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De Novo SNP Discovery in the Scandinavian Brown Bear (Ursus arctos)
Sveriges lantbruksuniversitet.
Umeå University, Faculty of Science and Technology, Department of Plant Physiology. Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC).ORCID iD: 0000-0001-6031-005X
Sveriges lantbruksuniversitet.
2013 (English)In: PLoS ONE, ISSN 1932-6203, Vol. 8, no 11, e81012- p.Article in journal (Refereed) Published
Abstract [en]

Information about relatedness between individuals in wild populations is advantageous when studying evolutionary, behavioural and ecological processes. Genomic data can be used to determine relatedness between individuals either when no prior knowledge exists or to confirm suspected relatedness. Here we present a set of 96 SNPs suitable for inferring relatedness for brown bears (Ursus arctos) within Scandinavia. We sequenced reduced representation libraries from nine individuals throughout the geographic range. With consensus reads containing putative SNPs, we applied strict filtering criteria with the aim of finding only high-quality, highly-informative SNPs. We tested 150 putative SNPs of which 96% were validated on a panel of 68 individuals. Ninety-six of the validated SNPs with the highest minor allele frequency were selected. The final SNP panel includes four mitochondrial markers, two monomorphic Y-chromosome sex-determination markers, three X-chromosome SNPs and 87 autosomal SNPs. From our validation sample panel, we identified two previously known parent-offspring dyads with reasonable accuracy. This panel of SNPs is a promising tool for inferring relatedness in the brown bear population in Scandinavia.

Place, publisher, year, edition, pages
Public Library of Science , 2013. Vol. 8, no 11, e81012- p.
National Category
Zoology Genetics Evolutionary Biology
URN: urn:nbn:se:umu:diva-85304DOI: 10.1371/journal.pone.0081012ISI: 000327308500190OAI: diva2:693951
Available from: 2014-02-05 Created: 2014-01-31 Last updated: 2015-04-29Bibliographically approved

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Street, Nathaniel Robert
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Department of Plant PhysiologyUmeå Plant Science Centre (UPSC)
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