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12.05.07

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Photograph by Steve Hahn
June Bugged: Mike Stiller, president of the Santa Cruz Commercial Fishermen's Association, wants his June salmon fishing back.

Home is Where the Genome Is

Scientists at Long Marine Lab are working on technology that could help save threatened salmon populations--while still allowing fishermen to harvest from healthy ones.

By Steve Hahn


Over the past month and a half, reports have been circulating among fishery biologists and recreational fishermen that the number of Chinook salmon returning to Central Valley riverbeds to spawn is lower than average. While the official counts won't be ready until the end of this month, some in the fishery biology field are already raising the alarm that the wild Chinook salmon population might be depressed below healthy numbers this year. In one instance, the Sacramento Bee reported that biologists counting salmon swimming upriver to the Sacramento River tributary Battle Creek to lay eggs have seen approximately 80 percent fewer Chinook salmon, popularly known as King salmon, than they would in an average year.

The low numbers do not constitute an emergency under California fishing regulations, which require that the same salmon population be counted below healthy numbers for three years in a row.

However, the depressed salmon population this year does bring back memories of the 2005-2007 salmon fishery closures for the Monterey Bay region during the month of June. Those closures were based on three successive years of the Klamath River Chinook populations falling below the federal conservation goal of 35,000 returning natural spawners. Allen Grover, fishery biologist for the California Department of Fish and Game, estimates the Klamath River Chinook population will reach the 35,000 mark this year. That means it is unlikely the salmon fishery will be restricted this year, although that decision won't officially be made until late January or early February.

In conjuring up memories of these previous closures, however, an important detail comes to light. From 2005 to 2007, the entire Monterey Bay region from Pigeon Point south was closed off in June because of the dearth of Klamath River salmon making it back to their breeding grounds. But at the time the Central Valley Chinook fall runs were considered to be at healthy numbers—or, in bureaucratic terms, they were reaching their conservation goal of 122,000 returning spawners.In theory it wouldn't have been a problem for the fishing fleets to harvest Central Valley Chinook during the fishery closure, but in reality, whether a particular fish is from the Klamath or the Sacramento River is impossible to determine from a fishing boat. So commercial salmon fishing was not allowed at all in specified areas during the closure.

This presented a major problem for Santa Cruz-based salmon fishermen, including those represented by Mike Stiller, president of the Santa Cruz Commercial Fisherman's Association.

"The month of June is a make-or-break time for us," explains Stiller. "The sea lions are gone and the fish are in the ocean [not swimming upriver or further north]. We've had that month closed off to us for the past three years now. We have to get that back." Thanks to genetics research currently taking place at Long Marine Lab in Santa Cruz, commercial fishermen like Stiller may have more flexibility in fishing during restricted months at some point in the future.

Dr. John Carlos Garza is a research geneticist for the National Oceanographic and Atmospheric Association. He has been working with others in his field over the past five years to create a genetic database of all the Chinook salmon runs from California to Alaska. With the database mostly complete, Garza and his associates are now able to clip off a small sample from the fin of a Chinook salmon in the ocean and determine its place of birth based on DNA readings. His research group has now traced about 2,600 samples to their location of birth.

While his research is still in the experimental stages, Garza sees potential use for the new genetic identification method in differentiating between plentiful and endangered populations of Chinook salmon in the ocean.

"What we've shown is that in the northern part of the San Francisco management area, the abundance of coastal Chinook and Klamath Chinook is much higher than in the Monterey Bay area," he says. "That indicates there may be opportunities to refine fishery management in such a way that you can relatively accurately identify regions where conservation stocks are and then direct fishing efforts away from those threatened stocks."

The genetic identification approach would replace the current clumsy process of implanting bits of wire into the heads of hatchery-born Chinook salmon, waiting for them to be caught by commercial fleets, and then correlating where the fish were hatched with where they ended up in the ocean.

But this new genetic approach to managing commercial fishing would require meddling with highly complex fishery regulations, which are influenced by everything from treaties with indigenous tribes to the Endangered Species Act. Garza warns that a long list of political factors make "a complete change in the way fishery management regulations are formulated" a very delicate process. After all, Garza says, it took years of negotiation between polarized political groups to hammer together the patchwork of regulations that exists now. But with the new genetic technology, there is an opportunity for change that could end up benefiting environmentalists and fishing fleets alike.

"In British Columbia they are already doing this," notes Garza. "It's been enormously successful. Their catch [overall] has tripled and the fishery impacts on their conservation stocks have gone way down. They've been collecting data on a weekly basis and then turning it over to fishery managers who can dynamically close or open small areas to fishing."

Fishermen like Stiller take a measure of hope from Garza's research that in the future they may be able to harvest healthy populations of salmon while dodging endangered stocks. This might mean that instead of entire blocks of the ocean being closed to salmon fishing, only certain genetically distinct populations in smaller areas would be off-limits.

Garza cautions that the unforeseen consequences of changing the current system should not be treated lightly.

"At some times in the year as much as 20 percent of the catch in British Columbia can be fish from California, which undoubtedly includes some of our conservation stocks," he says. While a host of similar complications make it difficult to predict exactly how the information provided by the genetic database will be used in fishery management, Garza is confident that genetic identification will soon become the key data collection tool used in the field.

"Given the success the Canadians have had in regards to salmon, the power of the technology and the fact that genomic technologies are becoming cheaper," he says, "I think it's becoming clear that over the next few years genetic methods are likely to become one of the primary data collection tools for use in fishery management."


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