[env-trinity] NYTimes: New tactics to save California's salmon - Iron Gate Hatchery

[Sari Sommarstrom]

http://www.nytimes.com/2016/01/19/science/new-tactics-to-save-californias-de
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Cover Photo: Salmon eggs at the Iron Gate Hatchery in California. Credit
Ruth Fremson/The New York Times  

  

To Save Its Salmon, California Calls In the Fish Matchmaker

 

At a hatchery on the Klamath River, biologists are using genetic techniques
to reduce inbreeding, though some argue natural methods are more effective.

 

By MATT RICHTELJAN. 15, 2016 

  

   

HORNBROOK, Calif. - On a frigid morning in a small metal-sided building, a
team of specialists prepared to orchestrate an elaborate breeding routine.
The work would be wet and messy, so they wore waders. Their tools included
egg trays and a rubber mallet, which they used to brain a fertile female
coho salmon, now hanging dead on a hook.

 

Diana Chesney, a biologist, studied a piece of paper with a matrix of
numbers, each one denoting a male salmon and potential match for the female
coho.

 

"This is the bible," she said of the matrix. "It's what Carlos says."

 

John Carlos Garza, a geneticist based a day's drive south in Santa Cruz, has
become a key figure in California's effort to preserve its decimated salmon
stocks. Using the latest genetic techniques, he and his team decide which
individual fish should be bred together. At several major state conservation
hatcheries, like the coho program here at Iron Gate, no two salmon are
spawned until after Dr. Garza gives counsel - a "salmon mating service," he
jokingly calls it.

 

Slide Show: A Scientific Matchmaker   CreditJim Wilson/The New York Times 

    

His painstaking work is the latest man-made solution to help fix a man-made
problem that is about 150 years old: Dams, logging, mining, farming, fishing
and other industries have so fractured and polluted the river system that
salmon can no longer migrate and thrive. In fact, today, owing to the
battered habitat, virtually all salmon in California are raised in
hatcheries.

 

Traditionally, the practice entailed killing fertile salmon and hand-mixing
eggs and male milt, or sperm, then raising the offspring packed in
containers or pools. When they were old enough to fend for themselves, they
were released to rivers or sometimes trucked or ferried to release points to
find the ocean on their own.

 

This practice gave them a necessary transition before they hit saltwater and
a semblance of the quintessential salmon experience of migrating to the sea
and back. To that end, they eventually swam back to hatcheries, where they
became the next breeders in the cycle.

 

While hatcheries have helped propagate the species, they have also created
new problems. The salmon they produce can be inbred and less hardy through
domestication, hurting their chances for surviving and thriving in the wild.

 

Dr. Garza hopes some high-tech ingenuity can help fix the salmon's troubles.
When the fish return to a hatchery, scientists there separate them into
individual tubes, clip their fins, then Fed-Ex the tissue samples to Dr.
Garza and his team. They then analyze each salmon's DNA, and match breeding
pairs that have no genetic relationship to each other.

 

The goal is to avoid breeding siblings or cousins, a break from traditional
methods of breeding the biggest fish (thought to be strong) without knowing
if the fish were related. At some smaller hatcheries, 50 percent or more of
salmon are inbred, Dr. Garza's work has shown.

 

"We're not trying to create the biggest, best, most productive fish," said
Dr. Garza, 51, who runs the molecular ecology and genetic analysis team for
the National Oceanic and Atmospheric Administration.

 

Those traditional methods led to homogeneity rather than the diversity that
makes a species more able to survive myriad challenges in nature, including
predators and disease.

 

"We're trying to mimic what's going on in nature," he added.

 

Photo: Unfertilized eggs scattered around salmon that were spawned at the
Iron Gate Hatchery. Credit Ruth Fremson/The New York Times  

 

His tactics, first used a decade ago and now used to breed half a million
offspring each year, inspire strong reactions, and hopes, in the passionate
community of scientists, environmentalists and commercial fish experts eager
to see the species preserved.

 

Underscoring the value of Dr. Garza's input, and of the genetic tools, he is
one of only a few people who consult with all 11 major hatcheries in
California.

 

"Carlos may hold the keys to the future," said John McManus, the executive
director of the Golden Gate Salmon Association, an advocacy group for
commercial and recreational fishermen. Perhaps the technology, Mr. McManus
said, can be expanded from a small subset of conservation hatcheries that
focus on the most endangered species to the bigger facilities relied upon by
the fishing industry and "infuse wildlike diversity back into hatchery
production."

 

But others question whether the mating service is just another misguided
step down a primrose path of human intervention. It is hubris, skeptics say,
to think that natural selection can be recreated through technology.

 

"It's a question of how much playing God will actually work," said Peter B.
Moyle, a distinguished professor emeritus of biology at the University of
California, Davis.

 

"Anytime you get tech solutions to natural problems," he added, "it seems to
me you wind up in trouble in the long run."

 

Re-evaluating Hatcheries

 

According to a Garza family story, Carlos was 4 years old when he first said
he wanted to be a scientist. But he would face several major detours as a
child.

 

He, his younger sister and his mother lived in a rough Philadelphia
neighborhood. Stubborn, angry and without his father around, Carlos battled
gang members, and wound up requiring the intervention of social services.

 

Photo: Bob Cook working with freshly fertilized salmon eggs at the Iron Gate
Hatchery. Credit Ruth Fremson/The New York Times  

 

Life did not improve much when he was 13 and the family moved to San Diego.
Carlos was kicked out of middle school for insolence and then dropped out of
high school because of a lack of interest, clashed with his family and left
home when he was 15. His sister, Mariel Garza, now an editorial writer for
The Los Angeles Times, thought "he'd be a bum of some variety," she said
with a laugh, knowing he is anything but.

 

Reviving his childhood dream of becoming a scientist, he attended community
college, then the University of California, San Diego, where he graduated
magna cum laude. He began researching monkeys in Thailand in 1990 - "the
dawn of molecular genetics," he said.

 

He earned his Ph.D. from the University of California, Berkeley, in
integrative biology. When he took a job at NOAA studying fish in 1999, he
remembered his Berkeley classmates being surprised he chose a job so
practical, so applied, as some scientists who favor theoretical work say
with derision.

 

Dr. Garza did not care much about fish. "Maybe to eat," he said. But he did
like solving real-world problems, even one involving the debate about
salmon. "It's not for the faint of heart," he said, adding: "I grew up in
that kind of environment."

 

Dr. Garza summarized the disagreement as one between what he called purists
and pragmatists. Purists want to see the tiny remaining population of wild
fish segregated from hatchery fish so that a native group can thrive;
pragmatists believe such segregation is impossible because of habitat loss
and the fact that hatcheries have already created genetic commingling. Once
the hatchery fish are released, the pragmatists say, you cannot control
where they swim, making segregation unrealistic.

 

The West Coast hatcheries, and the debates they inspire, date to the early
1870s. In 1875, Spencer Fullerton Baird, the first leader of the United
States Commission of Fish and Fisheries, wrote to the authorities in Oregon,
telling them that the way to preserve salmon was through hatcheries, said
Jim Lichatowich, a salmon biologist and historian. At the time, the
challenge to the salmon population was twofold: mining destroyed many rivers
and the fish were a popular source of protein for pioneers.

 

"Buy into these hatcheries and you will make salmon so abundant you won't
need to regulate the harvest," Mr. Baird wrote in the letter, according to
Mr. Lichatowich's description of its key message.

 

Was that prediction accurate? "Not by a long shot," the historian said.

 

Early hatcheries collected eggs from riverbeds, hatched them and released
months-old fry. "They did that until, in some cases, the stream ran out of
fish, and then moved on," Mr. Lichatowich said.

 

Photo: Salmon being checked to see if they are ready to be spawned at the
Iron Gate Hatchery. Credit Ruth Fremson/The New York Times  

 

In some cases, fish were released hundreds of miles from their native
streams. The fry lived in pools - early farms - over which a dead cow's head
was hung. Maggots would collect to devour the carcass, fall into the water
and become salmon food. It was the beginning of another self-defeating act:
It taught hatchery fish to wait for food to drop from the sky, and
short-circuited instincts that the shadows from above might be predators.
Finally, in other cases, fish were picked at random to spawn, their eggs and
sperm mixed in dishes, which led to inbreeding.

 

As damming and other water diversions reduced the natural habitat, the
hatcheries became indispensable. Today, in California, they produce 50
million offspring a year. Even so, the state has less than 10 percent of its
historic population of natural salmon, leaving 32 different kinds of salmon
and trout in the state as endangered, threatened or at risk, Dr. Moyle said.

 

But in 2012, Dr. Garza and other scientists wrote a critical report about
how hatcheries had done as much harm as good.

 

Among its key recommendations: Fish should no longer be inbred, a particular
problem for the most endangered species because dwindling populations leave
few mating choices (and a higher prospect of inbreeding).

 

"It's an extinction vortex," Dr. Garza said, "where inbreeding accelerates
the process of decline."

 

A Delicate Process

 

The story of F12, a female coho, shows the frantic intervention in the life
of an endangered salmon.

 

It began on Nov. 23 when she swam into the trap at the Iron Gate hatchery.
Her luck at having made it that far cannot be overstated. Each year, around
75,000 juvenile coho are released from the hatchery, which is at the base of
a dam on the Klamath River. On their swim to the ocean and back, the coho
face predatory birds, dry stream beds and disease. Most years, around 900
return in the coho salmon run. This year, fewer than 100 did.

 

By the time F12 reached the trap, her time was running out. Female salmon,
once they are ripe to spawn, typically drop their eggs in the gravel, then
die within days. On the Monday morning when F12 was plucked from the trap,
Ms. Chesney, the biologist, worked quickly. She clipped F12's fin with
scissors, put the sample into a manila coin envelope and, along with clips
from eight other fish, Fed-Exed it to Santa Cruz.

 

Photo: Bob Cook squeezing eggs from a female salmon, top, and milt from a
male salmon into a container of eggs, bottom. Credit Ruth Fremson/The New
York Times  

 

In the meantime, F12 was placed in a white tube and left in a round pool.
The tube separated her from other fish, each in its own tube, so they would
not become mixed up with one another when it was time to breed.

 

F12's fin clip arrived at 10:30 the next morning at the Southwest Fisheries
Science Center in Santa Cruz. Dr. Garza's team quickly processed the clip,
given F12's ticking clock. When fin clips arrive, Dr. Garza said, "it
pre-empts everything else."

 

In a lab with some $2 million of equipment, Libby Gilbert-Horvath, a
geneticist, put F12's clip into a solution to break the sample into
molecular parts, like proteins and nucleic acids. Then, F12's molecules were
processed by a machine that filters DNA. Next, a technique called enzymatic
amplification made millions of copies of F12's DNA to allow further study.

 

The next morning, Ms. Gilbert-Horvath used technology that allows fluids to
be studied at a nano scale; in this case, it let the team identify markers
at 96 of F12's individual gene sites. This technique, which Dr. Garza
developed, allows individual fish to be DNA fingerprinted. Finally, F12's
DNA was compared with that of the Iron Gate males to see which made the best
breeding partners.

 

At 5:07 p.m. on Nov. 25, the results were emailed to the hatchery. Because
of the Thanksgiving holiday, the breeding did not happen until Monday, Nov.
30. It was, in Ms. Chesney's words, "not romantic."

 

F12's tube was pulled onto a stainless steel table. Ms. Chesney studied the
mating matrix from Santa Cruz while hatchery staff members waited for
directions.

 

"Who's my home boy?" asked Bobby Cook, a staff member, wondering which males
would be spawned with F12.

 

Unfortunately, several top choices had died in their tubes over the long
weekend. The team was nervous. "We just hope they're alive. This is the
scary part," Ms. Chesney said.

 

Two matrix-approved males, named 28MN and 17MJ, were alive. Each was pulled
from its tube and smacked twice on the head with the mallet.

 

Photo : The Scott River near Hornbook, Calif., a spawning spot for salmon.
Credit Ruth Fremson/The New York Times  

 

It was time to breed F12, who now hung by her gills, dead, on a hook. Mr.
Cook stuck a needle into her side. This device forced air through F12's body
and caused bright orange roe to spill from her vents, about 1,500 eggs. Mr.
Cook divided them into two trays. Another staff member picked up each dead
male and squeezed milt into the eggs. The dead fish were tossed on a
conveyor belt for further study.

 

"It's a slaughterhouse," said Morgan Knechtle, the lead biologist at Iron
Gate, though he said the genetic sequencing tools provided a sharp contrast.
"In many places in the world, this level of technology is not provided to
humans."

 

It was a bittersweet day for the team. The good news was that it had spawned
four females, but, unfortunately, no new salmon returned to the trap.

 

"That's a run, folks," Mr. Cook said as the trap came up empty.

 

But Mr. Knechtle said he thought it would have been worse without the salmon
matchmaker, maybe only 50 coho over all, rather than the 100 they had seen.

 

Dr. Garza said he saw a bright future for this process. He wants to use
genetic tools at large hatcheries - not to dictate every mating but to get
DNA fingerprints and then track every hatchery fish from birth to death.
That way, he said, the hatcheries could deduce which spawning and management
techniques led to healthier fish.

 

Others agreed that there was no choice but to put these powerful
technologies to work. (They are also used in Idaho, Maine and Washington.)

 

"I know it's disheartening to people who want this kind of pure fish that
exists without us getting in the way of it doing its thing," said Jeanette
Howard, the associate director of science for the Nature Conservancy of
California. "But we're too far away from that."

 

"It's the best chance for saving this species," she added of Dr. Garza's
method. "He's created a great scientific enterprise."

 

But Dr. Moyle, from the University of California, Davis, said that while he
marveled at the technology, he feared that this may be another technological
fix that could create its own unforeseen problems.

 

"We think we can do better than Mother Nature," Dr. Moyle said. "You wind up
getting hooked on that system."

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