Keywords: Species and food webs, Fishes, Marine habitat, Estuarine habitat, Nearshore habitat, Freshwater habitat, Salish Sea Currents magazine, Salmonids, Tribes, Traditional ecological knowledge

Spring and fall Chinook salmon were thought to be alike until researchers discovered a gene for early migration. Now, federal biologists and legal experts are struggling to decide if spring Chinook should be granted their own legal protection under the Endangered Species Act.


Each year, as the dark days of winter surrendered to the rebirth of spring, the Twana people earnestly waited for a unique type of salmon to return to the rushing rivers of Tuwa'duxq Si’dak, known today as Hood Canal.

Throughout the Northwest, bands of native people followed their own ancient traditions, greeting the mysterious spring Chinook that would show up after the mountain snowpack began to melt.

Now, such arrivals are rare. More than half the spring Chinook runs in Puget Sound streams — including those in Hood Canal — have gone extinct since settlers first appeared in the 1800s. Essential habitat in the higher elevations, where the spring Chinook like to spawn, was cut off or damaged by logging, farming, dams and development. Although fall Chinook generally fared better, they too have experienced severe declines.

In 1999, federal authorities placed Puget Sound Chinook — spring and fall runs together — on the Endangered Species List.

Over the past few years, thanks to extraordinary advances in genetics, scientists are beginning to understand the unique nature of these fish as well as the genetic losses that occurred when spring runs disappeared. Experts are now confronting the resulting ecological, social and legal implications of these losses while trying to save the remaining spring populations and possibly restore historic runs to some streams.

A fishery technician holds up a large female spring chinook salmon.

Dean Bearden, fishery technician for the North Fork Skokomish Salmon Hatchery, holds up a large female spring chinook during operations to artificially spawn the fish to produce a new generation of springers. This fish was among 156 adults to return to this hatchery this year. Photo: Sarah Nystrom/Tacoma Power

Before they were gone

In the Twana culture, the first blooms on the dogwood trees would signal a welcome break from the dried fish and other foods of winter, according to Delbert Miller, a cultural leader with the Skokomish Tribe and a descendant of the first people to live along Hood Canal.

Spring Chinook salmon, with their high fat content, enriched the native people, not only by providing fresh fish to share among the local families but also by helping to renew spiritual bonds.

The hearty salmon were even seen as noble, with characteristics that humans could emulate, said Miller. In a stream, these fish would never show off, although they were sleek and strong and could swim fast. They would remain concealed in the shadows, he said. To find them, one would look along the banks and in logjams.

“You understood the humility of the springers,” Miller said. “They were not there for public attention.”

The southern resident orcas were sustained for a long time by the early returns of spring Chinook to the Fraser, but in recent years those runs too have declined along with the orca population.

The springers were also important to many other creatures in the Puget Sound region and throughout the Northwest — from eagles to bears to killer whales. Until recently, the fish-eating southern resident orcas gathered their families together each spring in northern Puget Sound. The whales feasted on those fish that returned early to North Puget Sound streams as well as Canada’s mighty Fraser River.

Since spring Chinook generally traveled farther upstream, their routes of travel and spawning grounds were more easily disrupted by human activities. Their populations were the first to decline, followed by fall Chinook and other species.

Map showing historic (left) and current (right) distribution of Chinook in the Skokomish River system, before and after construction of the Cushman Dam.

Historically (left), spring runs of Chinook salmon (“early timed”) were found in the upper reaches of the North Fork and South Fork of the Skokomish River, and fall Chinook (“late timed”) migrated into the lower reaches of its tributaries. Human activities, including the construction of two dams on the North Fork, led to a severe decline in spring and fall runs of native Chinook (right). Maps: SIT and WDFS 2017.

The southern resident orcas were sustained for a long time by the early returns of spring Chinook to the Fraser, but in recent years those runs too have declined along with the orca population. During the summer of 2019, the whales barely showed up at all, spending more and more time off the outer coast of Washington and British Columbia.

In Hood Canal, the Twana people shared the belief that the seal-eating killer whales, a separate population known as transients, escorted the spring Chinook back to their streams, the fish following in the whales’ shadows, Miller said. Once in the river, the springers would blaze a trail for other salmon by scraping moss off the rocks as they swam along the stream bottom.

“In this way, other salmon that came behind them would know the best way to travel,” Miller said. “You can go down there and see the trails in the gravel.”

Salmon were among the natural gifts provided to the people, and a positive frame of mind was essential for receiving these gifts, according to Miller. Like his ancestors before him, he talks about tribal customs and life’s important matters, not directly or with black-and-white facts, but through the retelling of oral traditions.

As Miller learned while growing up, the personal revelations that come from these retellings may arise suddenly or sink in over time, but the lessons are not easily forgotten.

Which tribal members get to fish for various salmon, where the fishing takes place and who shares in the bounty are the result of long-held family traditions, which remain somewhat guarded even today — in part because of lingering feelings about former government policies that tried to eliminate the memory of native beliefs.

“There is far more to this that is not public knowledge,” Miller said. “It is a long telling, and there are things that I would not talk about.”

In recent times, “first-salmon ceremonies” have been celebrated publicly among a few tribes throughout the Northwest. For the Skokomish, these gatherings are kept mainly within the families, Miller said. Some tribal members say this could change, however, now that a new salmon hatchery is in operation on the North Fork of the Skokomish River, where spring Chinook are returning for the first time in decades.

Spring Chinook stocks of Puget Sound

In 1999, when Puget Sound Chinook salmon were listed as threatened, salmon biologists believed that spring and fall Chinook in the same stream were pretty much alike. An analysis leading up to the listing identified 31 historical Chinook stocks, of which 14 were of the spring variety.

Of the 14 spring stocks that could be identified in the rivers of Puget Sound, eight were declared extinct:

  • Stillaguamish and Snohomish in North Puget Sound
  • Green/Duwamish in Central Puget Sound
  • Puyallup and Nisqually in South Puget Sound
  • Skokomish in Hood Canal
  • Elwha in the Strait of Juan de Fuca
  • Spring Chinook in “mid-Hood Canal” (Hamma Hamma, Duckabush and Dosewallips rivers) were grouped as a single extinct stock.

Spring Chinook stocks still hanging in the balance are those in:

  • The north and south forks of the Nooksack River in North Puget Sound
  • The upper Sauk, the Suiattle and the upper Cascade rivers, all tributaries of the Skagit River in North Puget Sound
  • The White River in South Puget Sound.

Of the 17 fall Chinook stocks, all but one still has some natural production, according to the federal endangered-species assessment. The fall Nooksack run was listed as extinct, and the fall run in the Skokomish comes from a hatchery stock.

Genetic differences

For years, researchers have understood that genetic differences among Chinook populations corresponded well with geographic distances. In other words, when the home streams were close together, the populations had similar DNA and were closely related. In contrast, Chinook from more distant streams might be considered more distant relatives.

That makes practical sense, researchers say. If a migrating salmon gets off track, it is more likely to stray into a neighboring stream to spawn, as opposed to a distant one.

With genetic techniques used up until 2017, spring and fall Chinook from the same stream looked much alike wherever they were found, with some exceptions in the upper tributaries of the Columbia River system. In streams where spring Chinook were extinct, biologists generally assumed that if the stream were restored to provide passage and habitat upstream, then fall Chinook would eventually find their way there. They could fill the empty niche left behind when the spring run disappeared.

Biologists understood that run timing was an inherited trait, but major differences between spring and fall Chinook went undetected for many years.

That’s why it came as a groundbreaking discovery when geneticists, using more focused genetic techniques, came to realize that the very existence of spring Chinook resulted from a tiny aberration in the DNA on chromosome 28. Suddenly, when looking at that one section of the genome, all the spring fish looked alike and quite different from their fall counterparts.

A juvenile Chinook salmon. Photo: Roger Tabor/USFWS (CC BY-NC 2.0)

A juvenile Chinook salmon. Photo: Roger Tabor/USFWS (CC BY-NC 2.0)

Scientists have hypothesized that the first spring Chinook came about eons ago, diverging from a single mutation or series of mutations in their DNA. The idea that a single rare event produced a unique innovation in evolutionary history has been supported by studies showing that all spring Chinook studied so far — from Washington to California — are practically alike in this one section of their genome.

If this idea holds up, it could mean that fall-run Chinook occupied many streams before this new type of Chinook arrived, according to Tasha Thompson of the University of California, Davis, one of the researchers involved in the new discovery. Descendants of the first spring Chinook then spread from stream to stream, finding success by swimming upstream, perhaps jumping waterfalls and traversing cascades, reaching places that the later-migrating fall populations could not go because of lower streamflows.

“They need an evolutionary reason to exist,” said Thompson of the spring Chinook. “We think that might be tied to their finding access to exclusive habitat, maybe an area that they couldn’t get to if they migrated in the fall.”

Lost salmon in the Skokomish

In the North Fork of the Skokomish River, Twana fishermen once traveled upriver to where salmon congregated below two waterfalls. The first was Little Falls, about 10 feet high. Farther upstream was Big Falls, some 12 to 15 feet high. The waterfalls helped to separate the spawning grounds of spring and fall Chinook, since the springers were better able to traverse the falls when the river was swollen from spring runoff.

In an interview in 1978, then-75-year-old Skokomish elder Georgia Miller recalled visiting both falls with her family and friends when she was a child. Chinook salmon were still thick in the pools in the early 1900s, she said, and tribal fishermen would take them with spears and nets, as their ancestors had done in the same location.

“The fish would jump into this pool, and then from that pool they’d jump into the next pool and then on up…” she told cultural anthropologist Karen James. “The falls, where the salmon jumped in the pools, is where they would spear fish for a night’s supper if they wanted it in a hurry. They set the net below, where the water was calmer.”

Increased hatchery production, damage to the natural habitat, and heavy fishing beginning in the 1970s led to the demise of the indigenous Skokomish Chinook — both spring and fall — during the 1990s.

In the 1800s, settlers began clearing the forests to set up farms in the Skokomish Valley. Through the years, wetlands were filled and dikes were built to control the river, cutting off side channels that provided habitat for migrating Chinook.

In higher elevations, loggers began clearing the forests, an enterprise that lasted more than a century. To move the logs to market, they used horses and oxen, built railroads and later constructed one the most extensive road networks in the West. Sediment washed into the streams, smothered salmon eggs and eventually altered the character of the Skokomish River.

In 1926, against the protests of the Skokomish Tribe, the state government and numerous landowners, the city of Tacoma completed a dam on the North Fork above Big Falls, blocking migration of spring Chinook into the upper river. The dam provided electrical power for a city growing rapidly after World War I.

In 1930, a second dam was built on the North Fork below Big Falls. The innovative design produced even more power by diverting the entire flow of the North Fork into pipes, moving the water downstream to a power plant on the edge of Hood Canal. With no flow coming through the dams, the river all but dried up entirely.

The severe decline of salmon in the Skokomish River led to construction of the George Adams Hatchery in 1961. The hatchery produced large numbers of Chinook, utilizing a stock imported from the Green River between Seattle and Tacoma. By then, only a remnant of the spring run was returning to the lower North Fork and South Fork of the Skokomish.

Increased hatchery production, damage to the natural habitat, and heavy fishing beginning in the 1970s led to the demise of the indigenous Skokomish Chinook — both spring and fall — during the 1990s.

Rebirth of spring stocks

In 2009, long-fought legal battles between the Skokomish Tribe and the city of Tacoma over damage to the North Fork were settled with the so-called Cushman Agreement. Provisions required Tacoma to release more flow into the North Fork, restore natural runs of spring Chinook and sockeye, and build facilities to move salmon upstream and downstream, bypassing the two dams.

The spring stock chosen for restoration was imported from the Marblemount Hatchery on the Cascade River, a tributary of the Skagit River in northern Puget Sound. The stock was chosen before the discovery of the early-migration gene on chromosome 28. But recent tests showed it was a good choice, as fish in the river are almost entirely a pure breed of spring Chinook.

As millions of dollars were being spent on habitat improvements throughout the Skokomish watershed, Tacoma Power constructed a new salmon hatchery on the North Fork. The facility is now rearing spring Chinook while boosting existing populations of coho and steelhead.

Aerial view of the North Fork Skokomish Salmon Hatchery.

Spring Chinook salmon are being reared at the North Fork of the Skokomish River. The hatchery is owned and operated by Tacoma Public Utilities. Photo: Tacoma Public Utilities

Last year, for the first time in decades, springers made their way to the North Fork of the Skokomish and continued upstream until they reached the base of the lower dam. These fish were the 113 survivors from 141,000 yearling Marblemount fry released into the river in 2016. This year, another 156 adult springers returned. Their eggs were fertilized to produce the next generation.

Eggs from the returning springers will be supplemented with eggs from Marblemount Hatchery until 375,000 young Chinook can be released each year without help from Marblemount, according to hatchery manager Andrew Ollenburg of Tacoma Power. If things go well, fish returning to the North Fork next year may provide all the eggs needed, he said.

As the spring Chinook population grows, surplus adults will be transported upstream to spawn naturally in higher elevations above the dams. It appears, based on stream surveys, that some of the fish are already spawning naturally below the dams, and that’s all for the best, Ollenburg said.

According to state records, some of the best salmon habitat in the North Fork was inundated by Lake Cushman, the 8-mile-long reservoir above the upper dam. Some tribal members dream of reclaiming that lost habitat, but discussions about dam removal and other restoration efforts must wait. The current hydropower license expires in 2048.

Genetic mysteries

It remains a wonder how a tiny change in the genome of Chinook salmon can shift the migration timing of a fish from fall to spring. But with advanced genetic techniques and whole-genome sequencing, researchers have discovered that even small DNA changes can produce large effects in a variety of species. Changes in pigmentation and coloration from a single gene have long been known for birds, lizards, fish and even humans, but now even behavioral effects from single genes or groups of genes are being recognized.

Spring and fall Chinook from the same river system are known to be closely related through more than 99 percent of their genome, yet a tiny fragment— the “migration gene” —  makes them behave like a totally different fish.

The so-called early-migration gene causes spring Chinook to enter the streams early, often in April or May, but it does not dramatically change their spawning time. Both types of salmon still spawn in the fall. The springers hunker down in streams, ponds and backwater areas through the summer as they become sexually mature. Meanwhile, the fall Chinook remain in saltwater longer, coming into the streams closer to their spawning time.

While in saltwater, both spring and fall Chinook grow and mature at the same rate, according to John Carlos Garza, supervisory research geneticist at NOAA’s Southwest Fisheries Science Center in Santa Cruz, Calif. Spring Chinook come into the streams an average of four months ahead and spawn about a month earlier. Perhaps the warmer waters in the streams advance the spawning time of the spring arrivals, he speculated.

Like Chinook, steelhead are influenced by the same genetic characteristics found on chromosome 28. Although different from the spring chinook in the same gene region, summer steelhead are endowed with a gene that tells them to return early — at a time when winter steelhead are still at sea.

What causes these fish to decide that it is time to head back to shore is a subject of considerable interest. One hypothesis is that the early-migration gene governs hormones that adjust the internal migration calendar — which may involve the ability of salmon to track the length of days and nights.

Upheaval over Endangered Species Act

As geneticists come to recognize the distinct difference between spring and fall Chinook, federal biologists and legal experts are struggling to decide if spring Chinook should be granted their own legal protection under the Endangered Species Act.

The outcome could determine whether discoveries in genetics, now coming rapidly, will play a stronger role in defining “species” under the law and determining which groupings of animals warrant federal protection.

"Applied conservation is hard because biology is complex and messy and every practical application involves interactions with human customs, laws and institutions that can differ from place to place."

Robin Waples, Northwest Fisheries Science Center

Much attention at the moment is focused on the Klamath River, which flows from the high desert of Southern Oregon to the California Coast. Before the beginning of gold mining, dams, logging and excessive fishing, spring Chinook numbered in the hundreds of thousands throughout in the extensive Klamath system, which includes the Trinity River and its tributaries. But over time, the spring population plummeted, with counts under 5,000 fish in recent years.

In 2011, the Center for Biological Diversity, an environmental group, petitioned the federal government to place the Klamath spring Chinook on the Endangered Species List. After consideration, the request was denied by the National Marine Fisheries Service, which said Klamath spring Chinook should remain grouped with fall Chinook — and the population as a whole was not threatened or endangered.

In light of the groundbreaking genetic findings, the petition was renewed in 2017 by the Karuk Tribe, which traditionally fished the Klamath. The tribe was joined by the nonprofit Salmon Restoration Council. The tribe expressed urgency, saying it is now clear that if spring Chinook in the Klamath were to go extinct, they could never be replaced.

In accepting the petition, NMFS said it would take another look at the entire spring-fall Chinook population in the Klamath. If a listing of threatened or endangered is warranted, one option would be to keep the spring and fall populations together and consider the overall population decline since the 2011 petition. Based on the new genetic information, the agency said it would also consider listing spring and fall runs separately.

For listing purposes, the Endangered Species Act serves to protect entire species and subspecies as well as “distinct population segments” — abbreviated as DPS — among vertebrates. For Pacific salmon, the smaller groups are called “evolutionarily significant units,” or ESUs.

NMFS can designate an ESU when a population is reproductively isolated and represents an important part of an “evolutionary legacy” of a species. Most ESUs are identified by the stream or close group of streams where the salmon originate. All Puget Sound Chinook — spring and fall — are listed as threatened under a single ESU.

The agency currently considers spring and fall Chinook in the Klamath-Trinity system as a single ESU, but it could create a new ESU for spring Chinook alone — an idea that has stirred up discussions over the future of the Endangered Species Act.

Spring and fall Chinook from the same river system are known to be closely related through more than 99.9 percent of their genome, yet a tiny fragment— the “migration gene” —  makes them behave like a totally different fish. As new genetic information is discovered, federal officials are challenged to sort it all out and provide appropriate protection to unique populations, said Robin Waples, a researcher with NMFS’ Northwest Fisheries Science Center who helped develop the current DPS/ESU framework for grouping salmon.

“Should each river be a separate DPS that includes both life history types?” he asked in a “perspective” paper published in the journal “Evolutionary Applications.”

“Should each existing DPS be split into two — one with all early-migrating populations, the other with all late-migrating populations? Should each early-migrating population be a separate DPS, with the late-migrating populations either lumped (together) or in separate DPSs? Pros and cons for each of these strategies as well as others can be imagined.”

As more genetic discoveries become linked to physical and behavioral traits among salmon and thousands of other species, it will be important to create a process for using the discoveries to meet conservation goals, Waples said. Identifying populations with unique qualities is one step, he added. Making sure those qualities persist is another.

“Applied conservation is hard because biology is complex and messy,” he wrote, “and every practical application involves interactions with human customs, laws and institutions that can differ from place to place.”

Advanced genetic approach unveils “early-migration gene”

Rapid advances in genetic techniques allowed researchers to compare smaller and smaller segments of DNA from one population of fish to another, leading to the 2017 discovery that a tiny segment of the Chinook genome determines whether the fish will migrate in the spring or the fall.

Chinook salmon genome depicted in a Circos plot. Image: 2018 Christensen et al. (CC BY 4.0)

Chinook salmon genome depicted in a Circos plot. Image: 2018 Christensen et al. (CC BY 4.0)  

That discovery, by researchers at the University of California, Davis, spawned further studies, which were aided by declining costs for automatic machines, called DNA sequencers, which can rapidly decode long chains of DNA.

Now, by sequencing the entire genome of spring and fall Chinook, researchers have more fully described the region of DNA that seems to dictate migration timing. The key region includes a gene called GREB1 L plus an adjacent gene called ROCK1, both associated with estrogen activity in other animals, according to Shawn Narum, a researcher with the Columbia River Inter-Tribal Fish Commission. Also in that key region, researchers found what they think is “regulatory DNA,” capable of turning genes on and off or adjusting their activity.

In some populations, researchers found other small DNA variations that could play a role in migration timing, said Narum, who led a study that involved collecting DNA samples from Chinook populations throughout the Northwest.

Because the fish inherit genes from both parents, it is possible to find fish that are half-spring and half-fall Chinook, known as heterozygotes. Fish with two early-migration genes or two late-migration genes are called homozygotes.

In a study in California, Carlos Garza’s research team at the Southwest Fisheries Science Center was able to obtain tissue samples of Chinook from fishermen, just as the fish returned to the Klamath River.

“What we found was extraordinary,” Garza said. “There was no overlap in the timing of entry for homozygotes of either the spring variant or the fall variant.”

In fact, just after the spring run finally tailed off in mid-July, a few fall Chinook began showing up. Although the people fishing didn’t know it at the time, there were also heterozygotes in their nets. Later testing revealed that these half-spring/half-fall fish first arrived about midway through the spring run and continued into the fall run.

Since most of the mixed heterozygotes arrive during the low flows of summer, their timing puts them at a selective disadvantage when it comes to reproduction, Garza said. Their chance of success is low compared to the majority of the spring or fall runs, particularly with dams on the Klamath controlling the water supply.

But the in-between heterozygotes are not doomed in all locations, he said. In some streams, such as the Salmon River in the upper Klamath, conditions are suitable for a fair number of heterozygotes to survive.

“Salmon move around, and they take their genes with them,” Garza said. “That is one of the hallmarks of their life history. When conditions can support a spring run, their life history will confer a selective advantage.”


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