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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>
Supporting trees and alignments for the publication: Cryptic and abundant marine viruses at the evolutionary origins of Earth's RNA virome
<div class="page"> <div class="layoutArea"> <div class="column"> <p>Whereas DNA viruses are known to be abundant, diverse, and commonly key ecosystem players, RNA viruses are relatively understudied outside disease settings. Here, we analyzed ≈28 terabases of Global Ocean RNA sequences to expand Earth's RNA virus catalogues and their taxonomy, investigate their evolutionary origins, and assess their marine biogeography from pole to pole. Using new approaches to optimize discovery and classification, we identified RNA viruses that necessitate substantive revisions of taxonomy (doubling phyla and adding >50% new classes) and evolutionary understanding. "Species"-rank abundance determination revealed that viruses of new phyla<span> </span><em>"Taraviricota"</em><span>, </span>a missing link in early RNA virus evolution, and<span> </span><em>"Arctiviricota"</em><span> </span>are widespread and dominant in the oceans. These efforts provide foundational knowledge critical to integrating RNA viruses into ecological and epidemiological models.</p> </div> </div> </div>
A new tree-based methodological framework to infer the evolutionary history of Mesopolyploid lineages: An application to the Brassiceae tribe (Brassicaceae)
<p>Whole genome duplication events are notably widespread in plants and this poses particular challenges for phylogenetic inference in allopolyploid lineages, i.e. lineages that result from the merging of two or more diverged genomes after interspecific hybridization. The nuclear genomes resulting from allopolyploidization contain homologous gene copies from different evolutionary origins called homoeologs, whose orthologs must be sorted out in order to reconstruct the evolutionary history of polyploid clades. In this study, we propose a methodological approach to resolve the phylogeny of allopolyploid clades focusing on mesopolyploid genomes, which experienced some level of genome reshuffling and gene fractionation across their subgenomes. To illustrate our methodological framework, we applied it to a clade belonging to the model Brassicaceae plant family, the Brassiceae tribe, that experienced a mesohexaploidy event. The dataset analysed consists of both publically available genomic sequences and new transcriptomic data according to taxa. The present methodology requires a well-annotated reference genome, for which the identification of the parental subgenome fragments has been performed (e.g. Brassica rapa and Brassica oleracea). Focusing on fully retained genes (i.e., genes for which all homoeologous gene copies inherited from the parental lineages are still present in the reference genome), the method constructs multilabelled gene trees that allow subsequent assignment of each gene copy to its diploid parental lineage. Once the orthologous copies are identified, genes from the same parental origin are concatenated and tree-building methods are used to reconstruct the species tree. This method allows resolving the phylogenetic relationships (i) among extant species within a mesopolyploid clade, (ii) among the parental lineages of a mesopolyploid lineage, and (iii) between the parental lineages and closely related extant species. We report here the first well-resolved nuclear-based phylogeny of the Brassiceae tribe.</p>
An integrative phylogenomic approach illuminates the evolutionary history of Old World tree frogs (Anura: Rhacophoridae)
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Data from: The interplay of past diversification and evolutionary isolation with present imperilment across the amphibian tree of life
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Data from: A 4-lineage statistical suite to evaluate the support of large-scale retrotransposon insertion data to reconstruct evolutionary trees
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A new tree-based methodological framework to infer the evolutionary history of Mesopolyploid lineages: An application to the Brassiceae tribe (Brassicaceae)
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Supporting trees and alignments for the publication: Cryptic and abundant marine viruses at the evolutionary origins of Earth’s RNA virome
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Data from: Evolutionary diversity in tropical tree communities peaks at intermediate precipitation
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Data from: Evolutionary constraints on tree size and aboveground biomass in tropical dry forests
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Global integration of phylogenomic data and fine-scale partitioning strategies refine the evolutionary tree of Adephaga beetles (Insecta: Coleoptera)
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Data from: Evolutionary history of almond tree domestication in the Mediterranean basin
Genetic diversity of contemporary domesticated species is shaped by both natural and human-driven processes. However, until now, little is known about how domestication has imprinted the variation of fruit tree species. In this study, we reconstruct the recent evolutionary history of the domesticated almond tree, Prunus dulcis, around the Mediterranean Basin, using a combination of nuclear and chloroplast microsatellites (i.e. SSRs) to investigate patterns of genetic diversity. Whereas conservative chloroplast SSRs show a widespread haplotype and rare locally distributed variants, nuclear SSRs show a pattern of isolation by distance with clines of diversity from the East to the West of the Mediterranean basin, while Bayesian genetic clustering reveals a substantial longitudinal genetic structure. Both kinds of markers thus support a single domestication event, in the eastern side of Mediterranean basin. In addition, model-based estimation of the timing of genetic divergence among those clusters is estimated sometime during the late Holocene, a result that is compatible with human-mediated dispersal of almonds out of its center of origin. Still, the detection of region-specific alleles suggests that gene flow from relictual wild pre-glacial populations (in North Africa) or from wild counterparts (in the Near-East) could account for a fraction of the diversity observed.
Data from: Relative impacts of environmental variation and evolutionary history on the nestedness and modularity of tree-herbivore networks.
Nestedness and modularity are measures of ecological networks whose causative effects are little understood. We analyzed antagonistic plant–herbivore bipartite networks using common gardens in two contrasting environments comprised of aspen trees with differing evolutionary histories of defence against herbivores. These networks were tightly connected owing to a high level of specialization of arthropod herbivores that spend a large proportion of the life cycle on aspen. The gardens were separated by ten degrees of latitude with resultant differences in abiotic conditions. We evaluated network metrics and reported similar connectance between gardens but greater numbers of links per species in the northern common garden. Interaction matrices revealed clear nestedness, indicating subsetting of the bipartite interactions into specialist divisions, in both the environmental and evolutionary aspen groups, although nestedness values were only significant in the northern garden. Variation in plant vulnerability, measured as the frequency of herbivore specialization in the aspen population, was significantly partitioned by environment (common garden) but not by evolutionary origin of the aspens. Significant values of modularity were observed in all network matrices. Trait-matching indicated that growth traits, leaf morphology, and phenolic metabolites affected modular structure in both the garden and evolutionary groups, whereas extra-floral nectaries had little influence. Further examination of module configuration revealed that plant vulnerability explained considerable variance in web structure. The contrasting conditions between the two gardens resulted in bottom-up effects of the environment, which most strongly influenced the overall network architecture, however, the aspen groups with dissimilar evolutionary history also showed contrasting degrees of nestedness and modularity. Our research therefore shows that, while evolution does affect the structure of aspen–herbivore bipartite networks, the role of environmental variations is a dominant constraint.
Data from: Phylogenetic relationships within the lizard clade Xantusiidae: using trees and divergence times to address evolutionary questions at multiple levels
Xantusiidae (night lizards) is a clade of small-bodied, cryptic lizards endemic to the New World. The clade is characterized by several features that would benefit from interpretation in a phylogenetic context, including: (1) monophyletic status of extant taxa Cricosaura, Lepidophyma, and Xantusia; (2) a species endemic to Cuba (Cricosaura typica) of disputed age; (3) origins of the parthenogenetic species of Lepidophyma; (4) pronounced micro-habitat differences accompanied by distinct morphologies in both Xantusia and Lepidophyma; and (5) placement of Xantusia riversiana, the only vertebrate species endemic to the California Channel Islands, which is highly divergent from its mainland relatives. This study incorporates extensive new character data from multiple gene regions to investigate the phylogeny of Xantusiidae using the most comprehensive taxonomic sampling available to date. Parsimony and partitioned Bayesian analyses of more than 7 kb of mitochondrial and nuclear sequence data from 11 loci all confirm that Xantusiidae is monophyletic, and comprises three well-supported clades: Cricosaura, Xantusia, and Lepidophyma. The Cuban endemic Cricosaura typica is well supported as the sister to all other xantusiids. Estimates of divergence time indicate that Cricosaura diverged from the (Lepidophyma + Xantusia) clade ∼81 million years ago (Ma), a time frame consistent with the separation of the Antilles from North America. Our results also confirm and extend an earlier study suggesting that parthenogenesis has arisen at least twice within Lepidophyma without hybridization, that rock-crevice ecomorphs evolved numerous times (>9) within Xantusia and Lepidophyma, and that the large-bodied Channel Island endemic X. riversiana is a distinct, early lineage that may form the sister group to the small-bodied congeners of the mainland.
Figure 3. Bayesian maximum clade credibility tree constructed from whole mitochondrial genome sequences, with a in Evolutionary history of Sundaland shrews (Eulipotyphla: Soricidae: Crocidura) with a focus on Borneo
Figure 3. Bayesian maximum clade credibility tree constructed from whole mitochondrial genome sequences, with a focus on Bornean Crocidura. Reconstructed with BEAST2. Dates are indicated on nodes and bar on bottom. Nodes used to calibrate the dating are marked with a black square. Uropsilus and Soricinae outgroups were included in the phylogenetic analysis for calibration purposes but removed from the figure for clarity. Since most nodes are highly supported (PP> 0.95), only less supported nodes (0.95 0.80) are marked with an orange circle. Colours on the vertical bar indicate geographical origin of sampled animals, and colors match the map. Samples from north of Kra are shown in grey.
Fig. 3 Maximum likelihood tree with 74 in Molecular evidence for the origin and evolutionary history of the rare American desert monotypic family Setchellanthaceae
Fig. 3 Maximum likelihood tree with 74 representative species of the families of the orders Brassicales and Malvales. Asterisks indicate nodal age constraints for the relaxed molecular clock analyses
FIGURE 2. Bayesian majority rule consensus tree inferred from the plastid DNA trnL-F in Evolutionary history of the tribe Astereae in the Flora Iranica area: Systematic implications
FIGURE 2. Bayesian majority rule consensus tree inferred from the plastid DNA trnL-F dataset. Numbers abovebranches are posterior probability (PP) and likelihood as well as parsimony bootstrap (BS) values, respectively. Values>50 % are shown.
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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.