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1,344 results for “phylogenomics”
Concordance and discordance in the phylogenomics of the wrasses and parrotfishes (Teleostei: Labridae)
<p>Phylogenomic analysis of large genome-wide sequence data sets can resolve phylogenetic tree topologies for large species groups, help test the accuracy of and improve resolution for earlier multilocus studies, and reveal the level of agreement or concordance within partitions of the genome for various tree topologies. Here we used a target-capture approach to sequence more than 1,000 single-copy exons for more than 200 labrid fishes together with more than 100 outgroup taxa to generate a new data-rich phylogeny for the family Labridae. Our time-calibrated phylogenetic analysis of exon-capture data pushes the root node age of the family Labridae back into the Cretaceous to about 79 Ma years ago. The monotypic Centrogenys vaigiensis, and the order Uranoscopiformes (stargazers) are identified as the sister lineages of Labridae. The phylogenetic relationships among major labrid subfamilies and within these clades was largely congruent with prior analyses of select mitochondrial and nuclear datasets. However, the position of the tribe Cirrhilabrini (fairy and flame wrasses) showed discordance, resolving either as the sister to a crown julidine clade or alternatively sister to a group formed by the labrines, cheilines and scarines. Exploration of this pattern using multiple approaches leads to slightly higher support for this latter hypothesis, highlighting the importance of genome-level data sets for resolving short internodes at key phylogenetic positions in large, economically important groups of coral reef fishes.</p>
Supporting Information for: Single-fly genome assemblies fill major phylogenomic gaps across the Drosophilidae Tree of Life
<p>This data repository contains supporting information, data, and code for figures and analysis pipelines the PLOS Biology article: "Single-fly genome assemblies fill major phylogenomic gaps across the Drosophilidae Tree of Life."</p> <ul> <li><strong>4d_full.treefile</strong>: Data underlying Figure 1 (note: tree was plotted as a cladogram and key groups collapsed on iToL; the treefile was not modified) and Figure S1.</li> <li><strong>S2_data.csv</strong>: Data underlying Figure 2.</li> <li><strong>S3_data.csv</strong>: Data underlying Figure 3.</li> <li>Data underlying Figure 4 is found in Table S4 of supplementary_tables.xlsx in the main manuscript</li> <li><strong>S5_data.csv</strong> Data underlying Figure 5</li> <li><strong>S6_data.csv</strong> Data underlying Figure S2 </li> <li><strong>illumina_only_assms.tar.gz</strong>: Archive of Illumina-only assemblies (FASTA) based on publicy available data that we did not generate. Assemblies generated from our own short-read data have been submitted to NCBI GenBank.</li> <li><strong>illumina_vcfs.tar.gz</strong>: Illumina-based variant calls and BED tracks of masked bases.</li> <li><strong>genomes.tar.gz</strong>: Genome files, for archival purposes.</li> <li><strong>repeatModeler-lib.tar.gz</strong>: RepeatModeler2 libraries.</li> <li><strong>diploid_genomes.tar.gz</strong>: diploid genomes and BED tracks of phased regions.</li> <li><strong>trees.tar.gz</strong>: phylogenies</li> </ul>
Phylogenomics of fresh and formalin specimens resolves the systematics of old world mud snakes (Serpentes: Homalopsidae) and expands biogeographic inference
<p>The known biodiversity of Asia and Australasia is continuously expanding with more focused studies on systematics of various groups and the respective biogeography. Historically, fluctuating sea-levels and cyclic connection and separation of now-disjunct landmasses have been invoked to explain the accumulation of biodiversity via species pump mechanisms. However, recent research has shown that geological shifts of the mainland and dispersal events may be better explanations of the biodiversity in these regions. We investigate these processes using the poorly-studied and geographically widespread Mud Snakes (Serpentes: Homalopsidae) using a target capture approach of ~4,800 nuclear loci from fresh tissues and supplemental mitochondrial data from formalin tissues from museum specimens. We use these datasets to reconstruct the first resolved phylogeny of the group, identify their biogeographic origins, and test hypotheses regarding the roles of sea-level change and habitat selection on their diversification. Divergence dating and ancestral range estimation yielded support for an Oligocene origin and diversification from mainland Southeast Asia and Sundaland in the rear-fanged group ~20 million years ago, followed by eastward and westward dispersal. GeoHiSSE models indicate that niche expansion of ancestral rear-fanged lineages into aquatic environments did not impact their diversification rates. Our results highlight that Pleistocene sea-level changes and habitat specificity did not primarily lead to the extant species richness of Homalopsidae, and that, alternatively, geological shifts in mainland Southeast Asia may be a major driver of diversity in this group. We also emphasize the importance of using fresh and degraded tissues, and both nuclear and mitochondrial DNA, for filling in knowledge gaps in poorly known, but highly diverse and conceptually important groups, constituting a non-traditional model study system for understanding transitions between terrestrial, marine, and freshwater environments.</p>
FIGURE 3 in Revised Evolutionary And Taxonomic Synthesis For Parrots (Order: Psittaciformes) Guided By Phylogenomic Analysis
FIGURE 3. Species-level topology of Psittacinae. Support values come from the maximum likelihood tree. Nodes have ultrafast bootstrap values of ≥95% otherwise noted.
FIGURE 8 in Revised Evolutionary And Taxonomic Synthesis For Parrots (Order: Psittaciformes) Guided By Phylogenomic Analysis
FIGURE 8. Photographs (not to scale) of Calyptomena hosii (left photo: Dubi Shapiro) a suboscine passerine of Borneo (Brunei, Indonesia) and Triclaria malachitacea (right photo: Marcos Eugênio) of southeastern Brazil showing presumably convergent evolution in ventral coloring. See text for discussion. Photographs reproduced with permission from the photographers.
FIGURE 16 in Revised Evolutionary And Taxonomic Synthesis For Parrots (Order: Psittaciformes) Guided By Phylogenomic Analysis
FIGURE 16. Dorsal view of specimens of Glossopsitta concinna from the Australian National Wildlife Collection (ANWC) showing variation within and between sexes and within and between mainland southeastern Australia versus Tasmania. Note the bluer coronal color in mainland males. Registration numbers from the bird collection at ANWC are shown. Photograph: Gordon Gullock.
Fig. 2. The red algal phylogenomic approaches. A. Concatenated multigene phylogeny using 170 in Algal genomics perspective: the pangenome concept beyond traditional molecular phylogeny and taxonomy
Fig. 2. The red algal phylogenomic approaches. A. Concatenated multigene phylogeny using 170 plastid genes (Muñoz-Gómez et al., 2017). B. Concatenated multigene phylogeny using 4,777 nuclear genes (Lee et al., 2019). C. Intertwining phylogenetic network tree of red algal plastid and nuclear multigene phylogenies.
Fig. 2 in Phylogenomics and deep convergence in cockroach hind-wing morphology
Fig. 2 Oulopteryx illuminata sp. nov. is demonstrative of a typical species with an apical folded membrane, but having a rare method of concealment at rest (i.e., coiling, a feature shared among Oulopterygidae, Theganopteryx, Prosoplecta, and possibly a few others). Forewing (a, b) and hind-wing (c) morphology to scale with full body (f, g). Folding occurs alone dashed lines. Method of rolling the hind-wing apical field at rest shown (h). Genital morphology (d, e) of male holotype from posterior dorsal views (d) and dorsal view (e). Labels identify genital sclerites using the nomenclature of Klass (1997). See supplementary figures for more details. Wing venation (b, c) nomenclature based on Li et al. (2018) with modification. *Pcu not identified. See Schubnel et al. (2019) for a discussion of Pcu's identity among Blattodea.
Anchored phylogenomics unravels the evolution of spider flies (Diptera, Acroceridae) and reveals discordance between nucleotides and amino acids
<p>Supplementary Material accompanying the manuscript titled "Anchored phylogenomics unravels the evolution of spider flies (Acroceridae) and reveals discordance between nucleotides and amino acids", including Supplementary Figures, Tables and Datasets.</p>
Data for: Why do phylogenomic analyses of early animal evolution continue to disagree? Sites in different structural environments yield different answers
<p>Supporting data for "Why do phylogenomic analyses of early animal evolution continue to disagree? Sites in different structural environments yield different answers" submitted by A Pandey and EL Braun. File is a gzipped tarball including protein multiple sequence alignments, phylogenetic trees, and other supporting data; see included README for details.</p>
Data for: Resolving the avian tree of life from top to bottom: The promise and potential boundaries of the phylogenomic era
<p>This data package includes multiple sequence alignments, information about base compositional variation, and phylogenetic analyses that support Figures 7 and 8 in Braun et al. (2019). There is a README in SuppInfo_Braun_et_al_chapter_Kraus_volume.tar.gz that provides a detailed description of the files in this data package.</p> <p>Braun, E.L., Cracraft, J., Houde, P. (2019). Resolving the Avian Tree of Life from Top to Bottom: The Promise and Potential Boundaries of the Phylogenomic Era. In: Kraus, R. (eds) Avian Genomics in Ecology and Evolution. Springer, Cham. https://doi.org/10.1007/978-3-030-16477-5_6</p>
Linked collectors and determiners for: Phylogenomic Species Delimitation, Taxonomy, and ' Bird Guide' Identification for the Neotropical Ant Genus Rasopone (Hymenoptera: Formicidae).
Natural history specimen data linked to collectors and determiners held within, "Phylogenomic Species Delimitation, Taxonomy, and ' Bird Guide' Identification for the Neotropical Ant Genus Rasopone (Hymenoptera: Formicidae)". Claims or attributions were made on Bionomia by volunteer Scribes, <a href="https://bionomia.net/dataset/430a96d1-f5cd-4234-a35d-3f324ed63974">https://bionomia.net/dataset/430a96d1-f5cd-4234-a35d-3f324ed63974</a> using specimen data from the dataset aggregated by the Global Biodiversity Information Facility, <a href="https://gbif.org/dataset/430a96d1-f5cd-4234-a35d-3f324ed63974">https://gbif.org/dataset/430a96d1-f5cd-4234-a35d-3f324ed63974</a>. Formatted as a Frictionless Data package.
Linked collectors and determiners for: Refining the phylogeny and taxonomy of the apple tribe Maleae (Rosaceae): insights from phylogenomic analyses of 563 plastomes and a taxonomic synopsis of Photinia and its allies in the Old World.
Natural history specimen data linked to collectors and determiners held within, "Refining the phylogeny and taxonomy of the apple tribe Maleae (Rosaceae): insights from phylogenomic analyses of 563 plastomes and a taxonomic synopsis of Photinia and its allies in the Old World". Claims or attributions were made on Bionomia by volunteer Scribes, <a href="https://bionomia.net/dataset/aa8d91fe-6fe4-4c59-8831-8103148e66f4">https://bionomia.net/dataset/aa8d91fe-6fe4-4c59-8831-8103148e66f4</a> using specimen data from the dataset aggregated by the Global Biodiversity Information Facility, <a href="https://gbif.org/dataset/aa8d91fe-6fe4-4c59-8831-8103148e66f4">https://gbif.org/dataset/aa8d91fe-6fe4-4c59-8831-8103148e66f4</a>. Formatted as a Frictionless Data package.
Linked collectors and determiners for: Phylogenomics and the rise of the angiosperms.
Natural history specimen data linked to collectors and determiners held within, "Phylogenomics and the rise of the angiosperms". Claims or attributions were made on Bionomia by volunteer Scribes, <a href="https://bionomia.net/dataset/4195e042-b632-47ba-9545-32a5e3033ff7">https://bionomia.net/dataset/4195e042-b632-47ba-9545-32a5e3033ff7</a> using specimen data from the dataset aggregated by the Global Biodiversity Information Facility, <a href="https://gbif.org/dataset/4195e042-b632-47ba-9545-32a5e3033ff7">https://gbif.org/dataset/4195e042-b632-47ba-9545-32a5e3033ff7</a>. Formatted as a Frictionless Data package.
Fig. 4 in Phylogenomics of the tropical plant family Ochnaceae using targeted enrichment of nuclear genes and 250+ taxa
Fig. 4. Distribution of specimen ages and the number of loci recovered in the phylogenomic study of Ochnaceae. A, Histogram of the collection years of all Ochnaceae specimens; B & C, Relationship between the year of collection of the specimens and the number of loci recovered for tissue obtained from herbarium material (excluding specimens with silica-dried leaf material), analysed for Ochneae and all the remaining Ochnaceae separately, either using the consensus-alignment (B) or the sample-specific (C) reference-based assembly approach. Pearson correlation coefficients and confidence intervals are given for each group.
Fig. 2 in Phylogenomics of the tropical plant family Ochnaceae using targeted enrichment of nuclear genes and 250+ taxa
Fig. 2. RAxML trees based on the concatenated nuclear loci of Ochnaceae. A, Early-diverging branches of Ochnaceae and relationships within Quiinoideae based on the FAM dataset; B, Phylogenetic relationships of Sauvagesieae, Luxemburgieae and Testuleeae based on the SLT dataset. Numbers on the branches are bootstrap values>50%. Numbers in parentheses after species names correspond to the specimen IDs (only for species with multiple accessions). The indicated classification of subfamilies and tribes follows Schneider & al. (2014).
Fig 1 in Phylogenomics and a revised tribal classification of subfamily Dipterocarpoideae (Dipterocarpaceae)
Fig 1. Chronogram of Dipterocarpoideae based on plastome and nuclear sequences (combined dataset) plus outgroups inferred by BEAST 2. Node ages (in Ma) shown at nodes, with the 95% highest posterior density intervals (HPD; blue bars). All nodes with posterior probability (PP) 1, except nodes indicated with blue circles (PP = 0.79–0.99) or grey circles (PP = 0.33–0.69). Overlay with revised tribal classification: A1: Vaterieae; A2: Dipterocarpeae; A3: Dryobalanopseae; A4: Shoreeae; A5: Doona + Anthoshorea + Neobalanocarpus + Hopea clade; A6: Shorea sect. Doona; A7: S. sect. Anthoshorea; A8: Richetioides + Parashorea + Shorea + Rubroshorea clade; A9: S. sect. Richetioides; A10: S. sect. Shorea; A11: S. sect. Rubroshorea. Fossils used in this study (red circles): I, the crown age of Malvales divergence from Brassicales (Magallón & al., 2015) (102.7 Ma); II, stem age for the ancestral node leading to Sterculioideae (Hernández-Gutiérrez & Magallón, 2019) (78.89 Mr); III, Bombacacidites anne (66–56 Ma) (Van Der Hammen, 1954); IV, Malvaciphyllum macondicus (61.6–56 Ma) (Carvalho & al., 2011). Geological time scale shown in millions of years.
Fig. 1 in Phylogenomics of the tropical plant family Ochnaceae using targeted enrichment of nuclear genes and 250+ taxa
Fig. 1. Overview of the phylogenetic relationships of the major clades of Ochnaceae based on the FAM dataset together with images of representative species. The classification follows Schneider & al. (2014). Ochninae is by far the most species-rich clade comprising about two-thirds of the family's species and six genera (Brack. = Brackenridgea; Cmp. = Campylospermum, clades A and B; I. = Idertia; Ochna; Ouratea; Rh. = Rhabdophyllum). Letters around the tree refer to the photos (mostly flowers except where indicated) and the relative position of the displayed taxa on the tree. A, Medusagyne oppositifolia (Medusagynoideae); B, Froesia venezuelensis (Quiinoideae); C, Luxemburgia schwackeana (Luxemburgieae); D, Rhytidanthera sulcata; E, Cespedesia spathulata; F, Poecilandra retusa; G, Godoya antioquiensis; H, Wallacea insignis; I, Sauvagesia semicylindrifolia; J, Sauvagesia erecta (Sauvagesieae); K, Infructescence of Lophira lanceolata with accrescent sepals (Lophirinae); L, Flower of Elvasia kollmannii (Elvasiinae); M, Perissocarpa umbellifera; N, Fruiting Rhabdophyllum arnoldianum; O, Brackenridgea nitida; P, Campylospermum glaberrimum; Q, Ochna serrulata; R, Fruit of Ochna integerrima with drupelets sitting on enlarged receptacle; S, Fruit of Ouratea sp. with enlarged red receptable; T, Ouratea sp. — Photos: A, K & N from www.africanplants.senckenberg.de (Dressler & al., 2014–); B by Julio Schneider; C by William Milliken/ Royal Botanic Gardens, Kew; D by Sandra Reinales; E by Reinaldo Aguilar; F, H & M by Francisco Farroñay; G by John Clark; I, J, S & T by Domingos Cardoso; L by Claudio Nicoletti de Fraga; O by John Elliott; P by Warran McCleland; Q by Marja Broersma; R by Pierre Grard.
Figure 2 in Reconstructing evolutionary timescales using phylogenomics
Figure 2. Phylogenomic estimates of the crown ages of major groups within mammals, birds, and insects. Black circles indicate median age estimates, whereas horizontal bars indicate the associated 95% credibility intervals. Ages for insect groups are according to Tong et al. (2015); ages of bird groups are according to Prum et al. (2015); and ages of placental mammal groups are according to dos Reis et al. (2012). The timings of four mass extinction events are also shown.
Figure 1 in Phylogenomic approaches in systematic studies
Figure 1. The number of annual publications with topic on phylogenomics in Web of Science database from 2009 to 2019.
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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.