Genetic and ecological divergence defines population structure of sockeye salmon populations returning to Bristol Bay, Alaska, and provides a tool for admixture analysis

We examined the population genetic diversity and structure of sockeye salmon Oncorhynchus nerka spawning in tributaries of Bristol Bay, Alaska, a region that supports the largest commercial fisheries for sockeye salmon in the world. Genetic variation among the sockeye salmon populations, as revealed by microsatellite data, was shallower than that found in other areas of comparable size around the Pacific Rim. This finding was driven by similarity among populations rearing in the four largest lake systems located on the southeastern side of the bay (upper and lower Ugashik, Becharof, Naknek-Grosvenor-Coville, and Iliamna lakes). Sockeye salmon in lakes located above known obstacles to migration on the southeastern side and in tributaries on the northwestern side showed variation and structure that were more typical of the species. Management of these important fisheries assumes knowledge of the composition of stock mixtures captured in each fishery. We investigated the potential of microsatellite data to provide stock composition estimates. We examined 58 collections and identified eight genetically discrete reporting groups. These reporting groups give fishery managers the opportunity to quantify stock components within fishing districts and thereby improve management precision.