2016 Genetic Stock Composition Analysis of the Chinook Salmon Bycatch Samples from the Gulf of Alaska Trawl Fisheries

December 11, 2016

A genetic analysis of samples from the Chinook salmon (Oncorhynchus tshawytscha) Prohibited Species Catch (bycatch) of the 2016 Gulf of Alaska (GOA) trawl fisheries for walleyepollock (Gadus chalcogrammus) and rockfish (Sebastes spp.), was undertaken to determine the stock composition of the sample sets. Samples were genotyped for 43 single nucleotide polymorphism (SNP) DNA markers and results were estimated using the Alaska Department of Fish and Game SNP baseline. In 2016, genetic samples were collected from Chinook salmon taken in the bycatch of the GOA pollock trawl fisheries using a simple random sample protocol with trip being the primary unit. This was the third year for this sampling protocol and which resulted in the largest available genetic sample set to date with 24% of the estimated salmon bycatch from the pollock fishery successfully genotyped. Based on analysis of 4,962 Chinook salmon bycatch samples, British Columbia (42%), West Coast US (40%), and Coastal Southeast Alaska (15%) comprised the largest stock groups, at an estimated 8,602, 8,301, and 3,080 Chinook salmon, respectively, out of 20,589 fish total. In 2016, genetic samples from the bycatch of the GOA rockfish CV fishery were collected by the fishing industry using a censussampling protocol. Based on the genotyping of 493 Chinook salmon bycatch samples collected from this fishery in NMFS Statistical Areas 620 and 630, West Coast US stocks represented the largest stock group (62%) with smaller contributions from British Columbia (27%), Coastal Southeast Alaska (7%), and Northwest GOA (4%) stock groups.

The Gulf of Alaska (GOA) is known as a feeding habitat for multiple brood years of Chinook salmon (Oncorhynchus tshawytscha) originating from many different localities in North America and Asia. Determining the geographic origin and stock composition of salmon caught in federally managed fisheries is essential to understanding whether fisheries management could address conservation concerns. This report provides genetic stock identification results for Chinook salmon Prohibited Species Catch (bycatch) samples collected in the GOA from the trawl fisheries for walleye pollock (Gadus chalcogrammus) and catcher vessel (CV) trawl fisheries for rockfish (Sebastes spp.). The National Marine Fisheries Service (NMFS) and Alaska Department of Fish and Game (ADF&G) geographical statistical areas associated with the groundfish fishery are shown in Figure 1 and are used later in the report to describe the spatial distribution of the Chinook salmon bycatch and genetic samples. All analyses used a single nucleotide polymorphism (SNP) baseline provided by ADF&G (Templin et al. 2011; Appendix 1), the same baseline used to estimate previous stock compositions of samples from the Chinook salmon bycatch of the federally managed GOA trawl fisheries (Guthrie et al. 2013, 2016, 2017; Guyon et al. 2014, 2015a,b; Larson et al. 2013). For additional information regarding background and methodology refer to the Chinook salmon bycatch report prepared previously for the 2008 Bering Sea trawl fishery (Guyon et al. 2010).

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Last updated by Alaska Fisheries Science Center on 06/06/2019

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