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165 results for “phylogenetic model”
Aligned bam files for "Phylogenetic modeling of enhancer shifts in mole-rats reveals regulatory changes associated with tissue-specific traits"
<p>Aligned bam files used for analysis in "Phylogenetic modeling of enhancer shifts in mole-rats reveals regulatory changes associated with tissue-specific traits".</p> <p>This is an accompanying dataset to Datasets and code for "Phylogenetic modeling of enhancer shifts in mole-rats reveals regulatory changes associated with tissue-specific traits" (https://zenodo.org/record/7442105).</p>
Supplement for "Using Phylogenetic Networks to Model Chinese Dialect History"
<p>This is the supplementary material accompanying the paper "Using Phylogenetic Networks to Model Chinese Dialect History", which appeared in 2014 in "Language Dynamics and Change" (volume 4, issue 2).</p>
Fig. 1 in Echinoderm model systems, homology, and phylogenetic inference: comment and reply to Paul (2021)
Fig. 1. Tree comparison between two phylogenetic inference methods with bootstrap support at the nodes. A. Phylogenetic hypothesis from Paul (2021) inferred via maximum parsimony. B. Phylogenetic hypothesis inferred via maximum likelihood.
figure 2 The dated phylogenetic trees using the cytb gene for G. subgutturosa. Blue bars show 95 in Unraveling goitered gazelle (Gazella subgutturosa) diversification: insights from phylogeography and species distribution modeling
figure 2 The dated phylogenetic trees using the cytb gene for G. subgutturosa. Blue bars show 95% highest posterior density intervals of the estimated node ages; numbers next to the nodes are mean node ages (Mya). The red and green lines show new haplotypes from this study.
Figure. The phylogenetic tree showing the relationship among Brevibacillus parabrevis strains SA2.2 and TJ2.3, Bacillus licheniformis MG4.2, and their phylogenetically closest type strains. The GenBank accession numbers of the type strains and studied strains are shown following species names. Distance matrix was calculated by Kimura's 2-parameter model. The scale bar indicates 0.02 substitutions per nucleotide position. Alicyclobacillus pohliae AJ564766 served as an out-group. in Distribution of extracellular enzyme-producing bacteria in the digestive tracts of 4 brackish water fish species
Figure. The phylogenetic tree showing the relationship among Brevibacillus parabrevis strains SA2.2 and TJ2.3, Bacillus licheniformis MG4.2, and their phylogenetically closest type strains. The GenBank accession numbers of the type strains and studied strains are shown following species names. Distance matrix was calculated by Kimura's 2-parameter model. The scale bar indicates 0.02 substitutions per nucleotide position. Alicyclobacillus pohliae AJ564766 served as an out-group.
FIG. 72 in Model-based analysis of postcranial osteology of marsupials from the Palaeocene of Itaboraí (Brazil) and the phylogenetics and biogeography of Metatheria
FIG. 72. — Comparison of left astragali and their articular patterns in selected metatherians to illustrate what were probably linear stages of transformation in the upper and lower ankle joints, as well as the astragalonavicular joint; A-C, a sudameridelphian (IMG I); A, dorsal view; B, plantar view; C, distal view; D-F, a didelphid (Marmosa); D, dorsal view; E, plantar view; F, distal view; G-I, a microbiothere (Dromiciops); G, dorsal view; H, plantar view; I, distal view; J-L, a dasyurid (Dasycercus); J, dorsal view; K, plantar view; L, distal view. Abbreviations: AFi, astragalofibular facet; ampt, astragalar medial plantar tuberosity; AN, astragalonavicular facet; ATil, lateral astragalotibial facet; ATim, medial astragalotibial facet; CaA, calcaneoastragalar facet; CaAd, distal calcaneoastragalar facet; CLAJP, continuous lower ankle joint pattern; Su, sustentacular facet. Scale bars: 1 mm.
FIG. 74 in Model-based analysis of postcranial osteology of marsupials from the Palaeocene of Itaboraí (Brazil) and the phylogenetics and biogeography of Metatheria
FIG. 74. — Simplified phylogeny of the taxa (thick vertical bars) and the hypothesized lineages leading to them (dashed lines). Numbered thick vertical arrows show points on the phylogeny where the stem of the various groups can be identified by diagnostic traits with respect to their ancestry. Only the entry of the stem of Sudameridelphia (1) is problematic in this regard because archaic metatherians outside of South America are less well known. Point 4 stands for the last common ancestor of Australidelphia, derivable from a bona fide didelphid (see text). Point 6 is the putative ancestry of the Gondwanadelphia, and as such it is queried. Thinner, and close to horizontal, arrows indicate both direction of phyletic derivations, as well as the direction of geographical dispersal. Note derivation and dispersal of australidelphians from a South American didelphid stem to Antarctica-Australia.
FIG. 71 in Model-based analysis of postcranial osteology of marsupials from the Palaeocene of Itaboraí (Brazil) and the phylogenetics and biogeography of Metatheria
FIG. 71. — Comparisons of several stages of monotreme and therian astragalocalcaneal patterns and articular relationships. For each of the six taxa the dorsal and distal views are shown in articulation above, and the lower ankle joint surfaces for the two left bones are shown below. In the metatherians the movement of the tarsus on the crus has one degree of freedom in rotation and another in translation, whereas in eutherians the stabilized upper ankle joint usually only allows one degree of freedom in rotation. Arrows on the tibial facet of the astragalus show rotational (and translational) freedom in the upper ankle joint, whereas the slimmer arrow on the astragalar fibular facet shows rotation of the calcaneus under the astragalus (i.e. movement in the lower ankle joint). Abbreviations: AFi, astragalofibular facet; ampt, astragalar medial plantar tuberosity; AN, astragalonavicular facet; ATil, lateral astragalotibial facet; ATim, medial astragalotibial facet; CaA, calcaneoastragalar facet; CaCu, calcaneocuboid facet; CaCua, auxiliary calcaneocuboid facet (australidelphian) CaCud, distal calcaneocuboid facet (didelphid); CaCul, lateral calcaneocuboid facet (australidelphian) CaCum, medial calcaneocuboid facet (australidelphian); CaCup, proximal calcaneocuboid facet (didelphid); CaFi, calcaneofibular facet; cpp, calcaneal peroneal process; ct, calcaneal tuber; Su, sustentacular facet.
FIG. 68 in Model-based analysis of postcranial osteology of marsupials from the Palaeocene of Itaboraí (Brazil) and the phylogenetics and biogeography of Metatheria
FIG. 68. — Comparisons of the distal end and head of the left humeri of the five extant didelphid species (A-E) with known habitus and the seven Itaboraí humeral groups (F-L); A, D. gliroides; B, R. raphanurus; C, M. domestica; D, C. derbianus; E, M. nudicaudatus. The drawings were prepared so that the distal width of the humerus was kept (approximately) constant, and the size of the head was then drawn at the same scale as the distal end of the same humerus. Anterior is toward the top of the page for the distal ends. From top to bottom, the size of the humeral groups (and possibly the body size as well) increases. Arrows point to the posterior and lateral extension of the curved (to various degrees) facet for the ulna. Scale bars: 2 mm.
FIG. 69 in Model-based analysis of postcranial osteology of marsupials from the Palaeocene of Itaboraí (Brazil) and the phylogenetics and biogeography of Metatheria
FIG. 69. — The patterns of bones in the carpus, viewed anteriorly, in some representatives of major groups of Metatheria. Lines between the patterns that can be found in the taxa (indicated under them by the taxonomic vernacular) represent approximate (or queried) transformations of these patterns. They do not stand for transformation of taxa from one into the other. Abbreviations: Cn, cuneiform; Lu, lunate; Mcp1-5, metacarpals; Mg, magnum; Pi, pisiform; Ra, radius; Sc, scaphocentrale; Tm, trapezium; Tr, trapezoid; Ul, ulna; Un, unciform.
FIG. 70 in Model-based analysis of postcranial osteology of marsupials from the Palaeocene of Itaboraí (Brazil) and the phylogenetics and biogeography of Metatheria
FIG. 70. — The calcaneus, astragalus, navicular, and cuboid of Pucadelphys andinus; A, B, a single left specimen, that has not been separated, of calcaneus, astragalus, and cuboid; A, dorsal view; B, plantar view; C, D, single left specimen of a calcaneus and an astragalus; C, distal view; D, proximal view; E, right specimen of a cuboid and navicular in articulation, dorsal view; F-H, right calcaneus; F, dorsal view; G, medial view; H, distal view; I-L, right astragalus; I, dorsal view; J, medial view; K, plantar view; L, distal view. Abbreviations: ac, astragalar canal; AFi, astragalofibular facet; ampt, astragalar medial plantar tuberosity; AN, astragalonavicular facet; ATil, lateral astragalotibial facet; ATim, medial astragalotibial facet; CaA, calcaneoastragalar facet; CaCu, calcaneocuboid facet; CaFi, calcaneofibular facet; cpp, calcaneal peroneal process; ct, calcaneal tuber; Cu, cuboid; Na, navicular; Su, sustentacular facet. Scale bar: 2 mm.
FIG. 67 in Model-based analysis of postcranial osteology of marsupials from the Palaeocene of Itaboraí (Brazil) and the phylogenetics and biogeography of Metatheria
FIG. 67. — Unguals that probably belong to metatherians from Itaboraí; A-F likely represent terrestrial species, whereas G-J suggest arboreal forms. For numbered designations see text. Scale bar: 2 mm.
FIG. 58. — Right IMG Femur 8 in Model-based analysis of postcranial osteology of marsupials from the Palaeocene of Itaboraí (Brazil) and the phylogenetics and biogeography of Metatheria
FIG. 58. — Right IMG Femur 8; A-C, the whole bone; A, anterior view; B, posterior view; C, medial view; D-G, details; D, anterior view; E, posterior view; F, proximal view; G, distal view. For numbered designations of specific characters see text. Scale bars: A- C, 4 mm; D-G, 2 mm.
FIG. 51. — A-C, left nearly complete IMG Femur 3 in Model-based analysis of postcranial osteology of marsupials from the Palaeocene of Itaboraí (Brazil) and the phylogenetics and biogeography of Metatheria
FIG. 51. — A-C, left nearly complete IMG Femur 3; A, proximal view; B, anteroir view; C, posterior view; D-F, left nearly complete IMG Femur 4; D, proximal view; E, anteroir view; F, posterior view. For numbered designations of specific characters see text. Scale bars: 2 mm.
FIG. 50. — A, B, left incomplete IMG Femur 1 in Model-based analysis of postcranial osteology of marsupials from the Palaeocene of Itaboraí (Brazil) and the phylogenetics and biogeography of Metatheria
FIG. 50. — A, B, left incomplete IMG Femur 1; A, anterior view; B, posterior view; C-F, left incomplete IMG Femur 2; C, E, anterior view; D, F, posterior view. For numbered designations of specific characters see text. Scale bar: 2 mm.
FIG. 46. — A in Model-based analysis of postcranial osteology of marsupials from the Palaeocene of Itaboraí (Brazil) and the phylogenetics and biogeography of Metatheria
FIG. 46. — A, lateral view of IMG Innominate 1 (DGM 1.145A-M), specimen from the left side; B, lateral view of IMG Innominate 3 (DGM 1.146B-M), specimen from the right side; C, lateral view of IMG Innominate 2 (DGM 1.146A-M), specimen from the left side. Scale bar: 4 mm.
FIG. 42 in Model-based analysis of postcranial osteology of marsupials from the Palaeocene of Itaboraí (Brazil) and the phylogenetics and biogeography of Metatheria
FIG. 42. — Plots of ulnar parameters. Regression line was drawn for living models only, and the fossil values were plotted subsequently in order to gauge some measure of their relationship to the arboreal-terrestrial dichotomy. The extremes of the living range are represented by the modern species. Abbreviations: CD, Caluromys derbianus; DG, Dromiciops gliroides; MF, Mayulestes ferox; MN, Metachirus nudicaudatus; RR, Rhyncholestes raphanurus; PA, Pucadelphys andinus. Roman numerals stand for Itaboraí Metatherian Group designations of ulnae.
FIG. 66. — A in Model-based analysis of postcranial osteology of marsupials from the Palaeocene of Itaboraí (Brazil) and the phylogenetics and biogeography of Metatheria
FIG. 66. — A, details of left IMG Tibia 2, proximal view; B-E, K, L, details of left IMG Tibia 3; B, proximal view; C, distal view; D, anterior view of distal end; E, posterior view; K, lateral view of distal end; L, posterior view of distal end; F, left distal tibia of Pucadelphys, anterior view; G, H, left distal tibia of Caluromys; G, lateral view; H, posterior view; I, J, left distal tibia of Metachirus; I, lateral view; J, posterior view. Abbreviations: ATil, lateral astragalotibial facet; ATim, medial astragalotibial facet; CaFi, calcaneofibular facet; FeTil, lateral femorotibial facet; TiFid, distal tibifibular facet; tmm, tibial medial malleolus. Scale bars: 2 mm.
FIG. 55 in Model-based analysis of postcranial osteology of marsupials from the Palaeocene of Itaboraí (Brazil) and the phylogenetics and biogeography of Metatheria
FIG. 55. — Details of left IMG Femur 5; A, B, proximal third; A, posterior view; B, anterior view; C, D, distal third; C, medial view; D, lateral view. For numbered designations of specific characters see text. Scale bar: 2 mm.
FIG. 35 in Model-based analysis of postcranial osteology of marsupials from the Palaeocene of Itaboraí (Brazil) and the phylogenetics and biogeography of Metatheria
FIG. 35. — Same as for Fig. 34, but with a different body weight surrogate that allows the inclusion of more (fragmentary) fossils.
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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.