Genetic Stock Identification and Full Parental Genotyping for Management of California’s Chinook Salmon Fisheries

Genetic tools have a long history in fishery management, with the use of genetic " tags " to distinguish hatchery and wild trout described more than 20 years ago (Taggart and Ferguson 1984). More recently, the use of genetic stock identification (GSI) techniques have been used to elucidate ocean migration patterns and to estimate stock proportions in a mixed stock fishery context (e.g. Teel et al. 2004). Such GSI for estimation of stock proportions can occur either post-season or in-season. An in-season GSI system requires a facility with dedicated staff and can typically produce stock proportion estimates from fishery or port samples within approximately one day of delivery (Beacham et al. 2004). Such stock composition estimates can then be used to adaptively focus fishery effort to avoid stocks of conservation concern, or to best target abundant stocks. Because of the current and potential future utility of GSI methods to assist in fishery management, the Pacific Salmon Commission has recently funded a collaborative effort to develop a coastwide genetic database for GSI of Chinook salmon. This $1.1 million effort has resulted in an unprecedented database of 13 microsatellite loci, which have been standardized across most major Pacific salmon genetics labs, typed in over 105 Chinook salmon populations (~120 fish per population) from Alaska to California and is capable of accurately distinguishing most major stocks of Chinook salmon in the northeast Pacific. The Southwest Fisheries Science Center in Santa Cruz is the California representative to this consortium of collaborating salmon genetics labs. The ability of the coastwide genetic database to distinguish Chinook salmon from the different basins and ESUs in California is straightforward and relatively trivial with this database, due to substantial genetic differences between CA Chinook salmon populations (Figure 1). These differences are also reflected in the performance of individual assignment tests, which correctly identify nearly every fish to basin/stock/ESU of origin. This is particularly true with salmon from the Klamath/Trinity basin, which are correctly distinguished from other California ESUs with near-perfect accuracy, because of their substantial genetic divergence from all other California Chinook salmon stocks (Figure 1; Waples et al. 2004). The coastwide GSI database can also identify individual fish to tributary of origin more than 80% of the time. Additional microsatellite genes in use by our lab can increase that accuracy to above 95%. The existence of this database for GSI thus provides a powerful tool for determining and …