State examines salmon DNA to pinpoint origins

Published on March 18th, 2010

By MARGARET BAUMAN

Scientists at the Alaska Department of Fish and Game are pushing the genetics frontier with a multi-million dollar study designed to verify stock composition of sockeye and chum salmon harvested in Western Alaska, from Chignik to Kotzebue.

The study is scheduled for release to the public in the summer of 2012, to allow time for writing allocation proposals to be considered at an Alaska Board of Fisheries meeting later that year.

Meanwhile in the Alaska Department of Fish and Game's gene conservation laboratory in Anchorage, geneticists and biologists are busy extracting and analyzing DNA from about 140,000 samples of tissue known as the axillary process from chum and sockeye salmon.

Eric Volk, chief fishery scientist for salmon with the state's Division of Commercial Fisheries, said the magnitude of the project, known as the Western Alaska salmon stock identification project, is unprecedented.

DNA is a nucleic acid that contains the genetic instructions used in development and functioning of all known living organisms. DNA is a blueprint or code carried in the genes. By comparing samples of DNA in fish harvested in Western Alaska with DNA samples taken from fish in natal streams, geneticists will know where the harvested fish were headed to spawn.

Stock composition is a heated issue in Western Alaska, where salmon harvesters north of the False Pass area, known as Area M, have voiced concern for years that their fish are being caught in Area M commercial fisheries, rather than the commercial and subsistence fisheries of Bristol Bay and the Arctic-Yukon-Kuskokwim region.

Yukon River commercial and subsistence harvesters likewise have expressed concern about the numbers of chum and chinook salmon caught incidentally in pollock fisheries in the Bering Sea, and a similar study will be used to verify the stock composition of those salmon harvested as bycatch by trawlers. Most of the sampling of salmon caught as bycatch in the Bering Sea is being done by National Marine Fisheries Service at its Auke Bay laboratory.

Chris Habicht, the agency's statewide stock status geneticist, is the project's ground level coordinator, charged with making sure deadlines are met for running samples, data analysis and statistical report writing, in advance of the December 2012 Board of Fisheries meeting. One of the challenges in getting the stock study started in the first place, said John Hilsiger, deputy commissioner of Fish and Game, is that all the money for all sampling had to be in place before testing of any samples could begin. The process also had to be approved by the stakeholders, represented by an advisory panel of varied interest groups.

Preserving fish value

Bill Templin, principal geneticist for the gene conservation laboratory, said biologists decided to take the DNA samples from the axillary process because it is easy to clip and does not decrease the value of the fish. Each sample is catalogued by date and place where the sample was taken and run through a series of chemical processes to identify its DNA markers. Test results are then compared with those of baseline studies of salmon from natal streams up and down the west coast of Alaska, so scientists can determine where harvested fish were headed.

Templin said to assure a high level of accuracy, the lab is also running new DNA analyses on all DNA baseline samples of chum and sockeye. "With one or two DNA markers, we can determine if they are from Asia or North America," he said. "The more markers, the more groups we can break into, and the more precise we can be in estimates."

Samples in the baseline studies themselves were gathered in a cooperative effort with the North Pacific Anadromous Fish Commission, whose membership includes Russia, Japan, Korea, Canada and the United States. Templin said the baseline studies are being done in collaboration with other salmon genetics laboratories from all these countries.

The Alaska Department of Fish and Game is also working with a technical committee of scientists from the National Marine Fisheries Service, the University of Washington and the University of Alaska Fairbanks, a group with broad background in biometrics, statistics, modeling, salmon ecology and genetics, Volk said. "The more complete the baseline is, the more likely the ability to match the fish to the specific areas" (using DNA identifiers)."

The more markers that geneticists can develop in the DNA tissue samples, the greater the chance of differentiating between different stocks of sockeye and chum salmon, he said.

The sockeye baseline includes tissue samples from more than 50,000 fish and the chum baseline will include more than 25,000 fish, he said.

To date geneticists have 45 markers for sockeye and are working toward 96 markers. For chum they have 53 markers and are working toward at least 96. The answers lie in the genes, a section of DNA that codes for specific proteins.

"It's kind of like a blueprint for building a house, Templin said. "We are looking for those little changes."

The use of genetic studies to determine stock identification dates back to 1980, when scientists from the University of Washington did a sockeye fish genetic stock study in Cook Inlet. Since then the process has seen great technical advancement, with new research and development of new chemical processes to identify markers in DNA.