DNA-Level variation of sockeye salmon in Southeast Alaska and the Nass and Skeena Rivers, British Columbia, with applications to stock identification

The variation at 14 microsatellite loci and 1 major histocompatibility complex locus was surveyed in 12,000 sockeye salmon Oncorhynchus nerka from 35 populations in the Skeena and Nass River drainages in British Columbia and 20 populations from Southeast Alaska. Genetic differentiation among populations was observed, with an overall F-ST of the microsatellite loci of 0.104. Evaluation of the utility of the microsatellite loci for stock identification applications indicated that the accuracy and precision of the estimated stock compositions generally increased as the number of observed alleles at the loci increased. Analysis of simulated mixtures of sockeye salmon from the Nass River, Skeena River, and Southeast Alaska indicated that DNA variation provides a practical way to estimate stock composition, yielding population and regional estimates within 1-3% of the actual values. The validity of the results from the simulated mixtures was evaluated with an analysis of a sample of known origin. Estimated stock compositions on a regional basis (derived from application of a 203-population baseline) were within 1% of the actual contributions, and for the Southeast Alaska component the individual population estimates were generally within 0.5% of the actual contributions. Analysis of fishery samples from a fishery near Tree Point in Southeast Alaska indicated that the major contributors to the fishery in 2001 were sockeye salmon of Nass River, Skeena River, and Southeast Alaska origin, with some components from the Stikine River. Analysis of fishery samples from a fishery near the entrance to Portland Inlet in northern British Columbia indicated that sockeye salmon of Nass River origin dominated the fishery in 2002. Thus, DNA variation provides an effective method for sockeye salmon stock identification.