NOAA Technical Memorandum NMFS-AFSC-310 doi:10.7289/V5/TM-AFSC-310 Genetic Stock Composition Analysis of the Chinook Salmon Bycatch from the 2014 Bering Sea Walleye Pollock (Gadus chalcogrammus) Trawl Fishery by C. M. Guthrie, III, Hv. T. Nguyen, and J. R. Guyon U.S. DEPARTMENT OF COMMERCE National Oceanic and Atmospheric Administration National Marine Fisheries Service Alaska Fisheries Science Center January 2016 NOAA Technical Memorandum NMFS The National Marine Fisheries Service's Alaska Fisheries Science Center uses the NOAA Technical Memorandum series to issue informal scientific and technical publications when complete formal review and editorial processing are not appropriate or feasible. Documents within this series reflect sound professional work and may be referenced in the formal scientific and technical literature. The NMFS-AFSC Technical Memorandum series of the Alaska Fisheries Science Center continues the NMFS-F/NWC series established in 1970 by the Northwest Fisheries Center. The NMFS-NWFSC series is currently used by the Northwest Fisheries Science Center. This document should be cited as follows: Guthrie, C. M. III, Hv. T. Nguyen, and J. R. Guyon. 2016. Genetic stock composition analysis of the Chinook salmon bycatch from the 2014 Bering Sea walleye pollock (Gadus chalcogrammus) trawl fishery. U.S. Dep. Commer., NOAA Tech. Memo. NMFS-AFSC-310, 25 p. http://dx.doi.org/10.7289/V5/TM-AFSC-310. Document available: http://www.afsc.noaa.gov/Publications/AFSC-TM/NOAA-TM-AFSC-310.pdf Reference in this document to trade names does not imply endorsement by the National Marine Fisheries Service, NOAA. NOAA Technical Memorandum NMFS-AFSC-310 doi:10.7289/V5/TM-AFSC-310 Genetic Stock Composition Analysis of the Chinook Salmon Bycatch from the 2014 Bering Sea Walleye Pollock (Gadus chalcogrammus) Trawl Fishery by C. M. Guthrie, III, Hv. T. Nguyen, and J. R. Guyon Alaska Fisheries Science Center Auke Bay Laboratories 17109 Pt. Lena Loop Road Juneau, AK 99801 www.afsc.noaa.gov U.S. DEPARTMENT OF COMMERCE Penny. S. Pritzker, Secretary National Oceanic and Atmospheric Administration Kathryn D. Sullivan, Under Secretary and Administrator National Marine Fisheries Service Eileen Sobeck, Assistant Administrator for Fisheries January 2015 This document is available to the public through: National Technical Information Service U.S. Department of Commerce 5285 Port Royal Road Springfield, VA 22161 www.ntis.gov iii ABSTRACT A genetic analysis of samples from the Chinook salmon (Oncorhynchus tshawytscha) bycatch of the 2014 Bering Sea-Aleutian Island (BSAI) trawl fishery for walleye pollock (Gadus chalcogrammus) was undertaken to determine the overall stock composition of the bycatch. Samples were genotyped for 43 single nucleotide polymorphism (SNP) DNA markers and results were estimated using the Alaska Department of Fish and Game (ADF&G) SNP baseline. In 2014, genetic samples from the Bering Sea were collected using a systematic random sampling protocol where one out of every 10 Chinook salmon encountered was sampled. Based on the analysis of 1,385 Chinook salmon bycatch samples collected throughout the 2014 BSAI walleye pollock trawl fishery, Coastal Western Alaska stocks dominated the sample set (49%) with smaller contributions from North Alaska Peninsula (18%), British Columbia (14%), and West Coast U.S. (WA/OR/CA) (7%) stocks. Analysis of temporal groupings within the pollock “A” and “B” seasons revealed changes in stock composition during the course of the year with lower contributions of Coastal Western Alaska, North Alaska Peninsula and Yukon stocks and higher contributions of West Coast U.S. (WA/OR/CA), British Columbia, NW Gulf of Alaska and Coastal Southeast Alaska stocks during the “B” season. iv v CONTENTS ABSTRACT _________________________________________________________________ iii CONTENTS _________________________________________________________________ v INTRODUCTION ____________________________________________________________ 1 SAMPLE DISTRIBUTION _____________________________________________________ 2 GENETIC STOCK COMPOSITION ______________________________________________ 6 COMPARISON WITH PREVIOUS ESTIMATES __________________________________ 13 SUMMARY ________________________________________________________________ 16 Sampling Issues __________________________________________________________________ 16 Stock Composition Estimates ________________________________________________________ 17 Application of These Estimates ______________________________________________________ 17 ACKNOWLEDGMENTS _____________________________________________________ 19 CITATIONS ________________________________________________________________ 21 APPENDIX _________________________________________________________________ 23 vi INTRODUCTION The Bering Sea and the Gulf of Alaska (GOA) are known feeding habitats 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 Pacific 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 the Chinook salmon bycatch samples collected from the U.S. Bering Sea-Aleutian Island (BSAI) pollock trawl fishery. National Marine Fisheries Service (NMFS) geographical statistical areas associated with the BSAI groundfish fishery (areas 509-524) are Figure 1. -- NMFS statistical areas associated with the Bering Sea-Aleutian Island (BSAI) and Gulf of Alaska (GOA) groundfish fisheries. 2 shown in Figure 1 and are used later in the report to describe the spatial distribution of the Chinook salmon bycatch and genetic samples. In 2014, genetic samples were collected by the AFSC’s North Pacific Groundfish Observer Program (NPGOP) from the Chinook salmon bycatch of the BSAI pollock fishery using the systematic sampling protocols recommended previously (Pella and Geiger 2009). The number of available samples and the unbiased methodology in which they were collected facilitated the extrapolation of the sample stock composition to the overall Chinook bycatch from the BSAI pollock trawl fishery in 2014. Stock composition analyses were performed using the single nucleotide polymorphism (SNP) baseline provided by the Alaska Department of Fish and Game (ADF&G) (Templin et al. 2011), the same baseline that was used previously to estimate stock composition of samples from the 2005-2013 Chinook salmon bycatch (NMFS 2009; Guyon et al. 2010a, b; Guthrie et al. 2012, 2013, 2014, and 2015; 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. 2010a). SAMPLE DISTRIBUTION Samples were collected from the Chinook salmon bycatch by the NPGOP for analysis at AFSC’s Auke Bay Laboratories (ABL). Amendment 91 to the North Pacific Fishery Management Council (NPFMC) fishery management plan for groundfish of the BSAI Management Area was enacted in 2010 and included retention of the salmon caught in the prohibited species catch. In 2011, a systematic random sampling design recommended by Pella and Geiger (2009) was implemented by the NPGOP to collect genetic samples from one out of every 10 Chinook salmon encountered as bycatch in the BSAI pollock fishery. Samples of