title: Application of SNPs for population genetics of nonmodel organisms: new opportunities and challenges.
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.
authors.affiliation: Molecular Ecology and Fisheries Genetics Laboratory, School of Biological Sciences, University of Bangor, Environment Centre Wales, Gwynedd, UK. s.helyar@bangor.ac.uk
authors.forename: S J
authors.initials: SJ
authors.lastname: Helyar
authors.forename: J
authors.initials: J
authors.lastname: Hemmer-Hansen
authors.forename: D
authors.initials: D
authors.lastname: Bekkevold
authors.forename: M I
authors.initials: MI
authors.lastname: Taylor
authors.forename: R
authors.initials: R
authors.lastname: Ogden
authors.forename: M T
authors.initials: MT
authors.lastname: Limborg
authors.forename: A
authors.initials: A
authors.lastname: Cariani
authors.forename: G E
authors.initials: GE
authors.lastname: Maes
authors.forename: E
authors.initials: E
authors.lastname: Diopere
authors.forename: G R
authors.initials: GR
authors.lastname: Carvalho
authors.forename: E E
authors.initials: EE
authors.lastname: Nielsen
mesh_terms: D000818:Animals; D005819:Genetic Markers; D023281:Genomics / Q000379:methods* / Q000639:trends; D020641:Polymorphism, Single Nucleotide; D017422:Sequence Analysis, DNA; D012984:Software
chemical_list: D005819:Genetic Markers