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Connecting the Dots

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Tiny samples of living tissue reveal the genetics of salmon recovery.

Fifteen bodies slip through murky water. Over, under, around each other they move together like dancers, like trapeze artists. They spin, pause, loop.

Then, in one instant, it’s chaos.

Water splashing, bodies collide as they slide from creek to walls; ethereal forms become solid, streaking back and forth across the cement bunker. A flex of muscle carries them upward to break the surface. Gravity shouts back and they crash down, torpedoing toward the shallow bottom. Their powerful movements boil the water, fill the air with raucous noise.

Waist-deep in the roiling water, a man in chest waders and a green rubber coat wields a net among the thrashing bodies. He muscles a slippery twenty-pounder onto a worktable. With an ordinary office single-hole punch, he quickly punctures out three dots of paper-thin tissue from the tail fin; with forceps, he plucks a few scales from the back. Quieting the movement for a moment, he calls up to a colleague standing above the tank: “Chinook, male, 93 centimeters.”

Jeff Feldner
OSU Extension fisheries specialist Jeff Feldner is the fleet manger for OSU's Project CROOS. Photo: Justin Bailie

The man standing above the tank snaps a picture of the fish; then the man in the green rubber coat slides the salmon gently into the creek next to the holding area. The big Chinook disappears upstream.

After recording data and registering samples, the two men repeat the process with the other 14 fish.

All of it—the splashing, the sampling, the setting free, the three dots— are part of ongoing research related to the long-term health of wild salmon populations in the Pacific Northwest. Call it the genetics of migration, or the genetics of recovery.

Currently, on the west coast of the United States, there are 28 distinct populations of Pacific salmon listed as either threatened or endangered under the Federal Endangered Species Act. Since listing began more than 20 years ago, and despite heroic efforts at recovery, none of these Pacific salmon populations have been removed from the list.

salmon jumping
Wild salmon face obstacles throughout their lives. Researchers hope that understanding genetic diversity in salmon will help wild populations survive. Photo: Justin Bailie

“We don’t have a great measure of what the historic abundance of salmon was, but we know that it greatly exceeded today’s returns,” says Carl Schreck, a U.S. Geological Survey scientist with an appointment at Oregon State University. “In the case of salmon, we didn’t even truly realize the fishery was sick until it was essentially dying.”

Schreck is one of a generation of fisheries scientists whose careers have witnessed the decline of salmon in Oregon. He is joined by a legion of researchers studying salmon survival, including David Noakes, the director of the Oregon Hatchery Research Center. Here at this research center, the cement holding tank detours salmon on their migration up Fall Creek on the central Oregon coast.

With three dots of fin tissue and a few scale scrapings, Noakes and his colleague Joseph O’Neil, a biologist with Oregon Department of Fish and Wildlife, are collecting genetic samples from each fish. The samples function like a unique Social Security number, impossible to steal or duplicate, that can reveal the birthplace and some of the migration history of that fish.

Because of the way salmon move in the ocean, Oregon’s commercial fishermen often catch Chinook salmon reared in the rivers of California’s Central Valley and the California and southern Oregon coasts. Once leaving their natal streams and entering the salt, these loose schools of fish move north along the coast of Oregon. These include migrating schools of threatened and endangered populations from the Sacramento and Klamath rivers.

For much of the 2010 salmon season, while fishing boomed off the north coast, commercial fishermen off Oregon’s central coast were catching an average of three Chinook a day, earning captains about $225 per trip. Subtract deckhand wages, fuel costs, licenses, and boat maintenance, and $225 doesn’t reach that far, says Jeff Feldner.

Feldner fished commercially out of Newport, Oregon for more than 30 years before joining OSU as the fleet manager for OSU’s Project CROOS— Collaborative Research on Oregon Ocean Salmon. As an OSU Extension fisheries specialist, he spends more time on the phone than setting lines these days, but he’s still a fishermen at heart, especially when he steps onboard his boat, the Granville. The dark wheelhouse is not much larger than a closet and piled with books, pictures, extension cords, coffee cups, and extra layers of waterproof clothes and gloves. Somehow the extra gear, the little bit of mess, makes it feel cozy, safe, like good things and great times have happened here. According to Feldner, they have.

salmon go to market
Big ocean-caught chinook salmon (above), king of the seafood market, record specifics of their life history in their DNA. Photo: Justin Bailie

“Commercial salmon fishing out of Newport is about the most fun I’ve ever had,” Feldner says. “But in the 36 years since I started we’ve seen changes in the fishery and in management.” Many of those changes are directly related to the decline and listing of those 28 populations of wild Pacific salmon under the Endangered Species Act. Increasingly, commercial salmon seasons have been shortened or closed to protect threatened runs.

Pacific salmon are born in the gravels of the region’s rivers and streams. As adults they spend much of their lives in the open ocean, growing strong on the sea’s plentiful food. They then return to their natal streams to spawn and die. This life cycle seems straightforward, but it is anything but simple. Depending on the species, the population, the individual, and the year, Pacific salmon may begin to migrate toward the ocean as soon as they leave the gravel, or they may wait a year or two before leaving their natal streams. Some linger for weeks in the estuary while others make a beeline for the strong offshore currents. Once in the ocean, some fish will remain for only one year, others may stay up to seven.

“There are shifts in ocean conditions, shifts in freshwater conditions, changes in predation and food sources,” says Schreck. “One year smolts migrate early, the next year they go late. Even in the same year, some move at different times than others. There’s nearly endless complexity to salmon life history.”

Pacific salmon have managed to survive in large part because of this great diversity, says Schreck. Variability hedges the bets for survival when widespread changes occur in rivers, the ocean, or both. It can only be taken so far, though.

The National Oceanic and Atmospheric Administration Fisheries Service, in its 2010 Report to Congress, stated that “over the course of their life cycle, salmonids require suitable habitat in mainstem rivers, tributaries, coastal estuaries, wetlands, and the Pacific Ocean.” Meeting these requirements is not always simple in today’s world, says Pete Lawson, a salmon ecologist in NOAA’s Northwest Fisheries Science Center. Some things can’t be overcome through adaptation.

Fish are not superheroes, and it would be tough to say that there is anything in the genetic make-up of Pacific salmon that would help them to deal with the development of 200-foot-tall dams, the over-allocation of water for out-of-stream uses, overfishing, clearcuts, and the construction of superstores in wetlands.

“Salmon are incredibly tough,” says Lawson. “But there are limits.”

salmon tissue sampling
Salmon are waylaid at the Oregon Hatchery Research Center, where researchers collect tiny samples of tissue before sending the fish on their way upstream. Photo: Justin Bailie

To better understand both limits and possibilities for recovery, managers needed new tools. For 40 years, scientists used coded-wire tags placed in the snouts of some hatchery-reared salmon to track the movement of fish in the ocean. When the fish were caught, these tags worked like tiny ID bracelets, providing rudimentary information about the origin of the hatchery fish.

“The information from the tags was useful but incomplete,” says Gil Sylvia, the superintendent of OSU’s Coastal Oregon Marine Experiment Station. “We needed the ability to discriminate salmon stocks in real time on the open ocean to avoid weak stocks and target healthy stocks.”

Hatfield Marine Science Center became an epicenter for a project to meet this need, says Sylvia. A collaborative team of scientists from academia and federal and state agencies joined with local commercial fishermen to begin identifying Pacific salmon by their genetic make-up.

Remember the hole-punch. Remember the three dots and the scale samples.

The researchers who formed Project CROOS asked fishermen to collect small samples of fin and scale from the fish they caught in the ocean, and to send these samples back to Hatfield. There, researchers dissolved the samples in a sea of chemicals, extracted DNA, and identified genetic markers. Comparing these markers to a library of other genetic markers, researchers could pinpoint specific runs of fish. The magic of all this is that it worked, and it worked fast.

“When the scientists at Hatfield first asked us to take part, we voluntarily collected about 200 samples from fish caught in the open ocean,” says Feldner. “A week later, we knew where 190 of the fish had come from—the specific rivers where they were reared.”

Of the 200 fish the fishermen sampled, only two carried coded-wire tags from hatcheries. It would have taken months for the information from those tags to be available to managers. The potential benefit of the new science was a revelation.

“Coded-wire tags were used only on hatchery fish so very little was known about wild fish,” says Michael Banks, the director of OSU’s Cooperative Institute for Marine Resource Studies. “Genetic sampling told us not just where one fish had come from, it told us who all these fish were and it did it in nearly real time. It was the beginning of uncovering the genes that trigger different life histories and different migrations in the ocean.”

That was five years ago. Since then, Project CROOS has steadily refined its approach using genetic information to reduce the unintended catch of weak salmon stocks, avoid the long-term and widespread closures of salmon fisheries, and possibly help to ensure the survival of Pacific salmon populations.

“Pacific salmon are thought to have discreet migratory paths in the ocean,” says Banks. “If we can understand the genetics that guide these migrations, we can direct fishermen to healthy runs and avoid those that are in trouble.”

In studying the genetics of migration, Banks and his colleagues have created genetic IDs of 7,448 individual fish. They’ve tracked adults back to their natal streams and determined not only the species and population, but also the time the fish migrated into the ocean and where they traveled once there. Those three little dots collected at the Oregon Hatchery Research Center are part of the genetic library used to help identify fish sampled in the open ocean.

“Populations of fish that breed separately will become different,” says Banks. “These differences make it possible for us to identify families of fish and to know where they came from.”

In the future, this knowledge might help managers protect specific fish populations in specific times and places. “For two seasons, the Pacific salmon fishery was closed off the coast of California and Oregon in order to protect one weak stock,” says Kathleen O’Malley, part of OSU’s Coastal Oregon Marine Experiment Station. “A primary goal is to use what we’re learning about genetics to help reestablish weak stocks while continuing to provide a fishery for commercial fishermen.”

O’Malley is exploring the genetics of migration timing. She’s asking not only which fish are which, but also where are these fish and when. By identifying the genes that influence when adult salmon return to spawn and when juveniles migrate to the ocean, she hopes to better understand how salmon populations adapt to their local environments.

salmon carcass
At the end of its journey, the carcass of a spawned-out salmon resets the cycle for another generation. Photo: Justin Bailie

Current thinking is that adults spawn at the time of year that most benefits the growth and survival of offspring as they emerge from the gravel. But O’Malley points out that another crucial component is the seasonal timing of juveniles entering the ocean. During the first few months of marine residence, juvenile salmon typically experience mortality rates greater than 90 percent, she says. Therefore, selection should favor timing of out-migration with optimal ocean conditions, such as suitable temperature regimes, vertical mixing, prey availability, and low numbers of competitors and predators.

This new focus on genetics is helping researchers better understand how Pacific salmon in the region live, move, and die. Just like the fish, the science isn’t simple. It’s not neat, and sometimes it’s not pretty.

It is hopeful, though, says Gil Sylvia from his office at Hatfield where he’s buried under paperwork requests and grant proposals seeking funding to keep Project CROOS running for another year. Those three dots—they are working.

Published in: Ecosystems