Conservation genetics of Chinook salmon in the Central Valley, CA and implications for the reintroduction of a currently extinct population

Background/Question/Methods

Chinook salmon (Oncorhynchus tshawytscha)were extirpated from the upper San Joaquin River, CA in the 1950s. As a result of a legal settlement, a multi-agency group is developing a plan to reintroduce spring-run Chinook salmon to the newly restored sections of the river, potentially using both direct translocations and individuals reared in a conservation hatchery. Much needs to be understood about the current state of the extant spring-run populations in the Central Valley, CA and their relationships with other Chinook salmon runs in the area to effectively conduct this reintroduction. We are using genetic tools to address pressing questions about these populations to inform the selection of source populations and management of the conservation hatchery. We used a panel of 96 single nucleotide polymorphisms (SNPs) to investigate the population structure of Chinook salmon in the Central Valley, evaluate the relationships between hatchery and wild populations, and estimate genetic diversity.

Results/Conclusions

We found there is a greater level of population differentiation within spring-run Chinook populations compared to fall-run Chinook populations. Interestingly, our results show the hatchery spring-run population clusters separately from the fall-run hatchery population in the same river, whereas past analyses have shown them to cluster together. SNP based estimates of diversity are relatively high, despite the small census sizes of many of the populations. We use this information to discuss different potential reintroduction strategies and implications for the San Joaquin River Chinook salmon reintroduction effort.