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1,598 results for “genetic diversity”
Molecular screening and genetic diversity of tick-borne pathogens associated with dogs and livestock ticks in Egypt
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Neutral processes and taxonomic scale drive beta species-genetic diversity correlations in a submesophotic tropical reef fish
<p>This dataset is associated to the following publication:</p> <p>Vilcot M, Faure N, Andrews KR, Bowen BW, Leprieur F, Manel S. (2024) <strong>Neutral processes and taxonomic scale drive beta species-genetic diversity correlations in a submesophotic tropical reef fish</strong>. <em>Molecular Ecology</em> <strong>33</strong>, e17423. (doi:<a href="https://doi.org/10.1111/mec.17423">10.1111/mec.17423</a>)</p> <p> </p> <h2><strong>Data: </strong></h2> <ul> <li> <p>"Report_DEtel22-6705_SNP_2_ordered_Bowen.csv": SNP data from Dart Sequencing on <em>Etelis coruscans</em>, from Andrews et al. (2020) samples</p> </li> <li>"PA_Mat_GaspObis.RDS": fish species presence data, gathered from an updated version of Albouy et al. (2019)</li> <li> <p>"metadata_samples_full.csv": all <em>Etelis coruscans</em> sample information, from Andrews et al. (2020) and the SEAMOUNTS project</p> </li> <li> <p>"metadata_samples.csv": <em>Etelis coruscans</em> sample information, only for samples that have passed the genetic filtering and were used for subsequent analyses </p> </li> <li> <p>"metadata_stations.csv": sampling station information</p> </li> <li> <p>"Taxonomy_Fishbase.csv": species taxonomic information, downloaded with rfishbase::load_taxa() </p> </li> <li> <p>"traits_Luiz_et_al_2013.csv": species trait information from Luiz et al. (2013) </p> </li> </ul> <h2><strong>Related dataset</strong><strong>: </strong></h2> <p><em>Etelis coruscans </em>SNP data on samples from the SEAMOUNTS project are available at <a href="https://doi.org/10.5281/zenodo.11201065">https://doi.org/10.5281/zenodo.11201065</a></p> <h2><strong>Scripts: </strong></h2> <p>Scripts used to reproduce the analyses and figures of the final article are available at <a href="https://github.com/mvilcot/etelis_SGDCs">https://github.com/mvilcot/etelis_SGDCs</a> </p> <p> </p> <h2><strong>References: </strong></h2> <p>Albouy, C., Archambault, P., Appeltans, W., Araújo, M. B., Beauchesne, D., Cazelles, K., Cirtwill, A. R., Fortin, M.-J., Galiana, N., Leroux, S. J., Pellissier, L., Poisot, T., Stouffer, D. B., Wood, S. A., & Gravel, D. (2019). The marine fish food web is globally connected. Nature Ecology & Evolution, 3(8), Article 8. <a href="https://doi.org/10.1038/s41559-019-0950-y" target="_blank" rel="noopener">https://doi.org/10.1038/s41559-019-0950-y</a> </p> <p>Andrews, K. R., Copus, J. M., Wilcox, C., Williams, A. J., Newman, S. J., Wakefield, C. B., & Bowen, B. W. (2020). Range-Wide population structure of 3 deepwater Eteline snappers across the Indo-Pacific Basin. Journal of Heredity, 111(5), 471‑485. <a href="https://doi.org/10.1093/jhered/esaa029" target="_blank" rel="noopener">https://doi.org/10.1093/jhered/esaa029</a> </p> <p>Luiz, O. J., Allen, A. P., Robertson, D. R., Floeter, S. R., Kulbicki, M., Vigliola, L., Becheler, R., & Madin, J. S. (2013). Adult and larval traits as determinants of geographic range size among tropical reef fishes. Proceedings of the National Academy of Sciences, 110(41), 16498‑16502. <a href="https://doi.org/10.1073/pnas.1304074110" target="_blank" rel="noopener">https://doi.org/10.1073/pnas.1304074110</a> </p> <p>Boettiger, C., Lang, D. T., & Wainwright, P. C. (2012). rfishbase: Exploring, manipulating and visualizing FishBase data from R. Journal of Fish Biology, 81(6), 2030‑2039. <a href="https://doi.org/10.1111/j.1095-8649.2012.03464.x" target="_blank" rel="noopener">https://doi.org/10.1111/j.1095-8649.2012.03464.x</a></p> <p> </p>
Genetic diversity and spread dynamics of SARS-CoV-2 variants present in African populations
<p>The dynamics of coronavirus disease-19 (COVID-19) have been extensively researched in many settings around the world, but little is known about these patterns in Africa. 7540 complete nucleotide genomes from 51 African nations were obtained and analysed from the National Center for Biotechnology Information (NCBI) and Global Initiative on Sharing Influenza Data (GISAID) databases to examine genetic diversity and spread dynamics of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) lineages circulating in Africa. Utilising a variety of clade and lineage nomenclature schemes, we looked at their diversity, and used maximum parsimony inference methods to recreate their evolutionary divergence and history. According to this study, only 465 of the 2610 Pango lineages found to have existed in the world circulated in Africa after three years of the COVID-19 pandemic outbreak, with five different lineages dominating at various points during the outbreak. We identified South Africa, Kenya, and Nigeria as key sources of viral transmissions between Sub-Saharan African nations. These findings provide insight into the viral strains that are circulating in Africa and their evolutionary patterns.</p>
Summary Statistics for Genetic determinants and phenotypic consequences of blood T-cell proportions in 207,000 diverse individuals
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Paternal lineages and genetic diversity in Holstein-Friesian cattle
<p>This database contains paternal lineages and genetic diversity data in Holstein-Friesian cattle (1950-2021).</p>
FIGURE 9 in Diversity of Tropidurus (Squamata: Tropiduridae) in Paraguay-an integrative taxonomic approach based on morphological and molecular genetic evidence
FIGURE 9. Dextral lateral views of specimens of T. catalanensis (A, SMF 100093) indicating inguinal (left arrow) and axillary (right arrow) folds, compared with T. etheridgei (B, SMF 87389), which lacks these folds.
FIGURE 8 in Diversity of Tropidurus (Squamata: Tropiduridae) in Paraguay-an integrative taxonomic approach based on morphological and molecular genetic evidence
FIGURE 8. Differences in the mucronation of dorsal scales of Tropidurus catalanensis (above, SMF 100091) and T. torquatus (below, SMF 100097).
FIGURE 5 in Diversity of Tropidurus (Squamata: Tropiduridae) in Paraguay-an integrative taxonomic approach based on morphological and molecular genetic evidence
FIGURE 5. Maximum Likelihood (left) and Bayesian (right) trees inferred using concatenated mitochondrial (16S and COI) and nuclear (PRLR) DNA genes for samples of Tropidurus from Paraguay. Support values on nodes represent SH-aLRT/ UFBoot (in percentages) for ML (only values above 65 are shown), and posterior probability for BI (only values above 70 are shown). See Appendix 3 and Figure 1 for geographic location of samples. Reference bar represents substitutions per site.
FIGURE 3 in Diversity of Tropidurus (Squamata: Tropiduridae) in Paraguay-an integrative taxonomic approach based on morphological and molecular genetic evidence
FIGURE 3. Location of genetic samples used for the analyses. See Appendix 1 for information on the specimens.
FIGURE 4 in Diversity of Tropidurus (Squamata: Tropiduridae) in Paraguay-an integrative taxonomic approach based on morphological and molecular genetic evidence
FIGURE 4. Phylogenetic trees of Paraguayan samples of Tropidurus inferred from 16S (A), COI (B), 16S+COI (C), and PRLR (D) partial gene sequences. For each analysis we present maximum likelihood (ML, left) and Bayesian inference (BI, right) trees. Red dots indicate support values (basedon on SH-aLRT/UFBoot for ML and posterior probability for BI) equal or superior to 80 for ML and 0.85 for BI. Roots to outgroup Plica plica (AMCC-106953). Reference bar represents substitutions per site.
FIGURE 11 in Diversity of Tropidurus (Squamata: Tropiduridae) in Paraguay-an integrative taxonomic approach based on morphological and molecular genetic evidence
FIGURE 11. Distribution maps of Tropidurus catalanensis (A), T. etheridgei (B), T. spinulosus (C), and T. lagunablanca (D).
FIGURE 13 in Diversity of Tropidurus (Squamata: Tropiduridae) in Paraguay-an integrative taxonomic approach based on morphological and molecular genetic evidence
FIGURE 13. Differences in the color of females of T. lagunablanca (above, SMF 103315) and T. spinulosus (below, SMF 103322). Note the black stripes (the upper one behind the eye, and the lower beyond the ear opening) of T. lagunablanca, absent in T. spinulosus.
FIGURE 12 in Diversity of Tropidurus (Squamata: Tropiduridae) in Paraguay-an integrative taxonomic approach based on morphological and molecular genetic evidence
FIGURE 12. Diagram showing the theory of a ring species, where populations accumulate gradual changes along temporal and spatial scales (represented here by black arrows), originating different species.
FIGURE 7 in Diversity of Tropidurus (Squamata: Tropiduridae) in Paraguay-an integrative taxonomic approach based on morphological and molecular genetic evidence
FIGURE 7. Detailed view of the left hind claws of T. torquatus (A, SMF 100097) showing a paler color than observed in T. catalanensis (B, SMF 100093). This coloration is also present in the fore claws.
FIGURE 6 in Diversity of Tropidurus (Squamata: Tropiduridae) in Paraguay-an integrative taxonomic approach based on morphological and molecular genetic evidence
FIGURE 6. Graphic visualization of genetic distances among specimens of the Tropidurus spinulosus group (red dots). The width of the lines refer to the p-distance between specimens (reference at the upper right corner). At the bottom is presented the mean p-distance between species of the torquatus group (T. catalanensis and T. etheridgei) and the two bigger clades of the spinulosus group.
FIGURE 10 in Diversity of Tropidurus (Squamata: Tropiduridae) in Paraguay-an integrative taxonomic approach based on morphological and molecular genetic evidence
FIGURE 10. Asulcate (left) and sulcate (right) views of the left hemipenes of T. lagunablanca (SMF 103316). White bar = 5 mm.
Genetic diversity of Avena ventricosa populations along an ecogeographical transect in Cyprus is correlated to environmental variables
<p>genetic data</p>
Figure 2 in Genetic diversity of Arabica coffee (Coffea arabica L.) collections
Figure 2. Dendrogram obtained by Ward's minimum variance among Arabica coffee collections based on 32 SSR markers (green colour = Ethiopian Arabica coffee, and red colour = cultivated varieties).
FIGURE 5 in Genetic and phenotypic diversity of Branchinecta sandiegonensis (Crustacea: Anostraca) in the vernal pools of Baja California, México
FIGURE 5. Plots of effective size trends through time generated by Vareff. The x-axis represents time to the past expressed as the product of the generation time (T) by the mutation rate. The y-axis represents the effective size expressed as the log10 of theta, where theta = 4Neu. For abbreviations, see Fig. 1.
FIGURE 1 in Genetic and phenotypic diversity of Branchinecta sandiegonensis (Crustacea: Anostraca) in the vernal pools of Baja California, México
FIGURE 1. Geographic location of the 15 naturally occurring vernal pools sampled in Baja California, México. The main map
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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.