An Update of Genetic Stock Identification of Chinook Salmon in the Pacific Northwest: Test Fisheries in California

Abstract

Analyzing the stock composition of mixed-stock fisheries using genetic stock identification (GSI) procedures was developed for chinook salmon in the early 1980s when an incipient baseline was focused in the Columbia River basin. The current coastwide baseline of allozyme (protein) genetic loci includes approximately 75% of the major contributing populations from California to western Alaska for over 30 polymorphic loci. We review the 2-decade history of GSI studies of chinook salmon in fishery applications in the Pacific Northwest. By summarizing GSI results for four test fisheries in California, we demonstrate the use of a regional segment of the current baseline to monitor critically depleted stocks. Average FST is 0.099, with 12 loci FST > 0.05, in a 28 locus/53 population dataset from southern Oregon to southern California. Seven stock groups are recognized based on a multilocus pattern of differentiation that coincides with watersheds and coastal affiliations. Simulated mixture analyses indicate that stock groups are well resolved: percent correct assignment is 83% for Central Valley spring-run, but >92% for all other groups. Simulated mixture analyses also indicated that it is difficult to distinguish between mixtures with low levels (<1%) of Central Valley winter- or spring-run stocks given the present dataset. GSI estimates for four test fisheries indicate that Central Valley fall- and late fall-run chinook salmon comprised the majority of each mixture (89 to 95%). Critical or endangered stock groups were detected in test fisheries in the 1997 Point Conception fishery (3% Sacramento River winter-run) and in the 1999 Bodega Bay fishery (2.8% Upper Klamath-Trinity rivers). Preliminary regional baselines for intron and microsatellite loci show promise for added stock discrimination among chinook salmon populations. GSI projects are increasingly involving multiple agencies and using multicharacter procedures. Continued GSI