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NEWPORT, Ore. – Commercial fishermen and scientists from Oregon, California and Washington have agreed to collaborate on a critical coast-wide study to learn more about salmon distribution, migration and behavior in the Pacific Ocean, but an alarming projected shortage of fish this year is putting their research in jeopardy.

Ironically the study, which expands a two-year pilot program began by Oregon State University researchers, is designed to help protect weak salmon stocks.

“We’ve got the funding, we’ve got the science and we’ve got the interest and cooperation of the fishing industry,” said Gil Sylvia, director of the Coastal Oregon Marine Experiment Station at OSU’s Hatfield Marine Science Center in Newport, Ore. “Now, we just need some salmon.”

During the pilot project, the OSU scientists found they could trace genetic markers of salmon caught in the ocean through small samples of fin or tissue and within 24 hours pinpoint an individual salmon’s river basin of origin. The hope, Sylvia says, is that an expanded study will allow the scientists to learn more about fish behavior in the ocean and whether salmon from, say, the Sacramento River or the Klamath River travel in clusters and feed in certain areas.

“This is ground-breaking research that could allow resource managers to keep much of the ocean open for fishing, yet protect weakened runs of fish,” Sylvia said. “There are preliminary indications that salmon destined for certain river systems do behave differently, but we need more data from a broader sampling before any management implications become clear.”

The Pacific Fisheries Management Council last month outlined three potential options for ocean chinook salmon fishing south of Cape Falcon (near Garibaldi, Ore.). The most optimistic scenario is a shortened season from April 15 to May 31 that would allow fishermen to catch a quota of fish and also share fins and tissue samples with scientists for genetic identification. A second option would preclude commercial fishing, but allow the scientists to catch and release a select number of salmon, maintaining only a piece of the tail fin for research.

The third, most dire option would close the ocean to all chinook fishing and not allow the take of any fish – even catch-and-release – for research.

The council is seeking to protect what may be a historic low return of salmon to the Sacramento River, a stock of fish that spend much of their time off the Oregon coast. The group will meet April 6-12 in Seattle, Wash., where it will decide on one of the three options – or another approach.

For the past two years, the Collaborative Research on Oregon Ocean Salmon project, or CROOS. has paired Oregon State University scientists and the state’s commercial fishing industry in a study to improve scientific knowledge about salmon behavior in the ocean. More than 190 salmon fishermen from 11 Oregon counties were trained in sampling protocols as part of the project, which was funded by the Oregon Watershed Enhancement Board.

The fishermen clipped fins and took tissues samples from the salmon before processing them, and logged when and where the fish were caught using a handheld GPS unit. The scientists brought the samples back to Hatfield Marine Science Center laboratories and conducted the genetic studies.

In the first year of the project, the scientists were able to match 2,100 salmon caught to a river, basin or specific region with 90 percent probability, according to Michael Banks, an OSU geneticist and director of the scientific portion of the project. Not all samples work flawlessly, Banks said, and genetic markers for some river systems are similar to others. Still, the scientists were able to confidently pinpoint the origin of roughly four out of every five salmon they tested.

Of those fish, 42 carried coded wire tags from hatcheries that identified where the fish were from. Without knowing that nugget of information, the scientists ran their genetic protocols and found they hit the mark on 41 of the 42 fish, Banks pointed out.

“That was pretty good validation that our methods work,” Banks said.

Buoyed by the results, the CROOS leaders sought to expand their studies in 2008. The two years of field study focused solely on the ocean off Oregon – and much of the study was concentrated off the central Oregon coast. Broadening the scope of the research to include Washington and California is critical, Sylvia says, because of the migratory nature of the salmon.

The CROOS project leaders have engaged the Oregon Salmon Commission, the California Salmon Commission and the Washington Department of Fish and Wildlife in the project, as well as NOAA’s National Marine Fisheries Service, and they are awaiting the final word from the Pacific Fisheries Management Council on the April decision.

Washington has used genetic identification methods to estimate fisheries stock composition for several years, but has not yet paired that with ocean sampling to determine at-sea stock distribution, the researchers say. California began its own genetic tracking project in 2006 and continued last year, although on a much smaller scale than Oregon.

Having the three states join forces will give scientists a much better idea of West Coast salmon migration, the researchers pointed out.

“The research is particularly important because some of the preliminary results suggest interesting patterns in salmon behavior that need to be validated,” said Renee Bellinger, an OSU faculty research assistant who is coordinating the three-state research effort. “We recorded ‘pulses’ of fish that would move at one time – from the Rogue River, for example – but we couldn’t gauge the range of movement or duration because the sampling period wasn’t long enough.”

If approved, scientists in all three states will work with commercial fishermen in their respective regions to collect the samples that they will test, using the CROOS protocols. They hope to look at different sampling blocks over time and space, covering the Pacific Ocean from northern Washington to the San Francisco Bay area.

In addition to their genetic studies, the scientists also are monitoring ocean conditions – including temperature, salinity, dissolved oxygen content and other factors – to determine their effect on salmon distribution, Sylvia said. Some of that information is collected by the fishermen, though most is supplied by unmanned undersea gliders that can be programmed to roam the same stretches of ocean where the fishermen are working.

“There is a tremendous amount of interest from the fishing industry in this project,” Sylvia said. “This is a case where science may help provide solutions to a complex and difficult management problem.”

Specific goals of the Oregon-based CROOS project include:

• Broadening the genetic stock identification (GSI) research to test different hypotheses on location and migration of salmon, and determine if hatchery fish behave differently than wild fish;

• Use data from vessels and undersea gliders to monitor ocean conditions that can be tied to biological data to determine if temperature, salinity or other factors influence migration;

• Sample tissues from harvested salmon to test for parasites that previously have infected Klamath basin fish;

• Evaluate different digital data logging instruments that can be used in real time on small fishing vessels;

• Track commercially harvested salmon through a barcode system from vessel to market and develop websites that allow consumers to learn more about their purchase;

• Design a “real time” genetic stock identification-based website to share data with multiple audiences;

• Develop potential management simulation scenarios based on the data to see if what the researchers learn through their data collection is sufficient to influence the in-season decision-making process.