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248 results for “tree of life”
Net effect of environmental fluctuations in multiple global-change drivers across the tree of life
<p>This dataset contains the raw data presented in the article and supplementary material by M. J. Cabrerizo and E. Marañón entitled: "<strong>Net effect of environmental fluctuations in multiple global-change drivers across the tree of life"</strong></p>
Phylogenomic analyses of 2,786 genes in 158 lineages support a root of the eukaryotic tree of life between opisthokonts and all other lineages
<p>Advances in phylogenetic methods and high-throughput sequencing have allowed the reconstruction of deep phylogenetic relationships in the evolutionary history of eukaryotes. Yet, the root of the eukaryotic tree of life remains elusive. The most 'popular' (i.e. in textbooks and reviews) hypothesis for the root is between Unikonta (Opisthokonta + Amoebozoa) and Bikonta (all other eukaryotes), which emerged from analyses of a single gene fusion and a limited sampling of eukaryotic lineages. Subsequent highly-cited studies based on concatenation of genes supported this hypothesis with some variations or proposed a root within the Excavata. However, concatenation of genes neither considers phylogenetically-informative events (i.e. gene duplications and losses) nor provides an estimate of the root. A more recent study using gene tree-species tree reconciliation methods suggested the root lies between Opisthokonta and all other eukaryotes, but only including 59 taxa and 20 genes. Here we apply a gene tree – species tree reconciliation approach to a gene-rich and taxon-rich dataset (i.e. 2,786 gene families from two sets of ~158 diverse eukaryotic lineages) to assess the root, and we iterate each analysis 100 times to quantify tree space uncertainty. Our results estimate a root between Fungi and all other eukaryotes, or between Opisthokonta and all other eukaryotes, and reject alternative popular roots from the literature. Based on further analysis of genome size, we propose Opisthokonta + others as the most likely root. Finding the root of the eukaryotic tree of life is critical for the field of comparative biology as it allows us to understand the timing and mode of evolution of characters across the evolutionary history of eukaryotes.</p>
Fig. 70 in The Amphibian Tree Of Life
Fig. 70. Generic changes suggested for bufonid taxa that we studied. This figure shows our
Fig. 68 in The Amphibian Tree Of Life
Fig. 68. Maximumlikelihood tree of predominantly New World Bufonidae suggested by
Fig. 31 in The Amphibian Tree Of Life
Fig. 31. Maximumlikelihood tree of various ranoids constructed by Van der Meijden et al. (
Fig. 16 in The Amphibian Tree Of Life
Fig. 16. Tree of amphibians provided by Roelants and Bossuyt (2005). This tree reflects a
Fig. 12 in The Amphibian Tree Of Life
Fig. 12. Salamandrid relationships suggested by Titus and Larson (1995) based on a
Fig. 11 in The Amphibian Tree Of Life
Fig. 11. Tree of Plethodontidae suggested by Chippindale et al. (2004) based on parsimony
Fig. 44 in The Amphibian Tree Of Life
Fig. 44. Maximumlikelihood tree of Holarctic Rana of Hillis and Wilcox (2005). The
Fig. 3 in The Amphibian Tree Of Life
Fig. 3. Currently accepted view of
Fig. 41 in The Amphibian Tree Of Life
Fig. 41. Consensus of two parsimony trees of Chinese ranids from Jiang and Zhou (2005).
Fig. 27 in The Amphibian Tree Of Life
Fig. 27. Implied consensus of two most parsimonious trees of African toads studied by
Fig. 54. Part 1 in The Amphibian Tree Of Life
Fig. 54. Part 1 of anurans from the general tree (fig. 50 [insert]): nonneobatrachian
AnnoTree: Functionally Annotated Tree of Life
<p><strong>Current version:</strong><br> 2019-02-01: This file is a MySQL (v5.7) dump for AnnoTree, a functionally annotated tree of life. It includes the databases 'gtdb_bacteria_RS86' and 'gtdb_archaea_RS86'. Both databases include <a href="https://pfam.xfam.org/">Pfam</a> (v27), <a href="https://www.genome.jp/kegg/">KEGG</a> Ontology (from the <a href="https://www.uniprot.org/help/uniref">UniRef100</a> database downloaded March 6, 2018), and <a href="http://tigrfams.jcvi.org/cgi-bin/index.cgi">TIGRFAM</a> (v15) annotations for the representative genomes in <a href="http://gtdb.ecogenomic.org/">GTDB</a> release 03-RS86.</p> <p>Please refer to <a href="http://annotree.uwaterloo.ca">http://annotree.uwaterloo.ca</a> for the full site.</p> <p> </p> <p><strong>Older versions:</strong><br> 2018-10-22: MySQL dump file (v5.7) containing the 'gtdb_bacteria' database for GTDB release 02-RS83 for use with AnnoTree. Functional annotations include <a href="https://pfam.xfam.org/">Pfam</a> (v27) and <a href="https://www.genome.jp/kegg/">KEGG</a> Ontology (from the <a href="https://www.uniprot.org/help/uniref">UniRef100</a> database downloaded March 6, 2018). Corresponds to AnnoTree version 1.0.0 before the integration of Archaea.</p>
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>
Tree of Life web
Tree of Life (ToL) project is a collaborative effort of biologists from around the world. On more than 10,000 World Wide Web pages, the project provides information about the diversity of organisms on Earth, their evolutionary history (phylogeny), and characteristics. ToL pages are linked to one another hierarchically, in the form of the evolutionary tree of life. Starting with the root of all Life on Earth and moving out along diverging branches to individual species, the structure of the ToL project thus illustrates the genetic connections between all living things. Once the EOL has established its infrastructure for disseminating species page content through web services, ToL will concentrate on collecting content about supra-specific taxa and phylogenetic relationships between species. <p></p>http://tolweb.org/
SKOS-based version of the open tree of life
<p>This is a <a href="https://www.w3.org/TR/skos-primer/">SKOS</a>-based representation of the data from :</p> <ul> <li>Open Tree of Life reference taxonomy version 3.6 <ul> <li>Version 3.6 draft 1 was generated on 18 September, 2023.</li> <li><a href="https://files.opentreeoflife.org/ott/ott3.6/ott3.6.tgz">Download</a></li> </ul> </li> </ul> <p>This SKOS representation was generated with the <a href="https://ontop-vkg.org/guide/cli.html#ontop-materialize">ontop tool </a>configuration files in <a href="https://github.com/digital-botanical-gardens-initiative/earth_metabolome_ontology/tree/main/ontop_config/open-tree-of-life">here</a> .</p> <p><strong>Version note:</strong> In this version, OS undesired files were deleted.</p>
Earth BioGenome Project: Authors and author contributions for publication "The Earth BioGenome Project Phase II: Illuminating the Eukaryotic Tree of Life"
<p>The zipped file cntains three tab-separated datasets (worksheets). These worksheets list</p> <p>The contributing authors for the manuscript "The Earth BioGenome Project Phase II: Illuminating the Eukaryotic Tree of Life" and the roles of these authors in the manuscript.</p> <p>The funding sources for these authors</p> <p>A list of the authors contributing to the "EBP Community of Scientists" collective authorship for the same manuscript.</p>
Truly ubiquitous CRESS DNA viruses scattered across the eukaryotic tree of life
<p>Until recently, most viruses detected and characterized were of economic significance, associated with agricultural and medical diseases. This was certainly true for the eukaryote-infecting circular Rep (replication-associated protein)-encoding single-stranded DNA (CRESS DNA) viruses, which were thought to be a relatively small group of viruses. With the explosion of metagenomic sequencing over the past decade and increasing use of rolling-circle replication for sequence amplification, scientists have identified and annotated copious numbers of novel CRESS DNA viruses – many without known hosts but which have been found in association with eukaryotes. Similar advances in cellular genomics have revealed that many eukaryotes have endogenous sequences homologous to viral Reps, which not only provide "fossil records" to reconstruct the evolutionary history of CRESS DNA viruses but also reveal potential host species for viruses known by their sequences alone. The Rep protein is a conserved protein that all CRESS DNA viruses use to assist rolling circle replication that is known to be endogenized in a few eukaryotic species (notably tobacco and water yam). A systematic search for endogenous Rep-like sequences in GenBank's non-redundant eukaryotic database was performed using tBLASTn. We utilized relaxed search criteria for the capture of integrated Rep sequence within eukaryotic genomes, identifying 93 unique species with an endogenized fragment of Rep in their nuclear (78 species), plasmid (1 species), mitochondrial (6 species) or chloroplast (8 species) genomes. These species come from 19 different phyla, scattered across the eukaryotic tree of life. Exogenous and endogenous CRESS DNA viral Rep tree topology suggested potential hosts for one family of uncharacterized viruses and supports a primarily fungal host range for genomoviruses.</p>
Data from: Remote homolog detection places insect chemoreceptors in a cryptic protein superfamily spanning the tree of life
<p><span>Many proteins exist in the so-called "twilight zone" of sequence alignment, where low pairwise sequence identity makes it difficult to determine homology and phylogeny. As protein tertiary structure is often more conserved, recent advances in<em> ab initio </em>protein folding have made structure-based identification of putative homologs feasible. However, structural screening and phylogenetics are in their infancy, particularly for twilight zone proteins. We present a pipeline for the identification and characterization of distant homologs, and apply it to 7-transmembrane domain ion channels (7TMICs), a protein group founded by insect Odorant and Gustatory receptors. Previous sequence and limited structure-based searches identified putatively-related proteins, mainly in other animals and plants. However, very few 7TMICs have been identified in non-animal, non-plant taxa. Moreover, these proteins' remarkable sequence dissimilarity made it uncertain if disparate 7TMIC types (Gr/Or, Grl, GRL, DUF3537, PHTF and GrlHz) are homologous or convergent, leaving their evolutionary history unresolved. Our pipeline identified thousands of new 7TMICs in archaea, bacteria and unicellular eukaryotes. Using graph-based analyses and protein language models to extract family-wide signatures, we demonstrate that 7TMICs have structure and sequence similarity, supporting homology. Through sequence and structure-based phylogenetics, we classify eukaryotic 7TMICs into two families (Class-A and Class-B), which are the result of a gene duplication predating the split(s) leading to Amorphea (animals, fungi and allies) and Diaphoretickes (plants and allies). Our work reveals 7TMICs as a cryptic superfamily with origins close to the evolution of cellular life. More generally, this study serves as a methodological proof of principle for the identification of extremely distant protein homologs.</span></p>
ScienceDex guides
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These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
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.