Reintroduction of Spring-Run Chinook Salmon to the San Joaquin River; Genetic Evaluation of Donor Stocks and Breeding Strategies

The San Joaquin River is the among the largest in California and drains the southern Sierra Nevada mountain range through the Golden Gate, after meeting the Sacramento River in the largest estuary on the west coast of North America. Since Friant Dam was built on the Upper San Joaquin River in 1942, nearly all of the river’s flow has been diverted for agriculture, leaving a ~70 mile stretch dry for most of every year. In 2006, multiple stakeholders, including federal and state agencies, water districts and conservation groups, signed a Settlement Agreement that prescribes sufficient dam releases to maintain connectivity to the confluence with the Merced River and the reintroduction of Chinook salmon by 2012. As a result, a large effort is underway to plan for the reintroduction of ESA listed Central Valley Spring-run Chinook salmon to a river where they were extirpated decades ago. Program plans include use of a new conservation hatchery facility and the parallel reintroduction of multiple stocks to evaluate relative fitness and provide sufficient genetic diversity. Questions remain about which stocks will be used and whether efforts will be made to maintain them separately or not.

 Although likely once the most abundant salmon stock in the Central Valley of California, spring-run salmon are now primarily relegated to two relictual populations in the northern Sacramento River basin, Butte Creek and Mill/Deer Creeks, with a third population in the Feather River, where it is heavily hatchery supported and has experienced introgression with Fall-run salmon. There are also a number of other Central Valley tributaries with small numbers of spring-run phenotype fish.

We used genetic analyses with a large number of single nucleotide polymorphism loci to evaluate genetic diversity in the three primary Spring-run Chinook salmon stocks as possible sources of fish for reintroduction. In addition, we evaluated the origin and stock affiliation of most of the small populations of spring-running fish in other tributaries, both to evaluate them as potential sources and also to better understand the process of recolonization. Two of these populations, which have increased substantially in size over the last decade, Battle and Clear Creeks, were found to have been recolonized by fish from two of the major Spring-run stocks. Ongoing evaluation of the patterns of mate choice and reproduction in these populations will inform the San Joaquin River Spring-run salmon reintroduction.