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727 results for “phylogenetic diversity”
Data from: Non-random patterns of invasion and extinction reduce phylogenetic diversity in island bird assemblages
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Taxonomic, functional and phylogenetic beta diversity of upland forest birds in the Amazon: The relative importance of biogeographic regions, climate, and geographic distance
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Data and code from: Echoes of the past: Long-term climate stability shapes functional and phylogenetic diversity in Euro-Mediterranean forests
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Data from: Unraveling the taxonomic, functional and phylogenetic diversity of lizard assemblages in riparian forest areas in the Amazon–Pantanal ecotone
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The counteracting effects of human-driven speciation and extinction on mammal species richness and phylogenetic diversity
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Tropical niche conservatism and dispersal limitation jointly determine taxonomic and phylogenetic β-diversities of Odonata in Eastern China
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Modern pollen–plant diversity relationships inform palaeoecological reconstructions of functional and phylogenetic diversity in calcareous fens
<p>Predicting the trajectory of ongoing diversity loss requires knowledge of historical development of community assemblages. Long-term data from paleoecological investigations combined with key biodiversity measures in ecology such as taxonomic richness, functional diversity (FD), phylogenetic diversity (PD) and environmental factors expressed as Ellenberg indicator values (EIVs) could provide that knowledge. We explored the modern pollen–plant (moss polster pollen vs. surrounding vegetation) diversity relationships for herbaceous and woody taxa in calcareous fens from two different regions in Estonia, NE Europe. Associations of taxonomic richness, vegetation composition, FD (including functional alpha diversity and trait composition), PD and EIVs in modern pollen vs. plant data were studied with correlation analysis, Procrustes analysis and linear regression models. To test their potential use in palaeoreconstructions, diversity measures were applied on pollen data from Kanna spring fen reflecting fen vegetation development over the last nine millennia and diversity changes through time were studied using generalized additive models. Results showed significant pollen–plant richness correlations for herbaceous taxa at vegetation estimate scales up to 6 m radius and Procrustes analysis showed significant compositional associations at all plant estimate scales (up to 100 m). Woody taxa had no significant pollen–plant richness correlations but composition relationships were significant at plant estimate scales of 6–100 m. Traits that were best reflected by pollen data (both in terms of trait composition and functional alpha diversity) among woody and herbaceous taxa were seed number, clonality, SLA and LDMC. PD of herbaceous species was reflected by pollen data. Among the EIVs, Ellenberg L and T were significantly reflected by pollen data for both woody and herbaceous communities. Palaeoreconstruction from Kanna fen indicates that trends of woody taxa are mostly related to long-term changes in climate while diversity variables of herbaceous taxa closely follow autogenic processes within the fen. We suggest that pollen-based diversity estimates should be calculated separately for woody and herbaceous taxa as they clearly represent different spatial scales. Present study suggests that linking sedimentary pollen data with FD, PD and EIVs provides possibilities to examine long-term trends in community assembly and ecosystem processes that would be undetectable from traditional pollen diagrams.</p>
Changes in taxonomic and phylogenetic diversity in the Anthropocene
<p>To better understand how ecosystems are changing, a multifaceted approach to measuring biodiversity that considers species richness and evolutionary history across spatial scales is needed. Here we compiled 162 datasets for fish, bird, and plant assemblages across the globe and measured how taxonomic and phylogenetic diversity changed at different spatial scales (within site α diversity and between sites spatial β diversity). Biodiversity change is measured from these datasets in three ways: across land use gradients, from species lists, and through sampling of the same locations across two time periods. We found that local species richness and phylogenetic α diversity (Faith's PD) increased for all taxonomic groups. However, when measured with a metric that is independent of species richness (phylogenetic species variation, PSV), phylogenetic α diversity declined for all taxonomic groups. Land use datasets showed declines in species richness, Faith's PD, and PSV. For all taxonomic groups and data types, spatial taxonomic and phylogenetic β diversity decreased when measured with Sorensen dissimilarity and phylogenetic Sorensen dissimilarity, respectively, providing strong evidence of global biotic homogenization. The decoupling of α and β diversity, as well as taxonomic and phylogenetic diversity, highlights the need for a broader perspective on contemporary biodiversity changes. Conservation and environmental policy decisions thus need to consider biodiversity beyond local species richness to protect biodiversity and ecosystem services.</p>
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>
Multi-dimensional biodiversity hotspots and the future of taxonomic, ecological, and phylogenetic diversity: a case study of North American rodents
<p>Aim: We investigate geographic patterns across taxonomic, ecological, and phylogenetic diversity to test for spatial (in)congruency and identify aggregate diversity hotspots in relation to present land-use and future climate. Simulating extinctions of imperiled species, we demonstrate where losses across diversity dimensions and geography are predicted.</p> <p>Location: North America</p> <p>Time period: Present-day, future</p> <p>Major taxa studied: Rodentia</p> <p>Methods: Using geographic range maps for rodent species, we quantified spatial patterns for eleven dimensions of diversity: taxonomic (species, range-weighted), ecological (body size, diet, habitat), phylogenetic (mean, variance, and nearest-neighbor patristic distances, phylogenetic distance, genus-to-species ratio) and phyloendemism. We tested for correlations across dimensions and used spatial residual analyses to illustrate regions of pronounced diversity. We aggregated diversity hotspots in relation to land-use and climate-change predictions and recalculated metrics following extinctions of IUCN-listed imperiled species.</p> <p>Results: Topographically-complex western North America hosts high diversity across multiple dimensions: phyloendemism and ecological diversity exceed predictions based on taxonomic richness and phylogenetic variance patterns indicate steep gradients in phylogenetic turnover. While an aggregate diversity hotspot emerges in the west, spatial incongruence exists across diversity dimensions at the continental scale. Notably, phylogenetic metrics are uncorrelated with ecological diversity. Diversity hotspots overlap with land-use and climate change, and extinctions predicted by IUCN status are unevenly distributed across space, phylogeny, or ecological groups.</p> <p>Main conclusions: Comparison of taxonomic, ecological, and phylogenetic diversity patterns for North American rodents clearly shows the multifaceted nature of biodiversity. Testing for geographic patterns and (in)congruency across dimensions of diversity facilitates investigation into underlying ecological and evolutionary processes. The geographic scope of this analysis suggests that several explicit regional challenges face North American rodent fauna in the future. Simultaneous consideration of multidimensional biodiversity allows us to assess what critical functions or evolutionary history we might lose with future extinctions and maximize the potential of our conservation efforts.</p>
A targeted phylogenetic approach helps explain New World functional diversity patterns of two eudicot lineages.
<p>Aim: </p> <p>Large-scale functional diversity studies typically examine isolated traits, often without phylogenetic context. Here, we integrate data from five life-history traits with phylogeny and occurrence records to asses: (1) correlated latitudinal gradients of trait combinations; (2) which traits show phylogenetic conservatism; (3) quantitative, clade-specific differences in trait syndromes, illustrating the phylogenetic scale of observable variation in ecological strategies.</p> <p>Location: </p> <p>The Americas.</p> <p>Taxon: </p> <p>Ericales (Asterids) and Fabales (Rosids).</p> <p>Methods: </p> <p>We used publicly-available trait data sets on height, seed mass, wood density, leaf mass per area (LMA), and growth form, an open-source phylogeny, and georeferenced occurrence records to investigate functional diversity patterns. We employed phylogenetic generalized least squares and phylogenetic principal components analyses (pPCA) to assess correlated trait evolution and quantify the trait syndrome, respectively. We employed the InfoMap Ecoregions web app to cluster species by bioregions. We used standard statistical tests and randomization simulations to assess statistical significance of results.</p> <p>Results:</p> <p>Ericales and Fabales exhibited a biogeographically-consistent, phylogenetically-conserved trait syndrome. Moving poleward, species exhibited progressively smaller trait values and more herbaceous and shrubby growth forms (except for LMA, which showed no consistent pattern). We quantified latitudinal variation in this trait syndrome using pPCA, and provide evidence for correlated trait evolution.</p> <p>Main conclusions:</p> <p>We demonstrate a functional trait syndrome involving height, seed mass, wood density, and growth form, but not LMA. Functional trait values showed consistent latitudinal patterns and evidence of correlated evolution, suggesting an underlying ecological strategy. Further, the two clades showed quantitative differences in the manifestation of this trait syndrome. Variation in the syndrome was best observed among species from con-ordinal families. We interpret this trait syndrome as a strategy of resource acquisition in which habitats with relatively greater soil nutrient content and a shorter growing season favor shorter stature, lower seed mass and wood density, and shrubby or herbaceous growth form.</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 diversity of two geographically overlapping species in the lichen genus Sticta (Ascomycota: Peltigeraceae): isolation by distance, environment, or fragmentation?
<p><span><b>Aim:</b> To test whether the degree of phylogenetic diversity differs in two congeneric, morphologically similar lichens that are both widespread and with a similar geographical range (Neotropics and Hawaii), but differ in altitudinal and habitat preferences, and whether the two species underwent isolation by distance (IBD), environment (IBE), or fragmentation (IBF).</span></p> <p><span><b>Location:</b> South and Central America, Caribbean, Hawaii, Azores.</span></p> <p><span><b>Taxon:</b> <i>Sticta</i> (Peltigeraceae).</span></p> <p><span><b>Methods:</b> Analysis of 395 specimens across the study area; ITS barcoding marker; maximum likelihood tree reconstruction within a broad taxonomic framework; TCS haplotype networks; Mantel test of genetic vs. geographic, environmental, and fragmentation distances; statistical comparison of BIOclim variables.</span></p> <p><span><b>Results:</b><b> </b><i>Sticta andina</i> exhibited high phenotypic variation and high reticulate phylogenetic diversity across its range, whereas the phenotypically more uniform <i>S. scabrosa</i> contained two main haplotypes, one unique to Hawaii (subsp. <i>hawaiiensis</i>). <i>Sticta andina</i> was restricted to well-preserved andine forests and paramos, habitats fragmented due to disruptive topology, whereas <i>S. scabrosa</i> was found in lowland to lower montane forests in rather exposed microsites, representing a more continuous habitat. These differences were statistically significant for several BIOclim variables. Mantel tests on genetic vs. geographic and environmental distances demonstrated that <i>S. scabrosa</i> followed a pattern of IBD across its full range but not within continental Central and South America. In contrast, <i>S. andina</i> did not exhibit IBD but showed weak, yet significant patterns of IBE at continental level and IBF in the northern Andes.</span></p> <p><b>Main Conclusions:</b> Autecology indirectly drives phylogenetic diversity in the two studied species. In the low altitude species, <i>S. scabrosa</i>, phylogenetic diversity is low and shows no correlation with geographic or environmental distances, except for the differentiation of the Hawaiian subspecies. We attribute this to rapid expansion and effective gene flow between populations across a more or less continuously distributed niche representing partially exposed microsites, including disturbed and anthropogenic vegetation, such as planted trees. In contrast, in the high altitude species, <i>S. andina</i>, phylogenetic diversity is high and correlated with both environmental niche differentiation (IBE) and fragmentation caused by the final Andean uplift (IBF). Therefore, an autoecological preference for high altitudes increases the likelihood for higher phylogenetic diversity.</p>
FIGURE 12 in Calling for a reassessment of rodent diversity in Colombia: description of a new species of Neacomys (Cricetidae: Oryzomyini) from the Magdalena Valley, with a new phylogenetic hypothesis for the genus and comments on its diversification
FIGURE 12. Illustration of Neacomys serranensis sp. nov. by wildlife artist and zoologist Velizar Simeonovski.
FIGURE 10 in Calling for a reassessment of rodent diversity in Colombia: description of a new species of Neacomys (Cricetidae: Oryzomyini) from the Magdalena Valley, with a new phylogenetic hypothesis for the genus and comments on its diversification
FIGURE 10. Comparison of the lateral profiles of the skulls of Trans-Andean species of Neacomys present in Colombia: A) Neacomys sp. nov. (UIS-MHN-M 1068, holotype). B) Neacomys tenuipes (UIS-MHN-M 1723). Note a more convex profile of the braincase, a thicker hamular process of the squamosal, a broader condylar process, a larger and laterally projected mental foramen, and the anterior margin of nasals without a hump in Neacomys sp. nov. con: condylar process; hp: hamular process of the squamosal; mf: mental foramen; nas: nasals.
FIGURE 8 in Calling for a reassessment of rodent diversity in Colombia: description of a new species of Neacomys (Cricetidae: Oryzomyini) from the Magdalena Valley, with a new phylogenetic hypothesis for the genus and comments on its diversification
FIGURE 8. Ventral perspectives of adult specimens illustrating the striking difference in ventral fur of the two Trans-Andean species of Neacomys present in Colombia: A) Holotype of Neacomys sp. nov (UIS-MHN-M 1068). B) Section of the holotype of Neacomys sp. nov. showing its characteristic gray-based ochraceous-buff ventral fur. C) Neacomys tenuipes (UIS-MHN-M 1723); note the contrasting entirely white ventral fur of this species.
FIGURE 7 in Calling for a reassessment of rodent diversity in Colombia: description of a new species of Neacomys (Cricetidae: Oryzomyini) from the Magdalena Valley, with a new phylogenetic hypothesis for the genus and comments on its diversification
FIGURE 7. Frontal perspectives of adult specimens belonging to the two Trans-Andean species of Neacomys present in Colombia: A) Holotype of Neacomys sp. nov (UIS-MHN-M 1068); note the distinctive broad ochraceous-orange patches in the sides of the muzzle of this species. B) Neacomys tenuipes (UIS-MHN-M 1723).
FIGURE 6 in Calling for a reassessment of rodent diversity in Colombia: description of a new species of Neacomys (Cricetidae: Oryzomyini) from the Magdalena Valley, with a new phylogenetic hypothesis for the genus and comments on its diversification
FIGURE 6. Dorsal perspectives of adult specimens belonging to the two Trans-Andean species of Neacomys present in Colombia: A) Holotype of Neacomys sp. nov (UIS-MHN-M 1068). B) Neacomys tenuipes (UIS-MHN-M 1723); note that a portion of the tail is missing in this specimen.
FIGURE 5. A in Calling for a reassessment of rodent diversity in Colombia: description of a new species of Neacomys (Cricetidae: Oryzomyini) from the Magdalena Valley, with a new phylogenetic hypothesis for the genus and comments on its diversification
FIGURE 5. A) Montane forest habitat along the left Bank of the La San Guillerma stream, adjacent to the type locality of Neacomys sp. nov. (municipality of El Carmen de Chucurí) (Photograph by Juliette Gualdrón) B) View of the forest remnant where the second specimen of Neacomys sp nov. was collected (municipality of Hato) (Photograph by Juliette Gualdrón). C) Topography of the western slope of the Serranía de los Yariguíes from the campsite "Finca Buenos Aires"; near the type locality of Neacomys sp. nov. D) Educational activity with members of the community in the municipality of El Carmen del Chucurí, Vereda la Bodega, Sector Manchurrias, illustrating the importance of government funded projects (like Santander BIO expeditions), not only to inventory the biodiversity of remote areas, but also to teach local people to preserve it.
FIGURE 4 in Calling for a reassessment of rodent diversity in Colombia: description of a new species of Neacomys (Cricetidae: Oryzomyini) from the Magdalena Valley, with a new phylogenetic hypothesis for the genus and comments on its diversification
FIGURE 4. Scatterplots of the Principal Components Analyses: PC1 and PC2 are represented in the graphics. A. PCA of the external and craniodental variables of all the small-bodied species of Neacomys; B. PCA of the craniodental variables of N. tenuipes and Neacomys sp. nov. Miniatures in the right side correspond to the Bayesian Cytb phylogeny recovered here (FIGURE 3): species in the scatterplots and the phylogenies are same colored.
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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)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
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.