50 years, pest abundance on city trees may foreshadow widespread outbreaks as natural forests also grow warmer. PMID:23544087

  18. Riparian Ficus Tree Communities: The Distribution and Abundance of Riparian Fig Trees in Northern Thailand

    PubMed Central

    Pothasin, Pornwiwan; Compton, Stephen G.; Wangpakapattanawong, Prasit

    2014-01-01

    Fig trees (Ficus) are often ecologically significant keystone species because they sustain populations of the many seed-dispersing animals that feed on their fruits. They are prominent components of riparian zones where they may also contribute to bank stability as well as supporting associated animals. The diversity and distributions of riparian fig trees in deciduous and evergreen forests in Chiang Mai Province, Northern Thailand were investigated in 2010–2012. To record the diversity and abundance of riparian fig trees, we (1) calculated stem density, species richness, and diversity indices in 20×50 m randomly selected quadrats along four streams and (2) measured the distances of individual trees from four streams to determine if species exhibit distinct distribution patterns within riparian zones. A total of 1169 individuals (from c. 4 ha) were recorded in the quadrats, representing 33 Ficus species (13 monoecious and 20 dioecious) from six sub-genera and about 70% of all the species recorded from northern Thailand. All 33 species had at least some stems in close proximity to the streams, but they varied in their typical proximity, with F. squamosa Roxb. and F. ischnopoda Miq the most strictly stream-side species. The riparian forests in Northern Thailand support a rich diversity and high density of Ficus species and our results emphasise the importance of fig tree within the broader priorities of riparian area conservation. Plans to maintain or restore properly functioning riparian forests need to take into account their significance. PMID:25310189

  19. Relationships between live tree diameter and cavity abundance in a Missouri oak-hickory forest

    USGS Publications Warehouse

    Allen, Arthur W.; Corn, Janelle G.

    1990-01-01

    We quantified relationships between mean dbh of live, dominant and codominant trees, and cavity abundance in an oak-hickory forest in southeast Missouri. Inspection of 3,981 trees >12.7 cm dbh in 107 0.1-ha plots indicated that cavities occurred in 19.9% of all trees. White oak, black oak, scarlet oak, and hickories composed 97% of the sample. Black oak contained the greatest number and frequency of cavities; white oak had the fewest cavities. In general, the proportion of trees with cavities increased as dbh increased, but mean tree dbh per plot explained little of the observed variance in cavity abundance. Correlations between tree diameter and cavity abundance were poor because of the wide variety of factors that affect cavity development in living trees. Differences in cavity occurrence among tree species suggest that black and scarlet oaks should be selected over hickories and white oak when managing for cavity trees.

  20. Effects of timber harvest on phlebotomine sand flies (Diptera: Psychodidae) in a production forest: abundance of species on tree trunks and prevalence of trypanosomatids.

    PubMed

    Pessoa, Felipe Arley Costa; Medeiros, Jansen Fernandes; Barrett, Toby Vincent

    2007-08-01

    The Amazon forest is being exploited for timber production. The harvest removes trees, used by sand flies as resting sites, and decreases the canopy, used as refuges by some hosts. The present study evaluated the impact of the timber harvest, the abundance of sand flies, and their trypanosomatid infection rates before and after selective logging. The study was accomplished in terra-firme production forest in an area of timber harvest, state of Amazonas, Brazil. Sand fly catches were carried out in three areas: one before and after the timber harvest, and two control areas, a nature preservation area and a previously exploited area. The flies were caught by aspiration on tree trunks. Samples of sand flies were dissected for parasitological examination. In the site that suffered a harvest, a larger number of individuals was caught before the selective extraction of timber, showing significant difference in relation to the number of individuals and their flagellate infection rates after the logging. The other two areas did not show differences among their sand fly populations. This fact is suggestive of a fauna sensitive to the environmental alterations associated with selective logging. PMID:17710304

  1. The abundance and diversity of legume-nodulating rhizobia in 28-year-old plantations of tropical, subtropical, and exotic tree species: a case study from the Forest Reserve of Bandia, Senegal.

    PubMed

    Sene, Godar; Thiao, Mansour; Samba-Mbaye, Ramatoulaye; Khasa, Damase; Kane, Aboubacry; Mbaye, Mame Samba; Beaulieu, Marie-Ève; Manga, Anicet; Sylla, Samba Ndao

    2013-01-01

    Several fast-growing and multipurpose tree species have been widely used in West Africa to both reverse the tendency of land degradation and restore soil productivity. Although beneficial effects have been reported on soil stabilization, there still remains a lack of information about their impact on soil microorganisms. Our investigation has been carried out in exotic and native tree plantations of 28 years and aimed to survey and compare the abundance and genetic diversity of natural legume-nodulating rhizobia (LNR). The study of LNR is supported by the phylogenetic analysis which clustered the isolates into three genera: Bradyrhizobium, Mesorhizobium, and Sinorhizobium. The results showed close positive correlations between the sizes of LNR populations estimated both in the dry and rainy seasons and the presence of legume tree hosts. There were significant increases in Rhizobium spp. population densities in response to planting with Acacia spp., and high genetic diversities and richness of genotypes were fittest in these tree plantations. This suggests that enrichment of soil Rhizobium spp. populations is host specific. The results indicated also that species of genera Mesorhizobium and Sinorhizobium were lacking in plantations of non-host species. By contrast, there was a widespread distribution of Bradyrhizobium spp. strains across the tree plantations, with no evident specialization in regard to plantation type. Finally, the study provides information about the LNR communities associated with a range of old tree plantations and some aspects of their relationships to soil factors, which may facilitate the management of man-made forest systems that target ecosystem rehabilitation and preservation of soil biota. PMID:22864803

  2. STRAW: Species TRee Analysis Web server

    PubMed Central

    Shaw, Timothy I.; Ruan, Zheng; Glenn, Travis C.; Liu, Liang

    2013-01-01

    The coalescent methods for species tree reconstruction are increasingly popular because they can accommodate coalescence and multilocus data sets. Herein, we present STRAW, a web server that offers workflows for reconstruction of phylogenies of species using three species tree methods—MP-EST, STAR and NJst. The input data are a collection of rooted gene trees (for STAR and MP-EST methods) or unrooted gene trees (for NJst). The output includes the estimated species tree, modified Robinson-Foulds distances between gene trees and the estimated species tree and visualization of trees to compare gene trees with the estimated species tree. The web sever is available at http://bioinformatics.publichealth.uga.edu/SpeciesTreeAnalysis/. PMID:23661681

  3. The Inference of Gene Trees with Species Trees

    PubMed Central

    Szöllősi, Gergely J.; Tannier, Eric; Daubin, Vincent; Boussau, Bastien

    2015-01-01

    This article reviews the various models that have been used to describe the relationships between gene trees and species trees. Molecular phylogeny has focused mainly on improving models for the reconstruction of gene trees based on sequence alignments. Yet, most phylogeneticists seek to reveal the history of species. Although the histories of genes and species are tightly linked, they are seldom identical, because genes duplicate, are lost or horizontally transferred, and because alleles can coexist in populations for periods that may span several speciation events. Building models describing the relationship between gene and species trees can thus improve the reconstruction of gene trees when a species tree is known, and vice versa. Several approaches have been proposed to solve the problem in one direction or the other, but in general neither gene trees nor species trees are known. Only a few studies have attempted to jointly infer gene trees and species trees. These models account for gene duplication and loss, transfer or incomplete lineage sorting. Some of them consider several types of events together, but none exists currently that considers the full repertoire of processes that generate gene trees along the species tree. Simulations as well as empirical studies on genomic data show that combining gene tree–species tree models with models of sequence evolution improves gene tree reconstruction. In turn, these better gene trees provide a more reliable basis for studying genome evolution or reconstructing ancestral chromosomes and ancestral gene sequences. We predict that gene tree–species tree methods that can deal with genomic data sets will be instrumental to advancing our understanding of genomic evolution. PMID:25070970

  4. Multiple peaks of species abundance distributions induced by sparse interactions.

    PubMed

    Obuchi, Tomoyuki; Kabashima, Yoshiyuki; Tokita, Kei

    2016-08-01

    We investigate the replicator dynamics with "sparse" symmetric interactions which represent specialist-specialist interactions in ecological communities. By considering a large self-interaction u, we conduct a perturbative expansion which manifests that the nature of the interactions has a direct impact on the species abundance distribution. The central results are all species coexistence in a realistic range of the model parameters and that a certain discrete nature of the interactions induces multiple peaks in the species abundance distribution, providing the possibility of theoretically explaining multiple peaks observed in various field studies. To get more quantitative information, we also construct a non-perturbative theory which becomes exact on tree-like networks if all the species coexist, providing exact critical values of u below which extinct species emerge. Numerical simulations in various different situations are conducted and they clarify the robustness of the presented mechanism of all species coexistence and multiple peaks in the species abundance distributions. PMID:27627322

  5. Non-phytoseiid Mesostigmata within citrus orchards in Florida: species distribution, relative and seasonal abundance within trees, associated vines and ground cover plants and additional collection records of mites in citrus orchards.

    PubMed

    Childers, Carl C; Ueckermann, Eduard A

    2015-03-01

    Seven citrus orchards on reduced- to no-pesticide spray programs in central and south central Florida were sampled for non-phytoseiid mesostigmatid mites. Inner and outer canopy leaves, fruits, twigs and trunk scrapings were sampled monthly between August 1994 and January 1996. Open flowers were sampled in March from five of the sites. A total of 431 samples from one or more of 82 vine or ground cover plants were sampled monthly in five of the seven orchards. Two of the seven orchards (Mixon I and II) were on full herbicide programs and vines and ground cover plants were absent. A total of 2,655 mites (26 species) within the families: Ascidae, Blattisociidae, Laelapidae, Macrochelidae, Melicharidae, Pachylaelapidae and Parasitidae were identified. A total of 685 mites in the genus Asca (nine species: family Ascidae) were collected from within tree samples, 79 from vine or ground cover plants. Six species of Blattisociidae were collected: Aceodromus convolvuli, Blattisocius dentriticus, B. keegani, Cheiroseius sp. near jamaicensis, Lasioseius athiashenriotae and L. dentatus. A total of 485 Blattisociidae were collected from within tree samples compared with 167 from vine or ground cover plants. Low numbers of Laelapidae and Macrochelidae were collected from within tree samples. One Zygoseius furciger (Pachylaelapidae) was collected from Eleusine indica. Four species of Melicharidae were identified from 34 mites collected from within tree samples and 1,190 from vine or ground cover plants: Proctolaelaps lobatus was the most abundant species with 1,177 specimens collected from seven ground cover plants. One Phorytocarpais fimetorum (Parasitidae) was collected from inner leaves and four from twigs. Species of Ascidae, Blattisociidae, Melicharidae, Laelapidae and Pachylaelapidae were collected from 31 of the 82 vine or ground cover plants sampled, representing only a small fraction of the total number of Phytoseiidae collected from the same plants. Including the

  6. Coalescent Histories for Lodgepole Species Trees.

    PubMed

    Disanto, Filippo; Rosenberg, Noah A

    2015-10-01

    Coalescent histories are combinatorial structures that describe for a given gene tree and species tree the possible lists of branches of the species tree on which the gene tree coalescences take place. Properties of the number of coalescent histories for gene trees and species trees affect a variety of probabilistic calculations in mathematical phylogenetics. Exact and asymptotic evaluations of the number of coalescent histories, however, are known only in a limited number of cases. Here we introduce a particular family of species trees, the lodgepole species trees (λn)n ≥ 0, in which tree λn has m = 2n+1 taxa. We determine the number of coalescent histories for the lodgepole species trees, in the case that the gene tree matches the species tree, showing that this number grows with m!! in the number of taxa m. This computation demonstrates the existence of tree families in which the growth in the number of coalescent histories is faster than exponential. Further, it provides a substantial improvement on the lower bound for the ratio of the largest number of matching coalescent histories to the smallest number of matching coalescent histories for trees with m taxa, increasing a previous bound of [Formula: see text] to [Formula: see text]. We discuss the implications of our enumerative results for phylogenetic computations. PMID:25973633

  7. Exact solutions for species tree inference from discordant gene trees.

    PubMed

    Chang, Wen-Chieh; Górecki, Paweł; Eulenstein, Oliver

    2013-10-01

    Phylogenetic analysis has to overcome the grant challenge of inferring accurate species trees from evolutionary histories of gene families (gene trees) that are discordant with the species tree along whose branches they have evolved. Two well studied approaches to cope with this challenge are to solve either biologically informed gene tree parsimony (GTP) problems under gene duplication, gene loss, and deep coalescence, or the classic RF supertree problem that does not rely on any biological model. Despite the potential of these problems to infer credible species trees, they are NP-hard. Therefore, these problems are addressed by heuristics that typically lack any provable accuracy and precision. We describe fast dynamic programming algorithms that solve the GTP problems and the RF supertree problem exactly, and demonstrate that our algorithms can solve instances with data sets consisting of as many as 22 taxa. Extensions of our algorithms can also report the number of all optimal species trees, as well as the trees themselves. To better asses the quality of the resulting species trees that best fit the given gene trees, we also compute the worst case species trees, their numbers, and optimization score for each of the computational problems. Finally, we demonstrate the performance of our exact algorithms using empirical and simulated data sets, and analyze the quality of heuristic solutions for the studied problems by contrasting them with our exact solutions. PMID:24131054

  8. The effects of urban warming on herbivore abundance and street tree condition.

    PubMed

    Dale, Adam G; Frank, Steven D

    2014-01-01

    Trees are essential to urban habitats because they provide services that benefit the environment and improve human health. Unfortunately, urban trees often have more herbivorous insect pests than rural trees but the mechanisms and consequences of these infestations are not well documented. Here, we examine how temperature affects the abundance of a scale insect, Melanaspis tenebricosa (Comstock) (Hemiptera: Diaspididae), on one of the most commonly planted street trees in the eastern U.S. Next, we examine how both pest abundance and temperature are associated with water stress, growth, and condition of 26 urban street trees. Although trees in the warmest urban sites grew the most, they were more water stressed and in worse condition than trees in cooler sites. Our analyses indicate that visible declines in tree condition were best explained by scale-insect infestation rather than temperature. To test the broader relevance of these results, we extend our analysis to a database of more than 2700 Raleigh, US street trees. Plotting these trees on a Landsat thermal image of Raleigh, we found that warmer sites had over 70% more trees in poor condition than those in cooler sites. Our results support previous studies linking warmer urban habitats to greater pest abundance and extend this association to show its effect on street tree condition. Our results suggest that street tree condition and ecosystem services may decline as urban expansion and global warming exacerbate the urban heat island effect. Although our non-probability sampling method limits our scope of inference, our results present a gloomy outlook for urban forests and emphasize the need for management tools. Existing urban tree inventories and thermal maps could be used to identify species that would be most suitable for urban conditions. PMID:25054326

  9. The Effects of Urban Warming on Herbivore Abundance and Street Tree Condition

    PubMed Central

    Dale, Adam G.; Frank, Steven D.

    2014-01-01

    Trees are essential to urban habitats because they provide services that benefit the environment and improve human health. Unfortunately, urban trees often have more herbivorous insect pests than rural trees but the mechanisms and consequences of these infestations are not well documented. Here, we examine how temperature affects the abundance of a scale insect, Melanaspis tenebricosa (Comstock) (Hemiptera: Diaspididae), on one of the most commonly planted street trees in the eastern U.S. Next, we examine how both pest abundance and temperature are associated with water stress, growth, and condition of 26 urban street trees. Although trees in the warmest urban sites grew the most, they were more water stressed and in worse condition than trees in cooler sites. Our analyses indicate that visible declines in tree condition were best explained by scale-insect infestation rather than temperature. To test the broader relevance of these results, we extend our analysis to a database of more than 2700 Raleigh, US street trees. Plotting these trees on a Landsat thermal image of Raleigh, we found that warmer sites had over 70% more trees in poor condition than those in cooler sites. Our results support previous studies linking warmer urban habitats to greater pest abundance and extend this association to show its effect on street tree condition. Our results suggest that street tree condition and ecosystem services may decline as urban expansion and global warming exacerbate the urban heat island effect. Although our non-probability sampling method limits our scope of inference, our results present a gloomy outlook for urban forests and emphasize the need for management tools. Existing urban tree inventories and thermal maps could be used to identify species that would be most suitable for urban conditions. PMID:25054326

  10. Clonal growth and plant species abundance

    PubMed Central

    Herben, Tomáš; Nováková, Zuzana; Klimešová, Jitka

    2014-01-01

    Background and Aims Both regional and local plant abundances are driven by species' dispersal capacities and their abilities to exploit new habitats and persist there. These processes are affected by clonal growth, which is difficult to evaluate and compare across large numbers of species. This study assessed the influence of clonal reproduction on local and regional abundances of a large set of species and compared the predictive power of morphologically defined traits of clonal growth with data on actual clonal growth from a botanical garden. The role of clonal growth was compared with the effects of seed reproduction, habitat requirements and growth, proxied both by LHS (leaf–height–seed) traits and by actual performance in the botanical garden. Methods Morphological parameters of clonal growth, actual clonal reproduction in the garden and LHS traits (leaf-specific area – height – seed mass) were used as predictors of species abundance, both regional (number of species records in the Czech Republic) and local (mean species cover in vegetation records) for 836 perennial herbaceous species. Species differences in habitat requirements were accounted for by classifying the dataset by habitat type and also by using Ellenberg indicator values as covariates. Key Results After habitat differences were accounted for, clonal growth parameters explained an important part of variation in species abundance, both at regional and at local levels. At both levels, both greater vegetative growth in cultivation and greater lateral expansion trait values were correlated with higher abundance. Seed reproduction had weaker effects, being positive at the regional level and negative at the local level. Conclusions Morphologically defined traits are predictive of species abundance, and it is concluded that simultaneous investigation of several such traits can help develop hypotheses on specific processes (e.g. avoidance of self-competition, support of offspring) potentially

  11. Lianas suppress seedling growth and survival of 14 tree species in a Panamanian tropical forest.

    PubMed

    Martínez-Izquierdo, Laura; García, María M; Powers, Jennifer S; Schnitzer, Stefan A

    2016-01-01

    Lianas are a common plant growth form in tropical forests, where they compete intensely with trees, decreasing tree recruitment, growth, and survival. If the detrimental effects of lianas vary significantly with tree species identity, as is often assumed, then lianas may influence tree species diversity and community composition. Furthermore, recent studies have shown that liana abundance and biomass are increasing relative to trees in neotropical forests, which will likely magnify the detrimental effects of lianas and may ultimately alter tree species diversity, relative abundances, and community composition. Few studies, however, have tested the responses of multiple tree species to the presence of lianas in robust, well-replicated experiments. We tested the hypotheses that lianas reduce tree seedling growth and survival, and that the effect of lianas varies with tree species identity. We used a large-scale liana removal experiment in Central Panama in which we planted 14 replicate seedlings of 14 different tree species that varied in shade tolerance in each of 16 80 x 80 m plots (eight liana-removal and eight unmanipulated controls; 3136 total seedlings). Over a nearly two-yr period, we found that tree seedlings survived 75% more, grew 300% taller, and had twice the aboveground biomass in liana-removal plots than seedlings in control plots, consistent with strong competition between lianas and tree seedlings. There were no significant differences in the response of tree species to liana competition (i.e., there was no species by treatment interaction), indicating that lianas had a similar negative effect on all 14 tree species. Furthermore, the effect of lianas did not vary with tree species shade tolerance classification, suggesting that the liana effect was not solely based on light. Based on these findings, recently observed increases in liana abundance in neotropical forests will substantially reduce tree regeneration, but will not significantly alter

  12. Reconciliation with Non-Binary Species Trees

    PubMed Central

    Vernot, Benjamin; Stolzer, Maureen; Goldman, Aiton

    2008-01-01

    Abstract Reconciliation extracts information from the topological incongruence between gene and species trees to infer duplications and losses in the history of a gene family. The inferred duplication-loss histories provide valuable information for a broad range of biological applications, including ortholog identification, estimating gene duplication times, and rooting and correcting gene trees. While reconciliation for binary trees is a tractable and well studied problem, there are no algorithms for reconciliation with non-binary species trees. Yet a striking proportion of species trees are non-binary. For example, 64% of branch points in the NCBI taxonomy have three or more children. When applied to non-binary species trees, current algorithms overestimate the number of duplications because they cannot distinguish between duplication and incomplete lineage sorting. We present the first algorithms for reconciling binary gene trees with non-binary species trees under a duplication-loss parsimony model. Our algorithms utilize an efficient mapping from gene to species trees to infer the minimum number of duplications in O(|VG| · (kS + hS)) time, where |VG| is the number of nodes in the gene tree, hS is the height of the species tree and kS is the size of its largest polytomy. We present a dynamic programming algorithm which also minimizes the total number of losses. Although this algorithm is exponential in the size of the largest polytomy, it performs well in practice for polytomies with outdegree of 12 or less. We also present a heuristic which estimates the minimal number of losses in polynomial time. In empirical tests, this algorithm finds an optimal loss history 99% of the time. Our algorithms have been implemented in Notung, a robust, production quality, tree-fitting program, which provides a graphical user interface for exploratory analysis and also supports automated, high-throughput analysis of large data sets. PMID:18808330

  13. Species Abundance Patterns in Complex Evolutionary Dynamics

    NASA Astrophysics Data System (ADS)

    Tokita, Kei

    2004-10-01

    An analytic theory of species abundance patterns (SAPs) in biological networks is presented. The theory is based on multispecies replicator dynamics equivalent to the Lotka-Volterra equation, with diverse interspecies interactions. Various SAPs observed in nature are derived from a single parameter. The abundance distribution is formed like a widely observed left-skewed lognormal distribution. As the model has a general form, the result can be applied to similar patterns in other complex biological networks, e.g., gene expression.

  14. Species Tree Inference Using a Mixture Model.

    PubMed

    Ullah, Ikram; Parviainen, Pekka; Lagergren, Jens

    2015-09-01

    Species tree reconstruction has been a subject of substantial research due to its central role across biology and medicine. A species tree is often reconstructed using a set of gene trees or by directly using sequence data. In either of these cases, one of the main confounding phenomena is the discordance between a species tree and a gene tree due to evolutionary events such as duplications and losses. Probabilistic methods can resolve the discordance by coestimating gene trees and the species tree but this approach poses a scalability problem for larger data sets. We present MixTreEM-DLRS: A two-phase approach for reconstructing a species tree in the presence of gene duplications and losses. In the first phase, MixTreEM, a novel structural expectation maximization algorithm based on a mixture model is used to reconstruct a set of candidate species trees, given sequence data for monocopy gene families from the genomes under study. In the second phase, PrIME-DLRS, a method based on the DLRS model (Åkerborg O, Sennblad B, Arvestad L, Lagergren J. 2009. Simultaneous Bayesian gene tree reconstruction and reconciliation analysis. Proc Natl Acad Sci U S A. 106(14):5714-5719), is used for selecting the best species tree. PrIME-DLRS can handle multicopy gene families since DLRS, apart from modeling sequence evolution, models gene duplication and loss using a gene evolution model (Arvestad L, Lagergren J, Sennblad B. 2009. The gene evolution model and computing its associated probabilities. J ACM. 56(2):1-44). We evaluate MixTreEM-DLRS using synthetic and biological data, and compare its performance with a recent genome-scale species tree reconstruction method PHYLDOG (Boussau B, Szöllősi GJ, Duret L, Gouy M, Tannier E, Daubin V. 2013. Genome-scale coestimation of species and gene trees. Genome Res. 23(2):323-330) as well as with a fast parsimony-based algorithm Duptree (Wehe A, Bansal MS, Burleigh JG, Eulenstein O. 2008. Duptree: a program for large-scale phylogenetic

  15. How selection structures species abundance distributions

    PubMed Central

    Magurran, Anne E.; Henderson, Peter A.

    2012-01-01

    How do species divide resources to produce the characteristic species abundance distributions seen in nature? One way to resolve this problem is to examine how the biomass (or capacity) of the spatial guilds that combine to produce an abundance distribution is allocated among species. Here we argue that selection on body size varies across guilds occupying spatially distinct habitats. Using an exceptionally well-characterized estuarine fish community, we show that biomass is concentrated in large bodied species in guilds where habitat structure provides protection from predators, but not in those guilds associated with open habitats and where safety in numbers is a mechanism for reducing predation risk. We further demonstrate that while there is temporal turnover in the abundances and identities of species that comprise these guilds, guild rank order is conserved across our 30-year time series. These results demonstrate that ecological communities are not randomly assembled but can be decomposed into guilds where capacity is predictably allocated among species. PMID:22787020

  16. Reconciliation of Gene and Species Trees

    PubMed Central

    Rusin, L. Y.; Lyubetskaya, E. V.; Gorbunov, K. Y.; Lyubetsky, V. A.

    2014-01-01

    The first part of the paper briefly overviews the problem of gene and species trees reconciliation with the focus on defining and algorithmic construction of the evolutionary scenario. Basic ideas are discussed for the aspects of mapping definitions, costs of the mapping and evolutionary scenario, imposing time scales on a scenario, incorporating horizontal gene transfers, binarization and reconciliation of polytomous trees, and construction of species trees and scenarios. The review does not intend to cover the vast diversity of literature published on these subjects. Instead, the authors strived to overview the problem of the evolutionary scenario as a central concept in many areas of evolutionary research. The second part provides detailed mathematical proofs for the solutions of two problems: (i) inferring a gene evolution along a species tree accounting for various types of evolutionary events and (ii) trees reconciliation into a single species tree when only gene duplications and losses are allowed. All proposed algorithms have a cubic time complexity and are mathematically proved to find exact solutions. Solving algorithms for problem (ii) can be naturally extended to incorporate horizontal transfers, other evolutionary events, and time scales on the species tree. PMID:24800245

  17. Attenuation of species abundance distributions by sampling.

    PubMed

    Shimadzu, Hideyasu; Darnell, Ross

    2015-04-01

    Quantifying biodiversity aspects such as species presence/ absence, richness and abundance is an important challenge to answer scientific and resource management questions. In practice, biodiversity can only be assessed from biological material taken by surveys, a difficult task given limited time and resources. A type of random sampling, or often called sub-sampling, is a commonly used technique to reduce the amount of time and effort for investigating large quantities of biological samples. However, it is not immediately clear how (sub-)sampling affects the estimate of biodiversity aspects from a quantitative perspective. This paper specifies the effect of (sub-)sampling as attenuation of the species abundance distribution (SAD), and articulates how the sampling bias is induced to the SAD by random sampling. The framework presented also reveals some confusion in previous theoretical studies. PMID:26064626

  18. Attenuation of species abundance distributions by sampling

    PubMed Central

    Shimadzu, Hideyasu; Darnell, Ross

    2015-01-01

    Quantifying biodiversity aspects such as species presence/ absence, richness and abundance is an important challenge to answer scientific and resource management questions. In practice, biodiversity can only be assessed from biological material taken by surveys, a difficult task given limited time and resources. A type of random sampling, or often called sub-sampling, is a commonly used technique to reduce the amount of time and effort for investigating large quantities of biological samples. However, it is not immediately clear how (sub-)sampling affects the estimate of biodiversity aspects from a quantitative perspective. This paper specifies the effect of (sub-)sampling as attenuation of the species abundance distribution (SAD), and articulates how the sampling bias is induced to the SAD by random sampling. The framework presented also reveals some confusion in previous theoretical studies. PMID:26064626

  19. Species richness, equitability, and abundance of ants in disturbed landscapes

    USGS Publications Warehouse

    Graham, J.H.; Krzysik, A.J.; Kovacic, D.A.; Duda, J.J.; Freeman, D.C.; Emlen, J.M.; Zak, J.C.; Long, W.R.; Wallace, M.P.; Chamberlin-Graham, C.; Nutter, J.P.; Balbach, H.E.

    2009-01-01

    Ants are used as indicators of environmental change in disturbed landscapes, often without adequate understanding of their response to disturbance. Ant communities in the southeastern United States displayed a hump-backed species richness curve against an index of landscape disturbance. Forty sites at Fort Benning, in west-central Georgia, covered a spectrum of habitat disturbance (military training and fire) in upland forest. Sites disturbed by military training had fewer trees, less canopy cover, more bare ground, and warmer, more compact soils with shallower A-horizons. We sampled ground-dwelling ants with pitfall traps, and measured 15 habitat variables related to vegetation and soil. Ant species richness was greatest with a relative disturbance of 43%, but equitability was greatest with no disturbance. Ant abundance was greatest with a relative disturbance of 85%. High species richness at intermediate disturbance was associated with greater within-site spatial heterogeneity. Species richness was also associated with intermediate values of the normalized difference vegetation index (NDVI), a correlate of net primary productivity (NPP). Available NPP (the product of NDVI and the fraction of days that soil temperature exceeded 25 ??C), however, was positively correlated with species richness, though not with ant abundance. Species richness was unrelated to soil texture, total ground cover, and fire frequency. Ant species richness and equitability are potential state indicators of the soil arthropod community. Moreover, equitability can be used to monitor ecosystem change. ?? 2008 Elsevier Ltd.

  20. Species composition and abundance of Brevipalpus spp. on different citrus species in Mexican orchards.

    PubMed

    Salinas-Vargas, D; Santillán-Galicia, M T; Valdez-Carrasco, J; Mora-Aguilera, G; Atanacio-Serrano, Y; Romero-Pescador, P

    2013-08-01

    We studied the abundance of Brevipalpus spp. in citrus orchards in the Mexican states of Yucatan, Quintana Roo and Campeche. Mites were collected from 100 trees containing a mixture of citrus species where sweet orange was always the main species. Eight collections were made at each location from February 2010 to February 2011. Mites from the genus Brevipalpus were separated from other mites surveyed and their abundance and relationships with the different citrus species were quantified throughout the collection period. A subsample of 25% of the total Brevipalpus mites collected were identified to species level and the interaction of mite species and citrus species were described. Brevipalpus spp. were present on all collection dates and their relative abundance was similar on all citrus species studies. The smallest number of mites collected was during the rainy season. Brevipalpus phoenicis (Geijskes) and Brevipalpus californicus (Banks) were the only two species present and they were found in all locations except Campeche, where only B. phoenicis was present. Yucatan and Campeche are at greater risk of leprosis virus transmission than Quintana Roo because the main vector, B. phoenicis, was more abundant than B. californicus. The implications of our results for the design of more accurate sampling and control methods for Brevipalpus spp. are discussed. PMID:23949863

  1. Pushing the pace of tree species migration.

    PubMed

    Lazarus, Eli D; McGill, Brian J

    2014-01-01

    Plants and animals have responded to past climate changes by migrating with habitable environments, sometimes shifting the boundaries of their geographic ranges by tens of kilometers per year or more. Species migrating in response to present climate conditions, however, must contend with landscapes fragmented by anthropogenic disturbance. We consider this problem in the context of wind-dispersed tree species. Mechanisms of long-distance seed dispersal make these species capable of rapid migration rates. Models of species-front migration suggest that even tree species with the capacity for long-distance dispersal will be unable to keep pace with future spatial changes in temperature gradients, exclusive of habitat fragmentation effects. Here we present a numerical model that captures the salient dynamics of migration by long-distance dispersal for a generic tree species. We then use the model to explore the possible effects of assisted colonization within a fragmented landscape under a simulated tree-planting scheme. Our results suggest that an assisted-colonization program could accelerate species-front migration rates enough to match the speed of climate change, but such a program would involve an environmental-sustainability intervention at a massive scale. PMID:25162663

  2. Pushing the Pace of Tree Species Migration

    PubMed Central

    Lazarus, Eli D.; McGill, Brian J.

    2014-01-01

    Plants and animals have responded to past climate changes by migrating with habitable environments, sometimes shifting the boundaries of their geographic ranges by tens of kilometers per year or more. Species migrating in response to present climate conditions, however, must contend with landscapes fragmented by anthropogenic disturbance. We consider this problem in the context of wind-dispersed tree species. Mechanisms of long-distance seed dispersal make these species capable of rapid migration rates. Models of species-front migration suggest that even tree species with the capacity for long-distance dispersal will be unable to keep pace with future spatial changes in temperature gradients, exclusive of habitat fragmentation effects. Here we present a numerical model that captures the salient dynamics of migration by long-distance dispersal for a generic tree species. We then use the model to explore the possible effects of assisted colonization within a fragmented landscape under a simulated tree-planting scheme. Our results suggest that an assisted-colonization program could accelerate species-front migration rates enough to match the speed of climate change, but such a program would involve an environmental-sustainability intervention at a massive scale. PMID:25162663

  3. Species abundance in a forest community in South China: A case of poisson lognormal distribution

    USGS Publications Warehouse

    Yin, Z.-Y.; Ren, H.; Zhang, Q.-M.; Peng, S.-L.; Guo, Q.-F.; Zhou, G.-Y.

    2005-01-01

    Case studies on Poisson lognormal distribution of species abundance have been rare, especially in forest communities. We propose a numerical method to fit the Poisson lognormal to the species abundance data at an evergreen mixed forest in the Dinghushan Biosphere Reserve, South China. Plants in the tree, shrub and herb layers in 25 quadrats of 20 m??20 m, 5 m??5 m, and 1 m??1 m were surveyed. Results indicated that: (i) for each layer, the observed species abundance with a similarly small median, mode, and a variance larger than the mean was reverse J-shaped and followed well the zero-truncated Poisson lognormal; (ii) the coefficient of variation, skewness and kurtosis of abundance, and two Poisson lognormal parameters (?? and ??) for shrub layer were closer to those for the herb layer than those for the tree layer; and (iii) from the tree to the shrub to the herb layer, the ?? and the coefficient of variation decreased, whereas diversity increased. We suggest that: (i) the species abundance distributions in the three layers reflects the overall community characteristics; (ii) the Poisson lognormal can describe the species abundance distribution in diverse communities with a few abundant species but many rare species; and (iii) 1/?? should be an alternative measure of diversity.

  4. Neutral theory and relative species abundance in ecology

    NASA Astrophysics Data System (ADS)

    Volkov, Igor; Banavar, Jayanth R.; Hubbell, Stephen P.; Maritan, Amos

    2003-08-01

    The theory of island biogeography asserts that an island or a local community approaches an equilibrium species richness as a result of the interplay between the immigration of species from the much larger metacommunity source area and local extinction of species on the island (local community). Hubbell generalized this neutral theory to explore the expected steady-state distribution of relative species abundance (RSA) in the local community under restricted immigration. Here we present a theoretical framework for the unified neutral theory of biodiversity and an analytical solution for the distribution of the RSA both in the metacommunity (Fisher's log series) and in the local community, where there are fewer rare species. Rare species are more extinction-prone, and once they go locally extinct, they take longer to re-immigrate than do common species. Contrary to recent assertions, we show that the analytical solution provides a better fit, with fewer free parameters, to the RSA distribution of tree species on Barro Colorado Island, Panama, than the lognormal distribution.

  5. Region effects influence local tree species diversity

    PubMed Central

    Ricklefs, Robert E.; He, Fangliang

    2016-01-01

    Global patterns of biodiversity reflect both regional and local processes, but the relative importance of local ecological limits to species coexistence, as influenced by the physical environment, in contrast to regional processes including species production, dispersal, and extinction, is poorly understood. Failure to distinguish regional influences from local effects has been due, in part, to sampling limitations at small scales, environmental heterogeneity within local or regional samples, and incomplete geographic sampling of species. Here, we use a global dataset comprising 47 forest plots to demonstrate significant region effects on diversity, beyond the influence of local climate, which together explain more than 92% of the global variation in local forest tree species richness. Significant region effects imply that large-scale processes shaping the regional diversity of forest trees exert influence down to the local scale, where they interact with local processes to determine the number of coexisting species. PMID:26733680

  6. Region effects influence local tree species diversity.

    PubMed

    Ricklefs, Robert E; He, Fangliang

    2016-01-19

    Global patterns of biodiversity reflect both regional and local processes, but the relative importance of local ecological limits to species coexistence, as influenced by the physical environment, in contrast to regional processes including species production, dispersal, and extinction, is poorly understood. Failure to distinguish regional influences from local effects has been due, in part, to sampling limitations at small scales, environmental heterogeneity within local or regional samples, and incomplete geographic sampling of species. Here, we use a global dataset comprising 47 forest plots to demonstrate significant region effects on diversity, beyond the influence of local climate, which together explain more than 92% of the global variation in local forest tree species richness. Significant region effects imply that large-scale processes shaping the regional diversity of forest trees exert influence down to the local scale, where they interact with local processes to determine the number of coexisting species. PMID:26733680

  7. Abundance of introduced species at home predicts abundance away in herbaceous communities

    USGS Publications Warehouse

    Firn, Jennifer; Moore, Joslin L.; MacDougall, Andrew S.; Borer, Elizabeth T.; Seabloom, Eric W.; HilleRisLambers, Janneke; Harpole, W. Stanley; Cleland, Elsa E.; Brown, Cynthia S.; Knops, Johannes M.H.; Prober, Suzanne M.; Pyke, David A.; Farrell, Kelly A.; Bakker, John D.; O'Halloran, Lydia R.; Adler, Peter B.; Collins, Scott L.; D'Antonio, Carla M.; Crawley, Michael J.; Wolkovich, Elizabeth M.; La Pierre, Kimberly J.; Melbourne, Brett A.; Hautier, Yann; Morgan, John W.; Leakey, Andrew D.B.; Kay, Adam; McCulley, Rebecca; Davies, Kendi F.; Stevens, Carly J.; Chu, Cheng-Jin; Holl, Karen D.; Klein, Julia A.; Fay, Phillip A.; Hagenah, Nicole; Kirkman, Kevin P.; Buckley, Yvonne M.

    2011-01-01

    Many ecosystems worldwide are dominated by introduced plant species, leading to loss of biodiversity and ecosystem function. A common but rarely tested assumption is that these plants are more abundant in introduced vs. native communities, because ecological or evolutionary-based shifts in populations underlie invasion success. Here, data for 26 herbaceous species at 39 sites, within eight countries, revealed that species abundances were similar at native (home) and introduced (away) sites - grass species were generally abundant home and away, while forbs were low in abundance, but more abundant at home. Sites with six or more of these species had similar community abundance hierarchies, suggesting that suites of introduced species are assembling similarly on different continents. Overall, we found that substantial changes to populations are not necessarily a pre-condition for invasion success and that increases in species abundance are unusual. Instead, abundance at home predicts abundance away, a potentially useful additional criterion for biosecurity programmes.

  8. Modeling species-abundance relationships in multi-species collections

    USGS Publications Warehouse

    Peng, S.; Yin, Z.; Ren, H.; Guo, Q.

    2003-01-01

    Species-abundance relationship is one of the most fundamental aspects of community ecology. Since Motomura first developed the geometric series model to describe the feature of community structure, ecologists have developed many other models to fit the species-abundance data in communities. These models can be classified into empirical and theoretical ones, including (1) statistical models, i.e., negative binomial distribution (and its extension), log-series distribution (and its extension), geometric distribution, lognormal distribution, Poisson-lognormal distribution, (2) niche models, i.e., geometric series, broken stick, overlapping niche, particulate niche, random assortment, dominance pre-emption, dominance decay, random fraction, weighted random fraction, composite niche, Zipf or Zipf-Mandelbrot model, and (3) dynamic models describing community dynamics and restrictive function of environment on community. These models have different characteristics and fit species-abundance data in various communities or collections. Among them, log-series distribution, lognormal distribution, geometric series, and broken stick model have been most widely used.

  9. Urbanization Level and Woodland Size Are Major Drivers of Woodpecker Species Richness and Abundance

    PubMed Central

    Myczko, Łukasz; Rosin, Zuzanna M.; Skórka, Piotr; Tryjanowski, Piotr

    2014-01-01

    Urbanization is a process globally responsible for loss of biodiversity and for biological homogenization. Urbanization may have a direct negative impact on species behaviour and indirect effects on species populations through alterations of their habitats, for example patch size and habitat quality. Woodpeckers are species potentially susceptible to urbanization. These birds are mostly forest specialists and the development of urban areas in former forests may be an important factor influencing their richness and abundance, but documented examples are rare. In this study we investigated how woodpeckers responded to changes in forest habitats as a consequence of urbanization, namely size and isolation of habitat patches, and other within-patch characteristics. We selected 42 woodland patches in a gradient from a semi-natural rural landscape to the city centre of Poznań (Western Poland) in spring 2010. Both species richness and abundance of woodpeckers correlated positively to woodland patch area and negatively to increasing urbanization. Abundance of woodpeckers was also positively correlated with shrub cover and percentage of deciduous tree species. Furthermore, species richness and abundance of woodpeckers were highest at moderate values of canopy openness. Ordination analyses confirmed that urbanization level and woodland patch area were variables contributing most to species abundance in the woodpecker community. Similar results were obtained in presence-absence models for particular species. Thus, to sustain woodpecker species within cities it is important to keep woodland patches large, multi-layered and rich in deciduous tree species. PMID:24740155

  10. Impact of gene family evolutionary histories on phylogenetic species tree inference by gene tree parsimony.

    PubMed

    Shi, Tao

    2016-03-01

    Complicated history of gene duplication and loss brings challenge to molecular phylogenetic inference, especially in deep phylogenies. However, phylogenomic approaches, such as gene tree parsimony (GTP), show advantage over some other approaches in its ability to use gene families with duplications. GTP searches the 'optimal' species tree by minimizing the total cost of biological events such as duplications, but accuracy of GTP and phylogenetic signal in the context of different gene families with distinct histories of duplication and loss are unclear. To evaluate how different evolutionary properties of different gene families can impact on species tree inference, 3900 gene families from seven angiosperms encompassing a wide range of gene content, lineage-specific expansions and contractions were analyzed. It was found that the gene content and total duplication number in a gene family strongly influence species tree inference accuracy, with the highest accuracy achieved at either very low or very high gene content (or duplication number) and lowest accuracy centered in intermediate gene content (or duplication number), as the relationship can fit a binomial regression. Besides, for gene families of similar level of average gene content, those with relatively higher lineage-specific expansion or duplication rates tend to show lower accuracy. Additional correlation tests support that high accuracy for those gene families with large gene content may rely on abundant ancestral copies to provide many subtrees to resolve conflicts, whereas high accuracy for single or low copy gene families are just subject to sequence substitution per se. Very low accuracy reached by gene families of intermediate gene content or duplication number can be due to insufficient subtrees to resolve the conflicts from loss of alternative copies. As these evolutionary properties can significantly influence species tree accuracy, I discussed the potential weighting of the duplication cost by

  11. A tree species inventory over Europe

    NASA Astrophysics Data System (ADS)

    Ambelas Skjøth, C.; Geels, C.; Hvidberg, M.; Hertel, O.; Brandt, J.; Frohn, L. M.; Hansen, K. M.; Hedegaard, G. B.; Christensen, J. H.; Moseholm, L.

    2009-04-01

    Atmospheric transport models are used in studies of atmospheric chemistry as well as aerobiology. Atmospheric transport models in general needs accurate emissions inventories, which includes biogenic emissions such as Volatile Organic Compounds (VOCs) and pollen. Trees are important VOC and pollen sources and a needed requirement is specie distribution which takes into account important species such as Betula and Alnus. We present here a detailed tree species inventory covering Europe, parts of Africa and parts of Asia. Forest inventories have been obtained for each European country, parts of Asia and parts of Africa. The national inventories vary with respect to number of species as well as the number of sub-regions each nation is divided into. The inventories are therefore harmonised within a GIS system and afterwards gridded to the model grid defined by the EMEP model: 50 km x 50 km. The inventory is designed to be used with existing land-use data, which separates forest cover into broad leaved, mixed and conifer forests. This will be exemplified by using two different remote sensing products with different grid resolution such as GLC2000 and CLC2000 in selected areas. The final inventory includes 16 conifer species and 23 broadleaved species that are important for biogenic VOCs or pollen emission calculations. For example: Oak (Quercus), poplar (Populus), pines (Pinus), spruce (Picea), birch (Betula) and alder (Alnus). 774 regions with forest inventories are included, mainly on sub-national level. The coverage of each specie ranges from national to European scale, where the latter includes VOC and allergy relevant species such as Quercus, Alnus and Betula. The inventory is gridded to the model grid defined by the EMEP model, which is also the basis for many emissions inventories throughout Europe. The inventory is therefore prepared for easy implementation into atmospheric transport models by providing an extension to already applied land use data such as the

  12. ABUNDANT OR RARE? A HYBRID APPROACH FOR DETERMINING SPECIES RELATIVE ABUNDANCE AT AN ECOREGOIONAL SCALE - 2014

    EPA Science Inventory

    Everyone knows what abundant and rare species are, but quantifying the concept proves elusive. As part of an EPA/USGS project to assess near-coastal species vulnerability to climate change affects, we designed a hybrid approach to determine species relative abundance at an ecoreg...

  13. ABUNDANT OR RARE? A HYBRID APPROACH FOR DETERMINING SPECIES RELATIVE ABUNDANCE AT AN ECOREGOIONAL SCALE

    EPA Science Inventory

    Everyone knows what abundant and rare species are, but quantifying the concept proves elusive. As part of an EPA/USGS project to assess near-coastal species vulnerability to climate change affects, we designed a hybrid approach to determine species relative abundance at an ecoreg...

  14. Reconstruction of Pacific salmon abundance from riparian tree-ring growth.

    PubMed

    Drake, D C; Naiman, Robert J

    2007-07-01

    We use relationships between modern Pacific salmon (Oncorhynchus spp.) escapement (migrating adults counted at weirs or dams) and riparian tree-ring growth to reconstruct the abundance of stream-spawning salmon over 150-350 years. After examining nine sites, we produced reconstructions for five mid-order rivers and four salmon species over a large geographic range in the Pacific Northwest: chinook (O. tschwatcha) in the Umpqua River, Oregon, USA; sockeye (O. nerka) in Drinkwater Creek, British Columbia, Canada; pink (O. gorbuscha) in Sashin Creek, southeastern Alaska, USA; chum (O. keta) in Disappearance Creek, southeastern Alaska, USA; and pink and chum in the Kadashan River, southeastern Alaska, USA. We first derived stand-level, non-climatic growth chronologies from riparian trees using standard dendroecology methods and differencing. When the chronologies were compared to 18-55 years of adult salmon escapement we detected positive, significant correlations at five of the nine sites. Regression models relating escapement to tree-ring growth at the five sites were applied to the differenced chronologies to reconstruct salmon abundance. Each reconstruction contains unique patterns characteristic of the site and salmon species. Reconstructions were validated by comparison to local histories (e.g., construction of dams and salmon canneries) and regional fisheries data such as salmon landings and aerial surveys and the Pacific Decadal Oscillation climate index. The reconstructions capture lower-frequency cycles better than extremes and are most useful for determination and comparison of relative abundance, cycles, and the effects of interventions. Reconstructions show lower population cycle maxima in both Umpqua River chinook and Sashin Creek pink salmon in recent decades. The Drinkwater Creek reconstruction suggests that sockeye abundance since the mid-1990s has been 15-25% higher than at any time since 1850, while no long-term deviations from natural cycles are

  15. Predator Diversity and Abundance Provide Little Support for the Enemies Hypothesis in Forests of High Tree Diversity

    PubMed Central

    Schuldt, Andreas; Both, Sabine; Bruelheide, Helge; Härdtle, Werner; Schmid, Bernhard; Zhou, Hongzhang; Assmann, Thorsten

    2011-01-01

    Predatory arthropods can exert strong top-down control on ecosystem functions. However, despite extensive theory and experimental manipulations of predator diversity, our knowledge about relationships between plant and predator diversity—and thus information on the relevance of experimental findings—for species-rich, natural ecosystems is limited. We studied activity abundance and species richness of epigeic spiders in a highly diverse forest ecosystem in subtropical China across 27 forest stands which formed a gradient in tree diversity of 25–69 species per plot. The enemies hypothesis predicts higher predator abundance and diversity, and concomitantly more effective top-down control of food webs, with increasing plant diversity. However, in our study, activity abundance and observed species richness of spiders decreased with increasing tree species richness. There was only a weak, non-significant relationship with tree richness when spider richness was rarefied, i.e. corrected for different total abundances of spiders. Only foraging guild richness (i.e. the diversity of hunting modes) of spiders was positively related to tree species richness. Plant species richness in the herb layer had no significant effects on spiders. Our results thus provide little support for the enemies hypothesis—derived from studies in less diverse ecosystems—of a positive relationship between predator and plant diversity. Our findings for an important group of generalist predators question whether stronger top-down control of food webs can be expected in the more plant diverse stands of our forest ecosystem. Biotic interactions could play important roles in mediating the observed relationships between spider and plant diversity, but further testing is required for a more detailed mechanistic understanding. Our findings have implications for evaluating the way in which theoretical predictions and experimental findings of functional predator effects apply to species-rich forest

  16. Liana competition with tropical trees varies seasonally but not with tree species identity.

    PubMed

    Leonor, Alvarez-Cansino; Schnitzer, Stefan A; Reid, Joseph P; Powers, Jennifer S

    2015-01-01

    Lianas in tropical forests compete intensely with trees for above- and belowground resources and limit tree growth and regeneration. Liana competition with adult canopy trees may be particularly strong, and, if lianas compete more intensely with some tree species than others, they may influence tree species composition. We performed the first systematic, large-scale liana removal experiment to assess the competitive effects of lianas on multiple tropical tree species by measuring sap velocity and growth in a lowland tropical forest in Panama. Tree sap velocity increased 60% soon after liana removal compared to control trees, and tree diameter growth increased 25% after one year. Although tree species varied in their response to lianas, this variation was not significant, suggesting that lianas competed similarly with all tree species examined. The effect of lianas on tree sap velocity was particularly strong during the dry season, when soil moisture was low, suggesting that lianas compete intensely with trees for water. Under the predicted global change scenario of increased temperature and drought intensity, competition from lianas may become more prevalent in seasonal tropical forests, which, according to our data, should have a negative effect on most tropical tree species. PMID:26236888

  17. Is abundance a species attribute? An example with haematophagous ectoparasites.

    PubMed

    Krasnov, Boris R; Shenbrot, Georgy I; Khokhlova, Irina S; Poulin, Robert

    2006-11-01

    Population density is a fundamental property of a species and yet it varies among populations of the same species. The variation comes from the interplay between intrinsic features of a species that tend to produce repeatable density values across all populations of the same species and extrinsic environmental factors that differ among localities and thus tend to produce spatial variation in density. Is inter-population variation in density too large for density to be considered a true species character? We addressed this question using data on abundance (number of parasites per individual host, i.e. equivalent to density) of fleas ectoparasitic on small mammals. The data included samples of 548 flea populations, representing 145 flea species and obtained from 48 different geographical regions. Abundances of the same flea species on the same host species, but in different regions, were more similar to each other than expected by chance, and varied significantly among flea species, with 46% of the variation among samples accounted by differences between flea species. Thus, estimates of abundance are repeatable within the same flea species. The same repeatability was also observed, but to a lesser extent, across flea genera, tribes and subfamilies. Independently of the identity of the flea species, abundance values recorded on the same host species, or in the same geographical region, also showed significant statistical repeatability, though not nearly as strong as that associated with abundance values from the same flea species. There were also no strong indications that regional differences in abiotic variables were an important determinant of variation in abundance of a given flea species on a given host species. Abundance thus appears to be a true species trait in fleas, although it varies somewhat within bounds set by species-specific life history traits. PMID:16896773

  18. The probability of topological concordance of gene trees and species trees.

    PubMed

    Rosenberg, Noah A

    2002-03-01

    The concordance of gene trees and species trees is reconsidered in detail, allowing for samples of arbitrary size to be taken from the species. A sense of concordance for gene tree and species tree topologies is clarified, such that if the "collapsed gene tree" produced by a gene tree has the same topology as the species tree, the gene tree is said to be topologically concordant with the species tree. The term speciodendric is introduced to refer to genes whose trees are topologically concordant with species trees. For a given three-species topology, probabilities of each of the three possible collapsed gene tree topologies are given, as are probabilities of monophyletic concordance and concordance in the sense of N. Takahata (1989), Genetics 122, 957-966. Increasing the sample size is found to increase the probability of topological concordance, but a limit exists on how much the topological concordance probability can be increased. Suggested sample sizes beyond which this probability can be increased only minimally are given. The results are discussed in terms of implications for molecular studies of phylogenetics and speciation. PMID:11969392

  19. Model reduction for stochastic chemical systems with abundant species.

    PubMed

    Smith, Stephen; Cianci, Claudia; Grima, Ramon

    2015-12-01

    Biochemical processes typically involve many chemical species, some in abundance and some in low molecule numbers. We first identify the rate constant limits under which the concentrations of a given set of species will tend to infinity (the abundant species) while the concentrations of all other species remains constant (the non-abundant species). Subsequently, we prove that, in this limit, the fluctuations in the molecule numbers of non-abundant species are accurately described by a hybrid stochastic description consisting of a chemical master equation coupled to deterministic rate equations. This is a reduced description when compared to the conventional chemical master equation which describes the fluctuations in both abundant and non-abundant species. We show that the reduced master equation can be solved exactly for a number of biochemical networks involving gene expression and enzyme catalysis, whose conventional chemical master equation description is analytically impenetrable. We use the linear noise approximation to obtain approximate expressions for the difference between the variance of fluctuations in the non-abundant species as predicted by the hybrid approach and by the conventional chemical master equation. Furthermore, we show that surprisingly, irrespective of any separation in the mean molecule numbers of various species, the conventional and hybrid master equations exactly agree for a class of chemical systems. PMID:26646867

  20. Model reduction for stochastic chemical systems with abundant species

    NASA Astrophysics Data System (ADS)

    Smith, Stephen; Cianci, Claudia; Grima, Ramon

    2015-12-01

    Biochemical processes typically involve many chemical species, some in abundance and some in low molecule numbers. We first identify the rate constant limits under which the concentrations of a given set of species will tend to infinity (the abundant species) while the concentrations of all other species remains constant (the non-abundant species). Subsequently, we prove that, in this limit, the fluctuations in the molecule numbers of non-abundant species are accurately described by a hybrid stochastic description consisting of a chemical master equation coupled to deterministic rate equations. This is a reduced description when compared to the conventional chemical master equation which describes the fluctuations in both abundant and non-abundant species. We show that the reduced master equation can be solved exactly for a number of biochemical networks involving gene expression and enzyme catalysis, whose conventional chemical master equation description is analytically impenetrable. We use the linear noise approximation to obtain approximate expressions for the difference between the variance of fluctuations in the non-abundant species as predicted by the hybrid approach and by the conventional chemical master equation. Furthermore, we show that surprisingly, irrespective of any separation in the mean molecule numbers of various species, the conventional and hybrid master equations exactly agree for a class of chemical systems.

  1. Model reduction for stochastic chemical systems with abundant species

    SciTech Connect

    Smith, Stephen; Cianci, Claudia; Grima, Ramon

    2015-12-07

    Biochemical processes typically involve many chemical species, some in abundance and some in low molecule numbers. We first identify the rate constant limits under which the concentrations of a given set of species will tend to infinity (the abundant species) while the concentrations of all other species remains constant (the non-abundant species). Subsequently, we prove that, in this limit, the fluctuations in the molecule numbers of non-abundant species are accurately described by a hybrid stochastic description consisting of a chemical master equation coupled to deterministic rate equations. This is a reduced description when compared to the conventional chemical master equation which describes the fluctuations in both abundant and non-abundant species. We show that the reduced master equation can be solved exactly for a number of biochemical networks involving gene expression and enzyme catalysis, whose conventional chemical master equation description is analytically impenetrable. We use the linear noise approximation to obtain approximate expressions for the difference between the variance of fluctuations in the non-abundant species as predicted by the hybrid approach and by the conventional chemical master equation. Furthermore, we show that surprisingly, irrespective of any separation in the mean molecule numbers of various species, the conventional and hybrid master equations exactly agree for a class of chemical systems.

  2. Ecological niche structure and rangewide abundance patterns of species

    PubMed Central

    Martínez-Meyer, Enrique; Díaz-Porras, Daniel; Peterson, A. Townsend; Yáñez-Arenas, Carlos

    2013-01-01

    Spatial abundance patterns across species' ranges have attracted intense attention in macroecology and biogeography. One key hypothesis has been that abundance declines with geographical distance from the range centre, but tests of this idea have shown that the effect may occur indeed only in a minority of cases. We explore an alternative hypothesis: that species' abundances decline with distance from the centroid of the species' habitable conditions in environmental space (the ecological niche). We demonstrate consistent negative abundance–ecological distance relationships across all 11 species analysed (turtles to wolves), and that relationships in environmental space are consistently stronger than relationships in geographical space. PMID:23134784

  3. Exploring tree species signature using waveform LiDAR data

    NASA Astrophysics Data System (ADS)

    Zhou, T.; Popescu, S. C.; Krause, K.

    2015-12-01

    Successful classification of tree species with waveform LiDAR data would be of considerable value to estimate the biomass stocks and changes in forests. Current approaches emphasize converting the full waveform data into discrete points to get larger amount of parameters and identify tree species using several discrete-points variables. However, ignores intensity values and waveform shapes which convey important structural characteristics. The overall goal of this study was to employ the intensity and waveform shape of individual tree as the waveform signature to detect tree species. The data was acquired by the National Ecological Observatory Network (NEON) within 250*250 m study area located in San Joaquin Experimental Range. Specific objectives were to: (1) segment individual trees using the smoothed canopy height model (CHM) derived from discrete LiDAR points; (2) link waveform LiDAR with above individual tree boundaries to derive sample signatures of three tree species and use these signatures to discriminate tree species in a large area; and (3) compare tree species detection results from discrete LiDAR data and waveform LiDAR data. An overall accuracy of the segmented individual tree of more than 80% was obtained. The preliminary results show that compared with the discrete LiDAR data, the waveform LiDAR signature has a higher potential for accurate tree species classification.

  4. Changes in the Relative Abundance of Two Saccharomyces Species from Oak Forests to Wine Fermentations.

    PubMed

    Dashko, Sofia; Liu, Ping; Volk, Helena; Butinar, Lorena; Piškur, Jure; Fay, Justin C

    2016-01-01

    Saccharomyces cerevisiae and its sibling species Saccharomyces paradoxus are known to inhabit temperate arboreal habitats across the globe. Despite their sympatric distribution in the wild, S. cerevisiae is predominantly associated with human fermentations. The apparent ecological differentiation of these species is particularly striking in Europe where S. paradoxus is abundant in forests and S. cerevisiae is abundant in vineyards. However, ecological differences may be confounded with geographic differences in species abundance. To compare the distribution and abundance of these two species we isolated Saccharomyces strains from over 1200 samples taken from vineyard and forest habitats in Slovenia. We isolated numerous strains of S. cerevisiae and S. paradoxus, as well as a small number of Saccharomyces kudriavzevii strains, from both vineyard and forest environments. We find S. cerevisiae less abundant than S. paradoxus on oak trees both within and outside the vineyard, but more abundant on grapevines and associated substrates. Analysis of the uncultured microbiome shows, that both S. cerevisiae and S. paradoxus are rare species in soil and bark samples, but can be much more common in grape must. In contrast to S. paradoxus, European strains of S. cerevisiae have acquired multiple traits thought to be important for life in the vineyard and dominance of wine fermentations. We conclude, that S. cerevisiae and S. paradoxus currently share both vineyard and non-vineyard habitats in Slovenia and we discuss factors relevant to their global distribution and relative abundance. PMID:26941733

  5. Changes in the Relative Abundance of Two Saccharomyces Species from Oak Forests to Wine Fermentations

    PubMed Central

    Dashko, Sofia; Liu, Ping; Volk, Helena; Butinar, Lorena; Piškur, Jure; Fay, Justin C.

    2016-01-01

    Saccharomyces cerevisiae and its sibling species Saccharomyces paradoxus are known to inhabit temperate arboreal habitats across the globe. Despite their sympatric distribution in the wild, S. cerevisiae is predominantly associated with human fermentations. The apparent ecological differentiation of these species is particularly striking in Europe where S. paradoxus is abundant in forests and S. cerevisiae is abundant in vineyards. However, ecological differences may be confounded with geographic differences in species abundance. To compare the distribution and abundance of these two species we isolated Saccharomyces strains from over 1200 samples taken from vineyard and forest habitats in Slovenia. We isolated numerous strains of S. cerevisiae and S. paradoxus, as well as a small number of Saccharomyces kudriavzevii strains, from both vineyard and forest environments. We find S. cerevisiae less abundant than S. paradoxus on oak trees both within and outside the vineyard, but more abundant on grapevines and associated substrates. Analysis of the uncultured microbiome shows, that both S. cerevisiae and S. paradoxus are rare species in soil and bark samples, but can be much more common in grape must. In contrast to S. paradoxus, European strains of S. cerevisiae have acquired multiple traits thought to be important for life in the vineyard and dominance of wine fermentations. We conclude, that S. cerevisiae and S. paradoxus currently share both vineyard and non-vineyard habitats in Slovenia and we discuss factors relevant to their global distribution and relative abundance. PMID:26941733

  6. Percolation Theory for the Distribution and Abundance of Species

    NASA Astrophysics Data System (ADS)

    He, Fangliang; Hubbell, Stephen P.

    2003-11-01

    We develop and test new models that unify the mathematical relationships among the abundance of a species, the spatial dispersion of the species, the number of patches occupied by the species, the edge length of the occupied patches, and the scale on which the distribution of species is mapped. The models predict that species distributions will exhibit percolation critical thresholds, i.e., critical population abundances at which the fragmented patches (as measured by the number of patches and edge length) start to coalesce to form large patches.

  7. An estimate of the number of tropical tree species

    PubMed Central

    Slik, J. W. Ferry; Arroyo-Rodríguez, Víctor; Aiba, Shin-Ichiro; Alvarez-Loayza, Patricia; Alves, Luciana F.; Ashton, Peter; Balvanera, Patricia; Bastian, Meredith L.; Bellingham, Peter J.; van den Berg, Eduardo; Bernacci, Luis; da Conceição Bispo, Polyanna; Blanc, Lilian; Böhning-Gaese, Katrin; Boeckx, Pascal; Bongers, Frans; Boyle, Brad; Bradford, Matt; Brearley, Francis Q.; Breuer-Ndoundou Hockemba, Mireille; Bunyavejchewin, Sarayudh; Calderado Leal Matos, Darley; Castillo-Santiago, Miguel; Catharino, Eduardo L. M.; Chai, Shauna-Lee; Chen, Yukai; Colwell, Robert K.; Chazdon, Robin L.; Clark, Connie; Clark, David B.; Clark, Deborah A.; Culmsee, Heike; Damas, Kipiro; Dattaraja, Handanakere S.; Dauby, Gilles; Davidar, Priya; DeWalt, Saara J.; Doucet, Jean-Louis; Duque, Alvaro; Durigan, Giselda; Eichhorn, Karl A. O.; Eisenlohr, Pedro V.; Eler, Eduardo; Ewango, Corneille; Farwig, Nina; Feeley, Kenneth J.; Ferreira, Leandro; Field, Richard; de Oliveira Filho, Ary T.; Fletcher, Christine; Forshed, Olle; Franco, Geraldo; Fredriksson, Gabriella; Gillespie, Thomas; Gillet, Jean-François; Amarnath, Giriraj; Griffith, Daniel M.; Grogan, James; Gunatilleke, Nimal; Harris, David; Harrison, Rhett; Hector, Andy; Homeier, Jürgen; Imai, Nobuo; Itoh, Akira; Jansen, Patrick A.; Joly, Carlos A.; de Jong, Bernardus H. J.; Kartawinata, Kuswata; Kearsley, Elizabeth; Kelly, Daniel L.; Kenfack, David; Kessler, Michael; Kitayama, Kanehiro; Kooyman, Robert; Larney, Eileen; Laumonier, Yves; Laurance, Susan; Laurance, William F.; Lawes, Michael J.; do Amaral, Ieda Leao; Letcher, Susan G.; Lindsell, Jeremy; Lu, Xinghui; Mansor, Asyraf; Marjokorpi, Antti; Martin, Emanuel H.; Meilby, Henrik; Melo, Felipe P. L.; Metcalfe, Daniel J.; Medjibe, Vincent P.; Metzger, Jean Paul; Millet, Jerome; Mohandass, D.; Montero, Juan C.; de Morisson Valeriano, Márcio; Mugerwa, Badru; Nagamasu, Hidetoshi; Nilus, Reuben; Ochoa-Gaona, Susana; Onrizal; Page, Navendu; Parolin, Pia; Parren, Marc; Parthasarathy, Narayanaswamy; Paudel, Ekananda; Permana, Andrea; Piedade, Maria T. F.; Pitman, Nigel C. A.; Poorter, Lourens; Poulsen, Axel D.; Poulsen, John; Powers, Jennifer; Prasad, Rama C.; Puyravaud, Jean-Philippe; Razafimahaimodison, Jean-Claude; Reitsma, Jan; dos Santos, João Roberto; Roberto Spironello, Wilson; Romero-Saltos, Hugo; Rovero, Francesco; Rozak, Andes Hamuraby; Ruokolainen, Kalle; Rutishauser, Ervan; Saiter, Felipe; Saner, Philippe; Santos, Braulio A.; Santos, Fernanda; Sarker, Swapan K.; Satdichanh, Manichanh; Schmitt, Christine B.; Schöngart, Jochen; Schulze, Mark; Suganuma, Marcio S.; Sheil, Douglas; da Silva Pinheiro, Eduardo; Sist, Plinio; Stevart, Tariq; Sukumar, Raman; Sun, I.-Fang; Sunderland, Terry; Suresh, H. S.; Suzuki, Eizi; Tabarelli, Marcelo; Tang, Jangwei; Targhetta, Natália; Theilade, Ida; Thomas, Duncan W.; Tchouto, Peguy; Hurtado, Johanna; Valencia, Renato; van Valkenburg, Johan L. C. H.; Van Do, Tran; Vasquez, Rodolfo; Verbeeck, Hans; Adekunle, Victor; Vieira, Simone A.; Webb, Campbell O.; Whitfeld, Timothy; Wich, Serge A.; Williams, John; Wittmann, Florian; Wöll, Hannsjoerg; Yang, Xiaobo; Adou Yao, C. Yves; Yap, Sandra L.; Yoneda, Tsuyoshi; Zahawi, Rakan A.; Zakaria, Rahmad; Zang, Runguo; de Assis, Rafael L.; Garcia Luize, Bruno; Venticinque, Eduardo M.

    2015-01-01

    The high species richness of tropical forests has long been recognized, yet there remains substantial uncertainty regarding the actual number of tropical tree species. Using a pantropical tree inventory database from closed canopy forests, consisting of 657,630 trees belonging to 11,371 species, we use a fitted value of Fisher’s alpha and an approximate pantropical stem total to estimate the minimum number of tropical forest tree species to fall between ∼40,000 and ∼53,000, i.e., at the high end of previous estimates. Contrary to common assumption, the Indo-Pacific region was found to be as species-rich as the Neotropics, with both regions having a minimum of ∼19,000–25,000 tree species. Continental Africa is relatively depauperate with a minimum of ∼4,500–6,000 tree species. Very few species are shared among the African, American, and the Indo-Pacific regions. We provide a methodological framework for estimating species richness in trees that may help refine species richness estimates of tree-dependent taxa. PMID:26034279

  8. An estimate of the number of tropical tree species.

    PubMed

    Slik, J W Ferry; Arroyo-Rodríguez, Víctor; Aiba, Shin-Ichiro; Alvarez-Loayza, Patricia; Alves, Luciana F; Ashton, Peter; Balvanera, Patricia; Bastian, Meredith L; Bellingham, Peter J; van den Berg, Eduardo; Bernacci, Luis; da Conceição Bispo, Polyanna; Blanc, Lilian; Böhning-Gaese, Katrin; Boeckx, Pascal; Bongers, Frans; Boyle, Brad; Bradford, Matt; Brearley, Francis Q; Breuer-Ndoundou Hockemba, Mireille; Bunyavejchewin, Sarayudh; Calderado Leal Matos, Darley; Castillo-Santiago, Miguel; Catharino, Eduardo L M; Chai, Shauna-Lee; Chen, Yukai; Colwell, Robert K; Chazdon, Robin L; Robin, Chazdon L; Clark, Connie; Clark, David B; Clark, Deborah A; Culmsee, Heike; Damas, Kipiro; Dattaraja, Handanakere S; Dauby, Gilles; Davidar, Priya; DeWalt, Saara J; Doucet, Jean-Louis; Duque, Alvaro; Durigan, Giselda; Eichhorn, Karl A O; Eisenlohr, Pedro V; Eler, Eduardo; Ewango, Corneille; Farwig, Nina; Feeley, Kenneth J; Ferreira, Leandro; Field, Richard; de Oliveira Filho, Ary T; Fletcher, Christine; Forshed, Olle; Franco, Geraldo; Fredriksson, Gabriella; Gillespie, Thomas; Gillet, Jean-François; Amarnath, Giriraj; Griffith, Daniel M; Grogan, James; Gunatilleke, Nimal; Harris, David; Harrison, Rhett; Hector, Andy; Homeier, Jürgen; Imai, Nobuo; Itoh, Akira; Jansen, Patrick A; Joly, Carlos A; de Jong, Bernardus H J; Kartawinata, Kuswata; Kearsley, Elizabeth; Kelly, Daniel L; Kenfack, David; Kessler, Michael; Kitayama, Kanehiro; Kooyman, Robert; Larney, Eileen; Laumonier, Yves; Laurance, Susan; Laurance, William F; Lawes, Michael J; Amaral, Ieda Leao do; Letcher, Susan G; Lindsell, Jeremy; Lu, Xinghui; Mansor, Asyraf; Marjokorpi, Antti; Martin, Emanuel H; Meilby, Henrik; Melo, Felipe P L; Metcalfe, Daniel J; Medjibe, Vincent P; Metzger, Jean Paul; Millet, Jerome; Mohandass, D; Montero, Juan C; de Morisson Valeriano, Márcio; Mugerwa, Badru; Nagamasu, Hidetoshi; Nilus, Reuben; Ochoa-Gaona, Susana; Onrizal; Page, Navendu; Parolin, Pia; Parren, Marc; Parthasarathy, Narayanaswamy; Paudel, Ekananda; Permana, Andrea; Piedade, Maria T F; Pitman, Nigel C A; Poorter, Lourens; Poulsen, Axel D; Poulsen, John; Powers, Jennifer; Prasad, Rama C; Puyravaud, Jean-Philippe; Razafimahaimodison, Jean-Claude; Reitsma, Jan; Dos Santos, João Roberto; Roberto Spironello, Wilson; Romero-Saltos, Hugo; Rovero, Francesco; Rozak, Andes Hamuraby; Ruokolainen, Kalle; Rutishauser, Ervan; Saiter, Felipe; Saner, Philippe; Santos, Braulio A; Santos, Fernanda; Sarker, Swapan K; Satdichanh, Manichanh; Schmitt, Christine B; Schöngart, Jochen; Schulze, Mark; Suganuma, Marcio S; Sheil, Douglas; da Silva Pinheiro, Eduardo; Sist, Plinio; Stevart, Tariq; Sukumar, Raman; Sun, I-Fang; Sunderland, Terry; Sunderand, Terry; Suresh, H S; Suzuki, Eizi; Tabarelli, Marcelo; Tang, Jangwei; Targhetta, Natália; Theilade, Ida; Thomas, Duncan W; Tchouto, Peguy; Hurtado, Johanna; Valencia, Renato; van Valkenburg, Johan L C H; Van Do, Tran; Vasquez, Rodolfo; Verbeeck, Hans; Adekunle, Victor; Vieira, Simone A; Webb, Campbell O; Whitfeld, Timothy; Wich, Serge A; Williams, John; Wittmann, Florian; Wöll, Hannsjoerg; Yang, Xiaobo; Adou Yao, C Yves; Yap, Sandra L; Yoneda, Tsuyoshi; Zahawi, Rakan A; Zakaria, Rahmad; Zang, Runguo; de Assis, Rafael L; Garcia Luize, Bruno; Venticinque, Eduardo M

    2015-06-16

    The high species richness of tropical forests has long been recognized, yet there remains substantial uncertainty regarding the actual number of tropical tree species. Using a pantropical tree inventory database from closed canopy forests, consisting of 657,630 trees belonging to 11,371 species, we use a fitted value of Fisher's alpha and an approximate pantropical stem total to estimate the minimum number of tropical forest tree species to fall between ∼ 40,000 and ∼ 53,000, i.e., at the high end of previous estimates. Contrary to common assumption, the Indo-Pacific region was found to be as species-rich as the Neotropics, with both regions having a minimum of ∼ 19,000-25,000 tree species. Continental Africa is relatively depauperate with a minimum of ∼ 4,500-6,000 tree species. Very few species are shared among the African, American, and the Indo-Pacific regions. We provide a methodological framework for estimating species richness in trees that may help refine species richness estimates of tree-dependent taxa. PMID:26034279

  9. Tree species richness affecting fine root biomass in European forests

    NASA Astrophysics Data System (ADS)

    Finér, Leena; Domisch, Timo; Vesterdal, Lars; Dawud, Seid M.; Raulund-Rasmussen, Karsten

    2016-04-01

    Fine roots are an important factor in the forest carbon cycle, contributing significantly to below-ground biomass and soil carbon storage. Therefore it is essential to understand the role of the forest structure, indicated by tree species diversity in controlling below-ground biomass and managing the carbon pools of forest soils. We studied how tree species richness would affect fine root biomass and its distribution in the soil profile and biomass above- and below-ground allocation patterns of different tree species. Our main hypothesis was that increasing tree species richness would lead to below-ground niche differentiation and more efficient soil exploitation by the roots, resulting in a higher fine root biomass in the soil. We sampled fine roots of trees and understorey vegetation in six European forest types in Finland, Poland, Germany, Romania, Italy and Spain, representing boreal, temperate and Mediterranean forests, established within the FunDivEUROPE project for studying the effects of tree species diversity on forest functioning. After determining fine root biomasses, we identified the percentages of different tree species in the fine root samples using the near infrared reflectance spectroscopy (NIRS) method. Opposite to our hypothesis we did not find any general positive relationship between tree species richness and fine root biomass. A weak positive response found in Italy and Spain seemed to be related to dry environmental conditions during Mediterranean summers. At the Polish site where we could sample deeper soil layers (down to 40 cm), we found more tree fine roots in the deeper layers under species-rich forests, as compared to the monocultures, indicating the ability of trees to explore more resources and to increase soil carbon stocks. Tree species richness did not affect biomass allocation patterns between above- and below-ground parts of the trees.

  10. Growth Strategies of Tropical Tree Species: Disentangling Light and Size Effects

    PubMed Central

    Rüger, Nadja; Berger, Uta; Hubbell, Stephen P.; Vieilledent, Ghislain; Condit, Richard

    2011-01-01

    An understanding of the drivers of tree growth at the species level is required to predict likely changes of carbon stocks and biodiversity when environmental conditions change. Especially in species-rich tropical forests, it is largely unknown how species differ in their response of growth to resource availability and individual size. We use a hierarchical Bayesian approach to quantify the impact of light availability and tree diameter on growth of 274 woody species in a 50-ha long-term forest census plot in Barro Colorado Island, Panama. Light reaching each individual tree was estimated from yearly vertical censuses of canopy density. The hierarchical Bayesian approach allowed accounting for different sources of error, such as negative growth observations, and including rare species correctly weighted by their abundance. All species grew faster at higher light. Exponents of a power function relating growth to light were mostly between 0 and 1. This indicates that nearly all species exhibit a decelerating increase of growth with light. In contrast, estimated growth rates at standardized conditions (5 cm dbh, 5% light) varied over a 9-fold range and reflect strong growth-strategy differentiation between the species. As a consequence, growth rankings of the species at low (2%) and high light (20%) were highly correlated. Rare species tended to grow faster and showed a greater sensitivity to light than abundant species. Overall, tree size was less important for growth than light and about half the species were predicted to grow faster in diameter when bigger or smaller, respectively. Together light availability and tree diameter only explained on average 12% of the variation in growth rates. Thus, other factors such as soil characteristics, herbivory, or pathogens may contribute considerably to shaping tree growth in the tropics. PMID:21966498

  11. Tree Species Traits Influence Soil Physical, Chemical, and Biological Properties in High Elevation Forests

    PubMed Central

    Ayres, Edward; Steltzer, Heidi; Berg, Sarah; Wallenstein, Matthew D.; Simmons, Breana L.; Wall, Diana H.

    2009-01-01

    Background Previous studies have shown that plants often have species-specific effects on soil properties. In high elevation forests in the Southern Rocky Mountains, North America, areas that are dominated by a single tree species are often adjacent to areas dominated by another tree species. Here, we assessed soil properties beneath adjacent stands of trembling aspen, lodgepole pine, and Engelmann spruce, which are dominant tree species in this region and are distributed widely in North America. We hypothesized that soil properties would differ among stands dominated by different tree species and expected that aspen stands would have higher soil temperatures due to their open structure, which, combined with higher quality litter, would result in increased soil respiration rates, nitrogen availability, and microbial biomass, and differences in soil faunal community composition. Methodology/Principal Findings We assessed soil physical, chemical, and biological properties at four sites where stands of aspen, pine, and spruce occurred in close proximity to one-another in the San Juan Mountains, Colorado. Leaf litter quality differed among the tree species, with the highest nitrogen (N) concentration and lowest lignin∶N in aspen litter. Nitrogen concentration was similar in pine and spruce litter, but lignin∶N was highest in pine litter. Soil temperature and moisture were highest in aspen stands, which, in combination with higher litter quality, probably contributed to faster soil respiration rates from stands of aspen. Soil carbon and N content, ammonium concentration, and microbial biomass did not differ among tree species, but nitrate concentration was highest in aspen soil and lowest in spruce soil. In addition, soil fungal, bacterial, and nematode community composition and rotifer, collembolan, and mesostigmatid mite abundance differed among the tree species, while the total abundance of nematodes, tardigrades, oribatid mites, and prostigmatid mites did not

  12. Slope variation and population structure of tree species from different ecological groups in South Brazil.

    PubMed

    Bianchini, Edmilson; Garcia, Cristina C; Pimenta, José A; Torezan, José M D

    2010-09-01

    Size structure and spatial arrangement of 13 abundant tree species were determined in a riparian forest fragment in Paraná State, South Brazil (23°16'S and 51°01'W). The studied species were Aspidosperma polyneuron Müll. Arg., Astronium graveolens Jacq. and Gallesia integrifolia (Spreng) Harms (emergent species); Alseis floribunda Schott, Ruprechtia laxiflora Meisn. and Bougainvillea spectabilis Willd. (shade-intolerant canopy species); Machaerium paraguariense Hassl, Myroxylum peruiferum L. and Chrysophyllum gonocarpum (Mart. & Eichler ex Miq.) Engl. (shade-tolerant canopy species); Sorocea bonplandii (Baill.) Bürger, Trichilia casaretti C. Dc, Trichilia catigua A. Juss. and Actinostemon concolor (Spreng.) Müll. Arg. (understory small trees species). Height and diameter structures and basal area of species were analyzed. Spatial patterns and slope correlation were analyzed by Moran's / spatial autocorrelation coefficient and partial Mantel test, respectively. The emergent and small understory species showed the highest and the lowest variations in height, diameter and basal area. Size distribution differed among emergent species and also among canopy shade-intolerant species. The spatial pattern ranged among species in all groups, except in understory small tree species. The slope was correlated with spatial pattern for A. polyneuron, A. graveolens, A. floribunda, R. laxiflora, M. peruiferum and T. casaretti. The results indicated that most species occurred in specific places, suggesting that niche differentiation can be an important factor in structuring the tree community. PMID:21562693

  13. Relation between rainfall intensity and savanna tree abundance explained by water use strategies.

    PubMed

    Xu, Xiangtao; Medvigy, David; Rodriguez-Iturbe, Ignacio

    2015-10-20

    Tree abundance in tropical savannas exhibits large and unexplained spatial variability. Here, we propose that differentiated tree and grass water use strategies can explain the observed negative relation between maximum tree abundance and rainfall intensity (defined as the characteristic rainfall depth on rainy days), and we present a biophysical tree-grass competition model to test this idea. The model is founded on a premise that has been well established in empirical studies, namely, that the relative growth rate of grasses is much higher compared with trees in wet conditions but that grasses are more susceptible to water stress and lose biomass more quickly in dry conditions. The model is coupled with a stochastic rainfall generator and then calibrated and tested using field observations from several African savanna sites. We show that the observed negative relation between maximum tree abundance and rainfall intensity can be explained only when differentiated water use strategies are accounted for. Numerical experiments reveal that this effect is more significant than the effect of root niche separation. Our results emphasize the importance of vegetation physiology in determining the responses of tree abundance to climate variations in tropical savannas and suggest that projected increases in rainfall intensity may lead to an increase in grass in this biome. PMID:26438847

  14. Diversity is maintained by seasonal variation in species abundance

    PubMed Central

    2013-01-01

    Background Some of the most marked temporal fluctuations in species abundances are linked to seasons. In theory, multispecies assemblages can persist if species use shared resources at different times, thereby minimizing interspecific competition. However, there is scant empirical evidence supporting these predictions and, to the best of our knowledge, seasonal variation has never been explored in the context of fluctuation-mediated coexistence. Results Using an exceptionally well-documented estuarine fish assemblage, sampled monthly for over 30 years, we show that temporal shifts in species abundances underpin species coexistence. Species fall into distinct seasonal groups, within which spatial resource use is more heterogeneous than would be expected by chance at those times when competition for food is most intense. We also detect seasonal variation in the richness and evenness of the community, again linked to shifts in resource availability. Conclusions These results reveal that spatiotemporal shifts in community composition minimize competitive interactions and help stabilize total abundance. PMID:24007204

  15. How tree species fill geographic and ecological space in eastern North America

    PubMed Central

    Ricklefs, Robert E.

    2015-01-01

    Background and Aims Ecologists broadly accept that the number of species present within a region balances regional processes of immigration and speciation against competitive and other interactions between populations that limit distribution and constrain diversity. Although ecological theory has, for a long time, addressed the premise that ecological space can be filled to ‘capacity’ with species, only with the availability of time-calibrated phylogenies has it been possible to test the hypothesis that diversification slows as the number of species in a region increases. Focusing on the deciduous trees of eastern North America, this study tested predictions from competition theory concerning the distribution and abundance of species. Methods Local assemblages of trees tabulated in a previous study published in 1950 were analysed. Assemblages were ordinated with respect to species composition by non-metric multidimensional scaling (NMS). Distributions of trees were analysed by taxonomically nested analysis of variance, discriminant analysis based on NMS scores, and canonical correlation analysis of NMS scores and Bioclim climate variables. Key Results Most of the variance in species abundance and distribution was concentrated among closely related (i.e. congeneric) species, indicating evolutionary lability. Species distribution and abundance were unrelated to the number of close relatives, suggesting that competitive effects are diffuse. Distances between pairs of congeneric species in NMS space did not differ significantly from distances between more distantly related species, in contrast to the predictions of both competitive habitat partitioning and ecological sorting of species. Conclusions Eastern deciduous forests of North America do not appear to be saturated with species. The distributions and abundances of individual species provide little evidence of being shaped by competition from related (i.e. ecologically similar) species and, by inference, that

  16. Abundance of green tree frogs and insects in artificial canopy gaps in a bottomland hardwood forest.

    SciTech Connect

    Horn, Scott; Hanula, James L.; Ulyshen, Michael D.; Kilgo, John C.

    2005-01-01

    Horn, Scott, James L. Hanula, Michael D. Ulyshen, and John C. Kilgo. 2005. Abundance of green tree frogs and insects in artificial canopy gaps in a bottomland hardwood forest. Am. Midl. Nat. 153:321-326. Abstract: We found more green tree frogs (Hyla cinerea) in canopy gaps than in closed canopy forest. Of the 331 green tree frogs observed, 88% were in canopy gaps. Likewise, higher numbers and biomasses of insects were captured in the open gap habitat. Flies were the most commonly collected insect group accounting for 54% of the total capture. These data suggest that one reason green tree frogs were more abundant in canopy gaps was the increased availability of prey and that small canopy gaps provide early successional habitats that are beneficial to green tree frog populations.

  17. Modelling occurrence and abundance of species when detection is imperfect

    USGS Publications Warehouse

    Royle, J. Andrew; Nichols, J.D.; Kery, M.

    2005-01-01

    Relationships between species abundance and occupancy are of considerable interest in metapopulation biology and in macroecology. Such relationships may be described concisely using probability models that characterize variation in abundance of a species. However, estimation of the parameters of these models in most ecological problems is impaired by imperfect detection. When organisms are detected imperfectly, observed counts are biased estimates of true abundance, and this induces bias in stated occupancy or occurrence probability. In this paper we consider a class of models that enable estimation of abundance/occupancy relationships from counts of organisms that result from surveys in which detection is imperfect. Under such models, parameter estimation and inference are based on conventional likelihood methods. We provide an application of these models to geographically extensive breeding bird survey data in which alternative models of abundance are considered that include factors that influence variation in abundance and detectability. Using these models, we produce estimates of abundance and occupancy maps that honor important sources of spatial variation in avian abundance and provide clearly interpretable characterizations of abundance and occupancy adjusted for imperfect detection.

  18. Abundance of Green Tree Frogs and Insects in Artificial Canopy Gaps in a Bottomland Hardwood Forest.

    SciTech Connect

    Horn, Scott; Hanula, James, L.; Ulyshen, Michael D.; Kilgo, John, C.

    2005-04-01

    ABSTRACT - We found more green tree frogs ( Hyla cinerea) n canopv gaps than in closed canopy forest. Of the 331 green tree frogs observed, 88% were in canopv gaps. Likewise, higher numbers and biomasses of insects were captured in the open gap habitat Flies were the most commonlv collected insect group accounting for 54% of the total capture. These data suggest that one reason green tree frogs were more abundant in canopy gaps was the increased availability of prey and that small canopy gaps provide early successional habitats that are beneficial to green tree frog populations.

  19. Inferring optimal species trees under gene duplication and loss.

    PubMed

    Bayzid, M S; Mirarab, S; Warnow, T

    2013-01-01

    Species tree estimation from multiple markers is complicated by the fact that gene trees can differ from each other (and from the true species tree) due to several biological processes, one of which is gene duplication and loss. Local search heuristics for two NP-hard optimization problems - minimize gene duplications (MGD) and minimize gene duplications and losses (MGDL) - are popular techniques for estimating species trees in the presence of gene duplication and loss. In this paper, we present an alternative approach to solving MGD and MGDL from rooted gene trees. First, we characterize each tree in terms of its "subtree-bipartitions" (a concept we introduce). Then we show that the MGD species tree is defined by a maximum weight clique in a vertex-weighted graph that can be computed from the subtree-bipartitions of the input gene trees, and the MGDL species tree is defined by a minimum weight clique in a similarly constructed graph. We also show that these optimal cliques can be found in polynomial time in the number of vertices of the graph using a dynamic programming algorithm (similar to that of Hallett and Lagergren(1)), because of the special structure of the graphs. Finally, we show that a constrained version of these problems, where the subtree-bipartitions of the species tree are drawn from the subtree-bipartitions of the input gene trees, can be solved in time that is polynomial in the number of gene trees and taxa. We have implemented our dynamic programming algorithm in a publicly available software tool, available at http://www.cs.utexas.edu/users/phylo/software/dynadup/. PMID:23424130

  20. How well can we predict forage species occurrence and abundance?

    Technology Transfer Automated Retrieval System (TEKTRAN)

    As part of a larger effort focused on forage species production and management, we have been developing a statistical modeling approach to predict the probability of species occurrence and the abundance for Orchard Grass over the Northeast region of the United States using two selected statistical m...

  1. Inconsistency of Species Tree Methods under Gene Flow.

    PubMed

    Solís-Lemus, Claudia; Yang, Mengyao; Ané, Cécile

    2016-09-01

    Coalescent-based methods are now broadly used to infer evolutionary relationships between groups of organisms under the assumption that incomplete lineage sorting (ILS) is the only source of gene tree discordance. Many of these methods are known to consistently estimate the species tree when all their assumptions are met. Nonetheless, little work has been done to test the robustness of such methods to violations of their assumptions. Here, we study the performance of two of the most efficient coalescent-based methods, ASTRAL and NJst, in the presence of gene flow. Gene flow violates the assumption that ILS is the sole source of gene tree conflict. We find anomalous gene trees on three-taxon rooted trees and on four-taxon unrooted trees. These anomalous trees do not exist under ILS only, but appear because of gene flow. Our simulations show that species tree methods (and concatenation) may reconstruct the wrong evolutionary history, even from a very large number of well-reconstructed gene trees. In other words, species tree methods can be inconsistent under gene flow. Our results underline the need for methods like PhyloNet, to account simultaneously for ILS and gene flow in a unified framework. Although much slower, PhyloNet had better accuracy and remained consistent at high levels of gene flow. PMID:27151419

  2. Selective logging in tropical forests decreases the robustness of liana-tree interaction networks to the loss of host tree species.

    PubMed

    Magrach, Ainhoa; Senior, Rebecca A; Rogers, Andrew; Nurdin, Deddy; Benedick, Suzan; Laurance, William F; Santamaria, Luis; Edwards, David P

    2016-03-16

    Selective logging is one of the major drivers of tropical forest degradation, causing important shifts in species composition. Whether such changes modify interactions between species and the networks in which they are embedded remain fundamental questions to assess the 'health' and ecosystem functionality of logged forests. We focus on interactions between lianas and their tree hosts within primary and selectively logged forests in the biodiversity hotspot of Malaysian Borneo. We found that lianas were more abundant, had higher species richness, and different species compositions in logged than in primary forests. Logged forests showed heavier liana loads disparately affecting slow-growing tree species, which could exacerbate the loss of timber value and carbon storage already associated with logging. Moreover, simulation scenarios of host tree local species loss indicated that logging might decrease the robustness of liana-tree interaction networks if heavily infested trees (i.e. the most connected ones) were more likely to disappear. This effect is partially mitigated in the short term by the colonization of host trees by a greater diversity of liana species within logged forests, yet this might not compensate for the loss of preferred tree hosts in the long term. As a consequence, species interaction networks may show a lagged response to disturbance, which may trigger sudden collapses in species richness and ecosystem function in response to additional disturbances, representing a new type of 'extinction debt'. PMID:26936241

  3. Effect of disjunct size distributions on foraminiferal species abundance determinations

    SciTech Connect

    Martin, R.E.; Liddell, W.D.

    1988-02-01

    Studies of foraminiferal distribution and abundance have typically employed a procedure (standard method) that entails counting approximately 300 specimens from a size range greater than some specified minimum (commonly 63 or 125 ..mu..m). This method fails to take into account that foraminifera may be found only within certain size fractions, either because of species specific size ranges or taphonomic processes (sorting, transport, abrasion). Use of a modified counting procedure (sieve method) takes into account foraminiferal size distributions. The sieve method uses counts of up to 300 specimens in each sand-size fraction (0.125-0.25, 0.25-0.5, 0.5-1, 1-2 mm) of each sample. Counts are then totaled for each sample (up to 1200 specimens per site) and used in determination of species abundances for each site. The sieve method has been of considerable utility in recognition of a foraminiferal bathymetric zonation preserved in sediment assemblages from fringing reef environments at Discovery Bay, north Jamaica. Well-documented reef zones (based on corals and physiography) are clearly defined in Q-mode cluster analysis (UPGMA) of species abundances determined using the sieve method. In contrast, individual fore reef zones are not recognized in cluster analysis of foraminiferal species abundances based on the standard method, nor by cluster analysis of species abundances within individual size fractions.

  4. Negative density dependence regulates two tree species at later life stage in a temperate forest.

    PubMed

    Piao, Tiefeng; Chun, Jung Hwa; Yang, Hee Moon; Cheon, Kwangil

    2014-01-01

    Numerous studies have demonstrated that tree survival is influenced by negative density dependence (NDD) and differences among species in shade tolerance could enhance coexistence via resource partitioning, but it is still unclear how NDD affects tree species with different shade-tolerance guilds at later life stages. In this study, we analyzed the spatial patterns for trees with dbh (diameter at breast height) ≥2 cm using the pair-correlation g(r) function to test for NDD in a temperate forest in South Korea after removing the effects of habitat heterogeneity. The analyses were implemented for the most abundant shade-tolerant (Chamaecyparis obtusa) and shade-intolerant (Quercus serrata) species. We found NDD existed for both species at later life stages. We also found Quercus serrata experienced greater NDD compared with Chamaecyparis obtusa. This study indicates that NDD regulates the two abundant tree species at later life stages and it is important to consider variation in species' shade tolerance in NDD study. PMID:25058660

  5. Relating species abundance distributions to species-area curves in two Mediterranean-type shrublands

    USGS Publications Warehouse

    Keeley, J.E.

    2003-01-01

    Based on both theoretical and empirical studies there is evidence that different species abundance distributions underlie different species-area relationships. Here I show that Australian and Californian shrubland communities (at the scale from 1 to 1000 m2) exhibit different species-area relationships and different species abundance patterns. The species-area relationship in Australian heathlands best fits an exponential model and species abundance (based on both density and cover) follows a narrow log normal distribution. In contrast, the species-area relationship in Californian shrublands is best fit with the power model and, although species abundance appears to fit a log normal distribution, the distribution is much broader than in Australian heathlands. I hypothesize that the primary driver of these differences is the abundance of small-stature annual species in California and the lack of annuals in Australian heathlands. Species-area is best fit by an exponential model in Australian heathlands because the bulk of the species are common and thus the species-area curves initially rise rapidly between 1 and 100 m2. Annuals in Californian shrublands generate very broad species abundance distributions with many uncommon or rare species. The power function is a better model in these communities because richness increases slowly from 1 to 100 m2 but more rapidly between 100 and 1000 m2 due to the abundance of rare or uncommon species that are more likely to be encountered at coarser spatial scales. The implications of this study are that both the exponential and power function models are legitimate representations of species-area relationships in different plant communities. Also, structural differences in community organization, arising from different species abundance distributions, may lead to different species-area curves, and this may be tied to patterns of life form distribution.

  6. Estimating abundance in the presence of species uncertainty

    USGS Publications Warehouse

    Chambert, Thierry A; Hossack, Blake R.; Fishback, LeeAnn; Davenport, Jon M.

    2016-01-01

    1.N-mixture models have become a popular method for estimating abundance of free-ranging animals that are not marked or identified individually. These models have been used on count data for single species that can be identified with certainty. However, co-occurring species often look similar during one or more life stages, making it difficult to assign species for all recorded captures. This uncertainty creates problems for estimating species-specific abundance and it can often limit life stages to which we can make inference. 2.We present a new extension of N-mixture models that accounts for species uncertainty. In addition to estimating site-specific abundances and detection probabilities, this model allows estimating probability of correct assignment of species identity. We implement this hierarchical model in a Bayesian framework and provide all code for running the model in BUGS-language programs. 3.We present an application of the model on count data from two sympatric freshwater fishes, the brook stickleback (Culaea inconstans) and the ninespine stickleback (Pungitius pungitius), ad illustrate implementation of covariate effects (habitat characteristics). In addition, we used a simulation study to validate the model and illustrate potential sample size issues. We also compared, for both real and simulated data, estimates provided by our model to those obtained by a simple N-mixture model when captures of unknown species identification were discarded. In the latter case, abundance estimates appeared highly biased and very imprecise, while our new model provided unbiased estimates with higher precision. 4.This extension of the N-mixture model should be useful for a wide variety of studies and taxa, as species uncertainty is a common issue. It should notably help improve investigation of abundance and vital rate characteristics of organisms’ early life stages, which are sometimes more difficult to identify than adults.

  7. Abundance of common species, not species richness, drives delivery of a real-world ecosystem service.

    PubMed

    Winfree, Rachael; Fox, Jeremy W; Williams, Neal M; Reilly, James R; Cariveau, Daniel P

    2015-07-01

    Biodiversity-ecosystem functioning experiments have established that species richness and composition are both important determinants of ecosystem function in an experimental context. Determining whether this result holds for real-world ecosystem services has remained elusive, however, largely due to the lack of analytical methods appropriate for large-scale, associational data. Here, we use a novel analytical approach, the Price equation, to partition the contribution to ecosystem services made by species richness, composition and abundance in four large-scale data sets on crop pollination by native bees. We found that abundance fluctuations of dominant species drove ecosystem service delivery, whereas richness changes were relatively unimportant because they primarily involved rare species that contributed little to function. Thus, the mechanism behind our results was the skewed species-abundance distribution. Our finding that a few common species, not species richness, drive ecosystem service delivery could have broad generality given the ubiquity of skewed species-abundance distributions in nature. PMID:25959973

  8. Indirect interactions among tropical tree species through shared rodent seed predators: a novel mechanism of tree species coexistence.

    PubMed

    Garzon-Lopez, Carol X; Ballesteros-Mejia, Liliana; Ordoñez, Alejandro; Bohlman, Stephanie A; Olff, Han; Jansen, Patrick A

    2015-08-01

    The coexistence of numerous tree species in tropical forests is commonly explained by negative dependence of recruitment on the conspecific seed and tree density due to specialist natural enemies that attack seeds and seedlings ('Janzen-Connell' effects). Less known is whether guilds of shared seed predators can induce a negative dependence of recruitment on the density of different species of the same plant functional group. We studied 54 plots in tropical forest on Barro Colorado Island, Panama, with contrasting mature tree densities of three coexisting large seeded tree species with shared seed predators. Levels of seed predation were far better explained by incorporating seed densities of all three focal species than by conspecific seed density alone. Both positive and negative density dependencies were observed for different species combinations. Thus, indirect interactions via shared seed predators can either promote or reduce the coexistence of different plant functional groups in tropical forest. PMID:25939379

  9. Tree Plantation Systems Influence Nitrogen Retention and the Abundance of Nitrogen Functional Genes in the Solomon Islands

    PubMed Central

    Reverchon, Frédérique; Bai, Shahla H.; Liu, Xian; Blumfield, Timothy J.

    2015-01-01

    Tree mono-plantations are susceptible to soil nutrient impoverishment and mixed species plantations have been proposed as a way of maintaining soil fertility while enhancing biodiversity. In the Solomon Islands, mixed species plantations where teak (Tectona grandis) is inter-planted with a local tree species (Flueggea flexuosa) have been used as an alternative to teak mono-plantations and are expected to increase soil microbial diversity and modify microbial biogeochemical processes. In this study, we quantified the abundance of microbial functional genes involved in the nitrogen (N) cycle from soil samples collected in teak, flueggea, and mixed species plantations. Furthermore, we measured soil properties such as pH, total carbon (C) and total N, stable N isotope composition (δ15N), and inorganic N pools. Soil pH and δ15N were higher under teak than under flueggea, which indicates that intercropping teak with flueggea may decrease bacterial activities and potential N losses. Higher C:N ratios were found under mixed species plantations than those under teak, suggesting an enhancement of N immobilization that would help preventing fast N losses. However, inorganic N pools remained unaffected by plant cover. Inter-planting teak with flueggea in mixed species plantations generally increased the relative abundance of denitrification genes and promoted the enrichment of nosZ-harboring denitrifiers. However, it reduced the abundance of bacterial amoA (ammonia monooxygenase) genes compared to teak mono-plantations. The abundance of most denitrification genes correlated with soil total N and C:N ratio, while bacterial and archeal nitrification genes correlated positively with soil NH4+ concentrations. Altogether, these results show that the abundance of bacterial N-cycling functional guilds vary under teak and under mixed species plantations, and that inter-planting teak with flueggea may potentially alleviate N losses associated with nitrification and denitrification

  10. Tree Plantation Systems Influence Nitrogen Retention and the Abundance of Nitrogen Functional Genes in the Solomon Islands.

    PubMed

    Reverchon, Frédérique; Bai, Shahla H; Liu, Xian; Blumfield, Timothy J

    2015-01-01

    Tree mono-plantations are susceptible to soil nutrient impoverishment and mixed species plantations have been proposed as a way of maintaining soil fertility while enhancing biodiversity. In the Solomon Islands, mixed species plantations where teak (Tectona grandis) is inter-planted with a local tree species (Flueggea flexuosa) have been used as an alternative to teak mono-plantations and are expected to increase soil microbial diversity and modify microbial biogeochemical processes. In this study, we quantified the abundance of microbial functional genes involved in the nitrogen (N) cycle from soil samples collected in teak, flueggea, and mixed species plantations. Furthermore, we measured soil properties such as pH, total carbon (C) and total N, stable N isotope composition (δ(15)N), and inorganic N pools. Soil pH and δ(15)N were higher under teak than under flueggea, which indicates that intercropping teak with flueggea may decrease bacterial activities and potential N losses. Higher C:N ratios were found under mixed species plantations than those under teak, suggesting an enhancement of N immobilization that would help preventing fast N losses. However, inorganic N pools remained unaffected by plant cover. Inter-planting teak with flueggea in mixed species plantations generally increased the relative abundance of denitrification genes and promoted the enrichment of nosZ-harboring denitrifiers. However, it reduced the abundance of bacterial amoA (ammonia monooxygenase) genes compared to teak mono-plantations. The abundance of most denitrification genes correlated with soil total N and C:N ratio, while bacterial and archeal nitrification genes correlated positively with soil NH4 (+) concentrations. Altogether, these results show that the abundance of bacterial N-cycling functional guilds vary under teak and under mixed species plantations, and that inter-planting teak with flueggea may potentially alleviate N losses associated with nitrification and

  11. Exploring the Taxonomy of Oaks and Related Tree Species

    ERIC Educational Resources Information Center

    McMaster, Robert T.

    2004-01-01

    A lab in Eastern North America conducted a study to determine the taxonomic relationship between deciduous trees and several species of oaks by calculating the similarity index of all species to be studied. The study enabled students to classify the different species of oaks according to their distinct characteristics.

  12. Temporal and Spatial Dynamics of Tree Species Composition in Temperate Mountains of South Korea

    NASA Astrophysics Data System (ADS)

    Lee, Boknam; Park, Juhan; Cho, Sungsik; Ryu, Daun; Zaw Wynn, Khine; Park, Minji; Cho, Sunhee; Yoon, Jongguk; Park, Jongyoung; Kim, Hyun Seok

    2015-04-01

    Long term studies on vegetation dynamics are important to identify changes of ecosystem-level responses to climate change. To learn how tree species composition and stand structure change across temperate mountains, the temporal and spatial variations in tree species diversity and structure were investigated using the species composition and DBH size collected over the fourteen-year period across 134 sites in Jiri and Baekoon Mountains, South Korea. The overall temporal changes over fourteen years showed significant increase in stand density, species diversity and evenness according to the indices of Shannon-Weiner diversity, Bray-Curtis dissimilarity, and Pielou's evenness, contributing to the increase of basal area and biomass growth. The change of tree species composition could be categorized into five species communities, representing gradual increase or decrease, establishment, extinction, fluctuation of species population. However, in general, the change in species composition appeared to have consistent and directional patterns of increase in the annual rate of change in the mean species traits including species richness, pole growth rate, adult growth rate, and adult stature with five common dominant species (Quercus mongolica, Quercus variabilis, Quercus serrata, Carpinus laxiflora, and Styrax japonicus). The spatial patterns of species composition appeared to have a higher stand density and species diversity along with the low latitude and high slope ecosystem. The climate change was another main driver to vary the distribution of species abundance. Overall, both temporal and spatial changes of composition in tree species community was clear and further analysis to clarify the reasons for such fast and species-specific changes is underway especially to separate the effect of successional change and climate change. Keywords species composition; climate change; temporal and spatial variation ; forest structure; temperate forest

  13. Mapping urban forest tree species using IKONOS imagery: preliminary results.

    PubMed

    Pu, Ruiliang

    2011-01-01

    A stepwise masking system with high-resolution IKONOS imagery was developed to identify and map urban forest tree species/groups in the City of Tampa, Florida, USA. The eight species/groups consist of sand live oak (Quercus geminata), laurel oak (Quercus laurifolia), live oak (Quercus virginiana), magnolia (Magnolia grandiflora), pine (species group), palm (species group), camphor (Cinnamomum camphora), and red maple (Acer rubrum). The system was implemented with soil-adjusted vegetation index (SAVI) threshold, textural information after running a low-pass filter, and brightness threshold of NIR band to separate tree canopies from non-vegetated areas from other vegetation types (e.g., grass/lawn) and to separate the tree canopies into sunlit and shadow areas. A maximum likelihood classifier was used to identify and map forest type and species. After IKONOS imagery was preprocessed, a total of nine spectral features were generated, including four spectral bands, three hue-intensity-saturation indices, one SAVI, and one texture image. The identified and mapped results were examined with independent ground survey data. The experimental results indicate that when classifying all the eight tree species/ groups with the high-resolution IKONOS image data, the identifying accuracy was very low and could not satisfy a practical application level, and when merging the eight species/groups into four major species/groups, the average accuracy is still low (average accuracy = 73%, overall accuracy = 86%, and κ = 0.76 with sunlit test samples). Such a low accuracy of identifying and mapping the urban tree species/groups is attributable to low spatial resolution IKONOS image data relative to tree crown size, to complex and variable background spectrum impact on crown spectra, and to shadow/shaded impact. The preliminary results imply that to improve the tree species identification accuracy and achieve a practical application level in urban area, multi-temporal (multi

  14. Abundance of introduced species at home predicts abundance away in herbaceous grasslands

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Many ecosystems worldwide are dominated by introduced plant species, leading to loss of biodiversity and ecosystem function. A common but rarely tested assumption is that these plants are more abundant in introduced versus native communities, because ecological or evolutionary based shifts in popula...

  15. Soil nutrients influence spatial distributions of tropical tree species

    PubMed Central

    John, Robert; Dalling, James W.; Harms, Kyle E.; Yavitt, Joseph B.; Stallard, Robert F.; Mirabello, Matthew; Hubbell, Stephen P.; Valencia, Renato; Navarrete, Hugo; Vallejo, Martha; Foster, Robin B.

    2007-01-01

    The importance of niche vs. neutral assembly mechanisms in structuring tropical tree communities remains an important unsettled question in community ecology [Bell G (2005) Ecology 86:1757–1770]. There is ample evidence that species distributions are determined by soils and habitat factors at landscape (<104 km2) and regional scales. At local scales (<1 km2), however, habitat factors and species distributions show comparable spatial aggregation, making it difficult to disentangle the importance of niche and dispersal processes. In this article, we test soil resource-based niche assembly at a local scale, using species and soil nutrient distributions obtained at high spatial resolution in three diverse neotropical forest plots in Colombia (La Planada), Ecuador (Yasuni), and Panama (Barro Colorado Island). Using spatial distribution maps of >0.5 million individual trees of 1,400 species and 10 essential plant nutrients, we used Monte Carlo simulations of species distributions to test plant–soil associations against null expectations based on dispersal assembly. We found that the spatial distributions of 36–51% of tree species at these sites show strong associations to soil nutrient distributions. Neutral dispersal assembly cannot account for these plant–soil associations or the observed niche breadths of these species. These results indicate that belowground resource availability plays an important role in the assembly of tropical tree communities at local scales and provide the basis for future investigations on the mechanisms of resource competition among tropical tree species. PMID:17215353

  16. Effectiveness of mosquito traps in measuring species abundance and composition

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Mosquito species abundance and composition estimates provided by trapping devices are commonly used to guide control efforts, but knowledge of trap biases is necessary for accurately interpreting results. We compared the Mosquito Magnet – Pro, the Mosquito Magnet – X and the CDC Miniature Light Trap...

  17. Capitalizing on opportunistic data for monitoring relative abundances of species.

    PubMed

    Giraud, Christophe; Calenge, Clément; Coron, Camille; Julliard, Romain

    2016-06-01

    With the internet, a massive amount of information on species abundance can be collected by citizen science programs. However, these data are often difficult to use directly in statistical inference, as their collection is generally opportunistic, and the distribution of the sampling effort is often not known. In this article, we develop a general statistical framework to combine such "opportunistic data" with data collected using schemes characterized by a known sampling effort. Under some structural assumptions regarding the sampling effort and detectability, our approach makes it possible to estimate the relative abundance of several species in different sites. It can be implemented through a simple generalized linear model. We illustrate the framework with typical bird datasets from the Aquitaine region in south-western France. We show that, under some assumptions, our approach provides estimates that are more precise than the ones obtained from the dataset with a known sampling effort alone. When the opportunistic data are abundant, the gain in precision may be considerable, especially for rare species. We also show that estimates can be obtained even for species recorded only in the opportunistic scheme. Opportunistic data combined with a relatively small amount of data collected with a known effort may thus provide access to accurate and precise estimates of quantitative changes in relative abundance over space and/or time. PMID:26496390

  18. Measuring β-diversity with species abundance data.

    PubMed

    Barwell, Louise J; Isaac, Nick J B; Kunin, William E

    2015-07-01

    In 2003, 24 presence-absence β-diversity metrics were reviewed and a number of trade-offs and redundancies identified. We present a parallel investigation into the performance of abundance-based metrics of β-diversity. β-diversity is a multi-faceted concept, central to spatial ecology. There are multiple metrics available to quantify it: the choice of metric is an important decision. We test 16 conceptual properties and two sampling properties of a β-diversity metric: metrics should be 1) independent of α-diversity and 2) cumulative along a gradient of species turnover. Similarity should be 3) probabilistic when assemblages are independently and identically distributed. Metrics should have 4) a minimum of zero and increase monotonically with the degree of 5) species turnover, 6) decoupling of species ranks and 7) evenness differences. However, complete species turnover should always generate greater values of β than extreme 8) rank shifts or 9) evenness differences. Metrics should 10) have a fixed upper limit, 11) symmetry (βA,B  = βB,A ), 12) double-zero asymmetry for double absences and double presences and 13) not decrease in a series of nested assemblages. Additionally, metrics should be independent of 14) species replication 15) the units of abundance and 16) differences in total abundance between sampling units. When samples are used to infer β-diversity, metrics should be 1) independent of sample sizes and 2) independent of unequal sample sizes. We test 29 metrics for these properties and five 'personality' properties. Thirteen metrics were outperformed or equalled across all conceptual and sampling properties. Differences in sensitivity to species' abundance lead to a performance trade-off between sample size bias and the ability to detect turnover among rare species. In general, abundance-based metrics are substantially less biased in the face of undersampling, although the presence-absence metric, βsim , performed well overall. Only

  19. Patterns of relative species abundance in rainforests and coral reefs.

    PubMed

    Volkov, Igor; Banavar, Jayanth R; Hubbell, Stephen P; Maritan, Amos

    2007-11-01

    A formidable many-body problem in ecology is to understand the complex of factors controlling patterns of relative species abundance (RSA) in communities of interacting species. Unlike many problems in physics, the nature of the interactions in ecological communities is not completely known. Although most contemporary theories in ecology start with the basic premise that species interact, here we show that a theory in which all interspecific interactions are turned off leads to analytical results that are in agreement with RSA data from tropical forests and coral reefs. The assumption of non-interacting species leads to a sampling theory for the RSA that yields a simple approximation at large scales to the exact theory. Our results show that one can make significant theoretical progress in ecology by assuming that the effective interactions among species are weak in the stationary states in species-rich communities such as tropical forests and coral reefs. PMID:17972874

  20. Analytical formulae for computing dominance from species-abundance distributions.

    PubMed

    Fung, Tak; Villain, Laura; Chisholm, Ryan A

    2015-12-01

    The evenness of an ecological community affects ecosystem structure, functioning and stability, and has implications for biodiversity conservation. In uneven communities, most species are rare while a few dominant species drive ecosystem-level properties. In even communities, dominance is lower, with possibly many species playing key ecological roles. The dominance aspect of evenness can be measured as a decreasing function of the proportion of species required to make up a fixed fraction (e.g., half) of individuals in a community. Here we sought general rules about dominance in ecological communities by linking dominance mathematically to the parameters of common theoretical species-abundance distributions (SADs). We found that if a community's SAD was log-series or lognormal, then dominance was almost inevitably high, with fewer than 40% of species required to account for 90% of all individuals. Dominance for communities with an exponential SAD was lower but still typically high, with fewer than 40% of species required to account for 70% of all individuals. In contrast, communities with a gamma SAD only exhibited high dominance when the average species abundance was below a threshold of approximately 100. Furthermore, we showed that exact values of dominance were highly scale-dependent, exhibiting non-linear trends with changing average species abundance. We also applied our formulae to SADs derived from a mechanistic community model to demonstrate how dominance can increase with environmental variance. Overall, our study provides a rigorous basis for theoretical explorations of the dynamics of dominance in ecological communities, and how this affects ecosystem functioning and stability. PMID:26409166

  1. Assessing introduction risk using species' rank-abundance distributions.

    PubMed

    Chan, Farrah T; Bradie, Johanna; Briski, Elizabeta; Bailey, Sarah A; Simard, Nathalie; MacIsaac, Hugh J

    2015-01-22

    Mixed-species assemblages are often unintentionally introduced into new ecosystems. Analysing how assemblage structure varies during transport may provide insights into how introduction risk changes before propagules are released. Characterization of introduction risk is typically based on assessments of colonization pressure (CP, the number of species transported) and total propagule pressure (total PP, the total abundance of propagules released) associated with an invasion vector. Generally, invasion potential following introduction increases with greater CP or total PP. Here, we extend these assessments using rank-abundance distributions to examine how CP : total PP relationships change temporally in ballast water of ocean-going ships. Rank-abundance distributions and CP : total PP patterns varied widely between trans-Atlantic and trans-Pacific voyages, with the latter appearing to pose a much lower risk than the former. Responses also differed by taxonomic group, with invertebrates experiencing losses mainly in total PP, while diatoms and dinoflagellates sustained losses mainly in CP. In certain cases, open-ocean ballast water exchange appeared to increase introduction risk by uptake of new species or supplementation of existing ones. Our study demonstrates that rank-abundance distributions provide new insights into the utility of CP and PP in characterizing introduction risk. PMID:25473007

  2. Tree Species Classification By Multiseasonal High Resolution Satellite Data

    NASA Astrophysics Data System (ADS)

    Elatawneh, Alata; Wallner, Adelheid; Straub, Christoph; Schneider, Thomas; Knoke, Thomas

    2013-12-01

    Accurate forest tree species mapping is a fundamental issue for sustainable forest management and planning. Forest tree species mapping with the means of remote sensing data is still a topic to be investigated. The Bavaria state institute of forestry is investigating the potential of using digital aerial images for forest management purposes. However, using aerial images is still cost- and time-consuming, in addition to their acquisition restrictions. The new space-born sensor generations such as, RapidEye, with a very high temporal resolution, offering multiseasonal data have the potential to improve the forest tree species mapping. In this study, we investigated the potential of multiseasonal RapidEye data for mapping tree species in a Mid European forest in Southern Germany. The RapidEye data of level A3 were collected on ten different dates in the years 2009, 2010 and 2011. For data analysis, a model was developed, which combines the Spectral Angle Mapper technique with a 10-fold- cross-validation. The analysis succeeded to differentiate four tree species; Norway spruce (Picea abies L.), Silver Fir (Abies alba Mill.), European beech (Fagus sylvatica) and Maple (Acer pseudoplatanus). The model success was evaluated using digital aerial images acquired in the year 2009 and inventory point records from 2008/09 inventory. Model results of the multiseasonal RapidEye data analysis achieved an overall accuracy of 76%. However, the success of the model was evaluated only for all the identified species and not for the individual.

  3. Soil nutrients influence spatial distributions of tropical trees species

    USGS Publications Warehouse

    John, R.; Dalling, J.W.; Harms, K.E.; Yavitt, J.B.; Stallard, R.F.; Mirabello, M.; Hubbell, S.P.; Valencia, R.; Navarrete, H.; Vallejo, M.; Foster, R.B.

    2007-01-01

    The importance of niche vs. neutral assembly mechanisms in structuring tropical tree communities remains an important unsettled question in community ecology [Bell G (2005) Ecology 86:1757-1770]. There is ample evidence that species distributions are determined by soils and habitat factors at landscape (0.5 million individual trees of 1,400 species and 10 essential plant nutrients, we used Monte Carlo simulations of species distributions to test plant-soil associations against null expectations based on dispersal assembly. We found that the spatial distributions of 36-51% of tree species at these sites show strong associations to soil nutrient distributions. Neutral dispersal assembly cannot account for these plant-soil associations or the observed niche breadths of these species. These results indicate that belowground resource availability plays an important role in the assembly of tropical tree communities at local scales and provide the basis for future investigations on the mechanisms of resource competition among tropical tree species. ?? 2007 by The National Academy of Sciences of the USA.

  4. Relative abundance and species richness of cerambycid beetles in partial cut and uncut bottomland hardwood forests

    USGS Publications Warehouse

    Newell, P.; King, S.

    2009-01-01

    Partial cutting techniques are increasingly advocated and used to create habitat for priority wildlife. However, partial cutting may or may not benefit species dependent on deadwood; harvesting can supplement coarse woody debris in the form of logging slash, but standing dead trees may be targeted for removal. We sampled cerambycid beetles during the spring and summer of 2006 and 2007 with canopy malaise traps in 1- and 2-year-old partial cut and uncut bottomland hardwood forests of Louisiana. We captured a total of 4195 cerambycid beetles representing 65 species. Relative abundance was higher in recent partial cuts than in uncut controls and with more dead trees in a plot. Total species richness and species composition were not different between treatments. The results suggest partial cuts with logging slash left on site increase the abundance of cerambycid beetles in the first few years after partial cutting and that both partial cuts and uncut forest should be included in the bottomland hardwood forest landscape.

  5. Experimental evidence of large changes in terrestrial chlorine cycling following altered tree species composition.

    PubMed

    Montelius, Malin; Thiry, Yves; Marang, Laura; Ranger, Jacques; Cornelis, Jean-Thomas; Svensson, Teresia; Bastviken, David

    2015-04-21

    Organochlorine molecules (Clorg) are surprisingly abundant in soils and frequently exceed chloride (Cl(-)) levels. Despite the widespread abundance of Clorg and the common ability of microorganisms to produce Clorg, we lack fundamental knowledge about how overall chlorine cycling is regulated in forested ecosystems. Here we present data from a long-term reforestation experiment where native forest was cleared and replaced with five different tree species. Our results show that the abundance and residence times of Cl(-) and Clorg after 30 years were highly dependent on which tree species were planted on the nearby plots. Average Cl(-) and Clorg content in soil humus were higher, at experimental plots with coniferous trees than in those with deciduous trees. Plots with Norway spruce had the highest net accumulation of Cl(-) and Clorg over the experiment period, and showed a 10 and 4 times higher Cl(-) and Clorg storage (kg ha(-1)) in the biomass, respectively, and 7 and 9 times higher storage of Cl(-) and Clorg in the soil humus layer, compared to plots with oak. The results can explain why local soil chlorine levels are frequently independent of atmospheric deposition, and provide opportunities for improved modeling of chlorine distribution and cycling in terrestrial ecosystems. PMID:25811074

  6. Widespread Discordance of Gene Trees with Species Tree in Drosophila: Evidence for Incomplete Lineage Sorting

    PubMed Central

    Pollard, Daniel A; Eisen, Michael B

    2006-01-01

    The phylogenetic relationship of the now fully sequenced species Drosophila erecta and D. yakuba with respect to the D. melanogaster species complex has been a subject of controversy. All three possible groupings of the species have been reported in the past, though recent multi-gene studies suggest that D. erecta and D. yakuba are sister species. Using the whole genomes of each of these species as well as the four other fully sequenced species in the subgenus Sophophora, we set out to investigate the placement of D. erecta and D. yakuba in the D. melanogaster species group and to understand the cause of the past incongruence. Though we find that the phylogeny grouping D. erecta and D. yakuba together is the best supported, we also find widespread incongruence in nucleotide and amino acid substitutions, insertions and deletions, and gene trees. The time inferred to span the two key speciation events is short enough that under the coalescent model, the incongruence could be the result of incomplete lineage sorting. Consistent with the lineage-sorting hypothesis, substitutions supporting the same tree were spatially clustered. Support for the different trees was found to be linked to recombination such that adjacent genes support the same tree most often in regions of low recombination and substitutions supporting the same tree are most enriched roughly on the same scale as linkage disequilibrium, also consistent with lineage sorting. The incongruence was found to be statistically significant and robust to model and species choice. No systematic biases were found. We conclude that phylogenetic incongruence in the D. melanogaster species complex is the result, at least in part, of incomplete lineage sorting. Incomplete lineage sorting will likely cause phylogenetic incongruence in many comparative genomics datasets. Methods to infer the correct species tree, the history of every base in the genome, and comparative methods that control for and/or utilize this

  7. Temporal variability of forest communities: empirical estimates of population change in 4000 tree species.

    PubMed

    Chisholm, Ryan A; Condit, Richard; Rahman, K Abd; Baker, Patrick J; Bunyavejchewin, Sarayudh; Chen, Yu-Yun; Chuyong, George; Dattaraja, H S; Davies, Stuart; Ewango, Corneille E N; Gunatilleke, C V S; Nimal Gunatilleke, I A U; Hubbell, Stephen; Kenfack, David; Kiratiprayoon, Somboon; Lin, Yiching; Makana, Jean-Remy; Pongpattananurak, Nantachai; Pulla, Sandeep; Punchi-Manage, Ruwan; Sukumar, Raman; Su, Sheng-Hsin; Sun, I-Fang; Suresh, H S; Tan, Sylvester; Thomas, Duncan; Yap, Sandra

    2014-07-01

    Long-term surveys of entire communities of species are needed to measure fluctuations in natural populations and elucidate the mechanisms driving population dynamics and community assembly. We analysed changes in abundance of over 4000 tree species in 12 forests across the world over periods of 6-28 years. Abundance fluctuations in all forests are large and consistent with population dynamics models in which temporal environmental variance plays a central role. At some sites we identify clear environmental drivers, such as fire and drought, that could underlie these patterns, but at other sites there is a need for further research to identify drivers. In addition, cross-site comparisons showed that abundance fluctuations were smaller at species-rich sites, consistent with the idea that stable environmental conditions promote higher diversity. Much community ecology theory emphasises demographic variance and niche stabilisation; we encourage the development of theory in which temporal environmental variance plays a central role. PMID:24805976

  8. Foraminifera Species Richness, Abundance, and Diversity Research in Bolinas, California

    NASA Astrophysics Data System (ADS)

    Brunwin, N.; Ingram, Z.; Mendez, M.; Sandoval, K.

    2015-12-01

    Foraminifera are abundant, diverse, respond rapidly to environmental change, and are present in all marine and estuarine environments, making them important indicator species. A survey of occurrence and distribution of foraminifera in the Bolinas Lagoon, Marin County, California was carried out by Hedman in 1975, but no study since has focused on foraminiferal composition within this important ecosystem. In July 2015, the Careers in Science (CiS) Intern Program collected samples at 12 sites previously examined in the 1975 study. Thirty-six samples were collected from the upper few centimeters of sediment from a variety of intertidal and subtidal environments within the lagoon. Foraminifera from each sample were isolated, identified and species richness, abundance and diversity quantified. Furthermore, comparisons of faunal composition represented in our recent collection and that of Hedman's 1975 report are made.

  9. Abundance anomaly of the 13C species of CCH

    NASA Astrophysics Data System (ADS)

    Sakai, N.; Saruwatari, O.; Sakai, T.; Takano, S.; Yamamoto, S.

    2010-03-01

    Aims: We have observed the N = 1-0 lines of CCH and its 13C isotopic species toward a cold dark cloud, TMC-1 and a star-forming region, L1527, to investigate the 13C abundances and formation pathways of CCH. Methods: The observations have been carried out with the IRAM 30 m telescope. Results: We have successfully detected the lines of 13CCH and C13CH toward the both sources and found a significant intensity difference between the two 13C isotopic species. The [C13CH] /[13CCH] abundance ratios are 1.6 ± 0.4 (3σ) and 1.6 ± 0.1 (3σ) for TMC-1 and L1527, respectively. The abundance difference between C13CH and 13CCH means that the two carbon atoms of CCH are not equivalent in the formation pathway. On the other hand, the [CCH]/[C13CH] and [CCH]/[13CCH] ratios are evaluated to be larger than 170 and 250 toward TMC-1, and to be larger than 80 and 135 toward L1527, respectively. Therefore, both of the 13C species are significantly diluted in comparison with the interstellar 12C/13C ratio of 60. The dilution is discussed in terms of a behavior of 13C in molecular clouds.

  10. Measurement scale in maximum entropy models of species abundance

    PubMed Central

    Frank, Steven A.

    2010-01-01

    The consistency of the species abundance distribution across diverse communities has attracted widespread attention. In this paper, I argue that the consistency of pattern arises because diverse ecological mechanisms share a common symmetry with regard to measurement scale. By symmetry, I mean that different ecological processes preserve the same measure of information and lose all other information in the aggregation of various perturbations. I frame these explanations of symmetry, measurement, and aggregation in terms of a recently developed extension to the theory of maximum entropy. I show that the natural measurement scale for the species abundance distribution is log-linear: the information in observations at small population sizes scales logarithmically and, as population size increases, the scaling of information grades from logarithmic to linear. Such log-linear scaling leads naturally to a gamma distribution for species abundance, which matches well with the observed patterns. Much of the variation between samples can be explained by the magnitude at which the measurement scale grades from logarithmic to linear. This measurement approach can be applied to the similar problem of allelic diversity in population genetics and to a wide variety of other patterns in biology. PMID:21265915

  11. Colloquium paper: how many tree species are there in the Amazon and how many of them will go extinct?

    PubMed

    Hubbell, Stephen P; He, Fangliang; Condit, Richard; Borda-de-Agua, Luís; Kellner, James; Ter Steege, Hans

    2008-08-12

    New roads, agricultural projects, logging, and mining are claiming an ever greater area of once-pristine Amazonian forest. The Millennium Ecosystems Assessment (MA) forecasts the extinction of a large fraction of Amazonian tree species based on projected loss of forest cover over the next several decades. How accurate are these estimates of extinction rates? We use neutral theory to estimate the number, relative abundance, and range size of tree species in the Amazon metacommunity and estimate likely tree-species extinctions under published optimistic and nonoptimistic Amazon scenarios. We estimate that the Brazilian portion of the Amazon Basin has (or had) 11,210 tree species that reach sizes >10 cm DBH (stem diameter at breast height). Of these, 3,248 species have population sizes >1 million individuals, and, ignoring possible climate-change effects, almost all of these common species persist under both optimistic and nonoptimistic scenarios. At the rare end of the abundance spectrum, however, neutral theory predicts the existence of approximately 5,308 species with <10,000 individuals each that are expected to suffer nearly a 50% extinction rate under the nonoptimistic deforestation scenario and an approximately 37% loss rate even under the optimistic scenario. Most of these species have small range sizes and are highly vulnerable to local habitat loss. In ensembles of 100 stochastic simulations, we found mean total extinction rates of 20% and 33% of tree species in the Brazilian Amazon under the optimistic and nonoptimistic scenarios, respectively. PMID:18695228

  12. [Dynamic changes of dominant tree species in broad-leaved Korean pine forest at different succession stages in Changbai Mountains].

    PubMed

    Guo, Li-ping; Ji, Lan-zhu; Wang, Zhen; Wang, Zhi-xuan

    2011-04-01

    Taking the broad-leaved Korean pine forest stands at four different succession stages after clear-cutting in Changbai Mountains as test objects, this paper studied the change characteristics of community composition and dominant species. The tree species richness, Shannon diversity index, and Simpson dominance index at different succession stages had less change, but the evenness and abundance changed greatly. As succession progressed, the community composition changed constantly, i.e., species number decreased, while the basal area sum and the maximum importance value of dominant tree species increased, suggesting that the dominance of dominant species was continuously improved with succession. In the succession process of broad-leaved Korean pine forest in Changbai Mountains, Betula platyphylla, Populus davidiana, Phellodendron amurense, Ulmus japonica, and other intolerant or semi-intolerant tree species decreased, while Tilia amurensis, Fraxinus mandshurica, Pinus koraiensis, Acer mono, and other shade-tolerant species increased. PMID:21774305

  13. Is tree species diversity or tree species identity the most important driver of European forest soil carbon stocks?

    NASA Astrophysics Data System (ADS)

    Vesterdal, Lars; Muhie Dawud, Seid; Raulund-Rasmussen, Karsten; Finér, Leena; Domisch, Timo

    2016-04-01

    Land management includes the selection of specific tree species and tree species mixtures for European forests. Studies of functional species diversity effects have reported positive effects for aboveground carbon (C) sequestration, but the question remains whether higher soil C stocks could also result from belowground niche differentiation including more efficient root exploitation of soils. We studied topsoil C stocks in tree species diversity gradients established within the FunDivEurope project to explore biodiversity-ecosystem functioning relationships in six European forest types in Finland, Poland, Germany, Romania, Spain and Italy. In the Polish forest type we extended the sampling to also include subsoils. We found consistent but modest effects of species diversity on total soil C stocks (forest floor and 0-20 cm) across the six European forest types. Carbon stocks in the forest floor alone and in the combined forest floor and mineral soil layers increased with increasing tree species diversity. In contrast, there was a strong effect of species identity (broadleaf vs. conifer) and its interaction with site-related factors. Within the Polish forest type we sampled soils down to 40 cm and found that species identity was again the main factor explaining total soil C stock. However, species diversity increased soil C stocks in deeper soil layers (20-40 cm), while species identity influenced C stocks significantly within forest floors and the 0-10 cm layer. Root biomass increased with diversity in 30-40 cm depth, and a positive relationship between C stocks and root biomass in the 30-40 cm layer suggested that belowground niche complementarity could be a driving mechanism for higher root carbon input and in turn a deeper distribution of C in diverse forests. We conclude that total C stocks are mainly driven by tree species identity. However, modest positive diversity effects were detected at the European scale, and stronger positive effects on subsoil C stocks

  14. Abundance and Relative Distribution of Frankia Host Infection Groups Under Actinorhizal Alnus glutinosa and Non-actinorhizal Betula nigra Trees.

    PubMed

    Samant, Suvidha; Huo, Tian; Dawson, Jeffrey O; Hahn, Dittmar

    2016-02-01

    Quantitative polymerase chain reaction (qPCR) was used to assess the abundance and relative distribution of host infection groups of the root-nodule forming, nitrogen-fixing actinomycete Frankia in four soils with similar physicochemical characteristics, two of which were vegetated with a host plant, Alnus glutinosa, and two with a non-host plant, Betula nigra. Analyses of DAPI-stained cells at three locations, i.e., at a distance of less than 1 m (near stem), 2.5 m (middle crown), and 3-5 m (crown edge) from the stems of both tree species revealed no statistically significant differences in abundance. Frankiae generally accounted for 0.01 to 0.04 % of these cells, with values between 4 and 36 × 10(5) cells (g soil)(-1). In three out of four soils, abundance of frankiae was significantly higher at locations "near stem" and/or "middle crown" compared to "crown edge," while numbers at these locations were not different in the fourth soil. Frankiae of the Alnus host infection group were dominant in all samples accounting for about 75 % and more of the cells, with no obvious differences with distance to stem. In three of the soils, all of these cells were represented by strain Ag45/Mut15. In the fourth soil that was vegetated with older A. glutinosa trees, about half of these cells belonged to a different subgroup represented by strain ArI3. In all soils, the remaining cells belonged to the Elaeagnus host infection group represented by strain EAN1pec. Casuarina-infective frankiae were not found. Abundance and relative distribution of Frankia host infection groups were similar in soils under the host plant A. glutinosa and the non-host plant B. nigra. Results did thus not reveal any specific effects of plant species on soil Frankia populations. PMID:26143359

  15. Are Tree Species Diversity and Genotypic Diversity Effects on Insect Herbivores Mediated by Ants?

    PubMed Central

    Campos-Navarrete, María José; Abdala-Roberts, Luis; Munguía-Rosas, Miguel A.; Parra-Tabla, Víctor

    2015-01-01

    Plant diversity can influence predators and omnivores and such effects may in turn influence herbivores and plants. However, evidence for these ecological feedbacks is rare. We evaluated if the effects of tree species (SD) and genotypic diversity (GD) on the abundance of different guilds of insect herbivores associated with big-leaf mahogany (Swietenia macrophylla) were contingent upon the protective effects of ants tending extra-floral nectaries of this species. This study was conducted within a larger experiment consisting of mahogany monocultures and species polycultures of four species and –within each of these two plot types– mahogany was represented by either one or four maternal families. We selected 24 plots spanning these treatment combinations, 10 mahogany plants/plot, and within each plot experimentally reduced ant abundance on half of the selected plants, and surveyed ant and herbivore abundance. There were positive effects of SD on generalist leaf-chewers and sap-feeders, but for the latter group this effect depended on the ant reduction treatment: SD positively influenced sap-feeders under ambient ant abundance but had no effect when ant abundance was reduced; at the same time, ants had negative effects on sap feeders in monoculture but no effect in polyculture. In contrast, SD did not influence specialist stem-borers or leaf-miners and this effect was not contingent upon ant reduction. Finally, GD did not influence any of the herbivore guilds studied, and such effects did not depend on the ant treatment. Overall, we show that tree species diversity influenced interactions between a focal plant species (mahogany) and ants, and that such effects in turn mediated plant diversity effects on some (sap-feeders) but not all the herbivores guilds studied. Our results suggest that the observed patterns are dependent on the combined effects of herbivore identity, diet breadth, and the source of plant diversity. PMID:26241962

  16. Are Tree Species Diversity and Genotypic Diversity Effects on Insect Herbivores Mediated by Ants?

    PubMed

    Campos-Navarrete, María José; Abdala-Roberts, Luis; Munguía-Rosas, Miguel A; Parra-Tabla, Víctor

    2015-01-01

    Plant diversity can influence predators and omnivores and such effects may in turn influence herbivores and plants. However, evidence for these ecological feedbacks is rare. We evaluated if the effects of tree species (SD) and genotypic diversity (GD) on the abundance of different guilds of insect herbivores associated with big-leaf mahogany (Swietenia macrophylla) were contingent upon the protective effects of ants tending extra-floral nectaries of this species. This study was conducted within a larger experiment consisting of mahogany monocultures and species polycultures of four species and -within each of these two plot types- mahogany was represented by either one or four maternal families. We selected 24 plots spanning these treatment combinations, 10 mahogany plants/plot, and within each plot experimentally reduced ant abundance on half of the selected plants, and surveyed ant and herbivore abundance. There were positive effects of SD on generalist leaf-chewers and sap-feeders, but for the latter group this effect depended on the ant reduction treatment: SD positively influenced sap-feeders under ambient ant abundance but had no effect when ant abundance was reduced; at the same time, ants had negative effects on sap feeders in monoculture but no effect in polyculture. In contrast, SD did not influence specialist stem-borers or leaf-miners and this effect was not contingent upon ant reduction. Finally, GD did not influence any of the herbivore guilds studied, and such effects did not depend on the ant treatment. Overall, we show that tree species diversity influenced interactions between a focal plant species (mahogany) and ants, and that such effects in turn mediated plant diversity effects on some (sap-feeders) but not all the herbivores guilds studied. Our results suggest that the observed patterns are dependent on the combined effects of herbivore identity, diet breadth, and the source of plant diversity. PMID:26241962

  17. When Can Species Abundance Data Reveal Non-neutrality?

    PubMed Central

    Al Hammal, Omar; Alonso, David; Etienne, Rampal S.; Cornell, Stephen J.

    2015-01-01

    Species abundance distributions (SAD) are probably ecology’s most well-known empirical pattern, and over the last decades many models have been proposed to explain their shape. There is no consensus over which model is correct, because the degree to which different processes can be discerned from SAD patterns has not yet been rigorously quantified. We present a power calculation to quantify our ability to detect deviations from neutrality using species abundance data. We study non-neutral stochastic community models, and show that the presence of non-neutral processes is detectable if sample size is large enough and/or the amplitude of the effect is strong enough. Our framework can be used for any candidate community model that can be simulated on a computer, and determines both the sampling effort required to distinguish between alternative processes, and a range for the strength of non-neutral processes in communities whose patterns are statistically consistent with neutral theory. We find that even data sets of the scale of the 50 Ha forest plot on Barro Colorado Island, Panama, are unlikely to be large enough to detect deviations from neutrality caused by competitive interactions alone, though the presence of multiple non-neutral processes with contrasting effects on abundance distributions may be detectable. PMID:25793889

  18. When can species abundance data reveal non-neutrality?

    PubMed

    Al Hammal, Omar; Alonso, David; Etienne, Rampal S; Cornell, Stephen J

    2015-03-01

    Species abundance distributions (SAD) are probably ecology's most well-known empirical pattern, and over the last decades many models have been proposed to explain their shape. There is no consensus over which model is correct, because the degree to which different processes can be discerned from SAD patterns has not yet been rigorously quantified. We present a power calculation to quantify our ability to detect deviations from neutrality using species abundance data. We study non-neutral stochastic community models, and show that the presence of non-neutral processes is detectable if sample size is large enough and/or the amplitude of the effect is strong enough. Our framework can be used for any candidate community model that can be simulated on a computer, and determines both the sampling effort required to distinguish between alternative processes, and a range for the strength of non-neutral processes in communities whose patterns are statistically consistent with neutral theory. We find that even data sets of the scale of the 50 Ha forest plot on Barro Colorado Island, Panama, are unlikely to be large enough to detect deviations from neutrality caused by competitive interactions alone, though the presence of multiple non-neutral processes with contrasting effects on abundance distributions may be detectable. PMID:25793889

  19. Which Models Are Appropriate for Six Subtropical Forests: Species-Area and Species-Abundance Models

    PubMed Central

    Wei, Shi Guang; Li, Lin; Chen, Zhen Cheng; Lian, Ju Yu; Lin, Guo Jun; Huang, Zhong Liang; Yin, Zuo Yun

    2014-01-01

    The species-area relationship is one of the most important topic in the study of species diversity, conservation biology and landscape ecology. The species-area relationship curves describe the increase of species number with increasing area, and have been modeled by various equations. In this paper, we used detailed data from six 1-ha subtropical forest communities to fit three species-area relationship models. The coefficient of determination and F ratio of ANOVA showed all the three models fitted well to the species-area relationship data in the subtropical communities, with the logarithm model performing better than the other two models. We also used the three species-abundance distributions, namely the lognormal, logcauchy and logseries model, to fit them to the species-abundance data of six communities. In this case, the logcauchy model had the better fit based on the coefficient of determination. Our research reveals that the rare species always exist in the six communities, corroborating the neutral theory of Hubbell. Furthermore, we explained why all species-abundance figures appeared to be left-side truncated. This was due to subtropical forests have high diversity, and their large species number includes many rare species. PMID:24755956

  20. Multilocus inference of species trees and DNA barcoding.

    PubMed

    Mallo, Diego; Posada, David

    2016-09-01

    The unprecedented amount of data resulting from next-generation sequencing has opened a new era in phylogenetic estimation. Although large datasets should, in theory, increase phylogenetic resolution, massive, multilocus datasets have uncovered a great deal of phylogenetic incongruence among different genomic regions, due both to stochastic error and to the action of different evolutionary process such as incomplete lineage sorting, gene duplication and loss and horizontal gene transfer. This incongruence violates one of the fundamental assumptions of the DNA barcoding approach, which assumes that gene history and species history are identical. In this review, we explain some of the most important challenges we will have to face to reconstruct the history of species, and the advantages and disadvantages of different strategies for the phylogenetic analysis of multilocus data. In particular, we describe the evolutionary events that can generate species tree-gene tree discordance, compare the most popular methods for species tree reconstruction, highlight the challenges we need to face when using them and discuss their potential utility in barcoding. Current barcoding methods sacrifice a great amount of statistical power by only considering one locus, and a transition to multilocus barcodes would not only improve current barcoding methods, but also facilitate an eventual transition to species-tree-based barcoding strategies, which could better accommodate scenarios where the barcode gap is too small or inexistent.This article is part of the themed issue 'From DNA barcodes to biomes'. PMID:27481787

  1. Tree Species Composition and Harvest Intensity Affect Herbivore Density and Leaf Damage on Beech, Fagus sylvatica, in Different Landscape Contexts.

    PubMed

    Mangels, Jule; Blüthgen, Nico; Frank, Kevin; Grassein, Fabrice; Hilpert, Andrea; Mody, Karsten

    2015-01-01

    Most forests are exposed to anthropogenic management activities that affect tree species composition and natural ecosystem processes. Changes in ecosystem processes such as herbivory depend on management intensity, and on regional environmental conditions and species pools. Whereas influences of specific forest management measures have already been addressed for different herbivore taxa on a local scale, studies considering effects of different aspects of forest management across different regions are rare. We assessed the influence of tree species composition and intensity of harvesting activities on arthropod herbivores and herbivore-related damage to beech trees, Fagus sylvatica, in 48 forest plots in three regions of Germany. We found that herbivore abundance and damage to beech trees differed between regions and that - despite the regional differences - density of tree-associated arthropod taxa and herbivore damage were consistently affected by tree species composition and harvest intensity. Specifically, overall herbivore damage to beech trees increased with increasing dominance of beech trees - suggesting the action of associational resistance processes - and decreased with harvest intensity. The density of leaf chewers and mines was positively related to leaf damage, and several arthropod groups responded to beech dominance and harvest intensity. The distribution of damage patterns was consistent with a vertical shift of herbivores to higher crown layers during the season and with higher beech dominance. By linking quantitative data on arthropod herbivore abundance and herbivory with tree species composition and harvesting activity in a wide variety of beech forests, our study helps to better understand the influence of forest management on interactions between a naturally dominant deciduous forest tree and arthropod herbivores. PMID:25938417

  2. Tree Species Composition and Harvest Intensity Affect Herbivore Density and Leaf Damage on Beech, Fagus sylvatica, in Different Landscape Contexts

    PubMed Central

    Mangels, Jule; Blüthgen, Nico; Frank, Kevin; Grassein, Fabrice; Hilpert, Andrea; Mody, Karsten

    2015-01-01

    Most forests are exposed to anthropogenic management activities that affect tree species composition and natural ecosystem processes. Changes in ecosystem processes such as herbivory depend on management intensity, and on regional environmental conditions and species pools. Whereas influences of specific forest management measures have already been addressed for different herbivore taxa on a local scale, studies considering effects of different aspects of forest management across different regions are rare. We assessed the influence of tree species composition and intensity of harvesting activities on arthropod herbivores and herbivore-related damage to beech trees, Fagus sylvatica, in 48 forest plots in three regions of Germany. We found that herbivore abundance and damage to beech trees differed between regions and that – despite the regional differences - density of tree-associated arthropod taxa and herbivore damage were consistently affected by tree species composition and harvest intensity. Specifically, overall herbivore damage to beech trees increased with increasing dominance of beech trees – suggesting the action of associational resistance processes – and decreased with harvest intensity. The density of leaf chewers and mines was positively related to leaf damage, and several arthropod groups responded to beech dominance and harvest intensity. The distribution of damage patterns was consistent with a vertical shift of herbivores to higher crown layers during the season and with higher beech dominance. By linking quantitative data on arthropod herbivore abundance and herbivory with tree species composition and harvesting activity in a wide variety of beech forests, our study helps to better understand the influence of forest management on interactions between a naturally dominant deciduous forest tree and arthropod herbivores. PMID:25938417

  3. Interspecific variation in growth responses to climate and competition of five eastern tree species.

    PubMed

    Rollinson, Christine R; Kaye, Margot W; Canham, Charles D

    2016-04-01

    Climate and competition are often presented from two opposing views of the dominant driver of individual tree growth and species distribution in temperate forests, such as those in the eastern United States. Previous studies have provided abundant evidence indicating that both factors influence tree growth, and we argue that these effects are not independent of one another and rather that interactions between climate, competition, and size best describe tree growth. To illustrate this point, we describe the growth responses of five common eastern tree species to interacting effects of temperature, precipitation, competition, and individual size using maximum likelihood estimation. Models that explicitly include interactions among these four factors explained over half of the variance in annual growth for four out of five species using annual climate. Expanding temperature and precipitation analyses to include seasonal interactions resulted in slightly improved models with a mean R2 of 0.61 (SD 0.10). Growth responses to individual factors as well their interactions varied greatly among species. For example, growth sensitivity to temperature for Quercus rubra increased with maximum annual precipitation, but other species showed no change in sensitivity or slightly reduced annual growth. Our results also indicate that three-way interactions among individual stem size, competition, and temperature may determine which of the five co-occurring species in our study could have the highest growth rate in a given year. Continued consideration and quantification of interactions among climate, competition, and individual-based characteristics are likely to increase understanding of key biological processes such as tree growth. Greater parameterization of interactions between traditionally segregated factors such as climate and competition may also help build a framework to reconcile drivers of individual-based processes such as growth with larger-scale patterns of species

  4. tropiTree: an NGS-based EST-SSR resource for 24 tropical tree species.

    PubMed

    Russell, Joanne R; Hedley, Peter E; Cardle, Linda; Dancey, Siobhan; Morris, Jenny; Booth, Allan; Odee, David; Mwaura, Lucy; Omondi, William; Angaine, Peter; Machua, Joseph; Muchugi, Alice; Milne, Iain; Kindt, Roeland; Jamnadass, Ramni; Dawson, Ian K

    2014-01-01

    The development of genetic tools for non-model organisms has been hampered by cost, but advances in next-generation sequencing (NGS) have created new opportunities. In ecological research, this raises the prospect for developing molecular markers to simultaneously study important genetic processes such as gene flow in multiple non-model plant species within complex natural and anthropogenic landscapes. Here, we report the use of bar-coded multiplexed paired-end Illumina NGS for the de novo development of expressed sequence tag-derived simple sequence repeat (EST-SSR) markers at low cost for a range of 24 tree species. Each chosen tree species is important in complex tropical agroforestry systems where little is currently known about many genetic processes. An average of more than 5,000 EST-SSRs was identified for each of the 24 sequenced species, whereas prior to analysis 20 of the species had fewer than 100 nucleotide sequence citations. To make results available to potential users in a suitable format, we have developed an open-access, interactive online database, tropiTree (http://bioinf.hutton.ac.uk/tropiTree), which has a range of visualisation and search facilities, and which is a model for the efficient presentation and application of NGS data. PMID:25025376

  5. tropiTree: An NGS-Based EST-SSR Resource for 24 Tropical Tree Species

    PubMed Central

    Russell, Joanne R.; Hedley, Peter E.; Cardle, Linda; Dancey, Siobhan; Morris, Jenny; Booth, Allan; Odee, David; Mwaura, Lucy; Omondi, William; Angaine, Peter; Machua, Joseph; Muchugi, Alice; Milne, Iain; Kindt, Roeland; Jamnadass, Ramni; Dawson, Ian K.

    2014-01-01

    The development of genetic tools for non-model organisms has been hampered by cost, but advances in next-generation sequencing (NGS) have created new opportunities. In ecological research, this raises the prospect for developing molecular markers to simultaneously study important genetic processes such as gene flow in multiple non-model plant species within complex natural and anthropogenic landscapes. Here, we report the use of bar-coded multiplexed paired-end Illumina NGS for the de novo development of expressed sequence tag-derived simple sequence repeat (EST-SSR) markers at low cost for a range of 24 tree species. Each chosen tree species is important in complex tropical agroforestry systems where little is currently known about many genetic processes. An average of more than 5,000 EST-SSRs was identified for each of the 24 sequenced species, whereas prior to analysis 20 of the species had fewer than 100 nucleotide sequence citations. To make results available to potential users in a suitable format, we have developed an open-access, interactive online database, tropiTree (http://bioinf.hutton.ac.uk/tropiTree), which has a range of visualisation and search facilities, and which is a model for the efficient presentation and application of NGS data. PMID:25025376

  6. Gene trees versus species trees: reassessing life-history evolution in a freshwater fish radiation.

    PubMed

    Waters, Jonathan M; Rowe, Diane L; Burridge, Christopher P; Wallis, Graham P

    2010-10-01

    Mechanisms of speciation are best understood in the context of phylogenetic relationships and as such have often been inferred from single gene trees, typically those derived from mitochondrial DNA (mtDNA) markers. Recent studies, however, have noted the potential for phylogenetic discordance between gene trees and underlying species trees (e.g., due to stochastic lineage sorting, introgression, or selection). Here, we employ a variety of nuclear DNA loci to reassess evolutionary relationships within a recent freshwater fish radiation to reappraise modes of speciation. New Zealand's freshwater-limited Galaxias vulgaris complex is thought to have evolved from G. brevipinnis, a widespread migratory species that retains a plesiomorphic marine juvenile phase. A well-resolved tree, based on four mtDNA regions, previously suggested that marine migratory ability has been lost on 3 independent occasions in the evolution of this species flock (assuming that loss of diadromy is irreversible). Here, we use pseudogene (galaxiid Numt: 1801 bp), intron (S: 903 bp), and exon (RAG-1: 1427 bp) markers, together with mtDNA, to reevaluate this hypothesis of parallel evolution. Interestingly, partitioned Bayesian analysis of concatenated nuclear sequences (3141 bp) and concatenated nuclear and mtDNA (4770 bp) both recover phylogenies implying a single loss of diadromy, not three parallel losses as previously inferred from mtDNA alone. This phylogenetic result is reinforced by a multilocus analysis performed using Bayesian estimation of species trees (BEST) software that estimates the posterior distribution of species trees under a coalescent model. We discuss factors that might explain the apparently misleading phylogenetic inferences generated by mtDNA. PMID:20603441

  7. Nitrogen Addition Enhances Drought Sensitivity of Young Deciduous Tree Species

    PubMed Central

    Dziedek, Christoph; Härdtle, Werner; von Oheimb, Goddert; Fichtner, Andreas

    2016-01-01

    Understanding how trees respond to global change drivers is central to predict changes in forest structure and functions. Although there is evidence on the mode of nitrogen (N) and drought (D) effects on tree growth, our understanding of the interplay of these factors is still limited. Simultaneously, as mixtures are expected to be less sensitive to global change as compared to monocultures, we aimed to investigate the combined effects of N addition and D on the productivity of three tree species (Fagus sylvatica, Quercus petraea, Pseudotsuga menziesii) in relation to functional diverse species mixtures using data from a 4-year field experiment in Northwest Germany. Here we show that species mixing can mitigate the negative effects of combined N fertilization and D events, but the community response is mainly driven by the combination of certain traits rather than the tree species richness of a community. For beech, we found that negative effects of D on growth rates were amplified by N fertilization (i.e., combined treatment effects were non-additive), while for oak and fir, the simultaneous effects of N and D were additive. Beech and oak were identified as most sensitive to combined N+D effects with a strong size-dependency observed for beech, suggesting that the negative impact of N+D becomes stronger with time as beech grows larger. As a consequence, the net biodiversity effect declined at the community level, which can be mainly assigned to a distinct loss of complementarity in beech-oak mixtures. This pattern, however, was not evident in the other species-mixtures, indicating that neighborhood composition (i.e., trait combination), but not tree species richness mediated the relationship between tree diversity and treatment effects on tree growth. Our findings point to the importance of the qualitative role (‘trait portfolio’) that biodiversity play in determining resistance of diverse tree communities to environmental changes. As such, they provide

  8. Nitrogen Addition Enhances Drought Sensitivity of Young Deciduous Tree Species.

    PubMed

    Dziedek, Christoph; Härdtle, Werner; von Oheimb, Goddert; Fichtner, Andreas

    2016-01-01

    Understanding how trees respond to global change drivers is central to predict changes in forest structure and functions. Although there is evidence on the mode of nitrogen (N) and drought (D) effects on tree growth, our understanding of the interplay of these factors is still limited. Simultaneously, as mixtures are expected to be less sensitive to global change as compared to monocultures, we aimed to investigate the combined effects of N addition and D on the productivity of three tree species (Fagus sylvatica, Quercus petraea, Pseudotsuga menziesii) in relation to functional diverse species mixtures using data from a 4-year field experiment in Northwest Germany. Here we show that species mixing can mitigate the negative effects of combined N fertilization and D events, but the community response is mainly driven by the combination of certain traits rather than the tree species richness of a community. For beech, we found that negative effects of D on growth rates were amplified by N fertilization (i.e., combined treatment effects were non-additive), while for oak and fir, the simultaneous effects of N and D were additive. Beech and oak were identified as most sensitive to combined N+D effects with a strong size-dependency observed for beech, suggesting that the negative impact of N+D becomes stronger with time as beech grows larger. As a consequence, the net biodiversity effect declined at the community level, which can be mainly assigned to a distinct loss of complementarity in beech-oak mixtures. This pattern, however, was not evident in the other species-mixtures, indicating that neighborhood composition (i.e., trait combination), but not tree species richness mediated the relationship between tree diversity and treatment effects on tree growth. Our findings point to the importance of the qualitative role ('trait portfolio') that biodiversity play in determining resistance of diverse tree communities to environmental changes. As such, they provide further

  9. Early positive effects of tree species richness on herbivory in a large-scale forest biodiversity experiment influence tree growth

    PubMed Central

    Schuldt, Andreas; Bruelheide, Helge; Härdtle, Werner; Assmann, Thorsten; Li, Ying; Ma, Keping; von Oheimb, Goddert; Zhang, Jiayong

    2015-01-01

    Despite the importance of herbivory for the structure and functioning of species-rich forests, little is known about how herbivory is affected by tree species richness, and more specifically by random vs. non-random species loss. We assessed herbivore damage and its effects on tree growth in the early stage of a large-scale forest biodiversity experiment in subtropical China that features random and non-random extinction scenarios of tree mixtures numbering between one and 24 species. In contrast to random species loss, the non-random extinction scenarios were based on the tree species’ local rarity and specific leaf area – traits that may strongly influence the way herbivory is affected by plant species richness. Herbivory increased with tree species richness across all scenarios and was unaffected by the different species compositions in the random and non-random extinction scenarios. Whereas tree growth rates were positively related to herbivory on plots with smaller trees, growth rates significantly declined with increasing herbivory on plots with larger trees. Our results suggest that the effects of herbivory on growth rates increase from monocultures to the most species-rich plant communities and that negative effects with increasing tree species richness become more pronounced with time as trees grow larger. Synthesis. Our results indicate that key trophic interactions can be quick to become established in forest plantations (i.e. already 2.5 years after tree planting). Stronger herbivory effects on tree growth with increasing tree species richness suggest a potentially important role of herbivory in regulating ecosystem functions and the structural development of species-rich forests from the very start of secondary forest succession. The lack of significant differences between the extinction scenarios, however, contrasts with findings from natural forests of higher successional age, where rarity had negative effects on herbivory. This indicates that

  10. Do ectomycorrhizal and arbuscular mycorrhizal temperate tree species systematically differ in root order-related fine root morphology and biomass?

    PubMed Central

    Kubisch, Petra; Hertel, Dietrich; Leuschner, Christoph

    2015-01-01

    While most temperate broad-leaved tree species form ectomycorrhizal (EM) symbioses, a few species have arbuscular mycorrhizas (AM). It is not known whether EM and AM tree species differ systematically with respect to fine root morphology, fine root system size and root functioning. In a species-rich temperate mixed forest, we studied the fine root morphology and biomass of three EM and three AM tree species from the genera Acer, Carpinus, Fagus, Fraxinus, and Tilia searching for principal differences between EM and AM trees. We further assessed the evidence of convergence or divergence in root traits among the six co-occurring species. Eight fine root morphological and chemical traits were investigated in root segments of the first to fourth root order in three different soil depths and the relative importance of the factors root order, tree species and soil depth for root morphology was determined. Root order was more influential than tree species while soil depth had only a small effect on root morphology All six species showed similar decreases in specific root length and specific root area from the 1st to the 4th root order, while the species patterns differed considerably in root tissue density, root N concentration, and particularly with respect to root tip abundance. Most root morphological traits were not significantly different between EM and AM species (except for specific root area that was larger in AM species), indicating that mycorrhiza type is not a key factor influencing fine root morphology in these species. The order-based root analysis detected species differences more clearly than the simple analysis of bulked fine root mass. Despite convergence in important root traits among AM and EM species, even congeneric species may differ in certain fine root morphological traits. This suggests that, in general, species identity has a larger influence on fine root morphology than mycorrhiza type. PMID:25717334

  11. Community structure influences species' abundance along environmental gradients.

    PubMed

    Eloranta, Antti P; Helland, Ingeborg P; Sandlund, Odd T; Hesthagen, Trygve; Ugedal, Ola; Finstad, Anders G

    2016-01-01

    Species' response to abiotic environmental variation can be influenced by local community structure and interspecific interactions, particularly in restricted habitats such as islands and lakes. In temperate lakes, future increase in water temperature and run-off of terrestrial (allochthonous) dissolved organic carbon (DOC) are predicted to alter community composition and the overall ecosystem productivity. However, little is known about how the present community structure and abiotic environmental variation interact to affect the abundance of native fish populations. We used a space-for-time approach to study how local community structure interact with lake morphometric and climatic characteristics (i.e. temperature and catchment productivity) to affect brown trout (Salmo trutta L.) yield in 283 Norwegian lakes located in different biogeographical regions. Brown trout yield (based on data from standardized survey gill net fishing; g 100 m(-2) gill net night(-1)) was generally lower in lakes where other fish species were present than in lakes with brown trout only. The yield showed an overall negative relationship with increasing temperature and a positive relationship with lake shoreline complexity. Brown trout yield was also negatively correlated with DOC load (measured using Normalized Difference Vegetation Index as a proxy) and lake size and depth (measured using terrain slope as a proxy), but only in lakes where other fish species were present. The observed negative response of brown trout yield to increasing DOC load and proportion of the pelagic open-water area is likely due to restricted (littoral) niche availability and competitive dominance of more pelagic fishes such as Arctic charr (Salvelinus alpinus (L.)). Our study highlights that, through competitive interactions, the local community structure can influence the response of a species' abundance to variation in abiotic conditions. Changes in biomass and niche use of top predators (such as the brown

  12. Analyzing fractal property of species abundance distribution and diversity indexes.

    PubMed

    Su, Qiang

    2016-03-01

    Community diversity is usually characterized by numerical indexes; however it indeed depends on the species abundance distribution (SAD). Diversity indexes and SAD are based on the same information but treating as separate themes. Ranking species abundance from largest to smallest, the decreasing pattern can give the information about the SAD. Frontier proposed such SAD might be a fractal structure, and first applied the Zipf-Mandelbrot model to the SAD study. However, this model fails to include the Zipf model, and also fails to ensure an integer rank. In this study, a fractal model of SAD was reconstructed, and tested with 104 community samples from 8 taxonomic groups. The results show that there was a good fit of the presented model. Fractal parameter (p) determines the SAD of a community. The ecological significance of p relates to the "dominance" of a community. The correlation between p and classical diversity indexes show that Shannon index decreases and Simpson index increases as p increases. The main purpose of this paper is not to compare with other SADs models; it simply provides a new interpretation of SAD model construction, and preliminarily integrates diversity indexes and SAD model into a broader perspective of community diversity. PMID:26746388

  13. Metagenomic abundance estimation and diagnostic testing on species level

    PubMed Central

    Lindner, Martin S.; Renard, Bernhard Y.

    2013-01-01

    One goal of sequencing-based metagenomic community analysis is the quantitative taxonomic assessment of microbial community compositions. In particular, relative quantification of taxons is of high relevance for metagenomic diagnostics or microbial community comparison. However, the majority of existing approaches quantify at low resolution (e.g. at phylum level), rely on the existence of special genes (e.g. 16S), or have severe problems discerning species with highly similar genome sequences. Yet, problems as metagenomic diagnostics require accurate quantification on species level. We developed Genome Abundance Similarity Correction (GASiC), a method to estimate true genome abundances via read alignment by considering reference genome similarities in a non-negative LASSO approach. We demonstrate GASiC’s superior performance over existing methods on simulated benchmark data as well as on real data. In addition, we present applications to datasets of both bacterial DNA and viral RNA source. We further discuss our approach as an alternative to PCR-based DNA quantification. PMID:22941661

  14. Multilocus inference of species trees and DNA barcoding

    PubMed Central

    2016-01-01

    The unprecedented amount of data resulting from next-generation sequencing has opened a new era in phylogenetic estimation. Although large datasets should, in theory, increase phylogenetic resolution, massive, multilocus datasets have uncovered a great deal of phylogenetic incongruence among different genomic regions, due both to stochastic error and to the action of different evolutionary process such as incomplete lineage sorting, gene duplication and loss and horizontal gene transfer. This incongruence violates one of the fundamental assumptions of the DNA barcoding approach, which assumes that gene history and species history are identical. In this review, we explain some of the most important challenges we will have to face to reconstruct the history of species, and the advantages and disadvantages of different strategies for the phylogenetic analysis of multilocus data. In particular, we describe the evolutionary events that can generate species tree—gene tree discordance, compare the most popular methods for species tree reconstruction, highlight the challenges we need to face when using them and discuss their potential utility in barcoding. Current barcoding methods sacrifice a great amount of statistical power by only considering one locus, and a transition to multilocus barcodes would not only improve current barcoding methods, but also facilitate an eventual transition to species-tree-based barcoding strategies, which could better accommodate scenarios where the barcode gap is too small or inexistent. This article is part of the themed issue ‘From DNA barcodes to biomes’. PMID:27481787

  15. Infer Metagenomic Abundance and Reveal Homologous Genomes Based on the Structure of Taxonomy Tree.

    PubMed

    Qiu, Yu-Qing; Tian, Xue; Zhang, Shihua

    2015-01-01

    Metagenomic research uses sequencing technologies to investigate the genetic biodiversity of microbiomes presented in various ecosystems or animal tissues. The composition of a microbial community is highly associated with the environment in which the organisms exist. As large amount of sequencing short reads of microorganism genomes obtained, accurately estimating the abundance of microorganisms within a metagenomic sample is becoming an increasing challenge in bioinformatics. In this paper, we describe a hierarchical taxonomy tree-based mixture model (HTTMM) for estimating the abundance of taxon within a microbial community by incorporating the structure of the taxonomy tree. In this model, genome-specific short reads and homologous short reads among genomes can be distinguished and represented by leaf and intermediate nodes in the taxonomy tree, respectively. We adopt an expectation-maximization algorithm to solve this model. Using simulated and real-world data, we demonstrate that the proposed method is superior to both flat mixture model and lowest common ancestry-based methods. Moreover, this model can reveal previously unaddressed homologous genomes. PMID:26451823

  16. SPECIES-ABUNDANCE-BIOMASS RESPONSES BY ESTUARINE MACROBENTHOS TO SEDIMENT CHEMICAL CONTAMINATION.

    EPA Science Inventory

    Macrobenthic community responses can be measured through concerted changes in univariate metrics, including species richness, total abundance, and total biomass. The classic model of pollution effects on marine macroinvertebrate communities recognizes that species/abundance/bioma...

  17. Widespread Discordance of Gene Trees with Species Tree inDrosophila: Evidence for Incomplete Lineage Sorting

    SciTech Connect

    Pollard, Daniel A.; Iyer, Venky N.; Moses, Alan M.; Eisen,Michael B.

    2006-08-28

    The phylogenetic relationship of the now fully sequencedspecies Drosophila erecta and D. yakuba with respect to the D.melanogaster species complex has been a subject of controversy. All threepossible groupings of the species have been reported in the past, thoughrecent multi-gene studies suggest that D. erecta and D. yakuba are sisterspecies. Using the whole genomes of each of these species as well as thefour other fully sequenced species in the subgenus Sophophora, we set outto investigate the placement of D. erecta and D. yakuba in the D.melanogaster species group and to understand the cause of the pastincongruence. Though we find that the phylogeny grouping D. erecta and D.yakuba together is the best supported, we also find widespreadincongruence in nucleotide and amino acid substitutions, insertions anddeletions, and gene trees. The time inferred to span the two keyspeciation events is short enough that under the coalescent model, theincongruence could be the result of incomplete lineage sorting.Consistent with the lineage-sorting hypothesis, substitutions supportingthe same tree were spatially clustered. Support for the different treeswas found to be linked to recombination such that adjacent genes supportthe same tree most often in regions of low recombination andsubstitutions supporting the same tree are most enriched roughly on thesame scale as linkage disequilibrium, also consistent with lineagesorting. The incongruence was found to be statistically significant androbust to model and species choice. No systematic biases were found. Weconclude that phylogenetic incongruence in the D. melanogaster speciescomplex is the result, at least in part, of incomplete lineage sorting.Incomplete lineage sorting will likely cause phylogenetic incongruence inmany comparative genomics datasets. Methods to infer the correct speciestree, the history of every base in the genome, and comparative methodsthat control for and/or utilize this information will be

  18. A multigene species tree for Western Mediterranean painted frogs (Discoglossus).

    PubMed

    Pabijan, Maciej; Crottini, Angelica; Reckwell, Dennis; Irisarri, Iker; Hauswaldt, J Susanne; Vences, Miguel

    2012-09-01

    Painted frogs (Discoglossus) are an anuran clade that originated in the Upper Miocene. Extant species are morphologically similar and have a circum-Mediterranean distribution. We assembled a multilocus dataset from seven nuclear and four mitochondrial genes for several individuals of all but one of the extant species and reconstructed a robust phylogeny by applying a coalescent-based species-tree method and a concatenation approach, both of which gave congruent results. The earliest phylogenetic split within Discoglossus separates D. montalentii from a clade comprising all other species. Discoglossus montalentii is monophyletic for haplotype variation at all loci and has distinct morphological, bioacoustic and karyotypic characters. We find moderate support for a sister-group relationship between the Iberian taxa and the Moroccan D. scovazzi, and high support for a D. pictus -D. sardus clade distributed around the Tyrrhenian basin. Topological discordance among gene trees during the speciation of D. galganoi, D. scovazzi, D. pictus and D. sardus is interpreted as the consequence of nearly simultaneous, vicariant diversification. The timing of these events is unclear, but possibly coincided with the final geotectonic rearrangement of the Western Mediterranean in the Middle Miocene or later during the Messinian salinity crisis. The Iberian taxa D. galganoi galganoi and D. g. jeanneae are reciprocally monophyletic in mitochondrial DNA but not in nuclear gene trees, and are therefore treated as subspecies of D. galganoi. PMID:22641173

  19. 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. PMID:27605507

  20. Neither Host-specific nor Random: Vascular Epiphytes on Three Tree Species in a Panamanian Lowland Forest

    PubMed Central

    LAUBE, STEFAN; ZOTZ, GERHARD

    2006-01-01

    • Background and Aims A possible role of host tree identity in the structuring of vascular epiphyte communities has attracted scientific attention for decades. Specifically, it has been suggested that each host tree species has a specific subset of the local species pool according to its own set of properties, e.g. physicochemical characteristics of the bark, tree architecture, or leaf phenology patterns. • Methods A novel, quantitative approach to this question is presented, taking advantage of a complete census of the vascular epiphyte community in 0·4 ha of undisturbed lowland forest in Panama. For three locally common host-tree species (Socratea exorrhiza, Marila laxiflora, Perebea xanthochyma) null models were created of the expected epiphyte assemblages assuming that epiphyte colonization reflected random distribution of epiphytes in the forest. • Key Results In all three tree species, abundances of the majority of epiphyte species (69–81 %) were indistinguishable from random, while the remaining species were about equally over- or under-represented compared with their occurrence in the entire forest plot. Permutations based on the number of colonized trees (reflecting observed spatial patchiness) yielded similar results. Finally, a third analysis (canonical correspondence analysis) also confirmed host-specific differences in epiphyte assemblages. In spite of pronounced preferences of some epiphytes for particular host trees, no epiphyte species was restricted to a single host. • Conclusions The epiphytes on a given tree species are not simply a random sample of the local species pool, but there are no indications of host specificity either. PMID:16574691

  1. Narrowing historical uncertainty: probabilistic classification of ambiguously identified tree species in historical forest survey data

    USGS Publications Warehouse

    Mladenoff, D.J.; Dahir, S.E.; Nordheim, E.V.; Schulte, L.A.; Guntenspergen, G.R.

    2002-01-01

    formerly present in maps of historic ecosystems for the region and can be applied to PLS datasets elsewhere, as well as other sources of ambiguous historical data. Mapping the newly classified data with ecological land units provides additional information on the distribution, abundance, and associations of tree species, as well as their relationships to environmental gradients before the industrial period, and clarifies the identities of species formerly mapped only to genus. We offer some caveats on the appropriate use of data derived in this way, as well as describing their potential.

  2. Astrochem: Abundances of chemical species in the interstellar medium

    NASA Astrophysics Data System (ADS)

    Maret, Sébastien; Bergin, Edwin A.

    2015-07-01

    Astrochem computes the abundances of chemical species in the interstellar medium, as function of time. It studies the chemistry in a variety of astronomical objects, including diffuse clouds, dense clouds, photodissociation regions, prestellar cores, protostars, and protostellar disks. Astrochem reads a network of chemical reactions from a text file, builds up a system of kinetic rates equations, and solves it using a state-of-the-art stiff ordinary differential equation (ODE) solver. The Jacobian matrix of the system is computed implicitly, so the resolution of the system is extremely fast: large networks containing several thousands of reactions are usually solved in a few seconds. A variety of gas phase process are considered, as well as simple gas-grain interactions, such as the freeze-out and the desorption via several mechanisms (thermal desorption, cosmic-ray desorption and photo-desorption). The computed abundances are written in a HDF5 file, and can be plotted in different ways with the tools provided with Astrochem. Chemical reactions and their rates are written in a format which is meant to be easy to read and to edit. A tool to convert the chemical networks from the OSU and KIDA databases into this format is also provided. Astrochem is written in C, and its source code is distributed under the terms of the GNU General Public License (GPL).

  3. Fuel breaks affect nonnative species abundance in Californian plant communities

    USGS Publications Warehouse

    Merriam, K.E.; Keeley, J.E.; Beyers, J.L.

    2006-01-01

    We evaluated the abundance of nonnative plants on fuel breaks and in adjacent untreated areas to determine if fuel treatments promote the invasion of nonnative plant species. Understanding the relationship between fuel treatments and nonnative plants is becoming increasingly important as federal and state agencies are currently implementing large fuel treatment programs throughout the United States to reduce the threat of wildland fire. Our study included 24 fuel breaks located across the State of California. We found that nonnative plant abundance was over 200% higher on fuel breaks than in adjacent wildland areas. Relative nonnative cover was greater on fuel breaks constructed by bulldozers (28%) than on fuel breaks constructed by other methods (7%). Canopy cover, litter cover, and duff depth also were significantly lower on fuel breaks constructed by bulldozers, and these fuel breaks had significantly more exposed bare ground than other types of fuel breaks. There was a significant decline in relative nonnative cover with increasing distance from the fuel break, particularly in areas that had experienced more numerous fires during the past 50 years, and in areas that had been grazed. These data suggest that fuel breaks could provide establishment sites for nonnative plants, and that nonnatives may invade surrounding areas, especially after disturbances such as fire or grazing. Fuel break construction and maintenance methods that leave some overstory canopy and minimize exposure of bare ground may be less likely to promote nonnative plants. ?? 2006 by the Ecological Society of America.

  4. Climatic extremes improve predictions of spatial patterns of tree species

    USGS Publications Warehouse

    Zimmermann, N.E.; Yoccoz, N.G.; Edwards, T.C., Jr.; Meier, E.S.; Thuiller, W.; Guisan, A.; Schmatz, D.R.; Pearman, P.B.

    2009-01-01

    Understanding niche evolution, dynamics, and the response of species to climate change requires knowledge of the determinants of the environmental niche and species range limits. Mean values of climatic variables are often used in such analyses. In contrast, the increasing frequency of climate extremes suggests the importance of understanding their additional influence on range limits. Here, we assess how measures representing climate extremes (i.e., interannual variability in climate parameters) explain and predict spatial patterns of 11 tree species in Switzerland. We find clear, although comparably small, improvement (+20% in adjusted D2, +8% and +3% in cross-validated True Skill Statistic and area under the receiver operating characteristics curve values) in models that use measures of extremes in addition to means. The primary effect of including information on climate extremes is a correction of local overprediction and underprediction. Our results demonstrate that measures of climate extremes are important for understanding the climatic limits of tree species and assessing species niche characteristics. The inclusion of climate variability likely will improve models of species range limits under future conditions, where changes in mean climate and increased variability are expected.

  5. Leaf and whole-tree water use relations of Australian rainforest species

    NASA Astrophysics Data System (ADS)

    Ishida, Yoko; Laurance, Susan; Liddell, Michael; Lloyd, Jonathan

    2015-04-01

    Climate change induces drought events and may therefore cause significant impact on tropical rainforests, where most plants are reliant on high water availability - potentially affecting the distribution, composition and abundance of plant species. Using an experimental approach, we are studying the effects of a simulated drought on lowland rainforest plants at the Daintree Rainforest Observatory (DRO), in tropical northern Australia. Before to build up the rainout infrastructure, we installed sap flow meters (HRM) on 62 rainforest trees. Eight tree species were selected with diverse ecological strategies including wood density values ranging from 0.34 to 0.88 g/cm3 and could be replicated within a 1ha plot: Alstonia scholaris (Apocynaceae), Argyrondendron peralatum (Malvaceae), Elaeocarpus angustifolius (Elaeocarpaceae), Endiandra microneura (Lauraceae), Myristica globosa (Myristicaceae), Syzygium graveolens (Myrtaceae), Normanbya normanbyi (Arecaceae), and Castanospermum australe (Fabaceae). Our preliminary results from sap flow data obtained from October 2013 to December of 2014 showed differences in the amount of water used by our trees varied in response to species, size and climate. For example Syzygium graveolens has used a maximum of 60 litres/day while Argyrondendrum peralatum used 13 litres/day. Other potential causes for differential water-use between species and the implications of our research will be discussed. We will continue to monitor sap flow during the rainfall exclusion (2014 to 2016) to determine the effects of plant physiological traits on water use strategies.

  6. Tree species effects on decomposition and forest floor dynamics in a common garden.

    PubMed

    Hobbie, Sarah E; Reich, Peter B; Oleksyn, Jacek; Ogdahl, Megan; Zytkowiak, Roma; Hale, Cynthia; Karolewski, Piotr

    2006-09-01

    We studied the effects of tree species on leaf litter decomposition and forest floor dynamics in a common garden experiment of 14 tree species (Abies alba, Acer platanoides, Acer pseudoplatanus, Betula pendula, Carpinus betulus, Fagus sylvatica, Larix decidua, Picea abies, Pinus nigra, Pinus sylvestris, Pseudotsuga menziesii, Quercus robur, Quercus rubra, and Tilia cordata) in southwestern Poland. We used three simultaneous litter bag experiments to tease apart species effects on decomposition via leaf litter chemistry vs. effects on the decomposition environment. Decomposition rates of litter in its plot of origin were negatively correlated with litter lignin and positively correlated with mean annual soil temperature (MAT(soil)) across species. Likewise, decomposition of a common litter type across all plots was positively associated with MAT(soil), and decomposition of litter from all plots in a common plot was negatively related to litter lignin but positively related to litter Ca. Taken together, these results indicate that tree species influenced microbial decomposition primarily via differences in litter lignin (and secondarily, via differences in litter Ca), with high-lignin (and low-Ca) species decomposing most slowly, and by affecting MAT(soil), with warmer plots exhibiting more rapid decomposition. In addition to litter bag experiments, we examined forest floor dynamics in each plot by mass balance, since earthworms were a known component of these forest stands and their access to litter in litter bags was limited. Forest floor removal rates estimated from mass balance were positively related to leaf litter Ca (and unrelated to decay rates obtained using litter bags). Litter Ca, in turn, was positively related to the abundance of earthworms, particularly Lumbricus terrestris. Thus, while species influence microbially mediated decomposition primarily through differences in litter lignin, differences among species in litter Ca are most important in

  7. Target strengths of two abundant mesopelagic fish species.

    PubMed

    Scoulding, Ben; Chu, Dezhang; Ona, Egil; Fernandes, Paul G

    2015-02-01

    Mesopelagic fish of the Myctophidae and Sternoptychidae families dominate the biomass of the oceanic deep scattering layers and, therefore, have important ecological roles within these ecosystems. Interest in the commercial exploitation of these fish is growing, so the development of techniques for estimating their abundance, distribution and, ultimately, sustainable exploitation are essential. The acoustic backscattering characteristics for two size classes of Maurolicus muelleri and Benthosema glaciale are reported here based on swimbladder morphology derived from digitized soft x-ray images, and empirical (in situ) measurements of target strength (TS) derived from an acoustic survey in a Norwegian Sea. A backscattering model based on a gas-filled prolate spheroid was used to predict the theoretical TS for both species across a frequency range between 0 and 250 kHz. Sensitivity analyses of the TS model to the modeling parameters indicate that TS is rather sensitive to the viscosity, swimbladder volume ratio, and tilt, which can result in substantial changes to the TS. Theoretical TS predictions close to the resonance frequency were in good agreement (±2 dB) with mean in situ TS derived from the areas acoustically surveyed that were spatially and temporally consistent with the trawl information for both species. PMID:25698030

  8. Daughter Species Abundances in Comet C/2014 Q2 (Lovejoy)

    NASA Astrophysics Data System (ADS)

    McKay, Adam; Cochran, Anita; Dello Russo, Neil; Kelley, Michael

    2015-11-01

    We present analysis of high spectral resolution optical spectra of C/2014 Q2 (Lovejoy) acquired with the Tull Coude spectrometer on the 2.7-meter Harlan J. Smith Telescope at McDonald Observatory and the ARCES spectrometer mounted on the 3.5-meter Astrophysical Research Consortium Telescope at Apache Point Observatory. Both Tull Coude and ARCES provide high spectral resolution (R=30,000-60,000) and a large spectral range of approximately 3500-10000 Angstroms. We obtained two observation epochs, one in February 2015 at a heliocentric distance of 1.3 AU, and another in May 2015 at a heliocentric distance of 1.9 AU. Another epoch in late August 2015 at a heliocentric distance of 3.0 AU is scheduled. We will present production rates of the daughter species CN, C3, CH, C2, and NH2. We will also present H2O production rates derived from the [OI]6300 emission, as well as measurements of the flux ratio of the [OI]5577 Angstrom line to the sum of the [OI]6300 and [OI]6364 Angstrom lines (sometimes referred to as the oxygen line ratio). This ratio is indicative of the CO2 abundance of the comet. As we have observations at several heliocentric distances, we will examine how production rates and mixing ratios of the various species change with heliocentric distance. We will compare our oxygen line measurements to observations of CO2 made with Spitzer, as well as our other daughter species observations to those of candidate parent molecules made at IR wavelengths.

  9. Abundance changes and habitat availability drive species' responses to climate change

    NASA Astrophysics Data System (ADS)

    Mair, Louise; Hill, Jane K.; Fox, Richard; Botham, Marc; Brereton, Tom; Thomas, Chris D.

    2014-02-01

    There is little consensus as to why there is so much variation in the rates at which different species' geographic ranges expand in response to climate warming. Here we show that the relative importance of species' abundance trends and habitat availability for British butterfly species vary over time. Species with high habitat availability expanded more rapidly from the 1970s to mid-1990s, when abundances were generally stable, whereas habitat availability effects were confined to the subset of species with stable abundances from the mid-1990s to 2009, when abundance trends were generally declining. This suggests that stable (or positive) abundance trends are a prerequisite for range expansion. Given that species' abundance trends vary over time for non-climatic as well as climatic reasons, assessment of abundance trends will help improve predictions of species' responses to climate change, and help us to understand the likely success of different conservation strategies for facilitating their expansions.

  10. Semi-supervised SVM for individual tree crown species classification

    NASA Astrophysics Data System (ADS)

    Dalponte, Michele; Ene, Liviu Theodor; Marconcini, Mattia; Gobakken, Terje; Næsset, Erik

    2015-12-01

    In this paper a novel semi-supervised SVM classifier is presented, specifically developed for tree species classification at individual tree crown (ITC) level. In ITC tree species classification, all the pixels belonging to an ITC should have the same label. This assumption is used in the learning of the proposed semi-supervised SVM classifier (ITC-S3VM). This method exploits the information contained in the unlabeled ITC samples in order to improve the classification accuracy of a standard SVM. The ITC-S3VM method can be easily implemented using freely available software libraries. The datasets used in this study include hyperspectral imagery and laser scanning data acquired over two boreal forest areas characterized by the presence of three information classes (Pine, Spruce, and Broadleaves). The experimental results quantify the effectiveness of the proposed approach, which provides classification accuracies significantly higher (from 2% to above 27%) than those obtained by the standard supervised SVM and by a state-of-the-art semi-supervised SVM (S3VM). Particularly, by reducing the number of training samples (i.e. from 100% to 25%, and from 100% to 5% for the two datasets, respectively) the proposed method still exhibits results comparable to the ones of a supervised SVM trained with the full available training set. This property of the method makes it particularly suitable for practical forest inventory applications in which collection of in situ information can be very expensive both in terms of cost and time.

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

    PubMed

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

    2015-07-01

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

  12. Inferring Species Trees from Gene Trees in a Radiation of California Trapdoor Spiders (Araneae, Antrodiaetidae, Aliatypus)

    PubMed Central

    Satler, Jordan D.; Starrett, James; Hayashi, Cheryl Y.; Hedin, Marshal

    2011-01-01

    Background The California Floristic Province is a biodiversity hotspot, reflecting a complex geologic history, strong selective gradients, and a heterogeneous landscape. These factors have led to high endemic diversity across many lifeforms within this region, including the richest diversity of mygalomorph spiders (tarantulas, trapdoor spiders, and kin) in North America. The trapdoor spider genus Aliatypus encompasses twelve described species, eleven of which are endemic to California. Several Aliatypus species show disjunct distributional patterns in California (some are found on both sides of the vast Central Valley), and the genus as a whole occupies an impressive variety of habitats. Methodology/Principal Findings We collected specimens from 89 populations representing all described species. DNA sequence data were collected from seven gene regions, including two newly developed for spider systematics. Bayesian inference (in individual gene tree and species tree approaches) recovered a general “3 clade” structure for the genus (A. gulosus, californicus group, erebus group), with three other phylogenetically isolated species differing slightly in position across different phylogenetic analyses. Because of extremely high intraspecific divergences in mitochondrial COI sequences, the relatively slowly evolving 28S rRNA gene was found to be more useful than mitochondrial data for identification of morphologically indistinguishable immatures. For multiple species spanning the Central Valley, explicit hypothesis testing suggests a lack of monophyly for regional populations (e.g., western Coast Range populations). Phylogenetic evidence clearly shows that syntopy is restricted to distant phylogenetic relatives, consistent with ecological niche conservatism. Conclusions/Significance This study provides fundamental insight into a radiation of trapdoor spiders found in the biodiversity hotspot of California. Species relationships are clarified and undescribed lineages

  13. Relating tree growth to rainfall in Bolivian rain forests: a test for six species using tree ring analysis.

    PubMed

    Brienen, Roel J W; Zuidema, Pieter A

    2005-11-01

    Many tropical regions show one distinct dry season. Often, this seasonality induces cambial dormancy of trees, particularly if these belong to deciduous species. This will often lead to the formation of annual rings. The aim of this study was to determine whether tree species in the Bolivian Amazon region form annual rings and to study the influence of the total amount and seasonal distribution of rainfall on diameter growth. Ring widths were measured on stem discs of a total of 154 trees belonging to six rain forest species. By correlating ring width and monthly rainfall data we proved the annual character of the tree rings for four of our study species. For two other species the annual character was proved by counting rings on trees of known age and by radiocarbon dating. The results of the climate-growth analysis show a positive relationship between tree growth and rainfall in certain periods of the year, indicating that rainfall plays a major role in tree growth. Three species showed a strong relationship with rainfall at the beginning of the rainy season, while one species is most sensitive to the rainfall at the end of the previous growing season. These results clearly demonstrate that tree ring analysis can be successfully applied in the tropics and that it is a promising method for various research disciplines. PMID:16012820

  14. 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 (Ec) 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 Gc at VPD = 1 kPa (Gcref) and the Gc sensitivity to VPD (−dGc/dlnVPD) across studied species as well as under contrasting soil water and Rs 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 Gcref. PMID:23118904

  15. Commonly Rare and Rarely Common: Comparing Population Abundance of Invasive and Native Aquatic Species

    PubMed Central

    Hansen, Gretchen J. A.; Vander Zanden, M. Jake; Blum, Michael J.; Clayton, Murray K.; Hain, Ernie F.; Hauxwell, Jennifer; Izzo, Marit; Kornis, Matthew S.; McIntyre, Peter B.; Mikulyuk, Alison; Nilsson, Erika; Olden, Julian D.; Papeş, Monica; Sharma, Sapna

    2013-01-01

    Invasive species are leading drivers of environmental change. Their impacts are often linked to their population size, but surprisingly little is known about how frequently they achieve high abundances. A nearly universal pattern in ecology is that species are rare in most locations and abundant in a few, generating right-skewed abundance distributions. Here, we use abundance data from over 24,000 populations of 17 invasive and 104 native aquatic species to test whether invasive species differ from native counterparts in statistical patterns of abundance across multiple sites. Invasive species on average reached significantly higher densities than native species and exhibited significantly higher variance. However, invasive and native species did not differ in terms of coefficient of variation, skewness, or kurtosis. Abundance distributions of all species were highly right skewed (skewness>0), meaning both invasive and native species occurred at low densities in most locations where they were present. The average abundance of invasive and native species was 6% and 2%, respectively, of the maximum abundance observed within a taxonomic group. The biological significance of the differences between invasive and native species depends on species-specific relationships between abundance and impact. Recognition of cross-site heterogeneity in population densities brings a new dimension to invasive species management, and may help to refine optimal prevention, containment, control, and eradication strategies. PMID:24194883

  16. Commonly rare and rarely common: comparing population abundance of invasive and native aquatic species.

    PubMed

    Hansen, Gretchen J A; Vander Zanden, M Jake; Blum, Michael J; Clayton, Murray K; Hain, Ernie F; Hauxwell, Jennifer; Izzo, Marit; Kornis, Matthew S; McIntyre, Peter B; Mikulyuk, Alison; Nilsson, Erika; Olden, Julian D; Papeş, Monica; Sharma, Sapna

    2013-01-01

    Invasive species are leading drivers of environmental change. Their impacts are often linked to their population size, but surprisingly little is known about how frequently they achieve high abundances. A nearly universal pattern in ecology is that species are rare in most locations and abundant in a few, generating right-skewed abundance distributions. Here, we use abundance data from over 24,000 populations of 17 invasive and 104 native aquatic species to test whether invasive species differ from native counterparts in statistical patterns of abundance across multiple sites. Invasive species on average reached significantly higher densities than native species and exhibited significantly higher variance. However, invasive and native species did not differ in terms of coefficient of variation, skewness, or kurtosis. Abundance distributions of all species were highly right skewed (skewness>0), meaning both invasive and native species occurred at low densities in most locations where they were present. The average abundance of invasive and native species was 6% and 2%, respectively, of the maximum abundance observed within a taxonomic group. The biological significance of the differences between invasive and native species depends on species-specific relationships between abundance and impact. Recognition of cross-site heterogeneity in population densities brings a new dimension to invasive species management, and may help to refine optimal prevention, containment, control, and eradication strategies. PMID:24194883

  17. Habitat fragmentation and effects of herbivore (howler monkey) abundances on bird species richness.

    PubMed

    Feeley, Kenneth J; Terborgh, John W

    2006-01-01

    Habitat fragmentation can alter herbivore abundances, potentially causing changes in the plant community that can propagate through the food web and eventually influence other important taxonomic groups such as birds. Here we test the relationship between the density of red howler monkeys (Alouatta seniculus) and bird species richness on a large set of recently isolated land-bridge islands in Lago Guri, Venezuela (n = 29 islands). Several of these islands host relict populations of howler monkeys at densities up to more than 30 times greater than those on the mainland. These "hyperabundant" herbivores previously have been shown to have a strong positive influence on aboveground plant productivity. We predicted that this should lead to a positive, indirect effect of howler monkey density on bird species richness. After accounting for passive sampling (the tendency for species richness to be positively associated with island area, regardless of differences in habitat quality) we found a significant positive correlation between howler monkey density and bird species richness. A path analysis incorporating data on tree growth rates from a subset of islands (n = 9) supported the hypothesis that the effect of howler monkeys on the resident bird communities is indirect and is mediated through changes in plant productivity and habitat quality. These results highlight the potential for disparate taxonomic groups to be related through indirect interactions and trophic cascades. PMID:16634305

  18. RELATIONSHIPS OF ALIEN PLANT SPECIES ABUNDANCE TO RIPARIAN VEGETATION, ENVIRONMENT, AND DISTURBANCE

    EPA Science Inventory

    Riparian ecosystems are often invaded by alien species. We evaluated vegetation, environment, and disturbance conditions and their interrelationships with alien species abundance along reaches of 29 streams in eastern Oregon, USA. Using flexible-BETA clustering, indicator species...

  19. Tree diversity and the role of non-host neighbour tree species in reducing fungal pathogen infestation

    PubMed Central

    Hantsch, Lydia; Bien, Steffen; Radatz, Stine; Braun, Uwe; Auge, Harald; Bruelheide, Helge

    2014-01-01

    The degree to which plant pathogen infestation occurs in a host plant is expected to be strongly influenced by the level of species diversity among neighbouring host and non-host plant species. Since pathogen infestation can negatively affect host plant performance, it can mediate the effects of local biodiversity on ecosystem functioning. We tested the effects of tree diversity and the proportion of neighbouring host and non-host species with respect to the foliar fungal pathogens of Tilia cordata and Quercus petraea in the Kreinitz tree diversity experiment in Germany. We hypothesized that fungal pathogen richness increases while infestation decreases with increasing local tree diversity. In addition, we tested whether fungal pathogen richness and infestation are dependent on the proportion of host plant species present or on the proportion of particular non-host neighbouring tree species. Leaves of the two target species were sampled across three consecutive years with visible foliar fungal pathogens on the leaf surface being identified macro- and microscopically. Effects of diversity among neighbouring trees were analysed: (i) for total fungal species richness and fungal infestation on host trees and (ii) for infestation by individual fungal species. We detected four and five fungal species on T. cordata and Q. petraea, respectively. High local tree diversity reduced (i) total fungal species richness and infestation of T. cordata and fungal infestation of Q. petraea and (ii) infestation by three host-specialized fungal pathogen species. These effects were brought about by local tree diversity and were independent of host species proportion. In general, host species proportion had almost no effect on fungal species richness and infestation. Strong effects associated with the proportion of particular non-host neighbouring tree species on fungal species richness and infestation were, however, recorded. Synthesis. For the first time, we experimentally

  20. Plant Trait-Species Abundance Relationships Vary with Environmental Properties in Subtropical Forests in Eastern China

    PubMed Central

    Yan, En-Rong; Yang, Xiao-Dong; Chang, Scott X.; Wang, Xi-Hua

    2013-01-01

    Understanding how plant trait-species abundance relationships change with a range of single and multivariate environmental properties is crucial for explaining species abundance and rarity. In this study, the abundance of 94 woody plant species was examined and related to 15 plant leaf and wood traits at both local and landscape scales involving 31 plots in subtropical forests in eastern China. Further, plant trait-species abundance relationships were related to a range of single and multivariate (PCA axes) environmental properties such as air humidity, soil moisture content, soil temperature, soil pH, and soil organic matter, nitrogen (N) and phosphorus (P) contents. At the landscape scale, plant maximum height, and twig and stem wood densities were positively correlated, whereas mean leaf area (MLA), leaf N concentration (LN), and total leaf area per twig size (TLA) were negatively correlated with species abundance. At the plot scale, plant maximum height, leaf and twig dry matter contents, twig and stem wood densities were positively correlated, but MLA, specific leaf area, LN, leaf P concentration and TLA were negatively correlated with species abundance. Plant trait-species abundance relationships shifted over the range of seven single environmental properties and along multivariate environmental axes in a similar way. In conclusion, strong relationships between plant traits and species abundance existed among and within communities. Significant shifts in plant trait-species abundance relationships in a range of environmental properties suggest strong environmental filtering processes that influence species abundance and rarity in the studied subtropical forests. PMID:23560114

  1. Plant trait-species abundance relationships vary with environmental properties in subtropical forests in eastern china.

    PubMed

    Yan, En-Rong; Yang, Xiao-Dong; Chang, Scott X; Wang, Xi-Hua

    2013-01-01

    Understanding how plant trait-species abundance relationships change with a range of single and multivariate environmental properties is crucial for explaining species abundance and rarity. In this study, the abundance of 94 woody plant species was examined and related to 15 plant leaf and wood traits at both local and landscape scales involving 31 plots in subtropical forests in eastern China. Further, plant trait-species abundance relationships were related to a range of single and multivariate (PCA axes) environmental properties such as air humidity, soil moisture content, soil temperature, soil pH, and soil organic matter, nitrogen (N) and phosphorus (P) contents. At the landscape scale, plant maximum height, and twig and stem wood densities were positively correlated, whereas mean leaf area (MLA), leaf N concentration (LN), and total leaf area per twig size (TLA) were negatively correlated with species abundance. At the plot scale, plant maximum height, leaf and twig dry matter contents, twig and stem wood densities were positively correlated, but MLA, specific leaf area, LN, leaf P concentration and TLA were negatively correlated with species abundance. Plant trait-species abundance relationships shifted over the range of seven single environmental properties and along multivariate environmental axes in a similar way. In conclusion, strong relationships between plant traits and species abundance existed among and within communities. Significant shifts in plant trait-species abundance relationships in a range of environmental properties suggest strong environmental filtering processes that influence species abundance and rarity in the studied subtropical forests. PMID:23560114

  2. The Impact of Missing Data on Species Tree Estimation.

    PubMed

    Xi, Zhenxiang; Liu, Liang; Davis, Charles C

    2016-03-01

    Phylogeneticists are increasingly assembling genome-scale data sets that include hundreds of genes to resolve their focal clades. Although these data sets commonly include a moderate to high amount of missing data, there remains no consensus on their impact to species tree estimation. Here, using several simulated and empirical data sets, we assess the effects of missing data on species tree estimation under varying degrees of incomplete lineage sorting (ILS) and gene rate heterogeneity. We demonstrate that concatenation (RAxML), gene-tree-based coalescent (ASTRAL, MP-EST, and STAR), and supertree (matrix representation with parsimony [MRP]) methods perform reliably, so long as missing data are randomly distributed (by gene and/or by species) and that a sufficiently large number of genes are sampled. When data sets are indecisive sensu Sanderson et al. (2010. Phylogenomics with incomplete taxon coverage: the limits to inference. BMC Evol Biol. 10:155) and/or ILS is high, however, high amounts of missing data that are randomly distributed require exhaustive levels of gene sampling, likely exceeding most empirical studies to date. Moreover, missing data become especially problematic when they are nonrandomly distributed. We demonstrate that STAR produces inconsistent results when the amount of nonrandom missing data is high, regardless of the degree of ILS and gene rate heterogeneity. Similarly, concatenation methods using maximum likelihood can be misled by nonrandom missing data in the presence of gene rate heterogeneity, which becomes further exacerbated when combined with high ILS. In contrast, ASTRAL, MP-EST, and MRP are more robust under all of these scenarios. These results underscore the importance of understanding the influence of missing data in the phylogenomics era. PMID:26589995

  3. Interannual Variation in Stand Transpiration is Dependent Upon Tree Species

    NASA Astrophysics Data System (ADS)

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

    2003-12-01

    In order to successfully predict transpirational water fluxes from forested watersheds, interannual variability in transpiration must be quantified and understood. In a heterogeneous forested landscape in northern Wisconsin, we quantified stand transpiration across four forest cover types representing more than 80 percent of the land area in order to 1) quantify differences in stand transpiration and leaf area over two years and 2) determine the mechanisms governing the changes in transpiration over two years. We measured sap flux in eight trees of each tree species in the four cover types. We found that in northern hardwoods, the leaf area of sugar maple increased between the two measurement years with transpiration per unit ground area increasing even more than could be explained by leaf area. In an aspen stand, tent caterpillars completely defoliated the stand for approximately a month until a new set of leaves flushed out. The new set of leaves resulted in a lower leaf area but the same transpiration per unit leaf area indicating there was no physiological compensation for the lower leaf area. At the same time, balsam fir growing underneath the aspen increased their transpiration rate in response to greater light penetration through the dominant aspen canopy Red pine had a thirty percent change in leaf area within a growing season due to multiple cohorts of leaves and transpiration followed this leaf area dynamic. In a forested wetland, white cedar transpiration was proportional to surface water depth between the two years. Despite the specific tree species' effects on stand transpiration, all species displayed a minimum water potential regulation resulting in a saturating response of transpiration to vapor pressure deficit that did not vary across the two years. This physiological set point will allow future water flux models to explain mechanistically interannual variability in transpiration of this and similar forests.

  4. Temporal dynamics of arthropods on six tree species in dry woodlands on the Caribbean Island of Puerto Rico.

    PubMed

    Beltrán, William; Wunderle, Joseph M

    2014-01-01

    The seasonal dynamics of foliage arthropod populations are poorly studied in tropical dry forests despite the importance of these studies for understanding arthropod population responses to environmental change. We monitored the abundance, temporal distributions, and body size of arthropods in five naturalized alien and one native tree species to characterize arthropod seasonality in dry novel Prosopis-Leucaena woodlands in Puerto Rico. A branch clipping method was used monthly to sample foliage arthropod abundance over 39 mo. Seasonal patterns of rainfall and abundance within various arthropod taxa were highly variable from year to year. Abundance for most taxa did not show significant seasonality over the 3 yr, although most taxa had abundance peaks each year. However, Homoptera displayed high seasonality with significant temporal aggregations in each year. Formicidae, Orthoptera, and Coleoptera showed high variation in abundance between wet and dry periods, whereas Hemiptera were consistently more abundant in the wet period. Seasonal differences in mean abundance were found only in a few taxa on Tamarindus indica L., Bucida buceras L., Pithecellobium dulce, and (Roxburgh) Benth. Mean arthropod abundance varied among tree species, with highest numbers on Prosopis juliflora, (Swartz) De Candolle, Pi. dulce, Leucaena leucocephala, and (Lamarck) de Wit. Abundance of Araneae, Orthoptera, Coleoptera, Lepidoptera larvae, and all arthropods showed weak relationships with one or more climatic variables (rainfall, maximum temperature, or relative humidity). Body size of arthropods was usually largest during the dry periods. Overall, total foliage arthropod abundance showed no consistent seasonality among years, which may become a more common trend in dry forests and woodlands in the Caribbean if seasonality of rainfall becomes less predictable. PMID:25502036

  5. Temporal Dynamics of Arthropods on Six Tree Species in Dry Woodlands on the Caribbean Island of Puerto Rico

    PubMed Central

    Beltrán, William; Wunderle, Joseph M.

    2014-01-01

    The seasonal dynamics of foliage arthropod populations are poorly studied in tropical dry forests despite the importance of these studies for understanding arthropod population responses to environmental change. We monitored the abundance, temporal distributions, and body size of arthropods in five naturalized alien and one native tree species to characterize arthropod seasonality in dry novel Prosopis–Leucaena woodlands in Puerto Rico. A branch clipping method was used monthly to sample foliage arthropod abundance over 39 mo. Seasonal patterns of rainfall and abundance within various arthropod taxa were highly variable from year to year. Abundance for most taxa did not show significant seasonality over the 3 yr, although most taxa had abundance peaks each year. However, Homoptera displayed high seasonality with significant temporal aggregations in each year. Formicidae, Orthoptera, and Coleoptera showed high variation in abundance between wet and dry periods, whereas Hemiptera were consistently more abundant in the wet period. Seasonal differences in mean abundance were found only in a few taxa on Tamarindus indica L., Bucida buceras L., Pithecellobium dulce, and (Roxburgh) Benth. Mean arthropod abundance varied among tree species, with highest numbers on Prosopis juliflora, (Swartz) De Candolle, Pi. dulce, Leucaena leucocephala, and (Lamarck) de Wit. Abundance of Araneae, Orthoptera, Coleoptera, Lepidoptera larvae, and all arthropods showed weak relationships with one or more climatic variables (rainfall, maximum temperature, or relative humidity). Body size of arthropods was usually largest during the dry periods. Overall, total foliage arthropod abundance showed no consistent seasonality among years, which may become a more common trend in dry forests and woodlands in the Caribbean if seasonality of rainfall becomes less predictable. PMID:25502036

  6. Nitrogen and phosphorus additions negatively affect tree species diversity in tropical forest regrowth trajectories.

    PubMed

    Siddique, Ilyas; Vieira, Ima Célia Guimarães; Schmidt, Susanne; Lamb, David; Carvalho, Cláudio José Reis; Figueiredo, Ricardo de Oliveira; Blomberg, Simon; Davidson, Eric A

    2010-07-01

    Nutrient enrichment is increasingly affecting many tropical ecosystems, but there is no information on how this affects tree biodiversity. To examine dynamics in vegetation structure and tree species biomass and diversity, we annually remeasured tree species before and for six years after repeated additions of nitrogen (N) and phosphorus (P) in permanent plots of abandoned pasture in Amazonia. Nitrogen and, to a lesser extent, phosphorus addition shifted growth among woody species. Nitrogen stimulated growth of two common pioneer tree species and one common tree species adaptable to both high- and low-light environments, while P stimulated growth only of the dominant pioneer tree Rollinia exsucca (Annonaceae). Overall, N or P addition reduced tree assemblage evenness and delayed tree species accrual over time, likely due to competitive monopolization of other resources by the few tree species responding to nutrient enrichment with enhanced establishment and/or growth rates. Absolute tree growth rates were elevated for two years after nutrient addition. However, nutrient-induced shifts in relative tree species growth and reduced assemblage evenness persisted for more than three years after nutrient addition, favoring two nutrient-responsive pioneers and one early-secondary tree species. Surprisingly, N + P effects on tree biomass and species diversity were consistently weaker than N-only and P-only effects, because grass biomass increased dramatically in response to N + P addition. The resulting intensified competition probably prevented an expected positive N + P synergy in the tree assemblage. Thus, N or P enrichment may favor unknown tree functional response types, reduce the diversity of coexisting species, and delay species accrual during structurally and functionally complex tropical rainforest secondary succession. PMID:20715634

  7. Tree Species Specific Soil Moisture Patterns and Dynamics

    NASA Astrophysics Data System (ADS)

    Heidbuechel, I.; Dreibrodt, J.; Guntner, A.; Blume, T.

    2014-12-01

    Land use has a major influence on the hydrologic processes that take place in soils. Soil compaction on pastures for example leads to infiltration patterns that differ considerably from the ones observable in forests. It is not clear, however, how different forest stands influence soil infiltration and soil moisture distributions. Factors that that vary amongst different stands and potentially affect soil moisture processes in forests are, amongst others, canopy density, throughfall patterns, the intensity and frequency of stem flow, litter type, root distributions and rooting depth. To investigate how different tree species influence the way soils partition, store and conduct incoming precipitation we selected 15 locations under different tree stands within the TERENO observatory in north-east Germany. The forest stands under investigation were mature oak, young pine, mature pine, young beech and mature beech. At each location we installed 30 FDR soil moisture sensors grouped into five depth profiles (monitoring soil moisture from 10 cm to 200 cm) and 5 additional near surface sensors. The profile locations within each forest stand covered most of the anticipated variability by ranging from minimum to maximum distance to the trees including locations under more and less dense canopy. Supplementary to the FDR sensors, throughfall measurements, tensiometers and groundwater data were available to observe dynamics of tree water availability, water fluxes within the soils and percolation towards the groundwater. To identify patterns in space and time we referred to the statistical methods of wavelet analysis and temporal stability analysis. Finally, we tried to link the results from these analyses to specific hydrologic processes at the different locations.

  8. Use of classification trees to apportion single echo detections to species: Application to the pelagic fish community of Lake Superior

    USGS Publications Warehouse

    Yule, Daniel L.; Adams, Jean V.; Hrabik, Thomas R.; Vinson, Mark R.; Woiak, Zebadiah; Ahrenstroff, Tyler D.

    2013-01-01

    Acoustic methods are used to estimate the density of pelagic fish in large lakes with results of midwater trawling used to assign species composition. Apportionment in lakes having mixed species can be challenging because only a small fraction of the water sampled acoustically is sampled with trawl gear. Here we describe a new method where single echo detections (SEDs) are assigned to species based on classification tree models developed from catch data that separate species based on fish size and the spatial habitats they occupy. During the summer of 2011, we conducted a spatially-balanced lake-wide acoustic and midwater trawl survey of Lake Superior. A total of 51 sites in four bathymetric depth strata (0–30 m, 30–100 m, 100–200 m, and >200 m) were sampled. We developed classification tree models for each stratum and found fish length was the most important variable for separating species. To apply these trees to the acoustic data, we needed to identify a target strength to length (TS-to-L) relationship appropriate for all abundant Lake Superior pelagic species. We tested performance of 7 general (i.e., multi-species) relationships derived from three published studies. The best-performing relationship was identified by comparing predicted and observed catch compositions using a second independent Lake Superior data set. Once identified, the relationship was used to predict lengths of SEDs from the lake-wide survey, and the classification tree models were used to assign each SED to a species. Exotic rainbow smelt (Osmerus mordax) were the most common species at bathymetric depths 100 m (384 million; 6.0 kt). Cisco (Coregonus artedi) were widely distributed over all strata with their population estimated at 182 million (44 kt). The apportionment method we describe should be transferable to other large lakes provided fish are not tightly aggregated, and an appropriate TS-to-L relationship for abundant pelagic fish species can be determined.

  9. Dependence of tree ring stable isotope abundances and ring width on climate in Finnish oak.

    PubMed

    Hilasvuori, Emmi; Berninger, Frank

    2010-05-01

    We measured ring widths and isotopic abundances of carbon, oxygen and hydrogen (delta(13)C, delta(18)O and delta(2)H) from the latewood of tree rings of pedunculate oak (Quercus robur L.) in its distributional northern limit in Southern Finland. Ring width was observed to be related to precipitation and relative humidity but not significantly to temperature. delta(13)C and delta(18)O were significantly related to all studied climatic variables, most strongly to cloud cover. Variations in delta(2)H were discovered to be complex combinations of signals from biochemical and physical processes. The results suggest that oaks in Finland can be used as a source of climate information. delta(18)O was discovered to be especially promising as it showed the strongest climate signal and highest common signal between trees. The relationship between climate and ring width indicates that water availability is the main control of ring radial growth. This is supported by the isotope data. High correlation between delta(13)C and delta(18)O time series indicates that photosynthetic carbon assimilation is limited by stomatal control. Therefore, in contrast to the expected temperature limitation, our data indicate that drought limits oak growth more than cold temperatures on the border of its northernmost distribution range. PMID:20357343

  10. Consistency and inconsistency of consensus methods for inferring species trees from gene trees in the presence of ancestral population structure.

    PubMed

    DeGiorgio, Michael; Rosenberg, Noah A

    2016-08-01

    In the last few years, several statistically consistent consensus methods for species tree inference have been devised that are robust to the gene tree discordance caused by incomplete lineage sorting in unstructured ancestral populations. One source of gene tree discordance that has only recently been identified as a potential obstacle for phylogenetic inference is ancestral population structure. In this article, we describe a general model of ancestral population structure, and by relying on a single carefully constructed example scenario, we show that the consensus methods Democratic Vote, STEAC, STAR, R(∗) Consensus, Rooted Triple Consensus, Minimize Deep Coalescences, and Majority-Rule Consensus are statistically inconsistent under the model. We find that among the consensus methods evaluated, the only method that is statistically consistent in the presence of ancestral population structure is GLASS/Maximum Tree. We use simulations to evaluate the behavior of the various consensus methods in a model with ancestral population structure, showing that as the number of gene trees increases, estimates on the basis of GLASS/Maximum Tree approach the true species tree topology irrespective of the level of population structure, whereas estimates based on the remaining methods only approach the true species tree topology if the level of structure is low. However, through simulations using species trees both with and without ancestral population structure, we show that GLASS/Maximum Tree performs unusually poorly on gene trees inferred from alignments with little information. This practical limitation of GLASS/Maximum Tree together with the inconsistency of other methods prompts the need for both further testing of additional existing methods and development of novel methods under conditions that incorporate ancestral population structure. PMID:27086043

  11. Neogene origins and implied warmth tolerance of Amazon tree species

    PubMed Central

    Dick, Christopher W; Lewis, Simon L; Maslin, Mark; Bermingham, Eldredge

    2013-01-01

    Tropical rain forest has been a persistent feature in South America for at least 55 million years. The future of the contemporary Amazon forest is uncertain, however, as the region is entering conditions with no past analogue, combining rapidly increasing air temperatures, high atmospheric carbon dioxide concentrations, possible extreme droughts, and extensive removal and modification by humans. Given the long-term Cenozoic cooling trend, it is unknown whether Amazon forests can tolerate air temperature increases, with suggestions that lowland forests lack warm-adapted taxa, leading to inevitable species losses. In response to this uncertainty, we posit a simple hypothesis: the older the age of a species prior to the Pleistocene, the warmer the climate it has previously survived, with Pliocene (2.6–5 Ma) and late-Miocene (8–10 Ma) air temperature across Amazonia being similar to 2100 temperature projections under low and high carbon emission scenarios, respectively. Using comparative phylogeographic analyses, we show that 9 of 12 widespread Amazon tree species have Pliocene or earlier lineages (>2.6 Ma), with seven dating from the Miocene (>5.6 Ma) and three >8 Ma. The remarkably old age of these species suggest that Amazon forests passed through warmth similar to 2100 levels and that, in the absence of other major environmental changes, near-term high temperature-induced mass species extinction is unlikely. PMID:23404439

  12. Evaluating Summary Methods for Multilocus Species Tree Estimation in the Presence of Incomplete Lineage Sorting.

    PubMed

    Mirarab, Siavash; Bayzid, Md Shamsuzzoha; Warnow, Tandy

    2016-05-01

    Species tree estimation is complicated by processes, such as gene duplication and loss and incomplete lineage sorting (ILS), that cause discordance between gene trees and the species tree. Furthermore, while concatenation, a traditional approach to tree estimation, has excellent performance under many conditions, the expectation is that the best accuracy will be obtained through the use of species tree estimation methods that are specifically designed to address gene tree discordance. In this article, we report on a study to evaluate MP-EST-one of the most popular species tree estimation methods designed to address ILS-as well as concatenation under maximum likelihood, the greedy consensus, and two supertree methods (Matrix Representation with Parsimony and Matrix Representation with Likelihood). Our study shows that several factors impact the absolute and relative accuracy of methods, including the number of gene trees, the accuracy of the estimated gene trees, and the amount of ILS. Concatenation can be more accurate than the best summary methods in some cases (mostly when the gene trees have poor phylogenetic signal or when the level of ILS is low), but summary methods are generally more accurate than concatenation when there are an adequate number of sufficiently accurate gene trees. Our study suggests that coalescent-based species tree methods may be key to estimating highly accurate species trees from multiple loci. PMID:25164915

  13. The complex biogeographic history of a widespread tropical tree species.

    PubMed

    Dick, Christopher W; Heuertz, Myriam

    2008-11-01

    Many tropical forest tree species have broad geographic ranges, and fossil records indicate that population disjunctions in some species were established millions of years ago. Here we relate biogeographic history to patterns of population differentiation, mutational and demographic processes in the widespread rainforest tree Symphonia globulifera using ribosomal (ITS) and chloroplast DNA sequences and nuclear microsatellite (nSSR) loci. Fossil records document sweepstakes dispersal origins of Neotropical S. globulifera populations from Africa during the Miocene. Despite historical long-distance gene flow, nSSR differentiation across 13 populations from Costa Rica, Panama, Ecuador (east and west of Andes) and French Guiana was pronounced (F(ST)= 0.14, R(ST)= 0.39, P < 0.001) and allele-size mutations contributed significantly (R(ST) > F(ST)) to the divergences between cis- and trans-Andean populations. Both DNA sequence and nSSR data reflect contrasting demographic histories in lower Mesoamerica and Amazonia. Amazon populations show weak phylogeographic structure and deviation from drift-mutation equilibrium indicating recent population expansion. In Mesoamerica, genetic drift was strong and contributed to marked differentiation among populations. The genetic structure of S. globulifera contains fingerprints of drift-dispersal processes and phylogeographic footprints of geological uplifts and sweepstakes dispersal. PMID:18764917

  14. Modelling community dynamics based on species-level abundance models from detection/nondetection data

    USGS Publications Warehouse

    Yamaura, Yuichi; Royle, J. Andrew; Kuboi, Kouji; Tada, Tsuneo; Ikeno, Susumu; Makino, Shun'ichi

    2011-01-01

    1. In large-scale field surveys, a binary recording of each species' detection or nondetection has been increasingly adopted for its simplicity and low cost. Because of the importance of abundance in many studies, it is desirable to obtain inferences about abundance at species-, functional group-, and community-levels from such binary data. 2. We developed a novel hierarchical multi-species abundance model based on species-level detection/nondetection data. The model accounts for the existence of undetected species, and variability in abundance and detectability among species. Species-level detection/nondetection is linked to species- level abundance via a detection model that accommodates the expectation that probability of detection (at least one individuals is detected) increases with local abundance of the species. We applied this model to a 9-year dataset composed of the detection/nondetection of forest birds, at a single post-fire site (from 7 to 15 years after fire) in a montane area of central Japan. The model allocated undetected species into one of the predefined functional groups by assuming a prior distribution on individual group membership. 3. The results suggest that 15–20 species were missed in each year, and that species richness of communities and functional groups did not change with post-fire forest succession. Overall abundance of birds and abundance of functional groups tended to increase over time, although only in the winter, while decreases in detectabilities were observed in several species. 4. Synthesis and applications. Understanding and prediction of large-scale biodiversity dynamics partly hinge on how we can use data effectively. Our hierarchical model for detection/nondetection data estimates abundance in space/time at species-, functional group-, and community-levels while accounting for undetected individuals and species. It also permits comparison of multiple communities by many types of abundance-based diversity and similarity

  15. Historical Human Footprint on Modern Tree Species Composition in the Purus-Madeira Interfluve, Central Amazonia

    PubMed Central

    Levis, Carolina; de Souza, Priscila Figueira; Schietti, Juliana; Emilio, Thaise; Pinto, José Luiz Purri da Veiga; Clement, Charles R.; Costa, Flavia R. C.

    2012-01-01

    Background Native Amazonian populations managed forest resources in numerous ways, often creating oligarchic forests dominated by useful trees. The scale and spatial distribution of forest modification beyond pre-Columbian settlements is still unknown, although recent studies propose that human impact away from rivers was minimal. We tested the hypothesis that past human management of the useful tree community decreases with distance from rivers. Methodology/Principal Findings In six sites, we inventoried trees and palms with DBH≥10 cm and collected soil for charcoal analysis; we also mapped archaeological evidence around the sites. To quantify forest manipulation, we measured the relative abundance, richness and basal area of useful trees and palms. We found a strong negative exponential relationship between forest manipulation and distance to large rivers. Plots located from 10 to 20 km from a main river had 20–40% useful arboreal species, plots between 20 and 40 km had 12–23%, plots more than 40 km had less than 15%. Soil charcoal abundance was high in the two sites closest to secondary rivers, suggesting past agricultural practices. The shortest distance between archaeological evidence and plots was found in sites near rivers. Conclusions/Significance These results strongly suggest that past forest manipulation was not limited to the pre-Columbian settlements along major rivers, but extended over interfluvial areas considered to be primary forest today. The sustainable use of Amazonian forests will be most effective if it considers the degree of past landscape domestication, as human-modified landscapes concentrate useful plants for human sustainable use and management today. PMID:23185264

  16. Fish and Phytoplankton Exhibit Contrasting Temporal Species Abundance Patterns in a Dynamic North Temperate Lake

    PubMed Central

    Hansen, Gretchen J. A.; Carey, Cayelan C.

    2015-01-01

    Temporal patterns of species abundance, although less well-studied than spatial patterns, provide valuable insight to the processes governing community assembly. We compared temporal abundance distributions of two communities, phytoplankton and fish, in a north temperate lake. We used both 17 years of observed relative abundance data as well as resampled data from Monte Carlo simulations to account for the possible effects of non-detection of rare species. Similar to what has been found in other communities, phytoplankton and fish species that appeared more frequently were generally more abundant than rare species. However, neither community exhibited two distinct groups of “core” (common occurrence and high abundance) and “occasional” (rare occurrence and low abundance) species. Both observed and resampled data show that the phytoplankton community was dominated by occasional species appearing in only one year that exhibited large variation in their abundances, while the fish community was dominated by core species occurring in all 17 years at high abundances. We hypothesize that the life-history traits that enable phytoplankton to persist in highly dynamic environments may result in communities dominated by occasional species capable of reaching high abundances when conditions allow. Conversely, longer turnover times and broad environmental tolerances of fish may result in communities dominated by core species structured primarily by competitive interactions. PMID:25651399

  17. Fish and phytoplankton exhibit contrasting temporal species abundance patterns in a dynamic north temperate lake.

    PubMed

    Hansen, Gretchen J A; Carey, Cayelan C

    2015-01-01

    Temporal patterns of species abundance, although less well-studied than spatial patterns, provide valuable insight to the processes governing community assembly. We compared temporal abundance distributions of two communities, phytoplankton and fish, in a north temperate lake. We used both 17 years of observed relative abundance data as well as resampled data from Monte Carlo simulations to account for the possible effects of non-detection of rare species. Similar to what has been found in other communities, phytoplankton and fish species that appeared more frequently were generally more abundant than rare species. However, neither community exhibited two distinct groups of "core" (common occurrence and high abundance) and "occasional" (rare occurrence and low abundance) species. Both observed and resampled data show that the phytoplankton community was dominated by occasional species appearing in only one year that exhibited large variation in their abundances, while the fish community was dominated by core species occurring in all 17 years at high abundances. We hypothesize that the life-history traits that enable phytoplankton to persist in highly dynamic environments may result in communities dominated by occasional species capable of reaching high abundances when conditions allow. Conversely, longer turnover times and broad environmental tolerances of fish may result in communities dominated by core species structured primarily by competitive interactions. PMID:25651399

  18. Tree competition and species coexistence in a Quercus--Betula forest in the Dongling Mountains in northern China

    NASA Astrophysics Data System (ADS)

    Hou, Ji-hua; Mi, Xiang-cheng; Liu, Can-ran; Ma, Ke-ping

    2006-09-01

    The population size structure, growth dynamics and mode of competition among adult trees (≥ 4 cm DBH) of six abundant tree species in a 5 ha study plot of a temperate deciduous forest in the Dongling Mountains in northern China were investigated using diffusion and growth dynamics models. In the year of 2000, two dominant species, Quercus liaotungensis and Betula dahurica accounted for ca. 68.69% of the total basal area and 52.71% of the total density of adult plants. Q. liaotungensis, Populus davidiana and Acer mono exhibited inverse J-shaped DBH distributions whereas Betula dahurica, B. platyphylla and Salix caprea had unimodal DBH distributions. One-sided interspecific competition was detected between some species combinations at the scale of the 5 ha study plot, and the competitive effect was mainly size-dependent rather than from species-specific interactions with large individuals in the canopy layer out competing smaller individuals in the understory. Symmetric competition was found between Q. liaotungensis and A. mono only. However, considering the straight line relationship of G ( t, x) - √{D(t, x)}, which suggests that competitive asymmetry is very low or absent, combined with the relatively low mortality of trees with a DBH larger than 4 cm, we speculate that asymmetric interspecific competition was not important in structuring this tree community. Regeneration characteristics of each species are most likely important in regulating species coexistence and stand dynamics in this forest.

  19. Firewood crops: shrub and tree species for energy production

    SciTech Connect

    Not Available

    1980-01-01

    In the face of global concern over the dwindling supply of fuelwood, the rate of forest decimation to provide basic human necessities in developing countries is alarming. We must look upon woody plants as renewable resources that, if effectively managed, could alleviate the problem not only for the present,but for posterity. This report suggests potential significant fuelwood species for introduction to suitable environments, although it does not suggest a solution for the fuelwood crisis. The emphasis is on species suitable for individual crops, but species suited to plantation cultivation for fueling small industrial factories, electric generators, and crop driers are also considered. Most of the plants are little known in traditional forest production. Some are woody shrubs rather than trees, but all are aggressive and quick growing. They should be introduced with care in areas where the climate and soil conditions are not harsh. The substitution of well-designed stoves, kilns, or boilers could improve fuel efficiency. Each species is illustrated with photographs and diagrams. (Refs. 420).

  20. About rats and jackfruit trees: modeling the carrying capacity of a Brazilian Atlantic Forest spiny-rat Trinomys dimidiatus (Günther, 1877) - Rodentia, Echimyidae - population with varying jackfruit tree (Artocarpus heterophyllus L.) abundances.

    PubMed

    Mello, J H F; Moulton, T P; Raíces, D S L; Bergallo, H G

    2015-01-01

    We carried out a six-year study aimed at evaluating if and how a Brazilian Atlantic Forest small mammal community responded to the presence of the invasive exotic species Artocarpus heterophyllus, the jackfruit tree. In the surroundings of Vila Dois Rios, Ilha Grande, RJ, 18 grids were established, 10 where the jackfruit tree was present and eight were it was absent. Previous results indicated that the composition and abundance of this small mammal community were altered by the presence and density of A. heterophyllus. One observed effect was the increased population size of the spiny-rat Trinomys dimidiatus within the grids where the jackfruit trees were present. Therefore we decided to create a mathematical model for this species, based on the Verhulst-Pearl logistic equation. Our objectives were i) to calculate the carrying capacity K based on real data of the involved species and the environment; ii) propose and evaluate a mathematical model to estimate the population size of T. dimidiatus based on the monthly seed production of jackfruit tree, Artocarpus heterophyllus and iii) determinate the minimum jackfruit tree seed production to maintain at least two T. dimidiatus individuals in one study grid. Our results indicated that the predicted values by the model for the carrying capacity K were significantly correlated with real data. The best fit was found considering 20~35% energy transfer efficiency between trophic levels. Within the scope of assumed premises, our model showed itself to be an adequate simulator for Trinomys dimidiatus populations where the invasive jackfruit tree is present. PMID:25945639

  1. Experimental warming studies on tree species and forest ecosystems: a literature review.

    PubMed

    Chung, Haegeun; Muraoka, Hiroyuki; Nakamura, Masahiro; Han, Saerom; Muller, Onno; Son, Yowhan

    2013-07-01

    Temperature affects a cascade of ecological processes and functions of forests. With future higher global temperatures being inevitable it is critical to understand and predict how forest ecosystems and tree species will respond. This paper reviews experimental warming studies in boreal and temperate forests or tree species beyond the direct effects of higher temperature on plant ecophysiology by scaling up to forest level responses and considering the indirect effects of higher temperature. In direct response to higher temperature (1) leaves emerged earlier and senesced later, resulting in a longer growing season (2) the abundance of herbivorous insects increased and their performance was enhanced and (3) soil nitrogen mineralization and leaf litter decomposition were accelerated. Besides these generalizations across species, plant ecophysiological traits were highly species-specific. Moreover, we showed that the effect of temperature on photosynthesis is strongly dependent on the position of the leaf or plant within the forest (canopy or understory) and the time of the year. Indirect effects of higher temperature included among others higher carbon storage in trees due to increased soil nitrogen availability and changes in insect performance due to alterations in plant ecophysiological traits. Unfortunately only a few studies extrapolated results to forest ecosystem level and considered the indirect effects of higher temperature. Thus more intensive, long-term studies are needed to further confirm the emerging trends shown in this review. Experimental warming studies provide us with a useful tool to examine the cascade of ecological processes in forest ecosystems that will change with future higher temperature. PMID:23689840

  2. Biogenic volatile organic compound emissions from nine tree species used in an urban tree-planting program

    NASA Astrophysics Data System (ADS)

    Curtis, A. J.; Helmig, D.; Baroch, C.; Daly, R.; Davis, S.

    2014-10-01

    The biogenic volatile organic compound (BVOC) emissions of nine urban tree species were studied to assess the air quality impacts from planting a large quantity of these trees in the City and County of Denver, Colorado, through the Mile High Million tree-planting initiative. The deciduous tree species studied were Sugar maple, Ohio buckeye, northern hackberry, Turkish hazelnut, London planetree, American basswood, Littleleaf linden, Valley Forge elm, and Japanese zelkova. These tree species were selected using the i-Tree Species Selector (itreetools.org). BVOC emissions from the selected tree species were investigated to evaluate the Species Selector data under the Colorado climate and environmental growing conditions. Individual tree species were subjected to branch enclosure experiments in which foliar emissions of BVOC were collected onto solid adsorbent cartridges. The cartridge samples were analyzed for monoterpenes (MT), sesquiterpenes (SQT), and other C10-C15 BVOC using thermal desorption-gas chromatography-flame ionization detection/mass spectroscopy (GC-FID/MS). Individual compounds and their emission rates (ER) were identified. MT were observed in all tree species, exhibiting the following total MT basal emission rates (BER; with a 1-σ lower bound, upper bound uncertainty window): Sugar maple, 0.07 (0.02, 0.11) μg g-1 h-1; London planetree, 0.15 (0.02, 0.27) μg g-1 h-1; northern hackberry, 0.33 (0.09, 0.57) μg g-1 h-1; Japanese zelkova, 0.42 (0.26, 0.58) μg g-1 h-1; Littleleaf linden, 0.71 (0.33, 1.09) μg g-1 h-1; Valley Forge elm, 0.96 (0.01, 1.92) μg g-1 h-1; Turkish hazelnut, 1.30 (0.32, 2.23) μg g-1 h-1; American basswood, 1.50 (0.40, 2.70) μg g-1 h-1; and Ohio buckeye, 6.61 (1.76, 11.47) μg g-1 h-1. SQT emissions were seen in five tree species with total SQT BER of: London planetree, 0.11 (0.01, 0.20) μg g-1 h-1; Japanese zelkova, 0.11 (0.05, 0.16) μg g-1 h-1; Littleleaf linden, 0.13 (0.06, 0.21) μg g-1 h-1; northern hackberry, 0.20 (0

  3. Some autecological characteristics of early to late successional tree species in Venezuela

    NASA Astrophysics Data System (ADS)

    Kammesheidt, Ludwig

    2000-01-01

    The breadth of the continuum concept of strategy with respect to succession was tested on 21 tree and shrub species common in either unlogged or logged stands, respectively, in the Forest Reserve of Caparo, Venezuela, by examining morphological, physiological and population characteristics. Based on a preliminary abundance analysis, `early', `mid' and `late' successional species as well as `generalists' were distinguished. Early successional species, i.e. Ochroma lagopus, Heliocarpus popayanensis and Cecropia peltata were similar in many autecological aspects, e.g. monolayered leaf arrangement, orthotropic architectural models, no adaptive reiteration, clumped distribution, but differed in gap association and distribution along a drainage gradient. Mid-successional species established themselves both in large and small gaps (> 300 m[sup2 ]; 80-300 m[sup2 ]) and showed a clumped to regular distribution pattern in logged areas; they exhibited more diverse crown and leaf characteristics than early successional species. Late successional species established themselves only in small gaps and understorey, and showed a regular spatial pattern in undisturbed areas. All late successional species displayed architectural models with plagiotropic lateral axes and showed a multilayered leaf arrangement. Adaptive reiteration was a common feature of late successional species which could be further subdivided into large, medium-sized and small trees, indicating different light requirements at maturity. Generalists were common treelet and shrub species in both disturbed and undisturbed sites where they are also capable of completing their life cycle. The light compensation point (LCP) of an individual plant was strongly influenced by its crown illuminance. Large late successional species showed the widest range of LCP values, reflecting the increasing light availability with increasing height in mature forest. On the basis of many autecological characteristics, it was found (i

  4. Tree species and functional traits but not species richness affect interrill erosion processes in young subtropical forests

    NASA Astrophysics Data System (ADS)

    Seitz, S.; Goebes, P.; Song, Z.; Bruelheide, H.; Härdtle, W.; Kühn, P.; Li, Y.; Scholten, T.

    2016-01-01

    Soil erosion is seriously threatening ecosystem functioning in many parts of the world. In this context, it is assumed that tree species richness and functional diversity of tree communities can play a critical role in improving ecosystem services such as erosion control. An experiment with 170 micro-scale run-off plots was conducted to investigate the influence of tree species and tree species richness as well as functional traits on interrill erosion in a young forest ecosystem. An interrill erosion rate of 47.5 Mg ha-1 a-1 was calculated. This study provided evidence that different tree species affect interrill erosion differently, while tree species richness did not affect interrill erosion in young forest stands. Thus, different tree morphologies have to be considered, when assessing soil erosion under forest. High crown cover and leaf area index reduced interrill erosion in initial forest ecosystems, whereas rising tree height increased it. Even if a leaf litter cover was not present, the remaining soil surface cover by stones and biological soil crusts was the most important driver for soil erosion control. Furthermore, soil organic matter had a decreasing influence on interrill erosion. Long-term monitoring of soil erosion under closing tree canopies is necessary, and a wide range of functional tree traits should be considered in future research.

  5. Higher levels of multiple ecosystem services are found in forests with more tree species.

    PubMed

    Gamfeldt, Lars; Snäll, Tord; Bagchi, Robert; Jonsson, Micael; Gustafsson, Lena; Kjellander, Petter; Ruiz-Jaen, María C; Fröberg, Mats; Stendahl, Johan; Philipson, Christopher D; Mikusiński, Grzegorz; Andersson, Erik; Westerlund, Bertil; Andrén, Henrik; Moberg, Fredrik; Moen, Jon; Bengtsson, Jan

    2013-01-01

    Forests are of major importance to human society, contributing several crucial ecosystem services. Biodiversity is suggested to positively influence multiple services but evidence from natural systems at scales relevant to management is scarce. Here, across a scale of 400,000 km(2), we report that tree species richness in production forests shows positive to positively hump-shaped relationships with multiple ecosystem services. These include production of tree biomass, soil carbon storage, berry production and game production potential. For example, biomass production was approximately 50% greater with five than with one tree species. In addition, we show positive relationships between tree species richness and proxies for other biodiversity components. Importantly, no single tree species was able to promote all services, and some services were negatively correlated to each other. Management of production forests will therefore benefit from considering multiple tree species to sustain the full range of benefits that the society obtains from forests. PMID:23299890

  6. Higher levels of multiple ecosystem services are found in forests with more tree species

    PubMed Central

    Gamfeldt, Lars; Snäll, Tord; Bagchi, Robert; Jonsson, Micael; Gustafsson, Lena; Kjellander, Petter; Ruiz-Jaen, María C.; Fröberg, Mats; Stendahl, Johan; Philipson, Christopher D.; Mikusiński, Grzegorz; Andersson, Erik; Westerlund, Bertil; Andrén, Henrik; Moberg, Fredrik; Moen, Jon; Bengtsson, Jan

    2013-01-01

    Forests are of major importance to human society, contributing several crucial ecosystem services. Biodiversity is suggested to positively influence multiple services but evidence from natural systems at scales relevant to management is scarce. Here, across a scale of 400,000 km2, we report that tree species richness in production forests shows positive to positively hump-shaped relationships with multiple ecosystem services. These include production of tree biomass, soil carbon storage, berry production and game production potential. For example, biomass production was approximately 50% greater with five than with one tree species. In addition, we show positive relationships between tree species richness and proxies for other biodiversity components. Importantly, no single tree species was able to promote all services, and some services were negatively correlated to each other. Management of production forests will therefore benefit from considering multiple tree species to sustain the full range of benefits that the society obtains from forests. PMID:23299890

  7. Temporal changes of soil respiration under different tree species.

    PubMed

    Akburak, Serdar; Makineci, Ender

    2013-04-01

    Soil respiration rates were measured monthly (from April 2007 to March 2008) under four adjacent coniferous plantation sites [Oriental spruce (Picea orientalis L.), Austrian pine (Pinus nigra Arnold), Turkish fir (Abies bornmulleriana L.), and Scots pine (Pinus sylvestris L.)] and adjacent natural Sessile oak forest (Quercus petraea L.) in Belgrad Forest-Istanbul/Turkey. Also, soil moisture, soil temperature, and fine root biomass were determined to identify the underlying environmental variables among sites which are most likely causing differences in soil respiration. Mean annual soil moisture was determined to be between 6.3 % and 8.1 %, and mean annual temperature ranged from 13.0°C to 14.2°C under all species. Mean annual fine root biomass changed between 368.09 g/m(2) and 883.71 g/m(2) indicating significant differences among species. Except May 2007, monthly soil respiration rates show significantly difference among species. However, focusing on tree species, differences of mean annual respiration rates did not differ significantly. Mean annual soil respiration ranged from 0.56 to 1.09 g C/m(2)/day. The highest rates of soil respiration reached on autumn months and the lowest rates were determined on summer season. Soil temperature, soil moisture, and fine root biomass explain mean annual soil respiration rates at the highest under Austrian pine (R (2) = 0.562) and the lowest (R (2) = 0.223) under Turkish fir. PMID:22828980

  8. Tree species identity and functional traits but not species richness affect interrill erosion processes in young subtropical forests

    NASA Astrophysics Data System (ADS)

    Seitz, S.; Goebes, P.; Song, Z.; Bruelheide, H.; Härdtle, W.; Kühn, P.; Li, Y.; Scholten, T.

    2015-06-01

    Soil erosion is seriously threatening ecosystem functioning in many parts of the world. In this context, it is assumed that tree species richness and functional diversity of tree communities can play a critical role in improving ecosystem services such as erosion control. An experiment with 170 micro-scale runoff plots was conducted to investigate the influence of tree species richness and identity as well as tree functional traits on interrill erosion in a young forest ecosystem. An interrill erosion rate of 47.5 t ha-1 a-1 was calculated. This study provided evidence that different tree species affect interrill erosion, but higher tree species richness did not mitigate soil losses in young forest stands. Thus, different tree morphologies have to be considered, when assessing erosion under forest. High crown cover and leaf area index reduced soil losses in initial forest ecosystems, whereas rising tree height increased them. Even if a leaf litter cover was not present, remaining soil surface cover by stones and biological soil crusts was the most important driver for soil erosion control. Furthermore, soil organic matter had a decreasing influence on soil loss. Long-term monitoring of soil erosion under closing tree canopies is necessary and a wide range of functional tree traits should be taken into consideration in future research.

  9. Species identity and neighbor size surpass the impact of tree species diversity on productivity in experimental broad-leaved tree sapling assemblages under dry and moist conditions

    PubMed Central

    Lübbe, Torben; Schuldt, Bernhard; Leuschner, Christoph

    2015-01-01

    Species diversity may increase the productivity of tree communities through complementarity (CE) and/or selection effects (SE), but it is not well known how this relationship changes under water limitation. We tested the stress-gradient hypothesis, which predicts that resource use complementarity and facilitation are more important under water-limited conditions. We conducted a growth experiment with saplings of five temperate broad-leaved tree species that were grown in assemblages of variable diversity (1, 3, or 5 species) and species composition under ample and limited water supply to examine effects of species richness and species identity on stand- and tree-level productivity. Special attention was paid to effects of neighbor identity on the growth of target trees in mixture as compared to growth in monoculture. Stand productivity was strongly influenced by species identity while a net biodiversity effect (NE) was significant in the moist treatment (mostly assignable to CE) but of minor importance. The growth performance of some of the species in the mixtures was affected by tree neighborhood characteristics with neighbor size likely being more important than neighbor species identity. Diversity and neighbor identity effects visible in the moist treatment mostly disappeared in the dry treatment, disproving the stress-gradient hypothesis. The mixtures were similarly sensitive to drought-induced growth reduction as the monocultures, which may relate to the decreased CE on growth upon drought in the mixtures. PMID:26579136

  10. Species identity and neighbor size surpass the impact of tree species diversity on productivity in experimental broad-leaved tree sapling assemblages under dry and moist conditions.

    PubMed

    Lübbe, Torben; Schuldt, Bernhard; Leuschner, Christoph

    2015-01-01

    Species diversity may increase the productivity of tree communities through complementarity (CE) and/or selection effects (SE), but it is not well known how this relationship changes under water limitation. We tested the stress-gradient hypothesis, which predicts that resource use complementarity and facilitation are more important under water-limited conditions. We conducted a growth experiment with saplings of five temperate broad-leaved tree species that were grown in assemblages of variable diversity (1, 3, or 5 species) and species composition under ample and limited water supply to examine effects of species richness and species identity on stand- and tree-level productivity. Special attention was paid to effects of neighbor identity on the growth of target trees in mixture as compared to growth in monoculture. Stand productivity was strongly influenced by species identity while a net biodiversity effect (NE) was significant in the moist treatment (mostly assignable to CE) but of minor importance. The growth performance of some of the species in the mixtures was affected by tree neighborhood characteristics with neighbor size likely being more important than neighbor species identity. Diversity and neighbor identity effects visible in the moist treatment mostly disappeared in the dry treatment, disproving the stress-gradient hypothesis. The mixtures were similarly sensitive to drought-induced growth reduction as the monocultures, which may relate to the decreased CE on growth upon drought in the mixtures. PMID:26579136

  11. From the Cover: Ecological community description using the food web, species abundance, and body size

    NASA Astrophysics Data System (ADS)

    Cohen, Joel E.; Jonsson, Tomas; Carpenter, Stephen R.

    2003-02-01

    Measuring the numerical abundance and average body size of individuals of each species in an ecological community's food web reveals new patterns and illuminates old ones. This approach is illustrated using data from the pelagic community of a small lake: Tuesday Lake, Michigan, United States. Body mass varies almost 12 orders of magnitude. Numerical abundance varies almost 10 orders of magnitude. Biomass abundance (average body mass times numerical abundance) varies only 5 orders of magnitude. A new food web graph, which plots species and trophic links in the plane spanned by body mass and numerical abundance, illustrates the nearly inverse relationship between body mass and numerical abundance, as well as the pattern of energy flow in the community. Species with small average body mass occur low in the food web of Tuesday Lake and are numerically abundant. Larger-bodied species occur higher in the food web and are numerically rarer. Average body size explains more of the variation in numerical abundance than does trophic height. The trivariate description of an ecological community by using the food web, average body sizes, and numerical abundance includes many well studied bivariate and univariate relationships based on subsets of these three variables. We are not aware of any single community for which all of these relationships have been analyzed simultaneously. Our approach demonstrates the connectedness of ecological patterns traditionally treated as independent. Moreover, knowing the food web gives new insight into the disputed form of the allometric relationship between body mass and abundance.

  12. Species Tree Estimation for the Late Blight Pathogen, Phytophthora infestans, and Close Relatives

    PubMed Central

    Blair, Jaime E.; Coffey, Michael D.; Martin, Frank N.

    2012-01-01

    To better understand the evolutionary history of a group of organisms, an accurate estimate of the species phylogeny must be known. Traditionally, gene trees have served as a proxy for the species tree, although it was acknowledged early on that these trees represented different evolutionary processes. Discordances among gene trees and between the gene trees and the species tree are also expected in closely related species that have rapidly diverged, due to processes such as the incomplete sorting of ancestral polymorphisms. Recently, methods have been developed for the explicit estimation of species trees, using information from multilocus gene trees while accommodating heterogeneity among them. Here we have used three distinct approaches to estimate the species tree for five Phytophthora pathogens, including P. infestans, the causal agent of late blight disease in potato and tomato. Our concatenation-based “supergene” approach was unable to resolve relationships even with data from both the nuclear and mitochondrial genomes, and from multiple isolates per species. Our multispecies coalescent approach using both Bayesian and maximum likelihood methods was able to estimate a moderately supported species tree showing a close relationship among P. infestans, P. andina, and P. ipomoeae. The topology of the species tree was also identical to the dominant phylogenetic history estimated in our third approach, Bayesian concordance analysis. Our results support previous suggestions that P. andina is a hybrid species, with P. infestans representing one parental lineage. The other parental lineage is not known, but represents an independent evolutionary lineage more closely related to P. ipomoeae. While all five species likely originated in the New World, further study is needed to determine when and under what conditions this hybridization event may have occurred. PMID:22615869

  13. A Bayesian Supertree Model for Genome-Wide Species Tree Reconstruction

    PubMed Central

    De Oliveira Martins, Leonardo; Mallo, Diego; Posada, David

    2016-01-01

    Current phylogenomic data sets highlight the need for species tree methods able to deal with several sources of gene tree/species tree incongruence. At the same time, we need to make most use of all available data. Most species tree methods deal with single processes of phylogenetic discordance, namely, gene duplication and loss, incomplete lineage sorting (ILS) or horizontal gene transfer. In this manuscript, we address the problem of species tree inference from multilocus, genome-wide data sets regardless of the presence of gene duplication and loss and ILS therefore without the need to identify orthologs or to use a single individual per species. We do this by extending the idea of Maximum Likelihood (ML) supertrees to a hierarchical Bayesian model where several sources of gene tree/species tree disagreement can be accounted for in a modular manner. We implemented this model in a computer program called guenomu whose inputs are posterior distributions of unrooted gene tree topologies for multiple gene families, and whose output is the posterior distribution of rooted species tree topologies. We conducted extensive simulations to evaluate the performance of our approach in comparison with other species tree approaches able to deal with more than one leaf from the same species. Our method ranked best under simulated data sets, in spite of ignoring branch lengths, and performed well on empirical data, as well as being fast enough to analyze relatively large data sets. Our Bayesian supertree method was also very successful in obtaining better estimates of gene trees, by reducing the uncertainty in their distributions. In addition, our results show that under complex simulation scenarios, gene tree parsimony is also a competitive approach once we consider its speed, in contrast to more sophisticated models. PMID:25281847

  14. Remnant Trees Affect Species Composition but Not Structure of Tropical Second-Growth Forest

    PubMed Central

    Sandor, Manette E.; Chazdon, Robin L.

    2014-01-01

    Remnant trees, spared from cutting when tropical forests are cleared for agriculture or grazing, act as nuclei of forest regeneration following field abandonment. Previous studies on remnant trees were primarily conducted in active pasture or old fields abandoned in the previous 2–3 years, and focused on structure and species richness of regenerating forest, but not species composition. Our study is among the first to investigate the effects of remnant trees on neighborhood forest structure, biodiversity, and species composition 20 years post-abandonment. We compared the woody vegetation around individual remnant trees to nearby plots without remnant trees in the same second-growth forests (“control plots”). Forest structure beneath remnant trees did not differ significantly from control plots. Species richness and species diversity were significantly higher around remnant trees. The species composition around remnant trees differed significantly from control plots and more closely resembled the species composition of nearby old-growth forest. The proportion of old-growth specialists and generalists around remnant trees was significantly greater than in control plots. Although previous studies show that remnant trees may initially accelerate secondary forest growth, we found no evidence that they locally affect stem density, basal area, and seedling density at later stages of regrowth. Remnant trees do, however, have a clear effect on the species diversity, composition, and ecological groups of the surrounding woody vegetation, even after 20 years of forest regeneration. To accelerate the return of diversity and old-growth forest species into regrowing forest on abandoned land, landowners should be encouraged to retain remnant trees in agricultural or pastoral fields. PMID:24454700

  15. Estimating Abundances of Interacting Species Using Morphological Traits, Foraging Guilds, and Habitat

    PubMed Central

    Dorazio, Robert M.; Connor, Edward F.

    2014-01-01

    We developed a statistical model to estimate the abundances of potentially interacting species encountered while conducting point-count surveys at a set of ecologically relevant locations – as in a metacommunity of species. In the model we assume that abundances of species with similar traits (e.g., body size) are potentially correlated and that these correlations, when present, may exist among all species or only among functionally related species (such as members of the same foraging guild). We also assume that species-specific abundances vary among locations owing to systematic and stochastic sources of heterogeneity. For example, if abundances differ among locations due to differences in habitat, then measures of habitat may be included in the model as covariates. Naturally, the quantitative effects of these covariates are assumed to differ among species. Our model also accounts for the effects of detectability on the observed counts of each species. This aspect of the model is especially important for rare or uncommon species that may be difficult to detect in community-level surveys. Estimating the detectability of each species requires sampling locations to be surveyed repeatedly using different observers or different visits of a single observer. As an illustration, we fitted models to species-specific counts of birds obtained while sampling an avian community during the breeding season. In the analysis we examined whether species abundances appeared to be correlated due to similarities in morphological measures (body mass, beak length, tarsus length, wing length, tail length) and whether these correlations existed among all species or only among species of the same foraging guild. We also used the model to estimate the effects of forested area on species abundances and the effects of sound power output (as measured by body size) on species detection probabilities. PMID:24727898

  16. Estimating abundances of interacting species using morphological traits, foraging guilds, and habitat

    USGS Publications Warehouse

    Dorazio, Robert M.; Connor, Edward F.

    2014-01-01

    We developed a statistical model to estimate the abundances of potentially interacting species encountered while conducting point-count surveys at a set of ecologically relevant locations - as in a metacommunity of species. In the model we assume that abundances of species with similar traits (e.g., body size) are potentially correlated and that these correlations, when present, may exist among all species or only among functionally related species (such as members of the same foraging guild). We also assume that species-specific abundances vary among locations owing to systematic and stochastic sources of heterogeneity. For example, if abundances differ among locations due to differences in habitat, then measures of habitat may be included in the model as covariates. Naturally, the quantitative effects of these covariates are assumed to differ among species. Our model also accounts for the effects of detectability on the observed counts of each species. This aspect of the model is especially important for rare or uncommon species that may be difficult to detect in community-level surveys. Estimating the detectability of each species requires sampling locations to be surveyed repeatedly using different observers or different visits of a single observer. As an illustration, we fitted models to species-specific counts of birds obtained while sampling an avian community during the breeding season. In the analysis we examined whether species abundances appeared to be correlated due to similarities in morphological measures (body mass, beak length, tarsus length, wing length, tail length) and whether these correlations existed among all species or only among species of the same foraging guild. We also used the model to estimate the effects of forested area on species abundances and the effects of sound power output (as measured by body size) on species detection probabilities.

  17. [Effect of Trichoderma species fungi on soil micromycetes, causing infectious conifer seedling lodging in Siberian tree nurseries].

    PubMed

    Iakimenko, E E; Grodinitskaia, I D

    2000-01-01

    Soils in the tree nurseries studied were characterized by a lower species diversity of fungi than adjacent virgin soils. In particular, the relative abundances of representatives of the genera Mucor, Chaetomium, and Trichoderma in the nursery soil were two times lower than in adjacent virgin soils. On the other hand, the nursery soil exhibited greater abundances of fungi of the genus Fusarium, which are causative agents of many diseases of conifer seedlings. To appreciate the efficiency of biocontrol of the infectious diseases of conifer seedlings, we introduced several indigenous Trichoderma strains into the nursery soil and found that this affected the species composition of soil microflora considerably. Changes in the species composition of mycobiota beneficially influenced the phytosanitary state of soils and reduced the infectious lodging of conifer seedlings. PMID:11195586

  18. The contribution of seed dispersers to tree species diversity in tropical rainforests.

    PubMed

    Kakishima, Satoshi; Morita, Satoru; Yoshida, Katsuhiko; Ishida, Atsushi; Hayashi, Saki; Asami, Takahiro; Ito, Hiromu; Miller, Donald G; Uehara, Takashi; Mori, Shigeta; Hasegawa, Eisuke; Matsuura, Kenji; Kasuya, Eiiti; Yoshimura, Jin

    2015-10-01

    Tropical rainforests are known for their extreme biodiversity, posing a challenging problem in tropical ecology. Many hypotheses have been proposed to explain the diversity of tree species, yet our understanding of this phenomenon remains incomplete. Here, we consider the contribution of animal seed dispersers to the species diversity of trees. We built a multi-layer lattice model of trees whose animal seed dispersers are allowed to move only in restricted areas to disperse the tree seeds. We incorporated the effects of seed dispersers in the traditional theory of allopatric speciation on a geological time scale. We modified the lattice model to explicitly examine the coexistence of new tree species and the resulting high biodiversity. The results indicate that both the coexistence and diversified evolution of tree species can be explained by the introduction of animal seed dispersers. PMID:26587246

  19. The contribution of seed dispersers to tree species diversity in tropical rainforests

    PubMed Central

    Kakishima, Satoshi; Morita, Satoru; Yoshida, Katsuhiko; Ishida, Atsushi; Hayashi, Saki; Asami, Takahiro; Ito, Hiromu; Miller, Donald G.; Uehara, Takashi; Mori, Shigeta; Hasegawa, Eisuke; Matsuura, Kenji; Kasuya, Eiiti; Yoshimura, Jin

    2015-01-01

    Tropical rainforests are known for their extreme biodiversity, posing a challenging problem in tropical ecology. Many hypotheses have been proposed to explain the diversity of tree species, yet our understanding of this phenomenon remains incomplete. Here, we consider the contribution of animal seed dispersers to the species diversity of trees. We built a multi-layer lattice model of trees whose animal seed dispersers are allowed to move only in restricted areas to disperse the tree seeds. We incorporated the effects of seed dispersers in the traditional theory of allopatric speciation on a geological time scale. We modified the lattice model to explicitly examine the coexistence of new tree species and the resulting high biodiversity. The results indicate that both the coexistence and diversified evolution of tree species can be explained by the introduction of animal seed dispersers. PMID:26587246

  20. Landscape Variation in Tree Species Richness in Northern Iran Forests

    PubMed Central

    Bourque, Charles P.-A.; Bayat, Mahmoud

    2015-01-01

    Mapping landscape variation in tree species richness (SR) is essential to the long term management and conservation of forest ecosystems. The current study examines the prospect of mapping field assessments of SR in a high-elevation, deciduous forest in northern Iran as a function of 16 biophysical variables representative of the area’s unique physiography, including topography and coastal placement, biophysical environment, and forests. Basic to this study is the development of moderate-resolution biophysical surfaces and associated plot-estimates for 202 permanent sampling plots. The biophysical variables include: (i) three topographic variables generated directly from the area’s digital terrain model; (ii) four ecophysiologically-relevant variables derived from process models or from first principles; and (iii) seven variables of Landsat-8-acquired surface reflectance and two, of surface radiance. With symbolic regression, it was shown that only four of the 16 variables were needed to explain 85% of observed plot-level variation in SR (i.e., wind velocity, surface reflectance of blue light, and topographic wetness indices representative of soil water content), yielding mean-absolute and root-mean-squared error of 0.50 and 0.78, respectively. Overall, localised calculations of wind velocity and surface reflectance of blue light explained about 63% of observed variation in SR, with wind velocity accounting for 51% of that variation. The remaining 22% was explained by linear combinations of soil-water-related topographic indices and associated thresholds. In general, SR and diversity tended to be greatest for plots dominated by Carpinus betulus (involving ≥ 33% of all trees in a plot), than by Fagus orientalis (median difference of one species). This study provides a significant step towards describing landscape variation in SR as a function of modelled and satellite-based information and symbolic regression. Methods in this study are sufficiently general to

  1. Landscape variation in tree species richness in northern Iran forests.

    PubMed

    Bourque, Charles P-A; Bayat, Mahmoud

    2015-01-01

    Mapping landscape variation in tree species richness (SR) is essential to the long term management and conservation of forest ecosystems. The current study examines the prospect of mapping field assessments of SR in a high-elevation, deciduous forest in northern Iran as a function of 16 biophysical variables representative of the area's unique physiography, including topography and coastal placement, biophysical environment, and forests. Basic to this study is the development of moderate-resolution biophysical surfaces and associated plot-estimates for 202 permanent sampling plots. The biophysical variables include: (i) three topographic variables generated directly from the area's digital terrain model; (ii) four ecophysiologically-relevant variables derived from process models or from first principles; and (iii) seven variables of Landsat-8-acquired surface reflectance and two, of surface radiance. With symbolic regression, it was shown that only four of the 16 variables were needed to explain 85% of observed plot-level variation in SR (i.e., wind velocity, surface reflectance of blue light, and topographic wetness indices representative of soil water content), yielding mean-absolute and root-mean-squared error of 0.50 and 0.78, respectively. Overall, localised calculations of wind velocity and surface reflectance of blue light explained about 63% of observed variation in SR, with wind velocity accounting for 51% of that variation. The remaining 22% was explained by linear combinations of soil-water-related topographic indices and associated thresholds. In general, SR and diversity tended to be greatest for plots dominated by Carpinus betulus (involving ≥ 33% of all trees in a plot), than by Fagus orientalis (median difference of one species). This study provides a significant step towards describing landscape variation in SR as a function of modelled and satellite-based information and symbolic regression. Methods in this study are sufficiently general to be

  2. ECOLOGICAL RESPONSE SURFACES FOR NORTH AMERICAN BOREAL TREE SPECIES AND THEIR USE IN FOREST CLASSIFICATION

    EPA Science Inventory

    Empirical ecological response surfaces were derived for eight dominant tree species in the boreal forest region of Canada. tepwise logistic regression was used to model species dominance as a response to five climatic predictor variables. he predictor variables (annual snowfall, ...

  3. The description of Paramblynotus delaneyi (Hymenoptera: Liopteridae), a new species from Joshua Tree National Park

    Technology Transfer Automated Retrieval System (TEKTRAN)

    A new species, Paramblynotus delaneyi (Hymenoptera: Liopteridae), is described and characters separating it from the Nearctic species P. zonatus Weld and P. virginianus Liu are discussed. A discussion of the insect biodiversity survey at Joshua Tree National Park is provided....

  4. New Insights on Jupiter's Deep Water Abundance from Disequilibrium Species

    NASA Astrophysics Data System (ADS)

    Wang, Dong; Gierasch, Peter; Lunine, Jonathan; Mousis, Olivier

    2014-11-01

    The bulk water abundance on Jupiter potentially constrains the planet's formation conditions. We aim to improve the chemical constraints on Jupiter's deep water abundance in this paper. The eddy diffusion coefficient is used to model vertical mixing in planetary atmosphere, and based on laboratory studies dedicated to turbulent rotating convection, we propose a new formulation of eddy diffusion coefficient. The new formulation predicts a smooth transition from slow rotation regime (near the equator) to the rapid rotation regime (near the pole). We estimate an uncertainty for newly derived coefficient of less than 25%, which is much better than the one order of magnitude uncertainty used in the literature. We then reevaluate the water constraintprovided by CO, using the newer eddy diffusion coefficient. We considered two updated CO kinetic models, one model constrains the water enrichment (relative to solar) between 0.1 and 0.75, while the other one constrains the water enrichment between 7 and 23. This difference calls for a better assessment of CO kinetic models.

  5. New insights on Jupiter's deep water abundance from disequilibrium species

    NASA Astrophysics Data System (ADS)

    Wang, Dong; Gierasch, Peter J.; Lunine, Jonathan I.; Mousis, Olivier

    2015-04-01

    The bulk water abundance on Jupiter potentially constrains the planet's formation conditions. We improve the chemical constraints on Jupiter's deep water abundance in this paper. The eddy diffusion coefficient is used to model vertical mixing in planetary atmosphere, and based on laboratory studies dedicated to turbulent rotating convection, we propose a new formulation of the eddy diffusion coefficient for the troposphere of giant planets. The new formulation predicts a smooth transition from the slow rotation regime (near the equator) to the rapid rotation regime (near the pole). We estimate an uncertainty for the newly derived coefficient of less than 25%, which is much better than the one order of magnitude uncertainty used in the literature. We then reevaluate the water constraint provided by CO, using the newer eddy diffusion coefficient. We considered two updated CO kinetic models, one model constrains the water enrichment (relative to solar) between 0.1 and 0.75, while the other constrains the water enrichment between 3 and 11.

  6. Fire controls population structure in four dominant tree species in a tropical savanna.

    PubMed

    Lehmann, Caroline E R; Prior, Lynda D; Bowman, David M J S

    2009-09-01

    The persistence of mesic savannas has been theorised as being dependent on disturbances that restrict the number of juveniles growing through the sapling size class to become fire-tolerant trees. We analysed the population structures of four dominant tropical savanna tree species from 30 locations in Kakadu National Park (KNP), northern Australia. We found that across KNP as a whole, the population size structures of these species do not exhibit recruitment bottlenecks. However, individual stands had multimodal size-class distributions and mixtures of tree species consistent with episodic and individualistic recruitment of co-occurring tree species. Using information theory and multimodel inference, we examined the relative importance of fire frequency, stand basal area and elevation difference between a site and permanent water in explaining variations in the proportion of sapling to adult stems in four dominant tree species. This showed that the proportion of the tree population made up of saplings was negatively related to both fire frequencies and stand basal area. Overall, fire frequency has density-dependent effects in the regulation of the transition of saplings to trees in this Australian savanna, due to interactions with stem size, regeneration strategies, growth rates and tree-tree competition. Although stable at the regional scale, the spatiotemporal variability of fire can result in structural and floristic diversity of savanna tree populations. PMID:19629532

  7. Indicator species of essential forest tree species in the Burdur district.

    PubMed

    Negiz, Mehmet Güvenç; Eser, Yunus; Kuzugüdenll, Emre; Izkan, Kürşad

    2015-01-01

    The forests of Burdur district for long have been subjected to over grazing and individual selection. As a result of this, majority of the forest areas in the district were degraded. In the district, afforestation efforts included majority of forestry implementations. It is well known that selecting suitable species plays an important role for achieving afforestation efforts. In this context, knowing the indicator species among the target species would be used in afforestation efforts, studies on the interrelationships between environmental factors and target species distribution is vital for selecting suitable species for a given area. In this study, Anatolian Black pine (Pinus nigra), Red pine (Pinus brutia), Crimean juniper (Juniperus excelsa) and Taurus cedar (Cedrus libani), essential tree species, were considered as target species. The data taken from 100 sample plots in Burdur district was used. Interspecific correlation analysis was performed to determine the positive and negative indicator species among each of the target species. As a result of ICA, 2 positive (Berberis crataegina, Juniperus oxycedrus), 2 negative (Phillyrea latifolia, Quercus coccifera) for Crimean Juniper, I positive (Juniperus oxycedrus), 3 negative (Onopordium acanthium, Fraxinus ornus, Phillyrea latifolia) for Anatolian black pine, 3 positive (Paliurus spina-christi, Quercus coccifer, Crataegus orientalis), 2 negative (Berberis crataegina, Astragalus nanus) for Red pine and 3 positive (Berberis crataegina, Rhamnus oleoides, Astragalus prusianus) 2 negative (Paliurus spina-christi, Quercus cerris) for Taurus cedarwere defined as indicator plant species. In this way, practical information was obtained for selecting the most suitable species, among the target species, for afforestation efforts in Burdur district. PMID:26591889

  8. Lactobacillus and Pediococcus species richness and relative abundance in the vagina of rhesus monkeys (Macaca mulatta)

    PubMed Central

    Gravett, Michael G.; Jin, Ling; Pavlova, Sylvia I.; Tao, Lin

    2012-01-01

    Background The rhesus monkey is an important animal model to study human vaginal health to which lactic acid bacteria play a significant role. However, the vaginal lactic acid bacterial species richness and relative abundance in rhesus monkeys is largely unknown. Methods Vaginal swab samples were aseptically obtained from 200 reproductive aged female rhesus monkeys. Following Rogosa agar plating, single bacterial colonies representing different morphotypes were isolated and analyzed for whole-cell protein profile, species-specifc PCR, and 16S rRNA gene sequence. Results A total of 510 Lactobacillus strains of 17 species and one Pediococcus acidilactici were identified. The most abundant species was L. reuteri, which colonized the vaginas of 86% monkeys. L. johnsonii was the second most abundant species, which colonized 36% of monkeys. The majority of monkeys were colonized by multiple Lactobacillus species. Conclusions The vaginas of rhesus monkeys are frequently colonized by multiple Lactobacillus species, dominated by L. reuteri. PMID:22429090

  9. Development, characterization, and cross-species/genera transferability of SSR markers for rubber tree (Hevea brasiliensis).

    PubMed

    Yu, Fei; Wang, Bao-Hua; Feng, Su-Ping; Wang, Jing-Yi; Li, Wei-Guo; Wu, Yao-Ting

    2011-03-01

    Genomic simple sequence repeat (SSR) markers are particularly valuable in studies of genetic diversity, evolution, genetic linkage map construction, quantitative trait loci tagging, and marker-assisted selection because of their multi-allelic nature, reproducibility, co-dominant inheritance, high abundance, and extensive genome coverage. The traditional methods of SSR marker development, such as genomic-SSR hybrid screening and microsatellite enrichment, have the disadvantages of high cost and complex operation. The selectively amplified microsatellite method is less costly and highly efficient as well as being simple and convenient. In this study, 252 sequences with SSRs were cloned from the rubber tree (Hevea brasiliensis) genome from which 258 SSR loci were obtained. The average repeat number was six. There were only 10 (3.9%) mononucleotide, trinucleotide, and pentanucleotide repeats, whereas the remaining 248 (96.1%) were dinucleotide repeats, including 128 (49.6%) GT/CA repeats, 118 (45.7%) GA/CT repeats, and 2 (0.8%) AT/TA repeats. A total of 126 primer pairs (see ESM) were successfully designed of which 36 primer pairs generated polymorphic products from 12 accessions of the cultivated species, 4 related species, and 3 species of the family Euphorbiaceae. In addition, investigations based on four genomic SSRs (GAR4, ACR22, CTR25, and GTR28) by cloning and sequencing provided evidence for cross-species/genera applicability, and homologous sequences were obtained from the rubber tree and Euphorbiaceae. Further analysis about the variation of the flanking regions of the four markers was carried out. PMID:20960206

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

    PubMed Central

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

    2015-01-01

    The very rare Mexican Picea chihuahuana tree community covers an area of no more than 300 ha in the Sierra Madre Occidental. This special tree community has been the subject of several studies aimed at learning more about the genetic structure and ecology of the species and the potential effects of climate change. The spatial distribution of trees is a result of many ecological processes and can affect the degree of competition between neighbouring trees, tree density, variability in size and distribution, regeneration, survival, growth, mortality, crown formation and the biological diversity within forest communities. Numerous scale-dependent measures have been established in order to describe spatial forest structure. The overall aim of most of these studies has been to obtain data to help design preservation and conservation strategies. In this study, we examined the spatial distribution pattern of trees in the P. chihuahuana tree community in 12 localities, in relation to i) tree stand density, ii) diameter distribution (vertical structure), iii) tree species diversity, iv) geographical latitude and v) tree dominance at a fine scale (in 0.25 ha plots), with the aim of obtaining a better understanding of the complex ecosystem processes and biological diversity. Because of the strongly mixed nature of this tree community, which often produces low population densities of each tree species and random tree fall gaps caused by tree death, we expect aggregated patterns in individual Picea chihuahuana trees and in the P. chihuahuana tree community, repulsive Picea patterns to other tree species and repulsive patterns of young to adult trees. Each location was represented by one plot of 50 x 50 m (0.25 ha) established in the centre of the tree community. The findings demonstrate that the hypothesis of aggregated tree pattern is not applicable to the mean pattern measured by Clark-Evans index, Uniform Angle index and Mean Directional index of the uneven-aged P

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

    PubMed

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

    2015-01-01

    The very rare Mexican Picea chihuahuana tree community covers an area of no more than 300 ha in the Sierra Madre Occidental. This special tree community has been the subject of several studies aimed at learning more about the genetic structure and ecology of the species and the potential effects of climate change. The spatial distribution of trees is a result of many ecological processes and can affect the degree of competition between neighbouring trees, tree density, variability in size and distribution, regeneration, survival, growth, mortality, crown formation and the biological diversity within forest communities. Numerous scale-dependent measures have been established in order to describe spatial forest structure. The overall aim of most of these studies has been to obtain data to help design preservation and conservation strategies. In this study, we examined the spatial distribution pattern of trees in the P. chihuahuana tree community in 12 localities, in relation to i) tree stand density, ii) diameter distribution (vertical structure), iii) tree species diversity, iv) geographical latitude and v) tree dominance at a fine scale (in 0.25 ha plots), with the aim of obtaining a better understanding of the complex ecosystem processes and biological diversity. Because of the strongly mixed nature of this tree community, which often produces low population densities of each tree species and random tree fall gaps caused by tree death, we expect aggregated patterns in individual Picea chihuahuana trees and in the P. chihuahuana tree community, repulsive Picea patterns to other tree species and repulsive patterns of young to adult trees. Each location was represented by one plot of 50 x 50 m (0.25 ha) established in the centre of the tree community. The findings demonstrate that the hypothesis of aggregated tree pattern is not applicable to the mean pattern measured by Clark-Evans index, Uniform Angle index and Mean Directional index of the uneven-aged P

  12. Characterizing tropical tree species growth strategies: learning from inter-individual variability and scale invariance.

    PubMed

    Le Bec, Jimmy; Courbaud, Benoit; Le Moguédec, Gilles; Pélissier, Raphaël

    2015-01-01

    Understanding how tropical tree species differ in their growth strategies is critical to predict forest dynamics and assess species coexistence. Although tree growth is highly variable in tropical forests, species maximum growth is often considered as a major axis synthesizing species strategies, with fast-growing pioneer and slow-growing shade tolerant species as emblematic representatives. We used a hierarchical linear mixed model and 21-years long tree diameter increment series in a monsoon forest of the Western Ghats, India, to characterize species growth strategies and question whether maximum growth summarizes these strategies. We quantified both species responses to biotic and abiotic factors and individual tree effects unexplained by these factors. Growth responses to competition and tree size appeared highly variable among species which led to reversals in performance ranking along those two gradients. However, species-specific responses largely overlapped due to large unexplained variability resulting mostly from inter-individual growth differences consistent over time. On average one-third of the variability captured by our model was explained by covariates. This emphasizes the high dimensionality of the tree growth process, i.e. the fact that trees differ in many dimensions (genetics, life history) influencing their growth response to environmental gradients, some being unmeasured or unmeasurable. In addition, intraspecific variability increased as a power function of species maximum growth partly as a result of higher absolute responses of fast-growing species to competition and tree size. However, covariates explained on average the same proportion of intraspecific variability for slow- and fast-growing species, which showed the same range of relative responses to competition and tree size. These results reflect a scale invariance of the growth process, underlining that slow- and fast-growing species exhibit the same range of growth strategies. PMID

  13. Characterizing Tropical Tree Species Growth Strategies: Learning from Inter-Individual Variability and Scale Invariance

    PubMed Central

    Le Bec, Jimmy; Courbaud, Benoit; Le Moguédec, Gilles; Pélissier, Raphaël

    2015-01-01

    Understanding how tropical tree species differ in their growth strategies is critical to predict forest dynamics and assess species coexistence. Although tree growth is highly variable in tropical forests, species maximum growth is often considered as a major axis synthesizing species strategies, with fast-growing pioneer and slow-growing shade tolerant species as emblematic representatives. We used a hierarchical linear mixed model and 21-years long tree diameter increment series in a monsoon forest of the Western Ghats, India, to characterize species growth strategies and question whether maximum growth summarizes these strategies. We quantified both species responses to biotic and abiotic factors and individual tree effects unexplained by these factors. Growth responses to competition and tree size appeared highly variable among species which led to reversals in performance ranking along those two gradients. However, species-specific responses largely overlapped due to large unexplained variability resulting mostly from inter-individual growth differences consistent over time. On average one-third of the variability captured by our model was explained by covariates. This emphasizes the high dimensionality of the tree growth process, i.e. the fact that trees differ in many dimensions (genetics, life history) influencing their growth response to environmental gradients, some being unmeasured or unmeasurable. In addition, intraspecific variability increased as a power function of species maximum growth partly as a result of higher absolute responses of fast-growing species to competition and tree size. However, covariates explained on average the same proportion of intraspecific variability for slow- and fast-growing species, which showed the same range of relative responses to competition and tree size. These results reflect a scale invariance of the growth process, underlining that slow- and fast-growing species exhibit the same range of growth strategies. PMID

  14. Process-based modeling of species' responses to climate change - a proof of concept using western North American trees

    NASA Astrophysics Data System (ADS)

    Evans, M. E.; Merow, C.; Record, S.; Menlove, J.; Gray, A.; Cundiff, J.; McMahon, S.; Enquist, B. J.

    2013-12-01

    Current attempts to forecast how species' distributions will change in response to climate change suffer under a fundamental trade-off: between modeling many species superficially vs. few species in detail (between correlative vs. mechanistic models). The goals of this talk are two-fold: first, we present a Bayesian multilevel modeling framework, dynamic range modeling (DRM), for building process-based forecasts of many species' distributions at a time, designed to address the trade-off between detail and number of distribution forecasts. In contrast to 'species distribution modeling' or 'niche modeling', which uses only species' occurrence data and environmental data, DRMs draw upon demographic data, abundance data, trait data, occurrence data, and GIS layers of climate in a single framework to account for two processes known to influence range dynamics - demography and dispersal. The vision is to use extensive databases on plant demography, distributions, and traits - in the Botanical Information and Ecology Network, the Forest Inventory and Analysis database (FIA), and the International Tree Ring Data Bank - to develop DRMs for North American trees. Second, we present preliminary results from building the core submodel of a DRM - an integral projection model (IPM) - for a sample of dominant tree species in western North America. IPMs are used to infer demographic niches - i.e., the set of environmental conditions under which population growth rate is positive - and project population dynamics through time. Based on >550,000 data points derived from FIA for nine tree species in western North America, we show IPM-based models of their current and future distributions, and discuss how IPMs can be used to forecast future forest productivity, mortality patterns, and inform efforts at assisted migration.

  15. The relationship between species diversity and genetic structure in the rare Picea chihuahuana tree species community, Mexico.

    PubMed

    Simental-Rodríguez, Sergio Leonel; Quiñones-Pérez, Carmen Zulema; Moya, Daniel; Hernández-Tecles, Enrique; López-Sánchez, Carlos Antonio; Wehenkel, Christian

    2014-01-01

    Species diversity and genetic diversity, the most basic elements of biodiversity, have long been treated as separate topics, although populations evolve within a community context. Recent studies on community genetics and ecology have suggested that genetic diversity is not completely independent of species diversity. The Mexican Picea chihuahuana Martínez is an endemic species listed as "Endangered" on the Red List. Forty populations of Chihuahua spruce have been identified. This species is often associated with tree species of eight genera in gallery forests. This rare Picea chihuahuana tree community covers an area no more than 300 ha and has been subject of several studies involving different topics such as ecology, genetic structure and climate change. The overall aim of these studies was to obtain a dataset for developing management tools to help decision makers implement preservation and conservation strategies. However, this unique forest tree community may also represent an excellent subject for helping us to understand the interplay between ecological and evolutionary processes in determining community structure and dynamics. The AFLP technique and species composition data were used together to test the hypothesis that species diversity is related to the adaptive genetic structure of some dominant tree species (Picea chihuahuana, Pinus strobiformis, Pseudotsuga menziesii and Populus tremuloides) of the Picea chihuahuana tree community at fourteen locations. The Hill numbers were used as a diversity measure. The results revealed a significant correlation between tree species diversity and genetic structure in Populus tremuloides. Because the relationship between the two levels of diversity was found to be positive for the putative adaptive AFLP detected, genetic and species structures of the tree community were possibly simultaneously adapted to a combination of ecological or environmental factors. The present findings indicate that interactions between

  16. The Relationship between Species Diversity and Genetic Structure in the Rare Picea chihuahuana Tree Species Community, Mexico

    PubMed Central

    Simental-Rodríguez, Sergio Leonel; Quiñones-Pérez, Carmen Zulema; Moya, Daniel; Hernández-Tecles, Enrique; López-Sánchez, Carlos Antonio; Wehenkel, Christian

    2014-01-01

    Species diversity and genetic diversity, the most basic elements of biodiversity, have long been treated as separate topics, although populations evolve within a community context. Recent studies on community genetics and ecology have suggested that genetic diversity is not completely independent of species diversity. The Mexican Picea chihuahuana Martínez is an endemic species listed as “Endangered” on the Red List. Forty populations of Chihuahua spruce have been identified. This species is often associated with tree species of eight genera in gallery forests. This rare Picea chihuahuana tree community covers an area no more than 300 ha and has been subject of several studies involving different topics such as ecology, genetic structure and climate change. The overall aim of these studies was to obtain a dataset for developing management tools to help decision makers implement preservation and conservation strategies. However, this unique forest tree community may also represent an excellent subject for helping us to understand the interplay between ecological and evolutionary processes in determining community structure and dynamics. The AFLP technique and species composition data were used together to test the hypothesis that species diversity is related to the adaptive genetic structure of some dominant tree species (Picea chihuahuana, Pinus strobiformis, Pseudotsuga menziesii and Populus tremuloides) of the Picea chihuahuana tree community at fourteen locations. The Hill numbers were used as a diversity measure. The results revealed a significant correlation between tree species diversity and genetic structure in Populus tremuloides. Because the relationship between the two levels of diversity was found to be positive for the putative adaptive AFLP detected, genetic and species structures of the tree community were possibly simultaneously adapted to a combination of ecological or environmental factors. The present findings indicate that interactions

  17. Tree species richness promotes productivity in temperate forests through strong complementarity between species.

    PubMed

    Morin, Xavier; Fahse, Lorenz; Scherer-Lorenzen, Michael; Bugmann, Harald

    2011-12-01

    Understanding the link between biodiversity and ecosystem functioning (BEF) is pivotal in the context of global biodiversity loss. Yet, long-term effects have been explored only weakly, especially for forests, and no clear evidence has been found regarding the underlying mechanisms. We explore the long-term relationship between diversity and productivity using a forest succession model. Extensive simulations show that tree species richness promotes productivity in European temperate forests across a large climatic gradient, mostly through strong complementarity between species. We show that this biodiversity effect emerges because increasing species richness promotes higher diversity in shade tolerance and growth ability, which results in forests responding faster to small-scale mortality events. Our study generalises results from short-term experiments in grasslands to forest ecosystems and demonstrates that competition for light alone induces a positive effect of biodiversity on productivity, thus providing a new angle for explaining BEF relationships. PMID:21955682

  18. Mortality rates associated with crown health for eastern forest tree species.

    PubMed

    Morin, Randall S; Randolph, KaDonna C; Steinman, Jim

    2015-03-01

    The condition of tree crowns is an important indicator of tree and forest health. Crown conditions have been evaluated during inventories of the US Forest Service Forest Inventory and Analysis (FIA) program since 1999. In this study, remeasured data from 55,013 trees on 2616 FIA plots in the eastern USA were used to assess the probability of survival among various tree species using the suite of FIA crown condition variables. Logistic regression procedures were employed to develop models for predicting tree survival. Results of the regression analyses indicated that crown dieback was the most important crown condition variable for predicting tree survival for all species combined and for many of the 15 individual species in the study. The logistic models were generally successful in representing recent tree mortality responses to multiyear infestations of beech bark disease and hemlock woolly adelgid. Although our models are only applicable to trees growing in a forest setting, the utility of models that predict impending tree mortality goes beyond forest inventory or traditional forestry growth and yield models and includes any application where managers need to assess tree health or predict tree mortality including urban forest, recreation, wildlife, and pest management. PMID:25655130

  19. Identifiability of the unrooted species tree topology under the coalescent model with time-reversible substitution processes, site-specific rate variation, and invariable sites.

    PubMed

    Chifman, Julia; Kubatko, Laura

    2015-06-01

    The inference of the evolutionary history of a collection of organisms is a problem of fundamental importance in evolutionary biology. The abundance of DNA sequence data arising from genome sequencing projects has led to significant challenges in the inference of these phylogenetic relationships. Among these challenges is the inference of the evolutionary history of a collection of species based on sequence information from several distinct genes sampled throughout the genome. It is widely accepted that each individual gene has its own phylogeny, which may not agree with the species tree. Many possible causes of this gene tree incongruence are known. The best studied is the incomplete lineage sorting, which is commonly modeled by the coalescent process. Numerous methods based on the coalescent process have been proposed for the estimation of the phylogenetic species tree given DNA sequence data. However, use of these methods assumes that the phylogenetic species tree can be identified from DNA sequence data at the leaves of the tree, although this has not been formally established. We prove that the unrooted topology of the n-leaf phylogenetic species tree is generically identifiable given observed data at the leaves of the tree that are assumed to have arisen from the coalescent process under a time-reversible substitution process with the possibility of site-specific rate variation modeled by the discrete gamma distribution and a proportion of invariable sites. PMID:25791286

  20. Species richness and relative abundance of breeding birds in forests of the Mississippi Alluvial Valley

    USGS Publications Warehouse

    Nelms, C.O.; Twedt, D.J.

    1993-01-01

    In 1992, the Vicksburg Field Research Station of the National Wetlands Research Center initiated research on the ecology of migratory birds within forests of the Mississippi Alluvial Valley (MAV). The MAV was historically a nearly contiguous bottomland hardwood forest, however, only remnants remain. These remnants are fragmented and often influenced by drainage projects, silviculture, agriculture, and urban development. Our objectives are to assess species richness and relative abundance, and to relate these to the size, quality, and composition of forest stands. Species richness and relative abundance were estimated for 53 randomly selected forest sites using 1 to 8 point counts per site, depending on the size of the forest fragment. However, statistical comparisons among sites will be restricted to an equal number ofpoint counts within the sites being compared. Point counts, lasting five minutes, were conducted from 11 May to 29 June 1992, foltowing Ralph, Sauer, and Droege (Point Count Standards; memo dated 9 March 1992). Vegetation was measured at the first three points on each site using a modification of the methods employed by Martin and Roper (Condor 90: 5 1-57; 1988). During 252 counts, 7 1 species were encountered, but only 62 species were encountered within a 50-m radius of point center. The mean number of species encountered within 50 m of a point, was 7.3 (s.d. = 2.7) and the mean number of individuals was 11.2 (s.d. = 4.2). The mean number of species detected at any distance was 9.6 (s.d, = 2.8) and the mean number of individuals was 15.6 (s.d. = 7.9). The most frequently encountered warblers in the MAV were Prothonotary Warbler and Northern Parula. Rarely encountered warblers were American Redstart and Worm-eating Warbler. The genera, Quercus, Ulmus, Carya, and Celtis were each encountered at 80 or more of the 152 points at which vegetation was sampled. Species most frequentlyencountered were: sugarberry (Celtis laevagata), water hickory (Caqa

  1. Independent domestications of cultivated tree peonies from different wild peony species.

    PubMed

    Yuan, Jun-Hui; Cornille, Amandine; Giraud, Tatiana; Cheng, Fang-Yun; Hu, Yong-Hong

    2014-01-01

    An understanding of plant domestication history provides insights into general mechanisms of plant adaptation and diversification and can guide breeding programmes that aim to improve cultivated species. Cultivated tree peonies (genus Paeonia L.) are among the most popular ornamental plants in the world; yet, the history of their domestication is still unresolved. Here, we explored whether the domestication in China of historically cultivated peonies, that is, the common and flare cultivated tree peonies, was a single event or whether independent domestications occurred. We used 14 nuclear microsatellite markers and a comprehensive set of 553 tree peonies collected across China, including common tree peonies, flare tree peonies and the wild species or subspecies that are potential contributors to the cultivated tree peonies, that is, Paeonia rockii ssp. rockii, P. rockii ssp. atava, P. jishanensis and P. decomposita. Assignment methods, a principal component analysis and approximate Bayesian computations provided clear evidence for independent domestications of these common tree and flare tree peonies from two distinct and allopatric wild species, P. jishanensis and P. rockii ssp. atava, respectively. This study provides the first example of independent domestications of cultivated trees from distinct species and locations. This work also yields crucial insight into the history of domestication of one of the most popular woody ornamental plants. The cultivated peonies represent an interesting case of parallel and convergent evolution. The information obtained in this study will be valuable both for improving current tree peony breeding strategies and for understanding the mechanisms of domestication, diversification and adaptation in plants. PMID:24138195

  2. Abundance of minor ion species at Mars: ASPERA-3 observations

    NASA Astrophysics Data System (ADS)

    Zhang, Yiteng; Nilsson, Hans; Barabash, Stas; Li, Lei

    2012-07-01

    The main species at Mars are O+, O2+, CO2+, while there are also some minor species. This article successfully separates minor species of O++, He+ and H2+ with about 12eV by integrating from two and a half years ASPERA-3 data on Mars Express and by integrating and taking some corrections and data processing. At the same time some space statistic Statistics of these Mars ions and estimating are taken place. The result indicates O++ ions density reduce quickly in the region without sunlight, and have moreis higher at subsolar than in the high alatitude place,. and reduces quickly in the region without sunlight. He+ and H2+ have similar distribution in space mainly above in the high altitude ionosphere, and relatively reduce sparse in the midnight space. O++ and He+ have a comparable volume density about 0.1% of O+, and H2+ is muchone order of magnitude lowerless for one order. Our results imply that O++ ions in the martian space are mainly the product of phtoionization in the ionosphere, while H2+ and He+ might also be originated in the planet.

  3. Species Composition and Abundance of Stink Bugs (Hemiptera: Heteroptera: Pentatomidae) in Minnesota Field Corn.

    PubMed

    Koch, Robert L; Pahs, Tiffany

    2015-04-01

    In response to concerns of increasing significance of stink bugs (Hemiptera: Heteroptera: Pentatomidae) in northern states, a survey was conducted over 2 yr in Minnesota to characterize the Pentatomidae associated with field corn, Zea mays L. Halyomorpha halys (Stål), an exotic species, was not detected in this survey, despite continued detection of this species as an invader of human-made structures in Minnesota. Five species of Pentatomidae (four herbivorous; one predatory) were collected from corn. Across years, Euschistus variolarius (Palisot de Beauvois) and Euschistus servus euschistoides (Vollenhoven) had the greatest relative abundances and frequencies of detection. In 2012, the abundance of herbivorous species exceeded 25 nymphs and adults per 100 plants (i.e., an economic threshold) in 0.48% of fields. However, the abundance of herbivorous species did not reach economic levels in any fields sampled in 2013. The frequency of detection of herbivorous species and ratio of nymphs to adults was highest during reproductive growth stages of corn. The predator species, Podisus maculiventris (Say), was detected in 0 to 0.32% of fields. These results provide baseline information on the species composition and abundance of Pentatomidae in Minnesota field corn, which will be necessary for documentation of changes to this fauna as a result of the invasion of H. halys and to determine if some native species continue to increase in abundance in field crops. PMID:26313176

  4. Unveiling the species-rank abundance distribution by generalizing the Good-Turing sample coverage theory.

    PubMed

    Chao, Anne; Hsieh, T C; Chazdon, Robin L; Colwell, Robert K; Gotelli, Nicholas J

    2015-05-01

    Based on a sample of individuals, we focus on inferring the vector of species relative abundance of an entire assemblage and propose a novel estimator of the complete species-rank abundance distribution (RAD). Nearly all previous estimators of the RAD use the conventional "plug-in" estimator Pi (sample relative abundance) of the true relative abundance pi of species i. Because most biodiversity samples are incomplete, the plug-in estimators are applied only to the subset of species that are detected in the sample. Using the concept of sample coverage and its generalization, we propose a new statistical framework to estimate the complete RAD by separately adjusting the sample relative abundances for the set of species detected in the sample and estimating the relative abundances for the set of species undetected in the sample but inferred to be present in the assemblage. We first show that P, is a positively biased estimator of pi for species detected in the sample, and that the degree of bias increases with increasing relative rarity of each species. We next derive a method to adjust the sample relative abundance to reduce the positive bias inherent in j. The adjustment method provides a nonparametric resolution to the longstanding challenge of characterizing the relationship between the true relative abundance in the entire assemblage and the observed relative abundance in a sample. Finally, we propose a method to estimate the true relative abundances of the undetected species based on a lower bound of the number of undetected species. We then combine the adjusted RAD for the detected species and the estimated RAD for the undetected species to obtain the complete RAD estimator. Simulation results show that the proposed RAD curve can unveil the true RAD and is more accurate than the empirical RAD. We also extend our method to incidence data. Our formulas and estimators are illustrated using empirical data sets from surveys of forest spiders (for abundance data) and

  5. Species-abundance--seed-size patterns within a plant community affected by grazing disturbance.

    PubMed

    Wu, Gao-lin; Shang, Zhan-huan; Zhu, Yuan-jun; Ding, Lu-ming; Wang, Dong

    2015-04-01

    Seed size has been advanced as a key factor that influences the dynamics of plant communities, but there are few empirical or theoretical predictions of how community dynamics progress based on seed size patterns. Information on the abundance of adults, seedlings, soil seed banks, seed rains, and the seed mass of 96 species was collected in alpine meadows of the Qinghai-Tibetan Plateau (China), which had different levels of grazing disturbance. The relationships between seed-mass-abundance patterns for adults, seedlings, the soil seed bank, and seed rain in the plant community were evaluated using regression models. Results showed that grazing levels affected the relationship between seed size and abundance properties of adult species, seedlings, and the soil seed bank, suggesting that there is a shift in seed-size--species-abundance relationships as a response to the grazing gradient. Grazing had no effect on the pattern of seed-size-seed-rain-abundance at four grazing levels. Grazing also had little effect on the pattern of seed-size--species-abundance and pattern of seed-size--soil-seed-bank-abundance in meadows with no grazing, light grazing, and moderate grazing), but there was a significant negative effect in meadows with heavy grazing. Grazing had little effect on the pattern of seed-size--seedling-abundance with no grazing, but had significant negative effects with light, moderate, and heavy grazing, and the |r| values increased with grazing levels. This indicated that increasing grazing pressure enhanced the advantage of smaller-seeded species in terms of the abundances of adult species, seedlings, and soil seed banks, whereas only the light grazing level promoted the seed rain abundance of larger-seeded species in the plant communities. This study suggests that grazing disturbances are favorable for increasing the species abundance for smaller-seeded species but not for the larger-seeded species in an alpine meadow community. Hence, there is a clear

  6. Positive effects of plant genotypic and species diversity on anti-herbivore defenses in a tropical tree species.

    PubMed

    Moreira, Xoaquín; Abdala-Roberts, Luis; Parra-Tabla, Víctor; Mooney, Kailen A

    2014-01-01

    Despite increasing evidence that plant intra- and inter-specific diversity increases primary productivity, and that such effect may in turn cascade up to influence herbivores, there is little information about plant diversity effects on plant anti-herbivore defenses, the relative importance of different sources of plant diversity, and the mechanisms for such effects. For example, increased plant growth at high diversity may lead to reduced investment in defenses via growth-defense trade-offs. Alternatively, positive effects of plant diversity on plant growth may lead to increased herbivore abundance which in turn leads to a greater investment in plant defenses. The magnitude of trait variation underlying diversity effects is usually greater among species than among genotypes within a given species, so plant species diversity effects on resource use by producers as well as on higher trophic levels should be stronger than genotypic diversity effects. Here we compared the relative importance of plant genotypic and species diversity on anti-herbivore defenses and whether such effects are mediated indirectly via diversity effects on plant growth and/or herbivore damage. To this end, we performed a large-scale field experiment where we manipulated genotypic diversity of big-leaf mahogany (Swietenia macrophylla) and tree species diversity, and measured effects on mahogany growth, damage by the stem-boring specialist caterpillar Hypsipyla grandella, and defensive traits (polyphenolics and condensed tannins in stem and leaves). We found that both forms of plant diversity had positive effects on stem (but not leaf) defenses. However, neither source of diversity influenced mahogany growth, and diversity effects on defenses were not mediated by either growth-defense trade-offs or changes in stem-borer damage. Although the mechanism(s) of diversity effects on plant defenses are yet to be determined, our study is one of the few to test for and show producer diversity effects on

  7. Positive Effects of Plant Genotypic and Species Diversity on Anti-Herbivore Defenses in a Tropical Tree Species

    PubMed Central

    Moreira, Xoaquín; Abdala-Roberts, Luis; Parra-Tabla, Víctor; Mooney, Kailen A.

    2014-01-01

    Despite increasing evidence that plant intra- and inter-specific diversity increases primary productivity, and that such effect may in turn cascade up to influence herbivores, there is little information about plant diversity effects on plant anti-herbivore defenses, the relative importance of different sources of plant diversity, and the mechanisms for such effects. For example, increased plant growth at high diversity may lead to reduced investment in defenses via growth-defense trade-offs. Alternatively, positive effects of plant diversity on plant growth may lead to increased herbivore abundance which in turn leads to a greater investment in plant defenses. The magnitude of trait variation underlying diversity effects is usually greater among species than among genotypes within a given species, so plant species diversity effects on resource use by producers as well as on higher trophic levels should be stronger than genotypic diversity effects. Here we compared the relative importance of plant genotypic and species diversity on anti-herbivore defenses and whether such effects are mediated indirectly via diversity effects on plant growth and/or herbivore damage. To this end, we performed a large-scale field experiment where we manipulated genotypic diversity of big-leaf mahogany (Swietenia macrophylla) and tree species diversity, and measured effects on mahogany growth, damage by the stem-boring specialist caterpillar Hypsipyla grandella, and defensive traits (polyphenolics and condensed tannins in stem and leaves). We found that both forms of plant diversity had positive effects on stem (but not leaf) defenses. However, neither source of diversity influenced mahogany growth, and diversity effects on defenses were not mediated by either growth-defense trade-offs or changes in stem-borer damage. Although the mechanism(s) of diversity effects on plant defenses are yet to be determined, our study is one of the few to test for and show producer diversity effects on

  8. Species tree discordance traces to phylogeographic clade boundaries in North American fence lizards (Sceloporus).

    PubMed

    Leaché, Adam D

    2009-12-01

    I investigated the impacts of phylogeographic sampling decisions on species tree estimation in the Sceloporus undulatus species group, a recent radiation of small, insectivorous lizards connected by parapatric and peripatric distribution across North America, using a variety of species tree inference methods (Bayesian estimation of species trees, Bayesian untangling of concordance knots, and minimize deep coalescences). Phylogenetic analyses of 16 specimens representing 4 putative species within S. "undulatus" using complete (8 loci, >5.5 kb) and incomplete (29 loci, >23.6 kb) nuclear data sets result in species trees that share features with the mitochondrial DNA (mtDNA) genealogy at the phylogeographic level but provide new insights into the evolutionary history of the species group. The concatenated nuclear data and mtDNA data both recover 4 major clades connecting populations across North America; however, instances of discordance are localized at the contact zones between adjacent phylogeographic groups. A random sub-sampling experiment designed to vary the phylogeographic samples included across hundreds of replicate species tree inferences suggests that inaccurate species assignments can result in inferred phylogenetic relationships that are dependent upon which particular populations are used as exemplars to represent species and can lead to increased estimates of effective population size. For the phylogeographic data presented here, reassigning specimens with introgressed mtDNA genomes to their prospective species, or excluding them from the analysis altogether, produces species tree topologies that are distinctly different from analyses that utilize mtDNA-based species assignments. Evolutionary biologists working at the interface of phylogeography and phylogenetics are likely to encounter multiple processes influencing gene trees congruence, which increases the relevance of estimating species trees with multilocus nuclear data and models that accommodate

  9. A Common Scaling Rule for Abundance, Energetics, and Production of Parasitic and Free-Living Species

    PubMed Central

    Hechinger, Ryan F.; Lafferty, Kevin D.; Dobson, Andy P.; Brown, James H.; Kuris, Armand M.

    2011-01-01

    The metabolic theory of ecology uses the scaling of metabolism with body size and temperature to explain the causes and consequences of species abundance. However, the theory and its empirical tests have never simultaneously examined parasites alongside free-living species. This is unfortunate because parasites represent at least half of species diversity. We show that metabolic scaling theory could not account for the abundance of parasitic or free-living species in three estuarine food webs until accounting for trophic dynamics. Analyses then revealed that the abundance of all species uniformly scaled with body mass to the −¾ power. This result indicates “production equivalence,” where biomass production within trophic levels is invariant of body size across all species and functional groups: invertebrate or vertebrate, ectothermic or endothermic, and free-living or parasitic. PMID:21778398

  10. Accounting for dispersal and biotic interactions to disentangle the drivers of species distributions and their abundances

    PubMed Central

    Boulangeat, Isabelle; Gravel, Dominique; Thuiller, Wilfried

    2014-01-01

    Although abiotic factors, together with dispersal and biotic interactions, are often suggested to explain the distribution of species and their abundances, species distribution models usually focus on abiotic factors only. We propose an integrative framework linking ecological theory, empirical data and statistical models to understand the distribution of species and their abundances together with the underlying community assembly dynamics. We illustrate our approach with 21 plant species in the French Alps. We show that a spatially nested modelling framework significantly improves the model’s performance and that the spatial variations of species presence–absence and abundances are predominantly explained by different factors. We also show that incorporating abiotic, dispersal and biotic factors into the same model bring new insights to our understanding of community assembly. This approach, at the crossroads between community ecology and biogeography, is a promising avenue for a better understanding of species co-existence and biodiversity distribution. PMID:22462813

  11. A common scaling rule for abundance, energetics, and production of parasitic and free-living species

    USGS Publications Warehouse

    Hechinger, Ryan F.; Lafferty, Kevin D.; Dobson, Andy P.; Brown, James H.; Kuris, Armand M.

    2011-01-01

    The metabolic theory of ecology uses the scaling of metabolism with body size and temperature to explain the causes and consequences of species abundance. However, the theory and its empirical tests have never simultaneously examined parasites alongside free-living species. This is unfortunate because parasites represent at least half of species diversity. We show that metabolic scaling theory could not account for the abundance of parasitic or free-living species in three estuarine food webs until accounting for trophic dynamics. Analyses then revealed that the abundance of all species uniformly scaled with body mass to the - 3/4 power. This result indicates "production equivalence," where biomass production within trophic levels is invariant of body size across all species and functional groups: invertebrate or vertebrate, ectothermic or endothermic, and free-living or parasitic.

  12. Species-specific effects on throughfall kinetic energy below 12 subtropical tree species are related to leaf traits and tree architecture

    NASA Astrophysics Data System (ADS)

    Goebes, Philipp; Seitz, Steffen; Kühn, Peter; Kröber, Wenzel; Bruelheide, Helge; Li, Ying; von Oheimb, Goddert; Scholten, Thomas

    2015-04-01

    Soil erosion impacts environmental systems widely, especially in subtropical China where high erosion rates occur. The comprehension about the mechanisms that induce soil erosion on agricultural land is broad, but erosion processes below forests are only rarely understood. Especially throughfall kinetic energy (TKE) is influenced by forests and their structure as well as their succession in many ways. Today, many forests are monoculture tree stands due to economic reasons by providing timber, fuel and pulp wood. Therefore, this study investigates the role of different monoculture forest stands on TKE that were afforestated in 2008. The main questions are: Is TKE species-specific? What are characteristic leaf traits and tree architectural parameters that induce a species-specific effect on TKE and by what extend do they contribute to a mediation of species-specific effects on TKE? We measured TKE of 12 different species in subtropical China using sand-filled splash cups during five rainfall events in summer 2013. In addition, 14 leaf traits and tree architectural parameters were registered to link species-specific effects on TKE to vegetation parameters. Our results show that TKE is highly species-specific. Highest TKE was found below Choerospondias axillaris and Sapindus mukorossi, while Schima superba showed lowest TKE. The latter species can be regarded as key species for reduced erosion occurrence. This species effect is mediated by leaf habit, leaf area, leaf pinnation, leaf margin, tree ground diameter, crown base height, tree height, number of branches and LAI as biotic factors and rainfall amount as abiotic factor. Moreover, leaf habit, tree height and LA show high effect sizes on TKE and can be considered as major drivers evoking TKE differences below vegetation.

  13. Macroalgal mats and species abundance: a field experiment

    NASA Astrophysics Data System (ADS)

    Hull, S. C.

    1987-11-01

    A field experiment was carried out whereby the density of macroalgae ( Enteromorpha spp.) was manipulated and the resultant changes in sediment infaunal density were monitored. Four densities of Enteromorpha spp. were used: 0,0·3, 1, and 3 kg FW m -2, corresponding to control, low-, medium-, and high-density plots. The experiment ran from May to October 1985 and was sampled on three occasions. By July, the density of Corophium volutator was reduced at all weed levels when compared to control plots, whereas densities of Hydrobia ulvae, Macoma balthica, Nereis diversicolor, and Capitella capitata, all increased. Samples taken in October when the weed mats were buried in the sediment showed fewer differences than in July. Macoma, Nereis, and Capitella were still significantly more abundant at medium and high weed densities. Corophium showed no significant treatment effect. There was, however, a highly significant difference in population size structure for Corophium. Measurements of sediment redox potential and silt content under medium- and high-density plots revealed rapid anoxia with a significant increase in siltation.

  14. Surface Water Storage Capacity of Twenty Tree Species in Davis, California.

    PubMed

    Xiao, Qingfu; McPherson, E Gregory

    2016-01-01

    Urban forestry is an important green infrastructure strategy because healthy trees can intercept rainfall, reducing stormwater runoff and pollutant loading. Surface saturation storage capacity, defined as the thin film of water that must wet tree surfaces before flow begins, is the most important variable influencing rainfall interception processes. Surface storage capacity is known to vary widely among tree species, but it is little studied. This research measured surface storage capacities of 20 urban tree species in a rainfall simulator. The measurement system included a rainfall simulator, digital balance, digital camera, and computer. Eight samples were randomly collected from each tree species. Twelve rainfall intensities (3.5-139.5 mm h) were simulated. Leaf-on and leaf-off simulations were conducted for deciduous species. Stem and foliar surface areas were estimated using an image analysis method. Results indicated that surface storage capacities varied threefold among tree species, 0.59 mm for crape myrtle ( L.) and 1.81 mm for blue spruce ( Engelm.). The mean value across all species was 0.86 mm (0.11 mm SD). To illustrate application of the storage values, interception was simulated and compared across species for a 40-yr period with different rainfall intensities and durations. By quantifying the potential for different tree species to intercept rainfall under a variety of meteorological conditions, this study provides new knowledge that is fundamental to validating the cost-effectiveness of urban forestry as a green infrastructure strategy and designing functional plantings. PMID:26828174

  15. No evidence for consistent long-term growth stimulation of 13 tropical tree species: results from tree-ring analysis.

    PubMed

    Groenendijk, Peter; van der Sleen, Peter; Vlam, Mart; Bunyavejchewin, Sarayudh; Bongers, Frans; Zuidema, Pieter A

    2015-10-01

    The important role of tropical forests in the global carbon cycle makes it imperative to assess changes in their carbon dynamics for accurate projections of future climate-vegetation feedbacks. Forest monitoring studies conducted over the past decades have found evidence for both increasing and decreasing growth rates of tropical forest trees. The limited duration of these studies restrained analyses to decadal scales, and it is still unclear whether growth changes occurred over longer time scales, as would be expected if CO2 -fertilization stimulated tree growth. Furthermore, studies have so far dealt with changes in biomass gain at forest-stand level, but insights into species-specific growth changes - that ultimately determine community-level responses - are lacking. Here, we analyse species-specific growth changes on a centennial scale, using growth data from tree-ring analysis for 13 tree species (~1300 trees), from three sites distributed across the tropics. We used an established (regional curve standardization) and a new (size-class isolation) growth-trend detection method and explicitly assessed the influence of biases on the trend detection. In addition, we assessed whether aggregated trends were present within and across study sites. We found evidence for decreasing growth rates over time for 8-10 species, whereas increases were noted for two species and one showed no trend. Additionally, we found evidence for weak aggregated growth decreases at the site in Thailand and when analysing all sites simultaneously. The observed growth reductions suggest deteriorating growth conditions, perhaps due to warming. However, other causes cannot be excluded, such as recovery from large-scale disturbances or changing forest dynamics. Our findings contrast growth patterns that would be expected if elevated CO2 would stimulate tree growth. These results suggest that commonly assumed growth increases of tropical forests may not occur, which could lead to erroneous

  16. Species tree estimation for a deep phylogenetic divergence in the New World monkeys (Primates: Platyrrhini).

    PubMed

    Perez, S Ivan; Klaczko, Julia; dos Reis, Sérgio F

    2012-11-01

    The estimation of a robust phylogeny is a necessary first step in understanding the biological diversification of the platyrrhines. Although the most recent phylogenies are generally robust, they differ from one another in the relationship between Aotus and other genera as well as in the relationship between Pitheciidae and other families. Here, we used coding and non-coding sequences to infer the species tree and embedded gene trees of the platyrrhine genera using the Bayesian Markov chain Monte Carlo method for the multispecies coalescent (*BEAST) for the first time and to compared the results with those of a Bayesian concatenated phylogenetic analysis. Our species tree, based on all available sequences, shows a closer phylogenetic relationship between Atelidae and Cebidae and a closer relationship between Aotus and the Cebidae clade. The posterior probabilities are lower for these conflictive tree nodes compared to those in the concatenated analysis; this finding could be explained by some gene trees showing no concordant topologies between Aotus and the other genera. Moreover, the topology of our species tree also differs from the findings of previous molecular and morphological studies regarding the position of Aotus. The existence of discrepancies between morphological data, gene trees and the species tree is widely reported and can be related to processes such as incomplete lineage sorting or selection. Although these processes are common in species trees with low divergence, they can also occur in species trees with deep and rapid divergence. The sources of the inconsistency of morphological and molecular traits with the species tree could be a main focus of further research on platyrrhines. PMID:22841656

  17. Phylogenomic species tree estimation in the presence of incomplete lineage sorting and horizontal gene transfer

    PubMed Central

    2015-01-01

    Background Species tree estimation is challenged by gene tree heterogeneity resulting from biological processes such as duplication and loss, hybridization, incomplete lineage sorting (ILS), and horizontal gene transfer (HGT). Mathematical theory about reconstructing species trees in the presence of HGT alone or ILS alone suggests that quartet-based species tree methods (known to be statistically consistent under ILS, or under bounded amounts of HGT) might be effective techniques for estimating species trees when both HGT and ILS are present. Results We evaluated several publicly available coalescent-based methods and concatenation under maximum likelihood on simulated datasets with moderate ILS and varying levels of HGT. Our study shows that two quartet-based species tree estimation methods (ASTRAL-2 and weighted Quartets MaxCut) are both highly accurate, even on datasets with high rates of HGT. In contrast, although NJst and concatenation using maximum likelihood are highly accurate under low HGT, they are less robust to high HGT rates. Conclusion Our study shows that quartet-based species-tree estimation methods can be highly accurate under the presence of both HGT and ILS. The study suggests the possibility that some quartet-based methods might be statistically consistent under phylogenomic models of gene tree heterogeneity with both HGT and ILS. PMID:26450506

  18. Seasonal variations of isoprene emissions from five oak tree species in East Asia

    NASA Astrophysics Data System (ADS)

    Lim, Yong-Jae; Armendariz, Al; Son, Youn-Suk; Kim, Jo-Chun

    2011-04-01

    Emissions of biogenic volatile organic compounds (BVOC) from trees can enhance the photochemical production of tropospheric ozone. Isoprene is one of the most environmentally important BVOCs, since its emission rate from certain tree species can be high and its chemical structure gives it high ozone forming potential. Understanding of isoprene emission rates from many tree species is limited, including influences of tree age, season, and other factors. Five oak species were studied which represent approximately 85 percent of the deciduous trees in South Korean forests. In general, there were obvious seasonal variations of isoprene emissions from five oak trees. Especially, Quercus aliena B. and Quercus mongolica F showed substantial seasonal variations of isoprene emissions; However, Quercus serrata T. and Quercus acutissima C. generally did not. It was found that Q. serrata T. showed the highest isoprene emission rates among the species tested (up to 130.5 μgC gdw -1 h -1) and its emission rates were highest during spring followed by summer and fall. The emission rates from two ( Q. acutissima C., Quercus variabilis B.) of the other tested oak species were lower by more than 3 orders of magnitude. Besides, two oak species, Q. aliena B. and Q. mongolica F. were chosen to determine the effect of tree age on isoprene emissions. Trees at the age of 21˜30 years had significantly higher isoprene emission rates than those at the age of 41˜50.

  19. Seabird nutrient subsidies benefit non-nitrogen fixing trees and alter species composition in South American coastal dry forests.

    PubMed

    Havik, Gilles; Catenazzi, Alessandro; Holmgren, Milena

    2014-01-01

    Marine-derived nutrients can increase primary productivity and change species composition of terrestrial plant communities in coastal and riverine ecosystems. We hypothesized that sea nutrient subsidies have a positive effect on nitrogen assimilation and seedling survival of non-nitrogen fixing species, increasing the relative abundance of non-nitrogen fixing species close to seashore. Moreover, we proposed that herbivores can alter the effects of nutrient supplementation by preferentially feeding on high nutrient plants. We studied the effects of nutrient fertilization by seabird guano on tree recruitment and how these effects can be modulated by herbivorous lizards in the coastal dry forests of northwestern Peru. We combined field studies, experiments and stable isotope analysis to study the response of the two most common tree species in these forests, the nitrogen-fixing Prosopis pallida and the non-nitrogen-fixing Capparis scabrida. We did not find differences in herbivore pressure along the sea-inland gradient. We found that the non-nitrogen fixing C. scabrida assimilates marine-derived nitrogen and is more abundant than P. pallida closer to guano-rich soil. We conclude that the input of marine-derived nitrogen through guano deposited by seabirds feeding in the Pacific Ocean affects the two dominant tree species of the coastal dry forests of northern Peru in contrasting ways. The non-nitrogen fixing species, C. scabrida may benefit from sea nutrient subsidies by incorporating guano-derived nitrogen into its foliar tissues, whereas P. pallida, capable of atmospheric fixation, does not. PMID:24466065

  20. Seabird Nutrient Subsidies Benefit Non-Nitrogen Fixing Trees and Alter Species Composition in South American Coastal Dry Forests

    PubMed Central

    Havik, Gilles; Catenazzi, Alessandro; Holmgren, Milena

    2014-01-01

    Marine-derived nutrients can increase primary productivity and change species composition of terrestrial plant communities in coastal and riverine ecosystems. We hypothesized that sea nutrient subsidies have a positive effect on nitrogen assimilation and seedling survival of non-nitrogen fixing species, increasing the relative abundance of non-nitrogen fixing species close to seashore. Moreover, we proposed that herbivores can alter the effects of nutrient supplementation by preferentially feeding on high nutrient plants. We studied the effects of nutrient fertilization by seabird guano on tree recruitment and how these effects can be modulated by herbivorous lizards in the coastal dry forests of northwestern Peru. We combined field studies, experiments and stable isotope analysis to study the response of the two most common tree species in these forests, the nitrogen-fixing Prosopis pallida and the non-nitrogen-fixing Capparis scabrida. We did not find differences in herbivore pressure along the sea-inland gradient. We found that the non-nitrogen fixing C. scabrida assimilates marine-derived nitrogen and is more abundant than P. pallida closer to guano-rich soil. We conclude that the input of marine-derived nitrogen through guano deposited by seabirds feeding in the Pacific Ocean affects the two dominant tree species of the coastal dry forests of northern Peru in contrasting ways. The non-nitrogen fixing species, C. scabrida may benefit from sea nutrient subsidies by incorporating guano-derived nitrogen into its foliar tissues, whereas P. pallida, capable of atmospheric fixation, does not. PMID:24466065

  1. Contrasting soil ciliate species richness and abundance between two tropical plant species: a test of the plant effect.

    PubMed

    Acosta-Mercado, D; Lynn, D H

    2006-05-01

    We still have a rudimentary understanding about the mechanism by which plant roots may stimulate soil microbial interactions. A biochemical model involving plant-derived biochemical fractions, such as exudates, has been used to explain this "rhizosphere effect" on bacteria. However, the variable response of other soil microbial groups, such as protozoa, to the rhizosphere suggests that other factors could be involved in shaping their communities. Thus, two experiments were designed to: (1) determine whether stimulatory and/or inhibiting factors associated with particular plant species regulate ciliate diversity and abundance and (2) obtain a better understanding about the mechanism by which these plant factors operate in the rhizosphere. Bacterial and chemical slurries were reciprocally exchanged between two plant species known to differ in terms of ciliate species richness and abundance (i.e., Canella winterana and plantation Tectona grandis). Analysis of variance showed that the bacteria plus nutrients and the nutrients only treatment had no significant effect on overall ciliate species richness and abundance when compared to the control treatment. However, the use of only colpodean species increased the taxonomic resolution of treatment effects revealing that bacterial slurries had a significant effect on colpodean ciliate species richness. Thus, for particular rhizosphere ciliates, biological properties, such as bacterial diversity or abundance, may have a strong influence on their diversity and possibly abundance. These results are consistent with a model of soil bacteria-mediated mutualisms between plants and protozoa. PMID:16645921

  2. Assessing variation in bacterial composition between the rhizospheres of two mangrove tree species

    NASA Astrophysics Data System (ADS)

    Gomes, Newton C. M.; Cleary, Daniel F. R.; Pires, Ana C. C.; Almeida, Adelaide; Cunha, Angela; Mendonça-Hagler, Leda C. S.; Smalla, Kornelia

    2014-02-01

    This study aimed to determine to what extent roots from the common mangrove tree species Avicennia schaueriana and Laguncularia racemosa are able to impose a selective force on the composition of sediment bacterial communities in mangrove intertidal sediments using barcoded pyrosequencing analysis of 16S rRNA gene fragments (V4 hyper-variable region). The novel results showed that root systems of A. schaueriana and L. racemosa are associated with increased bacterial dominance, lower richness and compositional shifts of sediment bacterial communities. The proportion of OTUs (operational taxonomc units) belonging to the orders Rhizobiales and Vibrionales were enriched in rhizosphere samples from both plant species and sulphur-reducing bacteria (SRB) belonging to the order Desulfobacterales and Desulfuromonadales were enriched in the rhizosphere of A. schaueriana. In addition, Clostridium and Vibrio populations were more abundant in different mangrove rhizospheres. A. schaueriana and L. racemosa roots appear to be able to impose a selective force on the composition of mangrove sediment bacterial communities and this phenomenon appears to be plant species specific. Our findings provide new insights into the potential ecological roles of bacterial guilds in plant-microbe interactions and may aid rhizoengineering approaches for replanting impacted mangrove areas.

  3. Assessing the sensitivity of avian species abundance to land cover and climate

    USGS Publications Warehouse

    LeBrun, Jaymi J.; Thogmartin, Wayne E.; Thompson, Frank R., III; Dijak, William D.; Millspaugh, Joshua J.

    2016-01-01

    Climate projections for the Midwestern United States predict southerly climates to shift northward. These shifts in climate could alter distributions of species across North America through changes in climate (i.e., temperature and precipitation), or through climate-induced changes on land cover. Our objective was to determine the relative impacts of land cover and climate on the abundance of five bird species in the Central United States that have habitat requirements ranging from grassland and shrubland to forest. We substituted space for time to examine potential impacts of a changing climate by assessing climate and land cover relationships over a broad latitudinal gradient. We found positive and negative relationships of climate and land cover factors with avian abundances. Habitat variables drove patterns of abundance in migratory and resident species, although climate was also influential in predicting abundance for some species occupying more open habitat (i.e., prairie warbler, blue-winged warbler, and northern bobwhite). Abundance of northern bobwhite increased with winter temperature and was the species exhibiting the most significant effect of climate. Models for birds primarily occupying early successional habitats performed better with a combination of habitat and climate variables whereas models of species found in contiguous forest performed best with land cover alone. These varied species-specific responses present unique challenges to land managers trying to balance species conservation over a variety of land covers. Management activities focused on increasing forest cover may play a role in mitigating effects of future climate by providing habitat refugia to species vulnerable to projected changes. Conservation efforts would be best served focusing on areas with high species abundances and an array of habitats. Future work managing forests for resilience and resistance to climate change could benefit species already susceptible to climate impacts.

  4. Spatial covariation of local abundance among different parasite species: the effect of shared hosts.

    PubMed

    Lagrue, C; Poulin, R

    2015-10-01

    Within any parasite species, abundance varies spatially, reaching higher values in certain localities than in others, presumably reflecting the local availability of host resources or the local suitability of habitat characteristics for free-living stages. In the absence of strong interactions between two species of helminths with complex life cycles, we might predict that the degree to which their abundances covary spatially is determined by their common resource requirements, i.e. how many host species they share throughout their life cycles. We test this prediction using five trematode species, all with a typical three-host cycle, from multiple lake sampling sites in New Zealand's South Island: Stegodexamene anguillae, Telogaster opisthorchis, Coitocaecum parvum, Maritrema poulini, and an Apatemon sp. Pairs of species from this set of five share the same host species at either one, two, or all three life cycle stages. Our results show that when two trematode species share the same host species at all three life stages, they show positive spatial covariation in abundance (of metacercarial and adult stages) across localities. When they share hosts at two life stages, they show positive spatial covariation in abundance in some cases but not others. Finally, if two trematode species share only one host species, at a single life stage, their abundances do not covary spatially. These findings indicate that the extent of resource sharing between parasite species can drive the spatial match-mismatch between their abundances, and thus influence their coevolutionary dynamics and the degree to which host populations suffer from additive or synergistic effects of multiple infections. PMID:26113509

  5. Soil magnetic susceptibility reflects soil moisture regimes and the adaptability of tree species to these regimes

    USGS Publications Warehouse

    Wang, J.-S.; Grimley, D.A.; Xu, C.; Dawson, J.O.

    2008-01-01

    Flooded, saturated or poorly drained soils are frequently anaerobic, leading to dissolution of the strongly magnetic minerals, magnetite and maghemite, and a corresponding decrease in soil magnetic susceptibility (MS). In this study of five temperate deciduous forests in east-central Illinois, USA, mean surface soil MS was significantly higher adjacent to upland tree species (31 ?? 10-5 SI) than adjacent to floodplain or lowland tree species (17 ?? 10-5 SI), when comparing regional soils with similar parent material of loessal silt. Although the sites differ in average soil MS for each tree species, the relative order of soil MS means for associated tree species at different locations is similar. Lowland tree species, Celtis occidentalis L., Ulmus americana L., Acer saccharinum L., Carya laciniosa (Michx. f.) Loud., and Fraxinus pennsylvanica Marsh. were associated with the lowest measured soil MS mean values overall and at each site. Tree species' flood tolerance rankings increased significantly, as soil MS values declined, the published rankings having significant correlations with soil MS values for the same species groups. The three published classifications of tree species' flood tolerance were significantly correlated with associated soil MS values at all sites, but most strongly at Allerton Park, the site with the widest range of soil drainage classes and MS values. Using soil MS measurements in forests with soil parent material containing similar initial levels of strongly magnetic minerals can provide a simple, rapid and quantitative method to classify soils according to hydric regimes, including dry conditions, and associated plant composition. Soil MS values thus have the capacity to quantify the continuum of hydric tolerances of tree species and guide tree species selection for reforestation. ?? 2007 Elsevier B.V. All rights reserved.

  6. Gradients in the Number of Species at Reef-Seagrass Ecotones Explained by Gradients in Abundance

    PubMed Central

    Tuya, Fernando; Vanderklift, Mathew A.; Wernberg, Thomas; Thomsen, Mads S.

    2011-01-01

    Gradients in the composition and diversity (e.g. number of species) of faunal assemblages are common at ecotones between juxtaposed habitats. Patterns in the number of species, however, can be confounded by patterns in abundance of individuals, because more species tend to be found wherever there are more individuals. We tested whether proximity to reefs influenced patterns in the composition and diversity (‘species density’ = number of species per area and ‘species richness’ = number of species per number of individuals) of prosobranch gastropods in meadows of two seagrasses with different physiognomy: Posidonia and Amphibolis. A change in the species composition was observed from reef-seagrass edges towards the interiors of Amphibolis, but not in Posidonia meadows. Similarly, the abundance of gastropods and species density was higher at edges relative to interiors of Amphibolis meadows, but not in Posidonia meadows. However, species richness was not affected by proximity to reefs in either type of seagrass meadow. The higher number of species at the reef-Amphibolis edge was therefore a consequence of higher abundance, rather than species richness per se. These results suggest that patterns in the composition and diversity of fauna with proximity to adjacent habitats, and the underlying processes that they reflect, likely depend on the physiognomy of the habitat. PMID:21629654

  7. Gradients in the number of species at reef-seagrass ecotones explained by gradients in abundance.

    PubMed

    Tuya, Fernando; Vanderklift, Mathew A; Wernberg, Thomas; Thomsen, Mads S

    2011-01-01

    Gradients in the composition and diversity (e.g. number of species) of faunal assemblages are common at ecotones between juxtaposed habitats. Patterns in the number of species, however, can be confounded by patterns in abundance of individuals, because more species tend to be found wherever there are more individuals. We tested whether proximity to reefs influenced patterns in the composition and diversity ('species density'  =  number of species per area and 'species richness'  =  number of species per number of individuals) of prosobranch gastropods in meadows of two seagrasses with different physiognomy: Posidonia and Amphibolis. A change in the species composition was observed from reef-seagrass edges towards the interiors of Amphibolis, but not in Posidonia meadows. Similarly, the abundance of gastropods and species density was higher at edges relative to interiors of Amphibolis meadows, but not in Posidonia meadows. However, species richness was not affected by proximity to reefs in either type of seagrass meadow. The higher number of species at the reef-Amphibolis edge was therefore a consequence of higher abundance, rather than species richness per se. These results suggest that patterns in the composition and diversity of fauna with proximity to adjacent habitats, and the underlying processes that they reflect, likely depend on the physiognomy of the habitat. PMID:21629654

  8. Remembrance of things past: modelling the relationship between species' abundances in living communities and death assemblages.

    PubMed

    Olszewski, Thomas D

    2012-02-23

    Accumulations of dead skeletal material are a valuable archive of past ecological conditions. However, such assemblages are not equivalent to living communities because they mix the remains of multiple generations and are altered by post-mortem processes. The abundance of a species in a death assemblage can be quantitatively modelled by successively integrating the product of an influx time series and a post-mortem loss function (a decay function with a constant half-life). In such a model, temporal mixing increases expected absolute dead abundance relative to average influx as a linear function of half-life and increases variation in absolute dead abundance values as a square-root function of half-life. Because typical abundance distributions of ecological communities are logarithmically distributed, species' differences in preservational half-life would have to be very large to substantially alter species' abundance ranks (i.e. make rare species common or vice-versa). In addition, expected dead abundances increase at a faster rate than their range of variation with increased time averaging, predicting greater consistency in the relative abundance structure of death assemblages than their parent living community. PMID:21653564

  9. Long-term changes in species composition and relative abundances of sharks at a provisioning site.

    PubMed

    Brunnschweiler, Juerg M; Abrantes, Kátya G; Barnett, Adam

    2014-01-01

    Diving with sharks, often in combination with food baiting/provisioning, has become an important product of today's recreational dive industry. Whereas the effects baiting/provisioning has on the behaviour and abundance of individual shark species are starting to become known, there is an almost complete lack of equivalent data from multi-species shark diving sites. In this study, changes in species composition and relative abundances were determined at the Shark Reef Marine Reserve, a multi-species shark feeding site in Fiji. Using direct observation sampling methods, eight species of sharks (bull shark Carcharhinus leucas, grey reef shark Carcharhinus amblyrhynchos, whitetip reef shark Triaenodon obesus, blacktip reef shark Carcharhinus melanopterus, tawny nurse shark Nebrius ferrugineus, silvertip shark Carcharhinus albimarginatus, sicklefin lemon shark Negaprion acutidens, and tiger shark Galeocerdo cuvier) displayed inter-annual site fidelity between 2003 and 2012. Encounter rates and/or relative abundances of some species changed over time, overall resulting in more individuals (mostly C. leucas) of fewer species being encountered on average on shark feeding dives at the end of the study period. Differences in shark community composition between the years 2004-2006 and 2007-2012 were evident, mostly because N. ferrugineus, C. albimarginatus and N. acutidens were much more abundant in 2004-2006 and very rare in the period of 2007-2012. Two explanations are offered for the observed changes in relative abundances over time, namely inter-specific interactions and operator-specific feeding protocols. Both, possibly in combination, are suggested to be important determinants of species composition and encounter rates, and relative abundances at this shark provisioning site in Fiji. This study, which includes the most species from a spatially confined shark provisioning site to date, suggests that long-term provisioning may result in competitive exclusion among shark

  10. Long-Term Changes in Species Composition and Relative Abundances of Sharks at a Provisioning Site

    PubMed Central

    Brunnschweiler, Juerg M.; Abrantes, Kátya G.; Barnett, Adam

    2014-01-01

    Diving with sharks, often in combination with food baiting/provisioning, has become an important product of today’s recreational dive industry. Whereas the effects baiting/provisioning has on the behaviour and abundance of individual shark species are starting to become known, there is an almost complete lack of equivalent data from multi-species shark diving sites. In this study, changes in species composition and relative abundances were determined at the Shark Reef Marine Reserve, a multi-species shark feeding site in Fiji. Using direct observation sampling methods, eight species of sharks (bull shark Carcharhinus leucas, grey reef shark Carcharhinus amblyrhynchos, whitetip reef shark Triaenodon obesus, blacktip reef shark Carcharhinus melanopterus, tawny nurse shark Nebrius ferrugineus, silvertip shark Carcharhinus albimarginatus, sicklefin lemon shark Negaprion acutidens, and tiger shark Galeocerdo cuvier) displayed inter-annual site fidelity between 2003 and 2012. Encounter rates and/or relative abundances of some species changed over time, overall resulting in more individuals (mostly C. leucas) of fewer species being encountered on average on shark feeding dives at the end of the study period. Differences in shark community composition between the years 2004–2006 and 2007–2012 were evident, mostly because N. ferrugineus, C. albimarginatus and N. acutidens were much more abundant in 2004–2006 and very rare in the period of 2007–2012. Two explanations are offered for the observed changes in relative abundances over time, namely inter-specific interactions and operator-specific feeding protocols. Both, possibly in combination, are suggested to be important determinants of species composition and encounter rates, and relative abundances at this shark provisioning site in Fiji. This study, which includes the most species from a spatially confined shark provisioning site to date, suggests that long-term provisioning may result in competitive exclusion

  11. Species-environment relationships and vegetation patterns: Effects of spatial scale and tree life-stage

    USGS Publications Warehouse

    Stohlgren, T.J.; Bachand, R.R.; Onami, Y.; Binkley, D.

    1998-01-01

    Do relationships between species and environmental gradients strengthen or weaken with tree life-stage (i.e., small seedlings, large seedlings, saplings, and mature trees)? Strengthened relationships may lead to distinct forest type boundaries, or weakening connections could lead to gradual ecotones and heterogeneous forest landscapes. We quantified the changes in forest dominance (basal area of tree species by life-stage) and environmental factors (elevation, slope, aspect, intercepted photosynthetically active radiation (PAR), summer soil moisture, and soil depth and texture) across 14 forest ecotones (n = 584, 10 m x 10 m plots) in Rocky Mountain National Park, Colorado, U.S.A. Local, ecotone-specific species-environment relationships, based on multiple regression techniques, generally strengthened from the small seedling stage (multiple R2 ranged from 0.00 to 0.26) to the tree stage (multiple R2 ranged from 0.20 to 0.61). At the landscape scale, combined canonical correspondence analysis (CCA) among species and for all tree life-stages suggested that the seedlings of most species became established in lower-elevation, drier sites than where mature trees of the same species dominated. However, conflicting evidence showed that species-environment relationships may weaken with tree life-stage. Seedlings were only found in a subset of plots (habitats) occupied by mature trees of the same species. At the landscape scale, CCA results showed that species-environment relationships weakened somewhat from the small seedling stage (86.4% of the variance explained by the first two axes) to the tree stage (76.6% of variance explained). The basal area of tree species co-occurring with Pinus contorta Doug. ex. Loud declined more gradually than P. contorta basal area declined across ecotones, resulting in less-distinct forest type boundaries. We conclude that broad, gradual ecotones and heterogeneous forest landscapes are created and maintained by: (1) sporadic establishment

  12. Regional species richness of families and the distribution of abundance and rarity in a local community of forest Hymenoptera

    NASA Astrophysics Data System (ADS)

    Ulrich, Werner

    2005-09-01

    Recent investigations about the relationship between the number of species of taxonomic lineages and regional patterns of species abundances gave indecisive results. Here, it is shown that mean densities of species of a species-rich community of forest Hymenoptera (673 species out of 25 families) were positively related to the number of European species per family. The fraction of abundant species per family declined and the fraction of rare species increased with species richness. Species rich families contained relatively more species, which were present in only one study year (occasional species), and relatively fewer species present during the whole study period (frequent species).

  13. Tissue culture and top-fruit tree species.

    PubMed

    Ochatt, S J; Davey, M R; Power, J B

    1990-01-01

    The commercial cultivation of rosaceous fruit trees (e.g., pear, apple, cherry, peach, plum) relies heavily upon the quality and performance of the rootstocks. This is even more the case now that self-rooted scions produce larger trees with a longer juvenile phase (1). It would, therefore, be of special interest for the fruit breeder to have general purpose rootstocks with a wide ecophysiological adaptation and high compatibility coupled with early cropping. In addition, many of the older and highly adapted scion varieties of fruit trees could benefit greatly from the introduction of stable, yet minor changes in their genome. Fruit trees are generally highly heterozygous, outbreeding, and thus are asexually propagated (see Chapter 10 , this vol.). Consequently, genetic improvement is likely to be based on protoplast technology, and achieved mainly through somatic methods, such as somaclonal variation or somatic hybridization. PMID:21390607

  14. Estimating species occurrence, abundance, and detection probability using zero-inflated distributions

    USGS Publications Warehouse

    Wenger, S.J.; Freeman, Mary C.

    2008-01-01

    Researchers have developed methods to account for imperfect detection of species with either occupancy (presence-absence) or count data using replicated sampling. We show how these approaches can be combined to simultaneously estimate occurrence, abundance, and detection probability by specifying a zero-inflated distribution for abundance. This approach may be particularly appropriate when patterns of occurrence and abundance arise from distinct processes operating at differing spatial or temporal scales. We apply the model to two data sets: (1) previously published data for a species of duck, Anas platyrhynchos, and (2) data for a stream fish species, Etheostoma scotti. We show that in these cases, an incomplete-detection zero-inflated modeling approach yields a superior fit to the data than other models. We propose that zero-inflated abundance models accounting for incomplete detection be considered when replicate count data are available.

  15. [Population structure and environmental relationships of the tropical tree Nectandra rudis (Lauraceae), a rare species in western Mexico].

    PubMed

    Guzmán, Ramón Cuevas; Moya, Edmundo García; García, J Antonio Vázquez; López, Nora M Núñez

    2008-03-01

    Population structure and environmental relationships of the tropical tree Nectandra rudis (Lauraceae), a rare species in western Mexico. The tree N. rudis is a rare species from western Mexico of which community and population features are unknown. We studied a population in an altitudinal gradient, from 550-1,850 m above sea level in the Sierra de Manantlan, Jalisco, Mexico. We established four 60x48 m sample sites at vertical distances of 100 m along this altitudinal gradient. Within each plot, ten 100 m2 circular sub-sampling units were randomly located. At each unit, we recorded diameter at breast height (dbh) and tree height for all woody vegetation > or =2.5 cm dbh. Basal area, tree density, frequency, species richness and importance values per species and plot. We estimated the vertical structure (total tree height) and diameter( as M=5log(10)N) for all N. rudis individuals. A direct ordination through Canonical Correspondence Analysis was done, involving amongst other species, edaphic and environmental data matrices. The record of 44 N. rudis individuals, in seven out the 56 plots sampled, represents the most septentrional record for the species and the first in Western Mexico. Its density and basal area represented 4.5 % and 8.7 % respectively of the total estimated for the community. The greatest importance values were observed at 1 650 m above sea level. The population structure of N. rudis is structured into five diameter categories in an inverse "J" shaped distribution. This is a typical behavior observed to occur in the Lauraceae, which produces big seeds of short viability that germinate when there is high soil moisture content. The species tend to form dense seedling banks although only a reduced number of them are able to survive. Species richness varies from 27 to 39 at plot level; the greatest importance values for the plots on which N. rudis was found, corresponds to Urera verrucosa (Liebm.) V.W. Steinm., N. rudis, Ficus sp., Beilschmiedia

  16. Designing Mixed Species Tree Plantations for the Tropics: Balancing Ecological Attributes of Species with Landholder Preferences in the Philippines

    PubMed Central

    Nguyen, Huong; Lamb, David; Herbohn, John; Firn, Jennifer

    2014-01-01

    A mixed species reforestation program known as the Rainforestation Farming system was undertaken in the Philippines to develop forms of farm forestry more suitable for smallholders than the simple monocultural plantations commonly used then. In this study, we describe the subsequent changes in stand structure and floristic composition of these plantations in order to learn from the experience and develop improved prescriptions for reforestation systems likely to be attractive to smallholders. We investigated stands aged from 6 to 11 years old on three successive occasions over a 6 year period. We found the number of species originally present in the plots as trees >5 cm dbh decreased from an initial total of 76 species to 65 species at the end of study period. But, at the same time, some new species reached the size class threshold and were recruited into the canopy layer. There was a substantial decline in tree density from an estimated stocking of about 5000 trees per ha at the time of planting to 1380 trees per ha at the time of the first measurement; the density declined by a further 4.9% per year. Changes in composition and stand structure were indicated by a marked shift in the Importance Value Index of species. Over six years, shade-intolerant species became less important and the native shade-tolerant species (often Dipterocarps) increased in importance. Based on how the Rainforestation Farming plantations developed in these early years, we suggest that mixed-species plantations elsewhere in the humid tropics should be around 1000 trees per ha or less, that the proportion of fast growing (and hence early maturing) trees should be about 30–40% of this initial density and that any fruit tree component should only be planted on the plantation margin where more light and space are available for crowns to develop. PMID:24751720

  17. Designing mixed species tree plantations for the tropics: balancing ecological attributes of species with landholder preferences in the Philippines.

    PubMed

    Nguyen, Huong; Lamb, David; Herbohn, John; Firn, Jennifer

    2014-01-01

    A mixed species reforestation program known as the Rainforestation Farming system was undertaken in the Philippines to develop forms of farm forestry more suitable for smallholders than the simple monocultural plantations commonly used then. In this study, we describe the subsequent changes in stand structure and floristic composition of these plantations in order to learn from the experience and develop improved prescriptions for reforestation systems likely to be attractive to smallholders. We investigated stands aged from 6 to 11 years old on three successive occasions over a 6 year period. We found the number of species originally present in the plots as trees >5 cm dbh decreased from an initial total of 76 species to 65 species at the end of study period. But, at the same time, some new species reached the size class threshold and were recruited into the canopy layer. There was a substantial decline in tree density from an estimated stocking of about 5000 trees per ha at the time of planting to 1380 trees per ha at the time of the first measurement; the density declined by a further 4.9% per year. Changes in composition and stand structure were indicated by a marked shift in the Importance Value Index of species. Over six years, shade-intolerant species became less important and the native shade-tolerant species (often Dipterocarps) increased in importance. Based on how the Rainforestation Farming plantations developed in these early years, we suggest that mixed-species plantations elsewhere in the humid tropics should be around 1000 trees per ha or less, that the proportion of fast growing (and hence early maturing) trees should be about 30-40% of this initial density and that any fruit tree component should only be planted on the plantation margin where more light and space are available for crowns to develop. PMID:24751720

  18. [Distribution patterns of canopy and understory tree species at local scale in a Tierra Firme forest, the Colombian Amazonia].

    PubMed

    Barreto-Silva, Juan Sebastian; López, Dairon Cárdenas; Montoya, Alvaro Javier Duque

    2014-03-01

    The effect of environmental variation on the structure of tree communities in tropical forests is still under debate. There is evidence that in landscapes like Tierra Firme forest, where the environmental gradient decreases at a local level, the effect of soil on the distribution patterns of plant species is minimal, happens to be random or is due to biological processes. In contrast, in studies with different kinds of plants from tropical forests, a greater effect on floristic composition of varying soil and topography has been reported. To assess this, the current study was carried out in a permanent plot of ten hectares in the Amacayacu National Park, Colombian Amazonia. To run the analysis, floristic and environmental variations were obtained according to tree species abundance categories and growth forms. In order to quantify the role played by both environmental filtering and dispersal limitation, the variation of the spatial configuration was included. We used Detrended Correspondence Analysis and Canonical Correspondence Analysis, followed by a variation partitioning, to analyze the species distribution patterns. The spatial template was evaluated using the Principal Coordinates of Neighbor Matrix method. We recorded 14 074 individuals from 1 053 species and 80 families. The most abundant families were Myristicaceae, Moraceae, Meliaceae, Arecaceae and Lecythidaceae, coinciding with other studies from Northwest Amazonia. Beta diversity was relatively low within the plot. Soils were very poor, had high aluminum concentration and were predominantly clayey. The floristic differences explained along the ten hectares plot were mainly associated to biological processes, such as dispersal limitation. The largest proportion of community variation in our dataset was unexplained by either environmental or spatial data. In conclusion, these results support random processes as the major drivers of the spatial variation of tree species at a local scale on Tierra Firme

  19. CpDNA-based species identification and phylogeography: application to African tropical tree species.

    PubMed

    Duminil, J; Heuertz, M; Doucet, J-L; Bourland, N; Cruaud, C; Gavory, F; Doumenge, C; Navascués, M; Hardy, O J

    2010-12-01

    Despite the importance of the African tropical rainforests as a hotspot of biodiversity, their history and the processes that have structured their biodiversity are understood poorly. With respect to past demographic processes, new insights can be gained through characterizing the distribution of genetic diversity. However, few studies of this type have been conducted in Central Africa, where the identification of species in the field can be difficult. We examine here the distribution of chloroplast DNA (cpDNA) diversity in Lower Guinea in two tree species that are difficult to distinguish, Erythrophleum ivorense and Erythrophleum suaveolens (Fabaceae). By using a blind-sampling approach and comparing molecular and morphological markers, we first identified retrospectively all sampled individuals and determined the limits of the distribution of each species. We then performed a phylogeographic study using the same genetic data set. The two species displayed essentially parapatric distributions that were correlated well with the rainfall gradient, which indicated different ecological requirements. In addition, a phylogeographic structure was found for E. suaveolens and, for both species, substantially higher levels of diversity and allelic endemism were observed in the south (Gabon) than in the north (Cameroon) of the Lower Guinea region. This finding indicated different histories of population demographics for the two species, which might reflect different responses to Quaternary climate changes. We suggest that a recent period of forest perturbation, which might have been caused by humans, favoured the spread of these two species and that their poor recruitment at present results from natural succession in their forest formations. PMID:21091558

  20. Colonization of Artificially Stressed Black Walnut Trees by Ambrosia Beetle, Bark Beetle, and Other Weevil Species (Coleoptera: Curculionidae) in Indiana and Missouri.

    PubMed

    Reed, Sharon E; Juzwik, Jennifer; English, James T; Ginzel, Matthew D

    2015-12-01

    Thousand cankers disease (TCD) is a new disease of black walnut (Juglans nigra L.) in the eastern United States. The disease is caused by the interaction of the aggressive bark beetle Pityophthorus juglandis Blackman and the canker-forming fungus, Geosmithia morbida M. Kolarik, E. Freeland, C. Utley & Tisserat, carried by the beetle. Other insects also colonize TCD-symptomatic trees and may also carry pathogens. A trap tree survey was conducted in Indiana and Missouri to characterize the assemblage of ambrosia beetles, bark beetles, and other weevils attracted to the main stems and crowns of stressed black walnut. More than 100 trees were girdled and treated with glyphosate (Riverdale Razor Pro, Burr Ridge, Illinois) at 27 locations. Nearly 17,000 insects were collected from logs harvested from girdled walnut trees. These insects represented 15 ambrosia beetle, four bark beetle, and seven other weevil species. The most abundant species included Xyleborinus saxeseni Ratzburg, Xylosandrus crassiusculus Motschulsky, Xylosandrus germanus Blandford, Xyleborus affinis Eichhoff, and Stenomimus pallidus Boheman. These species differed in their association with the stems or crowns of stressed trees. Multiple species of insects were collected from individual trees and likely colonized tissues near each other. At least three of the abundant species found (S. pallidus, X. crassiusculus, and X. germanus) are known to carry propagules of canker-causing fungi of black walnut. In summary, a large number of ambrosia beetles, bark beetles, and other weevils are attracted to stressed walnut trees in Indiana and Missouri. Several of these species have the potential to introduce walnut canker pathogens during colonization. PMID:26314028

  1. A survey of homopteran species (Auchenorrhyncha) from coffee shrubs and poró and laurel trees in shaded coffee plantations, in Turrialba, Costa Rica.

    PubMed

    Rojas, L; Godoy, C; Hanson, P; Hilje, L

    2001-01-01

    A survey of homopteran species (Auchenorryncha) was conducted in coffee plantations with no shade (C), and in those with shade of either poró (Erythrina poeppigiana) (CP) or poró plus laurel (Cordia alliodora) (CPL), in Turrialba, Costa Rica. A total of 130 species in ten families were collected, dominated by Cicadellidae (82 species). Species richness was highest in the CP system (88), followed by CPL (74) and C systems (60). Five most common species for all systems were Fusigonalia lativittata, Hebralebra nicaraguensis, Neocoelidia sp., Oliarus sp. and Clastoptera sp. Diversification of the coffee agroecosystem favors some species while limiting others, and have no effect on the majority of species. Thus, only F. lativittata, Neocoelidia sp. and Scaphytopius ca. latidens were well represented in all systems, but were more abundant in coffee shrubs. Additionally, the following were the dominant species in each system: Graphocephala sp. 1 (C), F. lativittata (CP) and H. nicaraguensis (CPL). Four species abundant on laurel trees, including H. nicaraguensis, appeared almost exclusively on these tree species. Species similarity was highest on the CP and CPL systems (51% of the species in common), followed by the C and CP (39%) and the C and CPL systems (38%). These findings show that even disturbed systems can harbor many insect species, so that they deserve attention from conservation advocates and biologists. PMID:12189787

  2. Concatenation and Species Tree Methods Exhibit Statistically Indistinguishable Accuracy under a Range of Simulated Conditions

    PubMed Central

    Tonini, João; Moore, Andrew; Stern, David; Shcheglovitova, Maryia; Ortí, Guillermo

    2015-01-01

    Phylogeneticists have long understood that several biological processes can cause a gene tree to disagree with its species tree. In recent years, molecular phylogeneticists have increasingly foregone traditional supermatrix approaches in favor of species tree methods that account for one such source of error, incomplete lineage sorting (ILS). While gene tree-species tree discordance no doubt poses a significant challenge to phylogenetic inference with molecular data, researchers have only recently begun to systematically evaluate the relative accuracy of traditional and ILS-sensitive methods. Here, we report on simulations demonstrating that concatenation can perform as well or better than methods that attempt to account for sources of error introduced by ILS. Based on these and similar results from other researchers, we argue that concatenation remains a useful component of the phylogeneticist’s toolbox and highlight that phylogeneticists should continue to make explicit comparisons of results produced by contemporaneous and classical methods. PMID:25901289

  3. Tree diversity and species identity effects on soil fungi, protists and animals are context dependent.

    PubMed

    Tedersoo, Leho; Bahram, Mohammad; Cajthaml, Tomáš; Põlme, Sergei; Hiiesalu, Indrek; Anslan, Sten; Harend, Helery; Buegger, Franz; Pritsch, Karin; Koricheva, Julia; Abarenkov, Kessy

    2016-02-01

    Plant species richness and the presence of certain influential species (sampling effect) drive the stability and functionality of ecosystems as well as primary production and biomass of consumers. However, little is known about these floristic effects on richness and community composition of soil biota in forest habitats owing to methodological constraints. We developed a DNA metabarcoding approach to identify the major eukaryote groups directly from soil with roughly species-level resolution. Using this method, we examined the effects of tree diversity and individual tree species on soil microbial biomass and taxonomic richness of soil biota in two experimental study systems in Finland and Estonia and accounted for edaphic variables and spatial autocorrelation. Our analyses revealed that the effects of tree diversity and individual species on soil biota are largely context dependent. Multiple regression and structural equation modelling suggested that biomass, soil pH, nutrients and tree species directly affect richness of different taxonomic groups. The community composition of most soil organisms was strongly correlated due to similar response to environmental predictors rather than causal relationships. On a local scale, soil resources and tree species have stronger effect on diversity of soil biota than tree species richness per se. PMID:26172210

  4. Temporal comparison and predictors of fish species abundance and richness on undisturbed coral reef patches

    PubMed Central

    Wismer, Sharon; Bshary, Redouan

    2015-01-01

    Large disturbances can cause rapid degradation of coral reef communities, but what baseline changes in species assemblages occur on undisturbed reefs through time? We surveyed live coral cover, reef fish abundance and fish species richness in 1997 and again in 2007 on 47 fringing patch reefs of varying size and depth at Mersa Bareika, Ras Mohammed National Park, Egypt. No major human or natural disturbance event occurred between these two survey periods in this remote protected area. In the absence of large disturbances, we found that live coral cover, reef fish abundance and fish species richness did not differ in 1997 compared to 2007. Fish abundance and species richness on patches was largely related to the presence of shelters (caves and/or holes), live coral cover and patch size (volume). The presence of the ectoparasite-eating cleaner wrasse, Labroides dimidiatus, was also positively related to fish species richness. Our results underscore the importance of physical reef characteristics, such as patch size and shelter availability, in addition to biotic characteristics, such as live coral cover and cleaner wrasse abundance, in supporting reef fish species richness and abundance through time in a relatively undisturbed and understudied region. PMID:26644988

  5. Temporal comparison and predictors of fish species abundance and richness on undisturbed coral reef patches.

    PubMed

    Wagner, Elena L E S; Roche, Dominique G; Binning, Sandra A; Wismer, Sharon; Bshary, Redouan

    2015-01-01

    Large disturbances can cause rapid degradation of coral reef communities, but what baseline changes in species assemblages occur on undisturbed reefs through time? We surveyed live coral cover, reef fish abundance and fish species richness in 1997 and again in 2007 on 47 fringing patch reefs of varying size and depth at Mersa Bareika, Ras Mohammed National Park, Egypt. No major human or natural disturbance event occurred between these two survey periods in this remote protected area. In the absence of large disturbances, we found that live coral cover, reef fish abundance and fish species richness did not differ in 1997 compared to 2007. Fish abundance and species richness on patches was largely related to the presence of shelters (caves and/or holes), live coral cover and patch size (volume). The presence of the ectoparasite-eating cleaner wrasse, Labroides dimidiatus, was also positively related to fish species richness. Our results underscore the importance of physical reef characteristics, such as patch size and shelter availability, in addition to biotic characteristics, such as live coral cover and cleaner wrasse abundance, in supporting reef fish species richness and abundance through time in a relatively undisturbed and understudied region. PMID:26644988

  6. Leapfrogging of tree species provenances? Interaction of microclimate and genetics on upward shifts in tree species' range limits

    NASA Astrophysics Data System (ADS)

    Reinhardt, K.; Castanha, C.; Germino, M. J.; Kueppers, L. M.

    2011-12-01

    The elevation limit of tree growth (alpine treeline) is considered to be constrained by environmental (i.e., thermal) and genetic (i.e., inability to adapt to climatic conditions) limitations to growth. Warming conditions due to climate change are predicted to cause upward shifts in the elevation of alpine treelines, through relief of cold-induced physiological limitations on seedling recruitment beyond current treeline boundaries. To determine how genetics and climate may interact to affect seedling establishment, we transplanted recently germinated seedlings from high- and low-elevation provenances (HI and LO, respectively) of Pinus flexilis in common gardens arrayed along an elevation and canopy gradient from subalpine forest into the alpine zone at Niwot Ridge, CO. We compared differences in microclimate and seedling ecophysiology among sites and between provenances. During the first summer of growth, frequently cloudy skies resulted in similar solar radiation incidence and air and soil temperatures among sites, despite nearly a 500 m-span in elevation across all sites. Preliminary findings suggest that survival of seedlings was similar between the lowest and highest elevations, with greater survival of LO (60%) compared to HI (40%) seedlings at each of these sites. Photosynthesis, carbon balance (photosynthesis/respiration), and conductance increased more than 2X with elevation for both provenances, and were 35-77% greater in LO seedlings compared to HI seedlings. There were no differences in dark-adapted chlorophyll fluorescence (Fv/Fm) among sites or between provenances. However, in a common-garden study at low elevation, we observed no differences in carbon or water relations between two naturally-germinated mitochondrial haplotypes of P. flexilis (of narrow and wide-ranging distributions). We did observe water-related thresholds on seedling carbon balance and survival that occurred when soil volumetric water content dropped below 10% and seedling water

  7. Coordination between water transport capacity, biomass growth, metabolic scaling and species stature in co-occurring shrub and tree species.

    PubMed

    Smith, Duncan D; Sperry, John S

    2014-12-01

    The significance of xylem function and metabolic scaling theory begins from the idea that water transport is strongly coupled to growth rate. At the same time, coordination of water transport and growth seemingly should differ between plant functional types. We evaluated the relationships between water transport, growth and species stature in six species of co-occurring trees and shrubs. Within species, a strong proportionality between plant hydraulic conductance (K), sap flow (Q) and shoot biomass growth (G) was generally supported. Across species, however, trees grew more for a given K or Q than shrubs, indicating greater growth-based water-use efficiency (WUE) in trees. Trees also showed slower decline in relative growth rate (RGR) than shrubs, equivalent to a steeper G by mass (M) scaling exponent in trees (0.77-0.98). The K and Q by M scaling exponents were common across all species (0.80, 0.82), suggesting that the steeper G scaling in trees reflects a size-dependent increase in their growth-based WUE. The common K and Q by M exponents were statistically consistent with the 0.75 of ideal scaling theory. A model based upon xylem anatomy and branching architecture consistently predicted the observed K by M scaling exponents but only when deviations from ideal symmetric branching were incorporated. PMID:25041417

  8. SIMULATION OF OZONE EFFECTS ON EIGHT TREE SPECIES AT SHENANDOAH NATIONAL PARK

    EPA Science Inventory

    As part of an assessment of potential effects of air pollutants on the vegetation of Shenandoah National Park (SHEN), we simulated the growth of eight important tree species using TREGRO, a mechanistic model of individual tree growth. Published TREGRO parameters for black cherry...

  9. Assessing the potential of native tree species for carbon sequestration forestry in Northeast China.

    PubMed

    Thomas, S C; Malczewski, G; Saprunoff, M

    2007-11-01

    Although the native forests of China are exceptionally diverse, only a small number of tree species have been widely utilized in forest plantations and reforestation efforts. We used dendrochronological sampling methods to assess the potential growth and carbon sequestration of native tree species in Jilin Province, Northeast China. Trees were sampled in and near the Changbaishan Biosphere Reserve, with samples encompassing old-growth, disturbed forest, and plantations. To approximate conditions for planted trees, sampling focused on trees with exposed crowns (dominant and co-dominant individuals). A log-linear relationship was found between diameter increment and tree diameter, with a linear decrease in increment with increasing local basal area; no significant differences in these patterns between plantations and natural stands were detected for two commonly planted species (Pinus koraiensis and Larix olgensis). A growth model that incorporates observed feedbacks with individual tree size and local basal area (in conjunction with allometric models for tree biomass), was used to project stand-level biomass increment. Predicted growth trajectories were then linked to the carbon process model InTEC to provide estimates of carbon sequestration potential. Results indicate substantial differences among species, and suggest that certain native hardwoods (in particular Fraxinus mandshurica and Phellodendron amurense), have high potential for use in carbon forestry applications. Increased use of native hardwoods in carbon forestry in China is likely to have additional benefits in terms of economic diversification and enhanced provision of "ecosystem services", including biodiversity protection. PMID:17188419

  10. Island invasion by a threatened tree species: evidence for natural enemy release of mahogany (Swietenia macrophylla) on Dominica, Lesser Antilles.

    PubMed

    Norghauer, Julian M; Martin, Adam R; Mycroft, Erin E; James, Arlington; Thomas, Sean C

    2011-01-01

    Despite its appeal to explain plant invasions, the enemy release hypothesis (ERH) remains largely unexplored for tropical forest trees. Even scarcer are ERH studies conducted on the same host species at both the community and biogeographical scale, irrespective of the system or plant life form. In Cabrits National Park, Dominica, we observed patterns consistent with enemy release of two introduced, congeneric mahogany species, Swietenia macrophylla and S. mahagoni, planted almost 50 years ago. Swietenia populations at Cabrits have reproduced, with S. macrophylla juveniles established in and out of plantation areas at densities much higher than observed in its native range. Swietenia macrophylla juveniles also experienced significantly lower leaf-level herbivory (∼3.0%) than nine co-occurring species native to Dominica (8.4-21.8%), and far lower than conspecific herbivory observed in its native range (11%-43%, on average). These complimentary findings at multiple scales support ERH, and confirm that Swietenia has naturalized at Cabrits. However, Swietenia abundance was positively correlated with native plant diversity at the seedling stage, and only marginally negatively correlated with native plant abundance for stems ≥1-cm dbh. Taken together, these descriptive patterns point to relaxed enemy pressure from specialized enemies, specifically the defoliator Steniscadia poliophaea and the shoot-borer Hypsipyla grandella, as a leading explanation for the enhanced recruitment of Swietenia trees documented at Cabrits. PMID:21533206

  11. Island Invasion by a Threatened Tree Species: Evidence for Natural Enemy Release of Mahogany (Swietenia macrophylla) on Dominica, Lesser Antilles

    PubMed Central

    Norghauer, Julian M.; Martin, Adam R.; Mycroft, Erin E.; James, Arlington; Thomas, Sean C.

    2011-01-01

    Despite its appeal to explain plant invasions, the enemy release hypothesis (ERH) remains largely unexplored for tropical forest trees. Even scarcer are ERH studies conducted on the same host species at both the community and biogeographical scale, irrespective of the system or plant life form. In Cabrits National Park, Dominica, we observed patterns consistent with enemy release of two introduced, congeneric mahogany species, Swietenia macrophylla and S. mahagoni, planted almost 50 years ago. Swietenia populations at Cabrits have reproduced, with S. macrophylla juveniles established in and out of plantation areas at densities much higher than observed in its native range. Swietenia macrophylla juveniles also experienced significantly lower leaf-level herbivory (∼3.0%) than nine co-occurring species native to Dominica (8.4–21.8%), and far lower than conspecific herbivory observed in its native range (11%–43%, on average). These complimentary findings at multiple scales support ERH, and confirm that Swietenia has naturalized at Cabrits. However, Swietenia abundance was positively correlated with native plant diversity at the seedling stage, and only marginally negatively correlated with native plant abundance for stems ≥1-cm dbh. Taken together, these descriptive patterns point to relaxed enemy pressure from specialized enemies, specifically the defoliator Steniscadia poliophaea and the shoot-borer Hypsipyla grandella, as a leading explanation for the enhanced recruitment of Swietenia trees documented at Cabrits. PMID:21533206

  12. Method for estimating potential tree-grade distributions for northeastern forest species. Forest Service research paper (Final)

    SciTech Connect

    Yaussy, D.A.

    1993-03-01

    The generalized logistic regression was used to distribute trees into four potential tree grades for 20 northeastern species groups. The potential tree grade is defined as the tree grade based on the length and amount of clear cuttings and defects only, disregarding minimum grading diameter. The algorithms described use site index and tree diameter as the predictive variables, allowing the equations to be incorporated into individual-tree growth and yield simulators such as NE-TWIGS.

  13. Net Assimilation Rate Determines the Growth Rates of 14 Species of Subtropical Forest Trees.

    PubMed

    Li, Xuefei; Schmid, Bernhard; Wang, Fei; Paine, C E Timothy

    2016-01-01

    Growth rates are of fundamental importance for plants, as individual size affects myriad ecological processes. We determined the factors that generate variation in RGR among 14 species of trees and shrubs that are abundant in subtropical Chinese forests. We grew seedlings for two years at four light levels in a shade-house experiment. We monitored the growth of every juvenile plant every two weeks. After one and two years, we destructively harvested individuals and measured their functional traits and gas-exchange rates. After calculating individual biomass trajectories, we estimated relative growth rates using nonlinear growth functions. We decomposed the variance in log(RGR) to evaluate the relationships of RGR with its components: specific leaf area (SLA), net assimilation rate (NAR) and leaf mass ratio (LMR). We found that variation in NAR was the primary determinant of variation in RGR at all light levels, whereas SLA and LMR made smaller contributions. Furthermore, NAR was strongly and positively associated with area-based photosynthetic rate and leaf nitrogen content. Photosynthetic rate and leaf nitrogen concentration can, therefore, be good predictors of growth in woody species. PMID:26953884

  14. Herbivory As A Driver For Biogenic Methanol Flux From North American Temperate Tree Species

    NASA Astrophysics Data System (ADS)

    Oikawa, P.; Lerdau, M.; Mak, J.

    2007-12-01

    Ecological relationships of plants and herbivores have implications for biosphere-atmosphere interactions. For instance, plant monoterpene emission response to herbivory can significantly impact air quality /(Litvak et al. /(1999/) Ecol. Appl. 9/(4/):1147-1159/). Studies on biogenic methanol emission response to herbivory have observed significant methanol emissions directly following herbivore attack and even larger emissions 24hrs later /(Penuelas et al. /(2005/) New Phytol. 167:851-857/). We investigated gypsy moth defoliation impacts on methanol emissions in the abundant North American temperate tree species big tooth aspen Populus grandidentata. Specifically, we measured methanol emission response to herbivory on both short and long time scales at a field site in northern Michigan. Our results suggest herbivory can significantly increase methanol emissions on both short and long time scales. Unlike previous investigations, we did not observe methanol emissions 24hrs post-attack to be significantly higher than emissions detected directly following attack. When compared to mechanical wounding, herbivory did not elicit a quantitatively different methanol emission response in this species. These results suggest that herbivory in temperate forests may be an important driver for biogenic methanol flux and may therefore be helpful in improving models of methanol dynamics.

  15. Net Assimilation Rate Determines the Growth Rates of 14 Species of Subtropical Forest Trees

    PubMed Central

    Li, Xuefei; Schmid, Bernhard; Wang, Fei; Paine, C. E. Timothy

    2016-01-01

    Growth rates are of fundamental importance for plants, as individual size affects myriad ecological processes. We determined the factors that generate variation in RGR among 14 species of trees and shrubs that are abundant in subtropical Chinese forests. We grew seedlings for two years at four light levels in a shade-house experiment. We monitored the growth of every juvenile plant every two weeks. After one and two years, we destructively harvested individuals and measured their functional traits and gas-exchange rates. After calculating individual biomass trajectories, we estimated relative growth rates using nonlinear growth functions. We decomposed the variance in log(RGR) to evaluate the relationships of RGR with its components: specific leaf area (SLA), net assimilation rate (NAR) and leaf mass ratio (LMR). We found that variation in NAR was the primary determinant of variation in RGR at all light levels, whereas SLA and LMR made smaller contributions. Furthermore, NAR was strongly and positively associated with area-based photosynthetic rate and leaf nitrogen content. Photosynthetic rate and leaf nitrogen concentration can, therefore, be good predictors of growth in woody species. PMID:26953884

  16. Early MESSENGER Results for Less Abundant or Weakly Emitting Species in Mercury's Exosphere

    NASA Technical Reports Server (NTRS)

    Vervack, Ronald J., Jr.; McClintock, William E.; Killen, Rosemary M.; Sprague, Ann L.; Burger, Matthew H.; Merkel, Aimee W.; Sarantos, Menelaos

    2011-01-01

    Now that the Messenger spacecraft is in orbit about Mercury, the extended observing time enables searches for exospheric species that are less abundant or weakly emitting compared with those for which emission has previously been detected. Many of these species cannot be observed from the ground because of terrestrial atmospheric absorption. We report here on the status of MESSENGER orbital-phase searches for additional species in Mercury's exosphere.

  17. Early MESSENGER Results for Less Abundant or Weakly Emitting Species in Mercury's Exosphere

    NASA Astrophysics Data System (ADS)

    Vervack, R. J., Jr.; Killen, R. M.; Sprague, A. L.; Burger, M. H.; Merkel, A. W.; Sarantos, M.

    2011-10-01

    Now that the MESSENGER spacecraft is in orbit about Mercury, the extended observing time enables searches for exospheric species that are less abundant or weakly emitting compared with those for which emission has previously been detected. Many of these species cannot be observed from the ground because of terrestrial atmospheric absorption. We report here on the status of MESSENGER orbitalphase searches for additional species in Mercury's exosphere.

  18. Pythium species Associated with Forest Tree Nurseries of Oregon and Washington

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Pythium species are one of several pathogen genera responsible for damping off of conifer seedlings in forest tree nurseries. Species identification has been traditionally based on morphology. However, DNA-based identification methods may allow more accurate identification of species associated wi...

  19. Herbs versus Trees: Influences on Teenagers' Knowledge of Plant Species

    ERIC Educational Resources Information Center

    Lückmann, Katrin; Menzel, Susanne

    2014-01-01

    The study reports on species knowledge among German adolescents (n = 507) as: (1) self-assessed evaluation of one's species knowledge; and (2) factual knowledge about popular local herbs and trees. Besides assessing species knowledge, we were interested in whether selected demographic factors, environmental attitude (as measured through the…

  20. Supercooling Capacity Increases from Sea Level to Tree Line in the Hawaiian Tree Species Metrosideros polymorpha.

    PubMed

    Melcher; Cordell; Jones; Scowcroft; Niemczura; Giambelluca; Goldstein

    2000-05-01

    Population-specific differences in the freezing resistance of Metrosideros polymorpha leaves were studied along an elevational gradient from sea level to tree line (located at ca. 2500 m above sea level) on the east flank of the Mauna Loa volcano in Hawaii. In addition, we also studied 8-yr-old saplings grown in a common garden from seeds collected from the same field populations. Leaves of low-elevation field plants exhibited damage at -2 degrees C, before the onset of ice formation, which occurred at -5.7 degrees C. Leaves of high-elevation plants exhibited damage at ca. -8.5 degrees C, concurrent with ice formation in the leaf tissue, which is typical of plants that avoid freezing in their natural environment by supercooling. Nuclear magnetic resonance studies revealed that water molecules of both extra- and intracellular leaf water fractions from high-elevation plants had restricted mobility, which is consistent with their low water content and their high levels of osmotically active solutes. Decreased mobility of water molecules may delay ice nucleation and/or ice growth and may therefore enhance the ability of plant tissues to supercool. Leaf traits that correlated with specific differences in supercooling capacity were in part genetically determined and in part environmentally induced. Evidence indicated that lower apoplastic water content and smaller intercellular spaces were associated with the larger supercooling capacity of the plant's foliage at tree line. The irreversible tissue-damage temperature decreased by ca. 7 degrees C from sea level to tree line in leaves of field populations. However, this decrease appears to be only large enough to allow M. polymorpha trees to avoid leaf tissue damage from freezing up to a level of ca. 2500 m elevation, which is also the current tree line location on the east flank of Mauna Loa. The limited freezing resistance of M. polymorpha leaves may be partially responsible for the occurrence of tree line at a relatively

  1. Predicting spatial variations of tree species richness in tropical forests from high-resolution remote sensing.

    PubMed

    Fricker, Geoffrey A; Wolf, Jeffrey A; Saatchi, Sassan S; Gillespie, Thomas W

    2015-10-01

    There is an increasing interest in identifying theories, empirical data sets, and remote-sensing metrics that can quantify tropical forest alpha diversity at a landscape scale. Quantifying patterns of tree species richness in the field is time consuming, especially in regions with over 100 tree species/ha. We examine species richness in a 50-ha plot in Barro Colorado Island in Panama and test if biophysical measurements of canopy reflectance from high-resolution satellite imagery and detailed vertical forest structure and topography from light detection and ranging (lidar) are associated with species richness across four tree size classes (>1, 1-10, >10, and >20 cm dbh) and three spatial scales (1, 0.25, and 0.04 ha). We use the 2010 tree inventory, including 204,757 individuals belonging to 301 species of freestanding woody plants or 166 ± 1.5 species/ha (mean ± SE), to compare with remote-sensing data. All remote-sensing metrics became less correlated with species richness as spatial resolution decreased from 1.0 ha to 0.04 ha and tree size increased from 1 cm to 20 cm dbh. When all stems with dbh > 1 cm in 1-ha plots were compared to remote-sensing metrics, standard deviation in canopy reflectance explained 13% of the variance in species richness. The standard deviations of canopy height and the topographic wetness index (TWI) derived from lidar were the best metrics to explain the spatial variance in species richness (15% and 24%, respectively). Using multiple regression models, we made predictions of species richness across Barro Colorado Island (BCI) at the 1-ha spatial scale for different tree size classes. We predicted variation in tree species richness among all plants (adjusted r² = 0.35) and trees with dbh > 10 cm (adjusted r² = 0.25). However, the best model results were for understory trees and shrubs (dbh 1-10 cm) (adjusted r² = 0.52) that comprise the majority of species richness in tropical forests. Our results indicate that high

  2. Decadal variability in abundances of the dominant euphausiid species in southern sectors of the California Current

    NASA Astrophysics Data System (ADS)

    Brinton, Edward; Townsend, Annie

    2003-08-01

    Euphausiid abundance data from broadly based California Cooperative Oceanic Fisheries Investigation surveys in California and Baja California sectors of the California Current provided a time series distinguishing periodic, rhythmic and irregular species patterns. Comparisons with environmental indexes indicate significant correlations with warm-water species, most notably in coastal Nyctiphanes simplex. Oceanic warm-water species were similarly, but less extremely, allied with an index. Coastal warm-water N. simplex was uncommon off southern California before the atmospheric regime shift of the 1970s. It assumed a post-1978 pattern of rhythmic biannual abundance increases and decreases during 1981-2000. The near-tropical oceanic Euphausia eximia and Pacific Central subtropicals patterned similarly, but was more periodic than rhythmic. Euphausia pacifica, the most dominant and broadly ranging Euphausia species, peaked at irregular but distinct bi-decadal abundances during 6 strong La Niña episodes. The peaks uniformly collapsed by 90%, becoming El Niño-associated minima. The cold-water coastal northern species Thysanoessa spinifera frequently ranged far south off Baja California before 1960 but became limited to Central California in the 1980s. The importance of T. spinifera off the Californias is small compared with northern regions, but it extends to southern upwelling centers contributing to dominance, here, by cold-water euphausiids. Decadal periodicity of species abundances decreased in the 1990s, when trends became more common. Differences among sectors were minimal between the two Californias, but were often distinct between southern California and Central Baja California. Species abundances, comparing pre- and post-climate shift species averages, differed insignificantly for all species when logarithmic values were used. With arithmetic values, most 1977-1998 average values were the greater, but with large standard deviations.

  3. Mountain landscapes offer few opportunities for high-elevation tree species migration

    USGS Publications Warehouse

    Bell, David M.; Bradford, John B.; Lauenroth, William K.

    2014-01-01

    Climate change is anticipated to alter plant species distributions. Regional context, notably the spatial complexity of climatic gradients, may influence species migration potential. While high-elevation species may benefit from steep climate gradients in mountain regions, their persistence may be threatened by limited suitable habitat as land area decreases with elevation. To untangle these apparently contradictory predictions for mountainous regions, we evaluated the climatic suitability of four coniferous forest tree species of the western United States based on species distribution modeling (SDM) and examined changes in climatically suitable areas under predicted climate change. We used forest structural information relating to tree species dominance, productivity, and demography from an extensive forest inventory system to assess the strength of inferences made with a SDM approach. We found that tree species dominance, productivity, and recruitment were highest where climatic suitability (i.e., probability of species occurrence under certain climate conditions) was high, supporting the use of predicted climatic suitability in examining species risk to climate change. By predicting changes in climatic suitability over the next century, we found that climatic suitability will likely decline, both in areas currently occupied by each tree species and in nearby unoccupied areas to which species might migrate in the future. These trends were most dramatic for high elevation species. Climatic changes predicted over the next century will dramatically reduce climatically suitable areas for high-elevation tree species while a lower elevation species, Pinus ponderosa, will be well positioned to shift upslope across the region. Reductions in suitable area for high-elevation species imply that even unlimited migration would be insufficient to offset predicted habitat loss, underscoring the vulnerability of these high-elevation species to climatic changes.

  4. Mountain landscapes offer few opportunities for high-elevation tree species migration.

    PubMed

    Bell, David M; Bradford, John B; Lauenroth, William K

    2014-05-01

    Climate change is anticipated to alter plant species distributions. Regional context, notably the spatial complexity of climatic gradients, may influence species migration potential. While high-elevation species may benefit from steep climate gradients in mountain regions, their persistence may be threatened by limited suitable habitat as land area decreases with elevation. To untangle these apparently contradictory predictions for mountainous regions, we evaluated the climatic suitability of four coniferous forest tree species of the western United States based on species distribution modeling (SDM) and examined changes in climatically suitable areas under predicted climate change. We used forest structural information relating to tree species dominance, productivity, and demography from an extensive forest inventory system to assess the strength of inferences made with a SDM approach. We found that tree species dominance, productivity, and recruitment were highest where climatic suitability (i.e., probability of species occurrence under certain climate conditions) was high, supporting the use of predicted climatic suitability in examining species risk to climate change. By predicting changes in climatic suitability over the next century, we found that climatic suitability will likely decline, both in areas currently occupied by each tree species and in nearby unoccupied areas to which species might migrate in the future. These trends were most dramatic for high elevation species. Climatic changes predicted over the next century will dramatically reduce climatically suitable areas for high-elevation tree species while a lower elevation species, Pinus ponderosa, will be well positioned to shift upslope across the region. Reductions in suitable area for high-elevation species imply that even unlimited migration would be insufficient to offset predicted habitat loss, underscoring the vulnerability of these high-elevation species to climatic changes. PMID:24353188

  5. Global patterns in sandy beach macrofauna: Species richness, abundance, biomass and body size

    NASA Astrophysics Data System (ADS)

    Defeo, Omar; McLachlan, Anton

    2013-10-01

    Global patterns in species richness in sandy beach ecosystems have been poorly understood until comparatively recently, because of the difficulty of compiling high-resolution databases at continental scales. We analyze information from more than 200 sandy beaches around the world, which harbor hundreds of macrofauna species, and explore latitudinal trends in species richness, abundance and biomass. Species richness increases from temperate to tropical sites. Abundance follows contrasting trends depending on the slope of the beach: in gentle slope beaches, it is higher at temperate sites, whereas in steep-slope beaches it is higher at the tropics. Biomass follows identical negative trends for both climatic regions at the whole range of beach slopes, suggesting decreasing rates in carrying capacity of the environment towards reflective beaches. Various morphodynamic variables determine global trends in beach macrofauna. Species richness, abundance and biomass are higher at dissipative than at reflective beaches, whereas a body size follows the reverse pattern. A generalized linear model showed that large tidal range (which determines the vertical dimension of the intertidal habitat), small size of sand particles and flat beach slope (a product of the interaction among wave energy, tidal range and grain size) are correlated with high species richness, suggesting that these parameters represent the most parsimonious variables for modelling patterns in sandy beach macrofauna. Large-scale patterns indicate a scaling of abundance to a body size, suggesting that dissipative beaches harbor communities with highest abundance and species with the smallest body sizes. Additional information for tropical and northern hemisphere sandy beaches (underrepresented in our compilation) is required to decipher more conclusive trends, particularly in abundance, biomass and body size. Further research should integrate meaningful oceanographic variables, such as temperature and primary

  6. Anonymous nuclear markers data supporting species tree phylogeny and divergence time estimates in a cactus species complex in South America.

    PubMed

    Perez, Manolo F; Carstens, Bryan C; Rodrigues, Gustavo L; Moraes, Evandro M

    2016-03-01

    Supportive data related to the article "Anonymous nuclear markers reveal taxonomic incongruence and long-term disjunction in a cactus species complex with continental-island distribution in South America" (Perez et al., 2016) [1]. Here, we present pyrosequencing results, primer sequences, a cpDNA phylogeny, and a species tree phylogeny. PMID:26900589

  7. Version 5 of Forecasts; Forecasts of Climate-Associated Shifts in Tree Species

    NASA Astrophysics Data System (ADS)

    Hargrove, W. W.; Kumar, J.; Potter, K. M.; Hoffman, F. M.

    2014-12-01

    Version 5 of the ForeCASTS tree range shift atlas (www.geobabble.org/~hnw/global/treeranges5/climate_change/atlas.html) now predicts global shifts in the suitable ranges of 335 tree species (essentially all woody species measured in Forest Inventory Analysis (FIA)) under forecasts from the Parallel Climate Model, and the Hadley Model, each under future climatic scenarios A1 and B1, each at two future dates (2050 and 2100). Version 5 includes more Global Biodiversity Information Facility (GBIF) occurrence points, uses improved heuristics for occurrence training, and recovers occurrence points that fall in water. A multivariate clustering procedure was used to quantitatively delineate 30 thousand environmentally homogeneous ecoregions across present and 8 potential future global locations at once, using global maps of 17 environmental characteristics describing temperature, precipitation, soils, topography and solar insolation. Occurrence of each tree species on FIA plots and in GBIF samples was used to identify a subset of suitable ecoregions from the full set of 30 thousand. This subset of suitable ecoregions was compared to the known current present range of the tree species. Predicted present ranges correspond well with existing ranges for all but a few of the 335 tree species. The subset of suitable ecoregions can then be tracked into the future to determine whether the suitable home range remains the same, moves, grows, shrinks, or disappears under each model/scenario combination. A quantitative niche breadth analysis allows sorting of the 17 environmental variables from the narrowest, most important, to the broadest, least restrictive environmental factors limiting each tree species. Potential tree richness maps were produced, along with a quantitative potential tree endemism map for present and future CONUS. Using a new empirical imputation method which associates sparse measurements of dependent variables with particular clustered combinations of the

  8. Extending the dormant bud cryopreservation method to new tree species

    Technology Transfer Automated Retrieval System (TEKTRAN)

    In cryopreservation of germplasm, using dormant winter buds (DB) as source plant material is economically favorable over tissue culture options. Although the DB cryopreservation method has been known for many years, the approach is feasible only for cryopreserving a select number of temperate tree s...

  9. Copepod abundance and species composition in the Eastern subtropical/tropical Atlantic

    NASA Astrophysics Data System (ADS)

    Schnack-Schiel, Sigrid B.; Mizdalski, Elke; Cornils, Astrid

    2010-12-01

    Abundance and species composition of copepods were studied during the expedition ANT XXI/1 on a latitudinal transect in the eastern Atlantic from 34°49.5'N to 27°28.1'S between 2-20 November 2002. Stratified zooplankton tows were carried out at 19 stations with a multiple opening-closing net between 300 m water depth and the surface. Cyclopoid and calanoid copepods showed similar patterns of distribution and abundance. Oithona was the most abundant cyclopoid genus, followed by Oncaea. A total of 149 calanoid copepod species were identified. Clausocalanus was by far the most abundant genus, comprising on average about 45% of all calanoids, followed by Calocalanus (13%), Delibus (9%), Paracalanus (6%), and Pleuromamma (5%). All other genera comprised on average less than 5% each, with 40 genera less than 1%. The calanoid copepod communities were distinguished broadly in accordance with sea surface temperature, separating the subtropical from the tropical stations, and were largely determined by variation in species composition and species abundance. Nine Clausocalanus species were identified. The most numerous Clausocalanus species was C. furcatus, which on average comprised half of all adult of this genus. C. pergens, C. paululus, and C. jobei, contributed an average of 19%, 9%, and 9%, respectively. The Clausocalanus species differed markedly in their horizontal and vertical distributions: C. furcatus, C. jobei, and C. mastigophorus had widespread distributions and inhabited the upper water layers. Major differences between the species were found in abundance. C. paululus and C. arcuicornis were biantitropical and were absent or occurred in very low numbers in the equatorial zone. C. parapergens was found at all stations and showed a bimodal distribution pattern with maxima in the subtropics. C. pergens occurred in higher numbers only at the southern stations, where it replaced C. furcatus in dominance. In contrast to the widespread species, the bulk of the C

  10. North American tree squirrels and ground squirrels with overlapping ranges host different Cryptosporidium species and genotypes.

    PubMed

    Stenger, Brianna L S; Clark, Mark E; Kváč, Martin; Khan, Eakalak; Giddings, Catherine W; Prediger, Jitka; McEvoy, John M

    2015-12-01

    Wildlife-associated Cryptosporidium are an emerging cause of cryptosporidiosis in humans. The present study was undertaken to determine the extent to which North American tree squirrels and ground squirrels host zoonotic Cryptosporidium species and genotypes. Fragments of the Cryptosporidium 18S rRNA and actin genes were amplified and sequenced from fecal samples obtained from three tree squirrel and three ground squirrel species. In tree squirrels, Cryptosporidium was identified in 40.5% (17/42) of American red squirrels (Tamiasciurus hudsonicus), 40.4% (55/136) of eastern gray squirrels (Sciurus carolinensis), and 28.6% (2/7) of fox squirrels (Sciurus niger). Human-pathogenic Cryptosporidium ubiquitum and Cryptosporidium skunk genotype were the most prevalent species/genotypes in tree squirrels. Because tree squirrels live in close proximity to humans and are frequently infected with potentially zoonotic Cryptosporidium species/genotypes, they may be a significant reservoir of infection in humans. In ground squirrels, Cryptosporidium was detected in 70.2% (33/47) of 13-lined ground squirrels (Ictidomys tridecemlineatus), 35.1% (27/77) of black-tailed prairie dogs (Cynomys ludovicianus), and the only golden-mantled ground squirrel (Callospermophilus lateralis) that was sampled. Cryptosporidium rubeyi and ground squirrel genotypes I, II, and III were identified in isolates from these ground squirrel species. In contrast to the Cryptosporidium infecting tree squirrels, these species/genotypes appear to be specific for ground squirrels and are not associated with human disease. PMID:26437239

  11. Long range correlations in tree ring chronologies of the USA: Variation within and across species

    NASA Astrophysics Data System (ADS)

    Bowers, M. C.; Gao, J. B.; Tung, W. W.

    2013-02-01

    Abstract <span class="hlt">Tree</span> ring width data are among the best proxies for reconstructing past temperature and precipitation records. The discovery of fractal scaling and long-memory in meteorological and hydrological signals motivates us to investigate such properties in <span class="hlt">tree</span> ring chronologies. Detrended fluctuation analysis and adaptive fractal analysis are utilized to estimate the Hurst parameter values of 697 <span class="hlt">tree</span> ring chronologies from the continental United States. We find significant differences in the Hurst parameter values across the 10 <span class="hlt">species</span> studied in the work. The long-range scaling relations found here suggest that the behavior of <span class="hlt">tree</span> ring growth observed in a short calibration period may be similar to the general behavior of <span class="hlt">tree</span> ring growth in a much longer period, and therefore, the limited calibration period may be more useful than originally thought. The variations of the long-range correlations within and across <span class="hlt">species</span> may be further explored in future to better reconstruct paleoclimatic records.</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://www.ncbi.nlm.nih.gov/pubmed/24649658','PUBMED'); return false;" href="http://www.ncbi.nlm.nih.gov/pubmed/24649658"><span id="translatedtitle">Secondary foundation <span class="hlt">species</span> as drivers of trophic and functional diversity: evidence from a <span class="hlt">tree</span>-epiphyte system.</span></a></p> <p><a target="_blank" href="https://www.ncbi.nlm.nih.gov/entrez/query.fcgi?DB=pubmed">PubMed</a></p> <p>Angelini, Christine; Silliman, Brian R</p> <p>2014-01-01</p> <p>Facilitation cascades arise where primary foundation <span class="hlt">species</span> facilitate secondary (dependent) foundation <span class="hlt">species</span>, and collectively, they increase habitat complexity and quality to enhance biodiversity. Whether such phenomena occur in nonmarine systems and if secondary foundation <span class="hlt">species</span> enhance food web structure (e.g., support novel feeding guilds) and ecosystem function (e.g., provide nursery for juveniles) remain unclear. Here we report on field experiments designed to test whether <span class="hlt">trees</span> improve epiphyte survival and epiphytes secondarily increase the number and diversity of adult and juvenile invertebrates in a potential live oak-Tillandsia usneoides (Spanish moss) facilitation cascade. Our results reveal that <span class="hlt">trees</span> reduce physical stress to facilitate Tillandsia, which, in turn, reduces desiccation and predation stress to facilitate invertebrates. In experimental removals, invertebrate total density, juvenile density, <span class="hlt">species</span> richness and H' diversity were 16, 60, 1.7, and 1.5 times higher, and feeding guild richness and H' were 5 and 11 times greater in Tillandsia-colonized relative to Tillandsia-removal limb plots. Tillandsia enhanced communities similarly in a survey across the southeastern United States. These findings reveal that a facilitation cascade organizes this widespread terrestrial assemblage and expand the role of secondary foundation <span class="hlt">species</span> as drivers of trophic structure and ecosystem function. We conceptualize the relationship between foundation <span class="hlt">species</span>' structural attributes and associated <span class="hlt">species</span> <span class="hlt">abundance</span> and composition in a Foundation <span class="hlt">Species</span>-Biodiversity (FSB) model. Importantly, the FSB predicts that, where secondary foundation <span class="hlt">species</span> form expansive and functionally distinct structures that increase habitat availability and complexity within primary foundation <span class="hlt">species</span>, they generate and maintain hot spots of biodiversity and trophic interactions. PMID:24649658</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://adsabs.harvard.edu/cgi-bin/nph-data_query?bibcode=2010CorRe..29..527H&link_type=ABSTRACT','NASAADS'); return false;" href="http://adsabs.harvard.edu/cgi-bin/nph-data_query?bibcode=2010CorRe..29..527H&link_type=ABSTRACT"><span id="translatedtitle">Predators reduce <span class="hlt">abundance</span> and <span class="hlt">species</span> richness of coral reef fish recruits via non-selective predation</span></a></p> <p><a target="_blank" href="http://adsabs.harvard.edu/abstract_service.html">NASA Astrophysics Data System (ADS)</a></p> <p>Heinlein, J. M.; Stier, A. C.; Steele, M. A.</p> <p>2010-06-01</p> <p>Predators have important effects on coral reef fish populations, but their effects on community structure have only recently been investigated and are not yet well understood. Here, the effect of predation on the diversity and <span class="hlt">abundance</span> of young coral reef fishes was experimentally examined in Moorea, French Polynesia. Effects of predators were quantified by monitoring recruitment of fishes onto standardized patch reefs in predator-exclosure cages or uncaged reefs. At the end of the 54-day experiment, recruits were 74% less <span class="hlt">abundant</span> on reefs exposed to predators than on caged ones, and <span class="hlt">species</span> richness was 42% lower on reefs exposed to predators. Effects of predators varied somewhat among families, however, rarefaction analysis indicated that predators foraged non-selectively among <span class="hlt">species</span>. These results indicate that predation can alter diversity of reef fish communities by indiscriminately reducing the <span class="hlt">abundance</span> of fishes soon after settlement, thereby reducing the number of <span class="hlt">species</span> present on reefs.</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://adsabs.harvard.edu/cgi-bin/nph-data_query?bibcode=2016JHyd..537....1S&link_type=ABSTRACT','NASAADS'); return false;" href="http://adsabs.harvard.edu/cgi-bin/nph-data_query?bibcode=2016JHyd..537....1S&link_type=ABSTRACT"><span id="translatedtitle">Inter- and intra-specific variation in stemflow for evergreen <span class="hlt">species</span> and deciduous <span class="hlt">tree</span> <span class="hlt">species</span> in a subtropical forest</span></a></p> <p><a target="_blank" href="http://adsabs.harvard.edu/abstract_service.html">NASA Astrophysics Data System (ADS)</a></p> <p>Su, Lei; Xu, Wenting; Zhao, Changming; Xie, Zongqiang; Ju, Hua</p> <p>2016-06-01</p> <p>Quantification of stemflow is necessary for the assessment of forest ecosystem hydrological effects. Nevertheless, variation of stemflow among plant functional groups is currently not well understood. Stemflow production of co-occurring evergreen broadleaved <span class="hlt">trees</span> (Cyclobalanopsis multinervis and Cyclobalanopsis oxyodon) and deciduous broadleaved <span class="hlt">trees</span> (Fagus engleriana and Quercus serrata var. brevipetiolata) was quantified through field observations in a mixed evergreen and deciduous broadleaved forest. The research results revealed that stemflow increased linearly with increasing rainfall magnitude, with precipitation depths of 6.9, 7.2, 10.0 and 14.8 mm required for the initiation of stemflow for C. multinervis, C. oxyodon, F. engleriana and Q. serrata, respectively. Stemflow percentage and funneling ratio (FR) increased with increasing rainfall in a logarithmic fashion. Stemflow percentage and FR tended to grow rapidly with increasing rainfall magnitude up to a rainfall threshold of 50 mm, above which, further rainfall increases brought about only small increases. For C. multinervis, C. oxyodon, F. engleriana and Q. serrata, FR averaged 19.8, 14.8, 8.9 and 2.8, respectively. The stemflow generating rainfall thresholds for evergreen <span class="hlt">species</span> were smaller than for deciduous <span class="hlt">species</span>. Furthermore, stemflow percentage and FR of the former was greater than the latter. For both evergreen <span class="hlt">species</span> and deciduous <span class="hlt">species</span>, overall funneling ratio (FRs) decreased with increasing basal area. We concluded that: (1) although stemflow partitioning represented a fairly low percentage of gross rainfall in mixed evergreen and deciduous broadleaved forests, it was capable of providing substantial amount of rainwater to <span class="hlt">tree</span> boles; (2) the evergreen <span class="hlt">species</span> were more likely to generate stemflow than deciduous <span class="hlt">species</span>, and directed more intercepted rainwater to the root zone; (3) small <span class="hlt">trees</span> were more productive in funneling stemflow than larger <span class="hlt">trees</span>, which may provide a favorable</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://www.ncbi.nlm.nih.gov/pubmed/27298428','PUBMED'); return false;" href="http://www.ncbi.nlm.nih.gov/pubmed/27298428"><span id="translatedtitle">Influence of Trap Height and Bait Type on <span class="hlt">Abundance</span> and <span class="hlt">Species</span> Diversity of Cerambycid Beetles Captured in Forests of East-Central Illinois.</span></a></p> <p><a target="_blank" href="https://www.ncbi.nlm.nih.gov/entrez/query.fcgi?DB=pubmed">PubMed</a></p> <p>Schmeelk, Thomas C; Millar, Jocelyn G; Hanks, Lawrence M</p> <p>2016-08-01</p> <p>We assessed how height of panel traps above the forest floor, and the type of trap bait used, influenced the <span class="hlt">abundance</span> and diversity of cerambycid beetles caught in forested areas of east-central Illinois. Panel traps were suspended from branches of hardwood <span class="hlt">trees</span> at three heights above the ground: understory (∼1.5 m), lower canopy (∼6 m), and midcanopy (∼12 m). Traps were baited with either a multispecies blend of synthesized cerambycid pheromones or a fermenting bait mixture. Traps captured a total of 848 beetles of 50 <span class="hlt">species</span> in the cerambycid subfamilies Cerambycinae, Lamiinae, Lepturinae, and Parandrinae, and one <span class="hlt">species</span> in the closely related family Disteniidae. The <span class="hlt">species</span> caught in highest numbers was the cerambycine Anelaphus pumilus (Newman), represented by 349 specimens. The 17 most <span class="hlt">abundant</span> <span class="hlt">species</span> (mean ± 1 SD: 45 ± 80 specimens per <span class="hlt">species</span>) included 12 cerambycine and five lamiine <span class="hlt">species</span>. Of these most <span class="hlt">abundant</span> <span class="hlt">species</span>, 13 (77%) were attracted to traps baited with the pheromone blend. Only the cerambycine Eburia quadrigeminata (Say) was attracted by the fermenting bait. Three <span class="hlt">species</span> were captured primarily in understory traps, and another five <span class="hlt">species</span> primarily in midcanopy traps. Variation among cerambycid <span class="hlt">species</span> in their vertical distribution in forests accounted for similar overall <span class="hlt">abundances</span> and <span class="hlt">species</span> richness across trap height treatments. These findings suggest that trapping surveys of native communities of cerambycids, and quarantine surveillance for newly introduced exotic <span class="hlt">species</span>, would be optimized by including a variety of trap baits and distributing traps across vertical strata of forests. PMID:27298428</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://adsabs.harvard.edu/cgi-bin/nph-data_query?bibcode=2016AcO....70...21F&link_type=ABSTRACT','NASAADS'); return false;" href="http://adsabs.harvard.edu/cgi-bin/nph-data_query?bibcode=2016AcO....70...21F&link_type=ABSTRACT"><span id="translatedtitle">Using <span class="hlt">species</span> <span class="hlt">abundance</span> distribution models and diversity indices for biogeographical analyses</span></a></p> <p><a target="_blank" href="http://adsabs.harvard.edu/abstract_service.html">NASA Astrophysics Data System (ADS)</a></p> <p>Fattorini, Simone; Rigal, François; Cardoso, Pedro; Borges, Paulo A. V.</p> <p>2016-01-01</p> <p>We examine whether <span class="hlt">Species</span> <span class="hlt">Abundance</span> Distribution models (SADs) and diversity indices can describe how <span class="hlt">species</span> colonization status influences <span class="hlt">species</span> community assembly on oceanic islands. Our hypothesis is that, because of the lack of source-sink dynamics at the archipelago scale, Single Island Endemics (SIEs), i.e. endemic <span class="hlt">species</span> restricted to only one island, should be represented by few rare <span class="hlt">species</span> and consequently have <span class="hlt">abundance</span> patterns that differ from those of more widespread <span class="hlt">species</span>. To test our hypothesis, we used arthropod data from the Azorean archipelago (North Atlantic). We divided the <span class="hlt">species</span> into three colonization categories: SIEs, archipelagic endemics (AZEs, present in at least two islands) and native non-endemics (NATs). For each category, we modelled rank-<span class="hlt">abundance</span> plots using both the geometric series and the Gambin model, a measure of distributional amplitude. We also calculated Shannon entropy and Buzas and Gibson's evenness. We show that the slopes of the regression lines modelling SADs were significantly higher for SIEs, which indicates a relative predominance of a few highly <span class="hlt">abundant</span> <span class="hlt">species</span> and a lack of rare <span class="hlt">species</span>, which also depresses diversity indices. This may be a consequence of two factors: (i) some forest specialist SIEs may be at advantage over other, less adapted <span class="hlt">species</span>; (ii) the entire populations of SIEs are by definition concentrated on a single island, without possibility for inter-island source-sink dynamics; hence all populations must have a minimum number of individuals to survive natural, often unpredictable, fluctuations. These findings are supported by higher values of the α parameter of the Gambin mode for SIEs. In contrast, AZEs and NATs had lower regression slopes, lower α but higher diversity indices, resulting from their widespread distribution over several islands. We conclude that these differences in the SAD models and diversity indices demonstrate that the study of these metrics is useful for</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://adsabs.harvard.edu/cgi-bin/nph-data_query?bibcode=2008ECSS...77..446F&link_type=ABSTRACT','NASAADS'); return false;" href="http://adsabs.harvard.edu/cgi-bin/nph-data_query?bibcode=2008ECSS...77..446F&link_type=ABSTRACT"><span id="translatedtitle">Habitat partitioning by five congeneric and <span class="hlt">abundant</span> Choerodon <span class="hlt">species</span> (Labridae) in a large subtropical marine embayment</span></a></p> <p><a target="_blank" href="http://adsabs.harvard.edu/abstract_service.html">NASA Astrophysics Data System (ADS)</a></p> <p>Fairclough, D. V.; Clarke, K. R.; Valesini, F. J.; Potter, I. C.</p> <p>2008-04-01</p> <p>The habitats occupied by the juveniles and adults of five morphologically similar, diurnally active and <span class="hlt">abundant</span> Choerodon <span class="hlt">species</span> in the large subtropical environment of Shark Bay, a "World Heritage Property" on the west coast of Australia, have been determined. The densities of the two life cycle stages of each Choerodon <span class="hlt">species</span> in those habitats were used in various analyses to test the hypotheses that: (1) habitats are partitioned among these <span class="hlt">species</span> and between their juveniles and adults; (2) such habitat partitioning is greatest in the case of the two Western Australian endemic <span class="hlt">species</span>, i.e. Choerodon rubescens and Choerodon cauteroma; and (3) the extent of habitat partitioning between both of these two <span class="hlt">species</span> and the only <span class="hlt">species</span> that is widely distributed in the Indo-West Pacific, i.e. Choerodon schoenleinii, will be less pronounced. Initially, catches of each of the five congeneric <span class="hlt">species</span>, obtained during other studies in Shark Bay by angling, spearfishing and otter trawling, were collated to elucidate the broad distribution of these <span class="hlt">species</span> in that embayment. Underwater visual census was then used to determine the densities of the juveniles and adults of each Choerodon <span class="hlt">species</span> at sites representing the four habitat types in which one or more of these <span class="hlt">species</span> had been caught, i.e. reefs in marine waters at the western boundary of the bay and seagrass, reefs and rocky shorelines in the two inner gulfs. The compositions of the Choerodon <span class="hlt">species</span> over marine (entrance channel) reefs and in seagrass were significantly different and each differed significantly from those in both inner gulf reefs and rocky shorelines, which were, however, not significantly different. Choerodon rubescens was restricted to exposed marine reefs, and thus occupied a different habitat and location of the bay than C. cauteroma, the other endemic <span class="hlt">species</span>, which was almost exclusively confined to habitats found in the inner gulfs. Choerodon cauteroma differed from other Choerodon</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://cfpub.epa.gov/si/si_public_record_report.cfm?dirEntryId=64306&keyword=Taxonomy&actType=&TIMSType=+&TIMSSubTypeID=&DEID=&epaNumber=&ntisID=&archiveStatus=Both&ombCat=Any&dateBeginCreated=&dateEndCreated=&dateBeginPublishedPresented=&dateEndPublishedPresented=&dateBeginUpdated=&dateEndUpdated=&dateBeginCompleted=&dateEndCompleted=&personID=&role=Any&journalID=&publisherID=&sortBy=revisionDate&count=50&CFID=65294418&CFTOKEN=71908534','EPA-EIMS'); return false;" href="http://cfpub.epa.gov/si/si_public_record_report.cfm?dirEntryId=64306&keyword=Taxonomy&actType=&TIMSType=+&TIMSSubTypeID=&DEID=&epaNumber=&ntisID=&archiveStatus=Both&ombCat=Any&dateBeginCreated=&dateEndCreated=&dateBeginPublishedPresented=&dateEndPublishedPresented=&dateBeginUpdated=&dateEndUpdated=&dateBeginCompleted=&dateEndCompleted=&personID=&role=Any&journalID=&publisherID=&sortBy=revisionDate&count=50&CFID=65294418&CFTOKEN=71908534"><span id="translatedtitle">ISOPRENE EMISSION CAPACITY FOR U.S. <span class="hlt">TREE</span> <span class="hlt">SPECIES</span></span></a></p> <p><a target="_blank" href="http://oaspub.epa.gov/eims/query.page">EPA Science Inventory</a></p> <p></p> <p></p> <p>Isoprene emission capacity measurements are presented from 18 North American oak <I>(Quercus)</I> <span class="hlt">species</span> and <span class="hlt">species</span> from six other genera previously found to emit significant quantities of isoprene. Sampling was conducted at physiographically diverse locations in North Carolina...</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://www.ncbi.nlm.nih.gov/pubmed/24233419','PUBMED'); return false;" href="http://www.ncbi.nlm.nih.gov/pubmed/24233419"><span id="translatedtitle">Ozone exposure : Areas of potential ozone risk for selected <span class="hlt">tree</span> <span class="hlt">species</span> in Austria.</span></a></p> <p><a target="_blank" href="https://www.ncbi.nlm.nih.gov/entrez/query.fcgi?DB=pubmed">PubMed</a></p> <p>Loibl, W; Smidt, S</p> <p>1996-12-01</p> <p>Increased tropospheric ozone concentrations cause damage to both human health and the environment. To assess the exposure of forest areas and selected <span class="hlt">tree</span> <span class="hlt">species</span> to ozone, it is necessary to calculate the ozone exposure distribution. The present article describes the application of an ozone interpolation model to the calculation of the ozone exposure distribution in combination with forest inventory data.The exposure of forest regions to ozone was assessed by means of an AOT40 map (accumulated ozone exposure over a threshold of 40 ppb). The calculation was performed by hourly running of the model during the summer term and accumulation of the patterns that exceeded 40 ppb.The exposure of the primary Austrian <span class="hlt">tree</span> <span class="hlt">species</span> to ozone can be assessed due to the spatial relation of ozone exposure and <span class="hlt">tree</span> <span class="hlt">species</span> patterns. This spatial relation also allows the verification of assumptions concerning ozone-related <span class="hlt">tree</span> damage. PMID:24233419</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://adsabs.harvard.edu/cgi-bin/nph-data_query?bibcode=2007ECSS...73..290T&link_type=ABSTRACT','NASAADS'); return false;" href="http://adsabs.harvard.edu/cgi-bin/nph-data_query?bibcode=2007ECSS...73..290T&link_type=ABSTRACT"><span id="translatedtitle"><span class="hlt">Species</span> composition and seasonal <span class="hlt">abundance</span> of Chaetognatha in the subtropical coastal waters of Hong Kong</span></a></p> <p><a target="_blank" href="http://adsabs.harvard.edu/abstract_service.html">NASA Astrophysics Data System (ADS)</a></p> <p>Tse, P.; Hui, S. Y.; Wong, C. K.</p> <p>2007-06-01</p> <p><span class="hlt">Species</span> composition, <span class="hlt">species</span> diversity and seasonal <span class="hlt">abundance</span> of chaetognaths were studied in Tolo Harbour and the coastal waters of eastern Hong Kong. Tolo Harbour is a semi-enclosed and poorly flushed bay with a long history of eutrophication. It opens into the eastern coast of Hong Kong which is fully exposed to water currents from the South China Sea. Zooplankton samples were collected monthly from July 2003 to July 2005 at six stations. Twenty <span class="hlt">species</span> of chaetognaths were identified. They included six <span class="hlt">species</span> of the genus Aidanosagitta ( Aidanosagitta neglecta, Aidanosagitta delicata, Aidanosagitta johorensis, Aidanosagitta regularis, Aidanosagitta bedfordii and Aidanosagitta crassa), four <span class="hlt">species</span> of the genus Zonosagitta ( Zonosagitta nagae, Zonosagitta bedoti, Zonosagitta bruuni and Zonosagitta pulchra), three <span class="hlt">species</span> of the genus Ferosagitta ( Ferosagitta ferox, Ferosagitta tokiokai and Ferosagitta robusta) and one <span class="hlt">species</span> each from the genera Serratosagitta ( Serratosagitta pacifica), Decipisagitta ( Decipisagitta decipiens), Flaccisagitta ( Flaccisagitta enflata), Krohnitta ( Krohnitta pacifica), Mesosagitta ( Mesosagitta minima), Pterosagitta ( Pterosagitta draco) and Sagitta ( Sagitta bipunctata). The most <span class="hlt">abundant</span> <span class="hlt">species</span> were Flaccisagitta enflata, A. neglecta and A. delicata. Averaged over the entire study period, the densities of Flaccisagitta enflata, A. neglecta and A. delicata were 9.3, 6.6 and 5.2 ind. m -3, respectively. Overall, these <span class="hlt">species</span> constituted 39.7%, 28.2% and 22.0% of all chaetognaths collected in the study. Averaged over the entire study, the density of most of the low <span class="hlt">abundance</span> <span class="hlt">species</span> was <0.6 ind. m -3. Flaccisagitta enflata occurred throughout the year at all sampling stations. Aidanosagitta neglecta occurred at all sampling stations, but was most common in summer. Aidanosagitta delicata was most common in Tolo Harbour during summer. Tolo Harbour supported larger populations, but fewer <span class="hlt">species</span> of chaetognaths than the</p> </li> </ol> <div class="pull-right"> <ul class="pagination"> <li><a href="#" onclick='return showDiv("page_1");'>«</a></li> <li><a href="#" onclick='return showDiv("page_13");'>13</a></li> <li><a href="#" onclick='return showDiv("page_14");'>14</a></li> <li class="active"><span>15</span></li> <li><a href="#" onclick='return showDiv("page_16");'>16</a></li> <li><a href="#" onclick='return showDiv("page_17");'>17</a></li> <li><a href="#" onclick='return showDiv("page_25");'>»</a></li> </ul> </div> </div><!-- col-sm-12 --> </div><!-- row --> </div><!-- page_15 --> <div id="page_16" class="hiddenDiv"> <div class="row"> <div class="col-sm-12"> <div class="pull-right"> <ul class="pagination"> <li><a href="#" onclick='return showDiv("page_1");'>«</a></li> <li><a href="#" onclick='return showDiv("page_14");'>14</a></li> <li><a href="#" onclick='return showDiv("page_15");'>15</a></li> <li class="active"><span>16</span></li> <li><a href="#" onclick='return showDiv("page_17");'>17</a></li> <li><a href="#" onclick='return showDiv("page_18");'>18</a></li> <li><a href="#" onclick='return showDiv("page_25");'>»</a></li> </ul> </div> </div> </div> <div class="row"> <div class="col-sm-12"> <ol class="result-class" start="301"> <li> <p><a target="_blank" onclick="trackOutboundLink('http://www.ncbi.nlm.nih.gov/pubmed/25761711','PUBMED'); return false;" href="http://www.ncbi.nlm.nih.gov/pubmed/25761711"><span id="translatedtitle">Glacial refugia and modern genetic diversity of 22 western North American <span class="hlt">tree</span> <span class="hlt">species</span>.</span></a></p> <p><a target="_blank" href="https://www.ncbi.nlm.nih.gov/entrez/query.fcgi?DB=pubmed">PubMed</a></p> <p>Roberts, David R; Hamann, Andreas</p> <p>2015-04-01</p> <p>North American <span class="hlt">tree</span> <span class="hlt">species</span>, subspecies and genetic varieties have primarily evolved in a landscape of extensive continental ice and restricted temperate climate environments. Here, we reconstruct the refugial history of western North American <span class="hlt">trees</span> since the last glacial maximum using <span class="hlt">species</span> distribution models, validated against 3571 palaeoecological records. We investigate how modern subspecies structure and genetic diversity corresponds to modelled glacial refugia, based on a meta-analysis of allelic richness and expected heterozygosity for 473 populations of 22 <span class="hlt">tree</span> <span class="hlt">species</span>. We find that <span class="hlt">species</span> with strong genetic differentiation into subspecies had widespread and large glacial refugia, whereas <span class="hlt">species</span> with restricted refugia show no differentiation among populations and little genetic diversity, despite being common over a wide range of environments today. In addition, a strong relationship between allelic richness and the size of modelled glacial refugia (r(2) = 0.55) suggest that population bottlenecks during glacial periods had a pronounced effect on the presence of rare alleles. PMID:25761711</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=4375868','PMC'); return false;" href="http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=4375868"><span id="translatedtitle">Glacial refugia and modern genetic diversity of 22 western North American <span class="hlt">tree</span> <span class="hlt">species</span></span></a></p> <p><a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?DB=pmc">PubMed Central</a></p> <p>Roberts, David R.; Hamann, Andreas</p> <p>2015-01-01</p> <p>North American <span class="hlt">tree</span> <span class="hlt">species</span>, subspecies and genetic varieties have primarily evolved in a landscape of extensive continental ice and restricted temperate climate environments. Here, we reconstruct the refugial history of western North American <span class="hlt">trees</span> since the last glacial maximum using <span class="hlt">species</span> distribution models, validated against 3571 palaeoecological records. We investigate how modern subspecies structure and genetic diversity corresponds to modelled glacial refugia, based on a meta-analysis of allelic richness and expected heterozygosity for 473 populations of 22 <span class="hlt">tree</span> <span class="hlt">species</span>. We find that <span class="hlt">species</span> with strong genetic differentiation into subspecies had widespread and large glacial refugia, whereas <span class="hlt">species</span> with restricted refugia show no differentiation among populations and little genetic diversity, despite being common over a wide range of environments today. In addition, a strong relationship between allelic richness and the size of modelled glacial refugia (r2 = 0.55) suggest that population bottlenecks during glacial periods had a pronounced effect on the presence of rare alleles. PMID:25761711</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://pubs.er.usgs.gov/publication/1015692','USGSPUBS'); return false;" href="http://pubs.er.usgs.gov/publication/1015692"><span id="translatedtitle">Relationships among environmental variables and distribution of <span class="hlt">tree</span> <span class="hlt">species</span> at high elevation in the Olympic Mountains</span></a></p> <p><a target="_blank" href="http://pubs.er.usgs.gov/pubs/index.jsp?view=adv">USGS Publications Warehouse</a></p> <p>Woodward, Andrea</p> <p>1998-01-01</p> <p>Relationships among environmental variables and occurrence of <span class="hlt">tree</span> <span class="hlt">species</span> were investigated at Hurricane Ridge in Olympic National Park, Washington, USA. A transect consisting of three plots was established down one north-and one south-facing slope in stands representing the typical elevational sequence of <span class="hlt">tree</span> <span class="hlt">species</span>. <span class="hlt">Tree</span> <span class="hlt">species</span> included subalpine fir (Abies lasiocarpa), Douglas-fir (Pseudotsuga menziesii), mountain hemlock (Tsuga mertensiana), and Pacific silver fir (Abies amabilis). Air and soil temperature, precipitation, and soil moisture were measured during three growing seasons. Snowmelt patterns, soil carbon and moisture release curves were also determined. The plots represented a wide range in soil water potential, a major determinant of <span class="hlt">tree</span> <span class="hlt">species</span> distribution (range of minimum values = -1.1 to -8.0 MPa for Pacific silver fir and Douglas-fir plots, respectively). Precipitation intercepted at plots depended on topographic location, storm direction and storm type. Differences in soil moisture among plots was related to soil properties, while annual differences at each plot were most often related to early season precipitation. Changes in climate due to a doubling of atmospheric CO2 will likely shift <span class="hlt">tree</span> <span class="hlt">species</span> distributions within, but not among aspects. Change will be buffered by innate tolerance of adult <span class="hlt">trees</span> and the inertia of soil properties.</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://www.ncbi.nlm.nih.gov/pubmed/15760366','PUBMED'); return false;" href="http://www.ncbi.nlm.nih.gov/pubmed/15760366"><span id="translatedtitle">Occurrence of nodulation in unexplored leguminous <span class="hlt">trees</span> native to the West African tropical rainforest and inoculation response of native <span class="hlt">species</span> useful in reforestation.</span></a></p> <p><a target="_blank" href="https://www.ncbi.nlm.nih.gov/entrez/query.fcgi?DB=pubmed">PubMed</a></p> <p>Diabate, Moussa; Munive, Antonio; de Faria, Sérgio Miana; Ba, Amadou; Dreyfus, Bernard; Galiana, Antoine</p> <p>2005-04-01</p> <p>Despite the <span class="hlt">abundance</span> and diversity of timber <span class="hlt">tree</span> legumes in the West African rainforest, their ability to form nitrogen-fixing nodules in symbiosis with rhizobia, and their response to rhizobial inoculation, remain poorly documented. In the first part of this study the occurrence of nodulation was determined in 156 leguminous <span class="hlt">species</span> growing in six natural forest areas in Guinea, mostly mature <span class="hlt">trees</span>. In the second part, an in situ experiment of rhizobial inoculation was performed on eight selected <span class="hlt">tree</span> <span class="hlt">species</span> belonging to three genera: Albizia, Erythrophleum and Millettia. Of the 97 plant <span class="hlt">species</span> and 14 genera that had never been examined before this study, 31 <span class="hlt">species</span> and four genera were reported to be nodulated. After 4 months of growing in a nursery and a further 11 months after transplantation of plants to the field, we observed a highly significant (P < 0.001) and positive effect of inoculation with Bradyrhizobium sp. strains on the growth of the eight <span class="hlt">tree</span> <span class="hlt">species</span> tested. The importance of determining the nodulation ability of unexplored local <span class="hlt">trees</span> and subsequently using this information for inoculation in reforestation programmes was demonstrated. PMID:15760366</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=4262173','PMC'); return false;" href="http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=4262173"><span id="translatedtitle">Loss of animal seed dispersal increases extinction risk in a tropical <span class="hlt">tree</span> <span class="hlt">species</span> due to pervasive negative density dependence across life stages</span></a></p> <p><a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?DB=pmc">PubMed Central</a></p> <p>Caughlin, T. Trevor; Ferguson, Jake M.; Lichstein, Jeremy W.; Zuidema, Pieter A.; Bunyavejchewin, Sarayudh; Levey, Douglas J.</p> <p>2015-01-01</p> <p>Overhunting in tropical forests reduces populations of vertebrate seed dispersers. If reduced seed dispersal has a negative impact on <span class="hlt">tree</span> population viability, overhunting could lead to altered forest structure and dynamics, including decreased biodiversity. However, empirical data showing decreased animal-dispersed <span class="hlt">tree</span> <span class="hlt">abundance</span> in overhunted forests contradict demographic models which predict minimal sensitivity of <span class="hlt">tree</span> population growth rate to early life stages. One resolution to this discrepancy is that seed dispersal determines spatial aggregation, which could have demographic consequences for all life stages. We tested the impact of dispersal loss on population viability of a tropical <span class="hlt">tree</span> <span class="hlt">species</span>, Miliusa horsfieldii, currently dispersed by an intact community of large mammals in a Thai forest. We evaluated the effect of spatial aggregation for all <span class="hlt">tree</span> life stages, from seeds to adult <span class="hlt">trees</span>, and constructed simulation models to compare population viability with and without animal-mediated seed dispersal. In simulated populations, disperser loss increased spatial aggregation by fourfold, leading to increased negative density dependence across the life cycle and a 10-fold increase in the probability of extinction. Given that the majority of <span class="hlt">tree</span> <span class="hlt">species</span> in tropical forests are animal-dispersed, overhunting will potentially result in forests that are fundamentally different from those existing now. PMID:25392471</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://www.ncbi.nlm.nih.gov/pubmed/25392471','PUBMED'); return false;" href="http://www.ncbi.nlm.nih.gov/pubmed/25392471"><span id="translatedtitle">Loss of animal seed dispersal increases extinction risk in a tropical <span class="hlt">tree</span> <span class="hlt">species</span> due to pervasive negative density dependence across life stages.</span></a></p> <p><a target="_blank" href="https://www.ncbi.nlm.nih.gov/entrez/query.fcgi?DB=pubmed">PubMed</a></p> <p>Caughlin, T Trevor; Ferguson, Jake M; Lichstein, Jeremy W; Zuidema, Pieter A; Bunyavejchewin, Sarayudh; Levey, Douglas J</p> <p>2015-01-01</p> <p>Overhunting in tropical forests reduces populations of vertebrate seed dispersers. If reduced seed dispersal has a negative impact on <span class="hlt">tree</span> population viability, overhunting could lead to altered forest structure and dynamics, including decreased biodiversity. However, empirical data showing decreased animal-dispersed <span class="hlt">tree</span> <span class="hlt">abundance</span> in overhunted forests contradict demographic models which predict minimal sensitivity of <span class="hlt">tree</span> population growth rate to early life stages. One resolution to this discrepancy is that seed dispersal determines spatial aggregation, which could have demographic consequences for all life stages. We tested the impact of dispersal loss on population viability of a tropical <span class="hlt">tree</span> <span class="hlt">species</span>, Miliusa horsfieldii, currently dispersed by an intact community of large mammals in a Thai forest. We evaluated the effect of spatial aggregation for all <span class="hlt">tree</span> life stages, from seeds to adult <span class="hlt">trees</span>, and constructed simulation models to compare population viability with and without animal-mediated seed dispersal. In simulated populations, disperser loss increased spatial aggregation by fourfold, leading to increased negative density dependence across the life cycle and a 10-fold increase in the probability of extinction. Given that the majority of <span class="hlt">tree</span> <span class="hlt">species</span> in tropical forests are animal-dispersed, overhunting will potentially result in forests that are fundamentally different from those existing now. PMID:25392471</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://www.ncbi.nlm.nih.gov/pubmed/12620063','PUBMED'); return false;" href="http://www.ncbi.nlm.nih.gov/pubmed/12620063"><span id="translatedtitle">Identification, measurement and interpretation of <span class="hlt">tree</span> rings in woody <span class="hlt">species</span> from mediterranean climates.</span></a></p> <p><a target="_blank" href="https://www.ncbi.nlm.nih.gov/entrez/query.fcgi?DB=pubmed">PubMed</a></p> <p>Cherubini, Paolo; Gartner, Barbara L; Tognetti, Roberto; Bräker, Otto U; Schoch, Werner; Innes, John L</p> <p>2003-02-01</p> <p>We review the literature dealing with mediterranean climate, vegetation, phenology and ecophysiology relevant to the understanding of <span class="hlt">tree</span>-ring formation in mediterranean regions. <span class="hlt">Tree</span> rings have been used extensively in temperate regions to reconstruct responses of forests to past environmental changes. In mediterranean regions, studies of <span class="hlt">tree</span> rings are scarce, despite their potential for understanding and predicting the effects of global change on important ecological processes such as desertification. In mediterranean regions, due to the great spatio-temporal variability of mediterranean environmental conditions, <span class="hlt">tree</span> rings are sometimes not formed. Often, clear seasonality is lacking, and vegetation activity is not always associated with regular dormancy periods. We present examples of <span class="hlt">tree</span>-ring morphology of five <span class="hlt">species</span> (Arbutus unedo, Fraxinus ornus, Quercus cerris, Q. ilex, Q. pubescens) sampled in Tuscany, Italy, focusing on the difficulties we encountered during the dating. We present an interpretation of anomalies found in the wood structure and, more generally, of cambial activity in such environments. Furthermore, we propose a classification of <span class="hlt">tree</span>-ring formation in mediterranean environments. Mediterranean <span class="hlt">tree</span> rings can be dated and used for dendrochronological purposes, but great care should be taken in selecting sampling sites, <span class="hlt">species</span> and sample <span class="hlt">trees</span>. PMID:12620063</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://www.ncbi.nlm.nih.gov/pubmed/24933814','PUBMED'); return false;" href="http://www.ncbi.nlm.nih.gov/pubmed/24933814"><span id="translatedtitle">The importance of long-distance seed dispersal for the demography and distribution of a canopy <span class="hlt">tree</span> <span class="hlt">species</span>.</span></a></p> <p><a target="_blank" href="https://www.ncbi.nlm.nih.gov/entrez/query.fcgi?DB=pubmed">PubMed</a></p> <p>Caughlin, T Trevor; Ferguson, Jake M; Lichstein, Jeremy W; Bunyavejchewin, Sarayudh; Levey, Douglas J</p> <p>2014-04-01</p> <p>Long-distance seed dispersal (LDD) is considered a crucial determinant of <span class="hlt">tree</span> distributions, but its effects depend on demographic processes that enable seeds to establish into adults and that remain poorly understood at large spatial scales. We estimated rates of seed arrival, germination, and survival and growth for a canopy <span class="hlt">tree</span> <span class="hlt">species</span> (Miliusa horsfieldii), in a landscape ranging from evergreen forest, where the <span class="hlt">species</span>' <span class="hlt">abundance</span> is high, to deciduous forest, where it is extremely low. We then used an individual-based model (IBM) to predict sapling establishment and to compare the relative importance of seed arrival and establishment in explaining the observed distribution of seedlings. Individuals in deciduous forest, far from the source population, experienced multiple benefits (e.g., increased germination rate and seedling survival and growth) from being in a habitat where conspecifics were almost absent. The net effect of these spatial differences in demographic processes was significantly higher estimated sapling establishment probabilities for seeds dispersed long distances into deciduous forest. Despite the high rate of establishment in this habitat, Miliusa is rare in the deciduous forest because the arrival of seeds at long distances from the source population is extremely low. Across the entire landscape, the spatial pattern of seed arrival is much more important than the spatial pattern of establishment for explaining observed seedling distributions. By using dynamic models to link demographic data to spatial patterns, we show that LDD plays a pivotal role in the distribution of this <span class="hlt">tree</span> in its native habitat. PMID:24933814</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://ntrs.nasa.gov/search.jsp?R=20040034206&hterms=Bird&qs=Ntx%3Dmode%2Bmatchall%26Ntk%3DAll%26N%3D0%26No%3D20%26Ntt%3DBird','NASA-TRS'); return false;" href="http://ntrs.nasa.gov/search.jsp?R=20040034206&hterms=Bird&qs=Ntx%3Dmode%2Bmatchall%26Ntk%3DAll%26N%3D0%26No%3D20%26Ntt%3DBird"><span id="translatedtitle">The Distribution and <span class="hlt">Abundance</span> of Bird <span class="hlt">Species</span>: Towards a Satellite, Data Driven Avian Energetics and <span class="hlt">Species</span> Richness Model</span></a></p> <p><a target="_blank" href="http://ntrs.nasa.gov/search.jsp">NASA Technical Reports Server (NTRS)</a></p> <p>Smith, James A.</p> <p>2003-01-01</p> <p>This paper addresses the fundamental question of why birds occur where and when they do, i.e., what are the causative factors that determine the spatio-temporal distributions, <span class="hlt">abundance</span>, or richness of bird <span class="hlt">species</span>? In this paper we outline the first steps toward building a satellite, data-driven model of avian energetics and <span class="hlt">species</span> richness based on individual bird physiology, morphology, and interaction with the spatio-temporal habitat. To evaluate our model, we will use the North American Breeding Bird Survey and Christmas Bird Count data for <span class="hlt">species</span> richness, wintering and breeding range. Long term and current satellite data series include AVHRR, Landsat, and MODIS.</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://adsabs.harvard.edu/abs/2014AGUFM.B51F0086M','NASAADS'); return false;" href="http://adsabs.harvard.edu/abs/2014AGUFM.B51F0086M"><span id="translatedtitle">Assessing the Impact of Central Appalachian <span class="hlt">Tree</span> <span class="hlt">Species</span> on Canopy Albedo via Measurement of Leaf Angles from Repeated Ground-based, Drone, and Hemispherical Photography</span></a></p> <p><a target="_blank" href="http://adsabs.harvard.edu/abstract_service.html">NASA Astrophysics Data System (ADS)</a></p> <p>McNeil, B. E.; Erazo, D.; Heimerl, T.</p> <p>2014-12-01</p> <p>Satellite measurements of forest albedo are directly used in climate models, and could be used in models of the C and N cycles if we more fully understood the mechanism causing a strong correlation of forest albedo with canopy N and C assimilation. One attractive mechanism posits that <span class="hlt">tree</span> <span class="hlt">species</span> have evolved convergent leaf and canopy traits. While the leaf traits of <span class="hlt">tree</span> <span class="hlt">species</span> are known to drive variability in canopy N and C assimilation, linking <span class="hlt">tree</span> <span class="hlt">species</span> to variability in albedo is challenging because of the difficulty in measuring important canopy traits like leaf angle. To refine techniques for measuring leaf angle, and test the hypothesis that high albedo in the central Appalachians could be linked to the <span class="hlt">abundance</span> of <span class="hlt">species</span> with canopy traits of more horizontal leaf angles, we conducted four tests with ground-based, drone, and hemispherical photographs. First, we used a leveled camera on a steep slope to repeatedly, and directly measure the leaf angle of over 400 leaves within the canopies of oak, maple, and beech <span class="hlt">trees</span>. Across all 21 repetitions (3 times a day on 7 dates between May and July), we observed consistent <span class="hlt">species</span> differences in mean leaf angle (MLA), with maple always being the most horizontal (MLA = 14-18°) and oak the most vertical (MLA = 19-28°). Second, we again found highly significant <span class="hlt">species</span> differences in MLA when we used a hexacopter drone with a camera on a self-leveling gimbal to make over 1020 direct measurements of leaf angle from six <span class="hlt">tree</span> <span class="hlt">species</span> in three broadleaf deciduous forest plots. Third, to measure MLA of a whole multi-<span class="hlt">species</span> canopy, we compared a <span class="hlt">species</span> <span class="hlt">abundance</span>-weighted plot average of the drone-measured MLA values with an indirect, ground-based hemispherical photograph method. The strong agreement of these direct and indirect plot-level methods finally led us to compare a broader set of 61 plot-level hemispherical photo MLA measurements with canopy albedo measured by AVIRIS in broadleaf deciduous forests. In</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://adsabs.harvard.edu/cgi-bin/nph-data_query?bibcode=2006PhRvE..74e1914V&link_type=ABSTRACT','NASAADS'); return false;" href="http://adsabs.harvard.edu/cgi-bin/nph-data_query?bibcode=2006PhRvE..74e1914V&link_type=ABSTRACT"><span id="translatedtitle"><span class="hlt">Species</span> <span class="hlt">abundance</span> distribution and population dynamics in a two-community model of neutral ecology</span></a></p> <p><a target="_blank" href="http://adsabs.harvard.edu/abstract_service.html">NASA Astrophysics Data System (ADS)</a></p> <p>Vallade, M.; Houchmandzadeh, B.</p> <p>2006-11-01</p> <p>Explicit formulas for the steady-state distribution of <span class="hlt">species</span> in two interconnected communities of arbitrary sizes are derived in the framework of Hubbell’s neutral model of biodiversity. Migrations of seeds from both communities as well as mutations in both of them are taken into account. These results generalize those previously obtained for the “island-continent” model and they allow an analysis of the influence of the ratio of the sizes of the two communities on the dominance/diversity equilibrium. Exact expressions for <span class="hlt">species</span> <span class="hlt">abundance</span> distributions are deduced from a master equation for the joint probability distribution of <span class="hlt">species</span> in the two communities. Moreover, an approximate self-consistent solution is derived. It corresponds to a generalization of previous results and it proves to be accurate over a broad range of parameters. The dynamical correlations between the <span class="hlt">abundances</span> of a <span class="hlt">species</span> in both communities are also discussed.</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://adsabs.harvard.edu/cgi-bin/nph-data_query?bibcode=2012ECSS..113..172L&link_type=ABSTRACT','NASAADS'); return false;" href="http://adsabs.harvard.edu/cgi-bin/nph-data_query?bibcode=2012ECSS..113..172L&link_type=ABSTRACT"><span id="translatedtitle">Does beach nourishment have long-term effects on intertidal macroinvertebrate <span class="hlt">species</span> <span class="hlt">abundance</span>?</span></a></p> <p><a target="_blank" href="http://adsabs.harvard.edu/abstract_service.html">NASA Astrophysics Data System (ADS)</a></p> <p>Leewis, Lies; van Bodegom, Peter M.; Rozema, Jelte; Janssen, Gerard M.</p> <p>2012-11-01</p> <p>Coastal squeeze is the largest threat for sandy coastal areas. To mitigate seaward threats, erosion and sea level rise, sand nourishment is commonly applied. However, its long-term consequences for macroinvertebrate fauna, critical to most ecosystem services of sandy coasts, are still unknown. Seventeen sandy beaches - nourished and controls - were sampled along a chronosequence to investigate the <span class="hlt">abundance</span> of four dominant macrofauna <span class="hlt">species</span> and their relations with nourishment year and relevant coastal environmental variables. Dean's parameter and latitude significantly explained the <span class="hlt">abundance</span> of the spionid polychaete Scolelepis squamata, Beach Index (BI), sand skewness, beach slope and latitude explained the <span class="hlt">abundance</span> of the amphipod Haustorius arenarius and Relative Tide Range (RTR), recreation and sand sorting explained the <span class="hlt">abundance</span> of Bathyporeia sarsi. For Eurydice pulchra, no environmental variable explained its <span class="hlt">abundance</span>. For H. arenarius, E. pulchra and B. sarsi, there was no relation with nourishment year, indicating that recovery took place within a year after nourishment. Scolelepis squamata initially profited from the nourishment with "over-recolonisation". This confirms its role as an opportunistic <span class="hlt">species</span>, thereby altering the initial community structure on a beach after nourishment. We conclude that the responses of the four dominant invertebrates studied in the years following beach nourishment are <span class="hlt">species</span> specific. This shows the importance of knowing the autecology of the sandy beach macroinvertebrate fauna in order to be able to mitigate the effects of beach nourishment and other environmental impacts.</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://adsabs.harvard.edu/cgi-bin/nph-data_query?bibcode=2015FrEaS...3...75C&link_type=ABSTRACT','NASAADS'); return false;" href="http://adsabs.harvard.edu/cgi-bin/nph-data_query?bibcode=2015FrEaS...3...75C&link_type=ABSTRACT"><span id="translatedtitle">Performance of seedlings of a shade-tolerant tropical <span class="hlt">tree</span> <span class="hlt">species</span> after moderate addition of N and P</span></a></p> <p><a target="_blank" href="http://adsabs.harvard.edu/abstract_service.html">NASA Astrophysics Data System (ADS)</a></p> <p>Cárate Tandalla, Daisy; Leuschner, Christoph; Homeier, Jürgen</p> <p>2015-12-01</p> <p>Nitrogen deposition to tropical forests is predicted to increase in future in many regions due to agricultural intensification. We conducted a seedling transplantation experiment in a tropical premontane forest in Ecuador with a locally <span class="hlt">abundant</span> late-successional <span class="hlt">tree</span> <span class="hlt">species</span> (Pouteria torta, Sapotaceae) aimed at detecting <span class="hlt">species</span>-specific responses to moderate N and P addition and to understand how increasing nutrient availability will affect regeneration. From locally collected seeds, 320 seedlings were produced and transplanted to the plots of the Ecuadorian Nutrient Manipulation Experiment (NUMEX) with three treatments (moderate N addition: 50 kg N ha-1 yr-1, moderate P addition: 10 kg P ha-1 yr-1 and combined N and P addition) and a control (80 plants per treatment). After 12 months, mortality, relative growth rate, leaf nutrient content and leaf herbivory rate were measured. N and NP addition significantly increased the mortality rate (70 % vs. 54 % in the control). However, N and P addition also increased the diameter growth rate of the surviving seedlings. N and P addition did not alter foliar nutrient concentrations and leaf N:P ratio, but N addition decreased the leaf C:N ratio and increased SLA. P addition (but not N addition) resulted in higher leaf area loss to herbivore consumption and also shifted carbon allocation to root growth. This fertilization experiment with a common rainforest <span class="hlt">tree</span> <span class="hlt">species</span> conducted in old-growth forest shows that already moderate doses of added N and P are affecting seedling performance which most likely will have consequences for the competitive strength in the understory and the recruitment success of P. torta. Simultaneous increases in growth, herbivory and mortality rates make it difficult to assess the <span class="hlt">species</span>' overall performance and predict how a future increase in nutrient deposition will alter the <span class="hlt">abundance</span> of this <span class="hlt">species</span> in the Andean tropical montane forests.</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://pubs.usgs.gov/of/1982/0443/report.pdf','USGSPUBS'); return false;" href="http://pubs.usgs.gov/of/1982/0443/report.pdf"><span id="translatedtitle">Plankton studies in San Francisco Bay; IV, Phytoplankton <span class="hlt">abundance</span> and <span class="hlt">species</span> composition, January 1980 - February 1981</span></a></p> <p><a target="_blank" href="http://pubs.er.usgs.gov/pubs/index.jsp?view=adv">USGS Publications Warehouse</a></p> <p>Wong, R.L.; Cloern, J.E.</p> <p>1982-01-01</p> <p>Data are presented on the phytoplankton <span class="hlt">species</span> composition and <span class="hlt">abundance</span> in San Francisco Bay from January 1980 through February 1981. Phytoplankton were identified and enumerated in surface samples collected approximately every two weeks at selected stations in the main channel of the Bay, and at shoal stations in the central portion of South San Francisco Bay, San Pablo Bay, and Suisun Bay. Also reported are separate <span class="hlt">species</span> lists for microphytoplankton (< 60 micrometers) and macrophytoplankton (> 60 micrometers). (Author 's abstract)</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://www.ncbi.nlm.nih.gov/pubmed/26601276','PUBMED'); return false;" href="http://www.ncbi.nlm.nih.gov/pubmed/26601276"><span id="translatedtitle">Individualistic sensitivities and exposure to climate change explain variation in <span class="hlt">species</span>' distribution and <span class="hlt">abundance</span> changes.</span></a></p> <p><a target="_blank" href="https://www.ncbi.nlm.nih.gov/entrez/query.fcgi?DB=pubmed">PubMed</a></p> <p>Palmer, Georgina; Hill, Jane K; Brereton, Tom M; Brooks, David R; Chapman, Jason W; Fox, Richard; Oliver, Tom H; Thomas, Chris D</p> <p>2015-10-01</p> <p>The responses of animals and plants to recent climate change vary greatly from <span class="hlt">species</span> to <span class="hlt">species</span>, but attempts to understand this variation have met with limited success. This has led to concerns that predictions of responses are inherently uncertain because of the complexity of interacting drivers and biotic interactions. However, we show for an exemplar group of 155 Lepidoptera <span class="hlt">species</span> that about 60% of the variation among <span class="hlt">species</span> in their <span class="hlt">abundance</span> trends over the past four decades can be explained by <span class="hlt">species</span>-specific exposure and sensitivity to climate change. Distribution changes were less well predicted, but nonetheless, up to 53% of the variation was explained. We found that <span class="hlt">species</span> vary in their overall sensitivity to climate and respond to different components of the climate despite ostensibly experiencing the same climate changes. Hence, <span class="hlt">species</span> have undergone different levels of population "forcing" (exposure), driving variation among <span class="hlt">species</span> in their national-scale <span class="hlt">abundance</span> and distribution trends. We conclude that variation in <span class="hlt">species</span>' responses to recent climate change may be more predictable than previously recognized. PMID:26601276</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://www.ncbi.nlm.nih.gov/pubmed/25460942','PUBMED'); return false;" href="http://www.ncbi.nlm.nih.gov/pubmed/25460942"><span id="translatedtitle">Influence of <span class="hlt">tree</span> canopy on N₂ fixation by pasture legumes and soil rhizobial <span class="hlt">abundance</span> in Mediterranean oak woodlands.</span></a></p> <p><a target="_blank" href="https://www.ncbi.nlm.nih.gov/entrez/query.fcgi?DB=pubmed">PubMed</a></p> <p>Carranca, C; Castro, I V; Figueiredo, N; Redondo, R; Rodrigues, A R F; Saraiva, I; Maricato, R; Madeira, M A V</p> <p>2015-02-15</p> <p>Symbiotic N2 fixation is of primordial significance in sustainable agro-forestry management as it allows reducing the use of mineral N in the production of mixed stands and by protecting the soils from degradation. Thereby, on a 2-year basis, N2 fixation was evaluated in four oak woodlands under Mediterranean conditions using a split-plot design and three replicates. (15)N technique was used for determination of N2 fixation rate. Variations in environmental conditions (temperature, rainfall, radiation) by the cork <span class="hlt">tree</span> canopy as well as the age of stands and pasture management can cause great differences in vegetation growth, legume N2 fixation, and soil rhizobial <span class="hlt">abundance</span>. In the present study, non-legumes dominated the swards, in particular beneath the <span class="hlt">tree</span> canopy, and legumes represented only 42% of total herbage. A 2-fold biomass reduction was observed in the oldest sown pasture in relation to the medium-age sward (6 t DW ha(-1)yr(-1)). Overall, competition of pasture growth for light was negligible, but soil rhizobial <span class="hlt">abundance</span> and symbiotic N2 fixation capacity were highly favored by this environmental factor in the spring and outside the influence of <span class="hlt">tree</span> canopy. Nitrogen derived from the atmosphere was moderate to high (54-72%) in unsown and sown swards. Inputs of fixed N2 increased from winter to spring due to more favorable climatic conditions (temperature and light intensity) for both rhizobia and vegetation growths. Assuming a constant fixation rate at each seasonal period, N2 fixation capacity increased from about 0.10 kg N ha(-1) per day in the autumn-winter period to 0.15 kg N ha(-1) per day in spring. Belowground plant material contributed to 11% of accumulated N in pasture legumes and was not affected by canopy. Size of soil fixing bacteria contributed little to explain pasture legumes N. PMID:25460942</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://www.ncbi.nlm.nih.gov/pubmed/27547317','PUBMED'); return false;" href="http://www.ncbi.nlm.nih.gov/pubmed/27547317"><span id="translatedtitle">Estimating <span class="hlt">species</span> - area relationships by modeling <span class="hlt">abundance</span> and frequency subject to incomplete sampling.</span></a></p> <p><a target="_blank" href="https://www.ncbi.nlm.nih.gov/entrez/query.fcgi?DB=pubmed">PubMed</a></p> <p>Yamaura, Yuichi; Connor, Edward F; Royle, J Andrew; Itoh, Katsuo; Sato, Kiyoshi; Taki, Hisatomo; Mishima, Yoshio</p> <p>2016-07-01</p> <p>Models and data used to describe <span class="hlt">species</span>-area relationships confound sampling with ecological process as they fail to acknowledge that estimates of <span class="hlt">species</span> richness arise due to sampling. This compromises our ability to make ecological inferences from and about <span class="hlt">species</span>-area relationships. We develop and illustrate hierarchical community models of <span class="hlt">abundance</span> and frequency to estimate <span class="hlt">species</span> richness. The models we propose separate sampling from ecological processes by explicitly accounting for the fact that sampled patches are seldom completely covered by sampling plots and that individuals present in the sampling plots are imperfectly detected. We propose a multispecies <span class="hlt">abundance</span> model in which community assembly is treated as the summation of an ensemble of <span class="hlt">species</span>-level Poisson processes and estimate patch-level <span class="hlt">species</span> richness as a derived parameter. We use sampling process models appropriate for specific survey methods. We propose a multispecies frequency model that treats the number of plots in which a <span class="hlt">species</span> occurs as a binomial process. We illustrate these models using data collected in surveys of early-successional bird <span class="hlt">species</span> and plants in young forest plantation patches. Results indicate that only mature forest plant <span class="hlt">species</span> deviated from the constant density hypothesis, but the null model suggested that the deviations were too small to alter the form of <span class="hlt">species</span>-area relationships. Nevertheless, results from simulations clearly show that the aggregate pattern of individual <span class="hlt">species</span> density-area relationships and occurrence probability-area relationships can alter the form of <span class="hlt">species</span>-area relationships. The plant community model estimated that only half of the <span class="hlt">species</span> present in the regional <span class="hlt">species</span> pool were encountered during the survey. The modeling framework we propose explicitly accounts for sampling processes so that ecological processes can be examined free of sampling artefacts. Our modeling approach is extensible and could be applied to a</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://adsabs.harvard.edu/cgi-bin/nph-data_query?bibcode=2015EGUGA..1712601J&link_type=ABSTRACT','NASAADS'); return false;" href="http://adsabs.harvard.edu/cgi-bin/nph-data_query?bibcode=2015EGUGA..1712601J&link_type=ABSTRACT"><span id="translatedtitle">Does deciduous <span class="hlt">tree</span> <span class="hlt">species</span> identity affect carbon storage in temperate soils?</span></a></p> <p><a target="_blank" href="http://adsabs.harvard.edu/abstract_service.html">NASA Astrophysics Data System (ADS)</a></p> <p>Jungkunst, Hermann; Schleuß, Per; Heitkamp, Felix</p> <p>2015-04-01</p> <p>Forest soils contribute roughly 70 % to the global terrestrial soil organic carbon (SOC) pool and thus play a vital role in the global carbon cycle. It is less clear, however, whether temperate <span class="hlt">tree</span> <span class="hlt">species</span> identity affects SOC storage beyond the coarse differentiation between coniferous and deciduous <span class="hlt">trees</span>. The most important driver for soil SOC storage definitely is the fine mineral fraction (clay and fine silt) because of its high sorption ability. It is difficult to disentangle any additional biotic effects since clay and silt vary considerably in nature. For experimental approaches, the process of soil carbon accumulation is too slow and, therefore, sound results cannot be expected for decades. Here we will present our success to distinguish between the effects of fine particle content (abiotic) and <span class="hlt">tree</span> <span class="hlt">species</span> composition (biotic) on the SOC pool in an old-growth broad-leaved forest plots along a <span class="hlt">tree</span> diversity gradient , i.e., 1- (beech), 3- (plus ash and lime <span class="hlt">tree</span>)- and 5-(plus maple and hornbeam) <span class="hlt">species</span>. The particle size fractions were separated first and then the carbon concentrations of each fraction was measured. Hence, the carbon content per unit clay was not calculated, as usually done, but directly measured. As expected, the variation in SOC content was mainly explained by the variations in clay content but not entirely. We found that the carbon concentration per unit clay and fine silt in the subsoil was by 30-35% higher in mixed than in monospecific stands indicating a significant <span class="hlt">species</span> identity or <span class="hlt">species</span> diversity effect on C stabilization. In contrast to the subsoil, no <span class="hlt">tree</span> <span class="hlt">species</span> effects was identified for the topsoil. Indications are given that the mineral phase was already carbon saturated and thus left no more room for a possible biotic effect. Underlying processes must remain speculative, but we will additionally present our latest microcosm results, including isotopic signatures, to underpin the proposed deciduous <span class="hlt">tree</span> <span class="hlt">species</span></p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://www.ncbi.nlm.nih.gov/pubmed/25643605','PUBMED'); return false;" href="http://www.ncbi.nlm.nih.gov/pubmed/25643605"><span id="translatedtitle">Habitat traits and <span class="hlt">species</span> interactions differentially affect <span class="hlt">abundance</span> and body size in pond-breeding amphibians.</span></a></p> <p><a target="_blank" href="https://www.ncbi.nlm.nih.gov/entrez/query.fcgi?DB=pubmed">PubMed</a></p> <p>Ousterhout, Brittany H; Anderson, Thomas L; Drake, Dana L; Peterman, William E; Semlitsch, Raymond D</p> <p>2015-07-01</p> <p>In recent studies, habitat traits have emerged as stronger predictors of <span class="hlt">species</span> occupancy, <span class="hlt">abundance</span>, richness and diversity than competition. However, in many cases, it remains unclear whether habitat also mediates processes more subtle than competitive exclusion, such as growth, or whether intra- and interspecific interactions among individuals of different <span class="hlt">species</span> may be better predictors of size. To test whether habitat traits are a stronger predictor of <span class="hlt">abundance</span> and body size than intra- and interspecific interactions, we measured the density and body size of three <span class="hlt">species</span> of larval salamanders in 192 ponds across a landscape. We found that the density of larvae was best predicted by models that included habitat features, while models incorporating interactions among individuals of different <span class="hlt">species</span> best explained the body size of larvae. Additionally, we found a positive relationship between focal <span class="hlt">species</span> density and congener density, while focal <span class="hlt">species</span> body size was negatively related to congener density. We posit that salamander larvae may not experience competitive exclusion and thus reduced densities, but instead compensate for increased competition behaviourally (e.g. reduced foraging), resulting in decreased growth. The discrepancy between larval density and body size, a strong predictor of fitness in this system, also highlights a potential shortcoming in using density or <span class="hlt">abundance</span> as a metric of habitat quality or population health. PMID:25643605</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://adsabs.harvard.edu/abs/1990IJBm...34...49V','NASAADS'); return false;" href="http://adsabs.harvard.edu/abs/1990IJBm...34...49V"><span id="translatedtitle">Seasonal <span class="hlt">abundance</span> of soil-surface arthropods in relation to some meteorological and edaphic variables of the grassland and <span class="hlt">tree</span>-planted areas in a tropical semi-arid savanna</span></a></p> <p><a target="_blank" href="http://adsabs.harvard.edu/abstract_service.html">NASA Astrophysics Data System (ADS)</a></p> <p>Vikram Reddy, M.; Venkataiah, B.</p> <p>1990-03-01</p> <p>Seasonality of relative population <span class="hlt">abundance</span> in different groups of soil-surface arthropods was investigated monthly by pit-fall traps during a 2-year period in the grassland and <span class="hlt">tree</span>-planted areas of a tropical semi-arid savanna at Warangal (south India). Densities of most groups were lowest during summer and highest during the rainy season. They were less <span class="hlt">abundant</span> during winter. Arthropods were recorded in higher numbers in <span class="hlt">tree</span>-planted compared to grassland areas. Certain arthropods that were found only during part of the year were recorded for a longer period in the <span class="hlt">tree</span>-planted area. Formicidae, Monomorium indicum Forel, Crematogaster sp. and Pachycondyla? tesserinoda (Emery), and Coleoptera, Pachycera sp. reached maximum densities in the rainy season and minimum numbers during winter and summer in the grassland area. However, these <span class="hlt">species</span> had lower densities during the rainy season and reached maximum densities during winter and summer in the <span class="hlt">tree</span>-planted area. The seasonal <span class="hlt">abundance</span> of arthropods showed significant linear correlations with different abiotic environmental variables such as rainfall, soil moisture, organic matter, soil and air temperatures, soil pH, relative humidity at the soil surface, and potassium and phosphorus of surface soil. Soil moisture and rainfall were generally the strongest correlates with densities, particularly in the grassland area.</p> </li> </ol> <div class="pull-right"> <ul class="pagination"> <li><a href="#" onclick='return showDiv("page_1");'>«</a></li> <li><a href="#" onclick='return showDiv("page_14");'>14</a></li> <li><a href="#" onclick='return showDiv("page_15");'>15</a></li> <li class="active"><span>16</span></li> <li><a href="#" onclick='return showDiv("page_17");'>17</a></li> <li><a href="#" onclick='return showDiv("page_18");'>18</a></li> <li><a href="#" onclick='return showDiv("page_25");'>»</a></li> </ul> </div> </div><!-- col-sm-12 --> </div><!-- row --> </div><!-- page_16 --> <div id="page_17" class="hiddenDiv"> <div class="row"> <div class="col-sm-12"> <div class="pull-right"> <ul class="pagination"> <li><a href="#" onclick='return showDiv("page_1");'>«</a></li> <li><a href="#" onclick='return showDiv("page_15");'>15</a></li> <li><a href="#" onclick='return showDiv("page_16");'>16</a></li> <li class="active"><span>17</span></li> <li><a href="#" onclick='return showDiv("page_18");'>18</a></li> <li><a href="#" onclick='return showDiv("page_19");'>19</a></li> <li><a href="#" onclick='return showDiv("page_25");'>»</a></li> </ul> </div> </div> </div> <div class="row"> <div class="col-sm-12"> <ol class="result-class" start="321"> <li> <p><a target="_blank" onclick="trackOutboundLink('http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=3302874','PMC'); return false;" href="http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=3302874"><span id="translatedtitle">Regular Patterns for Proteome-Wide Distribution of Protein <span class="hlt">Abundance</span> across <span class="hlt">Species</span></span></a></p> <p><a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?DB=pmc">PubMed Central</a></p> <p>Jiang, Ying; Ying, Wantao; Wu, Songfeng; Zhu, Yunping; Liu, Siqi; Yang, Pengyuan; Qian, Xiaohong; He, Fuchu</p> <p>2012-01-01</p> <p>A proteome of the bio-entity, including cell, tissue, organ, and organism, consists of proteins of diverse <span class="hlt">abundance</span>. The principle that determines the <span class="hlt">abundance</span> of different proteins in a proteome is of fundamental significance for an understanding of the building blocks of the bio-entity. Here, we report three regular patterns in the proteome-wide distribution of protein <span class="hlt">abundance</span> across <span class="hlt">species</span> such as human, mouse, fly, worm, yeast, and bacteria: in most cases, protein <span class="hlt">abundance</span> is positively correlated with the protein's origination time or sequence conservation during evolution; it is negatively correlated with the protein's domain number and positively correlated with domain coverage in protein structure, and the correlations became stronger during the course of evolution; protein <span class="hlt">abundance</span> can be further stratified by the function of the protein, whereby proteins that act on material conversion and transportation (mass category) are more <span class="hlt">abundant</span> than those that act on information modulation (information category). Thus, protein <span class="hlt">abundance</span> is intrinsically related to the protein's inherent characters of evolution, structure, and function. PMID:22427835</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://www.ncbi.nlm.nih.gov/pubmed/17665219','PUBMED'); return false;" href="http://www.ncbi.nlm.nih.gov/pubmed/17665219"><span id="translatedtitle">Population structure, physiology and ecohydrological impacts of dioecious riparian <span class="hlt">tree</span> <span class="hlt">species</span> of western North America.</span></a></p> <p><a target="_blank" href="https://www.ncbi.nlm.nih.gov/entrez/query.fcgi?DB=pubmed">PubMed</a></p> <p>Hultine, K R; Bush, S E; West, A G; Ehleringer, J R</p> <p>2007-11-01</p> <p>The global water cycle is intimately linked to vegetation structure and function. Nowhere is this more apparent than in the arid west where riparian forests serve as ribbons of productivity in otherwise mostly unproductive landscapes. Dioecy is common among <span class="hlt">tree</span> <span class="hlt">species</span> that make up western North American riparian forests. There are intrinsic physiological differences between male and female dioecious riparian <span class="hlt">trees</span> that may influence population structure (i.e., the ratio of male to female <span class="hlt">trees</span>) and impact ecohydrology at large scales. In this paper, we review the current literature on sex ratio patterns and physiology of dioecious riparian <span class="hlt">tree</span> <span class="hlt">species</span>. Then develop a conceptual framework of the mechanisms that underlie population structure of dominant riparian <span class="hlt">tree</span> <span class="hlt">species</span>. Finally, we identify linkages between population structure and ecohydrological processes such as evapotranspiration and streamflow. A more thorough understanding of the mechanisms that underlie population structure of dominant riparian <span class="hlt">tree</span> <span class="hlt">species</span> will enable us to better predict global change impacts on vegetation and water cycling at multiple scales. PMID:17665219</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://www.osti.gov/scitech/servlets/purl/861330','SCIGOV-STC'); return false;" href="http://www.osti.gov/scitech/servlets/purl/861330"><span id="translatedtitle">Ambrosia Beetle (Coleoptera: Scolytidae) <span class="hlt">Species</span>, Flight, and Attack on Living Eastern Cottonwood <span class="hlt">Trees</span>.</span></a></p> <p><a target="_blank" href="http://www.osti.gov/scitech">SciTech Connect</a></p> <p>Coyle, D R; D.C. Booth: M.S. Wallace</p> <p>2005-12-01</p> <p>ABSTRACT In spring 2002, ambrosia beetles (Coleoptera: Scolytidae) infested an intensively managed 22-ha <span class="hlt">tree</span> plantation on the upper coastal plain of South Carolina. Nearly 3,500 scolytids representing 28 <span class="hlt">species</span> were captured in ethanol-baited traps from 18 June 2002 to 18 April 2004. More than 88% of total captures were exotic <span class="hlt">species</span>. Five <span class="hlt">species</span> [Dryoxylon onoharaensum (Murayama), Euwallacea validus (Eichhoff), Pseudopityophthorus minutissimus (Zimmermann), Xyleborus atratus Eichhoff, and Xyleborus impressus Eichhoff]) were collected in South Carolina for the first time. Of four <span class="hlt">tree</span> <span class="hlt">species</span> in the plantation, eastern cottonwood, Populus deltoides Bartram, was the only one attacked, with nearly 40% of the <span class="hlt">trees</span> sustaining ambrosia beetle damage. Clone ST66 sustained more damage than clone S7C15. ST66 <span class="hlt">trees</span> receiving fertilization were attacked more frequently than <span class="hlt">trees</span> receiving irrigation, irrigation_fertilization, or controls, although the number of S7C15 <span class="hlt">trees</span> attacked did not differ among treatments. The study location is near major shipping ports; our results demonstrate the necessity for intensive monitoring programs to determine the arrival, spread, ecology, and impact of exotic scolytids.</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://adsabs.harvard.edu/cgi-bin/nph-data_query?bibcode=2013NatCC...3.1055J&link_type=ABSTRACT','NASAADS'); return false;" href="http://adsabs.harvard.edu/cgi-bin/nph-data_query?bibcode=2013NatCC...3.1055J&link_type=ABSTRACT"><span id="translatedtitle">Observed and predicted effects of climate change on <span class="hlt">species</span> <span class="hlt">abundance</span> in protected areas</span></a></p> <p><a target="_blank" href="http://adsabs.harvard.edu/abstract_service.html">NASA Astrophysics Data System (ADS)</a></p> <p>Johnston, Alison; Ausden, Malcolm; Dodd, Andrew M.; Bradbury, Richard B.; Chamberlain, Dan E.; Jiguet, Frédéric; Thomas, Chris D.; Cook, Aonghais S. C. P.; Newson, Stuart E.; Ockendon, Nancy; Rehfisch, Mark M.; Roos, Staffan; Thaxter, Chris B.; Brown, Andy; Crick, Humphrey Q. P.; Douse, Andrew; McCall, Rob A.; Pontier, Helen; Stroud, David A.; Cadiou, Bernard; Crowe, Olivia; Deceuninck, Bernard; Hornman, Menno; Pearce-Higgins, James W.</p> <p>2013-12-01</p> <p>The dynamic nature and diversity of <span class="hlt">species</span>' responses to climate change poses significant difficulties for developing robust, long-term conservation strategies. One key question is whether existing protected area networks will remain effective in a changing climate. To test this, we developed statistical models that link climate to the <span class="hlt">abundance</span> of internationally important bird populations in northwestern Europe. Spatial climate-<span class="hlt">abundance</span> models were able to predict 56% of the variation in recent 30-year population trends. Using these models, future climate change resulting in 4.0°C global warming was projected to cause declines of at least 25% for more than half of the internationally important populations considered. Nonetheless, most EU Special Protection Areas in the UK were projected to retain <span class="hlt">species</span> in sufficient <span class="hlt">abundances</span> to maintain their legal status, and generally sites that are important now were projected to be important in the future. The biological and legal resilience of this network of protected areas is derived from the capacity for turnover in the important <span class="hlt">species</span> at each site as <span class="hlt">species</span>' distributions and <span class="hlt">abundances</span> alter in response to climate. Current protected areas are therefore predicted to remain important for future conservation in a changing climate.</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://hdl.handle.net/2060/20010004212','NASA-TRS'); return false;" href="http://hdl.handle.net/2060/20010004212"><span id="translatedtitle">BOREAS TE-4 Branch Bag Data From Boreal <span class="hlt">Tree</span> <span class="hlt">Species</span></span></a></p> <p><a target="_blank" href="http://ntrs.nasa.gov/search.jsp">NASA Technical Reports Server (NTRS)</a></p> <p>Hall, Forrest G. (Editor); Papagno, Andrea (Editor); Berry, Joseph A.; Fu, Wei; Fredeen, Art; Gamon, John</p> <p>2000-01-01</p> <p>The BOREAS TE-4 team collected continuous records of gas exchange under ambient conditions from intact boreal forest <span class="hlt">trees</span> in the BOREAS NSA from 23-Jul-1996 until 14-Aug-1996. These measurements can be used to test models of photosynthesis, stomatal conductance, and leaf respiration, such as SiB2 (Sellers et al., 1996) or the leaf model (Collatz et al., 1991), and programs can be obtained from the investigators. The data are stored in tabular ASCII files. The data files are available on a CD-ROM (see document number 20010000884), or from the Oak Ridge National Laboratory (ORNL) Distributed Active Archive Center (DAAC).</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://www.ncbi.nlm.nih.gov/pubmed/20213151','PUBMED'); return false;" href="http://www.ncbi.nlm.nih.gov/pubmed/20213151"><span id="translatedtitle">Consequences of organic farming and landscape heterogeneity for <span class="hlt">species</span> richness and <span class="hlt">abundance</span> of farmland birds.</span></a></p> <p><a target="_blank" href="https://www.ncbi.nlm.nih.gov/entrez/query.fcgi?DB=pubmed">PubMed</a></p> <p>Smith, Henrik G; Dänhardt, Juliana; Lindström, Ake; Rundlöf, Maj</p> <p>2010-04-01</p> <p>It has been suggested that organic farming may benefit farmland biodiversity more in landscapes that have lost a significant part of its former landscape heterogeneity. We tested this hypothesis by comparing bird <span class="hlt">species</span> richness and <span class="hlt">abundance</span> during the breeding season in organic and conventional farms, matched to eliminate all differences not directly linked to the farming practice, situated in either homogeneous plains with only a little semi-natural habitat or in heterogeneous farmland landscapes with <span class="hlt">abundant</span> field borders and semi-natural grasslands. The effect of farm management on <span class="hlt">species</span> richness interacted with landscape structure, such that there was a positive relationship between organic farming and diversity only in homogeneous landscapes. This pattern was mainly dependent on the <span class="hlt">species</span> richness of passerine birds, in particular those that were invertebrate feeders. <span class="hlt">Species</span> richness of non-passerines was positively related to organic farming independent of the landscape context. Bird <span class="hlt">abundance</span> was positively related to landscape heterogeneity but not to farm management. This was mainly because the <span class="hlt">abundance</span> of passerines, particularly invertebrate feeders, was positively related to landscape heterogeneity. We suggest that invertebrate feeders particularly benefit from organic farming because of improved foraging conditions through increased invertebrate <span class="hlt">abundances</span> in otherwise depauperate homogeneous landscapes. Although many seed-eaters also benefit from increased insect <span class="hlt">abundance</span>, they may also utilize crop seed resources in homogeneous landscapes and conventional farms. The occurrence of an interactive effect of organic farming and landscape heterogeneity on bird diversity will have consequences for the optimal allocation of resources to restore the diversity of farmland birds. PMID:20213151</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://dx.doi.org/10.1890/11-1359.1','USGSPUBS'); return false;" href="http://dx.doi.org/10.1890/11-1359.1"><span id="translatedtitle">Do predators control prey <span class="hlt">species</span> <span class="hlt">abundance</span>? An experimental test with brown treesnakes on Guam</span></a></p> <p><a target="_blank" href="http://pubs.er.usgs.gov/pubs/index.jsp?view=adv">USGS Publications Warehouse</a></p> <p>Campbell, Earl W., III; Yackel Adams, Amy A.; Converse, Sarah J.; Fritts, Thomas H.; Rodda, Gordon H.</p> <p>2012-01-01</p> <p>The effect of predators on the <span class="hlt">abundance</span> of prey <span class="hlt">species</span> is a topic of ongoing debate in ecology; the effect of snake predators on their prey has been less debated, as there exists a general consensus that snakes do not negatively influence the <span class="hlt">abundance</span> of their prey. However, this viewpoint has not been adequately tested. We quantified the effect of brown treesnake (Boiga irregularis) predation on the <span class="hlt">abundance</span> and size of lizards on Guam by contrasting lizards in two 1-ha treatment plots of secondary forest from which snakes had been removed and excluded vs. two 1-ha control plots in which snakes were monitored but not removed or excluded. We removed resident snakes from the treatment plots with snake traps and hand capture, and snake immigration into these plots was precluded by electrified snake barriers. Lizards were sampled in all plots quarterly for a year following snake elimination in the treatment plots. Following the completion of this experiment, we used total removal sampling to census lizards on a 100-m2 subsample of each plot. Results of systematic lizard population monitoring before and after snake removal suggest that the <span class="hlt">abundance</span> of the skink, Carlia ailanpalai, increased substantially and the <span class="hlt">abundance</span> of two <span class="hlt">species</span> of gekkonids, Lepidodactylus lugubris and Hemidactylus frenatus, also increased on snake-free plots. No treatment effect was observed for the skink Emoia caeruleocauda. Mean snout–vent length of all lizard <span class="hlt">species</span> only increased following snake removal in the treatment plots. The general increase in prey density and mean size was unexpected in light of the literature consensus that snakes do not control the <span class="hlt">abundance</span> of their prey <span class="hlt">species</span>. Our findings show that, at least where alternate predators are lacking, snakes may indeed affect prey populations.</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://adsabs.harvard.edu/abs/2010AGUFM.B13B0476R','NASAADS'); return false;" href="http://adsabs.harvard.edu/abs/2010AGUFM.B13B0476R"><span id="translatedtitle">Wind Disturbance Produced Changes in <span class="hlt">Tree</span> <span class="hlt">Species</span> Assemblage in the Peruvian Amazon</span></a></p> <p><a target="_blank" href="http://adsabs.harvard.edu/abstract_service.html">NASA Astrophysics Data System (ADS)</a></p> <p>Rifai, S. W.; Chambers, J. Q.; Negron Juarez, R. I.; Ramirez, F.; Tello, R.; Alegria Muñoz, W.</p> <p>2010-12-01</p> <p>Wind disturbance has been a frequently overlooked abiotic cause of mass <span class="hlt">tree</span> mortality in the Amazon basin. In the Peruvian Amazon these wind disturbances are produced by meteorological events such as convective systems. Downbursts for example produce short term descendent wind speeds that can be in excess of 30 m s-1. These are capable of producing <span class="hlt">tree</span> blowdowns which have been reported to be as large as 33 km2 in the Amazon basin. We used the chronosequence of Landsat Satellite imagery to find and locate where these blowdowns have occurred in the Loreto region of the Peruvian Amazon. Spectral Mixture Analysis was used to estimate the proportion landcover of green vegetation, non-photosynthetic vegetation (NPV), soil and shade in each pixel. The change in NPV was calculated by subtracting the NPV signal in the Landsat image prior to the blowdown occurrence, from the image following the disturbance. Our prior research has established a linear relationship between <span class="hlt">tree</span> mortality and change in NPV. It is hypothesized that these mass <span class="hlt">tree</span> mortality events result in changes in the <span class="hlt">tree</span> <span class="hlt">species</span> assemblage of affected forests. Here we present preliminary <span class="hlt">tree</span> <span class="hlt">species</span> assemblage data from two sites in the Peruvian Amazon near Iquitos, Peru. The site (ALP) at the Allpahuayo Mishana reserve (3.945 S, 73.455 W) is 30 km south of Iquitos, Peru, and hosts the remnants of a 50 ha blowdown that occurred in either 1992 or 1993. Another site (NAPO) on the Napo river about 60 km north of Iquitos, is the location of an approximately 300 ha blowdown that occurred in 1998. At each site, a 3000 m x 10 m transect encompassing non disturbed and disturbed areas was installed, and <span class="hlt">trees</span> greater than 10 cm diameter at breast height were measured for diameter, height and were identified to the <span class="hlt">species</span>. Stem density of <span class="hlt">trees</span> with diameter at breast height > 10 cm, and <span class="hlt">tree</span> height appear to be similar both inside and outside the blowdown affected areas of the forests at both sites. At the ALP</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://www.ars.usda.gov/research/publications/Publications.htm?seq_no_115=238475','TEKTRAN'); return false;" href="http://www.ars.usda.gov/research/publications/Publications.htm?seq_no_115=238475"><span id="translatedtitle">Impact of Fumigation on Pythium <span class="hlt">Species</span> Associated with Forest <span class="hlt">Tree</span> Nurseries of Oregon and Washington</span></a></p> <p><a target="_blank" href="http://www.ars.usda.gov/services/TekTran.htm">Technology Transfer Automated Retrieval System (TEKTRAN)</a></p> <p></p> <p></p> <p>Pythium <span class="hlt">species</span> cause damping off of conifer seedlings in forest <span class="hlt">tree</span> nurseries. Identification of the <span class="hlt">species</span> responsible for the disease has been traditionally based on morphology. However, newer DNA-based identification methods may allow more accurate identification and assessment of soil popul...</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=3460976','PMC'); return false;" href="http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=3460976"><span id="translatedtitle">Spatial Distribution and Interspecific Associations of <span class="hlt">Tree</span> <span class="hlt">Species</span> in a Tropical Seasonal Rain Forest of China</span></a></p> <p><a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?DB=pmc">PubMed Central</a></p> <p>Lan, Guoyu; Getzin, Stephan; Wiegand, Thorsten; Hu, Yuehua; Xie, Guishui; Zhu, Hua; Cao, Min</p> <p>2012-01-01</p> <p>Studying the spatial pattern and interspecific associations of plant <span class="hlt">species</span> may provide valuable insights into processes and mechanisms that maintain <span class="hlt">species</span> coexistence. Point pattern analysis was used to analyze the spatial distribution patterns of twenty dominant <span class="hlt">tree</span> <span class="hlt">species</span>, their interspecific spatial associations and changes across life stages in a 20-ha permanent plot of seasonal tropical rainforest in Xishuangbanna, China, to test mechanisms maintaining <span class="hlt">species</span> coexistence. Torus-translation tests were used to quantify positive or negative associations of the <span class="hlt">species</span> to topographic habitats. The results showed: (1) fourteen of the twenty <span class="hlt">tree</span> <span class="hlt">species</span> were negatively (or positively) associated with one or two of the topographic variables, which evidences that the niche contributes to the spatial pattern of these <span class="hlt">species</span>. (2) Most saplings of the study <span class="hlt">species</span> showed a significantly clumped distribution at small scales (0–10 m) which was lost at larger scales (10–30 m). (3) The degree of spatial clumping deceases from saplings, to poles, to adults indicates that density-dependent mortality of the offspring is ubiquitous in <span class="hlt">species</span>. (4) It is notable that a high number of positive small-scale interactions were found among the twenty <span class="hlt">species</span>. For saplings, 42.6% of all combinations of <span class="hlt">species</span> pairs showed positive associations at neighborhood scales up to five meters, but only 38.4% were negative. For poles and adults, positive associations at these distances still made up 45.5% and 29.5%, respectively. In conclusion, there is considerable evidence for the presence of positive interactions among the <span class="hlt">tree</span> <span class="hlt">species</span>, which suggests that <span class="hlt">species</span> herd protection may occur in our plot. In addition, niche assembly and limited dispersal (likely) contribute to the spatial patterns of <span class="hlt">tree</span> <span class="hlt">species</span> in the tropical seasonal rain forest in Xishuangbanna, China. PMID:23029394</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://www.ncbi.nlm.nih.gov/pubmed/12625013','PUBMED'); return false;" href="http://www.ncbi.nlm.nih.gov/pubmed/12625013"><span id="translatedtitle">[Feasibility to introduce rare <span class="hlt">tree</span> <span class="hlt">species</span> Pinus sibirica into China].</span></a></p> <p><a target="_blank" href="https://www.ncbi.nlm.nih.gov/entrez/query.fcgi?DB=pubmed">PubMed</a></p> <p>Liu, Guifeng; Yang, Chuanping; Zhao, Guangyi</p> <p>2002-11-01</p> <p>Pinus sibirica growing mainly in Siberia of Russia is distributed over the Euro-Asia Taiga forest belt. There are many high-quality populations due to a great deal of variations. This kind of <span class="hlt">tree</span> has an advantage of standing up to frigid environment, and can spread out in such places that have cold weather and high altitude. In China, boreal forest is a wide-spreaded type of forest that has the largest area and high volume. For this reason, it is feasible to introduce Pinus sibirica into the region that the condition is suitable. Introducing this kind of <span class="hlt">tree</span> is a strategic project that can improve the structure and quality of our boreal forest. Introducing it can not only meet the demands of improved variety in short time, but also do the experiment of producing edible seeds and build up the developing center of nut, which can be a way of getting rid of poverty of forest region in heavy frigid area where is regarded as infertile area for farming formerly. PMID:12625013</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://www.ncbi.nlm.nih.gov/pubmed/26364482','PUBMED'); return false;" href="http://www.ncbi.nlm.nih.gov/pubmed/26364482"><span id="translatedtitle">Fuel wood properties of some oak <span class="hlt">tree</span> <span class="hlt">species</span> of Manipur, India.</span></a></p> <p><a target="_blank" href="https://www.ncbi.nlm.nih.gov/entrez/query.fcgi?DB=pubmed">PubMed</a></p> <p>Meetei, Shougrakpam Bijen; Singh, E J; Das, Ashesh Kumar</p> <p>2015-07-01</p> <p>Five indigenous oak <span class="hlt">tree</span> <span class="hlt">species</span>, i.e., Castanopsis indica (Roxb. ex Lindl.) A.DC., Lithocarpus fenestratus (Roxb.) Rehder, Lithocarpus pachyphyllus (Kurz) Rehder, Lithocarpus polystachyus (Wall. ex A.DC.) Rehder and Quercus serrata Murray were estimated for their wood properties such as calorific value, density, moisture content and ash content from a sub-tropical forest of Haraothel hill, Senapati District, Manipur. Wood biomass components were found to have higher calorific value (kJ g(-)) than bark components. The calorific values for <span class="hlt">tree</span> <span class="hlt">species</span> were found highest in L. pachyphyllus (17.99 kJ g(-1)) followed by C. indica (17.98 kJ g1), L. fenestratus (17.96 kJ g"), L. polystachyus (17.80 kJ g(-1)) and Q. serrata (17.49 kJ g(-1)). Calorific values for bole bark, bole wood and branch bark were found significantly different (F > 3.48 at p = 0.05) in five oak <span class="hlt">tree</span> <span class="hlt">species</span>. Percentage of ash on dry weight basis was found to be highest in Q. serrata (4.73%) and lowest in C. indica (2.19%). Ash content of <span class="hlt">tree</span> components gives a singnificant factor in determining fuelwood value index (FVI). Of all the five oak <span class="hlt">tree</span> <span class="hlt">species</span>, Q. serrata exhibited highest value of wood density (0.78 g cm-) and lowest was observed in C. indica (0.63 g cm(-3)). There was significant correlation between wood density (p<0.05), ash content (p<0.01) with calorific value in oak <span class="hlt">tree</span> <span class="hlt">species</span>. Fuelwood value index (FVI) was in the following order: C. indica (1109.70) > L. pachyphyllus (898.41)> L. polystachyus (879.02)> L. fenestratus (824.61)> Q. serrata (792.50). Thus, the present study suggests that C. indica may be considered as a fuelwood oak <span class="hlt">tree</span> <span class="hlt">species</span> in Manipur. PMID:26364482</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=4988811','PMC'); return false;" href="http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=4988811"><span id="translatedtitle">Early establishment of <span class="hlt">trees</span> at the alpine treeline: idiosyncratic <span class="hlt">species</span> responses to temperature-moisture interactions</span></a></p> <p><a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?DB=pmc">PubMed Central</a></p> <p>Loranger, Hannah; Zotz, Gerhard; Bader, Maaike Y.</p> <p>2016-01-01</p> <p>On a global scale, temperature is the main determinant of arctic and alpine treeline position. However on a local scale, treeline form and position vary considerably due to other climatic factors, <span class="hlt">tree</span> <span class="hlt">species</span> ecology and life-stage-dependent responses. For treelines to advance poleward or uphill, the first steps are germination and seedling establishment. These earliest life stages may be major bottlenecks for treeline <span class="hlt">tree</span> populations and will depend differently on climatic conditions than adult <span class="hlt">trees</span>. We investigated the effect of soil temperature and moisture on germination and early seedling survival in a field experiment in the French Alps near the local treeline (2100 m a.s.l.) using passive temperature manipulations and two watering regimes. Five European treeline <span class="hlt">tree</span> <span class="hlt">species</span> were studied: Larix decidua, Picea abies, Pinus cembra, Pinus uncinata and Sorbus aucuparia. In addition, we monitored the germination response of three of these <span class="hlt">species</span> to low temperatures under controlled conditions in growth chambers. The early establishment of these <span class="hlt">trees</span> at the alpine treeline was limited either by temperature or by moisture, the sensitivity to one factor often depending on the intensity of the other. The results showed that the relative importance of the two factors and the direction of the effects are highly <span class="hlt">species</span>-specific, while both factors tend to have consistent effects on both germination and early seedling survival within each <span class="hlt">species</span>. We show that temperature and water availability are both important contributors to establishment patterns of treeline <span class="hlt">trees</span> and hence to <span class="hlt">species</span>-specific forms and positions of alpine treelines. The observed idiosyncratic <span class="hlt">species</span> responses highlight the need for studies including several <span class="hlt">species</span> and life-stages to create predictive power concerning future treeline dynamics. PMID:27402618</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://www.ncbi.nlm.nih.gov/pubmed/27402618','PUBMED'); return false;" href="http://www.ncbi.nlm.nih.gov/pubmed/27402618"><span id="translatedtitle">Early establishment of <span class="hlt">trees</span> at the alpine treeline: idiosyncratic <span class="hlt">species</span> responses to temperature-moisture interactions.</span></a></p> <p><a target="_blank" href="https://www.ncbi.nlm.nih.gov/entrez/query.fcgi?DB=pubmed">PubMed</a></p> <p>Loranger, Hannah; Zotz, Gerhard; Bader, Maaike Y</p> <p>2016-01-01</p> <p>On a global scale, temperature is the main determinant of arctic and alpine treeline position. However on a local scale, treeline form and position vary considerably due to other climatic factors, <span class="hlt">tree</span> <span class="hlt">species</span> ecology and life-stage-dependent responses. For treelines to advance poleward or uphill, the first steps are germination and seedling establishment. These earliest life stages may be major bottlenecks for treeline <span class="hlt">tree</span> populations and will depend differently on climatic conditions than adult <span class="hlt">trees</span>. We investigated the effect of soil temperature and moisture on germination and early seedling survival in a field experiment in the French Alps near the local treeline (2100 m a.s.l.) using passive temperature manipulations and two watering regimes. Five European treeline <span class="hlt">tree</span> <span class="hlt">species</span> were studied: Larix decidua, Picea abies, Pinus cembra, Pinus uncinata and Sorbus aucuparia In addition, we monitored the germination response of three of these <span class="hlt">species</span> to low temperatures under controlled conditions in growth chambers. The early establishment of these <span class="hlt">trees</span> at the alpine treeline was limited either by temperature or by moisture, the sensitivity to one factor often depending on the intensity of the other. The results showed that the relative importance of the two factors and the direction of the effects are highly <span class="hlt">species</span>-specific, while both factors tend to have consistent effects on both germination and early seedling survival within each <span class="hlt">species</span>. We show that temperature and water availability are both important contributors to establishment patterns of treeline <span class="hlt">trees</span> and hence to <span class="hlt">species</span>-specific forms and positions of alpine treelines. The observed idiosyncratic <span class="hlt">species</span> responses highlight the need for studies including several <span class="hlt">species</span> and life-stages to create predictive power concerning future treeline dynamics. PMID:27402618</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://www.ncbi.nlm.nih.gov/pubmed/25412524','PUBMED'); return false;" href="http://www.ncbi.nlm.nih.gov/pubmed/25412524"><span id="translatedtitle"><span class="hlt">Species</span> richness and relative <span class="hlt">species</span> <span class="hlt">abundance</span> of Nymphalidae (Lepidoptera) in three forests with different perturbations in the North-Central Caribbean of Costa Rica.</span></a></p> <p><a target="_blank" href="https://www.ncbi.nlm.nih.gov/entrez/query.fcgi?DB=pubmed">PubMed</a></p> <p>Stephen, Carolyn; Sánchez, Ragde</p> <p>2014-09-01</p> <p>Measurements of <span class="hlt">species</span> richness and <span class="hlt">species</span> <span class="hlt">abundance</span> can have important implications for regulations and conservation. This study investigated <span class="hlt">species</span> richness and <span class="hlt">abundance</span> of butterflies in the family Nymphalidae at undisturbed, and disturbed habitats in Tirimbina Biological Reserve and Nogal Private Reserve, Sarapiquí, Costa Rica. Traps baited with rotten banana were placed in the canopy and the understory of three habitats: within mature forest, at a river/forest border, and at a banana plantation/forest border. In total, 71 <span class="hlt">species</span> and 487 individuals were caught and identified during May and June 2011 and May 2013. <span class="hlt">Species</span> richness and <span class="hlt">species</span> <span class="hlt">abundance</span> were found to increase significantly at perturbed habitats (p < 0.0001, p < 0.0001, respectively). The edge effect, in which <span class="hlt">species</span> richness and <span class="hlt">abundance</span> increase due to greater complementary resources from different habitats, could be one possible explanation for increased <span class="hlt">species</span> richness and <span class="hlt">abundance</span>. PMID:25412524</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://www.ncbi.nlm.nih.gov/pubmed/25377453','PUBMED'); return false;" href="http://www.ncbi.nlm.nih.gov/pubmed/25377453"><span id="translatedtitle">Multiple <span class="hlt">species</span> of wild <span class="hlt">tree</span> peonies gave rise to the 'king of flowers', Paeonia suffruticosa Andrews.</span></a></p> <p><a target="_blank" href="https://www.ncbi.nlm.nih.gov/entrez/query.fcgi?DB=pubmed">PubMed</a></p> <p>Zhou, Shi-Liang; Zou, Xin-Hui; Zhou, Zhi-Qin; Liu, Jing; Xu, Chao; Yu, Jing; Wang, Qiang; Zhang, Da-Ming; Wang, Xiao-Quan; Ge, Song; Sang, Tao; Pan, Kai-Yu; Hong, De-Yuan</p> <p>2014-12-22</p> <p>The origin of cultivated <span class="hlt">tree</span> peonies, known as the 'king of flowers' in China for more than 1000 years, has attracted considerable interest, but remained unsolved. Here, we conducted phylogenetic analyses of explicitly sampled traditional cultivars of <span class="hlt">tree</span> peonies and all wild <span class="hlt">species</span> from the shrubby section Moutan of the genus Paeonia based on sequences of 14 fast-evolved chloroplast regions and 25 presumably single-copy nuclear markers identified from RNA-seq data. The phylogeny of the wild <span class="hlt">species</span> inferred from the nuclear markers was fully resolved and largely congruent with morphology and classification. The incongruence between the nuclear and chloroplast <span class="hlt">trees</span> suggested that there had been gene flow between the wild <span class="hlt">species</span>. The comparison of nuclear and chloroplast phylogenies including cultivars showed that the cultivated <span class="hlt">tree</span> peonies originated from homoploid hybridization among five wild <span class="hlt">species</span>. Since the origin, thousands of cultivated varieties have spread worldwide, whereas four parental <span class="hlt">species</span> are currently endangered or on the verge of extinction. The documentation of extensive homoploid hybridization involved in <span class="hlt">tree</span> peony domestication provides new insights into the mechanisms underlying the origins of garden ornamentals and the way of preserving natural genetic resources through domestication. PMID:25377453</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=3436813','PMC'); return false;" href="http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=3436813"><span id="translatedtitle">Inferring duplications, losses, transfers and incomplete lineage sorting with nonbinary <span class="hlt">species</span> <span class="hlt">trees</span></span></a></p> <p><a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?DB=pmc">PubMed Central</a></p> <p>Stolzer, Maureen; Lai, Han; Xu, Minli; Sathaye, Deepa; Vernot, Benjamin; Durand, Dannie</p> <p>2012-01-01</p> <p>Motivation: Gene duplication (D), transfer (T), loss (L) and incomplete lineage sorting (I) are crucial to the evolution of gene families and the emergence of novel functions. The history of these events can be inferred via comparison of gene and <span class="hlt">species</span> <span class="hlt">trees</span>, a process called reconciliation, yet current reconciliation algorithms model only a subset of these evolutionary processes. Results: We present an algorithm to reconcile a binary gene <span class="hlt">tree</span> with a nonbinary <span class="hlt">species</span> <span class="hlt">tree</span> under a DTLI parsimony criterion. This is the first reconciliation algorithm to capture all four evolutionary processes driving <span class="hlt">tree</span> incongruence and the first to reconcile non-binary <span class="hlt">species</span> <span class="hlt">trees</span> with a transfer model. Our algorithm infers all optimal solutions and reports complete, temporally feasible event histories, giving the gene and <span class="hlt">species</span> lineages in which each event occurred. It is fixed-parameter tractable, with polytime complexity when the maximum <span class="hlt">species</span> outdegree is fixed. Application of our algorithms to prokaryotic and eukaryotic data show that use of an incomplete event model has substantial impact on the events inferred and resulting biological conclusions. Availability: Our algorithms have been implemented in Notung, a freely available phylogenetic reconciliation software package, available at http://www.cs.cmu.edu/~durand/Notung. Contact: mstolzer@andrew.cmu.edu PMID:22962460</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=4657984','PMC'); return false;" href="http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=4657984"><span id="translatedtitle">Discrimination of Deciduous <span class="hlt">Tree</span> <span class="hlt">Species</span> from Time Series of Unmanned Aerial System Imagery</span></a></p> <p><a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?DB=pmc">PubMed Central</a></p> <p>Lisein, Jonathan; Michez, Adrien; Claessens, Hugues; Lejeune, Philippe</p> <p>2015-01-01</p> <p>Technology advances can revolutionize Precision Forestry by providing accurate and fine forest information at <span class="hlt">tree</span> level. This paper addresses the question of how and particularly when Unmanned Aerial System (UAS) should be used in order to efficiently discriminate deciduous <span class="hlt">tree</span> <span class="hlt">species</span>. The goal of this research is to determine when is the best time window to achieve an optimal <span class="hlt">species</span> discrimination. A time series of high resolution UAS imagery was collected to cover the growing season from leaf flush to leaf fall. Full benefit was taken of the temporal resolution of UAS acquisition, one of the most promising features of small drones. The disparity in forest <span class="hlt">tree</span> phenology is at the maximum during early spring and late autumn. But the phenology state that optimized the classification result is the one that minimizes the spectral variation within <span class="hlt">tree</span> <span class="hlt">species</span> groups and, at the same time, maximizes the phenologic differences between <span class="hlt">species</span>. Sunlit <span class="hlt">tree</span> crowns (5 deciduous <span class="hlt">species</span> groups) were classified using a Random Forest approach for monotemporal, two-date and three-date combinations. The end of leaf flushing was the most efficient single-date time window. Multitemporal datasets definitely improve the overall classification accuracy. But single-date high resolution orthophotomosaics, acquired on optimal time-windows, result in a very good classification accuracy (overall out of bag error of 16%). PMID:26600422</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://www.ncbi.nlm.nih.gov/pubmed/26600422','PUBMED'); return false;" href="http://www.ncbi.nlm.nih.gov/pubmed/26600422"><span id="translatedtitle">Discrimination of Deciduous <span class="hlt">Tree</span> <span class="hlt">Species</span> from Time Series of Unmanned Aerial System Imagery.</span></a></p> <p><a target="_blank" href="https://www.ncbi.nlm.nih.gov/entrez/query.fcgi?DB=pubmed">PubMed</a></p> <p>Lisein, Jonathan; Michez, Adrien; Claessens, Hugues; Lejeune, Philippe</p> <p>2015-01-01</p> <p>Technology advances can revolutionize Precision Forestry by providing accurate and fine forest information at <span class="hlt">tree</span> level. This paper addresses the question of how and particularly when Unmanned Aerial System (UAS) should be used in order to efficiently discriminate deciduous <span class="hlt">tree</span> <span class="hlt">species</span>. The goal of this research is to determine when is the best time window to achieve an optimal <span class="hlt">species</span> discrimination. A time series of high resolution UAS imagery was collected to cover the growing season from leaf flush to leaf fall. Full benefit was taken of the temporal resolution of UAS acquisition, one of the most promising features of small drones. The disparity in forest <span class="hlt">tree</span> phenology is at the maximum during early spring and late autumn. But the phenology state that optimized the classification result is the one that minimizes the spectral variation within <span class="hlt">tree</span> <span class="hlt">species</span> groups and, at the same time, maximizes the phenologic differences between <span class="hlt">species</span>. Sunlit <span class="hlt">tree</span> crowns (5 deciduous <span class="hlt">species</span> groups) were classified using a Random Forest approach for monotemporal, two-date and three-date combinations. The end of leaf flushing was the most efficient single-date time window. Multitemporal datasets definitely improve the overall classification accuracy. But single-date high resolution orthophotomosaics, acquired on optimal time-windows, result in a very good classification accuracy (overall out of bag error of 16%). PMID:26600422</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=4604832','PMC'); return false;" href="http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=4604832"><span id="translatedtitle">PoMo: An Allele Frequency-Based Approach for <span class="hlt">Species</span> <span class="hlt">Tree</span> Estimation</span></a></p> <p><a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?DB=pmc">PubMed Central</a></p> <p>De Maio, Nicola; Schrempf, Dominik; Kosiol, Carolin</p> <p>2015-01-01</p> <p>Incomplete lineage sorting can cause incongruencies of the overall <span class="hlt">species</span>-level phylogenetic <span class="hlt">tree</span> with the phylogenetic <span class="hlt">trees</span> for individual genes or genomic segments. If these incongruencies are not accounted for, it is possible to incur several biases in <span class="hlt">species</span> <span class="hlt">tree</span> estimation. Here, we present a simple maximum likelihood approach that accounts for ancestral variation and incomplete lineage sorting. We use a POlymorphisms-aware phylogenetic MOdel (PoMo) that we have recently shown to efficiently estimate mutation rates and fixation biases from within and between-<span class="hlt">species</span> variation data. We extend this model to perform efficient estimation of <span class="hlt">species</span> <span class="hlt">trees</span>. We test the performance of PoMo in several different scenarios of incomplete lineage sorting using simulations and compare it with existing methods both in accuracy and computational speed. In contrast to other approaches, our model does not use coalescent theory but is allele frequency based. We show that PoMo is well suited for genome-wide <span class="hlt">species</span> <span class="hlt">tree</span> estimation and that on such data it is more accurate than previous approaches. PMID:26209413</p> </li> </ol> <div class="pull-right"> <ul class="pagination"> <li><a href="#" onclick='return showDiv("page_1");'>«</a></li> <li><a href="#" onclick='return showDiv("page_15");'>15</a></li> <li><a href="#" onclick='return showDiv("page_16");'>16</a></li> <li class="active"><span>17</span></li> <li><a href="#" onclick='return showDiv("page_18");'>18</a></li> <li><a href="#" onclick='return showDiv("page_19");'>19</a></li> <li><a href="#" onclick='return showDiv("page_25");'>»</a></li> </ul> </div> </div><!-- col-sm-12 --> </div><!-- row --> </div><!-- page_17 --> <div id="page_18" class="hiddenDiv"> <div class="row"> <div class="col-sm-12"> <div class="pull-right"> <ul class="pagination"> <li><a href="#" onclick='return showDiv("page_1");'>«</a></li> <li><a href="#" onclick='return showDiv("page_16");'>16</a></li> <li><a href="#" onclick='return showDiv("page_17");'>17</a></li> <li class="active"><span>18</span></li> <li><a href="#" onclick='return showDiv("page_19");'>19</a></li> <li><a href="#" onclick='return showDiv("page_20");'>20</a></li> <li><a href="#" onclick='return showDiv("page_25");'>»</a></li> </ul> </div> </div> </div> <div class="row"> <div class="col-sm-12"> <ol class="result-class" start="341"> <li> <p><a target="_blank" onclick="trackOutboundLink('http://www.ncbi.nlm.nih.gov/pubmed/21910838','PUBMED'); return false;" href="http://www.ncbi.nlm.nih.gov/pubmed/21910838"><span id="translatedtitle">Fruit availability, frugivore satiation and seed removal in 2 primate-dispersed <span class="hlt">tree</span> <span class="hlt">species</span>.</span></a></p> <p><a target="_blank" href="https://www.ncbi.nlm.nih.gov/entrez/query.fcgi?DB=pubmed">PubMed</a></p> <p>Ratiarison, Sandra; Forget, Pierre-Michel</p> <p>2011-09-01</p> <p>During a mast-fruiting event we investigated spatial variability in fruit availability, consumption, and seed removal at two sympatric <span class="hlt">tree</span> <span class="hlt">species</span>, Manilkara bidentata and M. huberi (Sapotaceae) at Nouragues Natural Reserve, French Guiana. We addressed the question of how Manilkara density and fruits at the community level might be major causes of variability in feeding assemblages between <span class="hlt">tree</span> <span class="hlt">species</span>. We thus explored how the frugivore assemblages differed between forest patches with contrasting relative Manilkara density and fruiting context. During the daytime, Alouatta seniculus was more often observed in M. huberi crowns at Petit Plateau (PP) with the greatest density of Manilkara spp. and the lowest fruit diversity and availability, whereas Cebus apella and Saguinus midas were more often observed in M. bidentata crowns at both Grand Plateau (GP), with a lowest density of M. bidentata and overall greater fruit supply, and PP. Overall, nearly 53% and 15% of the M. bidentata seed crop at GP and PP, respectively, and about 47% of the M. huberi seed crop were removed, otherwise either spit out or defecated beneath <span class="hlt">trees</span>, or dropped in fruits. Small-bodied primates concentrated fallen seeds beneath parent <span class="hlt">trees</span> while large-bodied primate <span class="hlt">species</span> removed and dispersed more seeds away from parents. However, among the latter, satiated A. seniculus wasted seeds under conspecific <span class="hlt">trees</span> at PP. Variations in feeding assemblages, seed removal rates and fates possibly reflected interactions with extra-generic fruit <span class="hlt">species</span> at the community level, according to feeding choice, habitat preferences and ranging patterns of primate <span class="hlt">species</span>. PMID:21910838</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=3335001','PMC'); return false;" href="http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=3335001"><span id="translatedtitle">Habitat Selection and Temporal <span class="hlt">Abundance</span> Fluctuations of Demersal Cartilaginous <span class="hlt">Species</span> in the Aegean Sea (Eastern Mediterranean)</span></a></p> <p><a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?DB=pmc">PubMed Central</a></p> <p>Maravelias, Christos D.; Tserpes, George; Pantazi, Maria; Peristeraki, Panagiota</p> <p>2012-01-01</p> <p>Predicting the occurrence of keystone top predators in a multispecies marine environment, such as the Mediterranean Sea, can be of considerable value to the long-term sustainable development of the fishing industry and to the protection of biodiversity. We analysed fisheries independent scientific bottom trawl survey data of two of the most <span class="hlt">abundant</span> cartilaginous fish <span class="hlt">species</span> (Scyliorhinus canicula, Raja clavata) in the Aegean Sea covering an 11-year sampling period. The current findings revealed a declining trend in R. clavata and S. canicula <span class="hlt">abundance</span> from the late ′90 s until 2004. Habitats with the higher probability of finding cartilaginous fish present were those located in intermediate waters (depth: 200–400 m). The present results also indicated a preferential <span class="hlt">species</span>' clustering in specific geographic and bathymetric regions of the Aegean Sea. Depth appeared to be one of the key determining factors for the selection of habitats for all <span class="hlt">species</span> examined. With cartilaginous fish <span class="hlt">species</span> being among the more biologically sensitive fish <span class="hlt">species</span> taken in European marine fisheries, our findings, which are based on a standardized scientific survey, can contribute to the rational exploitation and management of their stocks by providing important information on temporal <span class="hlt">abundance</span> trends and habitat preferences. PMID:22536389</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://adsabs.harvard.edu/cgi-bin/nph-data_query?bibcode=2007CorRe..26..895M&link_type=ABSTRACT','NASAADS'); return false;" href="http://adsabs.harvard.edu/cgi-bin/nph-data_query?bibcode=2007CorRe..26..895M&link_type=ABSTRACT"><span id="translatedtitle">Spatial predictability of juvenile fish <span class="hlt">species</span> richness and <span class="hlt">abundance</span> in a coral reef environment</span></a></p> <p><a target="_blank" href="http://adsabs.harvard.edu/abstract_service.html">NASA Astrophysics Data System (ADS)</a></p> <p>Mellin, C.; Andréfouët, S.; Ponton, D.</p> <p>2007-12-01</p> <p>Juvenile reef fish communities represent an essential component of coral reef ecosystems in the current focus of fish population dynamics and coral reef resilience. Juvenile fish survival depends on habitat characteristics and is, following settlement, the first determinant of the number of individuals within adult populations. The goal of this study was to provide methods for mapping juvenile fish <span class="hlt">species</span> richness and <span class="hlt">abundance</span> into spatial domains suitable for micro and meso-scale analysis and management decisions. Generalized Linear Models predicting juvenile fish <span class="hlt">species</span> richness and <span class="hlt">abundance</span> were developed according to spatial and temporal environmental variables measured from 10 m up to 10 km in the southwest lagoon of New Caledonia. The statistical model was further spatially generalized using a 1.5-m resolution, independently created, remotely sensed, habitat map. This procedure revealed that : (1) spatial factors at 10 to 100-m scale explained up to 71% of variability in juvenile <span class="hlt">species</span> richness, (2) a small improvement (75%) was gained when a combination of environmental variables at different spatial and temporal scales was used and (3) the coupling of remotely sensed data, geographical information system tools and point-based ecological data showed that the highest <span class="hlt">species</span> richness and <span class="hlt">abundance</span> were predicted along a narrow margin overlapping the coral reef flat and adjacent seagrass beds. Spatially explicit models of <span class="hlt">species</span> distribution may be relevant for the management of reef communities when strong relationships exist between faunistic and environmental variables and when models are built at appropriate scales.</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://www.ncbi.nlm.nih.gov/pubmed/16918900','PUBMED'); return false;" href="http://www.ncbi.nlm.nih.gov/pubmed/16918900"><span id="translatedtitle"><span class="hlt">Abundance</span>-based similarity indices and their estimation when there are unseen <span class="hlt">species</span> in samples.</span></a></p> <p><a target="_blank" href="https://www.ncbi.nlm.nih.gov/entrez/query.fcgi?DB=pubmed">PubMed</a></p> <p>Chao, Anne; Chazdon, Robin L; Colwell, Robert K; Shen, Tsung-Jen</p> <p>2006-06-01</p> <p>A wide variety of similarity indices for comparing two assemblages based on <span class="hlt">species</span> incidence (i.e., presence/absence) data have been proposed in the literature. These indices are generally based on three simple incidence counts: the number of <span class="hlt">species</span> shared by two assemblages and the number of <span class="hlt">species</span> unique to each of them. We provide a new probabilistic derivation for any incidence-based index that is symmetric (i.e., the index is not affected by the identity ordering of the two assemblages) and homogeneous (i.e., the index is unchanged if all counts are multiplied by a constant). The probabilistic approach is further extended to formulate <span class="hlt">abundance</span>-based indices. Thus any symmetric and homogeneous incidence index can be easily modified to an <span class="hlt">abundance</span>-type version. Applying the Laplace approximation formulas, we propose estimators that adjust for the effect of unseen shared <span class="hlt">species</span> on our <span class="hlt">abundance</span>-based indices. Simulation results show that the adjusted estimators significantly reduce the biases of the corresponding unadjusted ones when a substantial fraction of <span class="hlt">species</span> is missing from samples. Data on successional vegetation in six tropical forests are used for illustration. Advantages and disadvantages of some commonly applied indices are briefly discussed. PMID:16918900</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://www.treesearch.fs.fed.us/pubs/4893','USGSPUBS'); return false;" href="http://www.treesearch.fs.fed.us/pubs/4893"><span id="translatedtitle">Supplemental planting of early successional <span class="hlt">tree</span> <span class="hlt">species</span> during bottomland hardwood afforestation</span></a></p> <p><a target="_blank" href="http://pubs.er.usgs.gov/pubs/index.jsp?view=adv">USGS Publications Warehouse</a></p> <p>Twedt, D.J.; Wilson, R.R.</p> <p>2002-01-01</p> <p>Reforestation of former bottom land hardwood forests that have been cleared for agriculture (i.e., afforestation) has historically emphasized planting heavy-seeded oaks (Quercus spp.) and pecans (Carya spp.). These <span class="hlt">species</span> are slow to develop vertical forest structure. However, vertical forest structure is key to colonization of afforested sites by forest birds. Although early-successional <span class="hlt">tree</span> <span class="hlt">species</span> often enhance vertical structure, few of these <span class="hlt">species</span> invade afforested sites that are distant from seed sources. Furthermore, many land mangers are reluctant to establish and maintain stands of fast-growing plantation <span class="hlt">trees</span>. Therefore, on 40 afforested bottomland sites, we supplemented heavy-seeded seedlings with 8 patches of fast-growing <span class="hlt">trees</span>: 4 patches of 12 eastern cottonwood (Populus deltoides) stem cuttings and 4 patches of 12 American sycamore (Platanus occidentalis) seedlings. To enhance survival and growth, <span class="hlt">tree</span> patches were subjected to 4 weed control treatments: (1) physical weed barriers, (2) chemical herbicide, (3) both physical and chemical weed control, or (4) no weed control. Overall, first-year survival of cottonwood and sycamore was 25 percent and 47 percent, respectively. Second-year survival of extant <span class="hlt">trees</span> was 52 percent for cottonwood and 77 percent for sycamore. Physical weed barriers increased survival of cottonwoods to 30 percent versus 18 percent survival with no weed control. Similarly, sycamore survival was increased from 49 percent without weed control to 64 percent with physical weed barriers. Chemical weed control adversely impacted sycamore and reduced survival to 35 percent. <span class="hlt">Tree</span> heights did not differ between <span class="hlt">species</span> or among weed control treatments. Girdling of <span class="hlt">trees</span> by deer often destroyed saplings. Thus, little increase in vertical structure was detected between growing seasons. Application of fertilizer and protection via <span class="hlt">tree</span> shelters did not improve survival or vertical development of sycamore or cottonwood.</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=3615238','PMC'); return false;" href="http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=3615238"><span id="translatedtitle"><span class="hlt">Abundance</span> of biting midge <span class="hlt">species</span> (Diptera: Ceratopogonidae, Culicoides spp.) on cattle farms in Korea</span></a></p> <p><a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?DB=pmc">PubMed Central</a></p> <p>Oem, Jae-Ku; Chung, Joon-Yee; Kwon, Mee-Soon; Kim, Toh-Kyung; Lee, Tae-Uk</p> <p>2013-01-01</p> <p>Culicoides biting midges were collected on three cattle farms weekly using light traps overnight from May to October between 2010 and 2011 in the southern part of Korea. The seasonal and geographical <span class="hlt">abundance</span> of Culicodes spp. were measured. A total of 16,538 biting midges were collected from 2010 to 2011, including seven <span class="hlt">species</span> of Culicoides, four of which represented 98.42% of the collected specimens. These four <span class="hlt">species</span> were Culicodes (C.) punctatus (n = 14,413), C. arakawae (n = 1,120), C. oxystoma (n = 427), and C. maculatus (n = 318). C. punctatus was the predominant <span class="hlt">species</span> (87.15%). PMID:23388441</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=1461003','PMC'); return false;" href="http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=1461003"><span id="translatedtitle">Effects of colonization processes on genetic diversity: differences between annual plants and <span class="hlt">tree</span> <span class="hlt">species</span>.</span></a></p> <p><a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?DB=pmc">PubMed Central</a></p> <p>Austerlitz, F; Mariette, S; Machon, N; Gouyon, P H; Godelle, B</p> <p>2000-01-01</p> <p><span class="hlt">Tree</span> <span class="hlt">species</span> are striking for their high within-population diversity and low among-population differentiation for nuclear genes. In contrast, annual plants show much more differentiation for nuclear genes but much less diversity than <span class="hlt">trees</span>. The usual explanation for this difference is that pollen flow, and therefore gene flow, is much higher for <span class="hlt">trees</span>. This explanation is problematic because it relies on equilibrium hypotheses. Because <span class="hlt">trees</span> have very recently recolonized temperate areas, they have experienced many foundation events, which usually reduce within-population diversity and increase differentiation. Only extremely high levels of gene flow could counterbalance these successive founder effects. We develop a model to study the impact of life cycle of forest <span class="hlt">trees</span>, in particular of the length of their juvenile phase, on genetic diversity and differentiation during the glacial period and the following colonization period. We show that both a reasonably high level of pollen flow and the life-cycle characteristics of <span class="hlt">trees</span> are needed to explain the observed structure of genetic diversity. We also show that gene flow and life cycle both have an impact on maternally inherited cytoplasmic genes, which are characterized both in <span class="hlt">trees</span> and annual <span class="hlt">species</span> by much less diversity and much more differentiation than nuclear genes. PMID:10757772</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://www.ncbi.nlm.nih.gov/pubmed/26153693','PUBMED'); return false;" href="http://www.ncbi.nlm.nih.gov/pubmed/26153693"><span id="translatedtitle">Operational <span class="hlt">Tree</span> <span class="hlt">Species</span> Mapping in a Diverse Tropical Forest with Airborne Imaging Spectroscopy.</span></a></p> <p><a target="_blank" href="https://www.ncbi.nlm.nih.gov/entrez/query.fcgi?DB=pubmed">PubMed</a></p> <p>Baldeck, Claire A; Asner, Gregory P; Martin, Robin E; Anderson, Christopher B; Knapp, David E; Kellner, James R; Wright, S Joseph</p> <p>2015-01-01</p> <p>Remote identification and mapping of canopy <span class="hlt">tree</span> <span class="hlt">species</span> can contribute valuable information towards our understanding of ecosystem biodiversity and function over large spatial scales. However, the extreme challenges posed by highly diverse, closed-canopy tropical forests have prevented automated remote <span class="hlt">species</span> mapping of non-flowering <span class="hlt">tree</span> crowns in these ecosystems. We set out to identify individuals of three focal canopy <span class="hlt">tree</span> <span class="hlt">species</span> amongst a diverse background of <span class="hlt">tree</span> and liana <span class="hlt">species</span> on Barro Colorado Island, Panama, using airborne imaging spectroscopy data. First, we compared two leading single-class classification methods--binary support vector machine (SVM) and biased SVM--for their performance in identifying pixels of a single focal <span class="hlt">species</span>. From this comparison we determined that biased SVM was more precise and created a multi-<span class="hlt">species</span> classification model by combining the three biased SVM models. This model was applied to the imagery to identify pixels belonging to the three focal <span class="hlt">species</span> and the prediction results were then processed to create a map of focal <span class="hlt">species</span> crown objects. Crown-level cross-validation of the training data indicated that the multi-<span class="hlt">species</span> classification model had pixel-level producer's accuracies of 94-97% for the three focal <span class="hlt">species</span>, and field validation of the predicted crown objects indicated that these had user's accuracies of 94-100%. Our results demonstrate the ability of high spatial and spectral resolution remote sensing to accurately detect non-flowering crowns of focal <span class="hlt">species</span> within a diverse tropical forest. We attribute the success of our model to recent classification and mapping techniques adapted to <span class="hlt">species</span> detection in diverse closed-canopy forests, which can pave the way for remote <span class="hlt">species</span> mapping in a wider variety of ecosystems. PMID:26153693</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=4496029','PMC'); return false;" href="http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=4496029"><span id="translatedtitle">Operational <span class="hlt">Tree</span> <span class="hlt">Species</span> Mapping in a Diverse Tropical Forest with Airborne Imaging Spectroscopy</span></a></p> <p><a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?DB=pmc">PubMed Central</a></p> <p>Baldeck, Claire A.; Asner, Gregory P.; Martin, Robin E.; Anderson, Christopher B.; Knapp, David E.; Kellner, James R.; Wright, S. Joseph</p> <p>2015-01-01</p> <p>Remote identification and mapping of canopy <span class="hlt">tree</span> <span class="hlt">species</span> can contribute valuable information towards our understanding of ecosystem biodiversity and function over large spatial scales. However, the extreme challenges posed by highly diverse, closed-canopy tropical forests have prevented automated remote <span class="hlt">species</span> mapping of non-flowering <span class="hlt">tree</span> crowns in these ecosystems. We set out to identify individuals of three focal canopy <span class="hlt">tree</span> <span class="hlt">species</span> amongst a diverse background of <span class="hlt">tree</span> and liana <span class="hlt">species</span> on Barro Colorado Island, Panama, using airborne imaging spectroscopy data. First, we compared two leading single-class classification methods—binary support vector machine (SVM) and biased SVM—for their performance in identifying pixels of a single focal <span class="hlt">species</span>. From this comparison we determined that biased SVM was more precise and created a multi-<span class="hlt">species</span> classification model by combining the three biased SVM models. This model was applied to the imagery to identify pixels belonging to the three focal <span class="hlt">species</span> and the prediction results were then processed to create a map of focal <span class="hlt">species</span> crown objects. Crown-level cross-validation of the training data indicated that the multi-<span class="hlt">species</span> classification model had pixel-level producer’s accuracies of 94–97% for the three focal <span class="hlt">species</span>, and field validation of the predicted crown objects indicated that these had user’s accuracies of 94–100%. Our results demonstrate the ability of high spatial and spectral resolution remote sensing to accurately detect non-flowering crowns of focal <span class="hlt">species</span> within a diverse tropical forest. We attribute the success of our model to recent classification and mapping techniques adapted to <span class="hlt">species</span> detection in diverse closed-canopy forests, which can pave the way for remote <span class="hlt">species</span> mapping in a wider variety of ecosystems. PMID:26153693</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://www.ncbi.nlm.nih.gov/pubmed/26142389','PUBMED'); return false;" href="http://www.ncbi.nlm.nih.gov/pubmed/26142389"><span id="translatedtitle">Methanotrophic community <span class="hlt">abundance</span> and composition in plateau soils with different plant <span class="hlt">species</span> and plantation ways.</span></a></p> <p><a target="_blank" href="https://www.ncbi.nlm.nih.gov/entrez/query.fcgi?DB=pubmed">PubMed</a></p> <p>Dai, Yu; Wu, Zhen; Xie, Shuguang; Liu, Yong</p> <p>2015-11-01</p> <p>Aerobic methane-oxidizing bacteria (MOB) play an important role in mitigating the methane emission in soil ecosystems to the atmosphere. However, the impact of plant <span class="hlt">species</span> and plantation ways on the distribution of MOB remains unclear. The present study investigated MOB <span class="hlt">abundance</span> and structure in plateau soils with different plant <span class="hlt">species</span> and plantation ways (natural and managed). Soils were collected from unmanaged wild grassland and naturally forested sites, and managed farmland and afforested sites. A large variation in MOB <span class="hlt">abundance</span> and structure was found in these studied soils. In addition, both type I MOB (Methylocaldum) and type II MOB (Methylocystis) were detected in these soils, while type II MOB usually outnumbered type I MOB. The distribution of soil MOB community was found to be collectively regulated by plantation way, plant <span class="hlt">species</span>, the altitude of sampling site, and soil properties. PMID:26142389</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://pubs.er.usgs.gov/publication/70041741','USGSPUBS'); return false;" href="http://pubs.er.usgs.gov/publication/70041741"><span id="translatedtitle">Quantifying <span class="hlt">tree</span> mortality in a mixed <span class="hlt">species</span> woodland using multitemporal high spatial resolution satellite imagery</span></a></p> <p><a target="_blank" href="http://pubs.er.usgs.gov/pubs/index.jsp?view=adv">USGS Publications Warehouse</a></p> <p>Garrity, Steven R.; Allen, Craig D.; Brumby, Steven P.; Gangodagamage, Chandana; McDowell, Nate G.; Cai, D. Michael</p> <p>2013-01-01</p> <p>Widespread <span class="hlt">tree</span> mortality events have recently been observed in several biomes. To effectively quantify the severity and extent of these events, tools that allow for rapid assessment at the landscape scale are required. Past studies using high spatial resolution satellite imagery have primarily focused on detecting green, red, and gray <span class="hlt">tree</span> canopies during and shortly after <span class="hlt">tree</span> damage or mortality has occurred. However, detecting <span class="hlt">trees</span> in various stages of death is not always possible due to limited availability of archived satellite imagery. Here we assess the capability of high spatial resolution satellite imagery for <span class="hlt">tree</span> mortality detection in a southwestern U.S. mixed <span class="hlt">species</span> woodland using archived satellite images acquired prior to mortality and well after dead <span class="hlt">trees</span> had dropped their leaves. We developed a multistep classification approach that uses: supervised masking of non-<span class="hlt">tree</span> image elements; bi-temporal (pre- and post-mortality) differencing of normalized difference vegetation index (NDVI) and red:green ratio (RGI); and unsupervised multivariate clustering of pixels into live and dead <span class="hlt">tree</span> classes using a Gaussian mixture model. Classification accuracies were improved in a final step by tuning the rules of pixel classification using the posterior probabilities of class membership obtained from the Gaussian mixture model. Classifications were produced for two images acquired post-mortality with overall accuracies of 97.9% and 98.5%, respectively. Classified images were combined with land cover data to characterize the spatiotemporal characteristics of <span class="hlt">tree</span> mortality across areas with differences in <span class="hlt">tree</span> <span class="hlt">species</span> composition. We found that 38% of <span class="hlt">tree</span> crown area was lost during the drought period between 2002 and 2006. The majority of <span class="hlt">tree</span> mortality during this period was concentrated in piñon-juniper (Pinus edulis-Juniperus monosperma) woodlands. An additional 20% of the <span class="hlt">tree</span> canopy died or was removed between 2006 and 2011, primarily in areas</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=4457889','PMC'); return false;" href="http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=4457889"><span id="translatedtitle">Historic Mining and Agriculture as Indicators of Occurrence and <span class="hlt">Abundance</span> of Widespread Invasive Plant <span class="hlt">Species</span></span></a></p> <p><a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?DB=pmc">PubMed Central</a></p> <p>Calinger, Kellen; Calhoon, Elisabeth; Chang, Hsiao-chi; Whitacre, James; Wenzel, John; Comita, Liza; Queenborough, Simon</p> <p>2015-01-01</p> <p>Anthropogenic disturbances often change ecological communities and provide opportunities for non-native <span class="hlt">species</span> invasion. Understanding the impacts of disturbances on <span class="hlt">species</span> invasion is therefore crucial for invasive <span class="hlt">species</span> management. We used generalized linear mixed effects models to explore the influence of land-use history and distance to roads on the occurrence and <span class="hlt">abundance</span> of two invasive plant <span class="hlt">species</span> (Rosa multiflora and Berberis thunbergii) in a 900-ha deciduous forest in the eastern U.S.A., the Powdermill Nature Reserve. Although much of the reserve has been continuously forested since at least 1939, aerial photos revealed a variety of land-uses since then including agriculture, mining, logging, and development. By 2008, both R. multiflora and B. thunbergii were widespread throughout the reserve (occurring in 24% and 13% of 4417 10-m diameter regularly-placed vegetation plots, respectively) with occurrence and <span class="hlt">abundance</span> of each varying significantly with land-use history. Rosa multiflora was more likely to occur in historically farmed, mined, logged or developed plots than in plots that remained forested, (log odds of 1.8 to 3.0); Berberis thunbergii was more likely to occur in plots with agricultural, mining, or logging history than in plots without disturbance (log odds of 1.4 to 2.1). Mining, logging, and agriculture increased the probability that R. multiflora had >10% cover while only past agriculture was related to cover of B. thunbergii. Proximity to roads was positively correlated with the occurrence of R. multiflora (a 0.26 increase in the log odds for every 1-m closer) but not B. thunbergii, and roads had no impact on the <span class="hlt">abundance</span> of either <span class="hlt">species</span>. Our results indicated that a wide variety of disturbances may aid the introduction of invasive <span class="hlt">species</span> into new habitats, while high-impact disturbances such as agriculture and mining increase the likelihood of high <span class="hlt">abundance</span> post-introduction. PMID:26046534</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://www.ncbi.nlm.nih.gov/pubmed/26046534','PUBMED'); return false;" href="http://www.ncbi.nlm.nih.gov/pubmed/26046534"><span id="translatedtitle">Historic Mining and Agriculture as Indicators of Occurrence and <span class="hlt">Abundance</span> of Widespread Invasive Plant <span class="hlt">Species</span>.</span></a></p> <p><a target="_blank" href="https://www.ncbi.nlm.nih.gov/entrez/query.fcgi?DB=pubmed">PubMed</a></p> <p>Calinger, Kellen; Calhoon, Elisabeth; Chang, Hsiao-Chi; Whitacre, James; Wenzel, John; Comita, Liza; Queenborough, Simon</p> <p>2015-01-01</p> <p>Anthropogenic disturbances often change ecological communities and provide opportunities for non-native <span class="hlt">species</span> invasion. Understanding the impacts of disturbances on <span class="hlt">species</span> invasion is therefore crucial for invasive <span class="hlt">species</span> management. We used generalized linear mixed effects models to explore the influence of land-use history and distance to roads on the occurrence and <span class="hlt">abundance</span> of two invasive plant <span class="hlt">species</span> (Rosa multiflora and Berberis thunbergii) in a 900-ha deciduous forest in the eastern U.S.A., the Powdermill Nature Reserve. Although much of the reserve has been continuously forested since at least 1939, aerial photos revealed a variety of land-uses since then including agriculture, mining, logging, and development. By 2008, both R. multiflora and B. thunbergii were widespread throughout the reserve (occurring in 24% and 13% of 4417 10-m diameter regularly-placed vegetation plots, respectively) with occurrence and <span class="hlt">abundance</span> of each varying significantly with land-use history. Rosa multiflora was more likely to occur in historically farmed, mined, logged or developed plots than in plots that remained forested, (log odds of 1.8 to 3.0); Berberis thunbergii was more likely to occur in plots with agricultural, mining, or logging history than in plots without disturbance (log odds of 1.4 to 2.1). Mining, logging, and agriculture increased the probability that R. multiflora had >10% cover while only past agriculture was related to cover of B. thunbergii. Proximity to roads was positively correlated with the occurrence of R. multiflora (a 0.26 increase in the log odds for every 1-m closer) but not B. thunbergii, and roads had no impact on the <span class="hlt">abundance</span> of either <span class="hlt">species</span>. Our results indicated that a wide variety of disturbances may aid the introduction of invasive <span class="hlt">species</span> into new habitats, while high-impact disturbances such as agriculture and mining increase the likelihood of high <span class="hlt">abundance</span> post-introduction. PMID:26046534</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://www.ncbi.nlm.nih.gov/pubmed/19880241','PUBMED'); return false;" href="http://www.ncbi.nlm.nih.gov/pubmed/19880241"><span id="translatedtitle">Estimating <span class="hlt">tree</span> bole volume using artificial neural network models for four <span class="hlt">species</span> in Turkey.</span></a></p> <p><a target="_blank" href="https://www.ncbi.nlm.nih.gov/entrez/query.fcgi?DB=pubmed">PubMed</a></p> <p>Ozçelik, Ramazan; Diamantopoulou, Maria J; Brooks, John R; Wiant, Harry V</p> <p>2010-01-01</p> <p><span class="hlt">Tree</span> bole volumes of 89 Scots pine (Pinus sylvestris L.), 96 Brutian pine (Pinus brutia Ten.), 107 Cilicica fir (Abies cilicica Carr.) and 67 Cedar of Lebanon (Cedrus libani A. Rich.) <span class="hlt">trees</span> were estimated using Artificial Neural Network (ANN) models. Neural networks offer a number of advantages including the ability to implicitly detect complex nonlinear relationships between input and output variables, which is very helpful in <span class="hlt">tree</span> volume modeling. Two different neural network architectures were used and produced the Back propagation (BPANN) and the Cascade Correlation (CCANN) Artificial Neural Network models. In addition, <span class="hlt">tree</span> bole volume estimates were compared to other established <span class="hlt">tree</span> bole volume estimation techniques including the centroid method, taper equations, and existing standard volume tables. An overview of the features of ANNs and traditional methods is presented and the advantages and limitations of each one of them are discussed. For validation purposes, actual volumes were determined by aggregating the volumes of measured short sections (average 1 meter) of the <span class="hlt">tree</span> bole using Smalian's formula. The results reported in this research suggest that the selected cascade correlation artificial neural network (CCANN) models are reliable for estimating the <span class="hlt">tree</span> bole volume of the four examined <span class="hlt">tree</span> <span class="hlt">species</span> since they gave unbiased results and were superior to almost all methods in terms of error (%) expressed as the mean of the percentage errors. PMID:19880241</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://adsabs.harvard.edu/abs/2015ISPAnII22..175M','NASAADS'); return false;" href="http://adsabs.harvard.edu/abs/2015ISPAnII22..175M"><span id="translatedtitle">Identification and Mapping of <span class="hlt">Tree</span> <span class="hlt">Species</span> in Urban Areas Using WORLDVIEW-2 Imagery</span></a></p> <p><a target="_blank" href="http://adsabs.harvard.edu/abstract_service.html">NASA Astrophysics Data System (ADS)</a></p> <p>Mustafa, Y. T.; Habeeb, H. N.; Stein, A.; Sulaiman, F. Y.</p> <p>2015-10-01</p> <p>Monitoring and mapping of urban <span class="hlt">trees</span> are essential to provide urban forestry authorities with timely and consistent information. Modern techniques increasingly facilitate these tasks, but require the development of semi-automatic <span class="hlt">tree</span> detection and classification methods. In this article, we propose an approach to delineate and map the crown of 15 <span class="hlt">tree</span> <span class="hlt">species</span> in the city of Duhok, Kurdistan Region of Iraq using WorldView-2 (WV-2) imagery. A <span class="hlt">tree</span> crown object is identified first and is subsequently delineated as an image object (IO) using vegetation indices and texture measurements. Next, three classification methods: Maximum Likelihood, Neural Network, and Support Vector Machine were used to classify IOs using selected IO features. The best results are obtained with Support Vector Machine classification that gives the best map of urban <span class="hlt">tree</span> <span class="hlt">species</span> in Duhok. The overall accuracy was between 60.93% to 88.92% and κ-coefficient was between 0.57 to 0.75. We conclude that fifteen <span class="hlt">tree</span> <span class="hlt">species</span> were identified and mapped at a satisfactory accuracy in urban areas of this study.</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://adsabs.harvard.edu/cgi-bin/nph-data_query?bibcode=2008ECSS...78..739I&link_type=ABSTRACT','NASAADS'); return false;" href="http://adsabs.harvard.edu/cgi-bin/nph-data_query?bibcode=2008ECSS...78..739I&link_type=ABSTRACT"><span id="translatedtitle">Annual cycle of zooplankton <span class="hlt">abundance</span> and <span class="hlt">species</span> composition in Izmit Bay (the northeastern Marmara Sea)</span></a></p> <p><a target="_blank" href="http://adsabs.harvard.edu/abstract_service.html">NASA Astrophysics Data System (ADS)</a></p> <p>Isinibilir, Melek; Kideys, Ahmet E.; Tarkan, Ahmet N.; Yilmaz, I. Noyan</p> <p>2008-07-01</p> <p>The monthly <span class="hlt">abundance</span>, biomass and taxonomic composition of zooplankton of Izmit Bay (the northeastern Marmara Sea) were studied from October 2001 to September 2002. Most <span class="hlt">species</span> within the zooplankton community displayed a clear pattern of succession throughout the year. Generally copepods and cladocerans were the most <span class="hlt">abundant</span> groups, while the contribution of meroplankton increased at inner-most stations and dominated the zooplankton. Both <span class="hlt">species</span> number ( S) and diversity ( H') were positively influenced by the increase in salinity of upper layers ( r = 0.30 and r = 0.31, p < 0.001, respectively), while chlorophyll a was negatively affected ( r = -0.36, p < 0.001). Even though Noctiluca scintillans had a significant seasonality ( F11,120 = 8.45, p < 0.001, ANOVA), <span class="hlt">abundance</span> was not related to fluctuations in temperature and only chlorophyll a was adversely correlated ( r = -0.35, p < 0.001). In general, there are some minor differences in zooplankton assemblages of upper and lower layers. A comparison of the <span class="hlt">species</span> composition and <span class="hlt">abundance</span> of Izmit Bay with other Black Sea bays reveals a high similarity between them.</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://www.ncbi.nlm.nih.gov/pubmed/24587050','PUBMED'); return false;" href="http://www.ncbi.nlm.nih.gov/pubmed/24587050"><span id="translatedtitle">An empirical assessment and comparison of <span class="hlt">species</span>-based and habitat-based surrogates: a case study of forest vertebrates and large old <span class="hlt">trees</span>.</span></a></p> <p><a target="_blank" href="https://www.ncbi.nlm.nih.gov/entrez/query.fcgi?DB=pubmed">PubMed</a></p> <p>Lindenmayer, David B; Barton, Philip S; Lane, Peter W; Westgate, Martin J; McBurney, Lachlan; Blair, David; Gibbons, Philip; Likens, Gene E</p> <p>2014-01-01</p> <p>A holy grail of conservation is to find simple but reliable measures of environmental change to guide management. For example, particular <span class="hlt">species</span> or particular habitat attributes are often used as proxies for the <span class="hlt">abundance</span> or diversity of a subset of other taxa. However, the efficacy of such kinds of <span class="hlt">species</span>-based surrogates and habitat-based surrogates is rarely assessed, nor are different kinds of surrogates compared in terms of their relative effectiveness. We use 30-year datasets on arboreal marsupials and vegetation structure to quantify the effectiveness of: (1) the <span class="hlt">abundance</span> of a particular <span class="hlt">species</span> of arboreal marsupial as a <span class="hlt">species</span>-based surrogate for other arboreal marsupial taxa, (2) hollow-bearing <span class="hlt">tree</span> <span class="hlt">abundance</span> as a habitat-based surrogate for arboreal marsupial <span class="hlt">abundance</span>, and (3) a combination of <span class="hlt">species</span>- and habitat-based surrogates. We also quantify the robustness of <span class="hlt">species</span>-based and habitat-based surrogates over time. We then use the same approach to model overall <span class="hlt">species</span> richness of arboreal marsupials. We show that a <span class="hlt">species</span>-based surrogate can appear to be a valid surrogate until a habitat-based surrogate is co-examined, after which the effectiveness of the former is lost. The addition of a <span class="hlt">species</span>-based surrogate to a habitat-based surrogate made little difference in explaining arboreal marsupial <span class="hlt">abundance</span>, but altered the co-occurrence relationship between <span class="hlt">species</span>. Hence, there was limited value in simultaneously using a combination of kinds of surrogates. The habitat-based surrogate also generally performed significantly better and was easier and less costly to gather than the <span class="hlt">species</span>-based surrogate. We found that over 30 years of study, the relationships which underpinned the habitat-based surrogate generally remained positive but variable over time. Our work highlights why it is important to compare the effectiveness of different broad classes of surrogates and identify situations when either <span class="hlt">species</span>- or habitat-based surrogates are likely</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=3933686','PMC'); return false;" href="http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=3933686"><span id="translatedtitle">An Empirical Assessment and Comparison of <span class="hlt">Species</span>-Based and Habitat-Based Surrogates: A Case Study of Forest Vertebrates and Large Old <span class="hlt">Trees</span></span></a></p> <p><a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?DB=pmc">PubMed Central</a></p> <p>Lindenmayer, David B.; Barton, Philip S.; Lane, Peter W.; Westgate, Martin J.; McBurney, Lachlan; Blair, David; Gibbons, Philip; Likens, Gene E.</p> <p>2014-01-01</p> <p>A holy grail of conservation is to find simple but reliable measures of environmental change to guide management. For example, particular <span class="hlt">species</span> or particular habitat attributes are often used as proxies for the <span class="hlt">abundance</span> or diversity of a subset of other taxa. However, the efficacy of such kinds of <span class="hlt">species</span>-based surrogates and habitat-based surrogates is rarely assessed, nor are different kinds of surrogates compared in terms of their relative effectiveness. We use 30-year datasets on arboreal marsupials and vegetation structure to quantify the effectiveness of: (1) the <span class="hlt">abundance</span> of a particular <span class="hlt">species</span> of arboreal marsupial as a <span class="hlt">species</span>-based surrogate for other arboreal marsupial taxa, (2) hollow-bearing <span class="hlt">tree</span> <span class="hlt">abundance</span> as a habitat-based surrogate for arboreal marsupial <span class="hlt">abundance</span>, and (3) a combination of <span class="hlt">species</span>- and habitat-based surrogates. We also quantify the robustness of <span class="hlt">species</span>-based and habitat-based surrogates over time. We then use the same approach to model overall <span class="hlt">species</span> richness of arboreal marsupials. We show that a <span class="hlt">species</span>-based surrogate can appear to be a valid surrogate until a habitat-based surrogate is co-examined, after which the effectiveness of the former is lost. The addition of a <span class="hlt">species</span>-based surrogate to a habitat-based surrogate made little difference in explaining arboreal marsupial <span class="hlt">abundance</span>, but altered the co-occurrence relationship between <span class="hlt">species</span>. Hence, there was limited value in simultaneously using a combination of kinds of surrogates. The habitat-based surrogate also generally performed significantly better and was easier and less costly to gather than the <span class="hlt">species</span>-based surrogate. We found that over 30 years of study, the relationships which underpinned the habitat-based surrogate generally remained positive but variable over time. Our work highlights why it is important to compare the effectiveness of different broad classes of surrogates and identify situations when either <span class="hlt">species</span>- or habitat-based surrogates are likely</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=4906758','PMC'); return false;" href="http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=4906758"><span id="translatedtitle"><span class="hlt">Species</span> <span class="hlt">Abundance</span> Distribution of Ectoparasites on Norway Rats (Rattus norvegicus) from a Localized Area in Southwest China</span></a></p> <p><a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?DB=pmc">PubMed Central</a></p> <p>Guo, Xian Guo; Dong, Wen Ge; Men, Xing Yuan; Qian, Ti Jun; Wu, Dian; Ren, Tian Guang; Qin, Feng; Song, Wen Yu; Yang, Zhi Hua; Fletcher, Quinn E</p> <p>2016-01-01</p> <p>Background: The <span class="hlt">species</span> of ectoparasites that live on a specific host in a geographical region form an ectoparasite community. <span class="hlt">Species</span> <span class="hlt">abundance</span> distributions describe the number of individuals observed for each different <span class="hlt">species</span> that is encountered within a community. Based on properties of the <span class="hlt">species</span> <span class="hlt">abundance</span> distribution, the expected total number of <span class="hlt">species</span> present in the community can be estimated. Methods: Preston’s lognormal distribution model was used to fit the expected <span class="hlt">species</span> <span class="hlt">abundance</span> distribution curve. Using the expected <span class="hlt">species</span> <span class="hlt">abundance</span> distribution curve, we estimated the total number of expected parasite <span class="hlt">species</span> present and the amount of <span class="hlt">species</span> that were likely missed by our sampling in the field. Results: In total, 8040 ectoparasites (fleas, sucking lice, gamasid mites and chigger mites) were collected from 431 Norway rats (Rattus norvegicus) from a localized area in southwest China. These ectoparasites were identified to be 47 <span class="hlt">species</span> from 26 genera in 10 families. The majority of ectoparasite <span class="hlt">species</span> were chigger mites (family Trombiculidae) while the majority of individuals were sucking lice in the family Polyplacidae. The expected <span class="hlt">species</span> <span class="hlt">abundance</span> distribution curve demonstrated the classic pattern that the majority of ectoparasite <span class="hlt">species</span> were rare and that there were a few common <span class="hlt">species</span>. The total expected number of ectoparasite <span class="hlt">species</span> on R. norvegicus was estimated to be 85 <span class="hlt">species</span>, and 38 <span class="hlt">species</span> were likely missed by our sampling in the field. Conclusions: Norway rats harbor a large suite of ectoparasites. Future field investigations should sample large numbers of host individuals to assess ectoparasite populations. PMID:27308277</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://files.eric.ed.gov/fulltext/EJ1099325.pdf','ERIC'); return false;" href="http://files.eric.ed.gov/fulltext/EJ1099325.pdf"><span id="translatedtitle"><span class="hlt">Trees</span></span></a></p> <p><a target="_blank" href="http://www.eric.ed.gov/ERICWebPortal/search/extended.jsp?_pageLabel=advanced">ERIC Educational Resources Information Center</a></p> <p>Al-Khaja, Nawal</p> <p>2007-01-01</p> <p>This is a thematic lesson plan for young learners about palm <span class="hlt">trees</span> and the importance of taking care of them. The two part lesson teaches listening, reading and speaking skills. The lesson includes parts of a <span class="hlt">tree</span>; the modal auxiliary, can; dialogues and a role play activity.</p> </li> </ol> <div class="pull-right"> <ul class="pagination"> <li><a href="#" onclick='return showDiv("page_1");'>«</a></li> <li><a href="#" onclick='return showDiv("page_16");'>16</a></li> <li><a href="#" onclick='return showDiv("page_17");'>17</a></li> <li class="active"><span>18</span></li> <li><a href="#" onclick='return showDiv("page_19");'>19</a></li> <li><a href="#" onclick='return showDiv("page_20");'>20</a></li> <li><a href="#" onclick='return showDiv("page_25");'>»</a></li> </ul> </div> </div><!-- col-sm-12 --> </div><!-- row --> </div><!-- page_18 --> <div id="page_19" class="hiddenDiv"> <div class="row"> <div class="col-sm-12"> <div class="pull-right"> <ul class="pagination"> <li><a href="#" onclick='return showDiv("page_1");'>«</a></li> <li><a href="#" onclick='return showDiv("page_17");'>17</a></li> <li><a href="#" onclick='return showDiv("page_18");'>18</a></li> <li class="active"><span>19</span></li> <li><a href="#" onclick='return showDiv("page_20");'>20</a></li> <li><a href="#" onclick='return showDiv("page_21");'>21</a></li> <li><a href="#" onclick='return showDiv("page_25");'>»</a></li> </ul> </div> </div> </div> <div class="row"> <div class="col-sm-12"> <ol class="result-class" start="361"> <li> <p><a target="_blank" onclick="trackOutboundLink('http://adsabs.harvard.edu/abs/2012EGUGA..14.9592I','NASAADS'); return false;" href="http://adsabs.harvard.edu/abs/2012EGUGA..14.9592I"><span id="translatedtitle">The response of European <span class="hlt">tree</span> <span class="hlt">species</span> to drought: a meta-analysis</span></a></p> <p><a target="_blank" href="http://adsabs.harvard.edu/abstract_service.html">NASA Astrophysics Data System (ADS)</a></p> <p>Irschick, C.; Mayr, S.; Wohlfahrt, G.</p> <p>2012-04-01</p> <p>Here we provide first results of a meta-analysis of the response of European <span class="hlt">tree</span> <span class="hlt">species</span> to drought. A literature search was conducted in order to collect available studies of the response of the gas exchange of European <span class="hlt">tree</span> <span class="hlt">species</span> to either natural or imposed water shortage. The resulting publications were screened and parameters at organ (e.g. leaf or shoot), individual (i.e. <span class="hlt">tree</span>) and ecosystem scale were transferred to a data base. Here we present preliminary results from queries of the data base aiming at identifying differences in the drought response between <span class="hlt">species</span> that may have implications for forest productivity and composition under likely future warmer and drier conditions.</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=4840356','PMC'); return false;" href="http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=4840356"><span id="translatedtitle">Warming effects on photosynthesis of subtropical <span class="hlt">tree</span> <span class="hlt">species</span>: a translocation experiment along an altitudinal gradient</span></a></p> <p><a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?DB=pmc">PubMed Central</a></p> <p>Li, Yiyong; Liu, Juxiu; Zhou, Guoyi; Huang, Wenjuan; Duan, Honglang</p> <p>2016-01-01</p> <p>Ongoing climate warming induced by human activities may have great impacts on <span class="hlt">trees</span>, yet it remains unresolved how subtropical <span class="hlt">tree</span> <span class="hlt">species</span> respond to rising temperature in the field. Here, we used downward translocation to investigate the effects of climate warming on leaf photosynthesis of six common <span class="hlt">tree</span> <span class="hlt">species</span> in subtropical China. During the experimental period between 2012 and 2014, the mean average photosynthetic rates (Asat) under saturating light for Schima superba, Machilus breviflora, Pinus massoniana and Ardisia lindleyana in the warm site were7%, 19%, 20% and 29% higher than those in the control site. In contrast, seasonal Asat for Castanopsis hystrix in the warm site were lower compared to the control site. Changes in Asat in response to translocation were mainly associated with those in leaf stomatal conductance (gs) and photosynthetic capacity (RuBP carboxylation, RuBP regeneration capacity). Our results imply that climate warming could have potential impacts on <span class="hlt">species</span> composition and community structure in subtropical forests. PMID:27102064</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://adsabs.harvard.edu/cgi-bin/nph-data_query?bibcode=2007DSRII..54.1831S&link_type=ABSTRACT','NASAADS'); return false;" href="http://adsabs.harvard.edu/cgi-bin/nph-data_query?bibcode=2007DSRII..54.1831S&link_type=ABSTRACT"><span id="translatedtitle">Rich and rare—First insights into <span class="hlt">species</span> diversity and <span class="hlt">abundance</span> of Antarctic abyssal Gastropoda (Mollusca)</span></a></p> <p><a target="_blank" href="http://adsabs.harvard.edu/abstract_service.html">NASA Astrophysics Data System (ADS)</a></p> <p>Schwabe, Enrico; Michael Bohn, Jens; Engl, Winfried; Linse, Katrin; Schrödl, Michael</p> <p>2007-08-01</p> <p>, and all these 84 <span class="hlt">species</span> seem endemic to Antarctica south of the Polar Front. Comparing diversity and <span class="hlt">abundances</span> based on epibenthic sledge samples, there is no clear relationship between Antarctic deep-sea gastropod <span class="hlt">abundance</span> and <span class="hlt">species</span> richness with depth. However, both Antarctic and adjacent deep-sea areas are still far from being adequately sampled to allow more comprehensive conclusions.</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=4021425','PMC'); return false;" href="http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=4021425"><span id="translatedtitle">An empirical evaluation of two-stage <span class="hlt">species</span> <span class="hlt">tree</span> inference strategies using a multilocus dataset from North American pines</span></a></p> <p><a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?DB=pmc">PubMed Central</a></p> <p></p> <p>2014-01-01</p> <p>Background As it becomes increasingly possible to obtain DNA sequences of orthologous genes from diverse sets of taxa, <span class="hlt">species</span> <span class="hlt">trees</span> are frequently being inferred from multilocus data. However, the behavior of many methods for performing this inference has remained largely unexplored. Some methods have been proven to be consistent given certain evolutionary models, whereas others rely on criteria that, although appropriate for many parameter values, have peculiar zones of the parameter space in which they fail to converge on the correct estimate as data sets increase in size. Results Here, using North American pines, we empirically evaluate the behavior of 24 strategies for <span class="hlt">species</span> <span class="hlt">tree</span> inference using three alternative outgroups (72 strategies total). The data consist of 120 individuals sampled in eight ingroup <span class="hlt">species</span> from subsection Strobus and three outgroup <span class="hlt">species</span> from subsection Gerardianae, spanning ∼47 kilobases of sequence at 121 loci. Each “strategy” for inferring <span class="hlt">species</span> <span class="hlt">trees</span> consists of three features: a <span class="hlt">species</span> <span class="hlt">tree</span> construction method, a gene <span class="hlt">tree</span> inference method, and a choice of outgroup. We use multivariate analysis techniques such as principal components analysis and hierarchical clustering to identify <span class="hlt">tree</span> characteristics that are robustly observed across strategies, as well as to identify groups of strategies that produce <span class="hlt">trees</span> with similar features. We find that strategies that construct <span class="hlt">species</span> <span class="hlt">trees</span> using only topological information cluster together and that strategies that use additional non-topological information (e.g., branch lengths) also cluster together. Strategies that utilize more than one individual within a <span class="hlt">species</span> to infer gene <span class="hlt">trees</span> tend to produce estimates of <span class="hlt">species</span> <span class="hlt">trees</span> that contain clades present in <span class="hlt">trees</span> estimated by other strategies. Strategies that use the minimize-deep-coalescences criterion to construct <span class="hlt">species</span> <span class="hlt">trees</span> tend to produce <span class="hlt">species</span> <span class="hlt">tree</span> estimates that contain clades that are not present in <span class="hlt">trees</span></p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://www.ncbi.nlm.nih.gov/pubmed/27348264','PUBMED'); return false;" href="http://www.ncbi.nlm.nih.gov/pubmed/27348264"><span id="translatedtitle">The role of selected <span class="hlt">tree</span> <span class="hlt">species</span> in industrial sewage sludge/flotation tailing management.</span></a></p> <p><a target="_blank" href="https://www.ncbi.nlm.nih.gov/entrez/query.fcgi?DB=pubmed">PubMed</a></p> <p>Mleczek, Mirosław; Rutkowski, Paweł; Niedzielski, Przemysław; Goliński, Piotr; Gąsecka, Monika; Kozubik, Tomisław; Dąbrowski, Jędrzej; Budzyńska, Sylwia; Pakuła, Jarosław</p> <p>2016-11-01</p> <p>The aim of the study was to estimate the ability of ten <span class="hlt">tree</span> and bush <span class="hlt">species</span> to tolerate and accumulate Cd, Cu, Pb, Zn, and As <span class="hlt">species</span> [As(III), As(V), and total organic arsenic] in industrial sewage sludge extremely contaminated with arsenic (almost 27.5 g kg(-1)) in a pot experiment. The premise being that it will then be possible to select the most promising <span class="hlt">tree</span>/bush <span class="hlt">species</span>, able to grow in the vicinity of dams where sewage sludge/flotation tailings are used as landfill. Six of the ten tested <span class="hlt">tree</span> <span class="hlt">species</span> were able to grow on the sludge. The highest content of total As was observed in Betula pendula roots (30.0 ± 1.3 mg kg(-1) DW), where the dominant As <span class="hlt">species</span> was the toxic As(V). The highest biomass of Quercus Q1 robur (77.3 § 2.6 g) and Acer platanoides (76.0 § 4.9 g) was observed. A proper planting of selected <span class="hlt">tree</span> <span class="hlt">species</span> that are able to thrive on sewage sludge/flotation tailings could be an interesting and promising way to protect dams. By utilizing differences in their root systems and water needs, we will be able to reduce the risk of fatal environmental disasters. PMID:27348264</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://www.ncbi.nlm.nih.gov/pubmed/24620581','PUBMED'); return false;" href="http://www.ncbi.nlm.nih.gov/pubmed/24620581"><span id="translatedtitle">Diversity and utilization of <span class="hlt">tree</span> <span class="hlt">species</span> in Meitei homegardens of Barak Valley, Assam.</span></a></p> <p><a target="_blank" href="https://www.ncbi.nlm.nih.gov/entrez/query.fcgi?DB=pubmed">PubMed</a></p> <p>Devi, N Linthoingambi; Das, Ashesh Kumar</p> <p>2013-03-01</p> <p>An inventory of <span class="hlt">tree</span> diversity in traditional homegardens of Meitei community was conducted in a Bontarapur village in Cachar district of Barak Valley, Assam. Meitei homegarden locally called Ingkhol exhibits a wide diversity in size, shape, location and composition. Seventy one <span class="hlt">tree</span> <span class="hlt">species</span> were enumerated from 50 homegardens belonging to 60 genus and 35 families. Among the families encountered, Rutaceae was the dominant family (4 genus and 7 <span class="hlt">species</span>) followed by Meliaceae (5 genus and 5 <span class="hlt">species</span>), Arecaceae (4 genus and 4 <span class="hlt">species</span>) and Moraceae (3 genus and 5 <span class="hlt">species</span>). Total 7946 <span class="hlt">tree</span> individuals were recorded, with the density of 831 No ha(-1) of and total basal area of 9.54 m2 ha(-1). Areco catechu was the dominant <span class="hlt">species</span> with the maximum number of individuals. Other dominant <span class="hlt">trees</span> include Mangifera indica, Artocarpus heterophyllus, Citrus grandis, Parkia timoriana, Syzygium cumini and Psidium guajava. Being a cash crop, the intensification of betel nut has been preferred in many homegardens. Homegardens form an important component of land use of Meitei community which fulfills the socio-cultural and economic needs of the family and helps in conserving plant diversity through utilization. PMID:24620581</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://www.ncbi.nlm.nih.gov/pubmed/25145569','PUBMED'); return false;" href="http://www.ncbi.nlm.nih.gov/pubmed/25145569"><span id="translatedtitle">Effect of trophic status in lakes on fungal <span class="hlt">species</span> diversity and <span class="hlt">abundance</span>.</span></a></p> <p><a target="_blank" href="https://www.ncbi.nlm.nih.gov/entrez/query.fcgi?DB=pubmed">PubMed</a></p> <p>Pietryczuk, A; Cudowski, A; Hauschild, T</p> <p>2014-11-01</p> <p>The objective of this study was to determine the <span class="hlt">species</span> diversity and <span class="hlt">abundance</span> of fungi in relation to the hydrochemical conditions, with special emphasis on the trophic status and degree of pollution of lakes. The study was conducted in 14 lakes of the Augustów Lakeland (central Europe, NE Poland) with different hydrological conditions, type of stratification and trophic status. The analyses were performed in the hydrological year 2013. In the waters of the studied lakes, the mean <span class="hlt">abundance</span> of fungi was 5600±3600 CFU/mL. The minimum value (800 CFU/mL) was recorded for the mesotrophic Płaskie Lake, and the maximum value (14,000 CFU/mL) was recorded for the eutrophic Pobojno Lake. A total of 38 <span class="hlt">species</span> of fungi were identified, including 11 belonging to the aquatic hyphomycetes; up to 14 <span class="hlt">species</span> were potentially pathogenic fungi. The potentially pathogenic fungi, particularly Candida albicans and Scopulariopsis fusca, were found in lakes with increased concentrations of chloride and sulphate(VI) ions and may thus serve as indicators of the degree of water pollution. This paper illustrates that the <span class="hlt">species</span> diversity and <span class="hlt">abundance</span> of fungi in limnic waters depend on the concentration of organic matter, chlorophyll a concentration, and the degree of water pollution. The results suggest that aquatic fungi can be a valuable indicator of the degree of pollution and the sanitary quality of the water. PMID:25145569</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=2936647','PMC'); return false;" href="http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=2936647"><span id="translatedtitle">Niche and neutral models predict asymptotically equivalent <span class="hlt">species</span> <span class="hlt">abundance</span> distributions in high-diversity ecological communities</span></a></p> <p><a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?DB=pmc">PubMed Central</a></p> <p>Chisholm, Ryan A.; Pacala, Stephen W.</p> <p>2010-01-01</p> <p>A fundamental challenge in ecology is to understand the mechanisms that govern patterns of relative <span class="hlt">species</span> <span class="hlt">abundance</span>. Previous numerical simulations have suggested that complex niche-structured models produce <span class="hlt">species</span> <span class="hlt">abundance</span> distributions (SADs) that are qualitatively similar to those of very simple neutral models that ignore differences between <span class="hlt">species</span>. However, in the absence of an analytical treatment of niche models, one cannot tell whether the two classes of model produce the same patterns via similar or different mechanisms. We present an analytical proof that, in the limit as diversity becomes large, a strong niche model give rises to exactly the same asymptotic form of SAD as the neutral model, and we verify the analytical predictions for a Panamanian tropical forest data set. Our results strongly suggest that neutral processes drive patterns of relative <span class="hlt">species</span> <span class="hlt">abundance</span> in high-diversity ecological communities, even when strong niche structure exists. However, neutral theory cannot explain what generates high diversity in the first place, and it may not be valid in low-diversity communities. Our results also confirm that neutral theory cannot be used to infer an absence of niche structure or to explain ecosystem function. PMID:20733073</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://www.ncbi.nlm.nih.gov/pubmed/25761054','PUBMED'); return false;" href="http://www.ncbi.nlm.nih.gov/pubmed/25761054"><span id="translatedtitle">Culicoides monitoring in Belgium in 2011: analysis of spatiotemporal <span class="hlt">abundance</span>, <span class="hlt">species</span> diversity and Schmallenberg virus detection.</span></a></p> <p><a target="_blank" href="https://www.ncbi.nlm.nih.gov/entrez/query.fcgi?DB=pubmed">PubMed</a></p> <p>DE Regge, N; DE Deken, R; Fassotte, C; Losson, B; Deblauwe, I; Madder, M; Vantieghem, P; Tomme, M; Smeets, F; Cay, A B</p> <p>2015-09-01</p> <p>In 2011, Culicoides (Diptera: Ceratopogonidae) were collected at 16 locations covering four regions of Belgium with Onderstepoort Veterinary Institute (OVI) traps and at two locations with Rothamsted suction traps (RSTs). Quantification of the collections and morphological identification showed important variations in <span class="hlt">abundance</span> and <span class="hlt">species</span> diversity between individual collection sites, even for sites located in the same region. However, consistently higher numbers of Culicoides midges were collected at some sites compared with others. When <span class="hlt">species</span> <span class="hlt">abundance</span> and diversity were analysed at regional level, between-site variation disappeared. Overall, <span class="hlt">species</span> belonging to the subgenus Avaritia together with Culicoides pulicaris (subgenus Culicoides) were the most <span class="hlt">abundant</span>, accounting for 80% and 96% of all midges collected with RSTs and OVI traps, respectively. Culicoides were present during most of the year, with Culicoides obsoletus complex midges found from 9 February until 27 December. Real-time reverse-transcription polymerase chain reaction screening for Schmallenberg virus in the heads of collected midges resulted in the first detection of the virus in August 2011 and identified C. obsoletus complex, Culicoides chiopterus and Culicoides dewulfi midges as putative vector <span class="hlt">species</span>. At Libramont in the south of Belgium, no positive pools were identified. PMID:25761054</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=4458179','PMC'); return false;" href="http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=4458179"><span id="translatedtitle">Differential effects of cocaine exposure on the <span class="hlt">abundance</span> of phospholipid <span class="hlt">species</span> in rat brain and blood*</span></a></p> <p><a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?DB=pmc">PubMed Central</a></p> <p>Cummings, Brian S.; Pati, Sumitra; Sahin, Serap; Scholpa, Natalie E.; Monian, Prashant; Trinquero, Paul O.; Clark, Jason K.; Wagner, John J.</p> <p>2015-01-01</p> <p>Background Lipid profiles in the blood are altered in human cocaine users, suggesting that cocaine-exposure can induce lipid remodeling. Methods Cocaine-induced locomotor sensitization in rats was followed by shotgun lipidomics using electrospray ionization-mass spectrometry (ESI-MS) and determined changes in brain tissues. To determine if any lipidomic changes were also reflected in the blood, we performed principal component analysis (PCA) of lipidomic spectra isolated from cocaine-treated animals. Alterations in the <span class="hlt">abundance</span> of phospholipid <span class="hlt">species</span> were correlated with behavioral changes in the magnitude of either the initial response to drug or locomotor sensitization. Results Behavioral sensitization altered the relative <span class="hlt">abundance</span> of several phospholipid <span class="hlt">species</span> in the hippocampus and cerebellum, measured one week following the final exposure to cocaine. In contrast, relatively few effects on phospholipids in either the dorsal or the ventral striatum were observed. PCA analysis demonstrated that cocaine altered the relative <span class="hlt">abundance</span> of several glycerophospholipid <span class="hlt">species</span> as compared to saline-injected controls. Subsequent MS/MS analysis identified some of these lipids as phosphatidylethanolamines, phosphatidylserines and phosphatidylcholines. The relative <span class="hlt">abundance</span> of some of these phospholipid <span class="hlt">species</span> were well correlated (R2 of 0.7 or higher) with either the initial response to cocaine or locomotor sensitization. Conclusion Taken together, these data demonstrate that a cocaine-conditioning experience results in the remodeling of specific phospholipids in rat brain tissue in a region-specific manner and also alters the intensities and types of phospholipid <span class="hlt">species</span> in rat blood. These results further suggest that such changes may serve as biomarkers to assess the neuroadaptations occurring following repeated exposure to cocaine. PMID:25960140</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://pubs.er.usgs.gov/publication/70174943','USGSPUBS'); return false;" href="http://pubs.er.usgs.gov/publication/70174943"><span id="translatedtitle">Estimating <span class="hlt">species</span> – area relationships by modeling <span class="hlt">abundance</span> and frequency subject to incomplete sampling</span></a></p> <p><a target="_blank" href="http://pubs.er.usgs.gov/pubs/index.jsp?view=adv">USGS Publications Warehouse</a></p> <p>Yamaura, Yuichi; Connor, Edward F.; Royle, Andy; Itoh, Katsuo; Sato, Kiyoshi; Taki, Hisatomo; Mishima, Yoshio</p> <p>2016-01-01</p> <p>Models and data used to describe species–area relationships confound sampling with ecological process as they fail to acknowledge that estimates of <span class="hlt">species</span> richness arise due to sampling. This compromises our ability to make ecological inferences from and about species–area relationships. We develop and illustrate hierarchical community models of <span class="hlt">abundance</span> and frequency to estimate <span class="hlt">species</span> richness. The models we propose separate sampling from ecological processes by explicitly accounting for the fact that sampled patches are seldom completely covered by sampling plots and that individuals present in the sampling plots are imperfectly detected. We propose a multispecies <span class="hlt">abundance</span> model in which community assembly is treated as the summation of an ensemble of <span class="hlt">species</span>-level Poisson processes and estimate patch-level <span class="hlt">species</span> richness as a derived parameter. We use sampling process models appropriate for specific survey methods. We propose a multispecies frequency model that treats the number of plots in which a <span class="hlt">species</span> occurs as a binomial process. We illustrate these models using data collected in surveys of early-successional bird <span class="hlt">species</span> and plants in young forest plantation patches. Results indicate that only mature forest plant <span class="hlt">species</span> deviated from the constant density hypothesis, but the null model suggested that the deviations were too small to alter the form of species–area relationships. Nevertheless, results from simulations clearly show that the aggregate pattern of individual <span class="hlt">species</span> density–area relationships and occurrence probability–area relationships can alter the form of species–area relationships. The plant community model estimated that only half of the <span class="hlt">species</span> present in the regional <span class="hlt">species</span> pool were encountered during the survey. The modeling framework we propose explicitly accounts for sampling processes so that ecological processes can be examined free of sampling artefacts. Our modeling approach is extensible and could be applied</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://pubs.er.usgs.gov/publication/70028562','USGSPUBS'); return false;" href="http://pubs.er.usgs.gov/publication/70028562"><span id="translatedtitle">Effects of sample survey design on the accuracy of classification <span class="hlt">tree</span> models in <span class="hlt">species</span> distribution models</span></a></p> <p><a target="_blank" href="http://pubs.er.usgs.gov/pubs/index.jsp?view=adv">USGS Publications Warehouse</a></p> <p>Edwards, T.C., Jr.; Cutler, D.R.; Zimmermann, N.E.; Geiser, L.; Moisen, G.G.</p> <p>2006-01-01</p> <p>We evaluated the effects of probabilistic (hereafter DESIGN) and non-probabilistic (PURPOSIVE) sample surveys on resultant classification <span class="hlt">tree</span> models for predicting the presence of four lichen <span class="hlt">species</span> in the Pacific Northwest, USA. Models derived from both survey forms were assessed using an independent data set (EVALUATION). Measures of accuracy as gauged by resubstitution rates were similar for each lichen <span class="hlt">species</span> irrespective of the underlying sample survey form. Cross-validation estimates of prediction accuracies were lower than resubstitution accuracies for all <span class="hlt">species</span> and both design types, and in all cases were closer to the true prediction accuracies based on the EVALUATION data set. We argue that greater emphasis should be placed on calculating and reporting cross-validation accuracy rates rather than simple resubstitution accuracy rates. Evaluation of the DESIGN and PURPOSIVE <span class="hlt">tree</span> models on the EVALUATION data set shows significantly lower prediction accuracy for the PURPOSIVE <span class="hlt">tree</span> models relative to the DESIGN models, indicating that non-probabilistic sample surveys may generate models with limited predictive capability. These differences were consistent across all four lichen <span class="hlt">species</span>, with 11 of the 12 possible <span class="hlt">species</span> and sample survey type comparisons having significantly lower accuracy rates. Some differences in accuracy were as large as 50%. The classification <span class="hlt">tree</span> structures also differed considerably both among and within the modelled <span class="hlt">species</span>, depending on the sample survey form. Overlap in the predictor variables selected by the DESIGN and PURPOSIVE <span class="hlt">tree</span> models ranged from only 20% to 38%, indicating the classification <span class="hlt">trees</span> fit the two evaluated survey forms on different sets of predictor variables. The magnitude of these differences in predictor variables throws doubt on ecological interpretation derived from prediction models based on non-probabilistic sample surveys. ?? 2006 Elsevier B.V. All rights reserved.</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://www.ncbi.nlm.nih.gov/pubmed/26094447','PUBMED'); return false;" href="http://www.ncbi.nlm.nih.gov/pubmed/26094447"><span id="translatedtitle">[Biomass allometric equations of nine common <span class="hlt">tree</span> <span class="hlt">species</span> in an evergreen broadleaved forest of subtropical China].</span></a></p> <p><a target="_blank" href="https://www.ncbi.nlm.nih.gov/entrez/query.fcgi?DB=pubmed">PubMed</a></p> <p>Zuo, Shu-di; Ren, Yin; Weng, Xian; Ding, Hong-feng; Luo, Yun-jian</p> <p>2015-02-01</p> <p>Biomass allometric equation (BAE) considered as a simple and reliable method in the estimation of forest biomass and carbon was used widely. In China, numerous studies focused on the BAEs for coniferous forest and pure broadleaved forest, and generalized BAEs were frequently used to estimate the biomass and carbon of mixed broadleaved forest, although they could induce large uncertainty in the estimates. In this study, we developed the <span class="hlt">species</span>-specific and generalized BAEs using biomass measurement for 9 common broadleaved <span class="hlt">trees</span> (Castanopsis fargesii, C. lamontii, C. tibetana, Lithocarpus glaber, Sloanea sinensis, Daphniphyllum oldhami, Alniphyllum fortunei, Manglietia yuyuanensis, and Engelhardtia fenzlii) of subtropical evergreen broadleaved forest, and compared differences in <span class="hlt">species</span>-specific and generalized BAEs. The results showed that D (diameter at breast height) was a better independent variable in estimating the biomass of branch, leaf, root, aboveground section and total <span class="hlt">tree</span> than a combined variable (D2 H) of D and H (<span class="hlt">tree</span> height) , but D2H was better than D in estimating stem biomass. R2 (coefficient of determination) values of BAEs for 6 <span class="hlt">species</span> decreased when adding H as the second independent variable into D- only BAEs, where R2 value for S. sinensis decreased by 5.6%. Compared with generalized D- and D2H-based BAEs, standard errors of estimate (SEE) of BAEs for 8 <span class="hlt">tree</span> <span class="hlt">species</span> decreased, and similar decreasing trend was observed for different components, where SEEs of the branch decreased by 13.0% and 20.3%. Therefore, the biomass carbon storage and its dynamic estimates were influenced largely by <span class="hlt">tree</span> <span class="hlt">species</span> and model types. In order to improve the accuracy of the estimates of biomass and carbon, we should consider the differences in <span class="hlt">tree</span> <span class="hlt">species</span> and model types. PMID:26094447</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://www.ncbi.nlm.nih.gov/pubmed/25371435','PUBMED'); return false;" href="http://www.ncbi.nlm.nih.gov/pubmed/25371435"><span id="translatedtitle">Toward more accurate ancestral protein genotype-phenotype reconstructions with the use of <span class="hlt">species</span> <span class="hlt">tree</span>-aware gene <span class="hlt">trees</span>.</span></a></p> <p><a target="_blank" href="https://www.ncbi.nlm.nih.gov/entrez/query.fcgi?DB=pubmed">PubMed</a></p> <p>Groussin, Mathieu; Hobbs, Joanne K; Szöllősi, Gergely J; Gribaldo, Simonetta; Arcus, Vickery L; Gouy, Manolo</p> <p>2015-01-01</p> <p>The resurrection of ancestral proteins provides direct insight into how natural selection has shaped proteins found in nature. By tracing substitutions along a gene phylogeny, ancestral proteins can be reconstructed in silico and subsequently synthesized in vitro. This elegant strategy reveals the complex mechanisms responsible for the evolution of protein functions and structures. However, to date, all protein resurrection studies have used simplistic approaches for ancestral sequence reconstruction (ASR), including the assumption that a single sequence alignment alone is sufficient to accurately reconstruct the history of the gene family. The impact of such shortcuts on conclusions about ancestral functions has not been investigated. Here, we show with simulations that utilizing information on <span class="hlt">species</span> history using a model that accounts for the duplication, horizontal transfer, and loss (DTL) of genes statistically increases ASR accuracy. This underscores the importance of the <span class="hlt">tree</span> topology in the inference of putative ancestors. We validate our in silico predictions using in vitro resurrection of the LeuB enzyme for the ancestor of the Firmicutes, a major and ancient bacterial phylum. With this particular protein, our experimental results demonstrate that information on the <span class="hlt">species</span> phylogeny results in a biochemically more realistic and kinetically more stable ancestral protein. Additional resurrection experiments with different proteins are necessary to statistically quantify the impact of using <span class="hlt">species</span> <span class="hlt">tree</span>-aware gene <span class="hlt">trees</span> on ancestral protein phenotypes. Nonetheless, our results suggest the need for incorporating both sequence and DTL information in future studies of protein resurrections to accurately define the genotype-phenotype space in which proteins diversify. PMID:25371435</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=3543198','PMC'); return false;" href="http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=3543198"><span id="translatedtitle"><span class="hlt">Abundance</span>, <span class="hlt">species</span> composition of microzooplankton from the coastal waters of Port Blair, South Andaman Island</span></a></p> <p><a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?DB=pmc">PubMed Central</a></p> <p></p> <p>2012-01-01</p> <p>Background Microzooplankton consisting of protists and metazoa <200 μm. It displays unique feeding mechanisms and behaviours that allow them to graze cells up to five times their own volume. They can grow at rates which equal or exceed prey growth and can serve as a viable food source for metazoans. Moreover, they are individually inconspicuous, their recognition as significant consumers of oceanic primary production. The microzooplankton can be the dominant consumers of phytoplankton production in both oligo- and eutrophic regions of the ocean and are capable of consuming >100% of primary production. Results The microzooplankton of the South Andaman Sea were investigated during September 2011 to January 2012. A total of 44 <span class="hlt">species</span> belong to 19 genera were recorded in this study. Tintinnids made larger contribution to the total <span class="hlt">abundance</span> (34%) followed in order by dinoflagellates (24%), ciliates (20%) and copepod nauplii (18%). Foraminifera were numerically less (4%). Tintinnids were represented by 20 <span class="hlt">species</span> belong to 13 genera, Heterotrophic dinoflagellates were represented by 17 <span class="hlt">species</span> belong to 3 genera and Ciliates comprised 5 <span class="hlt">species</span> belong to 3 genera. Eutintinus tineus, Tintinnopsis cylindrical, T. incertum, Protoperidinium divergens, Lomaniella oviformes, Strombidium minimum were the most prevalent microzooplankton. Standing stock of tintinnids ranged from 30–80 cells.L-1 and showed a reverse distribution with the distribution of chlorophyll a relatively higher <span class="hlt">species</span> diversity and equitability was found in polluted harbour areas. Conclusions The change of environmental variability affects the <span class="hlt">species</span> composition and <span class="hlt">abundance</span> of microzooplankton varied spatially and temporarily. The observations clearly demonstrated that the harbor area differed considerably from other area in terms of <span class="hlt">species</span> present and phytoplankton biomass. Further, the phytoplankton <span class="hlt">abundance</span> is showed to be strongly influenced by tintinnid with respect to the relationship of</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://www.ncbi.nlm.nih.gov/pubmed/25413866','PUBMED'); return false;" href="http://www.ncbi.nlm.nih.gov/pubmed/25413866"><span id="translatedtitle"><span class="hlt">Abundance</span> and phenology patterns of two pond-breeding salamanders determine <span class="hlt">species</span> interactions in natural populations.</span></a></p> <p><a target="_blank" href="https://www.ncbi.nlm.nih.gov/entrez/query.fcgi?DB=pubmed">PubMed</a></p> <p>Anderson, Thomas L; Hocking, Daniel J; Conner, Christopher A; Earl, Julia E; Harper, Elizabeth B; Osbourn, Michael S; Peterman, William E; Rittenhouse, Tracy A G; Semlitsch, Raymond D</p> <p>2015-03-01</p> <p>Phenology often determines the outcome of interspecific interactions, where early-arriving <span class="hlt">species</span> often dominate interactions over those arriving later. The effects of phenology on <span class="hlt">species</span> interactions are especially pronounced in aquatic systems, but the evidence is largely derived from experimental studies. We examined whether differences in breeding phenology between two pond-breeding salamanders (Ambystoma annulatum and A. maculatum) affected metamorph recruitment and demographic traits within natural populations, with the expectation that the fall-breeding A. annulatum would negatively affect the spring-breeding A. maculatum. We monitored populations of each <span class="hlt">species</span> at five ponds over 4 years using drift fences. Metamorph <span class="hlt">abundance</span> and survival of A. annulatum were affected by intra- and interspecific processes, whereas metamorph size and date of emigration were primarily influenced by intraspecific effects. Metamorph <span class="hlt">abundance</span>, snout-vent length, date of emigration and survival for A. maculatum were all predicted by combinations of intra- and interspecific effects, but often showed negative relationships with A. annulatum metamorph traits and <span class="hlt">abundance</span>. Size and date of metamorphosis were strongly correlated within each <span class="hlt">species</span>, but in opposite patterns (negative for A. annulatum and positive for A. maculatum), suggesting that the two <span class="hlt">species</span> use alternative strategies to enhance terrestrial survival and that these factors may influence their interactions. Our results match predictions from experimental studies that suggest recruitment is influenced by intra- and interspecific processes which are determined by phenological differences between <span class="hlt">species</span>. Incorporating spatiotemporal variability when modeling population dynamics is necessary to understand the importance of phenology in <span class="hlt">species</span> interactions, especially as shifts in phenology occur under climate change. PMID:25413866</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://www.springerlink.com/content/g4295k8x56wj20g0/','USGSPUBS'); return false;" href="http://www.springerlink.com/content/g4295k8x56wj20g0/"><span id="translatedtitle">Complementary models of <span class="hlt">tree</span> <span class="hlt">species</span>-soil relationships in old-growth temperate forests</span></a></p> <p><a target="_blank" href="http://pubs.er.usgs.gov/pubs/index.jsp?view=adv">USGS Publications Warehouse</a></p> <p>Cross, Alison; Perakis, Steven S.</p> <p>2011-01-01</p> <p>Ecosystem level studies identify plant soil feed backs as important controls on soil nutrient availability,particularly for nitrogen and phosphorus. Although site and <span class="hlt">species</span> specific studies of <span class="hlt">tree</span> <span class="hlt">species</span> soil relationships are relatively common,comparatively fewer studies consider multiple coexisting speciesin old-growth forests across a range of sites that vary underlying soil fertility. We characterized patterns in forest floor and mineral soil nutrients associated with four common <span class="hlt">tree</span> <span class="hlt">species</span> across eight undisturbed old-growth forests in Oregon, USA, and used two complementary conceptual models to assess <span class="hlt">tree</span> <span class="hlt">species</span> soil relationships. Plant soil feedbacks that could reinforce sitelevel differences in nutrient availability were assessed using the context dependent relationships model, where by relative <span class="hlt">species</span> based differences in each soil nutrient divergedorconvergedas nutrient status changed across sites. <span class="hlt">Tree</span> <span class="hlt">species</span> soil relationships that did not reflect strong feedbacks were evaluated using a site independent relationships model, where by forest floor and surface mineral soil nutrient tools differed consistently by <span class="hlt">tree</span> <span class="hlt">species</span> across sites,without variation in deeper mineral soils. We found that theorganically cycled elements carbon, nitrogen, and phosphorus exhibited context-dependent differences among <span class="hlt">species</span> in both forest floor and mineral soil, and most of ten followed adivergence model,where by <span class="hlt">species</span> differences were greatest at high-nutrient sites. These patterns are consistent with the oryemphasizing biotic control of these elements through plant soil feedback mechanisms. Site independent <span class="hlt">species</span> differences were strongest for pool so if the weather able cations calcium, magnesium, potassium,as well as phosphorus, in mineral soils. Site independent <span class="hlt">species</span> differences in forest floor nutrients we reattributable too nespecies that displayed significant greater forest floor mass accumulation. Our finding confirmed that site-independent and</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://www.ncbi.nlm.nih.gov/pubmed/24361514','PUBMED'); return false;" href="http://www.ncbi.nlm.nih.gov/pubmed/24361514"><span id="translatedtitle"><span class="hlt">Species</span> <span class="hlt">abundance</span> distributions, statistical mechanics and the priors of MaxEnt.</span></a></p> <p><a target="_blank" href="https://www.ncbi.nlm.nih.gov/entrez/query.fcgi?DB=pubmed">PubMed</a></p> <p>Bowler, M G</p> <p>2014-03-01</p> <p>The methods of Maximum Entropy have been deployed for some years to address the problem of <span class="hlt">species</span> <span class="hlt">abundance</span> distributions. In this approach, it is important to identify the correct weighting factors, or priors, to be applied before maximising the entropy function subject to constraints. The forms of such priors depend not only on the exact problem but can also depend on the way it is set up; priors are determined by the underlying dynamics of the complex system under consideration. The problem is one of statistical mechanics and it is the properties of the system that yield the correct MaxEnt priors, appropriate to the way the problem is framed. Here I calculate, in several different ways, the <span class="hlt">species</span> <span class="hlt">abundance</span> distribution resulting when individuals in a community are born and die independently. In the usual formulation the prior distribution for the number of <span class="hlt">species</span> over the number of individuals is 1/n; the problem can be reformulated in terms of the distribution of individuals over <span class="hlt">species</span> classes, with a uniform prior. Results are obtained using master equations for the dynamics and separately through the combinatoric methods of elementary statistical mechanics; the MaxEnt priors then emerge a posteriori. The first object is to establish the log series <span class="hlt">species</span> <span class="hlt">abundance</span> distribution as the outcome of per capita guild dynamics. The second is to clarify the true nature and origin of priors in the language of MaxEnt. Finally, I consider how it may come about that the distribution is similar to log series in the event that filled niches dominate <span class="hlt">species</span> <span class="hlt">abundance</span>. For the general ecologist, there are two messages. First, that <span class="hlt">species</span> <span class="hlt">abundance</span> distributions are determined largely by population sorting through fractional processes (resulting in the 1/n factor) and secondly that useful information is likely to be found only in departures from the log series. For the MaxEnt practitioner, the message is that the prior with respect to which the entropy is to be</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://adsabs.harvard.edu/cgi-bin/nph-data_query?bibcode=2014EnMan..53..783S&link_type=ABSTRACT','NASAADS'); return false;" href="http://adsabs.harvard.edu/cgi-bin/nph-data_query?bibcode=2014EnMan..53..783S&link_type=ABSTRACT"><span id="translatedtitle">The Right <span class="hlt">Tree</span> for the Job? Perceptions of <span class="hlt">Species</span> Suitability for the Provision of Ecosystem Services</span></a></p> <p><a target="_blank" href="http://adsabs.harvard.edu/abstract_service.html">NASA Astrophysics Data System (ADS)</a></p> <p>Smaill, Simeon J.; Bayne, Karen M.; Coker, Graham W. R.; Paul, Thomas S. H.; Clinton, Peter W.</p> <p>2014-04-01</p> <p>Stakeholders in plantation forestry are increasingly aware of the importance of the ecosystem services and non-market values associated with forests. In New Zealand, there is significant interest in establishing <span class="hlt">species</span> other than Pinus radiata D. Don (the dominant plantation <span class="hlt">species</span>) in the belief that alternative <span class="hlt">species</span> are better suited to deliver these services. Significant risk is associated with this position as there is little objective data to support these views. To identify which <span class="hlt">species</span> were likely to be planted to deliver ecosystem services, a survey was distributed to examine stakeholder perceptions. Stakeholders were asked which of 15 <span class="hlt">tree</span> attributes contributed to the provision of five ecosystem services (amenity value, bioenergy production, carbon capture, the diversity of native habitat, and erosion control/water quality) and to identify which of 22 candidate <span class="hlt">tree</span> <span class="hlt">species</span> possessed those attributes. These data were combined to identify the <span class="hlt">species</span> perceived most suitable for the delivery of each ecosystem service. Sequoia sempervirens (D.Don) Endl. closely matched the stakeholder derived ideotypes associated with all five ecosystem services. Comparisons to data from growth, physiological and ecological studies demonstrated that many of the opinions held by stakeholders were inaccurate, leading to erroneous assumptions regarding the suitability of most candidate <span class="hlt">species</span>. Stakeholder perceptions substantially influence <span class="hlt">tree</span> <span class="hlt">species</span> selection, and plantations established on the basis of inaccurate opinions are unlikely to deliver the desired outcomes. Attitudinal surveys associated with engagement campaigns are essential to improve stakeholder knowledge, advancing the development of fit-for-purpose forest management that provides the required ecosystem services.</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://www.ncbi.nlm.nih.gov/pubmed/25292455','PUBMED'); return false;" href="http://www.ncbi.nlm.nih.gov/pubmed/25292455"><span id="translatedtitle">Stem CO2 efflux in six co-occurring <span class="hlt">tree</span> <span class="hlt">species</span>: underlying factors and ecological implications.</span></a></p> <p><a target="_blank" href="https://www.ncbi.nlm.nih.gov/entrez/query.fcgi?DB=pubmed">PubMed</a></p> <p>Rodríguez-Calcerrada, Jesús; López, Rosana; Salomón, Roberto; Gordaliza, Guillermo G; Valbuena-Carabaña, María; Oleksyn, Jacek; Gil, Luis</p> <p>2015-06-01</p> <p>Stem respiration plays a role in <span class="hlt">species</span> coexistence and forest dynamics. Here we examined the intra- and inter-specific variability of stem CO2 efflux (E) in dominant and suppressed <span class="hlt">trees</span> of six deciduous <span class="hlt">species</span> in a mixed forest stand: Fagus sylvatica L., Quercus petraea [Matt.] Liebl, Quercus pyrenaica Willd., Prunus avium L., Sorbus aucuparia L. and Crataegus monogyna Jacq. We conducted measurements in late autumn. Within <span class="hlt">species</span>, dominants had higher E per unit stem surface area (Es ) mainly because sapwood depth was higher than in suppressed <span class="hlt">trees</span>. Across <span class="hlt">species</span>, however, differences in Es corresponded with differences in the proportion of living parenchyma in sapwood and concentration of non-structural carbohydrates (NSC). Across <span class="hlt">species</span>, Es was strongly and NSC marginally positively related with an index of drought tolerance, suggesting that slow growth of drought-tolerant <span class="hlt">trees</span> is related to higher NSC concentration and Es . We conclude that, during the leafless period, E is indicative of maintenance respiration and is related with some ecological characteristics of the <span class="hlt">species</span>, such as drought resistance; that sapwood depth is the main factor explaining variability in Es within <span class="hlt">species</span>; and that the proportion of NSC in the sapwood is the main factor behind variability in Es among <span class="hlt">species</span>. PMID:25292455</p> </li> </ol> <div class="pull-right"> <ul class="pagination"> <li><a href="#" onclick='return showDiv("page_1");'>«</a></li> <li><a href="#" onclick='return showDiv("page_17");'>17</a></li> <li><a href="#" onclick='return showDiv("page_18");'>18</a></li> <li class="active"><span>19</span></li> <li><a href="#" onclick='return showDiv("page_20");'>20</a></li> <li><a href="#" onclick='return showDiv("page_21");'>21</a></li> <li><a href="#" onclick='return showDiv("page_25");'>»</a></li> </ul> </div> </div><!-- col-sm-12 --> </div><!-- row --> </div><!-- page_19 --> <div id="page_20" class="hiddenDiv"> <div class="row"> <div class="col-sm-12"> <div class="pull-right"> <ul class="pagination"> <li><a href="#" onclick='return showDiv("page_1");'>«</a></li> <li><a href="#" onclick='return showDiv("page_18");'>18</a></li> <li><a href="#" onclick='return showDiv("page_19");'>19</a></li> <li class="active"><span>20</span></li> <li><a href="#" onclick='return showDiv("page_21");'>21</a></li> <li><a href="#" onclick='return showDiv("page_22");'>22</a></li> <li><a href="#" onclick='return showDiv("page_25");'>»</a></li> </ul> </div> </div> </div> <div class="row"> <div class="col-sm-12"> <ol class="result-class" start="381"> <li> <p><a target="_blank" onclick="trackOutboundLink('http://www.ncbi.nlm.nih.gov/pubmed/21362638','PUBMED'); return false;" href="http://www.ncbi.nlm.nih.gov/pubmed/21362638"><span id="translatedtitle">Detecting phylogenetic breakpoints and discordance from genome-wide alignments for <span class="hlt">species</span> <span class="hlt">tree</span> reconstruction.</span></a></p> <p><a target="_blank" href="https://www.ncbi.nlm.nih.gov/entrez/query.fcgi?DB=pubmed">PubMed</a></p> <p>Ané, Cécile</p> <p>2011-01-01</p> <p>With the easy acquisition of sequence data, it is now possible to obtain and align whole genomes across multiple related <span class="hlt">species</span> or populations. In this work, I assess the performance of a statistical method to reconstruct the whole distribution of phylogenetic <span class="hlt">trees</span> along the genome, estimate the proportion of the genome for which a given clade is true, and infer a concordance <span class="hlt">tree</span> that summarizes the dominant vertical inheritance pattern. There are two main issues when dealing with whole-genome alignments, as opposed to multiple genes: the size of the data and the detection of recombination breakpoints. These breakpoints partition the genomic alignment into phylogenetically homogeneous loci, where sites within a given locus all share the same phylogenetic <span class="hlt">tree</span> topology. To delimitate these loci, I describe here a method based on the minimum description length (MDL) principle, implemented with dynamic programming for computational efficiency. Simulations show that combining MDL partitioning with Bayesian concordance analysis provides an efficient and robust way to estimate both the vertical inheritance signal and the horizontal phylogenetic signal. The method performed well both in the presence of incomplete lineage sorting and in the presence of horizontal gene transfer. A high level of systematic bias was found here, highlighting the need for good individual <span class="hlt">tree</span> building methods, which form the basis for more elaborate gene <span class="hlt">tree/species</span> <span class="hlt">tree</span> reconciliation methods. PMID:21362638</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://adsabs.harvard.edu/abs/1989NJSR...23...85A','NASAADS'); return false;" href="http://adsabs.harvard.edu/abs/1989NJSR...23...85A"><span id="translatedtitle"><span class="hlt">Species</span> composition, distribution and <span class="hlt">abundance</span> of chaetodontidae along reef transects in the Flores Sea</span></a></p> <p><a target="_blank" href="http://adsabs.harvard.edu/abstract_service.html">NASA Astrophysics Data System (ADS)</a></p> <p>Adrim, Mohammad; Hutomo, Malikusworo</p> <p></p> <p>Observations on chaetodontid fishes were made by applying a visual census technique at 13 coral reef locations in the Flores Sea region in October and November 1984. These observations were made along 50 m transect lines, parallel to the shore or the reef edge at depths between 3 to 12 m. Twenty-three <span class="hlt">species</span> of Chaetodontidae were observed, representing three genera: Chaetodon (20 <span class="hlt">species</span>), Heniochus (2 <span class="hlt">species</span>) and Forcipiger (1 <span class="hlt">species</span>). Chaetodon kleini, C. trifasciatus, C. melannotus and C. baronessa proved to be the most <span class="hlt">abundant</span> <span class="hlt">species</span>, and among them C. kleini and C. trifasciatus were the most widely distributed ones. Chaetodon semeion and C. mertensi were the rarest <span class="hlt">species</span>. The greatest number of individuals (77) was counted at station 4.268 near Tanjung Burung, Sumbawa, while the greatest number of <span class="hlt">species</span> (14) was observed at station 4.257, north of Komodo. The lowest number of individuals (17) was counted at station 4.175 near P. Bahuluang, Salayer, while station 4.251 near Teluk Slawi, Komodo, was inhabited by the smallest numbver of <span class="hlt">species</span> (2). Numerical classification by using the Bray Curtis dissimilarity index resulted in three groups of entities. The first group was characterized by predomination of C. kleini and the second by predomination of C. melannotus. The third one was a loose group not characterized by any predominant <span class="hlt">species</span>. The analyses indicated that the similarities of the chaetodontid communities between locations are not related to the distance between them, but rather to habitat conditions. For example predomination of C. melannotus is strongly related to the predomination of soft coral. Compared to other areas of Indonesia, e.g. Bali, Seribu Islands, Batam, Sunda Strait, and Ambon Bay, the Flores Sea reefs have a more <span class="hlt">abundant</span> and more diverse chaetodontid fauna.</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=4538783','PMC'); return false;" href="http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=4538783"><span id="translatedtitle"><span class="hlt">Tree</span> cover at fine and coarse spatial grains interacts with shade tolerance to shape plant <span class="hlt">species</span> distributions across the Alps</span></a></p> <p><a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?DB=pmc">PubMed Central</a></p> <p>Nieto-Lugilde, Diego; Lenoir, Jonathan; Abdulhak, Sylvain; Aeschimann, David; Dullinger, Stefan; Gégout, Jean-Claude; Guisan, Antoine; Pauli, Harald; Renaud, Julien; Theurillat, Jean-Paul; Thuiller, Wilfried; Van Es, Jérémie; Vittoz, Pascal; Willner, Wolfgang; Wohlgemuth, Thomas; Zimmermann, Niklaus E.; Svenning, Jens-Christian</p> <p>2015-01-01</p> <p>The role of competition for light among plants has long been recognised at local scales, but its importance for plant <span class="hlt">species</span> distributions at larger spatial scales has generally been ignored. <span class="hlt">Tree</span> cover modifies the local abiotic conditions below the canopy, notably by reducing light availability, and thus, also the performance of <span class="hlt">species</span> that are not adapted to low-light conditions. However, this local effect may propagate to coarser spatial grains, by affecting colonisation probabilities and local extinction risks of herbs and shrubs. To assess the effect of <span class="hlt">tree</span> cover at both the plot- and landscape-grain sizes (approximately 10-m and 1-km), we fit Generalised Linear Models (GLMs) for the plot-level distributions of 960 <span class="hlt">species</span> of herbs and shrubs using 6,935 vegetation plots across the European Alps. We ran four models with different combinations of variables (climate, soil and <span class="hlt">tree</span> cover) at both spatial grains for each <span class="hlt">species</span>. We used partial regressions to evaluate the independent effects of plot- and landscape-grain <span class="hlt">tree</span> cover on plot-level plant communities. Finally, the effects on <span class="hlt">species</span>-specific elevational range limits were assessed by simulating a removal experiment comparing the <span class="hlt">species</span> distributions under high and low <span class="hlt">tree</span> cover. Accounting for <span class="hlt">tree</span> cover improved the model performance, with the probability of the presence of shade-tolerant <span class="hlt">species</span> increasing with increasing <span class="hlt">tree</span> cover, whereas shade-intolerant <span class="hlt">species</span> showed the opposite pattern. The <span class="hlt">tree</span> cover effect occurred consistently at both the plot and landscape spatial grains, albeit most strongly at the former. Importantly, <span class="hlt">tree</span> cover at the two grain sizes had partially independent effects on plot-level plant communities. With high <span class="hlt">tree</span> cover, shade-intolerant <span class="hlt">species</span> exhibited narrower elevational ranges than with low <span class="hlt">tree</span> cover whereas shade-tolerant <span class="hlt">species</span> showed wider elevational ranges at both limits. These findings suggest that forecasts of climate-related range shifts for herb</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://adsabs.harvard.edu/cgi-bin/nph-data_query?bibcode=2016JPRS..119...79S&link_type=ABSTRACT','NASAADS'); return false;" href="http://adsabs.harvard.edu/cgi-bin/nph-data_query?bibcode=2016JPRS..119...79S&link_type=ABSTRACT"><span id="translatedtitle">Estimating forest <span class="hlt">species</span> <span class="hlt">abundance</span> through linear unmixing of CHRIS/PROBA imagery</span></a></p> <p><a target="_blank" href="http://adsabs.harvard.edu/abstract_service.html">NASA Astrophysics Data System (ADS)</a></p> <p>Stagakis, Stavros; Vanikiotis, Theofilos; Sykioti, Olga</p> <p>2016-09-01</p> <p>The advancing technology of hyperspectral remote sensing offers the opportunity of accurate land cover characterization of complex natural environments. In this study, a linear spectral unmixing algorithm that incorporates a novel hierarchical Bayesian approach (BI-ICE) was applied on two spatially and temporally adjacent CHRIS/PROBA images over a forest in North Pindos National Park (Epirus, Greece). The scope is to investigate the potential of this algorithm to discriminate two different forest <span class="hlt">species</span> (i.e. beech - Fagus sylvatica, pine - Pinus nigra) and produce accurate <span class="hlt">species</span>-specific <span class="hlt">abundance</span> maps. The unmixing results were evaluated in uniformly distributed plots across the test site using measured fractions of each <span class="hlt">species</span> derived by very high resolution aerial orthophotos. Landsat-8 images were also used to produce a conventional discrete-type classification map of the test site. This map was used to define the exact borders of the test site and compare the thematic information of the two mapping approaches (discrete vs <span class="hlt">abundance</span> mapping). The required ground truth information, regarding training and validation of the applied mapping methodologies, was collected during a field campaign across the study site. <span class="hlt">Abundance</span> estimates reached very good overall accuracy (R2 = 0.98, RMSE = 0.06). The most significant source of error in our results was due to the shadowing effects that were very intense in some areas of the test site due to the low solar elevation during CHRIS acquisitions. It is also demonstrated that the two mapping approaches are in accordance across pure and dense forest areas, but the conventional classification map fails to describe the natural spatial gradients of each <span class="hlt">species</span> and the actual <span class="hlt">species</span> mixture across the test site. Overall, the BI-ICE algorithm presented increased potential to unmix challenging objects with high spectral similarity, such as different vegetation <span class="hlt">species</span>, under real and not optimum acquisition conditions. Its</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://www.ncbi.nlm.nih.gov/pubmed/23376521','PUBMED'); return false;" href="http://www.ncbi.nlm.nih.gov/pubmed/23376521"><span id="translatedtitle">Forest floor leachate fluxes under six different <span class="hlt">tree</span> <span class="hlt">species</span> on a metal contaminated site.</span></a></p> <p><a target="_blank" href="https://www.ncbi.nlm.nih.gov/entrez/query.fcgi?DB=pubmed">PubMed</a></p> <p>Van Nevel, Lotte; Mertens, Jan; De Schrijver, An; Baeten, Lander; De Neve, Stefaan; Tack, Filip M G; Meers, Erik; Verheyen, Kris</p> <p>2013-03-01</p> <p><span class="hlt">Trees</span> play an important role in the biogeochemical cycling of metals, although the influence of different <span class="hlt">tree</span> <span class="hlt">species</span> on the mobilization of metals is not yet clear. This study examined effects of six <span class="hlt">tree</span> <span class="hlt">species</span> on fluxes of Cd, Zn, DOC, H(+) and base cations in forest floor leachates on a metal polluted site in Belgium. Forest floor leachates were sampled with zero-tension lysimeters in a 12-year-old post-agricultural forest on a sandy soil. The <span class="hlt">tree</span> <span class="hlt">species</span> included were silver birch (Betula pendula), oak (Quercus robur and Q. petraea), black locust (Robinia pseudoacacia), aspen (Populus tremula), Scots pine (Pinus sylvestris) and Douglas fir (Pseudotsuga menziesii). We show that total Cd fluxes in forest floor leachate under aspen were slightly higher than those in the other <span class="hlt">species</span>' leachates, yet the relative differences between the <span class="hlt">species</span> were considerably smaller when looking at dissolved Cd fluxes. The latter was probably caused by extremely low H(+) amounts leaching from aspen's forest floor. No <span class="hlt">tree</span> <span class="hlt">species</span> effect was found for Zn leachate fluxes. We expected higher metal leachate fluxes under aspen as its leaf litter was significantly contaminated with Cd and Zn. We propose that the low amounts of Cd and Zn leaching under aspen's forest floor were possibly caused by high activity of soil biota, for example burrowing earthworms. Furthermore, our results reveal that Scots pine and oak were characterized by high H(+) and DOC fluxes as well as low base cation fluxes in their forest floor leachates, implying that those <span class="hlt">species</span> might enhance metal mobilization in the soil profile and thus bear a potential risk for belowground metal dispersion. PMID:23376521</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://adsabs.harvard.edu/abs/2015AGUFM.B43C0563C','NASAADS'); return false;" href="http://adsabs.harvard.edu/abs/2015AGUFM.B43C0563C"><span id="translatedtitle">A Section-based Method For <span class="hlt">Tree</span> <span class="hlt">Species</span> Classification Using Airborne LiDAR Discrete Points In Urban Areas</span></a></p> <p><a target="_blank" href="http://adsabs.harvard.edu/abstract_service.html">NASA Astrophysics Data System (ADS)</a></p> <p>Chunjing, Y. C.; Hui, T.; Zhongjie, R.; Guikai, B.</p> <p>2015-12-01</p> <p>As a new approach to forest inventory utilizing, LiDAR remote sensing has become an important research issue in the past. Lidar researches initially concentrate on the investigation for mapping forests at the <span class="hlt">tree</span> level and identifying important structural parameters, such as <span class="hlt">tree</span> height, crown size, crown base height, individual <span class="hlt">tree</span> <span class="hlt">species</span>, and stem volume etc. But for the virtual city visualization and mapping, the traditional methods of <span class="hlt">tree</span> classification can't satisfy the more complex conditions. Recently, the advanced LiDAR technology has generated new full waveform scanners that provide a higher point density and additional information about the reflecting characteristics of <span class="hlt">trees</span>. Subsequently, it was demonstrated that it is feasible to detect individual overstorey <span class="hlt">trees</span> in forests and classify <span class="hlt">species</span>. But the important issues like the calibration and the decomposition of full waveform data with a series of Gaussian functions usually take a lot of works. What's more, the detection and classification of vegetation results relay much on the prior outcomes. From all above, the section-based method for <span class="hlt">tree</span> <span class="hlt">species</span> classification using small footprint and high sampling density lidar data is proposed in this paper, which can overcome the <span class="hlt">tree</span> <span class="hlt">species</span> classification issues in urban areas. More specific objectives are to: (1)use local maximum height decision and four direction sections certification methods to get the precise locations of the <span class="hlt">trees</span>;(2) develop new lidar-derived features processing techniques for characterizing the section structure of individual <span class="hlt">tree</span> crowns;(3) investigate several techniques for filtering and analyzing vertical profiles of individual <span class="hlt">trees</span> to classify the <span class="hlt">trees</span>, and using the expert decision skills based on percentile analysis;(4) assess the accuracy of estimating <span class="hlt">tree</span> <span class="hlt">species</span> for each <span class="hlt">tree</span>, and (5) investigate which type of lidar data, point frequency or intensity, provides the most accurate estimate of <span class="hlt">tree</span> <span class="hlt">species</span></p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=3360761','PMC'); return false;" href="http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=3360761"><span id="translatedtitle">Whitebark Pine Stand Condition, <span class="hlt">Tree</span> <span class="hlt">Abundance</span>, and Cone Production as Predictors of Visitation by Clark's Nutcracker</span></a></p> <p><a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?DB=pmc">PubMed Central</a></p> <p>Barringer, Lauren E.; Tomback, Diana F.; Wunder, Michael B.; McKinney, Shawn T.</p> <p>2012-01-01</p> <p>Background Accurately quantifying key interactions between <span class="hlt">species</span> is important for developing effective recovery strategies for threatened and endangered <span class="hlt">species</span>. Whitebark pine (Pinus albicaulis), a candidate <span class="hlt">species</span> for listing under the Endangered <span class="hlt">Species</span> Act, depends on Clark's nutcracker (Nucifraga columbiana) for seed dispersal. As whitebark pine succumbs to exotic disease and mountain pine beetles (Dendroctonus ponderosae), cone production declines, and nutcrackers visit stands less frequently, reducing the probability of seed dispersal. Methodology/Principal Findings We quantified whitebark pine forest structure, health metrics, and the frequency of nutcracker occurrence in national parks within the Northern and Central Rocky Mountains in 2008 and 2009. Forest health characteristics varied between the two regions, with the northern region in overall poorer health. Using these data, we show that a previously published model consistently under-predicts the proportion of survey hours resulting in nutcracker observations at all cone density levels. We present a new statistical model of the relationship between whitebark pine cone production and the probability of Clark's nutcracker occurrence based on combining data from this study and the previous study. Conclusions/Significance Our model clarified earlier findings and suggested a lower cone production threshold value for predicting likely visitation by nutcrackers: Although nutcrackers do visit whitebark pine stands with few cones, the probability of visitation increases with increased cone production. We use information theoretics to show that beta regression is a more appropriate statistical framework for modeling the relationship between cone density and proportion of survey time resulting in nutcracker observations. We illustrate how resource managers may apply this model in the process of prioritizing areas for whitebark pine restoration. PMID:22662186</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://pubs.er.usgs.gov/publication/ofr81214','USGSPUBS'); return false;" href="http://pubs.er.usgs.gov/publication/ofr81214"><span id="translatedtitle">Plankton studies in San Francisco Bay; II, Phytoplankton <span class="hlt">abundance</span> and <span class="hlt">species</span> composition, July 1977-December 1979</span></a></p> <p><a target="_blank" href="http://pubs.er.usgs.gov/pubs/index.jsp?view=adv">USGS Publications Warehouse</a></p> <p>Wong, Raymond L. J.; Cloern, James E.</p> <p>1981-01-01</p> <p>Data are presented on the phytoplankton <span class="hlt">species</span> composition and <span class="hlt">abundance</span> in San Francisco Bay from July 1977 through December 1979. Phytoplankton identification and enumerations were made at selected stations. Sample collections were made at selected stations in the main channel of the Bay from Rio Vista on the Sacramento River to Calaveras Point in South San Francisco Bay, and at shoal stations in the central portion of South San Francisco Bay, San Pablo Bay, and Suisun Bay. Also reported, from October 1978 through December 1979, are the calculated phytoplankton carbon and percent nondiatom carbon, and the <span class="hlt">species</span> list. This study is one component of an ongoing interdisciplinary study of San Francisco Bay. (USGS)</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://www.ncbi.nlm.nih.gov/pubmed/19637699','PUBMED'); return false;" href="http://www.ncbi.nlm.nih.gov/pubmed/19637699"><span id="translatedtitle">The fish fauna of Anambra river basin, Nigeria: <span class="hlt">species</span> <span class="hlt">abundance</span> and morphometry.</span></a></p> <p><a target="_blank" href="https://www.ncbi.nlm.nih.gov/entrez/query.fcgi?DB=pubmed">PubMed</a></p> <p>Odo, Gregory Ejikeme; Didigwu, Nwani Christopher; Eyo, Joseph Effiong</p> <p>2009-01-01</p> <p>The fish yields of most Nigeria inland waters are generally on the decline for causes that may range from inadequate management of the fisheries to degradation of the water bodies. Sustainable exploitation requires knowledge of the ichthyofaunal composition in the water bodies. We did a survey of fish <span class="hlt">species</span> in Anambra river basin for 22 months. Fish samples were collected using four different gears -hook and line of size 13, caste nets, gill nets, and cages of mesh sizes of 50 mm, 75 mm, and 100 mm each. We recorded 52 fish <span class="hlt">species</span> belonging to 17 families: 171, 236, and 169 individuals at Ogurugu, Otuocha, and Nsugbe stations respectively. Two families, Characidae, 19.5%, and Mochokidae, 11.8%, constituted the dominant fish families in the river. The dominant fish <span class="hlt">species</span> were Citherinus citherius, 9.02%, and Alestes nurse, 7.1%. Other fish <span class="hlt">species</span> with significant <span class="hlt">abundance</span> were Synodontis clarias 6.9%, Macrolepidotus curvier 5.7%, Labeo coubie 5.4%, Distichodus rostrtus 4.9%, and Schilbe mystus 4.5%. The meristic features of the two most <span class="hlt">abundant</span> fish <span class="hlt">species</span> caught are as follows: Citharinus citharius dorsal fins 20, anal fins 30, caudal fins 21, pectoral fins, 9 and 8 ventral fins, and Alestes nurse 10 dorsal fins, 14 anal fins, 31 caudal fins, 7 pectoral fins and 6 ventral fins. The morphometric features of the two most <span class="hlt">abundant</span> fish <span class="hlt">species</span> are Citharinus citharius total length 300 mm, standard length 231 mm, head length 69 mm, body length 101 mm, body girth 176 mm, body weight 900 mg. Alestes nurse total length 200, standard length 140 mm, head length 60 mm, body length 80 mm, body girth 120 mm, body weight 400 mg. The most <span class="hlt">abundant</span> animal utilizing the basin was Ardea cinerea (D3) with 22.2% occurrence (D4) and this was followed by Caprini with 13.51%, and Varanus niloticus, 10.04%. The least <span class="hlt">abundant</span> animals utilizing basin were Chephalophus rufilatus, and Erythrocebus patas, with 0.58% each of occurrence. PMID:19637699</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://www.ncbi.nlm.nih.gov/pubmed/26828175','PUBMED'); return false;" href="http://www.ncbi.nlm.nih.gov/pubmed/26828175"><span id="translatedtitle"><span class="hlt">Tree</span> <span class="hlt">Species</span> Suitability to Bioswales and Impact on the Urban Water Budget.</span></a></p> <p><a target="_blank" href="https://www.ncbi.nlm.nih.gov/entrez/query.fcgi?DB=pubmed">PubMed</a></p> <p>Scharenbroch, Bryant C; Morgenroth, Justin; Maule, Brian</p> <p>2016-01-01</p> <p>Water movement between soil and the atmosphere is restricted by hardscapes in the urban environment. Some green infrastructure is intended to increase infiltration and storage of water, thus decreasing runoff and discharge of urban stormwater. Bioswales are a critical component of a water-sensitive urban design (or a low-impact urban design), and incorporation of <span class="hlt">trees</span> into these green infrastructural components is believed to be a novel way to return stored water to the atmosphere via transpiration. This research was conducted in The Morton Arboretum's main parking lot, which is one of the first and largest green infrastructure installations in the midwestern United States. The parking lot is constructed of permeable pavers and <span class="hlt">tree</span> bioswales. <span class="hlt">Trees</span> in bioswales were evaluated for growth and condition and for their effects on water cycling via transpiration. Our data indicate that <span class="hlt">trees</span> in bioswales accounted for 46 to 72% of total water outputs via transpiration, thereby reducing runoff and discharge from the parking lot. By evaluating the stomatal conductance, diameter growth, and condition of a variety of <span class="hlt">tree</span> <span class="hlt">species</span> in these bioswales, we found that not all <span class="hlt">species</span> are equally suited for bioswales and that not all are equivalent in their transpiration and growth rates, thereby contributing differentially to the functional capacity of bioswales. We conclude that <span class="hlt">species</span> with high stomatal conductance and large mature form are likely to contribute best to bioswale function. PMID:26828175</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=3961351','PMC'); return false;" href="http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=3961351"><span id="translatedtitle">Are the Most Plastic <span class="hlt">Species</span> the Most <span class="hlt">Abundant</span> Ones? An Assessment Using a Fish Assemblage</span></a></p> <p><a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?DB=pmc">PubMed Central</a></p> <p>Vidal, Nicolás; Zaldúa, Natalia; D'Anatro, Alejandro; Naya, Daniel E.</p> <p>2014-01-01</p> <p>Few studies have evaluated phenotypic plasticity at the community level, considering, for example, plastic responses in an entire <span class="hlt">species</span> assemblage. In addition, none of these studies have addressed the relationship between phenotypic plasticity and community structure. Within this context, here we assessed the magnitude of seasonal changes in digestive traits (seasonal flexibility), and of changes during short-term fasting (flexibility during fasting), occurring in an entire fish assemblage, comprising ten <span class="hlt">species</span>, four trophic levels, and a 37-fold range in body mass. In addition, we analyzed the relationship between estimates of digestive flexibility and three basic assemblage structure attributes, i.e., <span class="hlt">species</span> trophic position, body size, and relative <span class="hlt">abundance</span>. We found that: (1) Seasonal digestive flexibility was not related with <span class="hlt">species</span> trophic position or with body size; (2) Digestive flexibility during fasting tended to be inversely correlated with body size, as expected from scaling relationships; (3) Digestive flexibility, both seasonal and during fasting, was positively correlated with <span class="hlt">species</span> relative <span class="hlt">abundance</span>. In conclusion, the present study identified two trends in digestive flexibility in relation to assemblage structure, which represents an encouraging departure point in the search of general patterns in phenotypic plasticity at the local community scale. PMID:24651865</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://pubs.er.usgs.gov/publication/70150320','USGSPUBS'); return false;" href="http://pubs.er.usgs.gov/publication/70150320"><span id="translatedtitle">Predicting probability of occurrence and factors affecting distribution and <span class="hlt">abundance</span> of three Ozark endemic crayfish <span class="hlt">species</span> at multiple spatial scales</span></a></p> <p><a target="_blank" href="http://pubs.er.usgs.gov/pubs/index.jsp?view=adv">USGS Publications Warehouse</a></p> <p>Nolen, Matthew S.; Magoulick, Daniel D.; DiStefano, Robert J.; Imhoff, Emily M.; Wagner, Brian K.</p> <p>2014-01-01</p> <p>We found that a range of environmental variables were important in predicting crayfish distribution and <span class="hlt">abundance</span> at multiple spatial scales and their importance was <span class="hlt">species</span>-, response variable- and scale dependent. We would encourage others to examine the influence of spatial scale on <span class="hlt">species</span> distribution and <span class="hlt">abundance</span> patterns.</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://adsabs.harvard.edu/cgi-bin/nph-data_query?bibcode=2013EnMan..51..524M&link_type=ABSTRACT','NASAADS'); return false;" href="http://adsabs.harvard.edu/cgi-bin/nph-data_query?bibcode=2013EnMan..51..524M&link_type=ABSTRACT"><span id="translatedtitle">Certified and Uncertified Logging Concessions Compared in Gabon: Changes in Stand Structure, <span class="hlt">Tree</span> <span class="hlt">Species</span>, and Biomass</span></a></p> <p><a target="_blank" href="http://adsabs.harvard.edu/abstract_service.html">NASA Astrophysics Data System (ADS)</a></p> <p>Medjibe, V. P.; Putz, Francis E.; Romero, Claudia</p> <p>2013-03-01</p> <p>Forest management certification is assumed to promote sustainable forest management, but there is little field-based evidence to support this claim. To help fill this gap, we compared a Forest Stewardship Council (FSC)-certified with an adjacent uncertified, conventionally logged concession (CL) in Gabon on the basis of logging damage, above-ground biomass (AGB), and <span class="hlt">tree</span> <span class="hlt">species</span> diversity and composition. Before logging, we marked, mapped, and measured all <span class="hlt">trees</span> >10 cm dbh in 20 and twelve 1-ha permanent plots in the FSC and CL areas, respectively. Soil and <span class="hlt">tree</span> damage due to felling, skidding, and road-related activities was then assessed 2-3 months after the 508 ha FSC study area and the 200 ha CL study area were selectively logged at respective intensities of 5.7 m3/ha (0.39 <span class="hlt">trees</span>/ha) and 11.4 m3/ha (0.76 <span class="hlt">trees</span>/ha). For each <span class="hlt">tree</span> felled, averages of 9.1 and 20.9 other <span class="hlt">trees</span> were damaged in the FSC and CL plots, respectively; when expressed as the impacts per timber volume extracted, the values did not differ between the two treatments. Skid trails covered 2.9 % more of the CL surface, but skid trail length per unit timber volume extracted was not greater. Logging roads were wider in the CL than FSC site and disturbed 4.7 % more of the surface. Overall, logging caused declines in AGB of 7.1 and 13.4 % at the FSC and CL sites, respectively. Changes in <span class="hlt">tree</span> <span class="hlt">species</span> composition were small but greater for the CL site. Based on these findings and in light of the pseudoreplicated study design with less-than perfect counterfactual, we cautiously conclude that certification yields environmental benefits even after accounting for differences in logging intensities.</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://www.ncbi.nlm.nih.gov/pubmed/23277438','PUBMED'); return false;" href="http://www.ncbi.nlm.nih.gov/pubmed/23277438"><span id="translatedtitle">Certified and uncertified logging concessions compared in Gabon: changes in stand structure, <span class="hlt">tree</span> <span class="hlt">species</span>, and biomass.</span></a></p> <p><a target="_blank" href="https://www.ncbi.nlm.nih.gov/entrez/query.fcgi?DB=pubmed">PubMed</a></p> <p>Medjibe, V P; Putz, Francis E; Romero, Claudia</p> <p>2013-03-01</p> <p>Forest management certification is assumed to promote sustainable forest management, but there is little field-based evidence to support this claim. To help fill this gap, we compared a Forest Stewardship Council (FSC)-certified with an adjacent uncertified, conventionally logged concession (CL) in Gabon on the basis of logging damage, above-ground biomass (AGB), and <span class="hlt">tree</span> <span class="hlt">species</span> diversity and composition. Before logging, we marked, mapped, and measured all <span class="hlt">trees</span> >10 cm dbh in 20 and twelve 1-ha permanent plots in the FSC and CL areas, respectively. Soil and <span class="hlt">tree</span> damage due to felling, skidding, and road-related activities was then assessed 2-3 months after the 508 ha FSC study area and the 200 ha CL study area were selectively logged at respective intensities of 5.7 m(3)/ha (0.39 <span class="hlt">trees</span>/ha) and 11.4 m(3)/ha (0.76 <span class="hlt">trees</span>/ha). For each <span class="hlt">tree</span> felled, averages of 9.1 and 20.9 other <span class="hlt">trees</span> were damaged in the FSC and CL plots, respectively; when expressed as the impacts per timber volume extracted, the values did not differ between the two treatments. Skid trails covered 2.9 % more of the CL surface, but skid trail length per unit timber volume extracted was not greater. Logging roads were wider in the CL than FSC site and disturbed 4.7 % more of the surface. Overall, logging caused declines in AGB of 7.1 and 13.4 % at the FSC and CL sites, respectively. Changes in <span class="hlt">tree</span> <span class="hlt">species</span> composition were small but greater for the CL site. Based on these findings and in light of the pseudoreplicated study design with less-than perfect counterfactual, we cautiously conclude that certification yields environmental benefits even after accounting for differences in logging intensities. PMID:23277438</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://www.ncbi.nlm.nih.gov/pubmed/27490180','PUBMED'); return false;" href="http://www.ncbi.nlm.nih.gov/pubmed/27490180"><span id="translatedtitle">Direct vs. Microclimate-Driven Effects of <span class="hlt">Tree</span> <span class="hlt">Species</span> Diversity on Litter Decomposition in Young Subtropical Forest Stands.</span></a></p> <p><a target="_blank" href="https://www.ncbi.nlm.nih.gov/entrez/query.fcgi?DB=pubmed">PubMed</a></p> <p>Seidelmann, Katrin N; Scherer-Lorenzen, Michael; Niklaus, Pascal A</p> <p>2016-01-01</p> <p>Effects of <span class="hlt">tree</span> <span class="hlt">species</span> diversity on decomposition can operate via a multitude of mechanism, including alterations of microclimate by the forest canopy. Studying such effects in natural settings is complicated by the fact that topography also affects microclimate and thus decomposition, so that effects of diversity are more difficult to isolate. Here, we quantified decomposition rates of standard litter in young subtropical forest stands, separating effects of canopy <span class="hlt">tree</span> <span class="hlt">species</span> richness and topography, and quantifying their direct and micro-climate-mediated components. Our litterbag study was carried out at two experimental sites of a biodiversity-ecosystem functioning field experiment in south-east China (BEF-China). The field sites display strong topographical heterogeneity and were planted with <span class="hlt">tree</span> communities ranging from monocultures to mixtures of 24 native subtropical <span class="hlt">tree</span> <span class="hlt">species</span>. Litter bags filled with senescent leaves of three native <span class="hlt">tree</span> <span class="hlt">species</span> were placed from Nov. 2011 to Oct. 2012 on 134 plots along the <span class="hlt">tree</span> <span class="hlt">species</span> diversity gradient. Topographic features were measured for all and microclimate in a subset of plots. Stand <span class="hlt">species</span> richness, topography and microclimate explained important fractions of the variations in litter decomposition rates, with diversity and topographic effects in part mediated by microclimatic changes. <span class="hlt">Tree</span> stands were 2-3 years old, but nevertheless <span class="hlt">tree</span> <span class="hlt">species</span> diversity explained more variation (54.3%) in decomposition than topography (7.7%). <span class="hlt">Tree</span> <span class="hlt">species</span> richness slowed litter decomposition, an effect that slightly depended on litter <span class="hlt">species</span> identity. A large part of the variance in decomposition was explained by <span class="hlt">tree</span> <span class="hlt">species</span> composition, with the presence of three <span class="hlt">tree</span> <span class="hlt">species</span> playing a significant role. Microclimate explained 31.4% of the variance in decomposition, and was related to lower soil moisture. Within this microclimate effect, <span class="hlt">species</span> diversity (without composition) explained 8.9% and topography 34.4% of</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=4973968','PMC'); return false;" href="http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=4973968"><span id="translatedtitle">Direct vs. Microclimate-Driven Effects of <span class="hlt">Tree</span> <span class="hlt">Species</span> Diversity on Litter Decomposition in Young Subtropical Forest Stands</span></a></p> <p><a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?DB=pmc">PubMed Central</a></p> <p>Seidelmann, Katrin N.; Scherer-Lorenzen, Michael; Niklaus, Pascal A.</p> <p>2016-01-01</p> <p>Effects of <span class="hlt">tree</span> <span class="hlt">species</span> diversity on decomposition can operate via a multitude of mechanism, including alterations of microclimate by the forest canopy. Studying such effects in natural settings is complicated by the fact that topography also affects microclimate and thus decomposition, so that effects of diversity are more difficult to isolate. Here, we quantified decomposition rates of standard litter in young subtropical forest stands, separating effects of canopy <span class="hlt">tree</span> <span class="hlt">species</span> richness and topography, and quantifying their direct and micro-climate-mediated components. Our litterbag study was carried out at two experimental sites of a biodiversity-ecosystem functioning field experiment in south-east China (BEF-China). The field sites display strong topographical heterogeneity and were planted with <span class="hlt">tree</span> communities ranging from monocultures to mixtures of 24 native subtropical <span class="hlt">tree</span> <span class="hlt">species</span>. Litter bags filled with senescent leaves of three native <span class="hlt">tree</span> <span class="hlt">species</span> were placed from Nov. 2011 to Oct. 2012 on 134 plots along the <span class="hlt">tree</span> <span class="hlt">species</span> diversity gradient. Topographic features were measured for all and microclimate in a subset of plots. Stand <span class="hlt">species</span> richness, topography and microclimate explained important fractions of the variations in litter decomposition rates, with diversity and topographic effects in part mediated by microclimatic changes. <span class="hlt">Tree</span> stands were 2–3 years old, but nevertheless <span class="hlt">tree</span> <span class="hlt">species</span> diversity explained more variation (54.3%) in decomposition than topography (7.7%). <span class="hlt">Tree</span> <span class="hlt">species</span> richness slowed litter decomposition, an effect that slightly depended on litter <span class="hlt">species</span> identity. A large part of the variance in decomposition was explained by <span class="hlt">tree</span> <span class="hlt">species</span> composition, with the presence of three <span class="hlt">tree</span> <span class="hlt">species</span> playing a significant role. Microclimate explained 31.4% of the variance in decomposition, and was related to lower soil moisture. Within this microclimate effect, <span class="hlt">species</span> diversity (without composition) explained 8.9% and topography 34.4% of</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=4134238','PMC'); return false;" href="http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=4134238"><span id="translatedtitle">Patterns of <span class="hlt">Tree</span> <span class="hlt">Species</span> Diversity in Relation to Climatic Factors on the Sierra Madre Occidental, Mexico</span></a></p> <p><a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?DB=pmc">PubMed Central</a></p> <p>Silva-Flores, Ramón; Pérez-Verdín, Gustavo; Wehenkel, Christian</p> <p>2014-01-01</p> <p>Biological diversity can be defined as variability among living organisms from all sources, including terrestrial organisms, marine and other aquatic ecosystems, and the ecological complexes which they are part of. This includes diversity within <span class="hlt">species</span>, between <span class="hlt">species</span>, and of ecosystems. Numerous diversity indices combine richness and evenness in a single expression, and several climate-based explanations have been proposed to explain broad-scale diversity patterns. However, climate-based water-energy dynamics appears to be an essential factor that determines patterns of diversity. The Mexican Sierra Madre Occidental occupies an area of about 29 million hectares and is located between the Neotropical and Holarctic ecozones. It shelters a high diversity of flora, including 24 different <span class="hlt">species</span> of Pinus (ca. 22% on the whole), 54 <span class="hlt">species</span> of Quercus (ca. 9–14%), 7 <span class="hlt">species</span> of Arbutus (ca. 50%) and many other <span class="hlt">trees</span> <span class="hlt">species</span>. The objectives of this study were to model how <span class="hlt">tree</span> <span class="hlt">species</span> diversity is related to climatic and geographic factors and stand density and to test the Metabolic Theory, Productivity-Diversity Hypothesis, Physiological Tolerance Hypothesis, Mid-Domain Effect, and the Water-Energy Dynamic Theory on the Sierra Madre Occidental, Durango. The results supported the Productivity-Diversity Hypothesis, Physiological Tolerance Hypothesis and Water-Energy Dynamic Theory, but not the Mid-Domain Effect or Metabolic Theory. The annual aridity index was the variable most closely related to the diversity indices analyzed. Contemporary climate was found to have moderate to strong effects on the minimum, median and maximum <span class="hlt">tree</span> <span class="hlt">species</span> diversity. Because water-energy dynamics provided a satisfactory explanation for the patterns of minimum, median and maximum diversity, an understanding of this factor is critical to future biodiversity research. Quantile regression of the data showed that the three diversity parameters of <span class="hlt">tree</span> <span class="hlt">species</span> are generally higher in cold</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://www.ncbi.nlm.nih.gov/pubmed/25127455','PUBMED'); return false;" href="http://www.ncbi.nlm.nih.gov/pubmed/25127455"><span id="translatedtitle">Patterns of <span class="hlt">tree</span> <span class="hlt">species</span> diversity in relation to climatic factors on the Sierra Madre Occidental, Mexico.</span></a></p> <p><a target="_blank" href="https://www.ncbi.nlm.nih.gov/entrez/query.fcgi?DB=pubmed">PubMed</a></p> <p>Silva-Flores, Ramón; Pérez-Verdín, Gustavo; Wehenkel, Christian</p> <p>2014-01-01</p> <p>Biological diversity can be defined as variability among living organisms from all sources, including terrestrial organisms, marine and other aquatic ecosystems, and the ecological complexes which they are part of. This includes diversity within <span class="hlt">species</span>, between <span class="hlt">species</span>, and of ecosystems. Numerous diversity indices combine richness and evenness in a single expression, and several climate-based explanations have been proposed to explain broad-scale diversity patterns. However, climate-based water-energy dynamics appears to be an essential factor that determines patterns of diversity. The Mexican Sierra Madre Occidental occupies an area of about 29 million hectares and is located between the Neotropical and Holarctic ecozones. It shelters a high diversity of flora, including 24 different <span class="hlt">species</span> of Pinus (ca. 22% on the whole), 54 <span class="hlt">species</span> of Quercus (ca. 9-14%), 7 <span class="hlt">species</span> of Arbutus (ca. 50%) and many other <span class="hlt">trees</span> <span class="hlt">species</span>. The objectives of this study were to model how <span class="hlt">tree</span> <span class="hlt">species</span> diversity is related to climatic and geographic factors and stand density and to test the Metabolic Theory, Productivity-Diversity Hypothesis, Physiological Tolerance Hypothesis, Mid-Domain Effect, and the Water-Energy Dynamic Theory on the Sierra Madre Occidental, Durango. The results supported the Productivity-Diversity Hypothesis, Physiological Tolerance Hypothesis and Water-Energy Dynamic Theory, but not the Mid-Domain Effect or Metabolic Theory. The annual aridity index was the variable most closely related to the diversity indices analyzed. Contemporary climate was found to have moderate to strong effects on the minimum, median and maximum <span class="hlt">tree</span> <span class="hlt">species</span> diversity. Because water-energy dynamics provided a satisfactory explanation for the patterns of minimum, median and maximum diversity, an understanding of this factor is critical to future biodiversity research. Quantile regression of the data showed that the three diversity parameters of <span class="hlt">tree</span> <span class="hlt">species</span> are generally higher in cold</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://www.ncbi.nlm.nih.gov/pubmed/21691855','PUBMED'); return false;" href="http://www.ncbi.nlm.nih.gov/pubmed/21691855"><span id="translatedtitle"><span class="hlt">Tree</span> <span class="hlt">species</span> identity and interactions with neighbors determine nutrient leaching in model tropical forests.</span></a></p> <p><a target="_blank" href="https://www.ncbi.nlm.nih.gov/entrez/query.fcgi?DB=pubmed">PubMed</a></p> <p>Ewel, John J; Bigelow, Seth W</p> <p>2011-12-01</p> <p>An ecosystem containing a mixture of <span class="hlt">species</span> that differ in phenology, morphology, and physiology might be expected to resist leaching of soil nutrients to a greater extent than one composed of a single <span class="hlt">species</span>. We tested the effects of <span class="hlt">species</span> identity and plant-life-form richness on nutrient leaching at a lowland tropical site where deep infiltration averages >2 m year(-1). Three indigenous <span class="hlt">tree</span> <span class="hlt">species</span> with contrasting leafing phenologies (evergreen, dry-season deciduous, and wet-season deciduous) were grown in monoculture and together with two other life-forms with which they commonly occur in tropical forests: a palm and a giant, perennial herb. To calculate nutrient leaching over an 11-year period, concentrations of nutrients in soil water were multiplied by drainage rates estimated from a water balance. The effect of plant-life-form richness on retention differed according to <span class="hlt">tree</span> <span class="hlt">species</span> identity and nutrient. Nitrate retention was greater in polycultures of the dry-season deciduous <span class="hlt">tree</span> <span class="hlt">species</span> (mean of 7.4 kg ha(-1) year(-1) of NO(3)-N lost compared to 12.7 in monoculture), and calcium and magnesium retention were greater in polycultures of the evergreen and wet-season deciduous <span class="hlt">tree</span> <span class="hlt">species</span>. Complementary use of light led to intensification of soil exploitation by roots, the main agent responsible for enhanced nutrient retention in some polycultures. Other mechanisms included differences in nutrient demand among <span class="hlt">species</span>, and avoidance of catastrophic failure due to episodic weather events or pest outbreaks. Even unrealistically simple multi-life-form mimics of tropical forest can safeguard a site's nutrient capital if careful attention is paid to <span class="hlt">species</span>' characteristics and temporal changes in interspecific interactions. PMID:21691855</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=4206468','PMC'); return false;" href="http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=4206468"><span id="translatedtitle">Data Concatenation, Bayesian Concordance and Coalescent-Based Analyses of the <span class="hlt">Species</span> <span class="hlt">Tree</span> for the Rapid Radiation of Triturus Newts</span></a></p> <p><a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?DB=pmc">PubMed Central</a></p> <p>Wielstra, Ben; Arntzen, Jan W.; van der Gaag, Kristiaan J.; Pabijan, Maciej; Babik, Wieslaw</p> <p>2014-01-01</p> <p>The phylogenetic relationships for rapid <span class="hlt">species</span> radiations are difficult to disentangle. Here we study one such case, namely the genus Triturus, which is composed of the marbled and crested newts. We analyze data for 38 genetic markers, positioned in 3-prime untranslated regions of protein-coding genes, obtained with 454 sequencing. Our dataset includes twenty Triturus newts and represents all nine <span class="hlt">species</span>. Bayesian analysis of population structure allocates all individuals to their respective <span class="hlt">species</span>. The branching patterns obtained by data concatenation, Bayesian concordance analysis and coalescent-based estimations of the <span class="hlt">species</span> <span class="hlt">tree</span> differ from one another. The data concatenation based <span class="hlt">species</span> <span class="hlt">tree</span> shows high branch support but branching order is considerably affected by allele choice in the case of heterozygotes in the concatenation process. Bayesian concordance analysis expresses the conflict between individual gene <span class="hlt">trees</span> for part of the Triturus <span class="hlt">species</span> <span class="hlt">tree</span> as low concordance factors. The coalescent-based <span class="hlt">species</span> <span class="hlt">tree</span> is relatively similar to a previously published <span class="hlt">species</span> <span class="hlt">tree</span> based upon morphology and full mtDNA and any conflicting internal branches are not highly supported. Our findings reflect high gene <span class="hlt">tree</span> discordance due to incomplete lineage sorting (possibly aggravated by hybridization) in combination with low information content of the markers employed (as can be expected for relatively recent <span class="hlt">species</span> radiations). This case study highlights the complexity of resolving rapid radiations and we acknowledge that to convincingly resolve the Triturus <span class="hlt">species</span> <span class="hlt">tree</span> even more genes will have to be consulted. PMID:25337997</p> </li> </ol> <div class="pull-right"> <ul class="pagination"> <li><a href="#" onclick='return showDiv("page_1");'>«</a></li> <li><a href="#" onclick='return showDiv("page_18");'>18</a></li> <li><a href="#" onclick='return showDiv("page_19");'>19</a></li> <li class="active"><span>20</span></li> <li><a href="#" onclick='return showDiv("page_21");'>21</a></li> <li><a href="#" onclick='return showDiv("page_22");'>22</a></li> <li><a href="#" onclick='return showDiv("page_25");'>»</a></li> </ul> </div> </div><!-- col-sm-12 --> </div><!-- row --> </div><!-- page_20 --> <div id="page_21" class="hiddenDiv"> <div class="row"> <div class="col-sm-12"> <div class="pull-right"> <ul class="pagination"> <li><a href="#" onclick='return showDiv("page_1");'>«</a></li> <li><a href="#" onclick='return showDiv("page_19");'>19</a></li> <li><a href="#" onclick='return showDiv("page_20");'>20</a></li> <li class="active"><span>21</span></li> <li><a href="#" onclick='return showDiv("page_22");'>22</a></li> <li><a href="#" onclick='return showDiv("page_23");'>23</a></li> <li><a href="#" onclick='return showDiv("page_25");'>»</a></li> </ul> </div> </div> </div> <div class="row"> <div class="col-sm-12"> <ol class="result-class" start="401"> <li> <p><a target="_blank" onclick="trackOutboundLink('http://adsabs.harvard.edu/abs/2015EGUGA..1712942H','NASAADS'); return false;" href="http://adsabs.harvard.edu/abs/2015EGUGA..1712942H"><span id="translatedtitle"><span class="hlt">Tree</span> <span class="hlt">species</span> specific soil moisture patterns and dynamics through the seasons</span></a></p> <p><a target="_blank" href="http://adsabs.harvard.edu/abstract_service.html">NASA Astrophysics Data System (ADS)</a></p> <p>Heidbüchel, Ingo; Dreibrodt, Janek; Simard, Sonia; Güntner, Andreas; Blume, Theresa</p> <p>2015-04-01</p> <p>Soil moisture patterns in the landscape are largely controlled by soil types (pore size distributions) and landscape position. But how strong is the influence of vegetation on patterns within a single soil type? While we would envision a clear difference in soil moisture patterns and responses between for example bare soil, a pasture and a forest, our conceptual images start to become less clear when we move on to different forest stands. Do different <span class="hlt">tree</span> <span class="hlt">species</span> cause different moisture patterns to emerge? Could it be possible to identify the dominant <span class="hlt">tree</span> <span class="hlt">species</span> of a site by classifying its soil moisture pattern? To investigate this question we analyzed data from 15 sensor clusters in the lowlands of north-eastern Germany (within the TERENO observatory) which were instrumented with soil moisture sensors (5 profiles per site), tensiometers, sap flow sensors, throughfall and stemflow gages. Data has been collected at these sites since May 2014. While the summer data has already been analyzed, the analysis of the winter data and thus the possible seasonal shifts in patterns will be carried out in the coming months. Throughout the last summer we found different dynamics of soil moisture patterns under pine <span class="hlt">trees</span> compared to beech <span class="hlt">trees</span>. While the soils under beech <span class="hlt">trees</span> were more often relatively wet and more often relatively dry, the soils under pine <span class="hlt">trees</span> showed less variability and more often average soil moisture. These differences are most likely due to differences in both throughfall patterns as well as root water uptake. Further analysis includes the use of throughfall and stemflow data as well as stable water isotope samples that were taken at different depths in the soil, in the groundwater and from the sapwood. The manifestation of <span class="hlt">tree</span> <span class="hlt">species</span> differences in soil moisture patterns and dynamics is likely to have implications for groundwater recharge, transit times and hydrologic partitioning.</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://pubs.er.usgs.gov/publication/70031880','USGSPUBS'); return false;" href="http://pubs.er.usgs.gov/publication/70031880"><span id="translatedtitle">Influences of calcium availability and <span class="hlt">tree</span> <span class="hlt">species</span> on Ca isotope fractionation in soil and vegetation</span></a></p> <p><a target="_blank" href="http://pubs.er.usgs.gov/pubs/index.jsp?view=adv">USGS Publications Warehouse</a></p> <p>Page, B.D.; Bullen, T.D.; Mitchell, M.J.</p> <p>2008-01-01</p> <p>The calcium (Ca) isotope system is potentially of great use for understanding biogeochemical processes at multiple scales in forest ecosystems, yet remains largely unexplored for this purpose. In order to further our understanding of Ca behavior in forests, we examined two nearly adjacent hardwood-dominated catchments with differing soil Ca concentrations, developed from crystalline bedrock, to determine the variability of 44Ca/ 40Ca ratios (expressed as ??44Ca) within soil and vegetation pools. For both sugar maple and American beech, the Ca isotope compositions of the measured roots and calculated bulk <span class="hlt">trees</span> were considerably lighter than those of soil pools at these sites, suggesting that the <span class="hlt">trees</span> were able to preferentially take up light Ca at the root-soil interface. The Ca isotope compositions of three of four root samples were among the lightest values yet reported for terrestrial materials (??44Ca ???-3.95???). Our results further indicate that Ca isotopes were fractionated along the transpiration streams of both <span class="hlt">tree</span> <span class="hlt">species</span> with roots having the least ??44Ca values and leaf litter the greatest. An approximately 2??? difference in ??44Ca values between roots and leaf litter of both <span class="hlt">tree</span> <span class="hlt">species</span> suggests a persistent fractionation mechanism along the transpiration stream, likely related to Ca binding in wood tissue coupled with internal ion exchange. Finally, our data indicate that differing <span class="hlt">tree</span> <span class="hlt">species</span> demand for Ca and soil Ca concentrations together may influence Ca isotope distribution within the <span class="hlt">trees</span>. Inter-catchment differences in Ca isotope distributions in soils and <span class="hlt">trees</span> were minor, indicating that the results of our study may have broad transferability to studies of forest ecosystems in catchments developed on crystalline substrates elsewhere. ?? 2008 Springer Science+Business Media B.V.</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://www.ncbi.nlm.nih.gov/pubmed/17204076','PUBMED'); return false;" href="http://www.ncbi.nlm.nih.gov/pubmed/17204076"><span id="translatedtitle">Large variation in whole-plant water-use efficiency among tropical <span class="hlt">tree</span> <span class="hlt">species</span>.</span></a></p> <p><a target="_blank" href="https://www.ncbi.nlm.nih.gov/entrez/query.fcgi?DB=pubmed">PubMed</a></p> <p>Cernusak, Lucas A; Aranda, Jorge; Marshall, John D; Winter, Klaus</p> <p>2007-01-01</p> <p>It is well known that whole-plant water-use efficiency (transpiration efficiency of carbon gain, TE(C)) varies among plant <span class="hlt">species</span> with different photosynthetic pathways. However, less is known of such variation among <span class="hlt">tree</span> <span class="hlt">species</span> within the C(3) group. Here we measured the TE(C) of seven C(3) tropical <span class="hlt">tree</span> <span class="hlt">species</span>. Isotopic analyses (delta(13)C, delta(18)O, and delta(15)N) and elemental analyses (carbon and nitrogen) were undertaken to provide insight into sources of variation in TE(C). Plants were grown over several months in approx. 80% full sunlight in individual 38-l containers in the Republic of Panama. Soil moisture content was nonlimiting. Significant variation was observed in TE(C) among the C(3) <span class="hlt">tree</span> <span class="hlt">species</span>. Values ranged from 1.6 mmol C mol(-1) H(2)O for teak (Tectona grandis) to 4.0 mmol C mol(-1) H(2)O for a legume, Platymiscium pinnatum. Variation in TE(C) was correlated with both leaf N concentration, a proxy for photosynthetic capacity, and oxygen-isotope enrichment, a proxy for stomatal conductance. The TE(C) varied with C-isotope discrimination within <span class="hlt">species</span>, but the relationship broke down among <span class="hlt">species</span>, reflecting the existence of <span class="hlt">species</span>-specific offsets. PMID:17204076</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://adsabs.harvard.edu/abs/2009AGUFM.B23A0359M','NASAADS'); return false;" href="http://adsabs.harvard.edu/abs/2009AGUFM.B23A0359M"><span id="translatedtitle">Leaf gas exchange traits of domestic and exotic <span class="hlt">tree</span> <span class="hlt">species</span> in Cambodia</span></a></p> <p><a target="_blank" href="http://adsabs.harvard.edu/abstract_service.html">NASA Astrophysics Data System (ADS)</a></p> <p>Miyazawa, Y.; Tateishi, M.; Kumagai, T.; Otsuki, K.</p> <p>2009-12-01</p> <p>In forests under the management by community villagers, exotic <span class="hlt">tree</span> <span class="hlt">species</span> with rapid growth rate are introduced in wide range of Cambodia. To evaluate the influence of the introduction on the forest gas exchange and water budget, we investigated the leaf gas exchange traits of two domestic (Dipterocarpus obtusifolius and Shorea roxburghii) and exotic <span class="hlt">tree</span> <span class="hlt">species</span> (Acasia auriculiformis and Eucalyptus camadilansis). We sampled shoots of each <span class="hlt">species</span> and measured the leaf gas exchange traits (photosynthetic rates under different CO2 concentrations, transpiration rate and stomatal conductance) (6 leaves x 3 <span class="hlt">trees</span> x 4 <span class="hlt">species</span>). We carried out this measurement at 2 months intervals for a year from the beginning of rainy season and compared the obtained traits among <span class="hlt">species</span>. Light saturated rate of net photosynthesis was higher in E. camadilansis but did not differ among other <span class="hlt">species</span> both in rainy and dry seasons. Seasonal patter in photosynthetic traits was not obvious. Each <span class="hlt">species</span> changed stomatal conductance in response to changes in environmental conditions. The response was more sensitive than reported values. In this presentation, we show details about the basic information about the leaf-level gas exchange traits, which are required to run soil- vegetation - atmosphere transfer model.</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://www.ncbi.nlm.nih.gov/pubmed/24392290','PUBMED'); return false;" href="http://www.ncbi.nlm.nih.gov/pubmed/24392290"><span id="translatedtitle">Sampling designs matching <span class="hlt">species</span> biology produce accurate and affordable <span class="hlt">abundance</span> indices.</span></a></p> <p><a target="_blank" href="https://www.ncbi.nlm.nih.gov/entrez/query.fcgi?DB=pubmed">PubMed</a></p> <p>Harris, Grant; Farley, Sean; Russell, Gareth J; Butler, Matthew J; Selinger, Jeff</p> <p>2013-01-01</p> <p>Wildlife biologists often use grid-based designs to sample animals and generate <span class="hlt">abundance</span> estimates. Although sampling in grids is theoretically sound, in application, the method can be logistically difficult and expensive when sampling elusive <span class="hlt">species</span> inhabiting extensive areas. These factors make it challenging to sample animals and meet the statistical assumption of all individuals having an equal probability of capture. Violating this assumption biases results. Does an alternative exist? Perhaps by sampling only where resources attract animals (i.e., targeted sampling), it would provide accurate <span class="hlt">abundance</span> estimates more efficiently and affordably. However, biases from this approach would also arise if individuals have an unequal probability of capture, especially if some failed to visit the sampling area. Since most biological programs are resource limited, and acquiring <span class="hlt">abundance</span> data drives many conservation and management applications, it becomes imperative to identify economical and informative sampling designs. Therefore, we evaluated <span class="hlt">abundance</span> estimates generated from grid and targeted sampling designs using simulations based on geographic positioning system (GPS) data from 42 Alaskan brown bears (Ursus arctos). Migratory salmon drew brown bears from the wider landscape, concentrating them at anadromous streams. This provided a scenario for testing the targeted approach. Grid and targeted sampling varied by trap amount, location (traps placed randomly, systematically or by expert opinion), and traps stationary or moved between capture sessions. We began by identifying when to sample, and if bears had equal probability of capture. We compared <span class="hlt">abundance</span> estimates against seven criteria: bias, precision, accuracy, effort, plus encounter rates, and probabilities of capture and recapture. One grid (49 km(2) cells) and one targeted configuration provided the most accurate results. Both placed traps by expert opinion and moved traps between capture sessions</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=3869179','PMC'); return false;" href="http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=3869179"><span id="translatedtitle">Sampling designs matching <span class="hlt">species</span> biology produce accurate and affordable <span class="hl