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138 results for “community phylogenetic”
Data from: A phylogenetic- and trait-based analysis of community assembly in a subtropical forest in central China
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Microbial communities of wild bees and comparative phylogenetics of key bacterial taxa across the bee tree of life
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Functional traits and phylogenetic structure based on root neighborhoods shape the mechanisms of species coexistence in underground communities
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Unravelling the factors affecting taxonomic, phylogenetic and functional beta diversity of stream macroinvertebrate communities in the World's Third Pole
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Data from: Examining differences in phylogenetic composition enhances understanding of the phylogenetic structure of the shrub community in the northeastern Qinghai-Tibetan Plateau
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The Community Coevolution Model with application to the study of evolutionary relationships between genes based on phylogenetic profiles
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Data from: Geography and ecology shape the phylogenetic composition of Amazonian tree communities
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Long-term nitrogen fertilization alters arbuscular mycorrhizal fungi community phylogenetic structure in plant roots across fine spatial scales
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Spatial phylogenetic and phenotypic patterns reveal ontogenetic shifts in ecological processes of plant community assembly
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Both source and recipient range phylogenetic community structure can predict the outcome of avian introductions
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Data from: Warming alters plant phylogenetic and functional community structure
<ol> <li><span>Climate change is known to affect many facets of the Earth's ecosystems.<b> </b>However, little is known about its impacts on phylogenetic and functional properties of ecological communities.<b> </b></span></li> <li><span>Here we studied the responses of plant communities in an alpine grassland on the Tibetan Plateau to environmental warming across taxonomic, phylogenetic, and functional levels in a six-year multiple-level warming experiment. </span></li> <li><span>While low-level warming did not alter either plant species richness or phylogenetic/functional community structure, high-level warming significantly decreased species richness. Higher-level warming more strongly reduced soil moisture and caused stronger environmental filtering, consequently changing species composition and community structure. At the plant functional trait level, high-level warming promoted species turnover through altering the effects of traits such as plant height on species extinction and specific leaf area on species colonization. As a result, high-, but not low-level warming drove phylogenetic/functional community structure from overdispersion to randomness, by filtering out species that were functionally dissimilar and distantly related to the resident species. </span></li> <li><span><i>Synthesis</i>. Our study provides evidence that the responses of plant phylogenetic and functional community structure to low warming differ from those in the future scenarios of increasing temperature. Importantly, the extinction of species that were functionally dissimilar and distantly related to the resident species contributed to alterations in plant community structure under high warming. Our study underscores the need to incorporate the phylogenetic and functional perspectives to gain a more complete understanding of community responses to climate warming.</span></li> </ol>
Data from: Using functional and phylogenetic diversity to infer avian community assembly along elevational gradients
<p><strong>Aim </strong>We present the first global analysis of elevational gradients in functional and phylogenetic diversity of birds and test for signals of deterministic processes (i.e., environmental filtering and limiting similarity) in community assembly. Further, we examine for latitudinal effects in the strength of these processes.</p> <p><strong>Location </strong>Forty-six elevational gradients across the globe.</p> <p><strong>Time period </strong>Current (between 1924 and 2016)</p> <p><strong>Major taxa </strong>Birds.</p> <p><strong>Methods </strong>We systematically selected, compiled and analyzed published data on bird diversity along elevational gradients. For each gradient, we calculated functional and phylogenetic diversity across elevations and described the main patterns for each diversity metric. Then, we calculated standardized effect sizes (SES) of each metric and used these SES values to (1) test the signals of deterministic processes shaping assemblages across elevations and (2) to compare changes in within-mountain diversity, among mountains located at different latitudes.</p> <p><strong>Results</strong> Birds displayed eight different patterns of functional and phylogenetic diversity across elevations, but no global pattern of increase or decrease was found. There is, however, a consistent global pattern of phylogenetic clustering, with mountain species being more closely related to each other at any given elevation. Latitude had a significant effect on within-mountain changes in functional and phylogenetic diversity across elevations, with more negative slopes (stronger decline in diversity metrics with increasing elevation) in tropical mountains.</p> <p><strong>Main conclusions</strong> Our findings challenge the idea that the decline of functional and phylogenetic diversity with elevation is a general pattern, emphasizing the uniqueness of each mountain system. In spite of this great variability, we found a latitudinal effect in the patterns of within-mountain functional and phylogenetic dispersion of birds after controlling for effects of species richness. Environmental filtering, thus, may act differently in tropical and temperate mountains, and calls for more comparative studies on the mechanisms driving community assembly at different latitudes.</p>
Scale-dependent drivers of the phylogenetic structure and similarity of tree communities in northwestern Amazonia
<p><span><span><span><span><span><span><span><span><span><span><span><span>1. The extent to which historical dispersal, environmental features and geographic barriers shape the phylogenetic structure and turnover of tree communities in northwestern Amazonia at multiple spatial scales remains poorly understood. </span></span></span></span></span></span></span></span></span></span></span></span></p> <p><span><span><span><span><span><span><span><span><span><span><span><span>2. We used 85 floristically standardized 0.1-ha plots (DBH ³ 2.5 cm) distributed in three subregions of northwestern (NW) Amazonia across three main habitat types (floodplain, swamp, terra firme forests), to hypothesize that: i) historical dispersal overcome geographical barriers, which meant low local phylogenetic relatedness and low phylogenetic turnover. ii) Geographical barriers triggered dispersal limitation, causing high local and subregional phylogenetic clustering and high regional phylogenetic turnover. iii) Edaphic properties and flooding were negatively associated to stem size and determined the tree phylogenetic structure and turnover at local and regional scales in Amazon forests.</span></span></span></span></span></span></span></span></span></span></span></span></p> <p><span><span><span><span><span><span><span><span><span><span><span><span>3. We found that the extent to which environmental or evolutionary features shaped the phylogenetic structure and phylogenetic similarity of tree communities in NW Amazonia was scale dependent. Specifically, we show that the relative importance of environmental factors increases as spatial scale and species pool decreases. Further, we find that these results are generally robust for both adult and juvenile trees. </span></span></span></span></span></span></span></span></span></span></span></span></p> <p><i>Synthesis</i><span><span><span><span><span><span><span><span><span><span><span><span>: Our analysis at the regional (NW Amazon) scale lends support to the idea of Amazonian forests as a large metacommunity</span></span></span></span></span></span></span></span></span></span></span></span><span><span><span><span><span><span><span><span><span><span><span><span> primarily structured by historical dispersal at large spatial scales with an increasing importance of environmental factors at finer spatial scales. The convergence of ancestral lineages across </span></span></span></span></span></span></span></span></span></span></span></span><span><span><span><span><span><span><span><span><span><span><span><span>habitat types </span></span></span></span></span></span></span></span></span></span></span></span><span><span><span><span><span><span><span><span><span><span><span><span>may have been due to the relatively recent formation of geographical barriers that promoted local isolation and allopatric speciation.</span></span></span></span></span></span></span></span></span></span></span></span></p>
Diversity and phylogenetic community structure across elevation during climate change in a family of hyperdiverse neotropical beetles (Staphylinidae)
<p>Environmental stress from abiotic conditions imposes physiological limits on individuals within communities, and these stressful conditions can act as a filter on the species present in any given environment. Such abiotic stressors can reduce a community's diversity and make its composition more phylogenetically clustered. Using a decade of staphylinid beetle (Staphylinidae, Coleoptera, rove beetles) collections made across a 1,500 m elevation gradient in northwestern Costa Rica (2008-2017) we asked what species lived there, how large and overlapping were the communities across this gradient, and what relationship was there between elevation and diversity. Using DNA barcodes for identification and phylogenetic estimates of community structure, we found high turnover across elevation, and that staphylinid diversity increased linearly with elevation. Because of this, we found staphylinid diversity was negatively related to surface area and temperature, and positively with precipitation. We suggest that historical biogeography and contemporary environmental stress have combined to produce these observed patterns. The forests in which these beetles are found are heating and drying rapidly and our finding that diversity increases with elevation suggests that there will be catastrophic biodiversity loss in the coming decades.</p>
Data from: Phylogenetic plant community structure along elevation is lineage specific
The trend of closely related taxa to retain similar environmental preferences mediated by inherited traits suggests that several patterns observed at the community scale originate from longer evolutionary processes. While the effects of phylogenetic relatedness have been previously studied within a single genus or family, lineage-specific effects on the ecological processes governing community assembly have rarely been studied for entire communities or flora. Here, we measured how community phylogenetic structure varies across a wide elevation gradient for plant lineages represented by 35 families, using a co-occurrence index and net relatedness index (NRI). We propose a framework that analyses each lineage separately and reveals the trend of ecological assembly at tree nodes. We found prevailing phylogenetic clustering for more ancient nodes and overdispersion in more recent tree nodes. Closely related species may thus rapidly evolve new environmental tolerances to radiate into distinct communities, while older lineages likely retain inherent environmental tolerances to occupy communities in similar environments, either through efficient dispersal mechanisms or the exclusion of older lineages with more divergent environmental tolerances. Our study illustrates the importance of disentangling the patterns of community assembly among lineages to better interpret the ecological role of traits. It also sheds light on studies reporting absence of phylogenetic signal, and opens new perspectives on the analysis of niche and trait conservatism across lineages.
Data from: Trophic position determines functional and phylogenetic recovery after disturbance within a community
1. The roles that functional traits and/or evolutionary history of species from co-occuring trophic groups have in determining community recovery following disturbance are poorly understood. Functional traits help determine how species interact with their environment, thus functional traits are likely to change with time since logging. However, traits of species may also be phylogenetically constrained depending on their evolutionary history. Because beetles are trophically diverse, the effects of phylogenetic and functional aspects of community recovery can be compared between co-occuring trophic groups. 2. Using a chronosequence of forest ages following logging, we applied a novel combination of functional trait and phylogenetic approaches to assess the extent to which taxonomic, functional and phylogenetic composition recovered after logging, and if these dimensions of composition approached those characteristic of mature forests, for both predators and decomposers/primary consumers. We also examined to what extent functional traits of both trophic groups were phylogenetically conserved. 3. Predator functional compostion had recovered ~45 years after logging, and this recovery preceded taxonomic recovery. Neither taxonomic nor functional composition had recovered for the decomposer/primary consumer communites by this time. 4. In contrast to decomposers/primary consumers, predator community recovery had no distinct phylogenetic signature, yet predator functional traits were more phylogenetically conserved than decomposers/primary consumer functional traits. 5. Trait syndromes that characterise forest recovery stages are identified and provide a basis for future work on community re-assembly following disturbance. 6. We demonstrate differential recovery of co-occuring beetle trophic groups following disturbance. We show that functional and phylogenetic composition may be disconnected from taxonomic composition; highlighting the advantages of integrating understanding of these three potentially independent components of ecological diversity to enable deeper understanding of animal community composition.
Data from: Investigating sensitivity of phylogenetic community structure metrics using North American desert bats
A relatively recent approach to characterizing structure of natural communities is to use phylogenies of species pools to compare patterns of relatedness between real and simulated communities. Such an approach can provide mechanistic insights into structure. Despite popularity of phylogenetic approaches, we do not yet fully understand how phylogenetic community structure (PCS) metrics might be impacted by changes to the phylogeny or community membership data from which they are calculated. We investigate metric sensitivity and examine PCS of bats from the 4 great desert regions of North America. We inferred a phylogeny of the regional species pool to calculate PCS metrics using community membership data delimited using 3 different methods. We also randomized our phylogeny to determine how reasonable changes to the tree affect PCS metrics. Overall, PCS metrics are quite robust to moderate changes in the phylogeny from which they are calculated. These metrics also are fairly insensitive to our 3 methods of delimiting communities. Additionally, we found that in general, communities are significantly phylogenetically clustered, suggesting habitat filtering has been important in community assembly.
Data from: Invasive species removal increases species and phylogenetic diversity of wetland plant communities
Plant invasions result in biodiversity losses and altered ecological functions, though quantifying loss of multiple ecosystem functions presents a research challenge. Plant phylogenetic diversity correlates with a range of ecosystem functions, and can be used as a proxy for ecosystem multifunctionality. Laurentian Great Lakes coastal wetlands are ideal systems for testing invasive species management effects because they support diverse biological communities, provide numerous ecosystem services, and are increasingly dominated by invasive macrophytes. Invasive cattails are among the most widespread and abundant of these taxa. We conducted a three-year study in two Great Lakes wetlands, testing the effects of a gradient of cattail removal intensities (mowing, harvest, complete biomass removal) within two vegetation zones (emergent marsh, wet meadow) on plant taxonomic and phylogenetic diversity. To evaluate native plant recovery potential, we paired this with a seed-bank emergence study that quantified diversity metrics in each zone under experimentally manipulated hydroperiods. Pre-treatment, we found that wetland zones had distinct plant community composition. Wet meadow seed banks had greater taxonomic and phylogenetic diversity than emergent marsh seed banks, and high-water treatments tended to inhibit diversity by reducing germination. Aboveground harvesting of cattails and their litter increased phylogenetic diversity and species richness in both zones, more than doubling richness compared to unmanipulated controls. In the wet meadow, harvesting shifted the community toward an early successional state, favoring seed-bank germination from early seral species, whereas emergent marsh complete removal treatments shifted the community toward an aquatic condition, favoring floating-leaved plants. Removing cattails and their litter increased taxonomic and phylogenetic diversity across water levels, a key environmental gradient, thereby potentially increasing the multifunctionality of these ecosystems. Killing invasive wetland macrophytes but leaving their biomass <i>in situ</i> does not address their underlying mechanism of dominance and is less effective than more intensive treatments that also remove their litter.
Data from: Multicontinental community phylogenetics of avian mixed-species flocks reveal the role of the stability of associations and of kleptoparasitism
If understood as a way to forage socially without incurring intra-specific competition for mates or other resources, mixed-species foraging flocks are predicted to be composed of functionally similar species. In the most intensively studied mixed-species foraging system, understory forest birds, relevant functional traits are however extremely difficult to measure and best replaced by phylogenetic relatedness. A multicontinental analysis of flock phylogenetic structure revealed departures from the expected phylogenetic clustering. Long-lasting associations (> one day) were phylogenetically overdispersed, indicating that these associations are affected by competitive exclusion or by mutualistic interactions. However, where kleptoparasites occurred, this effect disappeared completely, as expected if the dilution of kleptoparasitism risk compensated competition between related species. Mixed-species flocks should not be analyzed as a homogeneous phenomenon.
Data from: Phylogenetic measures of plant communities show long-term change and impacts of fire management in tallgrass prairie remnants
1. Phylogenies are increasingly incorporated into ecological studies on the basis that evolutionary relatedness broadly correlates with trait similarity. However, phylogenetic approaches have rarely been applied to monitoring long-term community change or guiding management. 2. We analysed a 25-year resampling data set (1976–2001) of 41 tallgrass prairie remnants (Illinois, USA) to test for phylogenetic signals of plant community structure, change, environmental associations, fire management and functional traits. A community phylogeny was constructed using GenBank sequences and trait data were acquired from the TRY consortium. Phylogenetic measures of alpha and beta diversity were compared with taxonomic and functional measures. 3. From 1976–2001, communities became more phylogenetically clustered relative to null model expectations, i.e. increasingly restricted to subsets of species more closely related than expected by chance. Phylogeny was a sensitive indicator of environmental gradients and fire management. There were strong relationships between phylogeny and traits: key traits were phylogenetically non-random and phylogenetic diversity was a necessary complement to species richness for explaining variation in trait diversity. 4. Phylogeny revealed a shift in community structure over time, with sites having been phylogenetically random in 1976 but becoming differentiated from each other by 2001. In contrast, measures of taxonomic and functional diversity showed differentiation at both time points. Phylogenetic patterns likely reflected changes in species' abundances mediated by the influence of environmental conditions and fire frequency. 5. Synthesis and applications. Phylogenetic analyses can elucidate factors central to sound monitoring and management of plant communities. In this system, phylogeny was not a proxy for other indicators, but provided information complementing taxonomic-based and trait-based approaches for understanding vegetation structure, change and response to fire management. Phylogenetic approaches to ecological analysis are increasingly accessible, but fuller understanding of phylogeny–trait relationships and further development of user-friendly analytical tools are needed for phylogenetics to widely inform restoration and management. In some systems, targeting phylogenetic diversity may be an effective means for restoring functionally diverse plant communities.
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Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
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DANDI Archive for NWB datasets
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International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.