Seven Millennia of Change: Comparison of Ancient and Modern Columbia River Chinook Salmon Using Mitochondrial DNA

Chinook salmon (Oncorhynchus tshawytscha) were historically abundant in the Columbia River Basin. Following the arrival of Europeans, salmon experienced declines. Of all the factors affecting salmon, hydropower development had the greatest impact on their distribution. The Grand Coulee Dam, completed in 1942, ended salmon runs into the upper-Columbia. Grand Coulee Fish Maintenance Project (GCFMP) aimed to redirect spawning efforts of fish that would naturally pass Grand Coulee Dam. Implemented in 1939, adult fish were captured and released in tributaries downstream of the dam or propagated as hatchery broodstock. We evaluated the genetic implications resulting from changes to the upper Columbia River Basin with a focus on the Grand Coulee Dam and the GCFMP. Using a 563 bp sequence of the mitochondrial displacement loop we compared ancient Chinook destined for upper-Columbia River spawning (~7627 to ~150 YBP) to contemporary stocks in the tributaries where salmon were transplanted during the GCFMP. Contemporary samples have significantly lower genetic diversity than their ancient counterpart, indicated by both a direct loss of haplotypes and overall reductions in genetic diversity. This work provides the first direct quantification of the genetic diversity present in Columbia River Chinook prior to European contact.