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Habitat and Marine Chemistry Program

Genetic Investigation of Chinook Bycatch in BSAI Pollock Fishery

figure 1, click image to enlarge
Figure 1.  Chuck Guthrie next to the Perkin Elmer Janus Robot. The new robot helps the ABL genetics laboratory set up over 500,000 genotyping reactions each year.  Photo by Jeff Guyon.

The Bering Sea/Aleutian Island (BSAI) pollock fishery will be partially regulated starting in 2011 through a cap limiting the total number of Chinook salmon that can be taken as bycatch.

The details for the cap can be found in Amendment 91 to the Bering Sea and Aleutian Islands Fishery Management Plan. Some of the impetus for enacting this limit was the potential effect of bycatch on declining stocks of western Alaska Chinook salmon and its consequence on subsistence fisheries.

This year, the genetics group at Auke Bay Laboratories (ABL) will be collaborating with the Alaska Department of Fish and Game (ADF&G) to complete a pilot project to analyze a limited number of samples from the Chinook bycatch from the 2008 BSAI groundfish fishery. These genetic samples were collected by the North Pacific Groundfish Observer Program as part of a feasibility study.

Although the samples may not be representative of the entire bycatch and, therefore, preclude the determination of unbiased stock estimations for the entire fishery, the data will give indications of presence or absence of specific stocks and establish efficient protocols for future analyses. For example, we are developing new MALDI-TOF (matrix-assisted laser desorption/ionization—time of flight) assays as a way to increase our genotyping capacity and significantly decrease SNP (single nucleotide polymorphism) assay costs.

Through contracting, these new MALDI-TOF assays will provide us with an almost unlimited genotyping capacity in a very cost-effective manner. The specific objectives of this bycatch project are to 1) identify the strata for which sufficient numbers of samples from the 2008 Chinook bycatch samples can be analyzed and 2) produce stock composition estimates for that limited strata. Results are anticipated in late 2010.

In addition to Chinook salmon, chum salmon are also captured as bycatch in the groundfish fishery. The largest bycatch occured in 2005 when approximately 700,000 non-Chinook salmon (mostly chum) were taken in the BSAI pollock trawl fishery. While chum bycatch stock composition estimates were produced by our laboratory for the 1994-96 fisheries, an ongoing project led by ABL scientist Chris Kondzela has refocused our efforts to learn about marine distributions of chum salmon populations or of regional aggregations of chum salmon in the Bering Sea by using chum bycatch samples collected from 1988 to 2005.

Chris is now working with both Colby Marvin, a contractor, and Tyler McCraney, our new technician, in the genotyping of 13 microsatellite markers for almost 8,000 chum salmon samples. This study and the development of a chum salmon genetic baseline are being done as part of a collaboration with Dr. Anthony Gharrett and Mike Garvin, a Ph.D. student from the University of Alaska.

As part of obligations under the Pacific Salmon Treaty, Chuck Guthrie (Fig. 1 above) of ABL has been working in collaboration with the ADF&G to quantify the numbers of Canadian sockeye salmon caught in some of the Alaskan fisheries. Chuck has been genotyping each salmon for 44 SNP DNA markers and performing genetic stock identification to determine the stock compositions of the catch.

To complete the analyses of the 2006 and 2007 northern boundary sockeye fisheries in Alaska Commercial Fishing Districts 101 and 104, Chuck is working with ABL's mathematical statistician Michele Masuda and biological science technician Hanhvan Nguyen. They will soon begin the analysis of 6,000 sockeye samples collected from the 2008 fishery.

The ABL genetics group is also investigating various forage species. In addition to supporting a significant commercial fishery in parts of Alaska, Pacific herring form a critical forage base for many high-profile species including whales, sea lions, Pacific salmon, and Pacific halibut.

The herring population in Lynn Canal (near Juneau, Alaska) has been struggling since the late 1970s. Although the commercial herring fishery has been closed since 1981, Lynn Canal herring have not fully recovered, and the National Marine Fisheries Service (NMFS) was petitioned in 2007 to list Pacific herring in Lynn Canal for protection under the Endangered Species Act.

Using 16 microsatellite markers, Sharon Wildes has been working to determine the uniqueness of Lynn Canal herring relative to other herring populations in Southeast Alaska. She is now in the process of analyzing her results and preparing them for publication.

By Jeff Guyon


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