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. ISSN 1755-098X

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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 Type:	Article
Uncontrolled Keywords:	ascertainment bias,nonneutral loci,outlier detection,population genomics,population structure,software
Faculty \ School:	Faculty of Science > School of Biological Sciences
UEA Research Groups:	Faculty of Science > Research Groups > Organisms and the Environment Faculty of Science > Research Centres > Centre for Ecology, Evolution and Conservation
Depositing User:	Pure Connector
Date Deposited:	02 Dec 2013 13:24
Last Modified:	28 Mar 2025 05:31
URI:	https://ueaeprints.uea.ac.uk/id/eprint/45077
DOI:	10.1111/j.1755-0998.2010.02943.x

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