Homogenization of Fall‐Run Chinook Salmon Gene Pools in the Central Valley of California, USA

Abstract

We assessed the population genetic structure and temporal stability of genetic diversity from 1999 to 2001 in collections of fall‐run Chinook salmon Oncorhynchus tshawytscha in California's Central Valley. Tests for genotypic differentiation at seven microsatellite loci revealed few significant pairwise comparisons between samples from five hatchery populations and eight naturally spawning populations throughout the Central Valley that were separated by 50–350 km. All collections were genetically homogeneous and failed to cluster with their nearest geographic neighbors. Likewise, evaluation of temporal change in genetic diversity revealed few changes over the 3 years of the study. Our results suggest that fall‐run Chinook salmon throughout the Central Valley comprise a genetically homogeneous population that has lower among‐population genetic diversity than fall‐run Chinook salmon populations examined elsewhere over similar geographic scales. The lack of genetic distinction and the lack of temporal differences in allele frequencies between hatchery and naturally spawning fish indicate that considerable gene flow occurs between fall‐run Chinook salmon throughout the Central Valley. Due to the prevalence of off‐site release of hatchery‐reared juveniles and the history of interbasin hatchery transfers and stocking within the Central Valley, homogenization of Central Valley fall‐run populations is most likely the result of hatchery practices for the past 140 years.