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

S. J. Helyar; J. Hemmer-Hansen; D. Bekkevold; M. I. Taylor; R. Ogden; M. T. Limborg; A. Cariani; G. E. Maes; E. Diopere; G. R. Carvalho; E. E. Nielsen

doi:10.1111/j.1755-0998.2010.02943.x

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

S. J. Helyar, J. Hemmer-Hansen, D. Bekkevold, M. I. Taylor, R. Ogden, M. T. Limborg, A. Cariani, G. E. Maes, E. Diopere, G. R. Carvalho, E. E. Nielsen

Research output: Contribution to journal › Article › peer-review

358 Citations (Scopus)

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.

Original language	English
Pages (from-to)	123-136
Number of pages	14
Journal	Molecular Ecology Resources
Volume	11
Issue number	S1
Early online date	10 Jan 2011
DOIs	https://doi.org/10.1111/j.1755-0998.2010.02943.x
Publication status	Published - 1 Mar 2011

Keywords

ascertainment bias
nonneutral loci
outlier detection
population genomics
population structure
software

Access to Document

10.1111/j.1755-0998.2010.02943.x

Cite this

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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.",

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AU - Helyar, S. J.

AU - Hemmer-Hansen, J.

AU - Bekkevold, D.

AU - Taylor, M. I.

AU - Ogden, R.

AU - Limborg, M. T.

AU - Cariani, A.

AU - Maes, G. E.

AU - Diopere, E.

AU - Carvalho, G. R.

AU - Nielsen, E. E.

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KW - ascertainment bias

KW - nonneutral loci

KW - outlier detection

KW - population genomics

KW - population structure

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DO - 10.1111/j.1755-0998.2010.02943.x

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