Saving the Chinook


In a dimly lit laboratory on a bluff overlooking the Pacific, Michael Banks pulls out a tray containing an orange, jello-like mass of baby salmon.

The fry don't look like much even to the trained eye, but Banks' fish represent a breakthrough in salmon biology, one that has implications for managing fish populations throughout California.

Banks, a research geneticist at the University of California Bodega Marine Laboratory, appears to have solved a deceptively simple problem: how to distinguish similar-looking but genetically distinct fish from one another.

The technique, which involves quick analysis of the genetic building blocks known as DNA, is now playing a key role in the effort to save the endangered winter-run Chinook salmon. Scientists say it could eventually be used to fundamentally change the way fish hatcheries operate.

"We're not just trying to pump out thousands of genetically similar fish," says Dave White, an assistant biologist from the Bodega lab. "What we're trying to do is enhance the gene pool at large. That's a real divergence from the way fisheries have been managed in the past."

The problem that gave rise to the new DNA identification technique is simple enough. The Sacramento River and its tributaries support four genetically different runs of salmon that migrate up the river to breed at different times of the year. The so-called winter-run Chinook are nearly extinct--and it's difficult to protect them because they look identical to the fish in the other runs.

The winter-run Chinook swim up the Sacramento River in their third year of life, beginning in November. Biologists believe they follow certain chemical cues in the water to smell their way home to the place they were born. The juvenile fish migrate to the ocean once the river is low--but that migration occurs at a time when water is being diverted from the river in many places for different uses, and many young fish never make it to the ocean.

There are 2,771 diversions on the Sacramento-San Joaquin River Delta, with two of the biggest pumpers--the Central Valley Project and the State Water Project--diverting about 7 million acre-feet of water per year to irrigate farms and supply drinking water around the state. Nearly 50% of the State Water Project water is pumped to Southern California, including Los Angeles.

Because the winter-run Chinook is endangered, state water regulators must assure that no more than 2% of its estimated population is being killed by the water pumps. If the toll is greater, the diversions must be stopped temporarily.

Until now, though, there has been no good way to tell if the fish being killed were from the winter run or one of the three other runs of Chinook. Biologists have mostly had to guess based on size, but fluctuations in water temperature and food availability--which affect growth rates--and overlapping releases from hatcheries made such identification inexact at best.

Enter Banks and his DNA technique. He takes a tiny sample of fin clipped from a salmon and places it in a gel, together with samples from as many as 96 other fish. A laser is then trained on the gel, which excites the material into emitting light. These light emissions, when passed through a set of filters, reveal the genetic pattern of each sample, which is then fed into a computer for analysis.

Banks looks for several specific, repeated genetic sequences that enable him to determine the type of salmon. He can analyze the 96 fish in just 30 to 45 minutes. The speed is critical for water managers, who in 1997 will rely on Banks for quick analysis of what kind of salmon are being killed at the pumps.

The technique has important applications in hatcheries as well. By knowing the heritage of specific fish, biologists are better equipped to prevent cross-breeding in captivity and to enhance diversity. There are now 791 adult winter-run Chinook in captivity and nearly 10,000 fry--the progeny of a $12.7-million state and federal effort to save the winter-run Chinook from extinction.

Maintaining the four runs of salmon separately is crucial, says Scott Hamelberg, a federal evaluator of the hatchery where winter-run Chinook are bred. "Genetic management has been looked at as critical to properly managing a fishery."

To enhance the captive winter-run Chinook's chances of survival, biologists also want to promote genetic diversity by making sure that plenty of unrelated parents are making babies in captivity.

"You want to have as much diversity as possible because there's no way of predicting what, in the future, might come up," says Banks.

Last year, biologists at the Coleman hatchery unwittingly mated winter run with spring run. Banks discovered the error using his new technique, and since then there has been a moratorium on mating wild fish. If the error had gone undetected, it could have threatened the small wild population, because the hatchery releases juveniles after just a few months in captivity. Hybridization--in which two runs are bred together--can quickly obliterate 10,000 years of evolution.

Already, the genetic work seems to be helping the winter-run Chinook: More than a thousand of the fish returned to breed last year, compared with only 189 in 1994.

Banks now wants to use the new technique to study other problems plaguing the Chinook. Tracking down disease agents and sampling for winter-run salmon at fishing docks will help biologists learn about the movements of these fish in the ocean. Banks is also interested in tracking the spring-run Chinook, a threatened population, and hopes to use the technique to help save the Coho salmon as well.

Freelance writer Linda Berlin can be reached by e-mail at

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