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591 results for “phylogenomic data”
New insights into infrageneric relationships of Lonicera (Caprifoliaceae) as revealed by nuclear ribosomal DNA cistron data and plastid phylogenomics
<p>The discontinuous geographic distribution pattern of plants in the north temperate zone has been a focus of biogeographic research, especially concerning the mechanisms behind the formation of such a pattern and the spatial and temporal evolution of this intermittent distribution pattern. Hypotheses of boreotropical origin, land bridge migration, and out-of-Tibet have been proposed to explain the formation of the discontinuous distribution pattern. The distribution of <em>Lonicera</em> shows a typical Europe-Asia-North America discontinuous distribution, which makes for a good case study to investigate the above three hypotheses. In this study, we inferred the phylogeny based on plastid genomes and a nuclear data set with broad taxon sampling, covering 83 species representing two subgenera and four sections. Both nuclear and plastid phylogenetic analyses found section <em>Isika</em> polyphyletic, while sections <em>Nintooa</em>, <em>Isoxylosteum</em>, and <em>Coelxylosteum</em> were monophyletic in subgenus <em>Chamaecerasus</em>. Based on the nuclear and chloroplast phylogeny, we suggest transferring L. <em>maximowiczii</em> and L. <em>tangutica</em> into section <em>Nintooa</em>. Reconstruction of ancestral areas suggests that <em>Lonicera</em> originated in the Qinghai-Tibetan Plateau (QTP) and/or Asia, and subsequently dispersed to other regions. The aridification of the Asian interior may have facilitated the rapid radiation of <em>Lonicera</em> in the region. At the same time, the uplifts of the Tibetan Plateau appear to have triggered the spread and recent rapid diversification of the genus on the QTP and adjacent areas. Overall, our results deepen the understanding of the evolutionary diversification history of <em>Lonicera</em>.</p>
Data from: Nightmare or delight: taxonomic circumscription meets reticulate evolution in the phylogenomic era
<p>Phylogenetic studies in the phylogenomics era have demonstrated that reticulate evolution greatly impedes the accuracy of phylogenetic inference, and consequently can obscure taxonomic treatments. However, the systematics community lacks a broadly applicable strategy for taxonomic delimitation in groups characterized by pervasive reticulate evolution. The red-fruit genus, <em>Stranvaesia</em>, provides an ideal model to examine the influence of reticulation on generic circumscription, particularly where hybridization and allopolyploidy dominate the evolutionary history. In this study, we conducted phylogenomic analyses integrating data from hundreds of single-copy nuclear (SCN) genes and plastomes, and interrogated nuclear paralogs to clarify the inter/intra-generic relationship of <em>Stranvaesia</em> and its allies in the framework of Maleae. Analyses of phylogenomic discord and phylogenetic networks showed that allopolyploidization and introgression promoted the origin and diversification of the Stranvaesia clade, a conclusion further bolstered by cytonuclear and gene tree discordance. With a well-inferred phylogenetic backbone, we propose an updated generic delimitation of <em>Stranvaesia</em> and introduce a new genus, <em>Weniomeles</em>. This new genus is distinguished by its purple-black fruits, thorns trunk and/or branches, and a distinctive fruit core anatomy characterized by multilocular separated by a layer of sclereids and a cluster of sclereids at the top of the locules. Through this study, we highlight a broadly applicable workflow that underscores the significance of reticulate evolution analyses in shaping taxonomic revisions from phylogenomic data.</p>
Data from: Phylogenomics, biogeography, and evolution of the blue- or white-fruited dogwoods
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Phylogenomic placement of a new genus and species of jumping spiders (Araneae: Salticidae: Spartaeini) based on UCE data
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Data from: Robust phylogenomics settles controversies of classification and reveals evolution of male embolic complex of the Laufeia clade (Araneae, Salticidae, Euophryini)
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Data from: Phylogenomics reveals rapid, simultaneous diversification of three major clades of Gondwanan frogs at the Cretaceous–Paleogene boundary
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Data from: Phylogenomics reveals three sources of adaptive variation during a rapid radiation
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Data from: Phylogenomic structure and speciation in an emerging model: The Sphagnum magellanicum complex (Bryophyta)
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Data from: Phylogenomic and ecological systematics of Melocactus (Cactaceae)
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Data from: A phylogenomic perspective on the biogeography of skinks in the Plestiodon brevirostris group inferred from target enrichment of ultraconserved elements
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Data for Concordance-based approaches in phylogenomics
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Data from: Phylogenomics reveals novel relationships among Neotropical crocodiles (Crocodylus spp.)
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Data for: Phylogenomic analyses of the Neotropical Artocarpeae (Moraceae) reveal a history of introgression and support the reinstatement of Acanthinophyllum
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Data from: Phylogenomic data reveal reticulation and incongruence among mitochondrial candidate species in Dusky Salamanders (Desmognathus)
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Data from: Phylogenomics supports island contribution to metapopulation dynamics in a predominantly continental bird species
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Data from: A phylogenomic perspective to diversity, hybridization and evolutionary affinities in the stickleback genus Pungitius
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Data from: Complex but clear allopolyploid pattern of subtribe Tussilagininae (Asteraceae: Senecioneae) revealed by robust phylogenomic evidence, with development of a novel homeolog-sorting pipeline
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Data from: Phylogenomics resolves major relationships and reveals significant diversification rate shifts in the evolution of silk moths and relatives
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Data from: Why do phylogenomic data sets yield conflicting trees? Data type influences the avian tree of life more than taxon sampling
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Data from: Parallel evolution of bower-building behavior in two groups of bowerbirds suggested by phylogenomics
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Allen Brain Atlas
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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.