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Background  By targeting SNPs contained in both coding and non-coding areas of the genome, we are able to identify genetic differences and characterize genome-wide patterns of variation among individuals, populations and species. We investigated the utility of 454 sequencing and MassARRAY genotyping for population genetics in natural populations of the teleost,  Fundulus heteroclitus  as well as closely related  Fundulus  species ( F. grandis ,  F. majalis  and  F. similis ).    Results  We used 454 pyrosequencing and MassARRAY genotyping technology to identify and type 458 genome-wide SNPs and determine genetic differentiation within and between populations and species of  Fundulus . Specifically, pyrosequencing identified 96 putative SNPs across coding and non-coding regions of the  F. heteroclitus  genome: 88.8% were verified as true SNPs with MassARRAY. Additionally, putative SNPs identified in  F. heteroclitus  EST sequences were verified in most (86.5%)  F. heteroclitus  individuals; fewer were genotyped in  F. grandis  (74.4%),  F. majalis  (72.9%), and  F. similis  (60.7%) individuals. SNPs were polymorphic and showed latitudinal clinal variation separating northern and southern populations and established isolation by distance in  F. heteroclitus  populations. In  F. grandis , SNPs were less polymorphic but still established isolation by distance. Markers differentiated species and populations.    Conclusions  In total, these approaches were used to quickly determine differences within the  Fundulus  genome and provide markers for population genetic studies.

SNP identification, verification, and utility for population genetics in a non-model genus