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FIGURE 10 in Unravelling the origin of the brown hyena (Parahyena brunnea) and its evolutionary and paleoecological implications for the Pachycrocuta lineage
FIGURE 10. Evolutionary and paleobiogeographic hypotheses proposed in this work illustrated with the plot of the first principal component for the lower dentition. Double horizontal lines indicate bidirectional migratory flows. Empty rectangles indicate the absence of barriers to dispersal between the last three regions considered, and solid rectangles indicate geographic isolation. See the text for a more detailed explanation.
FIGURE 9 in Unravelling the origin of the brown hyena (Parahyena brunnea) and its evolutionary and paleoecological implications for the Pachycrocuta lineage
FIGURE 9. Illustration of the two criteria used in this study as a practical guide to separate segments within a lineage. Successive values of a lineage with four populations and four fossils per population are shown. At the top, the range of variation observed for the variable considered in a related present-day biospecies. Taking the lowest value of the first population as an arbitrary reference point, the lineage will be divided into two segments for that time value at which the observed range for the biospecies is surpassed, and at the same time, the difference between the means of the two sets (C and C', respectively) becomes significant.
FIGURE 8 in Unravelling the origin of the brown hyena (Parahyena brunnea) and its evolutionary and paleoecological implications for the Pachycrocuta lineage
FIGURE 8. Relative size of the bone-breaking region of P4 versus the size of P4 for some localities of P. brevirostris. The correlation coefficient between both variables is significant (r = 0.844, p = 0.002). The ellipse corresponds to the expected region for the population at 95% confidence. Gi: Gigantopithecus Cave, Ke: Kedung Brubus, Lo: Longdan, LC: Longgu Cave, Re: Renzi Cave, Sa: Sainzelles, Um: Untermasfeld, Va: Val d'Arno, VM: Venta Micena, Yu: Yuanmou, Zo: Loc.1 of Zhoukoudian.
FIGURE 7 in Unravelling the origin of the brown hyena (Parahyena brunnea) and its evolutionary and paleoecological implications for the Pachycrocuta lineage
FIGURE 7. In A is shown a lateral view of an articulated skull and jaw of a H. hyaena specimen (EBD 33079M, Doñana Biological Station, Seville) and its corresponding schematic drawing in B, showing different functional regions of the dentition during the mandibular occlusion process. The main regions involved in cutting meat are the trigonid (Trig) of m1 in the lower dentition and the metastyle (Me) and the distal part of Paracone (P) of the upper fourth premolar (P4). The main elements involved in bone breaking are the two lower premolars (p4 and p3) that occlude with the upper third premolar (P3) and the mesial part of the paracone and the parastyle of the upper P4.
FIGURE 5 in Unravelling the origin of the brown hyena (Parahyena brunnea) and its evolutionary and paleoecological implications for the Pachycrocuta lineage
FIGURE 5. Bivariate plots of geological age on the scores for the lower dentition two first principal components. A-B, PC I for fossil individuals and paleontological localities, respectively. C-D, PC II for fossil individuals and paleontological localities, respectively. E: Elandsfontein. At the base of each figure are shown the ranges for the extant species and C. spelaea in each principal component.
FIGURE 4 in Unravelling the origin of the brown hyena (Parahyena brunnea) and its evolutionary and paleoecological implications for the Pachycrocuta lineage
FIGURE 4. Bivariate plots of the scores on the upper dentition two first principal components and their corresponding component loading plots for (A) analysis for fossil individuals and (B) analysis for paleontological localities. E: Elandsfontein. G: Gladysvale Cave. K: Kromdraai A. L: Longdan. S: Ségriès-le Réservoir.
FIGURE 2 in Unravelling the origin of the brown hyena (Parahyena brunnea) and its evolutionary and paleoecological implications for the Pachycrocuta lineage
FIGURE 2. Several examples of worn lower first molars. A, V 7296 from Baihaicum (from Qiu, 1987). B, Pliocrocuta perrieri (Se 312, Senèze, France). C, Crocuta crocuta (no id. Naturkundemuseum Berlin). D, plot of m1 trigonid length on m1 width for the species analyzed in this study. Note that there is a clear separation between Crocuta and Non Crocuta species. Additional explanations have been provided in the text.
FIGURE 1 in Unravelling the origin of the brown hyena (Parahyena brunnea) and its evolutionary and paleoecological implications for the Pachycrocuta lineage
FIGURE 1. Stratigraphic range of the species belonging to the analyzed lineages, their paleogeographic distribution (squares with gray background), and some examples of lower mandibles in labial view. IVPP V20801: Pliocrocuta perrieri from Zanclean (Zanda Basin, China), drawn from Tseng et al. (2016). KK 82-58: Parahyaena howelli (Laetoli, Tanzania), drawn from Werdelin and Dehghani (2011). MNHN 834: Pliocrocuta perrieri post-Zanclean (holotype from Mont Perrier, Muséum national d'histoire naturelle, Paris. C/C. 806: Pachycrocuta brevirostris (Zhoukoudian, China) drawn from Pei (1934). KA 55: Pachycrocuta bellax (Kromdraai A, South Africa) drawn from Ewer (1954a). 'Hyaena' prisca (holotype from Lunel-Viel, France) drawn from Brugal et al. (2021). NHM 35.9.1.286: Parahyaena brunnea (Karroo Valley, South Africa, housed at the Natural History Museum, London).
Figure 1 in Climatic preferences and distribution of 6 evolutionary lineages of Typhlops vermicularis Merrem, 1820 in Turkey using ecological niche modeling
Figure 1. Important mountain chains of Anatolia and ecological niche modeling of T. vermicularis in Turkey under current climatic conditions.
Figure 3 in Climatic preferences and distribution of 6 evolutionary lineages of Typhlops vermicularis Merrem, 1820 in Turkey using ecological niche modeling
Figure 3. Predicted models of lineages G, H, and I according to Last Interglacial (LIG) and Last Glacial Maximum (LGM; CCSM and MIROC) (4, 4A, 4B, 4C for lineage G; 5, 5A, 5B, 5C for lineage H; 6, 6A, 6B, 6C for lineage I).
Figure 2 in Climatic preferences and distribution of 6 evolutionary lineages of Typhlops vermicularis Merrem, 1820 in Turkey using ecological niche modeling
Figure 2. Predicted models of lineages B, C, and E according to Last Interglacial (LIG) and Last Glacial Maximum (LGM; CCSM and MIROC) (1, 1A, 1B, 1C for lineage B; 2, 2A, 2B, 2C for lineage C; 3, 3A, 3B, 3C for lineage E).
Data from: Ancestral hybridization yields evolutionary distinct hybrids lineages and species boundaries in crocodiles, posing unique conservation conundrums
<p>Interspecific hybridization can lead to adaptation and speciation, especially in the context of recent radiations. The emblematic <em>Crocodylus</em> (true crocodiles) is the most broadly distributed, ecologically diverse, and species-rich crocodylian genus. Nonetheless, their within-species evolutionary processes are poorly resolved mainly due to their potential for hybridization. Notably, the evolutionary outcomes when hybridization is ancient and involves long-lived species, like crocodiles, remain largely unexplored. Here, we evaluate the genomic admixture between the American (<em>Crocodylus</em> <em>acutus</em>) and the Morelet's (<em>Crocodylus</em> <em>moreletii</em>) species, and demonstrate that this hybridization system challenges the definition of species boundaries and poses a triple conservation conundrum: what has been recognized as <em>C. acutus</em> is actually two distinct species, therefore its taxonomic reassessment is needed; we identified two evolutionary distinct hybrids lineages, which are genetically discernible from the parental species; the remaining <em>C. moreletii </em>populations evidence its likely extinction as a species and/or evolution via hybridization. Hence, the crocodiles' distinct species and hybrids lineages warrant recognition and need urgent conservation efforts.</p>
Text-fig. 2. Phylogeography based on mitochondrial phylogeny showing several evolutionary lineages of Arvicola and the separation of the Italian lineage of Arvicola, currently A. italicus (lineage A1), from European and Euro-Asiatic groups. From Wust-Saucy (1998: fig. 27), modified. in Independent Water Vole (Mimomys Savini, Arvicola: Rodentia, Mammalia) Lineages In Italy And Central Europe
Text-fig. 2. Phylogeography based on mitochondrial phylogeny showing several evolutionary lineages of Arvicola and the separation of the Italian lineage of Arvicola, currently A. italicus (lineage A1), from European and Euro-Asiatic groups. From Wust-Saucy (1998: fig. 27), modified.
Genomic identification of direct seeding and evolutionary lineages by combining heterogeneous genomic resources
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Data from: Ancestral hybridization yields evolutionary distinct hybrids lineages and species boundaries in crocodiles, posing unique conservation conundrums
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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>
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>
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.