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501 results for “phylogenetic taxonomy”
FIGURE 8 in Integrative taxonomy reveals cryptic diversity in neotropical grasshoppers: taxonomy, phylogenetics, and evolution of the genus Sphenarium Charpentier, 1842 (Orthoptera: Pyrgomorphidae)
FIGURE 8. Type specimens of S. purpurascens: lectotype m (A) and paralectotype f (B); S. planum: lectotype m (C) and paralectotype f (D); S. macrophallicum: holotype m (E) and allotype f (F); S. minimum lectotype m (G); S. affine lecototype m (H) (Scale bars = 1cm).
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).
Figure 4 in Integrative taxonomy: molecular phylogenetics of Polypedilum (Cerobregma) and revisited morphology of Yaethauma and Collartomyia (Diptera: Chironomidae) reveals synonymy and supports new classification
Figure 4. Polypedilum (Collartomyia) longiligulatum. Pupa. A, frontal apotome; B, thorax; C, thorax horn; D, abdomen; E, caudolateral comb of segment VIII. (Scale bars. A, E, 100 µm; B, 400 µm; C, 20 µm; D, 200 µm.)
Figure 3 in Integrative taxonomy: molecular phylogenetics of Polypedilum (Cerobregma) and revisited morphology of Yaethauma and Collartomyia (Diptera: Chironomidae) reveals synonymy and supports new classification
Figure 3. Polypedilum (Collartomyia) longiligulatum. Colour images. Male. A, habitus, dorsal; B, hypopygium, dorsal view (Gc bulb, gonocoxite bulb; Gs, gonostylus); C, habitus, lateral. Pupa: D, habitus, dorsal; E, cephalothorax, lateral; F, thoracic horn, lateral. (Scale bars: A, C, D, E 400 µm; B, F,100 µm.)
Figure 1 in Integrative taxonomy: molecular phylogenetics of Polypedilum (Cerobregma) and revisited morphology of Yaethauma and Collartomyia (Diptera: Chironomidae) reveals synonymy and supports new classification
Figure 1. Phylogenetic tree from Bayesian inference for selected Polypedilum and relatives (see Table 1) based on six concatenated gene markers. Posterior probabilities (PP) and bootstrap support (BS from ML analysis) are indicated above branches, only nodes with PP> 0.95 or BS> 75 are labelled.
Figure 2 in Integrative taxonomy: molecular phylogenetics of Polypedilum (Cerobregma) and revisited morphology of Yaethauma and Collartomyia (Diptera: Chironomidae) reveals synonymy and supports new classification
Figure 2. Parsimony analysis for selected subgenera and species groups of Polypedilum Kieffer, related genera and Phaenopsectra Kieffer as outgroup under implied weighting. Numbers above branch Bremer values, with unlabeled branches unstable (0/1) between analyses, below line Bootstrap values of> 51. For analysis settings, see text.
Revised taxonomy of the Arctotis Annual Clade (Arctotideae, Asteraceae) from Southern Africa: integration of molecular phylogenetic and morphological evidence
<p>Previous phylogenetic analysis of ITS nrDNA sequence data for Arctotidinae species resolved a highly supported clade containing all but one of the showy annual <i>Arctotis </i>species (informally designated the '<i>Arctotis</i> Annual Clade')<i>.</i> In the present study, phylogenetic relationships in the <i>Arctotis </i>Annual<i> </i>Clade were investigated by Bayesian inference and maximum parsimony analyses of cpDNA (<i>trnT-trnL-trnF</i> and <i>trnH-psbA</i>) and nrDNA (ITS) sequence data. The cpDNA and nrDNA phylogenies were notably incongruent. <i>Arctotis venusta </i>and a putative unnamed species<i> </i>('sp. B') were highly supported as monophyletic by both datasets. The monophyly of <i>A. leiocarpa </i>was strongly supported by the ITS dataset, whereas the remaining accessions formed a poorly resolved complex (the '<i>A. fastuosa </i>complex'). Within the <i>A. fastuosa </i>complex, <i>A. hirsuta </i>was monophyletic with high support in the ITS phylogeny. A statistical parsimony-derived cpDNA haplotype network resolved five broad groups of haplotypes and showed no consistent geographical structure, but species-specific haplotype lineages<i> </i>for<i> A. venusta </i>and sp. B were resolved. <i>Arctotis fastuosa </i>accessions were distributed among four haplotype groups. Incongruence between the datasets and poor resolution within the <i>A. fastuosa </i>complex may reflect reticulate evolution, ancestral polymorphism, and incomplete lineage sorting, in tandem with the low information content of the datasets. The greatest phenotypic diversification in the clade is in cypsela morphology. Comparison of cypsela morphology with the phylogenies suggests a general trend for reduction in the sizes of the cypsela, abaxial wings, and pappus scales, and loss of pubescence during diversification. A revised taxonomy, integrating currently available evidence, accompanied by full descriptive accounts and a key to the taxa are presented. Eight species are recognized, including the nomenclatural novelties <span><b><i><span>Arctotis chrysantha</span></i></b></span> (sp. nov.) and <span><b><i><span>Arctotis namibiensis</span></i></b></span><i> </i>(sp. nov.). The names <i>Arctotis karasmontana</i>, <i>Venidium fugax</i>, and <i>Venidium macrocephalum</i> are lectotypified.</p>
Figure 34 in The genus Symmela Erichson, 1835 (Coleoptera, Scarabaeidae, Sericini): taxonomy and phylogenetic analysis
Figure 34. Strict consensus tree of three most parsimonious trees with a length of 658 steps (from the matrix of 113 characters). Squares along branches represent synapomorphies; black squares are nonhomoplastic synapomorphies and white squares are homoplastic synapomorphies. Support values: symmetric resampling/bootstrap.
Figure 32 in The genus Symmela Erichson, 1835 (Coleoptera, Scarabaeidae, Sericini): taxonomy and phylogenetic analysis
Figure 32. (a–k) Anterior legs of Symmela species (males), (l) pygidium (female). (a) S. clarki sp. nov.; (b) S. clypeata; (c, l) S. elegans; (d) S. instabilis; (e) S. jatahyensis; (f) S. mutabilis; (g) S. nunesorum sp. nov.; (h) S. opaca; (i) S. pseudopaca sp. nov.; (j) S. tarsalis; (k) S. nitidicollis (lectotype). Scale bars: 0.5 mm.
Figure 31 in The genus Symmela Erichson, 1835 (Coleoptera, Scarabaeidae, Sericini): taxonomy and phylogenetic analysis
Figure 31. Heads of Symmela species. (a) S. martinezi sp. nov.; (b) S. mutabilis; (c) S. nitida; (d) S. nitidicollis; (e) S. nunesorum sp. nov.; (f) S. opaca; (g) S. paschoali sp. nov.; (h) S. pseudopaca sp. nov.; (i) S. reischei sp. nov.; (j) S. tarsalis; (k) S. terezae sp. nov.; (l) S. unidentata sp. nov. Scale bars: 0.5 mm.
Figure 30 in The genus Symmela Erichson, 1835 (Coleoptera, Scarabaeidae, Sericini): taxonomy and phylogenetic analysis
Figure 30. Heads of Symmela species. (a) S. beskei sp. nov.; (b) S. brasiliensis; (c) S. capixaba sp. nov.; (d) S. clarki sp. nov.; (e) S. clypeata; (f) S. corumbana; (g) S. elegans; (h) S. erichsoni sp. nov.; (i) S. flavimana; (j) S. fuhrmanni sp. nov.; (k) S. guerlini sp. nov.; (l) S. iannuzziae sp. nov.; (m) S. instabilis; (n) S. jatahyensis; (o) S. longula. Scale bars: 0.5 mm.
Figure 28 in The genus Symmela Erichson, 1835 (Coleoptera, Scarabaeidae, Sericini): taxonomy and phylogenetic analysis
Figure 28. Symmela unidentata sp. nov., holotype ♂. (a) Habitus, dorsal view; (b) habitus, lateral view; (c) parameres, dorsal view; (d) aedeagus, dorsal view; (e) aedeagus, lateral view. Scale bars: a, b = 1 mm; c–e = 0.5 mm.
Figure 27 in The genus Symmela Erichson, 1835 (Coleoptera, Scarabaeidae, Sericini): taxonomy and phylogenetic analysis
Figure 27. Symmela terezae sp. nov., holotype ♂. (a) Habitus, dorsal view; (b) habitus, lateral view; (c) parameres, dorsal view; (d) aedeagus, lateral view. Scale bars: a, b = 1 mm; c, d = 0.5 mm.
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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.