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39 results for “Metazoa”
Metazoa-level USCOs as markers in species delimitation and classification
<p><span>Metazoa-level<strong> </strong>Universal Single-Copy Orthologs (USCOs) are universally applicable markers for DNA taxonomy in animals which can replace or supplement single-gene barcoding. While Metazoa-level USCOs from target enrichment data were shown to reliably distinguish species, it remains to be tested whether USCOs are an evenly distributed, representative sample of a given metazoan genome, and hence can facilitate detection of past hybridization events. Besides, unlinked loci are a principal assumption in coalescent-based species delimitation approaches. 239 chromosome-level genomes were analyzed to show that Metazoa-level<strong> </strong>USCOs are a representative sample of a genome: in terms of distances to each other on a chromosome, but also over the chromosomes, they are almost as evenly distributed as protein-coding genes in general are. We tested the suitability of Metazoa-level USCOs extracted from genomes for species delimitation and phylogeny in four case studies: <em>Anopheles</em> mosquitos, <em>Drosophila</em> fruit flies, <em>Heliconius </em>butterflies, and Darwin's finches. In almost all instances USCOs allowed delineating species and yielded phylogenies that correspond to those generated from whole genome data.<strong> </strong>Our results show<strong> </strong>that USCO genes can be considered as genetically unlinked for practical purposes and representative for an entire metazoan genome. Our phylogenetic analyses demonstrate that USCOs may complement single-gene barcoding and provide more accurate taxonomic inferences. Combining USCOs from sources that used different versions of ortholog reference libraries to infer marker orthology may be challenging and at times impact taxonomic conclusions. However, we expect this problem to become less severe as the size of genome reference libraries and their sampling of organismic lineages is rapidly increasing.</span></p>
Figure 16 in Deep - water hypoxic meiobenthic Protozoa and Metazoa taxa of the Istanbul Strait's (Bosporus) outlet area of the Black Sea
Figure 16. Proportion of the harpacticoids inhabiting different sediment layers along the depth gradient.
Figure 10 in Deep - water hypoxic meiobenthic Protozoa and Metazoa taxa of the Istanbul Strait's (Bosporus) outlet area of the Black Sea
Figure 10. Proportion of the main Metazoa taxa inhabiting along depth gradient at the Bosporus outlet area of the Black Sea.
Figure 9 in Deep - water hypoxic meiobenthic Protozoa and Metazoa taxa of the Istanbul Strait's (Bosporus) outlet area of the Black Sea
Figure 9. Proportion of soft-shelled foraminifera inhabiting different sediment layers along the depth gradient.
Figure 8 in Deep - water hypoxic meiobenthic Protozoa and Metazoa taxa of the Istanbul Strait's (Bosporus) outlet area of the Black Sea
Figure 8. Proportion of hard-shelled foraminifera inhabiting different sediment layers along the depth gradient.
Figure 7 in Deep - water hypoxic meiobenthic Protozoa and Metazoa taxa of the Istanbul Strait's (Bosporus) outlet area of the Black Sea
Figure 7. Distribution of the Foraminifera (hard-shelled and soft-shelled) abundance (N) along depth gradient at the Bosporus outlet area of the Black Sea.
Figure 6 in Deep - water hypoxic meiobenthic Protozoa and Metazoa taxa of the Istanbul Strait's (Bosporus) outlet area of the Black Sea
Figure 6. Proportion of the Ciliophora inhabiting different sediment layers along the depth gradient at the Bosporus outlet area of the Black Sea.
Figure 1 in Deep - water hypoxic meiobenthic Protozoa and Metazoa taxa of the Istanbul Strait's (Bosporus) outlet area of the Black Sea
Figure 1. Oxygen concentrations in the sediment and the overlying water at Stations 4 –6 (by Sergeeva et al 2013).
Gene/Protein BridgeDb ID Mapping Database (Ensembl Metazoa 49)
<p>Ensembl Metazoa 49 derived ID mapping databases for use with BridgeDb.<br> The scripts used to create these databases based on Ensembl BioMart can be found at <a href="https://github.com/bridgedb/create-bridgedb-genedb">https://github.com/bridgedb/create-bridgedb-genedb</a>.</p> <p>This work was funded by the <a href="https://fairplus-project.eu/">FAIRplus project</a> (grant agreement no 802750) and <a href="https://www.nwo.nl/en/researchprogrammes/open-science/open-science-fund/open-science-fund-2021-awarded-grants">NWO Open Science Fund</a> (grant no <a href="https://www.nwo.nl/en/projects/203001121">203.001.121</a>).<br> </p>
Standardized nuclear markers improve and homogenize species delimitation in Metazoa
<p><span>Species are the fundamental units of life and evolution. Their recognition is essential for science and society. Molecular methods have been increasingly employed for the identification of animal species, despite several challenges. </span></p> <p><span>Here, we explore with genomic data from nine animal lineages a set of nuclear</span><span> </span><span>markers, namely metazoan-level universal single-copy orthologs (metazoan USCOs), for their use in species delimitation. Our data sets include arthropods and vertebrates. We use various data assembly strategies and employ coalescent-based species inference as well as population admixture analyses and phenetic methods.</span></p> <p><span>We demonstrate that metazoan USCOs well distinguish closely related morphospecies and consistently outperform classical mitochondrial DNA barcoding in discriminating closely related species in different animal taxa. USCOs overcome the general shortcomings of mitochondrial DNA barcodes, and due to standardization across Metazoa, also those of other approaches. They accurately assign samples not only to lower but also to higher taxonomic levels. </span></p> <p><span>Metazoan USCOs provide a powerful and unifying framework for DNA-based species delimitation and taxonomy in animals and their employment could result in a more efficient use of research data and resources.</span></p>
Gene/Protein BridgeDb ID Mapping Database (Ensembl Metazoa 52)
<p>Mapping databases derived from Ensembl Metazoa 52. These files can be used with BridgeDb.<br> The scripts which were used to create these databases based on Ensembl BioMart can be found at <a href="https://github.com/bridgedb/create-bridgedb-genedb">https://github.com/bridgedb/create-bridgedb-genedb</a>.</p> <p>This work was funded by the <a href="https://fairplus-project.eu/">FAIRplus project</a> (grant agreement no 802750) and <a href="https://www.nwo.nl/en/researchprogrammes/open-science/open-science-fund/open-science-fund-2021-awarded-grants">NWO Open Science Fund</a> (grant no <a href="https://www.nwo.nl/en/projects/203001121">203.001.121</a>).</p>
Standardized nuclear markers improve and homogenize species delimitation in Metazoa
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Metazoa-level USCOs as markers in species delimitation and classification
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McMurdo Dry Valleys Soils Snowfence Nematode and Metazoa Survey Experiment
Increases in soil moisture from snow packs may influence distribution and abundances of soil invertebrates. In this study, two snow fences were erected in Lake Fryxell and Lake Bonney basins to trap snow and examine the effects of increased snow pack on soil physical, chemical and biological properties.
Figure 14 in Deep - water hypoxic meiobenthic Protozoa and Metazoa taxa of the Istanbul Strait's (Bosporus) outlet area of the Black Sea
Figure 14. Proportion of polychaetes inhabiting different sediment layers along the depth gradient.
Figure 4 in Deep - water hypoxic meiobenthic Protozoa and Metazoa taxa of the Istanbul Strait's (Bosporus) outlet area of the Black Sea
Figure 4. Proportion of gromiids inhabiting different sediment layers along the depth gradient.
The Tree of Life eDNA metabarcoding reveals a similar taxonomic richness but dissimilar evolutionary lineages between seaports and marine reserves (metazoa data)
<p>This dataset is associated to the following publication: <strong>Macé, B.</strong>, Mouillot, D., Dalongeville, A., Bruno, M., Deter, J., Varenne, A., Gudefin, A., Boissery, P., & Manel, S. (<strong>2024</strong>). The Tree of Life eDNA metabarcoding reveals a similar taxonomic richness but dissimilar evolutionary lineages between seaports and marine reserves. <em>Molecular Ecology</em>, e17373. <a href="https://doi.org/10.1111/mec.17373">https://doi.org/10.1111/mec.17373</a></p> <p>It contains the data obtained with the <strong>metazoa</strong> marker:</p> <ul> <li><em>fastq</em> files are the raw NGS eDNA sequencing outputs</li> <li><em>dat</em> file records the adapters names and oligos used for sequencing</li> </ul> <p>Metadata associated to each eDNA sample are also provided.</p> <p> </p> <p><strong>Methods</strong></p> <blockquote> <p>eDNA extractions were performed in a BSL-2 lab dedicated for eDNA samples following the protocol described in Polanco Fernández et al. (2021). Four PCR amplifications were conducted with different assays covering the whole tree of life. The teleo primer pair (Valentini et al., 2016) targets a 12S mitochondrial DNA marker from teleosts and elasmobranchs; the metazoa primer pair (Kelly et al., 2016) targets a 16S mitochondrial DNA marker from metazoans; the euka2 primer pair (Guardiola et al., 2015) targets a marker from eukaryotes located on the V7 region of the 18S ribosomal RNA; and the bact2 primer pair (Taberlet et al., 2018) targets a marker from prokaryotes located on the V4 region of the 16S ribosomal RNA. The idea of this experimental design is to give a holistic overview of communities, with a nested hierarchy euka2-metazoa-teleo to obtain a finer taxonomic resolution over animal communities, and particularly fish. Twelve PCR replicates per sample were run, with negative extractions and PCR positive and negative controls analyzed in parallel. Unique tags were used for each PCR replicate amplified with the teleo primers only, allowing to differentiate them in the bioinformatic analysis (see after). NGS library preparation and MiSeq paired-end sequencing (2 × 150 bp) were performed at DNA Gensee (Le Bourget-du-Lac, France).</p> </blockquote> <p> </p> <p><strong>References</strong></p> <p>Guardiola, M., Uriz, M. J., Taberlet, P., Coissac, E., Wangensteen, O. S., & Turon, X. (2015). Deep-Sea, Deep-Sequencing: Metabarcoding Extracellular DNA from Sediments of Marine Canyons. <em>PLOS ONE</em>, <em>10</em>(10), e0139633. https://doi.org/10.1371/journal.pone.0139633</p> <p>Kelly, R. P., O’Donnell, J. L., Lowell, N. C., Shelton, A. O., Samhouri, J. F., Hennessey, S. M., Feist, B. E., & Williams, G. D. (2016). Genetic signatures of ecological diversity along an urbanization gradient. <em>PeerJ</em>, <em>4</em>, e2444. https://doi.org/10.7717/peerj.2444</p> <p>Polanco Fernández, A., Marques, V., Fopp, F., Juhel, J.-B., Borrero-Pérez, G. H., Cheutin, M.-C., Dejean, T., González Corredor, J. D., Acosta-Chaparro, A., Hocdé, R., Eme, D., Maire, E., Spescha, M., Valentini, A., Manel, S., Mouillot, D., Albouy, C., & Pellissier, L. (2021). Comparing environmental DNA metabarcoding and underwater visual census to monitor tropical reef fishes. <em>Environmental DNA</em>, <em>3</em>(1), 142–156. https://doi.org/10.1002/edn3.140</p> <p>Taberlet, P., Bonin, A., Zinger, L., & Coissac, E. (2018). <em>Environmental DNA: For Biodiversity Research and Monitoring</em>. Oxford University Press.</p> <p>Valentini, A., Taberlet, P., Miaud, C., Civade, R., Herder, J., Thomsen, P. F., Bellemain, E., Besnard, A., Coissac, E., Boyer, F., Gaboriaud, C., Jean, P., Poulet, N., Roset, N., Copp, G. H., Geniez, P., Pont, D., Argillier, C., Baudoin, J.-M., … Dejean, T. (2016). Next-generation monitoring of aquatic biodiversity using environmental DNA metabarcoding. <em>Molecular Ecology</em>, <em>25</em>(4), 929–942. https://doi.org/10.1111/mec.13428</p>
Tudor genes of Holozoa: Early evolution and within Metazoa diversification of a multifaceted protein family
<p>Early metazoan evolution was characterized by the expansion of many gene families involved in novel multicellularity-related functions, like the Tudor family. In eukaryotes, Tudor genes are numerous and heterogeneous, mostly associated with gene expression regulation. However, the family underwent a lineage-specific expansion in animals, with novel elements almost exclusively involved in the germline-specific regulation of retrotransposons through piRNAs (as spatiotemporal regulators of the key-element Piwi, another previously supposedly animal-specific gene). In the present analysis, we used online-available proteomes for a total of 25 major taxonomic groups to characterize the Tudor gene family at a holozoan-wide level, and we confirmed the apomorphic expansion of piRNA-related Tudor genes in animals. However, we could also interestingly observe the presence of elements of the piRNA pathway, both Tudor and Piwi genes, in some Ichthyosporea species, suggesting that some elements of the pathway were already present in the last common ancestor of Holozoa. Moreover, we observed an outstanding variability (34-fold) of Tudor gene number both between and within metazoan phyla, that could be associated with convergent genomic and phenotypic evolutions. Expansions were usually sided by whole genome duplications and/or life history traits such as parthenogenesis, possibly leading to the expansion of retrotransposon silencing pathways. Reductions were instead mostly associated with overall phenotypic and genomic simplifications, like almost all endoparasites of our dataset. Lastly, we phylogenetically tested a previously proposed model for the evolution of the three possible secondary structures of the Tudor domains and we could mostly (but not completely) confirm the model.</p>
Tudor genes of Holozoa: Early evolution and within Metazoa diversification of a multifaceted protein family
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Data from: Endosymbiotic calcifying bacteria: a new cue for the origin of calcification in Metazoa?
Sponges show the highest diversity of associated bacteria among marine invertebrates. Immunological evidence traces the origin of the sponge bacterial symbioses to the Precambrian era. Hence, sponges appear to be ideally suited for studying the evolutionary origins of prokaryote-metazoan associations. Sponges produce either calcareous or siliceous skeletons, which only coexist in a relict group of demosponges, the sclerosponges. We report here, for the first time, intensive calcification in non-sclerosponge siliceous demosponges. Calcification is mediated by endosymbiotic bacteria (calcibacteria) located in archeocyte-like sponge cells. These calcibacteria are deprived from bacterial walls and divide within sponge cells until they became surrounded by a calcitic sheet, being subsequently extruded to the sponge subectosomal (subepithelial) zone. Thousands of bacteria-produced calcitic spherules cover the surface of the host sponges, forming a cortex-like structure that mimics a rudimentary peripheral skeleton. Calcibacteria are vertically transferred to the sponge larvae during embryogenesis. Calcium detoxification may have generated this symbiotic association, with some additional benefits for the sponges, such as skeletal formation and deterrence from predation. This unique symbiosis holds implications for sponge biology and may advance discussions on the role of bacteria in early biocalcification processes in metazoans.
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Allen Brain Atlas
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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.