Population Genetic Analysis of Chehalis River Basin Chinook Salmon (Oncorhynchus tshawytscha)

Understanding the population structure of wild salmonids in the Chehalis River is an important part of the Chehalis Flood and Aquatic Species Project and contributes to the Chehalis Basin Flood Hazard Project and Aquatic Species Enhancement Plan (The Aquatic Species Enhancement Plan Technical Committee 2014). Habitat conditions for salmon and steelhead in the Chehalis River are projected to change substantially over the next decade. The relative influence of these actions on salmon and steelhead will partially depend on the population structure within the watershed. Here we examined the population structure of wild Chinook salmon (Oncorhynchus tshawytscha) in the Chehalis river basin. Our objectives were to 1) identify population structure within the Chehalis River and its tributaries, 2) investigate if run timing (spring and fall runs) influenced the population structure within the Chehalis basin, and 3) determine the population structure of the Chehalis basin in relation to baseline populations from Washington state and British Columbia.

Genetic data indicate, that within the Chehalis basin, the population structure consists of two general clusters, 1) a downstream group (Wynoochee River, Wishkah River, Satsop River, Black River and the Chehalis mainstem) and 2) an upstream group (South Fork and Upper Chehalis River, Newaukum River and Skookumchuck River). This finding is supported by clustering analysis and low degrees of differentiation between downstream and upstream collections. This pattern of slight differentiation between downstream and upstream collections, appears to be largely driven by isolation by distance, which is a common driver of population structure in salmonid populations.

Generally, Chinook salmon run types display limited genetic differentiation, as population structure is typically driven by geographical proximity. This pattern holds true in the Chehalis River. Clustering and tests of genetic differentiation revealed that fall and spring runs were not genetically distinct. Similar patterns were found in other Washington Rivers with multiple Chinook salmon run types. The Hoh River showed little distinction between run types, displaying a similar structure to the Chehalis basin. Skagit River summer and fall Chinook salmon were not differentiated, but distinct population structure existed between spring and fall and spring and summer Chinook salmon. The Satsop River, Chehalis River mainstem, and Black River spring runs clustered more closely with the lower river fall runs than they did with upstream spring runs, indicating they likely belong to the same population. This may indicate that criteria used to label fish in the field are inaccurate, or that in the Chehalis, spring run Chinook salmon do not all migrate upriver.

Analysis of the population structure of the Chehalis basin and Washington state Chinook salmon baseline populations revealed three major branches 1: Puget Sound and British Columbia, 2) Lower Columbia, and 3) Washington Coast. Within the Washington Coast group, the Chehalis basin clustered most closely with Willapa Bay Rivers (North River, Fall River, Naselle River, Nemah River and Forks Creek). The results of Chehalis basin Chinook salmon population structure are largely in concordance with previous research. Other populations of salmonids, including Chinook salmon, tend to have population structure that is largely driven by geography (e.g. populations tend to be closely related to their nearest neighbors).