Analysis of microsatellite DNA resolves genetic structure and diversity ofchinook salmon (Oncorhynchus tshawytscha) in California's Central Valley

We use 10 microsatellite DNA markers to assess genetic diversity within and among the four runs (winter, spring, fall, and late fall) of chinook salmo n (Oncorhynchus tshawytscha) in California's Central Valley. Forty-one popu lation samples are studied, comprising naturally spawning and hatchery stoc ks collected from 1991 through 1997. Maximum likelihood methods are used to correct for kinship in juvenile samples and run admixture in adult samples . Through simulation, we determine the relationship between sample size and number of alleles observed at polymorphic microsatellite markers. Most sam ples have random-mating equilibrium proportions of single and multilocus ge notypes. Temporal and spatial genetic heterogeneity is minimal among sample s within subpopulations. An F-ST of 0.082 among subpopulations, however, in dicates substantial divergence among runs. Thus, with the exception of our discovery of two distinct lineages of spring run, genetic structure accords with the diverse chinook life histories seen in the Central Valley and pro vides a means for discrimination of protected populations.