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351 results for “gene tree”
Ancestral Genomes: a resource for reconstructed ancestral genes and genomes across the tree of life
<p>For each ancestral gene, we assign a stable identifier, and provide additional information designed to facilitate analysis: an inferred name (based on its descendants in extant genomes), a reconstructed protein sequence, a set of inferred Gene Ontology (GO) annotations, and a “proxy gene” for each ancestral gene, defined as the least-diverged descendant of the ancestral gene in a given extant genome.</p>
Genus level DNA sequence data for three genes (matK, rbcL, trnH-psbA) for the paper: A comprehensive, genus-level time-calibrated phylogeny of the tree flora of Mediterranean Europe and an assessment of its vulnerability
<p>This data file contains the consensus DNA sequences in fasta format, of 64 tree genera found in Mediterranean Europe, following the checklist of Médail et al. (2019). </p> <p>The data are used in a manuscript submitted for publication to Botany Letters and currently under revision. The manuscript is entitled: "<em>A comprehensive, genus-level time-calibrated phylogeny of the tree flora of Mediterranean Europe and an assessment of its vulnerability</em>". Its authors are: Marwan Cheikh Albassatneh, Marcial Escudero, Loic Ponge<sup>*</sup>, Anne-Christine Monnet, Juan Arroyo, Toni Nikolic, Gianluigi Bacchetta, Francesca Bagnoli, Panayotis Dimopoulos, Agathe Leriche, Frédéric Médail, Anne Roig, Ilaria Spanu, Giovanni Giuseppe Vendramin, Arndt Hampe, Bruno Fady.</p>
Dataset for "Divergent selection and primary gene flow shape incipient speciation of a riparian tree on Hawaii Island"
<p>HawaiiPopulation_Raw.bcf.gz</p> <p>- Unfiltered SNP + INDEL VCF file for Hawaii Island Metrosideros</p> <p> </p> <p>HawaiiPopulation_FILTERED_SNP.bcf.gz</p> <p>- Filtered SNP VCF for Hawaii Island Metrosideros</p> <p> </p> <p>Population_WithOutgroup_Raw.vcf.gz</p> <p>- Unfiltered SNP + INDEL VCF file used in analysis that grouped G<sub>H1</sub>, G<sub>H2</sub>, N subpopulation with the outgroup samples.</p> <p> </p> <p>Population_WithOutgroup_FILTERED_SNP.vcf.gz</p> <p>- Filtered SNP VCF file used in analysis that grouped G<sub>H1</sub>, G<sub>H2</sub>, N subpopulation with the outgroup samples.</p> <p> </p> <p>Population_WithOutgroup.geno.gz</p> <p>- Genotype file generated from the genomic_general from S. Martin and used as input for Dxy and Fst window analysis</p> <p> </p> <p>Popgene_stat*</p> <p>- 5, 10, and 50 kbp windows of calculating pi, Dxy, Fst, Omega, Hscan, and H12 statistics </p> <p> </p> <p>GPHOCS_INPUT.txt</p> <p>- Input data file for GPhoCS analysis</p> <p> </p> <p>GPHOCS_control_*</p> <p>- GPhoCS control file</p> <p> </p> <p>DADI_INPUT*</p> <p>- Input 2D-SFS file for dadi analysis</p>
Comparative transcriptomics reveals divergence in pathogen response gene families amongst twenty forest tree species
<p>Forest trees provide critical ecosystem services for humanity that are under threat due to ongoing global change. Measuring and characterizing genetic diversity is key to understanding adaptive potential and developing strategies to mitigate negative consequences arising from climate change. <span>In the area of forest genetic diversity, genetic divergence caused by large-scale changes at the chromosomal level has been largely understudied. In this study, </span>we used the RNA-seq data of twenty co-occurring forest tree species from genera including <em>Acer, Alnus, Amelanchier, Betula, Cornus, Corylus, Dirca, Fraxinus, Ostrya, Populus, Prunus, Quercus, Ribes, Tilia, </em>and<em> Ulmus </em>sampled from Upper Peninsula of Michigan. These data were used to infer the origin and maintenance of gene family variation, species divergence time, as well as gene family expansion and contraction. We identified a signal of common whole genome duplication events shared by core eudicots. We also found rapid evolution, namely fast expansion or fast contraction of gene families, in plant-pathogen interaction genes amongst the studied diploid species. Finally, the results lay the foundation for further research on the genetic diversity and adaptive capacity of forest trees, which will inform forest management and conservation policies.</p>
Newick Trees for EMERGE methanogen genome tree, and methylotrophic gene trees
<p>Newick trees provided for phylogenomic and phylogenetic analyses from Ellenbogen <em>et al. </em>(in prep). The methanogen genome tree (gtdbtk.ar53.decorated.tree) was built using a GTDB-Tk v12.1.1 r207 run with the de novo workflow. All other trees are RAxML gene trees built using ProtPipeliner (<a href="https://github.com/TheWrightonLab/Protpipeliner/blob/master/protpipeliner.py">https://github.com/TheWrightonLab/Protpipeliner/blob/master/protpipeliner.py</a>) to confirm the functional identity of identified methylotrophic genes from methanogens and bacteria. The names of the Newick trees correspond to relevant gene groupings as discussed in the associated manuscript.</p> <p>DRAM v1.3.2 raw annotations files for Stordalen methanogen MAGs also included.</p> <p>FUNDING:<br> This research is a contribution of the EMERGE Biology Integration Institute, funded by the National Science Foundation, Biology Integration Institutes Program, Award # 2022070.<br> We thank the Swedish Polar Research Secretariat and SITES for the support of the work done at the Abisko Scientific Research Station. SITES is supported by the Swedish Research Council's grant 4.3-2021-00164.<br> This study was also funded by the Genomic Science Program of the United States Department of Energy Office of Biological and Environmental Research, grant #s DE-SC0010580 and DE-SC0016440.</p>
DupLoss-2: Improved phylogenomic species tree inference under gene duplication and loss
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Genotype data of 970 Pedunculate oak trees (Quercus robur L.) in Russia and neighbouring countries at 385 gene loci covering the nuclear and organelle genome
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Comprehensive phylogenomic time tree of bryophytes reveals deep relationships and uncovers gene incongruences in the last 500 million years of diversification
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Allopatric speciation and interspecific gene flow driven by niche conservatism of Diploderma tree lizards in Taiwan
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Data and code from: How a territorial challenge changes sex steroid-related gene networks in the female brain: A field experiment with the tree swallow
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Data from: Sources of gene tree discordance and their implications for systematics and evolution of a megadiverse Australian plant radiation (subtribe Hakeinae, Proteaceae)
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Data from: Whole-genomes illuminate the drivers of gene tree discordance and the tempo of tinamou diversification (Aves: Tinamidae)
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Phylogenomic analyses in Phrymaceae reveal extensive gene tree discordance in relationships among major clades
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Genotype data of 1970 Pedunculate oak trees (Quercus robur L.) in 13 European countries at 381 gene loci covering the nuclear and organelle genome
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Data from: Phylogenomics reveals ancient gene tree discordance in the amphibian Tree of Life
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Dataset for: Smith et al., Phylogenomic analysis of the parrots of the world distinguishes artifactual from biological sources of gene tree discordance
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Disentangling sources of gene tree discordance in phylogenomic datasets: testing ancient hybridizations in Amaranthaceae s.l.
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Data from: Species tree estimation and the impact of gene loss following whole-genome duplication
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Contrasting the depths of divergence between gene-tree and coalescent estimates in the North American Racers (Colubridae: Coluber constrictor)
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Comparative transcriptomics reveals divergence in pathogen response gene families amongst 20 forest tree species
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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.