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Geneticist loading DNA plate for genotyping
Geneticist loading DNA plate for genotyping

The Genetics program at ABL provides research information required in regional, national, and international agreements and treaties on the management of marine resources including Pacific salmon, groundfish, and forage fish species. Legislation mandating this research includes the Pacific Salmon Treaty, the North Pacific Anadromous Stocks Act, and the Magnuson-Stevens Fishery Conservation and Management Act. Products of this program include peer reviewed manuscripts, technical reports, and briefings regarding genetic stock composition and population genetics. Program activities are designed to improve our understanding of the ocean ecology through stock assessments, identification of stocks to region or country of origin, determination of population and stock utilization of ocean rearing areas, and assessment of fishery interceptions. Information provided is used by:

and other international commissions.

Current projects include the following:
Chinook and chum salmon bycatch stock composition analysis for the Bering Sea and Gulf of Alaska pollock trawl fisheries - Samples are collected annually from fishery observers in Dutch Harbor, Anchorage and elsewhere for shipment to Auke Bay Laboratories. DNA is extracted using silica based column technology and the samples are genotyped for genetic markers including single nucleotide polymorphism (SNPs) and microsatellite repeats. Genetic mixed-stock analysis is performed using Bayes software developed at the Auke Bay Laboratories (Pella and Masuda, 2001) and results reported to the North Pacific Fishery Management Council.

Development of a standardized chum salmon genetic baseline – An improved chum salmon genetic baseline in needed to further delineate the stock composition of western Alaska chum salmon caught in the bycatch of the pollock fishery. Collaborative efforts are underway to improve the chum salmon genetic baseline (Alaska Department of Fish and Game and University of Alaska Fairbanks) by identifying new genetic markers and including additional salmon populations.

Identify stock origins of sockeye salmon harvested in Pacific Salmon Treaty delimited Northern Boundary Fisheries – In collaboration with ADF&G, genetic samples from 84 baseline stocks were grouped into 13 regions based on manager needs to match the scale pattern analysis groupings, geographical location and historical knowledge. Matched genetic and scale samples are collected each year by port samplers. SNP genotyping is performed using TaqMan chemistries for 45 SNP probes. Mixture analysis is completed statistically and resulting stock composition estimates for all 13 regions (including Nass and Skeena) are compared across weeks and areas to determine trends and identify the number of treaty delimited fish caught in the fishery. Results are communicated back to the Pacific Salmon Commission for treaty evaluation. This project is funded by the PSC Northern Boundary Fund.

Stock composition of Chinook salmon bycatch samples from the Bering Sea trawl fishery between 2008 and 2011
Comparison of yearly stock composition estimates (2008-2011) based on genetic samples collected from the Bering Sea Chinook salmon bycatch. “Coast W AK” refers to coastal western Alaska, “Mid Yukon” refers to middle Yukon, “Up Yukon” refers to upper Yukon, “N AK Pen” refers to north Alaskan Peninsula, “GOA” refers to the Gulf of Alaska, “Coast SE AK” refers to coastal southeast Alaska, and “BC” refers to British Columbia. Figure taken from Guthrie et al. 2013 (see

Stock composition analysis of juvenile Chinook and chum salmon collected off the mouth of the Yukon River during summer BASIS cruises – From past NMFS research cruises, samples were collected from juvenile salmon off the mouth of the Yukon River, an area which has been the subject of numerous fisheries disaster declarations from both the United States and State governments. The samples are being analyzed genetically to get a better understanding of stock specific, early life history migration patterns and potentially as an indicator of relative adult run strength. This project is predominantly funded with Alaska Sustainable Salmon Funds (AKSSF) and Arctic-Yukon-Kuskokwim Sustainable Salmon Initiative (AYK SSI) funds.

Stock composition analysis of Alaskan forage and pelagic fishes – Herring stock composition analysis is being completed in Prince William Sound to help determine the number of populations in the area, work funded through the Exxon Valdez Oil Spill Trustee Fund. Capelin and arctic cod are being collected as part of Arctic surveys and their stock structure will be used as a baseline in the Chukchi Sea. We are also involved in collaborations to identify new forage fish species using DNA sequence analysis and meristics.

Jeff Guyon, Ph.D.
Auke Bay Laboratories
Alaska Fisheries Science Center, NOAA Fisheries

Ted Stevens Marine Research Institute
17109 Pt Lena Loop Rd
Juneau AK 99801
(907) 789-6079

Recent Publications, Poster Presentations, Reports & Activities

  • Evidence of multiple paternity in quillback rockfish (Sebastes maliger).
    GRAY, A. K., C. J. RODGVELLER, and C. R. LUNSFORD. 2015. Evidence of multiple paternity in quillback rockfish (Sebastes maliger). U.S. Dep. Commer., NOAA Tech. Memo. NMFS-AFSC-303, 25 p. (.pdf, 1.14 MB).  Online.
  • Systematics of North Pacific sand lances of the genus Ammodytes based on molecular and morphological evidence, with the description of a new species from Japan.
    ORR, J. W., S. WILDES, Y. KAI, N. RARING, T. NAKABO, O. KATUGIN, and J. GUYON. 2015. Systematics of North Pacific sand lances of the genus Ammodytes based on molecular and morphological evidence, with the description of a new species from Japan. Fish. Bull., U.S. 113:129–156. (.pdf, 2.14 MB).  Online.
  • Inter-annual Distribution of Yukon River Juvenile Chum Salmon in the Eastern Bering Sea
    Conference:  NPAFC International Symposium on Pacific Salmon and Steelhead Production in a Changing Climate…, Kobe, Japan, May 2015
    (2015 poster, .pdf, 2.05 MB)   Online.

  • Yukon River Juvenile Chum Salmon in the Eastern Bering Sea
    Conference:  American Fisheries Society, Alaska Chapter Annual Meeting, Juneau, AK, Oct 2014
    (2014 poster, .pdf, 2.23 MB)   Online.


  • See the publications and posters databases for additional listings.

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