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351 results for “gene tree”
Supplementary material 3 from: Gutiérrez EE, Helgen KM, McDonough MM, Bauer F, Hawkins MTR, Escobedo-Morales LA, Patterson BD, Maldonado JE (2017) A gene-tree test of the traditional taxonomy of American deer: the importance of voucher specimens, geographic data, and dense sampling. ZooKeys 697: 87-131. https://doi.org/10.3897/zookeys.697.15124
Supplementary information figure : Authors: Eliécer E. Gutiérrez, Kristofer M. Helgen, Molly M. McDonough, Franziska Bauer, Melissa T. R. Hawkins, Luis A. Escobedo-Morales, Bruce D. Patterson, Jesús E. Maldonado
Supplementary material 2 from: Gutiérrez EE, Helgen KM, McDonough MM, Bauer F, Hawkins MTR, Escobedo-Morales LA, Patterson BD, Maldonado JE (2017) A gene-tree test of the traditional taxonomy of American deer: the importance of voucher specimens, geographic data, and dense sampling. ZooKeys 697: 87-131. https://doi.org/10.3897/zookeys.697.15124
Name and DNA sequences of pairs of primers used for amplification and sequencing of the CYTB gene : Data type: molecular data
FIGURE 2. Overview tree for the COI gene fragment. Bayesian inference tree using MrBayes 3.2.7a in The Oracle of Delphi-a molecular phylogenetic approach to Greek Cordulegaster Leach in Brewster, 1815 (Odonata: Anisoptera: Cordulegastridae)
FIGURE 2. Overview tree for the COI gene fragment. Bayesian inference tree using MrBayes 3.2.7a using the best-fit model (GTR+I+G) identified with JModeltest 2.1.10. Bayesian posterior probabilities values are depicted at the nodes. Included are our own sequences (PCR number next to the name) and those retrieved from GenBank (accession numbers next to the name), if specimens identify different taxa in the COI and ITS analysis they are considered hybrids. Haplotype analysis (TCS-network made in PopART 1.7) is shown in Figs. 5 and 6.
FIGURE 3. Overview tree from the ITS gene fragment. Bayesian inference tree using MrBayes 3.2.7a in The Oracle of Delphi-a molecular phylogenetic approach to Greek Cordulegaster Leach in Brewster, 1815 (Odonata: Anisoptera: Cordulegastridae)
FIGURE 3. Overview tree from the ITS gene fragment. Bayesian inference tree using MrBayes 3.2.7a using the best-fit model (HKY+G) identified with JModeltest 2.1.10. Bayesian posterior probabilities values are depicted at the nodes. Included are our isolated sequences (PCR number next to the name) and those retrieved from GenBank (accession numbers next to the name), if specimens identify different taxa in the COI and ITS analysis they are indicated hybrids.
Combining species delimitation, species trees, and tests for gene flow illuminates complex speciation in scrub-jays
<p class="MsoNormal"><span>Complex speciation, involving rapid divergence and multiple bouts of post-divergence gene flow, can obfuscate phylogenetic relationships and species limits. In North America, cases of complex speciation are common, due at least in part to the cyclical Pleistocene glacial history of the continent. Scrub-jays in the genus <em>Aphelocoma</em> provide a useful case study in complex speciation because their range throughout North America is structured by phylogeographic barriers with multiple cases of secondary contact between divergent lineages. Here, we show that a comprehensive approach to genomic reconstruction of evolutionary history, i.e., synthesizing results from species delimitation, species tree reconstruction, demographic model testing, and tests for gene flow, is capable of clarifying evolutionary history despite complex speciation. We find concordant evidence across all statistical approaches for the distinctiveness of an endemic southern Mexico lineage (<em>A. w. sumichrasti</em>), culminating in support for the species status of this lineage under any commonly applied species concept. We also find novel genomic evidence for the species status of a Texas endemic lineage <em>A. w. texana</em>, for which equivocal species delimitation results were clarified by demographic modeling and spatially explicit models of gene flow. Finally, we find that complex signatures of both ancient and modern gene flow between the non-sister California Scrub-Jay (<em>A. californica</em>) and Woodhouse's Scrub-Jay (<em>A. woodhouseii</em>), result in discordant gene trees throughout the species' genomes despite clear support for their overall isolation and species status. In sum, we find that a multi-faceted approach to genomic analysis can increase our understanding of complex speciation histories, even in well-studied groups. Given the emerging recognition that complex speciation is relatively commonplace, the comprehensive framework that we demonstrate for interrogation of species limits and evolutionary history using genomic data can provide a necessary roadmap for disentangling the impacts of gene flow and incomplete lineage sorting to better understand the systematics of other groups with similarly complex evolutionary histories.</span></p>
FIGURE 2. Bayesian tree for nuclear elongation complex protein 1 in Life-stage association of black flies, using a fast-evolving nuclear gene sequence, and description of the larva of Simulium lampangense Takaoka & Choochote (Diptera: Simuliidae) from Thailand
FIGURE 2. Bayesian tree for nuclear elongation complex protein 1 (ECP1) sequences of five nominal species and unknown (Unk) larvae in the Simulium multistriatum species group in Thailand. Bootstrap values for neighbor-joining and maximum likelihood and posterior probability of Bayesian analysis are shown above or near the branches. -- denotes bootstrap support less than 50%. Scale bar represents 0.03 substitutions per nucleotide position.
FIGURE 1. Neighbour joining COI gene tree using uncorrected p in Description of the final instar larva of Orthetrum borneense Kimmins, 1936 (Odonata, Libellulidae), using rearing and molecular methods
FIGURE 1. Neighbour joining COI gene tree using uncorrected p–distance for adults of nine species and subspecies of Orthetrum plus two outgroup taXa, and a larva of O. borneense.
FIGURES 133–137 in Revision of the Genus Leptogomphus Selys in Borneo, including gene trees and a two marker molecular phylogeny (Odonata: Anisoptera: Gomphidae)
FIGURES 133–137. Photographs in life of some Bornean Leptogomphus species: (133) L. coomansi male (left hand side, flipped to right for consistency with other images), Sungai Sbong, Kapit Division, Sarawak, photograph by G.T. Reels; (134) L. coomansi female, Ranchan Recreational Park, Serian, Serian Division, Sarawak; (135) L. pendleburyi female, Bukit Tanggan, Ulu Mujok, Lanjak Entimau Wildlife Sanctuary, Sarikei Division, Sarawak, photograph by Robin Ngiam; (136) L. pendleburyi male, Sungai Kahei area, Ulu Balui, Kapit Division, Sarawak, photograph by Robin Ngiam; (137) L. williamsoni immature male, semi-teneral, Sungai Kahei area, Ulu Balui, Kapit Division, Sarawak, photograph by Robin Ngiam.
FIGURE 126 in Revision of the Genus Leptogomphus Selys in Borneo, including gene trees and a two marker molecular phylogeny (Odonata: Anisoptera: Gomphidae)
FIGURE 126. Distribution of L. coomansi, confirmed (yellow square) and unconfirmed (blue triangle) records, and L. sp. cf coomansi (black circle).
FIGURES 130–132 in Revision of the Genus Leptogomphus Selys in Borneo, including gene trees and a two marker molecular phylogeny (Odonata: Anisoptera: Gomphidae)
FIGURES 130–132. Habitus of some Bornean Leptogomphus species: (130) L. pasia holotype (left hand side, flipped to right for consistency with other images); (131) L. sii holotype male; (132) L. williamsoni male SAR13_14_GOM56.
FIGURE 128 in Revision of the Genus Leptogomphus Selys in Borneo, including gene trees and a two marker molecular phylogeny (Odonata: Anisoptera: Gomphidae)
FIGURE 128. Distribution of L. pendleburyi (yellow circle), L. schieli (black square) and L. species from Pulong Tau National Park, Sarawak (white square).
FIGURES 118–119. Ventral view female abdominal S8 in Revision of the Genus Leptogomphus Selys in Borneo, including gene trees and a two marker molecular phylogeny (Odonata: Anisoptera: Gomphidae)
FIGURES 118–119. Ventral view female abdominal S8 (all scale bars 0.5mm): (118) L. coomansi SAR11_12_GOM48; (119) L. pasia SAB12_GOM2.
FIGURES 120–125 in Revision of the Genus Leptogomphus Selys in Borneo, including gene trees and a two marker molecular phylogeny (Odonata: Anisoptera: Gomphidae)
FIGURES 120–125. Female vulvar scale (all scale bars 0.5mm): (120) L. coomansi SAR11_12_GOM48; (121) L. pasia holotype; (122) L. pendleburyi SAR13_14_GOM15; (123) L. schieli paratype SAR15_GOM6; (124) L. sii paratype SAR13_14_GOM44; (125) L. williamsoni SAR13_14_GOM51.
FIGURES 106–111. Male anal appendages and abdominal S10 in Revision of the Genus Leptogomphus Selys in Borneo, including gene trees and a two marker molecular phylogeny (Odonata: Anisoptera: Gomphidae)
FIGURES 106–111. Male anal appendages and abdominal S10 in lateral view (all scale bars 0.5mm): (106) L. coomansi SAR09_10_GOM4; (107) L. pasia SAB12_GOM1; (108) L. pendleburyi SAR13_14_GOM13; (109) L. schieli holotype; (110) L. sii holotype; (111) L. williamsoni SAR11_12_GOM56.
FIGURES 112–117 in Revision of the Genus Leptogomphus Selys in Borneo, including gene trees and a two marker molecular phylogeny (Odonata: Anisoptera: Gomphidae)
FIGURES 112–117. Male anal appendages in ventral view (all scale bars 0.5mm): (112) L. coomansi SAR09_10_GOM4; (113) L. pasia SAB12_GOM1; (114) L. pendleburyi SAR13_14_GOM13; (115) L. schieli holotype; (116) L. sii holotype; (117) L. williamsoni SAR11_12_GOM56.
FIGURES 94–99 in Revision of the Genus Leptogomphus Selys in Borneo, including gene trees and a two marker molecular phylogeny (Odonata: Anisoptera: Gomphidae)
FIGURES 94–99. Penis in lateral view (all scale bars 0.5mm): (94) L. coomansi SAR07_8_GOM18; (95) L. pasia SAB12_GOM1; (96) L. pendleburyi SAB12_GOM3; (97) L. schieli holotype; (98) L. sii paratype SAR13_14_GOM49; (99) L. williamsoni SAR16_GOM1.
FIGURES 84–87 in Revision of the Genus Leptogomphus Selys in Borneo, including gene trees and a two marker molecular phylogeny (Odonata: Anisoptera: Gomphidae)
FIGURES 84–87. Female synthorax lateral: (84) L pendleburyi SAR16_GOM8; (85) L. schieli paratype SAR15_GOM6; (86) L. williamsoni SAR13_14_GOM51, right hand side, flipped for consistency; (87) L. sp. cf williamsoni SAR11_12_GOM59.
FIGURES 88–93 in Revision of the Genus Leptogomphus Selys in Borneo, including gene trees and a two marker molecular phylogeny (Odonata: Anisoptera: Gomphidae)
FIGURES 88–93. Male accessory genitalia, lateral view, all scale bars 1mm: (88) L. coomansi SAR09_10_GOM4; (89) L. pasia SAB12_GOM1; (90) L. pendleburyi SAR13_14_GOM13; (91) L. schieli holotype; (92) L. sii holotype; (93) L. williamsoni SAR11_12_GOM56.
FIGURES 100–105 in Revision of the Genus Leptogomphus Selys in Borneo, including gene trees and a two marker molecular phylogeny (Odonata: Anisoptera: Gomphidae)
FIGURES 100–105. Male anal appendages dorsal view (all scale bars 0.5mm): (100) L. coomansi SAR09_10_GOM4; (101) L. pasia SAB12_GOM1; (102) L. pendleburyi SAR13_14_GOM13; (103) L. schieli holotype; (104) L. sii holotype; (105) L. williamsoni SAR11_12_GOM56.
FIGURES 78–83 in Revision of the Genus Leptogomphus Selys in Borneo, including gene trees and a two marker molecular phylogeny (Odonata: Anisoptera: Gomphidae)
FIGURES 78–83. Female synthorax lateral: (78) L. coomansi SAR11_12_GOM48; (79) L. mariae holotype, right hand side, flipped for consistency; (80) L. sp. cf coomansi PomS260; (81) L. pasia holotype; (82) L. sii paratype SAR13_14_GOM44; (83) L. species SAR11_12_GOM33.
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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.