Management in a Complex Landscape: Sockeye Salmon in Southeast Alaska

Southeast Alaska is a complex landscape, consisting of both short coastal streams linked to lakes and large rivers that traverse the coastal mountain range from Canada.  Sockeye salmon, Oncorhynchus nerka, are found throughout this landscape, utilizing a variety of life history patterns in numerous small and large spawning aggregations.  Several large transmountain rivers contain important runs of sockeye salmon managed cooperatively by the United States and Canada under the Pacific Salmon Treaty to achieve conservation, allocation, and enhancement objectives.  Information on the stock composition of fishery harvests in and near these rivers is an important objective of management plans, and genetic stock identification has been identified as a tool to address this objective.  This study describes the genetic stock structure of sockeye salmon in transmountain rivers and adjacent areas of Southeast Alaska, and examines the utility of the baseline for use in stock composition estimates of fisheries harvests.  A survey of 125 sockeye spawning aggregates for 96 SNP markers suggests high levels of gene flow among lower transmountain river spawning aggregates and more reproductive isolation among island spawning aggregates, with coastal mainland and upper transmountain river spawning aggregates intermediate.  The patterns described here offer clues to the history of sockeye salmon in this area, and are indicative of geography, geology, colonization history, and life history differences in a dynamic landscape.