Development and testing of diagnostic molecular markers to differentiate among three species of Salvelinus : Arctic char, Dolly Varden, and Bull trout

The western North American Arctic char (AC, Salvelinus alpinus ), Dolly Varden (DV, Salvelinus malma ), and bull trout (BT, Salvelinus confluentus ) are described as a “species complex” due to their close inter-relationships, variable morphology, and tendency to hybridize. Consequently, there has been considerable historical debate about the taxonomic status of the three species, and their physical identification is often problematic. A genotyping-by-sequencing (GBS) library of AC, DV, and BT samples from across the North Pacific and Arctic Canada was exploited to find species-specific single nucleotide polymorphisms (SNPs) to design and test TaqMan™ assays for efficient species identification. A total of 10 AC/DV and 10 DV/BT TaqMan™ assays were developed and tested for efficient, cost-effective, and accurate genotyping of sympatric char species and their hybrids in samples from diverse subspecies, and phylogeographic lineages, and geographic groups. Both in silico and lab genotyping tests using these diagnostic SNPs resulted in highly concordant and accurate identification when compared to previous identifications using microsatellite, single copy nuclear DNA, GBS SNP data and information on geographic distributions. The TaqMan™ assays confirmed the utility of a relatively small number of diagnostic markers to identify these species and F 1 hybrids, and samples that were moderately admixed between species. This work represents the first SNP-based diagnostic markers for these three species that can be used for a wide variety of applications in research and monitoring in the char species complex.