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Post-season Stock Composition Analysis of Upper Cook Inlet Sockeye Salmon Harvest, 2005-2007

Habicht, C., Templin, W.D., Willette, T.M., Fair, L.F., Raborn, S.W., Seeb, L.W.

Genetic data were collected from sockeye salmon Oncorhynchus nerka originating from all major systems in Upper Cook Inlet, Alaska, that produce sockeye salmon. All individuals in the baseline were assayed for genotypes at 45 SNP markers. These DNA-based markers revealed population structure similar to that observed in the previous analyses with allozymes. Simulations indicated that seven regional groups (Kenai River, Susitna River, Yentna River, West Cook Inlet, Kasilof River, Northeast Cook Inlet, and Knik Arm) could be identified in mixtures at high levels of precision and accuracy. Samples taken from within the rivers at fish wheels were analyzed to evaluate the precision and accuracy possible using the baseline of new markers and statistical methods. Sockeye salmon from these drainages are commercially harvested in mixed-stock aggregations in Upper Cook Inlet. Genetic Stock Identification using Bayesian methods with data from 40 to 42 loci were performed to estimate the proportion of source populations in the harvest from set and drift gillnet fisheries during selected periods in the Central District of Upper Cook Inlet from 2005 to 2007. Samples from fisheries were analyzed postseason. Samples from the offshore test fishery were also analyzed. Patterns of stock proportions through time in the fishery were similar to results from allozyme data, indicating that Kenai River fish are present in the harvest later in the season relative to Kasilof River fish. High inter-annual variation in stock composition through space and time was detected, but this high level of variation might have been due, in part, to the unusual nature of the fishery during the 3 years investigated.

Citation

Habicht, C., Templin, W.D., Willette, T.M., Fair, L.F., Raborn, S.W., Seeb, L.W. "Post-season Stock Composition Analysis of Upper Cook Inlet Sockeye Salmon Harvest, 2005-2007" Alaska Department of Fish and Game, Fishery Manuscript No.07-07, Anchorage (2008):