Spring chinook salmon in a fish hatchery

Huge dam demolition could save salmon on the edge of extinction

Spring-run Chinook salmon, critical to Indigenous fishers along the Klamath River, are in steep decline. But two recent developments may offer a path to their recovery.

Spring chinook salmon come of age in a hatchery. Once their eggs mature, they will be released back into the wild. Chinooks that migrate in the late spring are becoming rarer primarily due to dams and climate change.

Photograph by Corey Arnold, National Geographic

When Karuk tribal member and cultural biologist Ron Reed was just a toddler in the early 1960s, he liked to crouch on a rounded rock poking out of the rushing water of California’s Klamath River, watching his family fish for the Chinook salmon that arrived in late spring. The fish crowded so thickly in the water that they looked nearly solid enough to walk across.

His family had waited through the long winter for these fish. They would fill sacks full of salmon, enough to feed them several times a day for months.

Those days of extreme abundance are decades gone. For the past few years Reed, fishing now with his own children, has taken only a few spring-run fish from the river. Dams, climate change, and other issues have wreaked havoc on salmon along the U.S. West Coast, and the declines have been particularly acute for the spring-run fish, which migrate farther upstream and so are more likely to have been cut off from their habitat by the dams.

But on November 17, a long-delayed project to remove some of the major dams on the Klamath cleared a major hurdle: The governors of California and Oregon agreed to take control of the dams from PacifiCorp, the utility that operates them. The states and the utility have also agreed on financing for the $450 million plan. Federal regulatory approval is still required, and nothing is certain—but for now the dams are back on track for removal starting in 2023.

And that raises the question: Can spring-run salmon still be saved on the Klamath?

With spring-run numbers at record lows in many rivers, tribes and conservation groups have pinned their hopes on getting the spring fish designated as a distinct population and protected under the Endangered Species Act. They think that would help to protect the fish long enough for the dams to come down and their habitat to be restored.

New research published last month in Science confirms that there is a genetic difference between the early- and late-migrating fish. The difference is crucial but tiny: “In the biological sense, they’re not different animals,” says John Carlos Garza, a fisheries scientist at NOAA and one of the authors of the study. That could complicate an ESA designation.

However, the gene that enables spring migration turns out to be more prevalent in fish that swim the Klamath and other rivers than scientists had thought—and that, Garza says, raises hopes that the spring-migrating fish could be restored once the dams are gone.

‘The trees are made of fish’

“A spring fish, for a tribal member, is worth five times a fall fish,” says Keith Parker, a Yurok tribal member and its fisheries biologist, who grew up fishing on rivers in the Klamath Basin. “They taste better, they’re fatter, they’re this wild, vibrant color. They’re amazing.”

For millennia they have been a crucial food source and an integral part of culture for tribes up and down the West Coast.

“The river is the vein, the artery of our existence,” says Charley Reed, Ron’s son and a graduate student studying salmon at Humboldt State University. The salmon are part of that river: a gift, a thing to be cared for, a manifestation of the cyclicity and reciprocity of a world in balance. “[They’re] a reminder of our responsibilities, whether that’s to harvest and sustain our lives, or our responsibilities to manage and care-take our environment.”

The core of their religion, adds Ron, “is to be true stewards of the forest.” And that stewardship intrinsically revolves around salmon.

Salmon was estimated to comprise half of the Karuk’s caloric intake before European contact. Even in Reed’s childhood, it was ubiquitous. “We ate so much we would get sick of it,” he says. But the loss of salmon and other traditional foods such as acorn and lamprey has completely shifted the dietary landscape. Today the Karuk tribe has the “dubious honor of having one of the most dramatic and recent diet shifts of any people in North America,” writes sociologist Kari Marie Norgaard. Research has shown a relationship between the decline in salmon and increases in diabetes and other health-related issues.

Before colonizers showed up and changed the rivers, and particularly when dams didn’t block their migrations, the spring fish would swim sometimes hundreds of miles upstream, to their spawning grounds. They parked in pools and streamlets for months, slowly drawing down their stores of fat as they sat out heat waves and dwindling water flows, patiently waiting for the moment to drop their eggs and sperm so they could finally rush back to the ocean.

The migration for fall salmon, in contrast, is shorter in distance and time—still remarkable, but more targeted.

Those different migration strategies meant that salmon could live in just about every pocket of habitat along a river, from the mouth to the very upper reaches, from the spring until the end of fall. Their journeys created an elegant ecological link, connecting the Pacific directly to verdant hillsides hundreds of miles away. Predators would swipe the fish from the water and drag them away to eat, leaving the carcasses to funnel vital, sea-sourced nutrients to a whole menagerie of plants and animals.

“The trees are made of fish,” says Parker.

For millennia, Native people managed the fish that swam up the rivers. They lit fires that laid thick clouds of smoke overhead when it got too hot in the summers, cooling the waters below; they built weirs to help some fish leap up waterfalls. They took fish from the glistening runs, but not more than they needed, leaving plenty to reproduce.

Everything changed by the mid-1800s. Miners, newly arrived and searching for gold, blew up hillsides, clogging them with sediment. Canneries pulled vast quantities of fish from the water; by the 1880s they were processing somewhere between 5 and 10 million pounds of salmon a year, many of them spring-run fish. Dams went in up and down the rivers.

Many springer populations disappeared. Those that are left are only fractions of what they once were. On the Salmon River, a tributary of the Klamath, the annual spring counts have turned up less than 200 fish for the past four years, down from 1,600 in 2011—and a far cry from what Reed remembers. The primary culprits are the enormous dams that keep spring salmon from their spawning grounds on the high river.

“Imagine: I’m a 50-pound, big, chunky fish. I’m gonna haul it up the river toward my spawning grounds, and then boom, I hit Iron Gate Dam [on the Klamath],” says Parker. “I have a phenotype and genotype that have developed over thousands of years that are telling me I’m supposed to run 300 miles upriver, but I can’t because there’s a dam in the way.”

From the 1960s on, many natural barriers along the rivers were dynamited, sometimes with the intention to help fall-run fish get higher up the river but often messing with more of the springers habitat. And climate change has boosted water temperatures in many parts of the Klamath basin nearly a degree Fahrenheit over the past decade—a big deal for cold-blooded animals.

Lose a gene now, lose it forever?

It was a 2017 study that first established something remarkable about Pacific salmon: Just one tiny area of their genome seemed to entirely control the timing of when a fish migrated.

It was clean and simple: If the fish had two copies of the “early” gene, they’d show up for their river migration early in the season. If they had two “late” genes, they’d show up late in the year. If they had both, they’d migrate somewhere in between.

That a behavior this important would be controlled by a tiny section of the genome—the new research suggests that it takes up just about 0.0000125 percent—was “really astounding,” says Nina Overgaard Therkildsen, a conservation geneticist at Cornell University.

The research—both from a few years ago and again now—also shows that this adaptation happened only one time, many thousands of years ago.

“The fact that it’s a trait that only evolved once and spread so widely has important implications for conservation,” says Therkildsen. “It means that the variant itself might not evolve so readily if we lose it.”

Communities invested in the springers’ survival latched onto the fact that there was a clear genetic difference between spring- and fall-run fish, albeit a small one. In 2017, the Karuk Tribe and a local nonprofit petitioned to have the spring Chinook salmon in the Klamath Basin considered for protection under the Endangered Species Act—independent of, and separate from, the fall-run fish.

Answers, deep in a fish genome

In collaboration with the Yurok Tribe, who routinely scoop spring-run salmon from near the mouth of the Klamath River for sustenance, Garza and the NOAA team collected hundreds of fish during all parts of the season and sequenced their genomes. They also looked at the traits that had long been noted as distinctions between the spring and fall fish, like their fattiness—a characteristic Reed, Parker, and other Indigenous fishers have long noted as distinct to the springers.

Once again, the data was crystal clear: A tiny gene region predicted 85 percent of the variation in migration timing.

But the spring and fall fish, the researchers found, were essentially the same in other crucial respects, like their fat content and maturity. They just looked different because the spring fish were getting caught earlier in the season, when they had not yet depleted their fat stores.

The NOAA study was detailed enough to also answer another question: whether the spring-run gene is present in enough of the rest of the salmon population that it would endure, even if the numbers of springers themselves dwindled further.

Sure enough, the researchers found a surprisingly large number of fish with one copy of the early-migrating gene and one copy of the late one. These “heterozygotes,” they argue, could potentially serve as a sort of living storehouse for the crucial early gene, making it fairly easy to reintroduce the springers to places they’ve disappeared from.

“This means it is as straightforward as introducing” fish with the early gene back into the rivers if the good habitat is restored, says Garza. And if the natural population doesn’t have enough of the spring version of the gene, he says, a simple hatchery breeding program could pump up its prevalence.

The planned removal of the Klamath River dams raises that tantalizing possibility.

No matter what, springers need help

Other scientists are skeptical.

“We all recognize that spring and fall run fish interbreed to some level and create these heterozygotes,” says Shawn Narum, a fish geneticist at the Columbia River Intertribal Fish Commission. “The question is, can they be a source for recovery?”

“In populations that don’t have the spring run phenotype anymore, you don’t find a lot of heterozygotes. So you don’t find a lot of ability for that to reemerge,” says Tasha Thompson, a geneticist at Michigan State University who studies salmon populations throughout the West. “It’s going to take monumental amounts of effort.”

This new science will likely be considered as the agencies overseeing the endangered designation decide whether the spring salmon deserve special protection. The decision is overdue but is expected within a few months.

The protections would be useful, but perhaps more critical is getting the springers’ habitat back, which the dam removal might accomplish as it re-opens huge swaths of the upper rivers to spring-run fish.

Until that happens, Parker, the Yurok biologist, will stay worried.

“The river is still our grocery store,” says Parker. “We go to the river for these keystone cultural species that we’ve lived with for thousands of years and let us maintain our way of life. It’s only been in the last 100 years that we’ve wiped out the salmon runs.”

Without the spring fish, Reed fears a dark future for his family and his tribe.

“We’re going extinct,” he says. “That’s the ultimate impact of no spring salmon.”

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