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95 results for “tree reconstruction”
Data from: Species tree reconstruction of a poorly resolved clade of salamanders (Ambystomatidae) using multiple nuclear loci
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Mesophication in temperate Europe: a dendrochronological reconstruction of tree succession and fires in a mixed deciduous stand in Białowieża Forest / supporting data
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Data from: Historical reconstruction of climatic and elevation preferences and the evolution of cloud forest-adapted tree ferns in Mesoamerica
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Newick trees for "Within-patient phylogenetic reconstruction reveals early events in Barrett's Esophagus"
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Data from: Using ultraconserved elements to reconstruct the termite tree of life
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Fig. 2. Bayesian majority rule consensus tree reconstructed for 90 in Phylogenetic analysis and systematic position of two new species of the ant genus Crematogaster (Hymenoptera, Formicidae) from Southeast Asia
Fig. 2. Bayesian majority rule consensus tree reconstructed for 90 taxa using five genes (ArgK, CAD, LWRh, Top1, Wg) in a MrBayes analysis. Most of the outgroups are not shown. Above node numbers indicate posterior probability, bootstrap value for MP, and bootstrap value for ML. Data were partitioned by PartitionFinder v.1.1.1 and analyzed using a best fit model for each gene and codon position, with 10 million generations and a burn-in of 25 %.
Genomic characterization and curation of UCEs improves species tree reconstruction: Supplementary Material S1
<p>Ultraconserved genomic elements (UCEs) are generally treated as independent loci in phylogenetic analyses. The identification pipeline for UCE probes does not require prior knowledge of genetic identity, only selecting loci that are highly conserved, single copy, without repeats, and of a particular length. Here we characterized UCEs from 11 phylogenomic studies across the animal tree of life, from birds to marine invertebrates. We found that within vertebrate lineages, UCEs are mostly intronic and intergenic, while in invertebrates, the majority are in exons. We then curated 4 different sets of UCE markers by genomic category from 5 different studies including: birds, mammals, fish, Hymenoptera (ants, wasps, and bees) and Coleoptera (beetles). Of genes captured by UCEs, we find that many are represented by 2 or more UCEs, corresponding to non-overlapping segments of a single gene. We considered these UCEs to be non-independent, merged all UCEs that belonged to a particular gene, constructed gene and species trees, and then evaluated the subsequent effect of merging co-genic UCEs on gene and species tree reconstruction. Average bootstrap support for merged UCE gene trees was significantly improved across all datasets apparently driven by the increase in loci length. Additionally, we conducted simulations and found that gene trees generated from merged UCEs were more accurate than those generated by unmerged UCEs. As loci length improves gene tree accuracy, this modest degree of UCE characterization and curation impacts downstream analyses and demonstrates the advantages of incorporating basic genomic characterizations into phylogenomic analyses.<br> </p>
Fig. 3. A neighbor-joining phylogenetic tree reconstructed from a in Report of two unrecorded yeast species in the class Tremellomycetes
Fig. 3. A neighbor-joining phylogenetic tree reconstructed from a comparative analysis of 26S rRNA gene sequences showing the relationships of strain DJ2-14-10C with closely related species. Bootstrap values (>70%) based on neighbor-joining methods are shown at the branch nodes. Bar, 0.01 substitutions per nucleotide position (Trees, 1987).
Data from: The shape of modern tree reconstruction methods
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Data from: A Bayesian supertree model for genome-wide species tree reconstruction
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Genomic characterization and curation of UCEs improves species tree reconstruction: Supplementary Material S1
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Data from: Graph splitting: a graph-based approach for superfamily-scale phylogenetic tree reconstruction
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Tree and sequence alignment used for diet reconstruction of Laurasiatheria
<p><b>Background:</b> Laurasiatheria contains taxa with diverse diets, while the molecular basis and evolutionary history underlying their dietary diversification are less clear.</p> <p><b>Results:</b> In this study, we used the recently developed molecular phyloecological approach to examine the adaptive evolution of digestive system-related genes across both carnivorous and herbivorous mammals within Laurasiatheria. Our results show an intensified selection of fat and/or protein utilization across all examined carnivorous lineages, which is consistent with their high-protein and high-fat diets. Intriguingly, for herbivorous lineages (ungulates), which have a high-carbohydrate diet, they show a similar selection pattern as that of carnivorous lineages. Our results suggest that for the ungulates, which have a specialized digestive system, the selection intensity of their digestive system-related genes does not necessarily reflect loads of the nutrient components in their diets but appears to be positively related to the loads of the nutrient components that are capable of being directly utilized by the herbivores themselves. Based on these findings, we reconstructed the dietary evolution within Laurasiatheria, and our results reveal the dominant carnivory during the early diversification of Laurasiatheria. In particular, our results suggest that the ancestral bats and the common ancestor of ruminants and cetaceans may be carnivorous as well. We also found evidence of the convergent evolution of one fat utilization-related gene, <i>APOB</i>, across carnivorous taxa.</p> <p><b>Conclusions: </b>Our molecular phyloecological results suggest that digestive system-related genes can be used to determine the molecular basis of diet differentiations and to reconstruct ancestral diets. </p>
Tree and sequence alignment used for diet reconstruction of Laurasiatheria
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RNA-Seq Based Reconstruction of the Phylogenetic Tree of the Genus Flaveria (Asteraceae)
GEO Series GSE54339. Flaveria cronquistii; Helenium autumnale; Flaveria kochiana; Flaveria sonorensis; Flaveria bidentis; Flaveria pubescens; Tragopogon dubius; Tanacetum parthenium; Flaveria angustifolia; Flaveria pringlei; Flaveria trinervia; Flaveria brownii; Flaveria palmeri; Flaveria vaginata. 21 samples. Type: Expression profiling by high throughput sequencing.
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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.