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3,663 results for “Phylogenetic analysis”
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>
Phylogenetic analysis of policistronic amino-acid sequences encoded by 116 flavivirus genomes
<p><span>Recently, Genome Biology and Evolution (11:3341-3352) published three statistical tests for testing whether alignments of sequence data violate the phylogenetic assumption of evolution under homogeneous conditions. The tests extend the matched-pairs tests of symmetry, marginal symmetry, and internal symmetry for pairs of aligned homologous sequences to the case where a whole alignment is considered. Here we reveal that the new tests are misleading. We explain why this is so, reveal how the tests of whole alignments may be done, and release new bioinformatics tools that implement statistically sound methods of dealing with multiple comparisons (i.e., by controlling the family-wise error rate or the false discovery rate). Using the new software to analyse an alignment of amino acids encoded by 116 flavivirus genomes, we reveal, for the first time, that these genomes are unlikely to have evolved under stationary, reversible, and homogeneous Markovian conditions.</span></p>
Fig. 32. Slaterocoris breviatus, male genitalia. A in Revision And Phylogenetic Analysis Of The North American Genus Slaterocoris Wagner With New Synonymy, The Description Of Five New Species And A New Genus From Mexico, And A Review Of The Genus Scalponotatus Kelton (Heteroptera: Miridae: Orthotylinae)
Fig. 32. Slaterocoris breviatus, male genitalia. A. Progress, BC. B, K. Cedar Creek Recreation Area, ID. C, O. Peshtigo River, WI. D–F, I. Washington, DC. J. Pine Grove Furnace State Park, PA. L. Slave Lake, AB. M. Ingonish, NS. N. Chiwaukee Prairie, WI.
Fig. 33. Slaterocoris pallidicornis, male genitalia. A, D, F–I in Revision And Phylogenetic Analysis Of The North American Genus Slaterocoris Wagner With New Synonymy, The Description Of Five New Species And A New Genus From Mexico, And A Review Of The Genus Scalponotatus Kelton (Heteroptera: Miridae: Orthotylinae)
Fig. 33. Slaterocoris pallidicornis, male genitalia. A, D, F–I. Theodore Roosevelt National Park, ND. B, C, E, J, K. Beddeck, NS. L. Pingree Park, CO.
Fig. 6 in Complete mitochondrial genome sequence of Bonasa sewerzowi (Galliformes: Phasianidae) and phylogenetic analysis
Fig. 6. The phylogenetic relationship of Bonasa among Galliformes based on the complete mitogenome. Branch lengths and topologies were obtained from Maximum Likelihood analyses. The numbers were the bootstrap values of MP/ML/BI trees in turn. * indicates that MP or BI tree was inconsistent with ML tree.
Fig. 4 in Complete mitochondrial genome sequence of Bonasa sewerzowi (Galliformes: Phasianidae) and phylogenetic analysis
Fig. 4. The structure of CR in Bonasa sewerzowi mitochondrial genome and comparasion with B. bonasia.
Fig. 5 in Complete mitochondrial genome sequence of Bonasa sewerzowi (Galliformes: Phasianidae) and phylogenetic analysis
Fig. 5. Nucleotide composition of different partitions from two Bonasa mitogenomes. AT-skew, (A-T)/(A+T); GC-skew, (G-C)/(G+C); PCG-1st, the first codon positions of PCGs; PCG-2nd, the second codon positions of PCGs; PCG-3rd, the third codon positions of PCGs.
Fig. 3 in Complete mitochondrial genome sequence of Bonasa sewerzowi (Galliformes: Phasianidae) and phylogenetic analysis
Fig. 3. The srRNA secondary structure of Bonasa sewerzowi mitogenome and comparasion with B. bonasia. The different nucleotides in B. bonasia was pointed out.
Fig. 1 in Complete mitochondrial genome sequence of Bonasa sewerzowi (Galliformes: Phasianidae) and phylogenetic analysis
Fig. 1. Gene map of the B. sewerzowi mitochondrial genome. Transfer RNA genes are designated by single-letter amino acid codes. L1, L2, S1, and S2 denote trnL (uur), trnL (cun), trnS (ucn) and trnS (agy), respectively.
Fig. 2 in Complete mitochondrial genome sequence of Bonasa sewerzowi (Galliformes: Phasianidae) and phylogenetic analysis
Fig. 2. The lrRNA secondary structure of Bonasa sewerzowi mitogenome and comparasion with B. bonasia. The different nucleotides in B.
Fig. 7 in A revision and phylogenetic analysis of the millipede genus Oxidus Cook, 1911 (Polydesmida, Paradoxosomatidae)
Fig. 7. Left gonopod of Oxidus riukiaria (Verhoeff, 1940), from sample IEBR-H470. A. Lateroventral view. B. Ventral view. C. Postfemoral region, ventral view. Note: z = spine z, but broken.
Fig. 10 in A revision and phylogenetic analysis of the millipede genus Oxidus Cook, 1911 (Polydesmida, Paradoxosomatidae)
Fig. 10. Phylogenetic tree of the genus Oxidus and some closely related groups based on Maximum Likelihood and Bayesian Inference Analysis of a 991 bp fragment of the combination of 16S rRNA and COI genes.
Fig. 9 in A revision and phylogenetic analysis of the millipede genus Oxidus Cook, 1911 (Polydesmida, Paradoxosomatidae)
Fig. 9. Phylogenetic tree of the genus Oxidus and some closely related groups based on Maximum Likelihood and Bayesian Inference Analysis of a 525 bp fragment of the COI gene (# = a value less than 65%).
Fig. 3 in A revision and phylogenetic analysis of the millipede genus Oxidus Cook, 1911 (Polydesmida, Paradoxosomatidae)
Fig. 3. Oxidus gigas (Attems, 1953) from Duc Xuan Commune, Ha Giang Prov., Vietnam. A. Entire body, length ca 34 mm. B–C. Segments 8–9–10. B. ♂. C. ♀. Scale bars = 1 mm. (photo by Anh Nguyen)
Fig. 10 in Phylogenetic analysis and systematics of the Acrapex unicolora Hampson species complex (Lepidoptera, Noctuidae, Noctuinae, Apameini), with the description of Fve new species from the Afrotropics
Fig. 10. Maximum likelihood tree resulting from the analysis of the combined dataset carried out with IQ-TREE. Support of major nodes is displayed as BV (only BV> 50% are shown). On the right, corresponding adult habitus (for species belonging to the A. unicolora species group) are also included for illustrative purposes. Results of PTP analyses are fgured using coloured branches and vertical side bars. Putative molecular species clusters are indicated using transitions between blue-coloured branches to red-coloured branches (vertical bars are also informative).
Fig. 8 in Phylogenetic analysis and systematics of the Acrapex unicolora Hampson species complex (Lepidoptera, Noctuidae, Noctuinae, Apameini), with the description of Fve new species from the Afrotropics
Fig. 8. Adults of species of Acrapex. – A–D. A. parvaclara Berio, 1973. A. ♂, upper side. B. ♂, under side. C. ♀, upper side. D. ♀, under side. – E–F. A. simillima le Ru sp. nov. E. ♀, upper side. F. ♀, under side. – G–J. A. unicolora (Hampson, 1910). G. ♂, upper side. H. ♂, under side. I. ♀, upper side. J. ♀, under side. Scale bars = 10 mm.
Fig. 9. Last instar larva. A in Phylogenetic analysis and systematics of the Acrapex unicolora Hampson species complex (Lepidoptera, Noctuidae, Noctuinae, Apameini), with the description of Fve new species from the Afrotropics
Fig. 9. Last instar larva. A. Acrapex simillima le Ru sp. nov. B. A. unicolora (Hampson, 1910). Scale bar = 10 mm.
Fig. 7 in Phylogenetic analysis and systematics of the Acrapex unicolora Hampson species complex (Lepidoptera, Noctuidae, Noctuinae, Apameini), with the description of Fve new species from the Afrotropics
Fig. 7. Adults of species of Acrapex. – A–E. A. mediopuncta (Bowden, 1956). A. ♂, upper side. B. ♂, under side. C. ♀, upper side. D. ♀, under side. E. ♀, original labels from BMNH. – F–G. A. miscantha le Ru sp. nov. F. ♀, upper side. G. ♀, under side. Scale bars = 10 mm.
Fig. 6 in Phylogenetic analysis and systematics of the Acrapex unicolora Hampson species complex (Lepidoptera, Noctuidae, Noctuinae, Apameini), with the description of Fve new species from the Afrotropics
Fig. 6. Adults of species of Acrapex. – A–B. A. kavumba le Ru sp. nov. A. ♂, upper side. B. ♂, under side. – C–F. A. kiakouama le Ru sp. nov. C. ♂, upper side. D. ♂, under side. E. ♀, upper side. F. ♀, under side. – G–I. A. malagasy Viette, 1967. G. ♂, upper side. H. ♂, under side. I. ♂, original labels from MNHH. Scale bars = 10 mm.
Fig. 3 in Phylogenetic analysis and systematics of the Acrapex unicolora Hampson species complex (Lepidoptera, Noctuidae, Noctuinae, Apameini), with the description of Fve new species from the Afrotropics
Fig. 3. Female genitalia of species of Acrapex. A. A. cuprescens (Hampson, 1910). B. A. kafula le Ru sp. nov. C. A. kiakouama le Ru sp. nov. D. A. mediopuncta (Bowden, 1956). E. A. miscantha le Ru sp. nov. F. A. parvaclara Berio, 1973. G. A. simillima le Ru sp. nov. H. A. unicolora (Hampson, 1910). Scale bars = 1 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.