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

被引：347

作者：

Helyar, S. J. ^{[1
]}

Hemmer-Hansen, J. ^{[2
]}

Bekkevold, D. ^{[2
]}

Taylor, M. I. ^{[1
]}

Ogden, R. ^{[3
]}

Limborg, M. T. ^{[2
]}

Cariani, A. ^{[4
]}

Maes, G. E. ^{[5
]}

Diopere, E. ^{[5
]}

Carvalho, G. R. ^{[1
]}

Nielsen, E. E. ^{[2
]}

机构：

[1] Univ Bangor, Environm Ctr Wales, MEFGL, Sch Biol Sci, Bangor LL57 2UW, Gwynedd, Wales

[2] Tech Univ Denmark, Natl Inst Aquat Resources, DK-8600 Silkeborg, Denmark

[3] Royal Zool Soc Scotland, TRACE Wildlife Forens Network, Edinburgh EH12 6TS, Midlothian, Scotland

[4] Univ Bologna, Interdept Ctr Res Environm Sci, Mol Genet Environm & Fishery Resources Lab GenMAP, I-48100 Bologna, Italy

[5] Catholic Univ Louvain, Lab Anim Div & Systemat, B-3000 Louvain, Belgium

来源：

MOLECULAR ECOLOGY RESOURCES | 2011年 / 11卷

关键词：

ascertainment bias; nonneutral loci; outlier detection; population genomics; population structure; software; SINGLE-NUCLEOTIDE POLYMORPHISMS; ASSESSING STATISTICAL POWER; MULTILOCUS GENOTYPE DATA; COMPUTER-PROGRAM; STRUCTURED POPULATIONS; ENVIRONMENTAL-FACTORS; FREQUENCY-SPECTRUM; POSITIVE SELECTION; ASCERTAINMENT BIAS; CANDIDATE LOCI;

D O I：

10.1111/j.1755-0998.2010.02943.x

中图分类号：

Q5 [生物化学]; Q7 [分子生物学];

学科分类号：

071010 ; 081704 ;

摘要：

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.

引用

页码：123 / 136

页数：14

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