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727 results for “phylogenetic diversity”
Data from: Historical and ecological controls on phylogenetic diversity in Californian plant communities
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Data from: Ploeotids represent much of the phylogenetic diversity of euglenids
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Data from: Phylogenetic niche conservatism and variations in species diversity-climate relationships
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Data from: Range shifting species reduce phylogenetic diversity in high latitude communities via competition
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Data from: Ranked tree shapes, nonrandom extinctions and the loss of phylogenetic diversity
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Data from: Galega orientalis is more diverse than Galega officinalis in Caucasus – whole-genome AFLP analysis and phylogenetics of symbiosis-related genes
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Data from: Rarefaction and extrapolation: making fair comparison of abundance-sensitive phylogenetic diversity among multiple assemblages
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Data from: Species richness, but not phylogenetic diversity, influences community biomass production and temporal stability in a re-examination of 16 grassland biodiversity studies
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Multigene phylogenetics of euglenids based on single-cell transcriptomics of diverse phagotrophs
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Data from: Phylogenetic beta diversity, similarity, and differentiation measures based on Hill numbers
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Data from: Geographical patterns in phylogenetic diversity of Chinese woody plants and its application for conservation planning
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Long-term trends in the phylogenetic and functional diversity of Anatidae in South China coastal wetlands
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The human Gut Chip “HuGChip”, an explorative phylogenetic microarray for determining gut microbiome diversity at Family level
GEO Series GSE44752. Bacteroides fragilis; Blautia producta; uncultured bacterium; Lactobacillus acidophilus; human gut metagenome; Escherichia coli; [Clostridium] leptum. 4 samples. Type: Expression profiling by array.
Randomized PAM depletion of phylogenetically-diverse Cas12a nucleases
GEO Series GSE130377. synthetic construct. 12 samples. Type: Other.
Phylogenetic, microbiological and glycoside hydrolase diversities within the extremely thermophilic, plant biomass-degrading genus Caldicellulosiruptor
GEO Series GSE23606. Caldicellulosiruptor owensensis; Caldicellulosiruptor acetigenus; Caldicellulosiruptor saccharolyticus; Caldicellulosiruptor hydrothermalis; Caldicellulosiruptor bescii; Caldicellulosiruptor kronotskyensis. 6 samples. Type: Genome variation profiling by array.
Warming stimulates cellulose decomposition by recruiting phylogenetically diverse but functionally similar microorganisms
GEO Series GSE237659. soil metagenome; uncultured soil microorganism; decomposition metagenome. 48 samples. Type: Other.
Data from: The effects of habitat management on the species, phylogenetic and functional diversity of bees are modified by the environmental context
Anthropogenic landscape elements, such as roadsides, hedgerows, field edges, and power line clearings, can be managed to provide important habitats for wild bees. However, the effects of habitat improvement schemes in power line clearings on components of diversity are poorly studied. We conducted a large-scale experiment to test the effects of different management practices on the species, phylogenetic, and functional diversity of wild bees in power line clearings (n = 19 sites across southeastern Norway) and explored whether any treatment effects were modified by the environmental context. At each site, we conducted the following treatments: (1) Cut: all trees cut and left to decay in the clearing; (2) Cut + Remove: all trees cut and removed from the plot; and (3) Uncut: uncleared. The site-specific environmental context (i.e., elevation and floral diversity) influenced the species, phylogenetic, and functional diversity within bee species assemblages. The largest number of species was found in the Cut + Remove treatment in plots with a high forb species richness, indicating that the outcome of management practices depends on the environmental context. Clearing of treatment plots with many forb species also appeared to alter the phylogenetic composition of bee species assemblages, that is, more closely related species were found in the Cut and the Cut + Remove plots than in the Uncut plots. Synthesis and applications: Our experimental simulation of management practices in power line clearings influenced the species, phylogenetic, and functional diversity of bee species assemblages. Frequent clearing and removal of the woody debris at low elevations with a high forb species richness can increase the value of power line clearings for solitary bees. It is therefore important for managers to consider the environmental context when designing habitat improvement schemes for solitary bees.
Data from: Species richness and phylogenetic diversity of seed plants across vegetation zones of Mount Kenya, East Africa
Mount Kenya is of ecological importance in tropical east Africa due to the dramatic gradient in vegetation types that can be observed from low to high elevation zones. However, species richness and phylogenetic diversity of this mountain have not been well studied. Here, we surveyed distribution patterns for a total of 1,335 seed plants of this mountain and calculated species richness and phylogenetic diversity across seven vegetation zones. We also measured phylogenetic structure using the net relatedness index (NRI) and the nearest species index (NTI). Our results show that lower montane wet forest has the highest level of species richness, density, and phylogenetic diversity of woody plants, while lower montane dry forest has the highest level of species richness, density, and phylogenetic diversity in herbaceous plants. In total plants, NRI and NTI of four forest zones were smaller than three alpine zones. In woody plants, lower montane wet forest and upper montane forest have overdispersed phylogenetic structures. In herbaceous plants, NRI of Afro‐alpine zone and nival zone are smaller than those of bamboo zone, upper montane forest, and heath zone. We suggest that compared to open dry forest, humid forest has fewer herbaceous plants because of the closed canopy of woody plants. Woody plants may have climate‐dominated niches, whereas herbaceous plants may have edaphic and microhabitat‐dominated niches. We also proposed lower and upper montane forests with high species richness or overdispersed phylogenetic structures as the priority areas in conservation of Mount Kenya and other high mountains in the Eastern Afro‐montane biodiversity hotspot regions.
Data from: A total evidence approach to understanding phylogenetic relationships and ecological diversity in Selaginella subg. Tetragonostachys
Premise of the Study: Several members of Selaginella are renowned for their ability to survive extreme drought and "resurrect" when conditions improve. Many of these belong to subgenus Tetragonostachys, a group of ∼45 species primarily found in North and Central America, with substantial diversity in the Sonoran and Chihuahuan Deserts. We evaluated the monophyly and the age of subgenus Tetragonostachys and assess how drought tolerance contributed to the evolution of this clade. Methods: Our study included most Tetragonostachys species, using plastid and nuclear sequences, fossil and herbarium records, and climate variables to describe the species diversity, phylogenetic relationships, divergence times, and climatic niche evolution in the subgenus. Key Results: We found that subgenus Tetragonostachys forms a monophyletic group sister to Selaginella lepidophylla and may have diverged from other Selaginella because of a Gondwanan–Laurasian vicariance event ca. 240 mya. The North American radiation of Tetragonostachys appears to be much more recent and to have occurred during the Early Cretaceous–late Paleocene interval. We identified two significant and nested ecological niche shifts during the evolution of Tetragonostachys associated with extreme drought tolerance and a more recent shift to cold climates. Our analyses suggest that drought tolerance evolved in the warm deserts of southwest North America and may have been advantageous for colonization of cold and dry boreal climates. Conclusions: Our investigation provides a foundation for future research addressing the genomics of ecological niche evolution and the potential role of reticulate evolution in Selaginella subgenus Tetragonostachys.
Targeted capture of hundreds of nuclear genes unravels phylogenetic relationships of the diverse Neotropical palm tribe Geonomateae.
<p>The tribe Geonomateae is a widely distributed group of 103 species of Neotropical palms which contains six ecologically important understory or subcanopy genera. Although it has been the focus of many studies, our understanding of the evolutionary history of this group, and in particular of the taxonomically complex genus <em>Geonoma</em>, is far from complete due to a lack of molecular data. Specifically, the previous Sanger sequencing-based studies used a few informative characters and partial sampling. To overcome these limitations, we used a recently developed Arecaceae-specific target capture bait set to undertake a phylogenomic analysis of the tribe Geonomateae. We sequenced 3,988 genes for 85% of the species of the tribe, including 84% of the species of the largest genus, <em>Geonoma</em>.<em> </em>Phylogenetic relationships were inferred using both concatenation and coalescent methods. Overall, our phylogenetic tree is highly supported and congruent with taxonomic delimitations although several morphological taxa were revealed to be non-monophyletic. It is the first time that such a large genomic dataset is provided for an entire tribe within the Arecaceae. Our study lays the groundwork not only for detailed macro- and micro-evolutionary studies within the group, but also sets a workflow for understanding other species complexes across the tree of life.</p>
ScienceDex guides
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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.