Canadian polar bear population structure using genome-wide markers
Predicting the consequences of environmental changes, including human-mediated climate change on species, requires that we quantify range-wide patterns of genetic diversity and identify the ecological, environmental, and historical factors that have contributed to it. Here, we generate baseline data...
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ftzenodo:oai:zenodo.org:4569046 2023-05-15T17:46:51+02:00 Canadian polar bear population structure using genome-wide markers Jensen, Evelyn Tschritter, Christina Van Coeverden de Groot, Peter Hayward, Kristen Branigan, Marsha Dyck, Markus Clemente-Carvalho, Rute Lougheed, Stephen 2021-02-28 https://zenodo.org/record/4569046 https://doi.org/10.5061/dryad.gb5mkkwkw unknown https://zenodo.org/communities/dryad https://zenodo.org/record/4569046 https://doi.org/10.5061/dryad.gb5mkkwkw oai:zenodo.org:4569046 info:eu-repo/semantics/openAccess https://creativecommons.org/publicdomain/zero/1.0/legalcode Ursus maritimus ddRAD Sequencing single nucleotide polymorphism info:eu-repo/semantics/other dataset 2021 ftzenodo https://doi.org/10.5061/dryad.gb5mkkwkw 2023-03-11T00:25:01Z Predicting the consequences of environmental changes, including human-mediated climate change on species, requires that we quantify range-wide patterns of genetic diversity and identify the ecological, environmental, and historical factors that have contributed to it. Here, we generate baseline data on polar bear population structure across most Canadian subpopulations (n=358) using 13,488 genome-wide single nucleotide polymorphisms (SNPs) identified with double digest restriction site-associated DNA sequencing (ddRAD). Our ddRAD dataset showed three genetic clusters in the sampled Canadian range, congruent with previous studies based on microsatellites across the same regions; however due to a lack of sampling in Norwegian Bay, we were unable to confirm the existence of a unique cluster in that subpopulation. These data on the genetic structure of polar bears using SNPs provide a detailed baseline against which future shifts in population structure can be assessed, and opportunities to develop new non-invasive tools for monitoring polar bears across their range. ddRAD libraries were constructed following the Peterson et al. (2012) protocol, using MluCI and PstI restriction enzymes and size selecting the DNA insert to 275-365 bp using a BluePippin Prep. Libraries were sequenced using paired-end 125 bp Illumina HiSeq 2500. PCR duplicates were removed and reads were assebled to the polar bear reference genome UrsMar_1.0 using BWA mem. Variant detection and genotype calling were done using samtools mpileup and bcftools call. Loci were filtered using VCFtools. Dataset Norwegian Bay Ursus maritimus Zenodo Norwegian Bay ENVELOPE(-91.535,-91.535,77.584,77.584) |
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Open Polar |
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unknown |
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Ursus maritimus ddRAD Sequencing single nucleotide polymorphism |
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Ursus maritimus ddRAD Sequencing single nucleotide polymorphism Jensen, Evelyn Tschritter, Christina Van Coeverden de Groot, Peter Hayward, Kristen Branigan, Marsha Dyck, Markus Clemente-Carvalho, Rute Lougheed, Stephen Canadian polar bear population structure using genome-wide markers |
topic_facet |
Ursus maritimus ddRAD Sequencing single nucleotide polymorphism |
description |
Predicting the consequences of environmental changes, including human-mediated climate change on species, requires that we quantify range-wide patterns of genetic diversity and identify the ecological, environmental, and historical factors that have contributed to it. Here, we generate baseline data on polar bear population structure across most Canadian subpopulations (n=358) using 13,488 genome-wide single nucleotide polymorphisms (SNPs) identified with double digest restriction site-associated DNA sequencing (ddRAD). Our ddRAD dataset showed three genetic clusters in the sampled Canadian range, congruent with previous studies based on microsatellites across the same regions; however due to a lack of sampling in Norwegian Bay, we were unable to confirm the existence of a unique cluster in that subpopulation. These data on the genetic structure of polar bears using SNPs provide a detailed baseline against which future shifts in population structure can be assessed, and opportunities to develop new non-invasive tools for monitoring polar bears across their range. ddRAD libraries were constructed following the Peterson et al. (2012) protocol, using MluCI and PstI restriction enzymes and size selecting the DNA insert to 275-365 bp using a BluePippin Prep. Libraries were sequenced using paired-end 125 bp Illumina HiSeq 2500. PCR duplicates were removed and reads were assebled to the polar bear reference genome UrsMar_1.0 using BWA mem. Variant detection and genotype calling were done using samtools mpileup and bcftools call. Loci were filtered using VCFtools. |
format |
Dataset |
author |
Jensen, Evelyn Tschritter, Christina Van Coeverden de Groot, Peter Hayward, Kristen Branigan, Marsha Dyck, Markus Clemente-Carvalho, Rute Lougheed, Stephen |
author_facet |
Jensen, Evelyn Tschritter, Christina Van Coeverden de Groot, Peter Hayward, Kristen Branigan, Marsha Dyck, Markus Clemente-Carvalho, Rute Lougheed, Stephen |
author_sort |
Jensen, Evelyn |
title |
Canadian polar bear population structure using genome-wide markers |
title_short |
Canadian polar bear population structure using genome-wide markers |
title_full |
Canadian polar bear population structure using genome-wide markers |
title_fullStr |
Canadian polar bear population structure using genome-wide markers |
title_full_unstemmed |
Canadian polar bear population structure using genome-wide markers |
title_sort |
canadian polar bear population structure using genome-wide markers |
publishDate |
2021 |
url |
https://zenodo.org/record/4569046 https://doi.org/10.5061/dryad.gb5mkkwkw |
long_lat |
ENVELOPE(-91.535,-91.535,77.584,77.584) |
geographic |
Norwegian Bay |
geographic_facet |
Norwegian Bay |
genre |
Norwegian Bay Ursus maritimus |
genre_facet |
Norwegian Bay Ursus maritimus |
op_relation |
https://zenodo.org/communities/dryad https://zenodo.org/record/4569046 https://doi.org/10.5061/dryad.gb5mkkwkw oai:zenodo.org:4569046 |
op_rights |
info:eu-repo/semantics/openAccess https://creativecommons.org/publicdomain/zero/1.0/legalcode |
op_doi |
https://doi.org/10.5061/dryad.gb5mkkwkw |
_version_ |
1766150731303223296 |