Connecting the Dots

Connecting the Dots header image
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

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

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

“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

“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

“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
. “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

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