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Alaska Department of Fish and Game


Gene Conservation Laboratory
Alaska Peninsula Chinook Project

Underwater photo of a sockeye salmon in a stream

In the 1990s, ADF&G contributed to the development of a genetic baseline for Chinook salmon using protein variation to infer genetic information about salmon populations (Crane et al. 2000 - PDF 2,253 kB ; Teel et al. 2000 - PDF). Record low runs of Chinook salmon (Oncorhynchus tshawytscha) in Alaska resulted in increased interest in developing a more comprehensive genetic baseline, a key component of performing mixed-stock analysis of fisheries using genetic data. At this time the GCL was continuing to develop baselines for use within river systems (Yukon River – Smith et al. 2005 ; Kuskokwim River – Templin et al. 2011 - PDF ; and Copper River – Seeb et al. 2009 - PDF 761 kB ) using newer, DNA-based genetic markers, especially single nucleotide polymorphisms (SNPs). Eventually, the GCL completed the first comprehensive genetic baseline for Alaska Chinook salmon and surrounding regions (Templin et al. 2011 - PDF) which allowed extension of genetic analyses to marine waters (e.g. Juvenile studies - Murphy et al. 2009 - PDF and Fishery bycatch – Templin et al. 2011; NMFS 2009 - PDF; Guyon et al. 2010 a,b.).

The more comprehensive genetic baseline allowed for examination of potential impacts of marine fisheries on Chinook salmon stocks. Recent studies have revealed that a larger than expected percentage (14-27%) of Chinook salmon of north Alaska Peninsula origin are caught incidentally in the Bering Sea Pollock fishery (NMFS 2009 - PDF ; Guyon et al. 2010 a,b; Guthrie et al. 2012 - PDF). While the north Alaska Peninsula populations were adequately represented within the existing baseline for large-scale analyses, there are several stocks in the Westward Region that do not have good representation in the genetic baseline, specifically on the north Alaska Peninsula and adjacent areas and on Kodiak Island (see Figures 1 and 2 below). This intensive survey and sampling of Chinook salmon spawning locations on the Alaska Peninsula and Kodiak Island will provide better knowledge of the distribution, size and biology of Chinook salmon populations in this remote area.

Some of the Chinook salmon production on Kodiak Island comes from Pillar Creek Hatchery which used Karluk River as the source of its original broodstock. Potential hatchery contributions to fisheries will be determined using parental based tagging of Pillar Creek Hatchery Chinook salmon. The access to hatchery broodstock and/or progeny samples provides an opportunity to assess the potential for parental-based tagging (PBT; Anderson and Garza 2006) of the hatchery production in tandem with traditional mixed stock analysis. If successful, PBT would allow for the identification of hatchery offspring in all fisheries where Pillar Creek Chinook salmon may be harvested. The potential for this application depends on the ability of single nucleotide polymorphisms (SNP) sets to identify offspring based upon parental genotypes and known mating pairs. The Gene Conservation Laboratory is currently investigating a large suite of SNPs for such applications.

This project plans to obtain samples of known Chinook salmon stocks to expand the genetic baseline and to investigate the existence of additional stocks that are not currently know by the department.

Other Works Cited

  • Guyon, J. R., Guthrie, C. M., and H. Nguyen. 2010a. Genetic stock composition analysis of Chinook salmon bycatch samples from the 2008 Bering Sea pollock fishery. Report to the North Pacific Fishery Management Council. pp. 32.
  • Guyon, J. R., Guthrie, C. M., and H. Nguyen. 2010b. Genetic Stock Composition Analysis of Chinook Salmon Bycatch Samples from the 2007 “B” Season and 2009 Bering Sea Trawl Fisheries, Report to the North Pacific Fisheries Management Council. pp. 32.

Figure 1—Map of the Alaska Peninsula with possible Chinook salmon spawning stocks targeted for sampling.
Figure 2—Map of the Kodiak area with possible Chinook salmon spawning stocks targeted for sampling.
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