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635 results for “comparative phylogenetics”
FIGURE 2 Phylogenetic relationships within the genus Longidorus. Bayesian 50 in Molecular phylogenetic analysis and comparative morphology reveals the diversity and distribution of needle nematodes of the genus Longidorus (Dorylaimida: Longidoridae) from Spain
FIGURE 2 Phylogenetic relationships within the genus Longidorus. Bayesian 50% majority rule consensus tree as inferred from ITS1 rRNA sequence alignment under a 3-parameter model with invariable sites and a gamma-shaped distribution (TPM3 µf + I + G). Posterior probabilities greater than 0.70 are given for appropriate clades. Newly obtained sequences in this study are shown in bold. Scale bar = expected changes per site. Downloaded from Brill.com08/29/2023 05:44:51PM via free access
Challenges of sampling and how phylogenetic comparative methods help: Supplementary data
<p>Supplementary data and results files for the paper:</p> <p>Macklin-Cordes, Jayden L. & Erich R. Round (2022). Challenges of sampling and how phylogenetic comparative methods help: With a case study of the Pama-Nyungan laminal contrast. <em>Linguistic Typology</em> (advance online publication). <a href="https://doi.org/10.1515/lingty-2021-0025">https://doi.org/10.1515/lingty-2021-0025</a></p>
Supplementary datasets, data analysis code, and R tutorials for: Phylogenetic analysis of adaptation in comparative physiology and biomechanics: overview and a case study of thermal physiology in treefrogs
<p>Comparative phylogenetic studies of adaptation are uncommon in biomechanics and physiology. Such studies require collecting data from many species, a challenge when data collection is experimentally intensive. Moreover, researchers struggle to employ the most biologically appropriate phylogenetic tools for identifying adaptive evolution. Here, we detail an established but greatly underutilized phylogenetic comparative framework—the Ornstein-Uhlenbeck process—that explicitly models long-term adaptation. We discuss challenges in implementing and interpreting the model, and we outline potential solutions. We demonstrate use of the model through studying the evolution of thermal physiology in treefrogs. Frogs of the family Hylidae have twice colonized the temperate zone from the tropics, and such colonization likely involved a fundamental change in physiology due to colder and more seasonal temperatures. However, which traits changed to allow colonization is unclear. We measured cold-temperature tolerance and characterized thermal performance curves in jumping for twelve species of treefrogs distributed from the Neotropics to temperate North America. We then conducted phylogenetic comparative analyses to examine how tolerances and performance curves evolved and to test whether that evolution was adaptive. We found that tolerance to low temperatures increased with the transition to the temperate zone. In contrast, jumping well at colder temperatures was unrelated to biogeography and thus did not adapt during dispersal. Overall, our paper shows how comparative phylogenetic methods can be leveraged in biomechanics and physiology to test the evolutionary drivers of variation among species.</p>
The chloroplast genomes of Sanicula (Apiaceae): plastome structure, comparative analyses, and phylogenetic relationships
<p><em>Sanicula</em> (Apiaceae subfamily Saniculoideae) is a taxonomically difficult genus of medicinal value. Its distribution center is in China, where there are 18 species (11 of which are endemic). To provide plastid genome resources, whole chloroplast genomes of five <em>Sanicula</em> species (<em>S. flavovirens</em>, <em>S. giraldii</em>, <em>S. lamelligera</em>, <em>S. odorata</em>, and <em>S. rubriflora</em>) were sequenced and compared to the previously published <em>S. orthacantha</em> plastome. These genomes exhibit a typical quadripartite structure. All contain 129 different genes, including 84 protein-coding, 37 tRNA, and 8 rRNA genes. Loci <em>rpl2</em>, <em>matK</em>, <em>psbA</em>, and <em>ycf1</em> are the most variable. Results of maximum likelihood analysis of 90 whole plastome sequences from Apioideae and Saniculoideae and the outgroup <em>Hydrocotyle</em> (Araliaceae) reveal sectional relationships in <em>Sanicula</em> different from the traditional classification system, support the monophyly of Apioideae and its sister group relationship to Saniculoideae, and show concordant topologies to nrDNA ITS and other plastome-based phylogenies. <em>Sanicula orthacantha</em> and <em>S. chinensis</em> form a clade sister group to <em>S. lamelligera</em> and <em>S. odorata</em>, consecutively. These four species comprise a clade sister group to the clade of <em>S. rubriflora</em> and <em>S. flavovirens</em>, with this entire group sister to <em>S. giraldii</em>. The plastid genome resources provided herein will be important for future systematic, evolutionary, phylogenomic, and population-level studies of <em>Sanicula</em>.</p>
Fig. 11. Coloborhynchinae comparative plate. A in A taxonomic and phylogenetic review of the anhanguerid pterosaur group Coloborhynchinae and the new clade Tropeognathinae
Fig. 11. Coloborhynchinae comparative plate. A. Coloborhynchus clavirostris in anterior (A1), right lateral (A2), and palatal (A3) views. B. Aerodraco sedgwickii in anterior (B1), right lateral (B2), and palatal (B3) views. C. Uktenadactylus wadleighi in anterior (C1), right lateral (C2), and palatal (C3) views. D. Uktenadactylus rodriguesae. in anterior (D1), left lateral (mirrored, D2), and palatal (D3) views. E. Nicorhynchus capito (holotype) in anterior (E1), right lateral (E2), and palatal (E3) views. F. Nicorhynchus capito (referred specimen, originally designated as the holotype of Ornithocheirus reedi, now presumed lost from CAMSM collections) in anterior (F1) and right lateral (F2) views. G. Nicorhynchus cf. capito in anterior (G1) and left lateral (mirrored, G2). H. Nicorhynchus fluviferox (holotype) in anterior (H1), right lateral (H2), and palatal (H3) views. Dark grey represents depressions, lighter gray with lines represents bulbous projections, white represents alveoli. Scale bars 50 mm. Drawings by RVP.
Fig. 6 in Comparative Analysis of Complete Mitogenomes of Two Gobies and Their Phylogenetic Implication.
Fig. 6. Termination-associated sequences (TAS), conserved sequence blocks (CSB-1, CSB-2, and CSB-3) and central conserved sequences (CSB-D) and GTGGG box in control region of two Oxyurichthys species mitogenomes.
Fig. 8 in Comparative Analysis of Complete Mitogenomes of Two Gobies and Their Phylogenetic Implication.
Fig. 8. Phylogenetic trees of goby derived from Maximum Likelihood (ML) method based on 13 PCGs + 2 rRNAs. The numbers at nodes are ultrafast bootstrap values. GenBank accession numbers are placed in front of species names.
Fig. 7 in Comparative Analysis of Complete Mitogenomes of Two Gobies and Their Phylogenetic Implication.
Fig. 7. Phylogenetic trees of goby derived from Bayesian Inference (BI) method based on 13 PCGs + 2 rRNAs. The numbers at nodes are posterior probability values. GenBank accession numbers are placed in front of species names.
Fig. 5 in Comparative Analysis of Complete Mitogenomes of Two Gobies and Their Phylogenetic Implication.
Fig. 5. The putative origin of L-strand replication (OL) of Oxyurichthys ophthalmonema (a) and Oxyurichthys microlepis (b).
Linked collectors and determiners for: Comparative geometric morphometrics of male genitalia in Xiphocentron subgenera (Trichoptera: Xiphocentronidae): new species, revision and phylogenetic systematics of the subgenus Sphagocentron.
Natural history specimen data linked to collectors and determiners held within, "Comparative geometric morphometrics of male genitalia in Xiphocentron subgenera (Trichoptera: Xiphocentronidae): new species, revision and phylogenetic systematics of the subgenus Sphagocentron". Claims or attributions were made on Bionomia by volunteer Scribes, <a href="https://bionomia.net/dataset/69a3ae72-af6c-4b7b-a4b1-7af0ed275a43">https://bionomia.net/dataset/69a3ae72-af6c-4b7b-a4b1-7af0ed275a43</a> using specimen data from the dataset aggregated by the Global Biodiversity Information Facility, <a href="https://gbif.org/dataset/69a3ae72-af6c-4b7b-a4b1-7af0ed275a43">https://gbif.org/dataset/69a3ae72-af6c-4b7b-a4b1-7af0ed275a43</a>. Formatted as a Frictionless Data package.
FIGURE 13 in New leontiniid Notoungulata (Mammalia) from Chile and Argentina: comparative anatomy, character analysis, and phylogenetic hypotheses
FIGURE 13. Cladogram of the "Toxodont" analysis. Strict consensus (left) and majority 50% consensus of the "Toxodont" phylogenetic analysis. Nodes: A, Colpodon; B, "Tropical clade"; C, Leontiniidae; D, "advanced Toxodontia"; E, Toxodontidae; F, "notohippid" + Toxodontidae. Numbers at nodes represent percent support when support is less than 100%.
FIGURE 7 in New leontiniid Notoungulata (Mammalia) from Chile and Argentina: comparative anatomy, character analysis, and phylogenetic hypotheses
FIGURE 7. Proximal (right) tarsals of leontiniids. A, calcaneum of cf. Elmerriggsia fieldia (PM 413); B, astragalus of cf. Elmerriggsia fieldia (PM 415); C, calcaneum of Scarrittia canquelensis (AMNH 29626), in dorsal and distal views; and D, astragalus of Scarrittia canquelensis (AMNH 29626), in dorsal and distal views. Abbreviations: cu, cuboid; ect, ectal; f, facet; fib, fibula; nav, navicular; sus, sustentacular.
FIGURE 4. 40 in New leontiniid Notoungulata (Mammalia) from Chile and Argentina: comparative anatomy, character analysis, and phylogenetic hypotheses
FIGURE 4. 40Ar/39Ar age spectra and inverse isochron plots for samples CH-31 (above) and CH-32 (opposite page). Age spectra illustrate apparent age versus cumulative fraction of 39Ar released. Shaded boxes indicate steps used to calculate weighted mean plateau ages. Plotting these steps suggests that most of them fall on simple isochrons with a 40Ar/36Ar ratio of the trapped component somewhat higher than atmospheric gas, giving a more reliable estimate of the ages at ~19.5 Ma, or ~19.8 Ma when corrected for a revised age of the Fish Canyon Tuff standard.
FIGURE 9 in New leontiniid Notoungulata (Mammalia) from Chile and Argentina: comparative anatomy, character analysis, and phylogenetic hypotheses
FIGURE 9. Selected dental characters of A, Anayatherium fortis, cast of holotype, alveoli of I3–P1 are exposed to show that A. fortis had a complete dental formula; B, m2 of Thomashuxleya externa (AMNH 28697) in occlusal (upper) and oblique (lower) views; and C, left m2 of Scarrittia canquelensis (AMNH 29592) in occlusal (upper) and lateral (lower) views. B and C illustrate the hypothetical evolution of the "paraconid" from the mesiolingual cingulid.
FIGURE 8 in New leontiniid Notoungulata (Mammalia) from Chile and Argentina: comparative anatomy, character analysis, and phylogenetic hypotheses
FIGURE 8. Knee region of leontiniids. A, left distal femur and proximal tibia-fibula (P 13632) in dorsal and lateral views of c.f. Elmerriggsia fieldia; and B, right (reversed to show as left) distal, femur of Anayatherium, cf. A. fortis in dorsal, lateral and distal views. Scale bar applies to all.
FIGURE 14 in New leontiniid Notoungulata (Mammalia) from Chile and Argentina: comparative anatomy, character analysis, and phylogenetic hypotheses
FIGURE 14. Cladogram of the "Typothere included" analysis. Strict consensus (left) and majority 50% consensus of the "Typothere included" phylogenetic analysis. Nodes: A, Colpodon; B, "Tropical clade"; C, Leontiniidae; D, "advanced Toxodontia"; E, Toxodontidae; F, "notohippid"+Toxodontidae (Eurygenium excluded); G, "advanced Toxodontia" plus interatheriine interatheriids. Numbers at nodes represent percent support when support is less than 100%.
FIGURE 12 in New leontiniid Notoungulata (Mammalia) from Chile and Argentina: comparative anatomy, character analysis, and phylogenetic hypotheses
FIGURE 12. Hypothetical pedal transition series in Notoungulata showing left pes in dorsal view (upper row), left calcaneum in dorsal view (middle row), and left calcaneum in medial view (lower row). Illustrations are not to scale. Abbreviations are as follows: ast, astragalus; calc, calcaneum; cu, cuboid; ect, ectocuneiform; f, facet; fib, fibula; Mt, metatarsal; nav, navicular; sus, sustentacular; troch, trochlea.
FIGURE 3 in New leontiniid Notoungulata (Mammalia) from Chile and Argentina: comparative anatomy, character analysis, and phylogenetic hypotheses
FIGURE 3. Left dentitions of Colpodon spp.: Colpodon antucoensis, new species (SGOPV 5704) in lateral (A) and occlusal (B) views; C, Colpodon propinquus (FMNH P 13310) in occlusal view. The numbers below the descriptors indicate character number (#) and state (see Character Analysis). Scale bar applies to all.
FIGURE 11 in New leontiniid Notoungulata (Mammalia) from Chile and Argentina: comparative anatomy, character analysis, and phylogenetic hypotheses
FIGURE 11. Hypothetical manual transition series in Notoungulata. All hands shown as left. Not drawn to scale. Abbreviations: Cun, cuneiform; Lu, lunate; Mg, magnum; Sc, scaphoid; Td, trapezoid; Tm, trapezium. Roman numerals indicate digit number.
FIGURE 5 in New leontiniid Notoungulata (Mammalia) from Chile and Argentina: comparative anatomy, character analysis, and phylogenetic hypotheses
FIGURE 5. Upper cheek teeth of Elmerriggsia fieldia, new taxon. A, P 13386, holotype, P2–M2; B, PM 61102, right M1; C, PM 61101, right P1–P3; and D, P 15060, unworn, right P3. Scale bar applies to all.
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Allen Brain Atlas
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DANDI Archive for NWB datasets
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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.