Genetic analyses provide insight into the early ocean stock distribution and survival of juvenile coho salmon off the coasts of Washington and Oregon

Estimating the stock proportions of mixed-stock fishery samples by means of genetic stock identification has played an important role in the management of salmon fisheries. In addition, stock identification of individual fish has applications for population studies, forensic cases, and management issues. We examined 11 microsatellite DNA loci in 84 populations of coho salmon Oncorhynchus kisutch sampled at 78 locations from southern British Columbia to northern California to construct a database of microsatellite allele frequencies. We then evaluated the applicability of the database for estimating stock proportions in a mixed fishery and assigning individuals to their regions of origin. The loci were highly polymorphic: observed heterozygosity ranged from 0.754 to 0.943. Using genetic distance calculations, we identified six major geographic regions and 15 smaller subregions into which the populations grouped. Computer simulations and a sample of 143 coho salmon with known origins showed that the database was sufficient to make accurate stock proportion estimates to the 15 subregions. For the sample of fish with known origins, individual assignments to region of origin were 82.5% accurate for all samples and 97.8% accurate for those where P was greater than 0.95. We used the database to estimate stock proportions and densities of 2,344 coho salmon sampled over eight summers in a juvenile marine ecology study conducted off the coasts of Washington and Oregon. Columbia River juveniles were caught at higher densities than coastal fish throughout the summer. Fish from Columbia River and coastal sources were captured both north and south of their points of sea entry in early summer and at higher densities than in late summer. September catch of Columbia River juveniles was correlated with adult abundance in the following year, indicating that year-class strength for this stock is largely set during the first summer in the ocean.