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8 results for “tree dissimilarity”
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>
Love thy neighbour? Tropical tree growth and its response to climate anomalies is mediated by neighbourhood hierarchy and dissimilarity in carbon and water related traits
<div> <div>Data and R code to reproduce all analyses, figures and tables for Krebber et al. 2024, Ecology Letters:<br>Love thy neighbour? Tropical tree growth and its response to climate anomalies is mediated by neighbourhood hierarchy and dissimilarity in carbon and water related traits. </div> <div> </div> <div>All analyses have been conducted and produced in the R environment (R version 4.1.2; R Core Team, 2021; RStudio Team, 2020). Bayesian hierarchical models have been run using the R package brms (Version 2.19.0; Bürkner, 2017). The data and R files containing the code to reproduce the results, figures and tables are described in the README file and code in more detailed is described in <em>RCode_xxx</em> files. Please note that the analyses are highly computational intensive and the scripts should be run on a high performance cluster (models and scripts running models and handeling model outputs presented here have been run with 16 cpus and with 50 - 100 GB of RAM). Packages needed are loaded at the beginning of each script. Please ensure that these and all their dependencies have been previously installed. The R code in the files has been carefully commented.</div> </div>
Data from: Trait hierarchies are stronger than trait dissimilarities in structuring spatial co-occurrence patterns of common tree species in a subtropical forest
<p>1. The dissimilarity and hierarchy of trait values that characterize niche and fitness differences, respectively, have been increasingly applied to infer mechanisms driving community assembly and to explain species co-occurrence patterns. Here, we predict that limiting similarity should result in the spatial segregation of functionally similar species, while functionally similar species will be more likely to co-occur either due to environmental filtering or competitive exclusion of inferior competitors (hereafter hierarchical competition).</p> <p>2. We used a fully mapped 50-ha subtropical forest plot in southern China to explore how pairwise spatial associations between saplings and between adult trees were influenced by trait dissimilarity and hierarchy in order to gain insight into assembly mechanisms. We assessed pairwise spatial associations using two summary statistics of spatial point patterns at different spatial scales and compared the effects of trait dissimilarity and trait hierarchy of different functional traits on the interspecific spatial associations. These comparisons allow us to disentangle the effects of limiting similarity, environmental filtering and hierarchical competition on species co-occurrence.</p> <p>3. We found that trait dissimilarity was generally negatively related with interspecific spatial associations for both saplings and adult trees across spatial scales, meaning that species with similar trait values were more likely to co-occur and thus supporting environmental filtering or hierarchical competition. We further found that trait hierarchy outweighed trait dissimilarity in structuring pairwise spatial associations, suggesting that hierarchical competition played a more important role in structuring our forest community than environmental filtering across life stages.</p> <p>4. This study employed a novel method, by offering the integration of pairwise spatial association and trait dissimilarity as well as trait hierarchy, to disentangle the relative importance of multiple assembly mechanisms in structuring co-occurrence patterns, especially the mechanisms of environmental filtering and hierarchical competition, which lead to indistinguishable co-occurrence patterns. This study also reinforced the importance of trait hierarchy rather than trait dissimilarity in driving neighborhood competition.</p>
Functionally dissimilar neighbors improve tree water use efficiency through increases in leaf phosphorus concentration
<p><span>Water use efficiency (WUE) is central to the global cycles of water and carbon.</span> However, whether increasing tree diversity in plantation can increase WUE remain poorly understood. Here, we conduct a forest biodiversity experiment with 32 tree species spread in 14 ha in subtropical China to assess the effects of neighboring tree diversity on foliar WUE of <em>Cunninghamia lanceolata</em>, a widespread tree plantation species in China. We measure foliar <span>δ<sup>13</sup>C as the proxies of changes in intrinsic WUE. Folia P concentrations of focal trees increase with trait dissimilarities between focal trees and neighbors, and the increased foliar P concentrations improve foliar WUE of focal trees. This neighborhood complementarity effect on WUE is stronger under more shaded neighborhood. However, neighborhood biodiversity did not significantly affect foliar δ<sup>18</sup>O, a surrogate for stomatal conductance. These findings suggest that tree biodiversity increases WUE through the complementary usages of soil P between neighboring tree species.</span></p>
Functionally dissimilar neighbors improve tree water use efficiency through increases in leaf phosphorus concentration
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