Examining Genetic Lineages of Chinook Salmon in the Columbia River Basin

We examined 13 microsatellite loci from 51 collections of Chinook salmon Oncorhynchus tshawytscha throughout the Columbia River basin to determine membership in one of three major genetic lineages, introgression of genetic lineages within specific populations, and genetic structure at the subbasin level. Results confirm those of previous studies that three major lineages of Chinook salmon persist in the drainage, representing two interior life histories (ocean and stream types) and one lineage in the lower Columbia River. Novel observations of introgression were noted in specific collections, including three from the lower Columbia River (Sandy River, Kalama Hatchery, and Lewis Hatchery) and one stream-type population (Klickitat River). Estimates of genetic distance were larger in comparisons between ocean-and stream-type populations (G(ST)' = 0.429) and among stream-type and lower Columbia River populations (G(ST)' = 0.418) than between ocean-type and lower Columbia River populations (G(ST)' = 0.271). Significant geographic structure was observed within lineages at the regional and subbasin scale, particularly for stream-type Chinook salmon, which is consistent with the philopatric nature of the species. The stream-type lineage typically had a lower effective population size than did the other lineages. In particular, natural populations from Big Creek and West Fork Yankee Fork had estimates of less than 50 effective individuals, warranting conservation concern. Overall, the differing life histories and genetic characteristics of the three lineages discussed here make them high priorities for long-term conservation of the species.