A Case of Mistaken Identity

DNA--the acronym is familiar to most of us. This genetic discovery --which holds the essence of all living things -- has helped solve murders, identify missing people, and unravel medical mysteries. The Department is now hoping deoxyribonucleic acid, DNA, will soon crack a trying case of mistaken identity.

The case involves four runs of chinook salmon that look alike as juveniles. One run is endangered; another is a candidate for listing, and the others are not protected. Mistaking one run for another could impact the water delivered by California's two major water projects. How can DWR and other agencies protect both fish and water supply? Part of the answer may lie within the double-stranded DNA molecule.

A Crucial Count
Each Central Valley chinook salmon run is named for the season the adult fish migrate through the Sacramento-San Joaquin Delta to spawn upstream in the Sacramento and San Joaquin rivers and their tributaries. Their progeny later emigrate to the ocean through the Delta, where some wind up at State and federal pumping plants. These juveniles are collected at salvage facilities, counted and recorded then returned to the waterway to resume their journey. But if identified as winter-run, listed under the federal and State endangered species acts in 1989, the count becomes crucial.

When that number reaches the designated "take" level at these facilities, water operators such as the State Water Project must consult with regulatory agencies. The results could mean that exports from the Delta are slowed or stopped, as has happened in 1993 and 1994. (The take number is determined by a complex extrapolation of the actual number salvaged and reflects losses in Clifton Court Forebay and at fish screens.)

The dilemma is that these runs as juveniles often intermix. Identifying the winter- run from other runs, up until recently, has been a matter of length (at a certain date) -a method that has yielded questionable results in the Delta.

To resolve this identity crisis, the Department began a three-year, $594,000 contract in 1994 with University of California at Davis' Bodega Marine Laboratory to study if genetics could be used to identify differences among the four Central Valley chinook runs--winter, fall, late fall and spring.

"The initial motivation for the contract was the take issue," says Randy Brown, Chief of DWR's Environmental Services Office. "But, more importantly, the study will provide management in DWR and other agencies with information they need to make water operations decisions that will benefit juvenile winter-run chinook as well as assist fish biologists on how to best manage the different chinook runs.

"With the new candidacy of the spring-run chinook and the possible listing of some other chinook runs, DNA will prove to be a useful tool in managing the system -- both fish and water."

The Winter-Run
"The winter-run is unique. It's found only in California and its life history is different from the other runs," says Sheila Greene, DWR fish biologist and project coordinator of the DNA studies. Before Shasta Dam was built, the winter-run's spawning was separated from other runs by season and geography.

"In addition, every phase of their lives--migrating from the ocean, spawning, emerging from their gravel nests, emigrating to the ocean--occurs over a wider time range than for other runs. These time range distinctions, at the same time, cause their juvenile life phase to overlap with other runs, in particular the late fall and spring runs."

The geographic lines that distinguished the winter-run chinook spawning have blurred. Before Shasta Dam was built, the winter run would migrate through the Sacramento-San Joaquin River Delta in the winter to the McCloud and Pitt rivers. They would spawn and lay their eggs in the summer where spring-fed rivers provided cool waters needed for survival of these eggs. But now Greene says the adult winter-run can be found in the same parts of the upper Sacramento River as the late fall and spring runs.

"Dams have blocked the historic spawning grounds of various stocks, " says Greene. "The situation raises questions about how the runs have adapted by changing life history strategies. Data from the DNA study may help us answer some of those questions."

Genetic Markers
From 1993-96, tissue samples, about one square millimeter taken from the fin (nonlethal), were collected from adult and juvenile chinook of known origins such as spawned adult fall-run carcasses from the upper Sacramento River, winter-run carcasses near Redding, late-fall run chinook returning to the Coleman National Fish Hatchery, and spring-run adults and juveniles from Mill and Deer creeks. Samples were also taken from juveniles of unknown origin such as those from within the Bay-Delta estuary and State and federal salvage facilities in the Delta. (All samples are archived at a Fish and Game facility in Rancho Cordova.)

What biologists at the Bodega laboratory look for in these samples are benign mutations that have occurred in the winter-run and not in other runs. They are concentrating on microsatellites, sections of the double-stranded DNA molecule which mutate at a much higher rate. When such mutations occur in a small population, like the winter-run, some will become much more prevalent than in other populations, providing a means of identifying the run. This work has resulted in a number of findings where striking frequency differences between the runs enable run discrimination.

"Five markers were found to have mutations that occur at a much higher frequency in the winter-run," explains Greene. "Two at an extremely high rate, the other three not quite as high. But the more markers you can use, the more statistically significant the findings, meaning the greater the confidence that these markers are identifying winter-run."

The results, though preliminary, look promising. So far, the potential to identify winter-run by their genetic markers is greater than for any other run.

So how will this discovery help SWP operators when facing a take level? The Department hopes that the analysis will gain acceptance among fish biologists and will be used to identify winter-run within days after samples are taken from fish salvaged at State and federal facilities.

The premise was tested in 1997 during the first "rapid turnaround" analysis of salvaged chinook salmon. Though the sample size (95) was small, results were ready four days after the lab received the fin tissues. "Small numbers can be done in 24 hours," Greene explains. "But hundreds of samples would take several, days."

As for the accuracy of the analysis, that's a question to be answered by a validation test to be completed this fall.

"Because these results are preliminary," says Greene. "we can't say how regulatory agencies will deal with the information. They support the work, but more research is needed."

Future Efforts
This summer the UCD staff submitted their results for publication, which will open the data and interpretation to scrutiny by other geneticists.

Under a new three-year contract which will begin in November, the Bodega Marine Laboratory scientists will conduct further analysis, and more samples will be collected to confirm that the genetic markers that appear to distinguish winter-run remain so from year to year. Attention will also focus on developing a near real-time demonstration project that will estimate winter-run chinook losses at SWP and CVP Delta intakes.

The ultimate results of the DNA study will do more than estimate take for regulatory agencies and water project operators. The information will lead to a better understanding of the different chinook runs, as well as provide insight to the species' future survival.

"Fishery biologists have a good understanding of adult chinook salmon, but are uncertain about what happens to the juveniles when they're in the Delta," says Sheila Greene. "More than one run are in the estuary at the same time, and it's especially hard to determine when the winter-run reach the Delta. Their numbers are low and there is the potential for them to enter over a wide range of time.

"What if we modified SWP operations to benefit the winter-run and they weren't there? We need to learn when they are at risk and how we can best protect them. We're hopeful the DNA study will help us make the right decisions."



sidebar
Projects that Protect
When the Bay-Delta Accord was signed in December 1994, water users agreed to share in the funding of nonflow-related habitat programs. These address factors other than water exports that affect the ecological health of the region.

Water users contributed $22 million to pay for nearly 40 environmental restoration projects of which a second DNA study of spring-run chinook salmon is one. Its focus is on finding the genetic markers that identify the spring-run as well as the different spring run populations in several Central Valley streams.

Other Category III projects include fish screens and ladders, watershed conservancy and management, a study of exotic species, pollution control, and a winter-run salmon captive broodstock program.