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1,344 results for “: phylogenomics”
Data from: A phylogenomic analysis of turtles
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Data from: Combining phylogenomic and supermatrix approaches, and a time-calibrated phylogeny for squamate reptiles (lizards and snakes) based on 52 genes and 4162 species
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Phylogenomics of monitor lizards and the role of competition in dictating body size disparity
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Comprehensive phylogenomic analyses re-write the evolution of parasitism within cynipoid wasps
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A phylogenomic perspective on gene tree conflict and character evolution in Caprifoliaceae using target enrichment data, with Zabelioideae recognized as a new subfamily
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Data from: A comprehensive and dated phylogenomic analysis of butterflies
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Data from: Comparison of taxon-specific versus general locus sets for targeted sequence capture for plant phylogenomics
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Data from: Phylogenomic analysis of a rapid radiation of misfit fishes (Syngnathiformes) using ultraconserved elements
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Data from: Phylogenomic incongruence, hypothesis testing, and taxonomic sampling: the monophyly of characiform fishes
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Valenzuela phylogenomic dataset from: Illumina whole genome sequencing indicates ploidy level differences within the Valenzuela flavidus (Psocodea: Psocomorpha: Caeciliusidae) species complex
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Data from: Anchored phylogenomics improves the resolution of evolutionary relationships in the rapid radiation of Protea L.
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Phylogenomics and biogeography of Castanea (chestnut) and Hamamelis (witch-hazel): Choosing between RAD-seq and Hyb-Seq approaches
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Revisiting the evolution of Ostrinia moths with phylogenomics (Pyraloidea: Crambidae: Pyraustinae)
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Data from: Plotting for change: an analytic framework to aid decisions on which lineages are candidate species in phylogenomic species discovery
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Tempo and mode of evolution of Oryzomyine rodents (Rodentia, Cricetidae, Sigmodontinae): a phylogenomic approach
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Phylogenomic analysis does not support a classic but controversial hypothesis of progenitor-derivative origins for the serpentine endemic Clarkia franciscana
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Fig. 9 in Phylogenomic Species Delimitation, Taxonomy, and 'Bird Guide' Identification for the Neotropical Ant Genus Rasopone (Hymenoptera: Formicidae)
Fig. 9. Distribution map, face view, and lateral view of petiole of Rasopone costaricensis (holotype worker), R. politognatha (holotype worker), R. JTL035 (worker, Mexico, CASENT0640453), and Rasopone JTL049 (worker, Colombia, CASENT0644557). On distribution maps, red dots are sites with UCE sequence data. Red boxes are type locality.
Fig. 10 in Phylogenomic Species Delimitation, Taxonomy, and 'Bird Guide' Identification for the Neotropical Ant Genus Rasopone (Hymenoptera: Formicidae)
Fig. 10. Distribution map, face view, and lateral view of petiole of Rasopone costaricensis form b (worker, Costa Rica, INB0003223929), R. JTL047 (worker, French Guiana, CASENT0645960), R. panamensis (worker, Costa Rica, CASENT0644252), and R. subcubitalis (holotype worker). On distribution maps, red dots are sites with UCE sequence data. Red boxes are type locality.
A combined approach of mitochondrial DNA and anchored nuclear phylogenomics sheds light on unrecognized diversity, phylogeny, and historical biogeography of the cascade frogs, genus Amolops (Anura: Ranidae)
<p><i>Amolops</i> is one of the most species-rich genera in Ranidae, with 59 recognized species. This genus currently includes six species groups diagnosed mainly by morphology. Several recent molecular studies indicated that the classification of species groups within <i>Amolops</i> remains controversial, and key nodes in the phylogeny have been inadequately resolved. In addition, the diversity of cascade frogs remains poorly understood, especially for those from incompletely sampled regions. Herein, we investigate the species-level diversity within genus <i>Amolops</i> throughout southern China and Southeast Asia, and infer evolutionary relationships among the species using mtDNA data (16S, <i>COI</i>, and <i>ND2</i>). Molecular analyses indicate nine new unnamed species, mostly distributed in the Himalayas. We then utilized anchored hybrid enrichment to generate a dataset representing major mitochondrial lineages to resolve phylogenetic relationships, biogeography, and pattern of species diversification. Our resulting phylogeny strongly supports the monophyly of three previously identified species groups (the <i>A. ricketti</i>, <i>A. daiyunensis</i>,<i> </i>and <i>A. hainanensis</i> groups), the paraphyly of the <i>A. mantzorum</i> and <i>A. marmoratus</i> groups, as previously defined, and monophyly of the <i>A. monticola</i> group. We erect one new species group, the <i>A. viridimaculatus</i> group, and recognize Dubois (1992) 'subgenus' <i>Amo</i> as the <i>A. larutensis</i> species group. Biogeographic analysis suggests that <i>Amolops</i> originated on the Indo-Burma/Tai-Malay Peninsula at the Eocene/Oligocene boundary, and dispersed outward, exemplifying a common pattern observed for the origin of Asia's biodiversity. The early divergence within <i>Amolops</i> coincides with the Himalayas uplift, and the lateral extrusion of Indochina at the Oligocene/Miocene boundary. Our results show that paleoclimatic and geomorphological events have profoundly influenced the pattern of lineage diversification within <i>Amolops</i>.</p>
Target-capture phylogenomics provide insights on gene and species tree discordances in Old World Treefrogs (Anura: Rhacophoridae)
<p>Genome-scale data have greatly facilitated the resolution of recalcitrant nodes that Sanger-based datasets have been unable to resolve. However, phylogenomic studies continue to utilize traditional methods such as bootstrapping to estimate branch support; and high bootstrap values are still interpreted as providing strong support for the correct topology. Furthermore, relatively little attention is given to assessing discordances between gene and species trees, and the underlying processes that produce phylogenetic conflict. We generated novel genomic datasets to characterize and determine the causes of discordance in Old World Treefrogs (Family: Rhacophoridae)—a group that is fraught with conflicting and poorly supported topologies among major clades. We showed that incomplete lineage sorting was present at all nodes that exhibited high levels of discordance, which was caused by extremely short internal branches. We also clearly demonstrate that bootstrap values do not reflect uncertainty or confidence for the correct topology, and hence, should not be used as a measure of branch support in phylogenomic datasets. Overall, we showed that species tree inference can be improved using a total-evidence and multi-faceted approach that utilizes the most amount of data and considers results from different analytical methods and datasets.</p>
ScienceDex guides
Understand access before you commit
These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
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.