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87 results for “Animal evolution”
LukProt - an animal evolution-centric eukaryotic protein database
<p>LukProt is the EukProt database with additional species added, mostly the undersampled animal and some holozoan taxa. The database is composed of sequences translated from annotated genomes, transcriptomes or ESTs. <strong>The main purposes of the database are to consolidate sequences from undersampled animal taxa</strong> and provide usable search tools. The publication associated with LukProt can be found here: <a href="https://doi.org/10.1093/gbe/evae231">https://doi.org/10.1093/gbe/evae231</a>.</p> <p>The current version of the database (v1.5.1) is based on <a href="https://doi.org/10.24072/pcjournal.173">EukProt v3</a>. The home of all public versions of LukProt is this page (Zenodo).</p> <p>Proteomes that are novel in LukProt are denoted as LPXXXXX and those coming from AniProtDB are called APXXXXX. The sequence IDs from EukProt are conserved in LukProt. This means that each sequence is assigned an ID in the following format:</p> <pre><code>(A/E/L)PXXXXX_Species_epithet_(strain)_PYYYYYY</code></pre> <p>where XXXXX is a number from 00001 to 99999 and YYYYYY is a number from 000001 to 999999. Each sequence is assigned a unique number YYYYYY, and each taxon XXXXXX. All the IDs are compatible with BLAST v5 "-parse_seqids" option and the database can be readily deployed, for example on a server running <a href="https://doi.org/10.1093/molbev/msz185">SequenceServer</a>. Within each of the source fasta files, the source sequence identifier was kept after a blank space, so that it can still be retrieved if needed.</p> <p>A publicly available BLAST server providing LukProt search is available at: <a title="LukProt BLAST server" href="https://lukprot.hirszfeld.pl/" target="_blank" rel="noopener">https://lukprot.hirszfeld.pl/</a>.</p> <p>Comparison of EukProt v2/v3, LukProt 1.4.1 and LukProt v1.5.1 in their main areas of difference:</p> <table> <tbody> <tr> <th>Taxogroup</th> <th>EukProt v2</th> <th>EukProt v3</th> <th>LukProt v1.4.1</th> <th>LukProt v1.5.1</th> </tr> <tr> <th> <p>Holozoa</p> <p>(excluding Metazoa)</p> </th> <td>31</td> <td>40</td> <td>39</td> <td>43</td> </tr> <tr> <th>Ctenophora</th> <td>2</td> <td>2</td> <td>35</td> <td>38</td> </tr> <tr> <th>Porifera</th> <td>4</td> <td>5</td> <td>30</td> <td>47</td> </tr> <tr> <th>Placozoa</th> <td>2</td> <td>2</td> <td>3</td> <td>6</td> </tr> <tr> <th>Cnidaria</th> <td>3</td> <td>5</td> <td>65</td> <td>88</td> </tr> <tr> <th>Bilateria</th> <td>51</td> <td>51</td> <td>94</td> <td>142</td> </tr> </tbody> </table> <p>Included with the database are:</p> <ul> <li>ready to use main database files: <ul> <li><em>LukProt_v1.5.1_single_species_FASTA.7z</em> – a FASTA file with the sequences - <a href="https://en.wikipedia.org/wiki/7z">7-zipped</a>, <strong>uncompressed size: 17.6 GB</strong><br> <ul> <li>to concatenate all into one file, run this in the parent directory: <code>for file in $(find . -type f -name "*.fasta"); do awk 'FNR==1{print ""}1' $file >> LukProt_v1.5.1.fa; done</code>. This will create single FASTA file with all the sequences in the parent directory. <code>awk</code> is used to insert a new line after every file because <code>cat</code> would sometimes merge the last sequence with the header of the first sequence.</li> </ul> </li> <li><em>LukProt_v1.5.1_full_BLAST_db.7z</em> – a preformatted, full BLAST database (NCBI BLAST database format version: v5, masked with segmasker), <strong>uncompressed size: 28.3 GB</strong></li> <li><em>LukProt_v1.5.1_taxogroup_BLAST_db.7z</em> – a collection of BLAST databases where each proteome is one taxogroup and is placed within the eukaryotic tree of life directory structure, <strong>uncompressed size: 26.3 GB</strong></li> <li><em>LukProt_v1.5.1_single_species_BLAST_db.7z</em> – a collection of BLAST databases where each proteome is one BLAST database and is placed within the eukaryotic tree of life directory structure, <strong>uncompressed size: 26.4 GB</strong></li> </ul> </li> <li>auxiliary database files: <ul> <li><em>LukProt_v1.5.1.cdhit70.7z</em> – the full database clustered at 70% identity using CD-HIT with the following command: <code>cd-hit -g 1 -d 0 -T 20 -M 90000 -c 0.7 -uL 0.2 -uS 0.9 -s 0.2</code>, <strong>uncompressed sizes: fasta file - 11 GB, clstr file - 2.5 GB</strong></li> <li><em>LukProt_IDs_mapped.txt.gz</em> – a text file mapping the LukProt IDs to the AniProtDB IDs and EukProt IDs that are different</li> <li><em>BUSCO_tables.ods</em> – a spreadsheet with full result tables generated by BUSCO analysis</li> <li><em>OMAmer_output.zip</em> – a folder with full results of OMAmer analyses (includes per-sequence taxonomy classification)</li> <li><em>OMArk_output.zip</em> – a folder with the results of all OMArk analyses</li> </ul> </li> <li>metadata: <ul> <li><em>README.md</em> – a README file describing the metadata</li> <li><strong><em>LukProt_metadata_sheet.ods</em> – main metadata file. A spreadsheet with information about each proteome (in an open .ods format, most compatible with <a href="https://www.libreoffice.org/">LibreOffice</a>)</strong></li> <li><em>LukProt_metadata_other.zip</em> – an archive with other metadata files, documented in the README. Contents include:<br> <ul> <li>the LukProt taxonomy in various formats</li> <li>supporting scripts for data manipulation and visualization</li> </ul> </li> <li>a recoloring script (modified by LFS, originally by Dr. Celine Petitjean). The script is in <a title="formatFigtree2" href="https://doi.org/10.5281/zenodo.10654583">public domain</a> and reuploaded here only for convenience. </li> <li>other files - see README</li> </ul> </li> <li><em>changelog.md</em> – database changelog</li> </ul> <p>Words of caution:</p> <ul> <li>The database has been synchronized to EukProt v3 in version v1.5.1. This means that identifiers were modified in comparison to LukProt v1.4.1. The convention is not expected to change any more in future updates.</li> <li>Many proteomes, especially those transcriptome-based, may contain contamination from different species. In addition, the translation algorithms often introduce errors (e.g. the transcript may not represent a full length protein). For this reason, to get accurate sequences from each organism, users are directed to source data and to the included OMAmer, OMArk and BUSCO data for details.</li> <li>The taxonomy is different to UniEuk/EukMap, but UniEuk data were integrated where possible.</li> <li>A few NCBI taxids are missing and will be added in due course.</li> <li>Proteomes from NCBI and UniProt will be updated to current versions.</li> <li>A number of proteomes present in some metadata, are unpublished and were held back.</li> <li>While the database contains metadata that present a particular phylogeny of animals, holozoans and other eukaryotes, no particular claims or hypotheses are made by the author(s). However, in the future efforts will be made to name clades officially, once they are more firmly established.</li> </ul> <p><strong>Please report any problems or suggestions to Lukasz Sobala: lukasz.sobala (at) hirszfeld.pl.</strong></p> <p> </p> <p>Acknowledgements:</p> <ul> <li> <p>Andrew E. Allen Lab for creating the original <a href="https://allenlab.ucsd.edu/data/" target="_blank" rel="noopener">PhyloDB</a>.</p> </li> <li> <p>Daniel Richter <em>et al.</em> for creating <a href="https://doi.org/10.6084/m9.figshare.12417881">EukProt</a> and keeping it updated.</p> </li> <li> <p>Members of <a href="https://multicellgenome.com/">the Multicellgenome Lab</a>, especially Michelle Leger (for donating her database), for the bioinformatics support and for doing great science.</p> </li> <li> <p>All the authors of the original data.</p> </li> <li> <p>National Science Centre of Poland for funding of the project 2020/36/C/NZ8/00081, "The role of glycosylation in the emergence of animal multicellularity", which enabled the creation of this database.</p> </li> </ul>
Data for: Why do phylogenomic analyses of early animal evolution continue to disagree? Sites in different structural environments yield different answers
<p>Supporting data for "Why do phylogenomic analyses of early animal evolution continue to disagree? Sites in different structural environments yield different answers" submitted by A Pandey and EL Braun. File is a gzipped tarball including protein multiple sequence alignments, phylogenetic trees, and other supporting data; see included README for details.</p>
Supplementary Data: Evolution of the cholesterol biosynthesis pathway in animals
<p>Cholesterol plays essential roles in animal development and disease progression. Here, we characterize the evolutionary pattern of the canonical cholesterol biosynthesis pathway (CBP) in the animal kingdom using both genome-wide analyses and functional experiments. CBP genes in the basal metazoans were inherited from their last common eukaryotic ancestor and evolutionarily conserved for cholesterol biosynthesis. The genomes of both the basal metazoans and deuterostomes retain almost the full set of CBP genes, while Cnidaria and many protostomes have independently experienced multiple massive losses of CBP genes that might be due to the geologic events during the Ediacaran period, such as the appearance of an exogenous sterol supply and the frequent perturbation of ocean oxygenation. Meanwhile, the indispensable utilization processes of cholesterol potentially strengthened the maintenance of the complete set of CBP genes in vertebrates. These results strengthen both biotic and abiotic roles in the macroevolution of a biosynthesis pathway in animals.</p>
Linked collectors and determiners for: Invertebrata Collection of Institute of Systematics and Evolution of Animals.
Natural history specimen data linked to collectors and determiners held within, "Invertebrata Collection of Institute of Systematics and Evolution of Animals". Claims or attributions were made on Bionomia by volunteer Scribes, <a href="https://bionomia.net/dataset/eca72f80-3330-11de-8db7-b8a03c50a862">https://bionomia.net/dataset/eca72f80-3330-11de-8db7-b8a03c50a862</a> using specimen data from the dataset aggregated by the Global Biodiversity Information Facility, <a href="https://gbif.org/dataset/eca72f80-3330-11de-8db7-b8a03c50a862">https://gbif.org/dataset/eca72f80-3330-11de-8db7-b8a03c50a862</a>. Formatted as a Frictionless Data package.
Linked collectors and determiners for: Aves Collection of Institute of Systematics and Evolution of Animals.
Natural history specimen data linked to collectors and determiners held within, "Aves Collection of Institute of Systematics and Evolution of Animals". Claims or attributions were made on Bionomia by volunteer Scribes, <a href="https://bionomia.net/dataset/c1b0f4a0-3330-11de-8db7-b8a03c50a862">https://bionomia.net/dataset/c1b0f4a0-3330-11de-8db7-b8a03c50a862</a> using specimen data from the dataset aggregated by the Global Biodiversity Information Facility, <a href="https://gbif.org/dataset/c1b0f4a0-3330-11de-8db7-b8a03c50a862">https://gbif.org/dataset/c1b0f4a0-3330-11de-8db7-b8a03c50a862</a>. Formatted as a Frictionless Data package.
Linked collectors and determiners for: Mammalia Collection of Institute of Systematics and Evolution of Animals.
Natural history specimen data linked to collectors and determiners held within, "Mammalia Collection of Institute of Systematics and Evolution of Animals". Claims or attributions were made on Bionomia by volunteer Scribes, <a href="https://bionomia.net/dataset/1933e8e0-3331-11de-8db8-b8a03c50a862">https://bionomia.net/dataset/1933e8e0-3331-11de-8db8-b8a03c50a862</a> using specimen data from the dataset aggregated by the Global Biodiversity Information Facility, <a href="https://gbif.org/dataset/1933e8e0-3331-11de-8db8-b8a03c50a862">https://gbif.org/dataset/1933e8e0-3331-11de-8db8-b8a03c50a862</a>. Formatted as a Frictionless Data package.
Deep-time convergent evolution in animal communication presented by shared adaptations for coping with noise in lizards and other animals
<p>Convergence in communication appears rare compared to other forms of adaptation. This is puzzling, given communication is acutely dependent on the environment and expected to converge in form when animals communicate in similar habitats. We uncover deep-time convergence in territorial communication between two groups of tropical lizards separated by over 140 million years of evolution: the Southeast Asian Draco and Caribbean Anolis. These groups have repeatedly converged in multiple aspects of display along common environmental gradients. Robot playbacks to free-ranging lizards confirmed the most prominent convergence in display is adaptive, as it improves signal detection. We then provide evidence from a sample of the literature to further show convergent adaptation among highly divergent animal groups is almost certainly widespread in nature. Signal evolution is therefore curbed towards the same set of adaptive solutions, especially when animals are challenged with the problem of communicating effectively in noisy environments.</p>
Figure 11 in Hybridization in the evolution of animal form and life-cycle
Figure 11. Four mid-Cambrian species from the Burgess Shale of British Columbia. A, Laggania cambria (= Anomalocaris nathorsti), ventral; B, Anomalocaris canadensis, ventral; C, Amiskwia sagittiformis; D, Nectocaris pteryx. Scale bar = ∼200 mm (A, B), ∼5 mm (C, D). [A, B reproduced with permission from S M Gonn III (from 'The Anomalocarid Bauplan' http://www.geocities.com/goniagnostus/background3.html); C, D, from Marianne Collins in Gould, 1989.]
Figure 9 in Hybridization in the evolution of animal form and life-cycle
Figure 9. Reticulate phylogeny of adults and larvae of extant hemichordates and echinoderms, showing probable sequence of events. Time (horizontal) not to scale. Ord/Sil, Ordovician/Silurian boundary; pres, present; thick black lines, adults; thin black lines, larvae; grey arrows, larval transfers.
Figure 7. Two Cambrian trilobites. A–D in Hybridization in the evolution of animal form and life-cycle
Figure 7. Two Cambrian trilobites. A–D, stages in the development of Sao hirsute: A, protaspis; B–D, early segmented stages. E, adult Agnostus pisiformis. Scale bar = ∼1 mm (A–D from Borradaile et al., 1935; E redrawn after Fortey, 2000.)
Figure 6 in Hybridization in the evolution of animal form and life-cycle
Figure 6. Stages in the development of the branchiopod crustacean Leptestheria syriaca, to different magnifications. (From Gurney, 1942; as Estheria.)
Figure 5. A in Hybridization in the evolution of animal form and life-cycle
Figure 5. A, nauplius of Penaeus sp. (recent Crustacea: Penaeidae). B, C, Martinssonia elongata (upper Cambrian): B, paranauplius II (left first appendage omitted); C, oldest known stage. Scale bar = ∼0.1 mm (A after Gurney, 1942; B, C adapted from Müller & Walossek, 1986b.)
Figure 4 in Hybridization in the evolution of animal form and life-cycle
Figure 4. Enteropneust and pterobranch hemichordates and a planctosphere. A–E, enteropneusta: A, adult Dolichoglossus, B, tornaria larva; C–E, stages in metamorphosis; F, G, Pterobranchia: F, adult Rhabdopleara; G, pterobranch larva. H, Planctosphaeromorpha: adult Planctoshaera pelagica. Scale bar = ∼10 mm (A), ∼1 mm (B–E, G), ∼5 mm (F, H). (Adapted from Borradaile et al., 1935; Hyman, 1959.)
Figure 3. Bryozoan larvae and adult. A in Hybridization in the evolution of animal form and life-cycle
Figure 3. Bryozoan larvae and adult. A, trochophore larva of Alcyonidium; B, cyphonautes larva of Membranipora; C, adult zooid of Electra. (After Williamson, 1992.)
Figure 2 in Hybridization in the evolution of animal form and life-cycle
Figure 2. Examples of overlapping metamorphosis. A, Luidia sarsi (Echinodermata): swimming bipinnaria larva and detached juvenile starfish; B, Polygordius sp. (Annelida): two stages showing segmented polychaete worm protruding from swimming trochophore larva; C, Cerebratulus sp. (Nemertea): juvenile nemertean worm within swimming pilidium larva; D, Doliolum mulleri (Urochordata): juvenile doliolid tunicate within cuticle of tadpole larva. Juvenile stippled in each case. (A, C adapted from Williamson, 1992; B, D adapted from Borradaile et al., 1935.)
Figure 1 in Hybridization in the evolution of animal form and life-cycle
Figure 1. Hydroid and medusae of Hebella (Hydrozoa: Thecata). A, gonophores of H. parasitica; B, male and female medusae of H. parasitica; C, medusa of H. furax. (A, B adapted from Boero, 1980; C adapted from Migotto & de Andrade, 2000.)
Figure 10. A in Hybridization in the evolution of animal form and life-cycle
Figure 10. A phylogram of some metazoans, based on 18S rRNA. (From Williamson, 2002; after Michael Syvanen, unpubl. data)
Figure 8 in Hybridization in the evolution of animal form and life-cycle
Figure 8. Larvae of an enteropneust hemichordate and echinoderms. A, tornaria larva of an acorn-worm (Enteropneusta); B, auricularia larva of a sea-cucumber (Holothuromorpha); C, bipinnaria larva of a starfish (Asteromorpha); D, echinopluteus larva of a sea-urchin (Echinomorpha); E, ophiopluteus larva of a brittle-star (Ophiuromorpha); F, doliolaria larva of a sea-lily (Crinomorpha). Scale bar = ∼1 mm (Adapted from Williamson, 1992, 2003.)
Fig. 9 in Ordovician opabiniid-like animals and the role of the proboscis in euarthropod head evolution
Fig. 9 | Details of posterior body and tail fan of Castle Bank euarthropod A (NMW.2021.3 G.8). cb-l leftcaudal blade, cb-r rightcaudalblade, df dorsalfurrow, fl lateral flap, sp spine.
Fig. 4 in Ordovician opabiniid-like animals and the role of the proboscis in euarthropod head evolution
Fig. 4 | Details of anterior of Mieridduryn bonniae nov. gen. et sp. (NMW.2021.3 G.7) photographed using fluorescence. a Anterior of the head regionincludingproboscis,mouth, and gut. b Dorsalsclerite. c Mouthand anterior flaps with strengthening rays. d Proboscis with spines. ds dorsal sclerite, pr proboscis, sp spine, sr strengthening rays.
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.