Genomic Analysis of Parallel Evolution of Chinook Salmon (Oncorhynchus tschawytscha) In the Columbia River Basin

A topic of great interest among conservation scientists and evolutionary biologists is whether traits relevant to the long-term fitness of a population will evolve repeatedly in response to similar environmental influences. If the same genetic loci are involved in these processes, the potential to adapt to changing environments is contingent on the genetic diversity at these loci. Chinook salmon (Oncorhynchus tshawytscha) found in the Columbia River drainage in the Pacific Northwest of the USA exhibit a diversity of life-history strategies as a result of local adaptation. There is evidence that some traits, such as run timing, have evolved rapidly in native and introduced populations, and that parallel evolution has sometimes played a role. Here, we used RAD (Restriction site Associated DNA) sequencing, an approach that provides substantial information on genetic diversity, to perform a “genome scan” between population pairs of coastal Chinook that show repeated (parallel) evolution of run timing. We used this approach to detect markers linked to genes under selection and to determine whether similar genome regions respond to selection. This study provides markers linked to genomic regions that have played a major role in Chinook salmon evolution, greatly improves the understanding of mechanisms involved in evolution, and provides the basis for measuring changes in fitness related traits.