Extinction

It is the nature of salmon and steelhead to populate discrete habitats and adapt to unique environmental conditions over time. When conditions change, the fish either adapt, move to another location or become extinct.

Earthquakes, floods, geologic upheavals and other natural processes altered salmon and steelhead habitats over time. Human activities did the same thing, but in different ways and, with the possible exception of earthquakes and floods, more quickly.

Large-scale, human-caused impacts to salmon and steelhead, impacts that led to deteriorated habitat conditions and could have hastened the extinction of species, date to the earliest economic activities in the Columbia River Basin. In 1820, for example, the Hudson's Bay Company, bristling over the 1818 treaty that established joint occupancy of the Columbia Basin with the United States, ordered its trappers to do their best to eliminate beavers from all of the territory south and east of the Columbia River in the Snake River region. The company expected the Americans to try to occupy the area. Eliminating beavers would discourage American fur traders from occupying an area the company considered its own.

The new policy was successful, and beaver populations were decimated. As beavers went, so did salmon. Beaver dams created ponds that provided rearing habitat for young salmon, as well as insects and other food organisms for the fish. The ponds also slowed stream flows and created quiet areas where the fish could rest and hide from predators. Beavers maintained environments favorable to salmon. The policy of deliberately overhunting beaver undermined salmon survival, particularly east of the Cascade Mountains, by reducing the amount of debris in the stream habitat, causing streams to be more linear as a result and therefore making it more difficult for young salmon to hide from predators and seek refuge in sheltered, shadowy areas.

Salmon and steelhead habitat also suffered from multiple impacts of dams, including inundation of spawning and rearing habitat, changes in water flows and temperatures, and restricted or blocked access to habitat. Excessive commercial fishing impacted salmon and steelhead runs by the turn of the 20th century, as did logging and agricultural practices that altered or destroyed habitat. Poor hatchery practices also contributed to the decline of salmon and steelhead runs. The precise contribution of each impact can’t be determined, but all played a part.

Today, salmon are extinct in almost 40 percent of the rivers where they were known to exist in California, Oregon, Washington, and Idaho, fisheries scientist and author Jim Lichatowich has reported. The National Research Council reported in 1996 that salmon populations are at risk of extinction in 44 percent of the streams where they remain. In 1991, Lichatowich and two other scientists, Willa Nehlsen and Jack Williams, reported in Fisheries, the journal of the American Fisheries Society, that 214 native, naturally spawning runs of salmon, steelhead and sea-run cutthroat trout in those states were at risk of extinction, and of these 101 were at high risk, 58 were at moderate risk, 54 were considered stocks of special concern, and one was classified as a threatened species under the Endangered Species Act. Of the 214 stocks considered at some risk of extinction, 76 were in the Columbia River Basin. The authors also reported that at least 106 major stocks in the four states already had gone extinct.

In March 2000, scientists for the National Marine Fisheries Service (NMFS) reported on their updated computer modeling of extinction probabilities for Columbia River Basin salmon and steelhead stocks. Their conclusion: the fish were worse off than had been believed previously. Outmigrations of juvenile salmon and steelhead from Idaho between 1990 and 1994 were the worst since fish and wildlife agencies began keeping records, and the adult returns that resulted were low, the scientists reported.

On a hopeful note, the scientists reported that ocean conditions appeared to be improving, citing the huge jack (immature salmon) returns of 1999 (as expected, adult fish returns in the early 2000s also were impressive and, for some stocks, record-breaking). But overall, the scientists reported, the condition of salmon and steelhead stocks in the Columbia Basin appeared to be worsening.

In 2003, the Fisheries Service reported on the status of ESA-listed salmon and steelhead. he paper is posted on the Web site of the Service’s Northwest Fisheries Science Center. According to the paper, based on the criterion of self-sustainability, the following Columbia River Basin evolutionarily significant units (ESUs) were considered in danger of extinction: Upper Columbia River spring Chinook, Upper Columbia River steelhead, Lower Columbia River coho, and Snake River sockeye. Eight other ESUs were considered “likely to become endangered in the foreseeable future.” These included Snake River fall Chinook, Snake River spring/summer Chinook, Lower Columbia River Chinook, Upper Willamette River Chinook, Snake River steelhead, Lower Columbia River steelhead, Upper Willamette River steelhead, and Lower Columbia River chum. The Fisheries Service defines an ESU as a population that: 1) is substantially reproductively isolated from other populations in the same geographic area, and 2) represents an important component in the evolutionary legacy of the species.

The 2003 Status Report does not speculate on the specific causes of the decline of the ESUs, but in its Federal Register notices announcing the ESA listing decisions for the fish, the Fisheries Service identified the so-called 4H factors for decline - habitat degradation and loss, hydropower development, overharvest, and the impacts of hatchery fish on fish that spawn in the wild - as well as other factors.

Case in point: The demise of Snake River coho

Snake River coho are just one of the 106 runs of Columbia River Basin anadromous fish that became extinct over time. But the story of these fish is unique because their extinction occurred recently and almost nothing was done to stop it.

In 1986, five years before petitions would be filed to add Snake River Chinook and sockeye salmon to the federal endangered species list, a single adult Snake River coho salmon crossed Lower Granite Dam on its futile return to spawn. With none of the news media fanfare that would accompany the 1991 Endangered Species Act petitions, in fact in a year when 6,895 spring Chinook, 3,934 summer Chinook, 449 fall Chinook and 15 sockeye crossed the dam, a single coho returning to spawn somewhere in one of the lower Snake River tributaries that once ran thick with them was virtually unnoticed. But with no mate, there would be no spawning. A single coho had returned in 1985, as well, but in 1987 the count was zero, and it would remain zero until 1997.

No more Snake River coho.

No agency or entity officially declared Snake River coho extinct, although many acknowledged it after the fact. The fish simply were gone, and very few people noticed.

Snake River coho never were listed as endangered or threatened under state or federal law. They were not included among the salmon species addressed in the Lower Snake River Compensation Plan, the artificial production program that produces salmon to compensate for the impact of the four federal dams on the lower Snake River.

While the precise reason for this non-action is not clear, a 1972 report prepared by state fish and wildlife agencies in Idaho, Oregon, and Washington, which summarized the effects of the four lower Snake River dams on fish and wildlife, focused on spring Chinook and steelhead, which had greater value as sport fish. The 1972 report was prepared by the U.S. Fish and Wildlife Service and the National Marine Fisheries Service and submitted to the U.S. Army Corps of Engineers as the final report on the impacts of the four dams, in compliance with the federal Fish and Wildlife Coordination Act. This report formed the basis of the 1975 Lower Snake River Compensation Plan and a companion environmental impact statement in 1976.

Historically, coho were abundant in the lower Snake River Basin and provided important late-summer and fall fisheries for the Nez Perce Tribe in the Wallowa, Grand Ronde, and Imnaha rivers of Oregon, and Asotin Creek, in Washington, and in two tributaries of Idaho’s Clearwater River: Potlatch Creek and the North Fork Clearwater. Coho are not known to have spawned in streams or rivers above the Hells Canyon Complex of dams (Hells Canyon, Oxbow and Brownlee).

Dams, primarily, eliminated the Clearwater coho. In 1910, Harpster Dam was built on the lower South Fork Clearwater, blocking salmon passage. In 1927, Washington Water Power Company built a diversion dam just above the mouth of the Clearwater, and despite a diversion channel, the dam all but eliminated salmon runs into the Clearwater Basin. Harpster Dam was removed in 1963 and the Water Power dam in 1972, but the damage was done. The fish ladder at the Washington Water Power dam was improperly designed and did not pass the basin’s Chinook and coho salmon effectively. Both populations were extirpated. A rebuilding effort, the Chinook Reintroduction Program, began in 1958 and was moderately successful. Federal and state biologists had collected eggs from the native Chinook stocks in the Clearwater and taken them to the Carson National Fish Hatchery in Washington prior to the extirpation — anticipating that the Water Power dam would wipe them out — and it was the progeny of these eggs that the biologists used to re-establish Chinook runs in the Selway River, a Clearwater tributary, in the late 1950s.

The Idaho Department of Fish and Game began supplementation projects for the declining Clearwater coho in 1962. These continued for eight years, but were unsuccessful. Also in 1962, the Idaho Department of Fish and Game released 375,000 coho yearlings at Oxbow Dam as part of an experiment to test whether the fish would return to spawn naturally in that part of the Snake River Basin. A few adults returned in November and December 1965, but the return rate was very small — 0.05 percent of those released. At that time of the year, the tributary rivers were too cold for coho spawning, and no spawning was observed in the mainstem Snake River. At about the same time, Canadian sockeye were planted as an experiment in the upper Salmon River system, but they did not adapt.

The extinction of Snake River coho was not a secret. There were efforts to re-establish coho runs as they declined, both in Idaho and in Oregon tributaries of the Snake such as the Grande Ronde. But these amounted to too little, too late. There was finger-pointing when it was clear the fish were gone — perhaps more money should have been spent or perhaps the reintroduction efforts should have been more aggressive. But in the end, the reintroduction efforts just didn’t work.

It wasn’t just a one-time failure. According to a 1999 environmental impact statement prepared by the Corps of Engineers, which operates the four lower Snake River dams, the wild coho population in the Grande Ronde River was eliminated in the early 1900s at a time when many upriver runs were decimated by dams, habitat destruction and, particularly, overfishing downstream. The Oregon Fish Commission attempted a reintroduction in the Wallowa River in the 1950s, but it failed, evidently for the same reasons that it failed in the Clearwater. According to the EIS, “the progeny of the reintroduction, not native Wallowa River coho, became extinct in 1986.” The native fish had disappeared long ago. Also according to the EIS, as late as 1968 as many as 6,000 coho returned to the Snake River, and most of them spawned in the Grande Ronde River. These were the last Snake River wild coho.

In July 1987, the Northwest Power Planning Council (today the Northwest Power and Conservation Council) took up the Snake River coho issue when Willa Nehlsen, then a biologist on the Council staff, made a presentation at a Council meeting in Post Falls, Idaho, on the status of Snake River salmon and steelhead stocks. At the time, the Council was working on an effort called system planning, which was an attempt to identify areas of genetic risk and marginal stocks of salmon and steelhead for attention in the Council’s Columbia River Basin Fish and Wildlife Program. Nehlsen said her analysis of the Snake River stocks was inspired by concerns of the Idaho Department of Fish and Game that many stocks were at critically low levels. According to the minutes of the Council meeting, “she pointed out that these stocks are uniquely adapted to making the long spawning migrations to get to and through the Snake River system and that preserving these stocks could be an important part of fulfilling the Council’s policy of emphasizing the importance of upriver runs in system planning.”

Nehlsen identified 22 Snake River stocks that were candidates for extinction, stocks in which fewer than 1,000 adult fish returned to spawn annually. She said the hypothesis used by the National Marine Fisheries Service was that a stock does not survive if there are fewer than 400 spawners. Among the 22 stocks, the most critical were spring and summer Chinook in the Salmon River and the South Fork Salmon, and in the Imnaha River. Snake River coho, she said, had “disappeared very abruptly.”

This caught the attention of Kai Lee, a University of Washington professor and Council member. According to the minutes, “Member Lee stated that with regard to the loss of the coho, he had hoped that the passage of the Northwest Power Act meant that no stocks of fish would go extinct after 1980. Today’s briefing indicates that a number of stocks are at very low levels.”

During the public comment period following Nehlsen’s presentation, Al Wright, who then was the director of the Pacific Northwest Utilities Conference Committee in Portland, criticized the fish managers for giving up on Snake River coho and said electric utilities had proposed to the fish managers in 1982 to help pay for restoring or replacing some of the coho runs, but were rebuffed. According to the minutes, Wright said the utilities “were told by the management agencies that there was no way [the coho] were going to be restored or replaced. He stated that these coho runs could have been saved, but the Council or Bonneville was never asked to preserve that run, and that the Council should not take the responsibility for the loss of the run.”

In the 1991 article in Fisheries, Nehlsen and her co-authors wrote: “Native coho stocks that once ranged into Snake River and mid-Columbia tributaries of the Columbia River Basin are now extinct above Bonneville Dam, with the exception of a remnant population in the Hood River. The loss of these populations is attributed primarily to mainstem passage problems, habitat damage, overharvest and interactions with hatchery fish.”

In the late 1970s, the American Fisheries Society (AFS) took the lead in preparing petitions to add Snake River Chinook, sockeye and coho to the federal Endangered Species List but withdrew the petitions when Congress passed the Northwest Power Act. The Act authorized the four Northwest states to form the Power Council and directed the Council to prepare a program to “protect, mitigate and enhance” fish and wildlife affected by hydropower in the Columbia River Basin.

The petitioners waited a decade to see whether the fish and wildlife mitigation authorized under the Power Act would boost the runs. But the runs did not recover, and the petitions were filed in 1991. By then, the ESA was too late for the coho. A petition was filed in 1992 to add Snake River coho to the federal endangered species list, but the Fisheries Service rejected it because it did not include “substantial scientific or commercial information” that would warrant listing. Accordingly, the agency declined to initiate a status review of the coho.

In 1995, the Nez Perce Tribe of Idaho began a reintroduction program by releasing into the Clearwater River Basin 630,000 coho fry reared in Mitchell Act hatcheries in the lower Columbia River. The program has been moderately successful. Coho are known to be opportunistic, prolific spawners, and the first adult returns were noted at Lower Granite Dam in 1997, a total of 85 fish. The number of returning adults grew steadily. In 2000, a total of 891 adults and 36 jacks were counted, a smolt-to-adult return ratio of less than one-tenth of one percent compared to the number of juveniles that had been released, a rate that scientists consider low. The count at Lower Granite topped 1,000 fish for the first time in 2003, and was more than 3,000 in 2004 and more than 2,000 in 2005. Jack counts have increased, as well, consistently topping 100 fish per year. In 2006, for example, a total of 263 jacks were counted at Lower Granite, the highest since 460 were counted in 1976. Since then, through 2015, jack counts have varied annually from a low of 202 in 2012 to a high of 1,312 in 2008. The 2006 adult coho count was lower than in recent years — 1,141 — but the trend remains upward. Since then, Lower Granite count has varied year to year, from a low of 1,440 in 2015 to a high of 18,098 just the year before, in 2014. The average for the 10 years 2006-2015 was 4,240 per year.

The returns are not spectacular, but the fish aren’t failing, either. This is good news for an important salmon population that was swept under the rug and then revived, at least in the native habitat if not with native fish.

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