De novo SNP discovery in the Scandinavian brown bear (Ursus arctos).

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. Her...

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Autores principales:	Anita J Norman, Nathaniel R Street, Göran Spong
Formato:	article
Lenguaje:	EN
Publicado:	Public Library of Science (PLoS) 2013
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/04f0855a75ea45ad8993ce50b927213d
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id	oai:doaj.org-article:04f0855a75ea45ad8993ce50b927213d
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spelling	oai:doaj.org-article:04f0855a75ea45ad8993ce50b927213d2021-11-18T08:46:06ZDe novo SNP discovery in the Scandinavian brown bear (Ursus arctos).1932-620310.1371/journal.pone.0081012https://doaj.org/article/04f0855a75ea45ad8993ce50b927213d2013-01-01T00:00:00Zhttps://www.ncbi.nlm.nih.gov/pmc/articles/pmid/24260529/?tool=EBIhttps://doaj.org/toc/1932-6203Information 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.Anita J NormanNathaniel R StreetGöran SpongPublic Library of Science (PLoS)articleMedicineRScienceQENPLoS ONE, Vol 8, Iss 11, p e81012 (2013)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Anita J Norman Nathaniel R Street Göran Spong De novo SNP discovery in the Scandinavian brown bear (Ursus arctos).
description	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.
format	article
author	Anita J Norman Nathaniel R Street Göran Spong
author_facet	Anita J Norman Nathaniel R Street Göran Spong
author_sort	Anita J Norman
title	De novo SNP discovery in the Scandinavian brown bear (Ursus arctos).
title_short	De novo SNP discovery in the Scandinavian brown bear (Ursus arctos).
title_full	De novo SNP discovery in the Scandinavian brown bear (Ursus arctos).
title_fullStr	De novo SNP discovery in the Scandinavian brown bear (Ursus arctos).
title_full_unstemmed	De novo SNP discovery in the Scandinavian brown bear (Ursus arctos).
title_sort	de novo snp discovery in the scandinavian brown bear (ursus arctos).
publisher	Public Library of Science (PLoS)
publishDate	2013
url	https://doaj.org/article/04f0855a75ea45ad8993ce50b927213d
work_keys_str_mv	AT anitajnorman denovosnpdiscoveryinthescandinavianbrownbearursusarctos AT nathanielrstreet denovosnpdiscoveryinthescandinavianbrownbearursusarctos AT goranspong denovosnpdiscoveryinthescandinavianbrownbearursusarctos
_version_	1718421303924359168

De novo SNP discovery in the Scandinavian brown bear (Ursus arctos).

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