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Dryad Translation missing: fr.blacklight.search.logo
de Greef, Evelien; Brashear, Wesley; Delmore, Kira; Fraser, Kevin 2022-03-01 <p>Genetic variation is a fundamental component of biodiversity, and studying population structure, gene flow, and demographic history can help guide conservation strategies for many species. Like other aerial insectivores, the purple martin (<em>Progne subis</em>) is in decline, and yet their genetic background remains largely unknown. To address this knowledge gap, we assessed population structure in the nominate eastern subspecies (<em>P. s. subis</em>) with relation to natal dispersal and examined historical genetic patterns in all three subspecies (<em>P. s. subis, P. s. arboricola, P. s. hesperia</em>) across their North American breeding range by estimating effective population sizes over time. We used next-generation sequencing strategies for genomic analyses, integrating whole-genome resequencing data with continent-wide band encounter records to examine natal dispersal. We documented population structure across <em>P. s. subis</em>, with the highest differentiation between the northern (Alberta) and more southern colonies and following patterns of isolation-by-distance. Consistent with spatial patterns of genetic differentiation, we also found greater longitudinal than latitudinal natal dispersal distances, signifying potential latitudinal constraints on gene flow. Earlier contractions in effective population sizes in the western <em>P. s. arboricola</em> and <em>P. s. hesperia</em> compared to the eastern <em>P. s. subis</em> subspecies suggest these subspecies originated from two different glacial refugia. Together, these findings support latitudinal distinction in <em>P. s. subis</em>, and elucidate the origin of subspecies differentiation, highlighting the importance to conserve populations across the range to maximize genetic diversity and adaptive potential in the purple martin.</p>
Zenodo Translation missing: fr.blacklight.search.logo
Zenodo
de Greef, Evelien; Müller, Claudio; Thorstensen, Matt; Ferguson, Steven; Watt, Cortney; Marcoux, Marianne; Petersen, Stephen; Garroway, Colin 2024-09-20 This dataset contains resequencing data used in our Arctic whale genomics research exaiming population structure and demographic history in bowhead whales and narwhal, including unfiltered genomic variants and filtered SNPs. Source code for genomic analyses is available at github.com/edegreef/arctic-whales-resequencing. Data uploaded here contain: bowhead_sample_info.csv - metadata for bowhead whale samples bowhead_RWmap_allvariants.vcf.gz - all variant calls in bowhead whales, including indels and SNPs (n = 21) bowhead_RWmap_snps.filtered.autosomes.vcf.gz - bowhead whale SNPs filtered for quality, bi-allelic sites, and autosomes (n = 21) bowhead_RWmap_snps.filtered.autosomes.hwe_maf_LDprunedr08_n20.vcf.gz - bowhead whale SNPs filtered for quality, bi-allelic sites, out of HWE, MAF > 0.05, LD-pruned, removal of close kin (n = 20). narwhal_sample_info.csv - metadata for narwhal samples narwhal_allvariants.vcf.gz - all variant calls in narwhals, including indels and SNPs for bowhead whales (n = 62*) narwhal_snps.filtered.autosomes.vcf.gz - narwhal SNPs filtered for quality, bi-allelic sites, and autosomes (n = 62*) narwhal_snps.filtered.autosomes.hwe_maf_LDprunedr08_n57.vcf.gz - narwhal SNPs filtered for quality, bi-allelic sites, out of HWE, MAF > 0.05, LD-pruned, removal of duplicates, close kin, and samples with high missingness (n = 57) The asterisk* is to note this includes 2 duplicate samples that were removed from the analyses and respective manuscript. https://creativecommons.org/licenses/by/4.0/legalcode
Zenodo Translation missing: fr.blacklight.search.logo
Zenodo
Garroway, Colin J.; de Greef, Evelien; Lefort, Kyle J.; Thorstensen, Matt J.; Foote, Andrew D.; Matthews, Cory J.D.; Higdon, Jeff W.; Kucheravy, Caila E.; Petersen, Stephen D.; Rosing-Asvid, Aqqalu; Ugarte, Fernando; Dietz, Rune; Ferguson, Steven H. 2024-05-15 This dataset contains resequencing data used in our killer whale genomics research exaiming population structure and demographic history, including unfiltered genomic variants and filtered SNPs. Source code for genomic analyses is available at github.com/edegreef/killerwhale-resequencing. Data uploaded here contain: orca_sample_info.csv - metadata for the killer whale samples orca_unfiltered_diploid.vcf.gz - all variant calls, including indels and SNPs (n = 29) orca_snps_q30_biallelic.vcf.gz - SNPs filtered for quality and bi-allelic sites (n = 29) orca_snps_q30_biallelic_HWE0.005_miss0.4.vcf.gz - SNPs filtered for quality, bi-allelic sites, out of HWE, and missingness > 0.4 (n = 29). orca_snps_q30_biallelic_HWE0.005_miss0.4_maf0.05_LDprunedr08_n24.vcf.gz - SNPs further filtered for MAF, LD-pruned, and removal of kin & duplicates (n = 24). https://creativecommons.org/licenses/by/4.0/legalcode

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