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29 results for “diversification analyses”
Phylogenomic analyses of the East Asian endemic Abelia (Caprifoliaceae) shed insights into the temporal and spatial diversification history with widespread hybridization
<p><b>• </b><b>Background and Aims </b><i>Abelia</i> (Caprifoliaceae) is a small genus with five species, including one man-made hybrid and several natural hybrids. The genus has a discontinuous distribution in Mainland China, the Taiwan Island, and the Ryukyu Islands, providing a model system to explore mechanisms of species dispersal in the East Asian flora. However, the current phylogenetic relationships within <i>Abelia</i> remain uncertain.</p> <p><b>• Methods</b> In this study, we reconstructed the phylogenetic relationships within <i>Abelia</i> using nuclear loci generated by target enrichment and plastomes from genome skimming. Divergence time estimation, ancestral area reconstruction, and ecological niche modelling (ENM) were used to examine the diversification history of <i>Abelia</i>.</p> <p><b>• Key Results </b>We found extensive cytonuclear discordance across the genus<i>. </i>By integrating lines of evidence from molecular phylogenies, divergence times, and morphology, we propose to merge<i> A. macrotera </i>var.<i> zabelioides </i>into<i> A. uniflora.</i><i> </i>Network analyses suggested that there have been widespread and multiple hybridization events among<i> Abelia</i> species. These hybridization events may have contributed to the speciation mechanism and resulted in a high observed morphological diversity. The diversification of <i>Abelia</i> began in the early Eocene, followed by <i>A. chinensis</i> var. <i>ionandra </i>colonizing the Taiwan Island in the Middle Miocene. The ENM results suggested an expansion of climatically suitable areas during the Last Glacial Maximum and range contraction during the Last Interglacial. Disjunction between the Himalayan-Hengduan Mountain region (HHM) and the Taiwan Island is most likely the consequence of topographic isolation and postglacial contraction.</p> <p><b>• Conclusions </b>We used genomic data to reconstruct the phylogeny of <i>Abelia</i> and found a clear pattern of reticulate evolution in the group.<b> </b>In addition, our results support shrinkage of postglacial range and the heterogeneity of the terrain have led to the disjunction of the Mainland China-Taiwan Island. This study provides important new insights into the speciation process and taxonomy of<i> Abelia</i>.</p>
Data from: Macroevolutionary analyses suggest that environmental factors, not venom apparatus, play key role in Terebridae marine snail diversification
<p><span>How species diversification occurs remains an unanswered question in predatory marine invertebrates, such as sea snails of the family Terebridae. However, the anatomical disparity found throughput the Terebridae provides a unique perspective for investigating diversification patterns in venomous predators. In this study, a new dated molecular phylogeny of the Terebridae is used as a framework for investigating diversification of the family through time, and for testing the putative role of intrinsic and extrinsic traits, such as shell size, larval ecology, bathymetric distribution, and anatomical features of the venom apparatus, as drivers of terebrid species diversification. Macroevolutionary analysis revealed that when diversification rates do not vary across Terebridae clades, the whole family has been increasing its global diversification rate since 25 Ma. We recovered evidence for a concurrent increase in diversification of depth ranges, while shell size appeared to have undergone a fast divergence early in terebrid evolutionary history. Our data also confirm that planktotrophy is the ancestral larval ecology in terebrids, and evolutionary modeling highlighted that shell size is linked to larval ecology of the Terebridae, with species with long-living pelagic larvae tending to be larger and have a broader size range than lecithotrophic species. Although we recovered patterns of size and depth trait diversification through time and across clades, the presence or absence of a venom gland (VG) did not appear to have impacted Terebridae diversification. Terebrids have lost their venom apparatus several times and we confirm that the loss of a VG happened in phylogenetically clustered terminal taxa and that reversal is extremely unlikely. Our findings suggest that environmental factors, and not venom, have had more influence on terebrid evolution.</span></p>
FIGURE 1 Maximum Parsimony phylogenetic analyses. A in Dating the origin and diversiFIcation of Pan-Chelidae (Testudines, Pleurodira) under multiple molecular clock approaches
FIGURE 1 Maximum Parsimony phylogenetic analyses. A: Morphological phylogeny. B: Molecular phylogeny. C: Total-evidence phylogeny. Bootstrap supports are coded in grayscale. Australasian species are shown in red; South American species are shown in green. Abbreviations: A, Acanthochelys; B, Bonapartemys; Ch, Chelodina; El, Elseya; H, Hydromedusa; L, Lomalatachelys; M, Mesoclemmys; Me, Mendozachelys; My, Myuchelys; Pa, Palaeophrynops; Ph, Phrynops; Pl, Platemys; Pr, Prochelidella; Ps, Pseudemydura; Ri, Rionegrochelys; Y, Yaminuechelys. †, extinct taxa.
Concatenated DNA matrix and BEAST tree used for phylogenetic, dating, biogeographic and diversification analyses of Caribbean Podocarpus
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Data from: Macroevolutionary analyses suggest that environmental factors, not venom apparatus, play key role in Terebridae marine snail diversification
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Phylogenomic analyses of the East Asian endemic Abelia (Caprifoliaceae) shed insights into the temporal and spatial diversification history with widespread hybridization
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A Total-Group Phylogenetic Metatree for Cetacea and the Importance of Fossil Data in Diversification Analyses
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Data from: Post K-Pg diversification of the mammalian order Eulipotyphla as suggested by phylogenomic analyses of ultra-conserved elements
The origin of the mammalian order Eulipotyphla has been debated intensively with arguments around whether they began diversifying before or after the Cretaceous-Palaeogene (K-Pg) boundary at 66 Ma. Here, we used an in-solution nucleotide capture method and next generation DNA sequencing to determine the sequence of hundreds of ultra-conserved elements (UCEs), and conducted phylogenomic and molecular dating analyses for the four extant eulipotyphlan lineages—Erinaceidae, Solenodontidae, Soricidae, and Talpidae. Concatenated maximum-likelihood analyses with single or partitioned models and a coalescent species-tree analysis showed that divergences among the four major eulipotyphlan lineages occurred within a short period of evolutionary time, but did not resolve the interrelationships among them. Alternative suboptimal phylogenetic hypotheses received consistently the same amount of support from different UCE loci, and were not significantly different from the maximum likelihood tree topology, suggesting the prevalence of stochastic lineage sorting. Molecular dating analyses that incorporated among-lineage evolutionary rate differences supported a scenario where the four eulipotyphlan families diversified between 57.8 and 63.2 Ma. Given short branch lengths with low support values, traces of rampant genome-wide stochastic lineage sorting, and post K-Pg diversification, we concluded that the crown eulipotyphlan lineages arose through a rapid diversification after the K-Pg boundary when novel niches were created by the mass extinction of species.
Data from: Post K-Pg diversification of the mammalian order Eulipotyphla as suggested by phylogenomic analyses of ultra-conserved elements
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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.