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501 results for “Phylogenetic tree”
Phylogenetic tree of 1819 YfaL protein sequences identified in 2053 E. coli genomes.
<p><strong><span>Phylogenetic tree of 1819 YfaL protein sequences identified in 2053 <em>E. coli</em> genomes. </span></strong><span>The purple circles on the branches represent bootstrap values > 0.8. The different strain’s phylogroups are displayed outside of the tree.</span></p>
Complex ecological phenotypes on phylogenetic trees: a Markov process model for comparative analysis of multivariate count data
The evolutionary dynamics of complex ecological traits – including multistate representations of diet, habitat, and behavior – remain poorly understood. Reconstructing the tempo, mode, and historical sequence of transitions involving such traits poses many challenges for comparative biologists, owing to their multidimensional nature. Continuous-time Markov chains (CTMC) are commonly used to model ecological niche evolution on phylogenetic trees but are limited by the assumption that taxa are monomorphic and that states are univariate categorical variables. A necessary first step in the analysis of many complex traits is therefore to categorize species into a pre-determined number of univariate ecological states, but this procedure can lead to distortion and loss of information. This approach also confounds interpretation of state assignments with effects of sampling variation because it does not directly incorporate empirical observations for individual species into the statistical inference model. In this study, we develop a Dirichlet-multinomial framework to model resource use evolution on phylogenetic trees. Our approach is expressly designed to model ecological traits that are multidimensional and to account for uncertainty in state assignments of terminal taxa arising from effects of sampling variation. The method uses multivariate count data for individual species to simultaneously infer the number of ecological states, the proportional utilization of different resources by different states, and the phylogenetic distribution of ecological states among living species and their ancestors. The method is general and may be applied to any data expressible as a set of observational counts from different categories.
Fig. 3 in New Tools for Phylogenetic reconstruction using character state trees
Fig. 3: Result of a Camin-Sokal parsimony phylogenetic reconstruction using the data from tab. 2a.
Fig. 2 in New Tools for Phylogenetic reconstruction using character state trees
Fig. 2: Result of a Camin-Sokal parsimony phylogenetic reconstruction using the data from tab. 1.
Figure 4. Tree 1 in Genets and 'genet-like' taxa (Carnivora, Viverrinae): phylogenetic analysis, systematics and biogeographic implications
Figure 4. Tree 1 rooted with the Viverridae (intergeneric analysis).
Figure 5. Tree 2 in Genets and 'genet-like' taxa (Carnivora, Viverrinae): phylogenetic analysis, systematics and biogeographic implications
Figure 5. Tree 2 rooted with the Herpestidae (intergeneric analysis).
Figure 7. Tree 4 in Genets and 'genet-like' taxa (Carnivora, Viverrinae): phylogenetic analysis, systematics and biogeographic implications
Figure 7. Tree 4 rooted both with the Felidae and the Canidae (intergeneric analysis).
Figure 6. Tree 3 in Genets and 'genet-like' taxa (Carnivora, Viverrinae): phylogenetic analysis, systematics and biogeographic implications
Figure 6. Tree 3 rooted with the Felidae (intergeneric analysis).
Alignments and phylogenetic tree from: A new endemic species of Loasa ser. Macrospermae from northern Chile
<p><span></span></p> <p>Alignments used for the phylogenetic work and raw phylogenetic trees obtained.</p> <p>A new species of Loasa, endemic to the northern Andes of Chile is described and evaluated, under the IUCN criteria for conservation, as critically endangered. Molecular analyses based on plastid markers place the new species within the Loasa ser. Macrospermae, with high support, and specifically as sister to Loasa acerifolia. A key to and comparative plates including all the 13 known species of Loasa ser. Macrospermae, are provided.</p>
Cephalopod retinal development shows vertebrate-like mechanisms of neurogenesis: Multiple sequence alignments and phylogenetic trees
<p>Coleoid cephalopods, including squid, cuttlefish and octopus, have large and complex nervous systems and camera-type eyes that are comparable only to features that have independently evolved in the vertebrate lineage. The changes in development that result in the evolution of nervous system size and diversity of neural cell-types are not well understood. Here, we have pioneered live-imaging techniques and performed functional interrogation to show the squid, <em>Doryteuthis</em> <em>pealeii</em>, utilizes mechanisms during retinal neurogenesis that are hallmarks of vertebrate processes. Given the convergent evolution of elaborate visual systems in cephalopods and vertebrates, these results reveal common mechanisms that underlie the growth of highly proliferative neurogenic primordia that may alter ontogenetic allometry and contribute to the evolution of complex nervous systems.</p>
Aligned DNA sequence matrix for phylogenetic analyses in the article "A new species of spiny-backed tree frog, genus Osteocephalus (Anura: Hylidae), from the Yanachaga Chemillén National Park in central Peru"
<p>Aligned DNA sequence matrix for phylogenetic analyses of the article "Systematics of Huicundomantis, a new subgenus of Pristimantis (Anura, Strabomantidae) with extraordinary cryptic diversity and eleven new species"</p> <p>The matrix is in NEXUS format and has 14791 bp and 38 terminals.</p> <p>Partitions are as follows:</p> <p>charset 12S_16S = 1-2442;<br> charset mtGenome_other_genes = 2443-9180; charset nonCoding = 3132- 3138 4776- 4857 5203- 5214;<br> charset codonPos1 = 2443-3130\3 3139-4774\3 4858-5200\3 5215-9178\3;<br> charset codonPos2 = 2444-3131\3 3140-4775\3 4859-5201\3 5216-9179\3;<br> charset codonPos3 = 2445-3129\3 3141-4773\3 4860-5202\3 5217-9180\3;<br> charset 16S_ND1nonCoding = 9181- 9428 10390- 10506 ;<br> charset 16S_ND1codonPos1 = 9429-10389\3;<br> charset 16S_ND1codonPos2 = 9430-10387\3;<br> charset 16S_ND1codonPos3 = 9431-10388\3;<br> charset POMCcodonPos1 = 10507-11068\3;<br> charset POMCcodonPos2 = 10508-11066\3;<br> charset POMCcodonPos3 = 10509-11067\3;<br> charset CO1codonPos1 = 11069-12608\3;<br> charset CO1codonPos2 = 11070-12609\3;<br> charset CO1codonPos3 = 11071-12610\3;<br> charset CytbcodonPos1 = 12611-13757\3;<br> charset CytbcodonPos2 = 12612-13758\3;<br> charset CytbcodonPos3 = 12613-13759\3;<br> charset ND2codonPos1 = 13760-14789\3;<br> charset ND2codonPos2 = 13761-14790\3;<br> charset ND2codonPos3 = 13762-14791\3;</p>
Species-level phylogenetic trees of all angiosperm species (100 trees)
<p>One hundred species-level trees of all angiosperms (zip file) comprising all 329,798 species recognized by version 6 of the World Checklist of Vascular Plants. Details of how these trees were compiled is provided, as well as a spreadsheet listing the familial and ordinal assignation of each species in the trees. </p> <p> </p>
Phylogenetic alignments and trees (16S, COI, 16S+COI) of Haploniscidae (Crustacea: Isopoda) from the Northwest Pacific Ocean
<p>The role of geomorphological features as drivers for benthic deep-sea biodiversity remains poorly understood. By disentangling the putative <em>Haploniscus belyaevi </em>Birstein, 1963 species complex from the abysso-hadal Kuril-Kamchatka Trench (KKT) region in the Northwest Pacific Ocean, we aim to shed light on deep-sea differentiation and how it is related to potential bathymetric barriers such as the KKT and the Kuril-Island Ridge (KIR). Our integrative taxonomic approach featured morphological and molecular delimitation methods, also considering the post-marsupial development due to pronounced sexual dimorphism. Mitochondrial 16S and COI markers were sequenced and several molecular species delimitation methods were applied. By combining the different results we were able to delineate six distinct species within the <em>belyaevi </em>complex, including several morphologically cryptic species, and found hints of three additional species groups in the complex. Even though several of these species were distributed across the KKT and/or KIR, limited gene flow and depth-differentiation were indicated supporting previous notions that these geomorphological features play a role in deep-sea benthos speciation.</p> <p>These files comprise the 16S, COI and 16S+COI alignments of these analyses and their phylogenetic trees as calculated by IQTree.</p>
Figure S1: Phylogenetic tree of HIV-1 subtype D
<p>Figure S1: Phylogenetic tree of HIV-1 subtype D, branches with Brazilian sequences are highlighted: (a) Maximum likelihood tree of 1945 HIV-1 subtype D sequences; (b) Highlighted branch with Brazilian sequences from Rio Grande do Sul; (c) Highlighted branch with a Brazilian sequence from Pará; (d) Highlighted branch with a Brazilian sequence from Goiás; (e) Highlighted branch with a Brazilian sequence from São Paulo; (f) Highlighted branch with another Brazilian sequence from Pará; (g) Highlighted branch with Brazilian sequences from Rio de Janeiro; (h) Highlighted branch with a Brazilian sequence from Rio de Janeiro; (i) Highlighted branch of the major Brazilian clade; (j) Highlighted branch with another Brazilian sequence from Pará.</p>
Nucleotide alignment and phylogenetic tree illustrating tick-derived Mycoplasma cynos
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Data from: AUTOEB: A software for systematically evaluating bipartitions in a phylogenetic tree employing an approximately unbiased test
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Alignments and tree files from: Phylogenetic relationships within tribe Hibisceae (Malvaceae) reveal complex patterns of polyphyly in Hibiscus and Pavonia
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A new Lower Permian ray-finned fish (Actinopterygii) from South Dakota and the use of tree space to find rogue taxa in phylogenetic analysis of morphological data
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Phylogenetic data for construction of bryophyte tree using published sanger data
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Alignments and phylogenetic tree from: A new endemic species of Loasa ser. Macrospermae from northern Chile
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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.