Genetic analysis of interior Pacific Northwest Oncorhynchus mykiss reveals apparent ancient hybridization with westslope cutthroat trout

Seventeen populations of Oncorhynchus mykiss were analyzed for mitochondrial haplotype diversity through either polymerase chain reaction-restriction fragment length polymorphism analysis or mitochondrial DNA sequencing. Six new mitochondrial haplotypes were observed among these populations, five in steelhead and one in Harney Basin rainbow trout. Although no distinct patterns were observed between steelhead and rainbow trout with mitochondrial DNA sequencing, Harney Basin rainbow trout populations from southeastern Oregon exhibited a high frequency of a unique new haplotype designated MYS22. Fourteen of 17 individuals within the Harney Basin rainbow trout populations possessed this haplotype. Additionally, the mitochondrial DNA haplotypes of six westslope cutthroat trout O. clarki lewisi were observed among 90 steelhead from the Tucannon River, Washington, a river in which no native or introduced cutthroat trout have been documented. Analysis of other introduced hatchery and wild stocks of steelhead and rainbow trout from throughout the interior Pacific Northwest revealed only rainbow trout and steelhead mitochondrial haplotypes. Analysis of 90 wild Tucannon River steelhead using 16 nuclear DNA markers detected only one individual with a single nuclear allele consistent with westslope cutthroat trout, although the marker may be a rare rainbow trout or steelhead nuclear allele. This suggests that a hybridization event of ancient origin probably occurred within the Tucannon River basin. This hybridization event may have occurred between Tucannon River steelhead and a now extinct native population of westslope cutthroat trout that probably arrived as a result of late Wisconsin glacial outburst floods (Missoula Floods) occurring 19,000-10,000 years before the present.