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1,344 results for “: phylogenomics”
Data from: Phylogenomic analysis of yellowjackets and hornets (Hymenoptera: Vespidae, Vespinae)
The phylogenetic relationships among genera of the subfamily Vespinae (yellowjackets and hornets) remain unclear. Yellowjackets and hornets constitute one of the only two lineages of highly eusocial wasps, and the distribution of key behavioral traits correlates closely with the current classification of the group. The potential of the Vespinae to elucidate the evolution of social life, however, remains limited due to ambiguous genus-level relationships. Here, we address the relationships among genera within the Vespinae using transcriptomic (RNA-seq) data. We sequenced the transcriptomes of six vespid wasps, including three of the four genera recognized in the Vespinae, combined our data with publicly available transcriptomes, and assembled two matrices comprising 1,507 and 3,356 putative single-copy genes. The results of our phylogenomic analyses recover Dolichovespula as more closely related to Vespa than to Vespula, therefore challenging the prevailing hypothesis of yellowjacket (Vespula + Dolichovespula) monophyly. This suggests that traits such as large colony size and high paternity arose in the genus Vespula following its early divergence from the remaining vespine genera.
Disentangling lousy relationships: Comparative phylogenomics of two sucking louse lineages parasitizing chipmunks
<p><span><span><span><span><span><span><span><span><span><span><span>The evolution of obligate parasites is often interpreted in light of their hosts' evolutionary history. An expanded approach is to examine the histories of multiple lineages of parasites that inhabit similar environments on a particular host lineage. Western North American chipmunks (genus <i>Tamias</i>) have a broad distribution, a history of divergence with gene flow, and host two species of sucking lice (Anoplura), <i>Hoplopleura arboricola</i> and <i>Neohaematopinus pacificus</i>. From total genomic sequencing, we obtained sequences of over 1100 loci sampled across the genomes of these lice to compare their evolutionary histories and examine the roles of host association in structuring louse relationships. Within each louse species, clades are largely associated with closely related chipmunk host species. Exceptions to this pattern appear to have a biogeographic component, but differ between the two louse species. Phylogenetic relationships among these major louse clades, in both species, are not congruent with chipmunk relationships. In the context of host associations, each louse lineage has a different evolutionary history, supporting the hypothesis that host-parasite assemblages vary both across the landscape and with the taxa under investigation. In addition,<i> </i>the louse <i>Hoplopleura erratica </i>(parasitizing the eastern <i>Tamias striatus</i>) is embedded within <i>H. arboricola</i>, rendering it paraphyletic. This phylogenetic result, together with comparable divergences within <i>H. arboricola</i>, indicate a need for taxonomic revision. Both host divergence and biogeographic components shape parasite diversification as demonstrated by the distinctive diversification patterns of these two independently evolving lineages that parasitize the same hosts.</span></span></span></span></span></span></span></span></span></span></span></p>
Figure 2 in Integrating phylogenomic and morphological data to assess candidate species-delimitation models in brown and red-bellied snakes (Storeria)
Figure 2. Map of Storeria ranges and sampling locations, showing geographical extent of populations, and range of former species with respect to re-delimited taxa. A, previous geographical extent of Storeria occipitomaculata is shown in red; circles indicate sampling localities. The asterisk indicates the sample of Storeria 'hidalgoensis' examined for morphology, with the range of this subpopulation, now considered part of S. occipitomaculata, indicated in pink. The range of Storeria storerioides is indicated in blue, with the sampling locality indicated by a square. B, previous geographical extent of Storeria dekayi is shown in yellow, with pentagons indicating sampling localities of S. dekayi, triangles indicating Storeria victa, and a line drawn to approximate the range boundary. The asterisk in the Central American population indicates the collection location of the specimen of Storeria 'tropica' examined for morphology, which is now considered part of S. dekayi.
Figures 25–30 in Taxonomy in the phylogenomic era: species boundaries and phylogenetic relationships among North American ants of the Crematogaster scutellaris group (Formicidae: Hymenoptera)
Figures 25–30. Crematogaster workers, showing lateral view of body (A), full-face view of head (B) and dorsal view of body (C). 25, C. opuntiae (CASENT0922738); 26, C. marioni (CASENT0922734); 27, C. coarctata (CASENT0005667); 28, C. hespera holotype (USNMENT00529501); 29, C. browni (CASENT0922722); 30, C. emeryana (CASENT0922729). Images courtesy of AntWeb (www.antweb.org); photographers Wade Lee (25, 26, 29, 30), April Nobile (27), Michele Esposito (28).
Figures 31–36 in Taxonomy in the phylogenomic era: species boundaries and phylogenetic relationships among North American ants of the Crematogaster scutellaris group (Formicidae: Hymenoptera)
Figures 31–36. Crematogaster workers, showing lateral view of body (A), full-face view of head (B) and dorsal view of body (C). 31, C. cerasi lectotype (USNMENT00529078); 32, C. vermiculata (CASENT0914534); 33, C. rifelna holotype (LACMENT164556); 34, C. ashmeadi (CASENT0922720); 35, C. pinicola (CASENT0172943); 36, C. pilosa (CASENT0914530). Images courtesy of AntWeb (www.antweb.org); photographers Michele Esposito (31, 33), Zach (Ziv) Lieberman (32, 36), Wade Lee (34), April Nobile (35).
Figures 3–12. Crematogaster worker features useful for identification. 3 in Taxonomy in the phylogenomic era: species boundaries and phylogenetic relationships among North American ants of the Crematogaster scutellaris group (Formicidae: Hymenoptera)
Figures 3–12. Crematogaster worker features useful for identification. 3, petiole shape, dorsal view, C. lineolata (CASENT0863235) (3A) and C. torosa (CASENT0795540) (3B); 4, sculpture on declivitous face of propodeum, C. dentinodis (CASENT0863070) (4A) and C. depilis (CASENT0863478) (4B); 5, mesosomal pilosity, C. punctulata (CASENT0863277) (5A) and C. emeryana (CASENT0863099) (5B); 6, position and shape of propodeal spines, dorsal view, C. isolata (CASENT0863072) (6A) and C. pinicola (CASENT0882129) (6B); 7, petiole shape, dorsal view, C. mutans (CASENT0862488); 8, subpetiolar tooth, lateral view, C. mutans (CASENT0862488); 9, promesonotal sculpture, C. californica (CASENT0221085) (9A) and C. coarctata (CASENT0221962) (9B); 10, postpetiolar seta, C. browni (CASENT0863144) (10A) and C. cerasi (CASENT0795541) (10B); 11, cephalic pilosity, C. torosa (CASENT0795540) (11A) and C. missouriensis (CASENT0221041) (11B); 12, mesosomal profile, C. crinosa (CASENT0795543) (12A) and C. torosa (CASENT0863226) (12B).
Figures 40–47 in Taxonomy in the phylogenomic era: species boundaries and phylogenetic relationships among North American ants of the Crematogaster scutellaris group (Formicidae: Hymenoptera)
Figures 40–47. Bivariate plots of selected worker measurements in the Crematogaster scutellaris group. 40, PP-SL (postpetiole seta length) by HW (head width) in C. browni (N = 16) and C. cerasi (N = 17); 41, ED (eye diameter) by MtFL (metafemur length) in C. californica (N = 22) and C. coarctata (N = 21); 42, MtFL (metafemur length) by HW (head width) in C. californica (N = 22), C. colei (N = 12) and C. opuntiae (N = 10); 43, MtFL (metafemur length) by HW (head width) in C. depilis (N = 15), C. detecta (N = 11) and C. larreae (N = 5); 44, MtTL (metatibia length) by HW (head width) in C. depilis (N = 15), C. detecta (N = 11) and C. larreae (N = 5); 45, SPL (propodeal spine length) by HW (head width) in workers of C. hespera (N = 18), C. laeviuscula (N = 25) and C. parapilosa (N = 15); 46, SL (scape length) by HW (head width) in C. emeryana (N = 12) and C. marioni (N = 18); 47, SPTD (propodeal spine tip distance) by HW (head width) in C. lineolata (N = 26) and C. punctulata (N = 15).
Figures 37–39 in Taxonomy in the phylogenomic era: species boundaries and phylogenetic relationships among North American ants of the Crematogaster scutellaris group (Formicidae: Hymenoptera)
Figures 37–39. Crematogaster workers, showing lateral view of body (A), full-face view of head (B), and dorsal view of body (C). 37, C. parapilosa holotype (CASENT0863386); 38, C. laeviuscula (CASENT0104828); 39, C. lineolata (CASENT0922733). Images courtesy of AntWeb (www.antweb.org); photographers Zachary Griebenow (37), April Nobile (338), Wade Lee (39).
Figures 13–18 in Taxonomy in the phylogenomic era: species boundaries and phylogenetic relationships among North American ants of the Crematogaster scutellaris group (Formicidae: Hymenoptera)
Figures 13–18. Crematogaster workers, showing lateral view of body (A), full-face view of head (B) and dorsal view of body (C). 13, C. dentinodis (CASENT0102830); 14. C. vetusta holotype (CASENT0863254); 15, C. navajoa worker (CASENT0064826); 16, C. punctulata lectotype (CASENT0923318); 17, C. isolata (CASENT0922731); 18, C. sp. cf. opaca (MCZENT00589113). Images courtesy of AntWeb (www.antweb.org); photographers Jen Fogarty (13), Michele Esposito (14, 16), April Nobile (15), Wade Lee (17), Zachary Griebenow (18).
Figure 2 in Taxonomy in the phylogenomic era: species boundaries and phylogenetic relationships among North American ants of the Crematogaster scutellaris group (Formicidae: Hymenoptera)
Figure 2. Biogeography and nesting preference of the Crematogaster scutellaris group. Time-calibrated phylogeny estimated with mcmctree and codeml in PAMLv.4.9. The analysis is based on the 90% completeness matrix after application of spruceup trimming with a cut-off of 0.98 (90%-0.98-spruceup), and the best maximum likelihood tree resulting from SWSC-EN partitioning of this matrix. This matrix and tree was pruned to a reduced dataset of 34 taxa for dating analysis. Node numbers refer to Table 1, where median ages and 95% highest posterior densities (HPD) are given. Biogeographic range reconstructions with BioGeoBEARS v.1.1.2 are mapped on this chronogram as E = eastern US and north-east Mexico (orange), W = western US and north-west Mexico (dark blue), C = the Caribbean (grey), M = southern Mexico to Honduras (red), EW = combined E and W distributions (light blue), EM = combined E and M distributions (purple), EC = combined E and C distributions (dark green), WM = combined W and M distributions (peach). Respective probabilities for ancestral ranges are given in Table 1. Ancestral states for nesting preference, estimated with the R package corHMM v.2.5, are further mapped on the phylogeny; pie colours are: light green = arboreal; brown = ground-dwelling.
Figure 1 in Taxonomy in the phylogenomic era: species boundaries and phylogenetic relationships among North American ants of the Crematogaster scutellaris group (Formicidae: Hymenoptera)
Figure 1. Phylogeny of the North American Crematogaster scutellaris group. Maximum likelihood phylogenetic tree estimated from the 90% taxon completeness matrix after application of spruceup trimming with a 0.98 cut-off (90%-0.98-spruceup), using a combined best tree and ultrafast bootstrap (N = 1000) search in IQ-TREE v.1.6.12 and implementing 746 partitions. The analysis was rooted using the most distantly related outgroup taxon C. cf. rogenhoferi; the long branch leading to this taxon has been shortened for space-saving purposes. All nodes have bootstrap support = 100% unless labelled otherwise. Species images courtesy of AntWeb (www.antweb.org).
Fig. 7 in UCE Phylogenomics of New World Cryptopone (Hymenoptera: Formicidae) Elucidates Genus Boundaries, Species Boundaries, and the Vicariant History of a
Fig. 7. Shape of third abdominal sternite, Cryptopone vs.Wadeura. Cryptopone gilvagrande (CASENT064143), lateral view (A), oblique ventral view (B). Wadeura guianensis (CASENT0640149), lateral view (C), oblique ventral view (D). Scale bars are 0.2 mm.
Fig. 6 in UCE Phylogenomics of New World Cryptopone (Hymenoptera: Formicidae) Elucidates Genus Boundaries, Species Boundaries, and the Vicariant History of a
Fig. 6. Biogeography of the Cryptopone gilva complex within Central America. Chronogram inferred using BEAST2, 300 UCE loci, and a fixed topology (all UCE samples and SWSC-EN partitioning). Only results for the C. gilva complex are shown (see Supp Fig. 6 [online only] for the full results). Numbers on nodes are mean ages in millions of years ago and node bars are 95% Highest Posterior Densities (HPD).The map inset shows the distribution of C. gilva-clade samples within Central America. Colored dots match tip labels of the chronogram. Sites where specimens were identified by morphology alone (no sequencing) are shown as x for C. gilvagrande and a small black dot for C. guatemalensis. Samples of true C. gilva from the United States are not shown in the map.
Fig. 16–18 in Species Paraphyly and Social Parasitism: Phylogenomics, Morphology, and Geography Clarify the Evolution of the Pseudomyrmex elongatulus Group (Hymenoptera:
Fig. 16–18. Pseudomyrmex elongatulus group, workers, full-face dorsal view of head (a) and lateral profile of body (b). 16, P. nimbus, holotype, Costa Rica (CASENT0863541); 17, P. salvini, syntype, Mexico (CASENT0902879); 18, P. veracruzensis, holotype, Mexico (CASENT0863542). Images from AntWeb (www. antweb.org); photographers Phil Ward (16, 18), Zach (Ziv) Lieberman (17).
Fig. 3. Phylorate plot from a in Phylogenomics and Fossil Data Inform the Systematics and Geographic Range Evolution of a Diverse Neotropical Ant Lineage
Fig. 3. Phylorate plot from a diversification rate-shift analysis in BAMM. A single rate regime is inferred without any rate shifts detected. Diversification rate gradient legend is in units of species/million years.
Fig. 14 in UCE Phylogenomics of New World Cryptopone (Hymenoptera: Formicidae) Elucidates Genus Boundaries, Species Boundaries, and the Vicariant History of a
Fig. 14. Wadeura species, petiole lateral views. (A) W. guianensis (CASENT0640150). (B) W. pauli (CASENT0637806). (C) W. holmgreni (CASENT0373370). (D) W. holmgrenita (CASENT0637779). Scale bars are 0.2 mm.
Fig. 3 in Species Paraphyly and Social Parasitism: Phylogenomics, Morphology, and Geography Clarify the Evolution of the Pseudomyrmex elongatulus Group (Hymenoptera:
Fig. 3. Bivariate plots of measurements and indices concerned with eye size and petiole shape, in workers of P. apache (n = 17) and P. arcanus (n = 17). (a) PL/ LHT (petiole length/metatibia length) by HW (head width); (b) REL2 (eye length/head width) by PLI (petiole height/petiole length).
Fig. 1 in Phylogenomics and Fossil Data Inform the Systematics and Geographic Range Evolution of a Diverse Neotropical Ant Lineage
Fig. 1. Cephalotes topology inferred with RAxML, with species groups inferred in this study annotated with reference to previous species group designations. Numbers along the phylogeny correspond to species groups listed in the inset. Black circles indicate nodes with bootstrap support <95%, with corresponding bootstrap values displayed. Species (and photo credit) imaged, from top: Cephalotes persimilis de Andrade, 1999 (Hymenoptera: Formicidae) (April Nobile), Cephalotes pellans de Andrade, 1999 (Hymenoptera: Formicidae) (April Nobile), Cephalotes pusillus (Klug, 1824) (Hymenoptera: Formicidae) (April Nobile), Cephalotes guayaki de Andrade, 1999 (Hymenoptera: Formicidae) (April Nobile), Cephalotes umbraculatus (Fabricius, 1804) (Hymenoptera: Formicidae) (Shannon Hartman), Cephalotes manni (Kempf, 1951) (Hymenoptera: Formicidae) (Will Ericson), Cephalotes depressus (Klug, 1824) (Hymenoptera: Formicidae) (Wade Lee), Cephalotes setulifer (Emery, 1894) (Hymenoptera: Formicidae) (Wade Lee),Cephalotes kukulcan (Ryan Perry),Cephalotes multispinosus (Norton, 1868) (Hymenoptera: Formicidae) (Wade Lee), Cephalotes rohweri (Wheeler, 1916) (Hymenoptera: Formicidae) (Wade Lee), Cephalotes complanatus (Guérin-Méneville, 1844) (Hymenoptera: Formicidae) (Wade Lee), Cephalotes clypeatus (Fabricius, 1804) (Hymenoptera: Formicidae) (April Nobile), Cephalotes unimaculatus (Smith, 1853) (Hymenoptera: Formicidae) (Wade Lee), Cephalotes opacus Santschi, 1920 (Hymenoptera: Formicidae) (Shannon Hartman). Images from antweb.org under a Creative Commons Attribution License. Accessed August 24, 2020.
Fig. 2 in Phylogenomics and Fossil Data Inform the Systematics and Geographic Range Evolution of a Diverse Neotropical Ant Lineage
Fig. 2. MCMCTree time-scaled phylogeny (RAxML topology pruned to one tip per species) with historical biogeographic range inferences from the four-node fossil-constrained BioGeoBEARS analysis mapped onto nodes. An asterisk (*) indicates the location of a fossil node calibration.The light purple shading spans the proposed start and end dates (35–32 Mya) of the GAARlandia land bridge linking South America to the Antilles.The light gold shading spans the potential early start date and the complete closure date of the Panamanian land bridge (10–3.5 Mya).Transitions with boxes outlined in red denote differences from the historical geographic range inference without fossil constraints (Supp Fig. S7 [online only]). A, Antilles; C, Central America; S, South America.
Fig. 13–15 in Species Paraphyly and Social Parasitism: Phylogenomics, Morphology, and Geography Clarify the Evolution of the Pseudomyrmex elongatulus Group (Hymenoptera:
Fig. 13–15. Pseudomyrmex elongatulus group, workers, full-face dorsal view of head (a), and lateral profile of body (b). 13, P. capillatus, holotype, Mexico (CASENT0863535); 14, P. exoratus, holotype worker, Mexico (CASENT0863539); 15, P. fasciatus, holotype, Costa Rica (CASENT0863540). Images from AntWeb (www.antweb.org); photographer Phil Ward.
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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.