Discerning patterns and causes for introgressive hybridization of three major Columbia River basin Chinook salmon lineages within the Klickitat River sub-basin

Three genetically distinct lineages of Chinook salmon, Oncorhynchus tshawytscha, occur in the Columbia River Basin (Lower Columbia, interior ocean-type, and interior stream-type Chinook salmon), each with distinguishing life history traits (e.g. juvenile migration and adult run timing).  Most Chinook salmon in the Columbia River Basin assign with high probability to one of the three lineages; however, spring-run Chinook salmon in the Klickitat River have been difficult to classify due to their intermediate relationship to these lineages both geographically and genetically.  We used a baseline of 2233 fish (21 collections) genotyped for 91 SNP loci to accomplish two goals: 1) to clarify which of the three lineages share greatest genetic similarity with Klickitat spring-run Chinook, and 2) to determine whether the intermediate genetic status of the Klickitat spring-run is a product of recent (~5 generations) or historical (> 200 generations) admixture, isolation-by-distance gene-flow, or natural selection.  We conclude that spring run Chinook salmon in the Klickitat River likely experienced recent introgression because our collections were composed of a large proportion of stream-type backcrosses and the alternative explanations were found to lack support.  We discuss both the potential natural and human-mediated causes for the introgression, and associated management implications.