Keywords: Species and food webs, Fishes, Freshwater habitat, Salmonids, Species of concern, Elwha River, Salish Sea Currents magazine

Our series 'Returning home: The Elwha's genetic legacy' continues with a look at the possible return of spring Chinook to the upper portions of the Elwha River. We bring you part three of seven.

Given a clear path upstream after dam removal, Chinook salmon in the Elwha wasted no time swimming past the first dam and later the second. Yet, unlike steelhead, Chinook still have not ventured into the upper watershed in large numbers, according to recent surveys. Ongoing genetic studies are now trying to determine if the powerful spring Chinook that once fought their way through the river's upper rapids have become extinct, as many experts suspect.   

Bull trout actually won the prize for being the first anadromous fish to pass upstream of Glines Canyon Dam, sneaking through before dam demolition was even complete. A few days after workers blasted away the last chunk of the dam, biologists noticed a Chinook salmon swimming in upstream waters. It was Sept. 2, 2014, when a team of volunteers was preparing to deploy a net to see what they might catch.

“I walked over to the edge of the stream, and right in front of me was a big, fat, bright female,” said Mel Elofson, assistant habitat manager for the Lower Elwha Klallam Tribe. “It was like a godsend. This was something that my grandparents, aunts and uncles all wanted to see.”

Elofson, a tribal member, said the Elwha Dam was built while his grandparents were children. He recalls his grandmother, Louisa Sampson, telling him about the tragedy of seeing salmon leap up against an unyielding concrete wall. Tribal members, whose ancestors practiced fishing traditions for thousands of years, never lost hope that the dams would someday be gone.

“I used to hang out with the elders; they taught me how to fish,” he said, noting that his elders would have been delighted to see the return of the salmon. “I got to be their eyes,” he added. “I was ecstatic.”

Elofson said the female Chinook he saw was about 2½ feet long. A week later, biologists snorkeling above Glines Canyon spotted three Chinook, all between 2½ and 3 feet long. Still, the numbers of Chinook moving upstream remained relatively small.

Finding the early-migration gene in the remnant population of Elwha Chinook could provide hope that a growing population of spring Chinook might emerge over time.

More complete snorkel surveys in 2018 and 2019 showed that while fair numbers of Chinook were moving into spawning habitat above the lower Elwha Dam, few were making it upstream past the site of the former Glines Canyon Dam, and fewer still were occupying the 18 miles of upstream habitat. For the two years of surveys, snorkel teams counted fish in early September along 22 river segments, going from high elevations down to the river mouth. Similar surveys were conducted in 2008 and 2009 before dam removal.

A person swimming in a river wearing snorkeling gear.

A fish biologist snorkeling to count fish in the upper Elwha River, Olympic National Park. Photo: NPS

A person wearing snorkeling gear standing in a river pointing to an area with lighter colored river rocks.

A snorkeler in the Elwha River points out a Chinook redd (lighter colored river rocks). Photo: NPS/USBR/USGS (CC BY-SA 2.0)

The tendency of Elwha Chinook to cluster between the dam sites was generally confirmed by researchers looking for signs of spawning by searching for gravel mounds created when females bury their eggs in the riverbed. These salmon nests, called redds, generally mark the end of a female Chinook’s migration. In a 2019 survey, 66 percent of the redds counted in the river were between the two dam sites, while 28 percent were below the Elwha Dam and only 6 percent were above the Glines Canyon Dam. This survey was part of a long-term study led by the Lower Elwha Klallam Tribe.

A similar distribution also was seen in a 2017 survey of Chinook carcasses found along the river after spawning. Tests on the dead fish revealed that 96 percent were released from hatcheries, primarily a state hatchery on the Elwha.

Experts have offered three possible explanations for why more Chinook have not yet migrated farther upstream, as the steelhead have done.

  • First, the low numbers of migrating Chinook result in less crowding, which could encourage them to spawn in the first suitable stream habitat.
  • Second, the vast majority of Chinook returning to the Elwha have been reared in a hatchery in the lower Elwha, which could create a greater affinity for downstream areas.
  • Third, the surviving Chinook population may lack the innate drive or the physical ability to ascend higher-elevation rapids, including the Grand Canyon of the Elwha. Perhaps the powerful spring Chinook that once fought their way through raging waters are now extinct.

The Grand Canyon of the Elwha could present a major challenge for migrating fish, although the issue has not been thoroughly studied. Among kayakers and river-rafters, this Grand Canyon is viewed as a world-renowned challenge at the edge of extreme. Class 5 and Class 4 rapids, with names like Goblin Gate and Nightmare, are characterized by whitewater rushing through narrow, sheer-walled canyons where boulders and logs are constant impediments.  The stretch of river called Nightmare is considered especially dangerous because of a blind corner where wild water surges through a steep and narrow passageway, making scouting and portage next to impossible.

River rushing through a canyon with a bridge across it at the top of the photo and person on standing on the left side of the bridge

Dodger Point Bridge in the Grand Canyon of the Elwha River. Narrow canyons and whitewater rapids of the upper Elwha may serve as a partial barrier that helps separate spring from fall Chinook. Photo:, CC BY-SA 3.0 via Wikimedia Commons

“The upper reach of the Elwha is an incredibly powerful place, not just for the force of the river but for qualities that inspire awe and wonder,” said Tom O’Keefe, an aquatic ecologist who serves as the Pacific Northwest stewardship director for American Whitewater. “You are in a canyon that is incredibly inaccessible yet magical with a real diversity of geology and a beautiful tapestry of botanical resources.”

While the magnificent old-growth forest suggests an ecosystem frozen in time, the canyon is a dynamic landscape, O’Keefe said. Heavy rainfall, rushing water and constant erosion trigger falling trees, rockfalls and even landslides. “You have to be aware of the constant change.”

Some experts believe that the wild waters of the upper Elwha could act as a partial barrier, helping to separate summer from winter steelhead, and perhaps spring from fall Chinook. In some rivers, early-run populations have evolved to move upstream during spring runoff, before the summer low-flow period. That could be the case for the Elwha, but it is not yet proven.

“Fish are so remarkable,” said O’Keefe. “What can be a very challenging environment for kayakers looks different when you’re in the water and realize how flow moves in three dimensions, with eddies here and there and pockets behind boulders. I’m sure there are places that create partial velocity barriers to fish, but I believe that if we give these fish time, some will find ways to make it through.”

Before the dams were built, it is possible that a unique breed of Chinook, perhaps larger or with special swimming abilities, were routinely making it through the Grand Canyon and other challenging rapids during the spring runoff.

As with steelhead, many Chinook salmon studied along the West Coast contain genes that help determine when the fish will enter a river and how far upstream they will go. Before the dams were built, the Elwha apparently had a large number of early-migrating spring Chinook, which were a key part of Native American culture and celebration. 

Studies are underway to determine if any of the Chinook returning to the Elwha still contain the early-migration variant within the GREB1L region of the genome, said Garrett McKinney, a research scientist at the Washington Department of Fish and Wildlife who is leading the study. Finding the early-migration gene in the remnant population of Elwha Chinook could provide hope that a growing population of spring Chinook might emerge over time. Since the fish now have access to extensive spawning habitat in the upper watershed, Chinook that make it through the Grand Canyon might be successful in producing ever more offspring able to make the trip.

Returning adults have been observed farther upstream as their numbers increase in the Elwha, although most are still spawning downstream of Glines Canyon, where the upper dam was located.

The number of spawners increased nearly threefold from 2016 to 2019, when the estimated number reached 7,600, based on sonar detections, net captures and redd surveys. This increase was seen during an upward trend for Chinook throughout Puget Sound, but the Elwha increase was more dramatic. The 2019 spawners produced more than 1 million juveniles leaving the river the following the spring. That’s nearly 22 times higher than the average number of subyearling migrants leaving the Elwha during the eight years before dam removal.

A single small fish swimming underwater with rocks in the background

Juvenile Chinook salmon in the Elwha River. Photo: John McMillan/ NOAA NWFSC (CC BY-NC-ND 2.0)

Because of lower ocean survival, the years 2020 and 2021 were down years for counts of adult Chinook in the Elwha. The number of Elwha spawners dropped to an estimated 3,250 in 2020 then to 2,630 in 2021, as declines occurred throughout Puget Sound. 

While fewer spawners produced fewer young out-migrants, it was encouraging to see that the number of surviving offspring per female increased after dam removal and has remained high the past three years, said Mike McHenry, fisheries habitat manager for the Lower Elwha Klallam Tribe. The latest productivity rate of 274 subyearling migrants per female is more than double what was observed before dam removal, he noted. An ongoing increase in natural spawning could, in turn, lead to greater ocean survival and more returns in the future.

While natural recovery of a spring Chinook population would be a pleasant surprise, it is still too early to tell whether any of the current Elwha Chinook population — dominated by hatchery fish — have maintained the GREB1L variant, assuming they once did. Of the Chinook returning to the Elwha today, almost none arrive in an early time period expected for spring Chinook. And researchers see no clear break in timing, as expected for a separate population. Furthermore, other research — including studies on the effects of a dam in Oregon’s Klamath and Rogue rivers — suggest that the early-migration gene is easily lost when spring Chinook can no longer separate themselves from other Chinook, as they do by spawning in upstream reaches.

The rapid revival of steelhead in the Elwha may well be driven by genes that still reside in the resident form of the species. But for Chinook — a species that has followed a different evolutionary pathway — researchers don’t normally find long-term residents hanging out in any stream. A few isolated exceptions exist where “landlocked” Chinook became trapped behind man-made dams, such as Lake Cushman on the Skokomish River in Hood Canal. Landlocked Chinook have not been found in the Elwha.

By sampling the full run of Elwha Chinook, genetic studies should reveal whether any early-migration genes remain in today’s population, said McKinney, the WDFW scientist. Since these fish inherit one gene from each parent, it is possible for an offspring with mixed parentage to have genes for both early and late migration. In many systems, these “heterozygous” Chinook have been found to return at an intermediate time — often in summer when chances of survival are reduced.

“Some studies have shown that the spring alleles are gone where spring Chinook are lost; other studies have found low levels of spring alleles,” McKinney said. “This is something worth looking for in the Elwha.”

McKinney says genetic techniques have advanced so rapidly that he expects that researchers will soon connect more regions of the genome with identifiable characteristics for many species. For Chinook, McKinney has published two papers showing that the age of maturity in males can be influenced by a genetic region on the Y chromosome. Since the Y chromosome is found only in males and is passed on completely to all male offspring, if a male Chinook matures early, all of his male offspring will also mature early. If he matures late, all of his male offspring will mature late and so on through the generations.

So far, McKinney has confirmed these findings for the Wenatchee River in Washington and certain rivers in Alaska, although there are three variants in the Wenatchee and four variants in Alaska, each variant having a different effect. He intends to continue this work for Elwha Chinook. One additional complication is that the genetic influence is reduced for hatchery fish, which seem to mature faster because of how they are fed, he said.

“I would like to look at that in the Elwha as well,” he said. “We would need to have a lot of wild individuals to compare. I really don’t know what to expect.”

Next week: Our series continues with a look at the return of other salmonids to the Elwha, including sockeye, bull trout, cohos, pinks and chums. We'll also report on the remarkable recovery of another spawning fish, the prehistoric-looking lamprey.  


View of the Elwha River above the site of the former Glines Canyon Dam in 2021. Photo: Sylvia Kantor

Following dam removal, migratory salmon have been free to swim into the upper Elwha River for the first time in 100 years. Their actual behaviors and reproductive success may well be driven by changes in their genetic makeup. Our seven-part series 'Returning home' examines how the fish are doing and whether the Elwha's genetic legacy remains intact. 


A single steelhead trout swimming under water with rocks in background

Migration patterns have apparently reawakened for the Elwha River's wild steelhead. Studies show that the fish may have retained much of their genetic drive despite 100 years of being trapped behind dams. We continue our series 'Returning home: The Elwha's genetic legacy' with part two of seven. 


Three salmon with green heads and red bodies seen underwater

The return of sockeye to the Elwha River is intriguing scientists. Could nearby freshwater kokanee help re-establish resident populations? We continue with part four of our series 'Returning home: The Elwha's genetic legacy.' 


Underwater view of a large group of silver and grey fish

Restoration managers are hopeful that populations of coho, chum and pink salmon will rebound on the Elwha River as the fish take advantage of newly accessible habitat. Part five of our series 'Returning home' examines the importance of genetically distinct salmon runs.


Underwater view of a single fish with red and white spots swimming above rocks

Bull trout appear to be thriving in nearly every section of the Elwha River. Populations there have at least doubled in the years since dam removal, signaling good news for a species that has struggled throughout the West. We bring you part six of our series 'Returning home: The Elwha's genetic legacy.'


Underwater view of two Pacific lamprey resting on rocks and sand.

Prehistoric-looking lamprey are recolonizing parts of the Elwha River that they have not occupied for more than 100 years. Like salmon, the culturally and ecologically important fish also move from saltwater into rivers to spawn. And like salmon, lamprey were devastated by the dams that once blocked their way. We conclude our series 'Returning home: The Elwha's genetic legacy.'   

About the author: Christopher Dunagan is a senior writer at the Puget Sound Institute.

Returning home: The Elwha's genetic legacy

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