Genetic Composition of Pacific Trout Species in Relation to Landscape Features in the Upper Snoqualmie River Watershed, WA

The upper Snoqualmie River watershed (USRW) is located above an 82 m vertical barrier to anadromous fishes. Main stem rivers and tributaries in the USRW contain wild populations of coastal and westslope cutthroat trout, rainbow trout, and hybrids among these species. Releases of hatchery-raised strains of Pacific trout were widespread throughout the watershed between 1930’s and 1990’s and continue in alpine lakes that drain into tributaries and main stem rivers. Trout identified in the field as rainbow, coastal cutthroat, westslope cutthroat, and hybrids were sampled in main stem and tributary habitats in the USRW and analyzed to describe the various species and lineages inhabiting the watershed and the magnitude of introgression by hatchery strains of Pacific trout. Fish were genotyped at seven microsatellite DNA loci and 96 single nucleotide polymorphism loci (SNPs) and results differentiated between putative native and hatchery strains of coastal and westslope cutthroat, rainbow and hybrids between all of these species. Hybrids were composed of first generation types (F1) and descendants of hybrids (beyond F1 or introgressed). Many samples contained a mixture of native and hatchery strains indicating that hatchery-raised trout have introgressed into the populations and even dominate the genetic structure in discrete segments of the watershed. Dominant lineages (native or hatchery ancestry) were generally homogenous within each fork but varied between the forks, indicating that some native subpopulations were probably more vulnerable to displacement by hatchery-raised species or the area was unoccupied prior to hatchery introductions. Current spatial distribution of the genetic composition of Pacific trout revealed possible causal mechanisms of the distribution of salmonids during and after the last glacial recession (c. 10,000 to 15,000 years before present).