Cutthroat Trout Subspecies Delineation Using Diagnostic Single Nucleotide Polymorphisms

Advances in sequencing technologies have made it relatively cheap and easy to generate genomic data in comparison to traditional sequencing methods, even in non-model organisms for which genomic resources have not been as readily available. Cutthroat trout is a geographically widespread non-model species that exhibits pronounced phenotypic and genetic variation. This widespread variation has long been recognized, and resulted in an often changing taxonomic history. There are several currently recognized subspecies, often corresponding to western North American watershed boundaries, and other subspecies which have been subject to much debate. We used genomic and bioinformatic techniques to develop a panel of 125 single nucleotide polymorphisms (SNPs) for use in characterizing the genetic structure of cutthroat trout subspecies in western North America. These SNP loci are able to differentiate among nine subspecies of cutthroat trout.