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Fig. 64. A in The Amphibian Tree Of Life
Fig. 64. A, Original tree of Jiang et al. (2005; from fig. 42) of Paini and (on right) its undirected network; B, Tree rerooted and with augmented resolution as implied by our general
Data for: Resolving the avian tree of life from top to bottom: The promise and potential boundaries of the phylogenomic era
<p>This data package includes multiple sequence alignments, information about base compositional variation, and phylogenetic analyses that support Figures 7 and 8 in Braun et al. (2019). There is a README in SuppInfo_Braun_et_al_chapter_Kraus_volume.tar.gz that provides a detailed description of the files in this data package.</p> <p>Braun, E.L., Cracraft, J., Houde, P. (2019). Resolving the Avian Tree of Life from Top to Bottom: The Promise and Potential Boundaries of the Phylogenomic Era. In: Kraus, R. (eds) Avian Genomics in Ecology and Evolution. Springer, Cham. https://doi.org/10.1007/978-3-030-16477-5_6</p>
TreeGOER Holdridge Life Zone Distributions: Observations for 48,129 tree species across 45 historical (1901-1920) and contemporary (1979-2013) terrestrial life zones
<p><strong>TreeGOER (Tree Globally Observed Environmental Ranges)</strong> is a database that documents the environmental ranges (minimum, maximum, median, mean and 5%, 25%, 75% and 95% quantiles) for 48,129 tree species and for 51 environmental variables, including 38 bioclimatic variables, 8 soil variables and 3 topographic variables. TreeGOER is available from the following Zenodo archives: <a href="https://doi.org/10.5281/zenodo.7922927">https://doi.org/10.5281/zenodo.7922927.</a></p> <p>The TreeGOER ranges were calculated after cleaning occurrence records and standardizing species names with the <a href="https://bsapubs.onlinelibrary.wiley.com/doi/10.1002/aps3.11388">WorldFlora</a> R package to <a href="https://onlinelibrary.wiley.com/doi/10.1002/tax.12373">World Flora Online</a> or the <a href="https://www.nature.com/articles/s41597-021-00997-6">World Checklist of Vascular Plants</a> for a global GBIF occurrence download of 44,267,164 occurrences (GBIF.org 2021 <strong>GBIF Occurrence Download</strong> <a href="https://doi.org/10.15468/dl.77gcvq">https://doi.org/10.15468/dl.77gcvq</a>). The process of compilation of TreeGOER with 30 arc-seconds global grid layers, two examples of BIOCLIM applications that investigated the effects of climate change on global tree diversity patterns and R scripts to repeat these analyses have been described by Kindt, R. (2023). <strong>TreeGOER: A database with globally observed environmental ranges for 48,129 tree species</strong>. Global Change Biology 29: 6303–6318. <a href="https://onlinelibrary.wiley.com/doi/10.1111/gcb.16914">https://onlinelibrary.wiley.com/doi/10.1111/gcb.16914</a>.</p> <p>This Zenodo archive documents the occurrence of the same previously compiled and cleaned observations for the TreeGOER across global raster layers that document the contemporary (1979-1920) and historical (1901-1920) distribution of 45 <strong>Terrestrial Life Zones</strong>. These global raster layers were created for the following article:</p> <ul> <li>Elsen, P. R., Saxon, E. C., Simmons, B. A., Ward, M., Williams, B. A., Grantham, H. S., Kark, S., Levin, N., Perez-Hammerle, K.-V., Reside, A. E., & Watson, J. E. M. (2022). Accelerated shifts in terrestrial life zones under rapid climate change. <em>Global Change Biology</em>, 28, 918–935. <a href="https://doi.org/10.1111/gcb.15962">https://doi.org/10.1111/gcb.15962</a></li> </ul> <p>and are <a href="https://datadryad.org/stash/dataset/doi:10.5061/dryad.41ns1rnff">available for download from DRYAD</a>:</p> <ul> <li>Elsen, Paul R.; Saxon, Earl C.; Simmons, B. Alexander; Ward, Michelle; Williams, Brooke A.; Grantham, Hedley S.; Kark, Salit; Levin, Noam; Perez-Hammerle, Katharina-Victoria; Reside, April E.; Watson, James E. M.; Perez‐Hammerle, Katharina‐Victoria. 2021. Data from: Accelerated shifts in terrestrial life zones under rapid climate change.<strong> </strong>Nov 05 2021 version files. <a href="https://doi.org/10.5061/dryad.41ns1rnff">https://doi.org/10.5061/dryad.41ns1rnff</a></li> </ul> <p>The raster layers were processed using <em>R</em> and <em>Google Earth Engine</em> following the methodology described in Elsen et al (<a href="https://doi.org/10.1111/gcb.15962">2022</a>). Documentation of the different zones are partially available from this README file: <a href="https://datadryad.org/stash/downloads/file_stream/1145694">https://datadryad.org/stash/downloads/file_stream/1145694</a></p> <p>For each of the 48,129 tree species, the distribution is given for:</p> <ul> <li>Contemporary climate: number of observations in life zones mapped by <a href="https://datadryad.org/stash/downloads/file_stream/1145680">https://datadryad.org/stash/downloads/file_stream/1145680</a></li> <li>Historical climate: number of observations in life zones mapped by <a href="https://datadryad.org/stash/downloads/file_stream/1145681">https://datadryad.org/stash/downloads/file_stream/1145681</a></li> <li>Mixed climate: number of observations for contemporary life zones if GBIF observations were from 1979 or later, and number of observations for historical life zones if GBIF observations were from before 1979</li> <li>Static climate: number of observations in the same zone in the contemporary and historical climate. The number of observations in areas where the life zone changed are listed in the variable of 'H-0'.</li> </ul> <p>Observations outside the life zone maps are listed in the variable of 'H-1'.</p> <p> </p> <p>The development of this data set archive supported by the <strong>Darwin Initiative</strong> to project DAREX001 of <em>Developing a Global Biodiversity Standard certification for tree-planting and restoration</em>, by <strong>Norway’s International Climate and Forest Initiative through the Royal Norwegian Embassy in Ethiopia</strong> to the <em>Provision of Adequate Tree Seed Portfolio</em> project in Ethiopia, by the <strong>Green Climate Fund</strong> through the IUCN-led <em>Transforming the Eastern Province of Rwanda through Adaptation</em> and through the <em>Readiness proposal on Climate Appropriate Portfolios of Tree Diversity for Burkina Faso</em> projects, by the <strong>Bezos Earth Fund</strong> to the <em>Quality Tree Seed for Africa in Kenya and Rwanda</em> project and by the <strong>German International Climate Initiative (IKI)</strong> to the regional tree seed programme on <em>The Right Tree for the Right Place for the Right Purpose in Africa</em>.</p>
Eye morphology contributes to the ecology and evolution of the avian tree of life
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Data and code from: Efficient inference of macrophylogenies: Insights from the avian tree of life
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Data from: Meta-analytical evidence for frequency-dependent selection across the tree of life
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Data from: Enriching the ant tree of life: enhanced UCE bait set for genome-scale phylogenetics of ants and other Hymenoptera
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DateLife: leveraging databases and analytical tools to reveal the dated Tree of Life
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Empirical data for: Extending phylogenetic regression models for comparing within-species patterns across the Tree of Life
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A comprehensive phylogenomic platform for exploring the angiosperm Tree of Life
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Data from: Evolutionary innovation through fusion of sequences from across the tree of life
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Data from: An R package and online resource for macroevolutionary studies using the ray-finned fish tree of life
1. Comprehensive, time-scaled phylogenies provide a critical resource for many questions in ecology, evolution, and biodiversity. Methodological advances have increased the breadth of taxonomic coverage in phylogenetic data; however, accessing and reusing these data remain challenging. 2. We introduce the Fish Tree of Life website and associated R package fishtree to provide convenient access to sequences, phylogenies, fossil calibrations, and diversification rate estimates for the most diverse group of vertebrate organisms, the ray-finned fishes. The Fish Tree of Life website presents subsets and visual summaries of phylogenetic and comparative data, and is complemented by the R package, which provides flexible programmatic access to the same underlying data source for advanced users wishing to extend or reanalyze the data. 3. We demonstrate functionality with an overview of the website, and show three examples of advanced usage through the R package. First, we test for the presence of long branch attraction artifacts across the fish tree of life. The second example examines the effects of habitat on diversification rate in the pufferfishes. The final example demonstrates how a community phylogenetic analysis could be conducted with the package. 4. This resource makes a large comparative vertebrate dataset easily accessible via the website, while the R package enables the rapid reuse and reproducibility of research results via its ability to easily integrate with other R packages and software for molecular biology and comparative methods.
Data from: Phylogenomics reveals ancient gene tree discordance in the amphibian Tree of Life
<p>Molecular phylogenies have yielded strong support for many parts of the amphibian Tree of Life, but poor support for the resolution of deeper nodes, including relationships among families and orders. To clarify these relationships, we provide a phylogenomic perspective on amphibian relationships by developing a taxon-specific Anchored Hybrid Enrichment protocol targeting hundreds of conserved exons which are effective across the class. After obtaining data from 220 loci for 286 species (representing 94% of the families and 44% of the genera), we estimate a phylogeny for extant amphibians and identify gene tree–species tree conflict across the deepest branches of the amphibian phylogeny. We perform locus-by-locus genealogical interrogation of alternative topological hypotheses for amphibian monophyly, focusing on interordinal relationships. We find that phylogenetic signal deep in the amphibian phylogeny varies greatly across loci in a manner that is consistent with incomplete lineage sorting in the ancestral lineage of extant amphibians. Our results overwhelmingly support amphibian monophyly and a sister relationship between frogs and salamanders, consistent with the Batrachia hypothesis. Species tree analyses converge on a small set of topological hypotheses for the relationships among extant amphibian families. These results clarify several contentious portions of the amphibian Tree of Life, which in conjunction with a set of vetted fossil calibrations, support a surprisingly younger timescale for crown and ordinal amphibian diversification than previously reported. More broadly, our study provides insight into the sources, magnitudes, and heterogeneity of support across loci in phylogenomic data sets.</p>
Tree of Life
Please Like Before Downloading. Thank You! Carriage Hill Metro Park Huber Heights Ohio De-lighting needed Created in RealityCapture by Capturing Reality from 452 images Update: This Tree no longer stands. Great model for a Heritage or Spooky scene. Source: Objaverse 1.0 / Sketchfab
Data from: hiding in plain sight: phylogenomics reveals a new branch on the Noctuoidea tree of life
<p>We analyze anchored hybrid enrichment data (AHE) from densely sampled tribes and subfamilies of Notodontidae (Prominent Moths). Notodontidae are monophyletic except for an assemblage of genera related to <em>Thacona</em> Walker (=<em>Scrancia</em> Holland), which had been recognized at either the tribal or subfamilial rank within Notodontidae. We elevate and re-describe Scranciidae, stat. nov. as a family distinct from the six currently recognized noctuoid families (Noctuidae, Erebidae, Euteliidae, Nolidae, Notodontidae, and Oenosandridae). Scranciidae include 22 genera comprising approximately 100 species—distributed in Africa, Asia, and Australia. We re-interpret morphological synapomorphies previously proposed for Notodontidae (including Scranciidae) and for the trifid Noctuoidea more broadly. Deep-level relationships within Noctuoidea are not well resolved outside the clade comprising the four quadrifid families (Noctuidae, Erebidae, Euteliidae, and Nolidae). The phylogenetic position of Scranciidae relative to Notodontidae, Oenosandridae, and the quadrifids varied markedly depending on data type (amino acid vs. nucleotide) and analytical framework (maximum likelihood, multi-species coalescent, and parsimony). We discuss the possible roles of missing data and short branch lengths in resolving the placement of Scranciidae. In the topology best supported by the most available data, Scranciidae are sister to the remaining Noctuoidea, highlighting their phylogenetic significance. We provide a provisional list of the genera included in Scranciidae.</p>
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>
The Tree of Life eDNA metabarcoding reveals a similar taxonomic richness but dissimilar evolutionary lineages between seaports and marine reserves (bact2 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>bact2</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>
The Tree of Life eDNA metabarcoding reveals a similar taxonomic richness but dissimilar evolutionary lineages between seaports and marine reserves (euka2 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>euka2</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>
The Tree of Life eDNA metabarcoding reveals a similar taxonomic richness but dissimilar evolutionary lineages between seaports and marine reserves (teleo 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>teleo</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> <p> </p>
Ignacio Ribera's Tree of Life
<p>Supplementary Data with phylogenetic trees built with the COI sequences from Coleoptera that were uploaded to GenBank by studies including Ignacio Ribera as author. Those trees also include sequences from other studies to highlight the impressive work done Ignacio Ribera to contribute to the Coleoptera Tree of Life. This upload also includes the python scripts written to parse GenBank entries and the files to upload in iTOL webpage to highlight on trees the samples coming from Ignacio’s studies. Finally, we also include the 17,499 entries for nucleotide sequences deposited from Ignacio’s articles.</p>
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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.