1. Application of SNPs for population genetics of nonmodel organisms: new opportunities and challenges
- Author
-
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., Nielsen, E.E., 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, and E. E. NIELSEN
- Subjects
POPULATION STRUCTURE ,Population genetics ,Bias (Statistics) ,OUTLIER DETECTION ,SOFTWARE ,Population structure ,ASCERTAINMENT BIAS ,Software ,POPULATION GENOMICS - Abstract
Recent improvements in the speed, cost and accuracy of next generation sequencing are revolutionising the discovery of single nucleotide polymorphisms (SNPs). SNPs are increasingly being used as an addition to the molecular ecology toolkit in non-model 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 non-neutral loci in a marker panel. We provide a critique of considerations specifically associated with the application and population genetic analysis of SNPs in non-model taxa, focusing specifically on some of the most commonly applied methods
- Published
- 2011