Application of SNPs for population genetics of nonmodel organisms: new opportunities and challenges

Helyar, S.J., Hemmer-Hansen, J., Bekkevold, D., Taylor, M.I., Ogden, R., Limborg, M.T., Cariani, A., Maes, G.E., Diopere, E., Carvalho, G.R., and Nielsen, E.E. (2011) Application of SNPs for population genetics of nonmodel organisms: new opportunities and challenges. Molecular Ecology Resources, 11 (S1). pp. 123-136.

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Abstract

Recent improvements in the speed, cost and accuracy of next generation sequencing are revolutionizing the discovery of single nucleotide polymorphisms (SNPs). SNPs are increasingly being used as an addition to the molecular ecology toolkit in nonmodel organisms, but their efficient use remains challenging. Here, we discuss common issues when employing SNP markers, including the high numbers of markers typically employed, the effects of ascertainment bias and the inclusion of nonneutral loci in a marker panel. We provide a critique of considerations specifically associated with the application and population genetic analysis of SNPs in nonmodel taxa, focusing specifically on some of the most commonly applied methods.

Item ID: 27628
Item Type: Article (Research - C1)
ISSN: 1755-0998
Keywords: ascertainment bias, nonneutral loci, outlier detection, population genomics, population structure, software
Date Deposited: 07 Jun 2013 09:37
FoR Codes: 06 BIOLOGICAL SCIENCES > 0604 Genetics > 060408 Genomics @ 50%
06 BIOLOGICAL SCIENCES > 0604 Genetics > 060411 Population, Ecological and Evolutionary Genetics @ 50%
SEO Codes: 96 ENVIRONMENT > 9608 Flora, Fauna and Biodiversity > 960808 Marine Flora, Fauna and Biodiversity @ 100%
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