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50 results for “phylogenetic community structure”
FIGURE 2 in Using community phylogenetics to assess phylogenetic structure in the Fitzcarrald region of Western Amazonia
FIGURE 2 | Ultrametric cladogram of the Fitzcarrald region fish fauna (modified from S2) showing distributions of species in habitats and river basins. Red boxes indicate species presences in: Rivers, Stream, Lakes, Purus, Yuruá, Urubamba and Las Piedras. Note phylogenetic clustering in the Urubamba basin and the stream habitat.
Species introductions cause phylogenetically structured successional pathways in natural wood-inhabiting fungal communities
<p>These files include the data and the scripts for reproducing the results presented in the manuscript "Species introductions cause phylogenetically structured successional pathways in natural wood-inhabiting fungal communities".</p> <p>Description of the files can be found from the README.docx file.</p>
Data for: Historical and contemporary processes drive global phylogenetic structure across geographical scales: Insights from bat communities
<p><strong>Aim</strong>: Patterns of evolutionary relatedness among co-occurring species are driven by scale-dependent contemporary and historical processes. Yet, we still lack a detailed understanding of how these drivers impact the phylogenetic structure of biological communities. Here, we focused on bats – one of the most speciose and vagile groups of mammals – and test the predictions of three general biogeographical hypotheses that are particularly relevant to understanding how paleoclimatic stability, local diversification rates, and geographical scales shaped their present-day phylogenetic community structure.</p> <p><strong>Location</strong>: Worldwide, across restrictive geographical extents: global, east-west hemispheres, biogeographical realms, tectonic plates, biomes, and ecoregions.</p> <p><strong>Time period</strong>: Last Glacial Maximum (~22,000 years ago) to the present.</p> <p><strong>Major taxa studied</strong>: Bats (Chiroptera)</p> <p><strong>Methods</strong>: We estimated bat phylogenetic community structure across restrictive geographical extents and modelled it as a function of paleoclimatic stability, and in situ net diversification rates.</p> <p><strong>Results</strong>: Limiting geographical extents from larger to smaller scales strongly changed the phylogenetic structure of bat communities. The magnitude of these effects is less noticeable in the western hemisphere, where frequent among-realm biota interchange could have been maintained through bats' adaptive traits. Highly phylogenetically related bat communities are generally more common in regions that changed less in climate since the last glacial maximum, supporting the expectation that stable climates allow for increased phylogenetic clustering. Finally, increased in situ net diversification rates are associated with greater phylogenetic clustering in bat communities.</p> <p><strong>Main conclusions</strong>: We show that the worldwide phylogenetic structure of bat assemblages varies as a function of geographical extents, dispersal barriers, paleoclimatic stability and in situ diversification. The integrative framework used in our study, which can be applied to other taxonomic groups, has proven useful to not only explain the evolutionary dynamics of community assembly but could also help tackle questions related to scale dependence in community ecology and biogeography.</p>
Data for: Environmental responses of fruiting fungal communities are phylogenetically structured
<p class="MsoNormal"><span>Through their ephemeral reproductive structures (fruiting bodies), ectomycorrhizal forest soil fungi provide a resource for a plethora of organisms. Thus, resolving what biotic and abiotic factors determine the occurrence and abundance of fruiting bodies is fundamental for understanding the dynamics of forest trophic networks. While the influence of abiotic factors such as moisture and temperature on fungal fruiting are relatively well established, little is known about how these processes interact with the evolutionary history of fungal species to determine when, where, and in which abundance fungal fruiting bodies will emerge. A specific knowledge gap relates to whether species' responses to their environment are phylogenetically structured. Here, we ask whether related fungal taxa respond similarly to climatic factors and forest habitat characteristics, and whether such correlated responses will affect the assembly of fungal fruiting communities. To resolve these questions, we fitted joint species distribution models combining data on the species composition and abundance of fungal fruiting bodies, environmental variation, and phylogenetic relationships among fungal taxa. Our results show that both site-level forest characteristics (dominant tree species and forest age) and climatic factors related to phenology (effective heat sum) greatly influence the occurrence and abundance of fruiting bodies. More importantly, while different fungal species responded unequally to their shared environment, there was a strong <span>phylogenetic signal in their responses, so that related fungal species tended to fruit under similar environmental conditions. </span>Thus, not only are fruiting bodies short-lived and patchily distributed, but the availability of similar resources will be further aggregated in time and space. These strong constraints on resource availability for fungus-associated taxa highlight the potential of fungus-based networks as a model system for studies on the ecology and evolution of resource–consumer relations in ephemeral systems of high spatiotemporal patchiness.</span></p>
Data for: Environmental responses of fruiting fungal communities are phylogenetically structured
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Data for: Historical and contemporary processes drive global phylogenetic structure across geographical scales: Insights from bat communities
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Both source and recipient range phylogenetic community structure can predict the outcome of avian introductions
<p>Competing phylogenetic models have been proposed to explain the success of species introduced to other communities. Here, we present a study predicting the establishment success of birds introduced to Florida, Hawaii, and New Zealand using several alternative models, considering species' phylogenetic relatedness to source and recipient range taxa, propagule pressure, and traits. We find consistent support for the predictive ability of source region phylogenetic structure. However, we find that the effects of recipient region phylogenetic structure vary in sign and magnitude depending on inclusion of source region phylogenetic structure, delineation of the recipient species pool, and the use of phylogenetic correction in the models. We argue that tests of alternative phylogenetic hypotheses including the both source and recipient community phylogenetic structure, as well as important covariates such as propagule pressure, are likely to be critical for identifying general phylogenetic patterns in introduction success, predicting future invasions, and for stimulating further exploration of the underlying mechanisms of invasibility.</p>
Long-term nitrogen fertilization alters arbuscular mycorrhizal fungi community phylogenetic structure in plant roots across fine spatial scales
<p><span>Purpose:</span><span> Nitrogen deposition due to human activities is known to have a substantial impact on arbuscular mycorrhizal fungi (AMF) community in plant roots. However, the influence of elevated nitrogen on the phylogenetic structure of AMF across fine spatial scales, as well as the mechanisms behind such alterations, are remained poorly understood. </span></p> <p><span>Results:</span><span> Nitrogen addition significantly increased the phylogenetic alpha diversity (diversity within a plot) and the 'within-treatment' phylogenetic beta diversity (dissimilarity among replicate plots) of AMF communities, which resulted in an increased 'within-treatment' phylogenetic gamma diversity (overall diversity among all the replicate plots within a treatment). These changes were caused by the relative abundance decline of a dominant genus (</span><span>Glomus</span><span>) and an increase in non-dominant genera. Mechanically, nitrogen addition affected phylogenetic alpha diversity mainly by influencing soil properties. Likewise, the increased 'within-treatment' dissimilarity of plant community composition and changes in soil properties caused by nitrogen addition and plot distance contributed to an increase in within-treatment phylogenetic beta diversity. </span></p> <p><span>Conclusions:</span><span> We conclude that deterministic environmental filtering (both abiotic and biotic) and dispersal limitation effect played critical roles in AMF community assembly under global change scenarios. Insightfully, this study provides a mechanistic understanding of the response of AMF to nitrogen addition across fine scales.</span></p>
Intra-specific variation in plant associated herbivore communities is phylogenetically structured in Brassicaceae
<p>As a result of co-evolution between plants and herbivores, related plants often interact with similar herbivore communities. Variation in plant-herbivore interactions is determined by variation in underlying functional traits and by ecological and stochastic processes. Hence, typically only a subset of possible interactions is realized on individual plants. We show that insect herbivore communities assembling on individual plants are structured by plant phylogeny among twelve species in two phylogenetic lineages of Brassicaceae. This community sorting to plant phylogeny was retained when splitting the community according to herbivore feeding guilds. Relative abundance of herbivores as well as the size of the community structured community dissimilarity among plant species. Importantly, the amount of intra-specific variation in realized plant-herbivore interactions is also phylogenetically structured. We argue that variability in realized interactions that is not directly structured by plant traits is ecologically relevant and must be considered in the evolution of plant defences.</p>
Environment differentially affects the functional and phylogenetic structures of plant communities in a dry evergreen Afromontane tropical forest
<p class="MsoNormal"><span>Testing how local environmental conditions influence plant community assembly is important to understand the underlying mechanisms that promote and/or maintain biodiversity. Functional traits are used to find the broad spectrum of resource use strategies that plants use to</span><span> respond to environmental variation</span><span>. The patterns and drivers of plant community assembly through the lens of traits and phylogeny, however, remain to be studied in a uniquely biodiversity rich but poorly known fragmented dry Afromontane forest of Ethiopia. Here, we combined trait and community phylogenetic data from thirty sampling plots of 20 × 20 m size to determine the functional and phylogenetic structures and their drivers in a fragmented, human-dominated dry evergreen Afromontane forest. We found phylogenetic and functional clustering of plants in which the effect of environment was found to be trait specific. A weak phylogenetic signal for traits was detected suggesting that species resource use strategies may not be inferred using species phylogenetic distance. Additionally, we found functional traits to be weak in predicting species abundance distribution. Overall, while this study shows a non-random community assembly pattern, it also highlights the importance of deterministic processes being trait specific. </span></p>
Data from: Nitrogen fertilization, not water addition, alters plant phylogenetic community structure in a semi-arid steppe
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Intra-specific variation in plant associated herbivore communities is phylogenetically structured in Brassicaceae
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Data from: Grassland restoration characteristics influence phylogenetic and taxonomic structure of plant communities and suggest assembly mechanisms
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Environment differentially affects the functional and phylogenetic structures of plant communities in a dry evergreen Afromontane tropical forest
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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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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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Long-term nitrogen fertilization alters arbuscular mycorrhizal fungi community phylogenetic structure in plant roots across fine spatial scales
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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>
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>
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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.