Do No Harm

Ted Williams

Jul 1, 2018
Zach Sheller, hatchery manager, and Rachel Gorich, assistant manager, check salmon parr in the Peter Gray Conservation Hatchery in East Machias, Maine.
In published screeds over the last 40 years, I’ve been making some of the points Dr. Kyle Young made in “Kicking the Habit” (ASJ, Autumn 2017). Some fish managers still suffer from a malady I call Hatchery Narcosis—growing salmon and trout as if they were cabbages. In a process of reverse selection, these substandard replicas are transformed into everything wild fish aren’t. They do poorly in the natural world; and when they mix with wild fish they degrade native genetics and deplete food sources.

In the words of Dr. Peter Moyle, associate director of the Center for Watershed Sciences, University of California at Davis, “Domestic [salmonids] are as different from their wild ancestors as a dog is from a wolf or a cow from an auroch.”

In 1970, Montana’s Fish, Wildlife and Parks Department stopped stocking brown and rainbow trout in a section of the Madison River. Four years later, large trout (three years and older) were up 942 percent. This was a fact anglers didn’t want to know. The study area was sabotaged with trout from a private hatchery, and the towing hitch on the department’s truck was loosened so that boat and trailer parted company on the highway. The illegal stocking only corroborated the department’s data because the brown trout biomass dipped 24 percent.

Then, with two more years of no stocking, it shot back up. Since then Montana has not stocked its moving water.

The bad reputation of North American hatcheries is well deserved, and much of it is the result of hideous abuses in the Pacific Northwest that have squandered wild runs of salmon and steelhead.

Some West Coast hatcheries are trying to conserve or rebuild wild stocks, but the overwhelming majority produce fish strictly for recreational and commercial harvest, swamping wild salmon and steelhead. The lament of former Washington Department of Fish and Wildlife director, and wild-fish advocate, Bernard Shanks is nearly as true today as when he uttered it in 1997: “If you cross a sacred cow with a military base in Washington State, you get a fish hatchery.”

Washington State has 12 federal hatcheries, 51 tribal hatcheries and 87 state hatcheries. When Shanks gently floated the idea of closing a few ancient facilities, some of which were cranking out salmon at a cost of $300 each, he was cursed from hell to breakfast by sportsmen, politicians, media and the Northwest Treaty Tribes —all whipped to furor by the department’s hatchery bureaucracy which constituted one quarter of its employees. Instead of closing hatcheries the state built new ones and Shanks was hounded out of office.

Under orders from the National Marine Fisheries Service, the department has phased out its Chambers Creek steelhead stocking on the lower Columbia river’s threatened steelhead habitat. But it continues to pollute Puget Sound Rivers with these grossly inbred and domesticated fish, aptly described by retired Montana State fisheries professor Dr. Ray White as “farm animals developed for living in hatcheries.” Wild Chambers Creek steelhead, long extinct, evolved in a low, warm basin so they spawned early. This allowed managers to produce smolts in one year instead of two or three.

And consider the not-so-atypical Leavenworth Hatchery, a production facility for Chinook salmon on Washington State’s Icicle Creek run by the U.S. Fish and Wildlife Service as “mitigation” for the Grand Coulee Dam. The hatchery impedes migration of threatened Upper Columbia River steelhead, threatened bull trout, coho salmon and endangered spring Chinook, which it also exposes to genetic contamination from its domestic stock. On top of all this, it violates the Clean Water Act by polluting Icicle Creek and the Wenatchee Basin with phosphorus from feed and feces.
Large parr at the Peter Gray Conservation Hatchery
A decade ago, the Wild Fish Conservancy filed a Clean-Water-Act violation enforcement case against the Leavenworth Hatchery, forcing the Fish and Wildlife Service to do a “401 certification” analysis that included chemical as well as biological impacts. The Service agreed to open a downstream dam on Icicle Creek, provided no more than 50 Chinooks ascended.

Officials worried the upstream migration might shed pathogens into the hatchery’s water source. But during spring runoff, when native fish attempt to migrate up that historic channel, they hit a fire-hose-like flow from a water-control dam. “The Service’s new 401 analysis, all of six pages, ignores instream flow,” reports Wild Fish Conservancy executive director Kurt Beardslee. “It’s absolutely insane. We’ll be filing a new case soon.”

From an ecological perspective you can’t “improve” production hatcheries because their function is purely to pump out fish for harvest. But you could greatly lessen damage they do to wild fish by moving them down to river mouths, or by merely trucking or barging smolts there, thus creating terminal fisheries. You’d get increased survival, and wild fish would suffer less genetic contamination because hatchery stocks wouldn’t imprint to upriver routes.

The biggest salmonid producer on California’s Sacramento River system is the Coleman Hatchery, 250 miles from the sea. That means stocked fish have to negotiate a highly modified flow with all its dams and predation issues. One of the few upsides of the recent five-year drought was that the river was so low and warm that Coleman fish had to be trucked down to the Sacramento-San Joaquin River Delta. Another upside is that these hatchery fish strayed, creating a robust Chinook run in Putah Creek, a lower Sacramento tributary.

Straying of hatchery fish might be good for barren rivers, but it threatens wild salmonids and it’s happening worldwide. The Japanese, Russians and Alaskans have festooned the North Pacific with millions of salmon from their production hatcheries. Now chums and pinks are showing up from California to Newfoundland.
Corey Clarke helps transfer salmon from the Grand Manan sea cage site at Dark Harbour to the trucks that will transport the fish to Fundy National Park.
Hatcheries are like drugs. Everything depends on who’s administering them and why. Drugs can cause brain damage and death, but with no drugs few of us would make it past 40. Had it not been for hatcheries, lake-trout recovery in the Great Lakes could not have happened; there would be no landlocked Atlantic salmon in Lakes Champlain and Ontario and no hope for anadromous Atlantic salmon in the U.S. or inner Bay of Fundy.

With no hatcheries the planet would be without Lahontan cutthroat trout and greenback cutthroat trout (both declared extinct until rediscovered by Dr. Robert Behnke) and we would have lost most or possibly all our westslope cutthroats, Bonneville cutthroats, Rio Grande cutthroats, bull trout, golden trout, Apache trout and Gila trout. Then there’s a long list of imperiled non-salmonids.

“Stocking,” writes Young, “should only be considered for wild populations facing an immediate risk of extirpation.” That’s what faced inner Bay of Fundy runs at the turn of the 21st Century when adult salmon returns had dropped from something like 40,000 to less than 250. For reasons that include climate change and salmon aquaculture, fish weren’t surviving at sea. It became clear that once the few wild juveniles left such rivers as the Upper Salmon in Fundy National Park, most would never make it back as adults.

So the park had two choices: give up or attempt CPR on an expiring river with a revolutionary approach called “live gene banking.” Juvenile fish are collected from the wild and reared in a hatchery to produce broodstock. These are selectively mated to maintain genetic diversity, and their offspring are released to maximize natural selection.

This from Corey Clarke, the park’s salmon-recovery team leader: “What we found with our monitoring, and published in 2016, was that fish with less exposure to captive conditions exhibited higher levels of wild fitness. This agreed with a growing body of literature.

We weren’t able to suggest that our number-one concern, at-sea survival, would improve; but we observed multiple other measures of wild fitness that improved when we decreased captive exposure. So perhaps our best chance of improving at-sea survival was to raise and release adult salmon whose progeny would have no captive exposure.”

The park has been trapping wild smolts and taking them to the world’s only wild-salmon aquaculture operation just off Grand Manan Island. The net pens are operated by Cooke Aquaculture largely at its expense. For the last three years, adult salmon reared there have been transported by Canadian Coast Guard helicopters to prime habitat in the Upper Salmon River. Just about everywhere survey crews have been electro-fishing—in places barren for 20 years—they’re finding progeny of these fish. And, while it’s too early to assess ocean survival of resulting smolts, some adults are returning. “We got eight back in 2016 and 30 back last year,” says Clarke. “For the inner Bay of Fundy that’s huge.”

As a control, Fundy National Park has stocked its other river, the Point Wolf, with fry only and there have been no adult returns. Now, with the encouraging results from the Upper Salmon, the park will start live gene banking on the Point Wolf, too.

A similar project is being administered by the Fort Folly First Nation on the Petitcodiac River, which flows into the Bay of Fundy at Moncton. Here there’s road access so adult salmon from the pens are being trucked to release sites.

Whether or not the strategy can restore wild salmon runs remains to be seen, but the University of New Brunswick has already documented positive effects on the Upper Salmon River ecosystem, which has been infused with 2,200 adult fish. With their excretions, eggs, milt and sometimes their decaying carcasses they’ve returned some of the traditional nutrient load.

That new richness is cascading up the food chain to all manner of life forms, juvenile salmon included.

Returning nutrients to aquatic ecosystems could be at least as important as returning salmon, opines the University of New Brunswick’s Dr. Tommi Linnansaari, who serves as research coordinator for the Collaboration for Atlantic Salmon Tomorrow (CAST). He’s the leading proponent of a “smolt-to-adult supplementation” (SAS) proposal for the Miramichi. “I’m spending 95 percent of my time on SAS because there has been a resistance movement,” says Linnansaari. “We don’t understand where it’s coming from.

I think there are a lot of misconceptions.”
A coast guard helicopter assists Parks Canada staff with the salmon release at Dark Hole, an inaccessible stretch of the Upper Salmon River.
At least on the Miramichi River, where the Miramichi Salmon Association wants a SAS program, part of that resistance is coming from DFO. The CAST partners agreed to a review in 2016 through the Canadian Science Advisory Secretariat (CSAS), which provides peer-reviewed scientific advice to the Canadian government on fisheries issues.

That review expressed concern that captured smolts will take two and a half years to mature, swimming around in tanks and never be exposed to the many natural-selection influences of the marine environment. How this might affect progeny is unknown. Another CSAS concern was that by randomly collecting smolts, CAST may have unintentionally selected for poor-performing genes.

A recent international conference on stocking organized by the North Atlantic Salmon Conservation Organization (NASCO), involving highly respected salmon scientists from Canada, the United States, Wales, Switzerland, France and Norway, reached the same conclusions.

Even using today’s low marine survival rates of two to three percent, there could have been 100 or more wild and supremely fit adults returning to the Northwest Miramichi each of the past two years, had CAST not captured some 9,000 smolts for the hatchery.

“The Miramichi still has a relatively healthy wild salmon population—very different from those of the Bay of Fundy and Gulf of Maine,” says Jonathan Carr, ASF’s vice president of research and environment. “There are lots of other choices that can effectively increase salmon survival such as improvements to habitat and predator-prey balances. What has been proposed is significant—potentially stocking more SAS adults into the river than returning wild salmon.

Until a full assessment of SAS is completed, doing this in the Miramichi is like playing Russian Roulette. If it succeeds, you’d be considered a genius; but if it fails, this world-renowned salmon river could lose big on many fronts. I think the SAS technique is worth trying on rivers like the Tobique, Upper Salmon and Petitcodiac. If the strategy is proven successful—taking at least one salmon generation or likely more to evaluate—it could be an effective tool. But to run such an experiment on the Miramichi, at the scale being proposed, and not knowing the outcome is a big risk.”

For Linnansaari it’s about prevention. “Typically when intervention is initiated, you are looking at a river that is already extirpated or on its last legs. In the case of the Upper Salmon the patient was dead. If I’m sick, I’d much rather have the doctors intervene when I’m alive rather than waiting until I die and then trying to resuscitate me.”

Except for the Penobscot, U.S. salmon rivers also “face a risk of immediate extirpation.” All 12 are in Maine. On a good year the Machias and East Machias Rivers might get 14 adults each. The others usually get single numbers.
Adult salmon from sea cages arrive at the Pollett River, a tributary of the Petitcodiac.
Last May, I visited the Downeast Salmon Federation’s Peter Gray Conservation Hatchery on the East Machias. Unlike many traditional hatcheries this one uses river water. So fish hatched from East Machias eggs, provided by the U.S. Fish and Wildlife Service’s Craig Brook National Hatchery gene bank, are exposed to the bacteria and fluctuations in temperature and pH they’ll encounter in the wild. Substrate incubation boxes act as artificial redds, allowing alevins to emerge on their own, using energy from yolk-sacs for growth rather than locomotion.

The holding tanks are painted black rather than the traditional blue so that fry take on darker, more natural coloration. As they grow, water velocity is increased to tone muscles. Parr are stocked in late fall when their metabolisms are lower and competition for reduced food declines.

What the Downeast Salmon Federation is doing has never been attempted in North America. But the method, conceived by Peter Gray (1941- 2013) at the Kielder Hatchery on England’s River Tyne, may have been instrumental in one of Europe’s most dramatic salmon recoveries. Average annual catch rates on the Tyne have increased from a few hundred to around 4,000. Gray believed that traditional salmon hatcheries fail because they produce inferior fish. He advocated production of “little athletes” that can better handle challenges of river life and, especially, survival in an increasingly hostile ocean.

On the Tyne there was scant monitoring. Habitat, pollution control and a suspension of commercial netting in the estuary doubtless played a part in salmon recovery; and sea trout, which weren’t stocked, surged back along with the salmon. On the other hand, salmon runs on rivers with similar water-quality and habitat improvements remain depressed.

Part of the Peter Gray philosophy is to saturate habitat with as many parr as possible. The Downeast Salmon Federation put out 200,000 in 2017. And it will double that annual number when it finishes adding 15 more tanks.

“The East Machias system is infested with smallmouth and largemouth bass, chain pickerel, yellow perch and white perch,” says Federation director Dwayne Shaw. “So there’s probably no better test as to whether salmon can make it in Maine. The uppermost lake, Pocomoonshine, has been managed by the state as a trophy largemouth fishery almost since the illegal introduction. That’s ridiculous. But despite all this, parr survival is amazing.”

Even with the Peter Gray approach, parr may be somewhat degraded by hatchery life. But like Fundy National Park, the Fort Folly First Nation and DFO, the Downeast Salmon Federation has two choices: give up or try a new approach.
An East Machias smolt ready to “better handle challenges of river life and, especially, survival in an increasingly hostile ocean.”
Hatcheries have been blamed for failure of salmon recovery on the 407-mile-long Connecticut River, which once sustained the continent’s largest Atlantic salmon runs. But having been heavily involved and invested in that effort almost from the start until the Feds pulled the plug in 2012, I’m convinced that’s a bum rap. Our native stock was extinct; so we had to fashion a new native with succeeding generations of fry from the few fish fit enough to make it back from Greenland. It was simulated natural selection run at fast-forward, and it was close to succeeding. What failed was not the hatchery stock, but the habitat and the environment.

Steve Gephard, Connecticut’s supervising fisheries biologist, agrees. “

In my mind a major factor has been climate change,” he says. “We’re at the southern extent of the range. Long Island Sound is getting warmer every year. Maine has the nice, cold Gulf of Maine and quicker access to the ocean and Greenland, and even their Downeast-river returns are abysmal. Our fish had to go around Cape Cod. It’s not easy for me to talk about this because I’ve put my career into it.”

Wild fish stray, too. It’s part of their survival strategy. As the earth heats up hundreds of rivers above the Arctic Circle, previously incapable of sustaining Pacific salmon, are being colonized. While data is scarce on the East Coast, Atlantic salmon are being reported in Greenland and Baffin Island streams previously inhabited by char only. Is the new salmon habitat good news? Only if you ignore all the displaced fish and wildlife.

Maybe hatchery managers won’t be able to adapt to the challenges of global warming and ocean mortality. But at least they’re trying, especially with Atlantic salmon.

Ted Williams, a member of the Journal’s editorial board, serves as national chair of the Native Fish Coalition ( and writes the monthly “Recovery” column for The Nature Conservancy’s online magazine Cool Green Science (