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Causes of Decline and Factors Limiting Recovery

Idaho Fish & Game Report to the Director 5/1/98


Many natural and artificial fluctuations and changes to the fishes' ecosystem have occurred over time. The most dramatic changes resulted from human development of the region, and included overharvest of adults, hydropower development, flood control, water diversion and storage for irrigation, grazing, logging, mining, and commerce. There have also been natural disturbances, such as drought, floods, fire and shifts in ocean productivity and predator cycles. These natural events are important regulators of population abundance and are part of the natural evolutionary legacy of Idaho's wild salmon and steelhead and are not the primary cause of the current crisis facing these fish (NMFS 1995; Harza Northwest 1996; Marmorek and Peters 1996; Williams et al. 1996; Harrison 1998; Stelle 1998).

It is unrealistic to assume society can restore the ecosystem to pristine pre-European development conditions and regain the estimated 1.5 million spring/summer chinook salmon adults that returned to the Snake River annually (Matthews and Waples 1991). But we do not have to go back in time very far to find ecosystem conditions that supported stable and viable runs of wild salmon and steelhead. During the 1960s wild salmon and steelhead runs into the Snake River averaged over 100,000 adults annually (Figure 1). These runs provided sustainable natural production and consistent tribal, sport and commercial fisheries.

Idaho's wild salmon and steelhead declined dramatically in the mid and late 1970s and have not recovered (Figure 1). Currently all of Idaho's native salmon and steelhead are either extinct or threatened with extinction. Snake River coho salmon were declared extinct in 1986. Sockeye and chinook were listed as endangered and threatened, respectively, under the federal Endangered Species Act (ESA) in 1991 and 1992. Steelhead were added to this list as threatened in 1997.

It is generally accepted that hydropower development on the lower Snake and Columbia rivers is the primary cause of decline and continued suppression of Snake River salmon and steelhead (USGAO 1990; CBFWA 1991a; NPPC 1992; NMFS 1995, 1997; NRC 1995; Williams et al. 1996; State of Idaho 1997; State of Idaho 1998). The region is particularly unified with respect to mainstem hydropower development being the primary cause of decline; there is less unified agreement that the hydropower system is the primary factor currently limiting recovery (Marmorek and Peters 1998). It has been hypothesized that the detrimental effect of the dams has been compensated for by the smolt transportation program, and that high fish mortality now occurs primarily in the ocean unrelated to the mainstem dams. It is important to understand the merits, risks and uncertainties of these opposing hypotheses in order to implement effective recovery measures.

Two primary aggregate hypotheses regarding the current major factors limiting recovery are being analyzed by PATH scientists2. Appendix 3.6 provides a summary of these hypotheses.

State and Tribal Hypothesis: In basic terms, the aggregate hypothesis developed and supported by the state and tribal salmon managers states that cumulative direct and delayed mortality of juveniles and adults associated with the mainstem hydropower system has not been compensated for by the smolt transportation program and recent dam improvements. The primary reason smolt transportation has failed to compensate for the dams is the delayed mortality associated with stress from reservoir and dam passage, collection, handling, barging and disruption of natural migration timing.

Alternative Hypothesis: In basic terms, the alternative aggregate hypothesis developed and supported by BPA, COE and some of NMFS' scientists states that the smolt transportation program and recent dam improvements have compensated for direct and delayed mortality associated with the mainstem hydrosystem. The primary reason adults are not returning to Idaho is due to a mid-1970s shift in ocean conditions, coupled with disease, genetics, predators, and other unspecified factors that cause selectively high ocean mortality for upriver stocks.

PATH is currently modeling predicted outcomes of recovery options based on these two hypotheses. They have completed preliminary results for spring/summer chinook (Marmorek and Peters 1998) and are currently working on model runs for fall chinook, followed by steelhead. PATH has not yet fully analyzed which aggregate hypothesis has the best ecological rationale and scientific support. PATH will attempt to resolve this important issue next fall and winter. Currently, both hypotheses are being modeled equally.

Department staff believe the level of ecological and scientific support for the state and tribal hypothesis, and the level of ecological and scientific uncertainty for the alternative hypothesis, do not warrant delay in clarifying the primary factor limiting recovery. Without this clarification we believe the 1999 Decision Point will likely be deferred.

The 1950s and 1960s provide a reasonable standard for recovery. The Commission, State of Idaho and NMFS have adopted a 2-6% smolt-to-adult survival standard for recovery based on this earlier time period (Toole et al. 1996; IFG Commission 1997; State of Idaho 1998). We examine the following factors in the context of what has changed dramatically in the fishes ecosystem since this period of sustainable runs thirty to forty years ago.

Spawning and Rearing Habitat

The quality of Idaho's salmon and steelhead habitat range from pristine to degraded to inaccessible, but no significant deterioration in the condition of accessible habitat has occurred since the 1960s that could account for the dramatic decline in fish numbers (Marorek and Peters 1996; Appendix 2.3). Important spawning and rearing areas have been blocked by dam construction during this time period, but this cannot account for reduced escapements into accessible areas. Idaho currently has about 3,700 total miles of spawning and/or rearing habitat for spring/summer chinook, which represents 62% of predevelopment condition (Hassemer et al. 1997, Appendix 3.12). Approximately 30% of the habitat is locate within boundaries of designated wilderness or wild and scenic river corridors (State of Idaho 1991; Appendix 3.12) and has been protected from development. Idaho's current habitat could produce several million smolts (IDFG et al. 1990; NPT and IDFG 1990, IDFG 1992a).

Adult escapements into accessible habitat have declined dramatically since the 1960s, regardless of the relative quality of the habitat (Figure 2; Appendix 3.12). In contrast, the productivity or survival of juvenile salmon and steelhead in these freshwater habitats has declined only slightly since the 1960s (Petrosky and Schaller 1996; Appendix 3.12).

The quantity and quality of habitat in Idaho does not preclude recovery of wild Snake River salmon and steelhead. Habitat protection remains important in helping ensure the persistence and resilience of the species (Quigley and Arbelbide 1997; Appendix 3.12).

Migration Habitat

Idaho's spring migrating salmon and steelhead prospered for thousands of years by utilizing headwate tributaries for spawning and nursery areas and then sending their young to the ocean on the wave of snowmelt each spring. The most important change to the ecosystem that nurtured this process as recent as 30 years ago is the construction of additional dams on the lower Snake and Columbia rivers in Washington. The dramatic decline of Idaho's salmon and steelhead coincides directly with completion of these dams (Figure 1 not shown on this web site). The newly impounded reach lost many of the ecosystem components historically required by steelhead and salmon for smolt migration (e.g., relatively unimpeded passage without dams, substrate and riparian cover for resting and predator avoidance, high water velocity and velocity gradients, preferred temperatures, etc.)(Williams et al. 1996).

Water velocity, which is only one component of the complex ecosystem requirements of migrating salmon and steelhead smolts, is up to 15 times slower in the lower Snake River reservoirs than in the natural river (CBFWA 1991b; IDFG and IDWR 1993; Dreher 1998). This altered environment results in slower migration and greater exposure to predators. Historically, Idaho's salmon and steelhead smolts migrated through the lower Snake and Columbia rivers in less than two weeks, which was crucial to their physiological changes from a freshwater to saltwater fish. The journey for in-river migrants now requires two to three times longer as a result of the slack water (Raymond 1979).

Independent scientists, hired by the Northwest Power Planning Council to assess their recovery plan, were very clear regarding the dams in their Return to the River document.

"Key among the conditions we define as normative is the availability of a continuum of high-quality habitat throughout the salmon life cycle, from freshwater streams along the entire migratory path into and back out of the Pacific Ocean . . . The dams severed the continuum of habitat, leaving very little riverine habitat left in the mainstem and isolating other types of habitat." (Williams et al. 1996).
PATH scientists reported in their conclusions document:
"We are highly confident that the differences in stream-type chinook indicators of productivity and survival rates between upstream (Snake River sub-basins) and downstream (Lower Columbia sub-basin) stocks are coincident in space and time with development of the hydrosystem."

"We are reasonably confident that aggregate effects of the hydrosystem have contributed to reduced survival rates of Snake River stocks during the post-1974 period, as compared to the pre-1970 period."

"We are reasonably confident that the hydrosystem has contributed to decreased juvenile survival in the downstream corridor for Snake River stocks in the post-1974 period." (Marmorek and Peters 1996).

Some groups claim the development of Idaho's upriver irrigation storage and flood control reservoirs is to blame for the loss of good springtime migration flows into the lower Snake River. Analysis show that these reservoirs have minimal impact on springtime and summer water velocity and flows (IDFG and IDWR 199s; Dreher 1998). In contrast, construction of dams in the lower Snake River during the 1960s and early 1970s significantly reduced water velocity and altered numerous other ecosystem components vital to migrating fish (NMFS 1995; Williams et al. 1996; Dreher 1998).

The smolt transportation program was implemented in the mid-1970s in an attempt to compensate for adverse migration conditions caused by hydropower development. Available data and scientific reviews indicate smolt transportation has not compensated for the dams and is unlikely to provide recovery (Appendices 3.11 and 3.12).

Estuary and Ocean Conditions

Estuary and ocean conditions are important regulators of population abundance but are not the primary factors limiting recovery of Idaho's salmon and steelhead (Harrison 1998; Stelle 1998; Appendices 3.2 and 3.6). Cyclic and stochastic fluctuations in ocean productivity, temperature and predators have occurred for thousands of years and are part of the evolutionary legacy of anadromous fish. These conditions can have a profound effect on survival and relative year-class strength of Idaho's salmon and steelhead, but can these conditions account for the dramatic decline toward extinction since the 1960s?

Dr. Robert Francis, and oceanographer from the University of Washington and member of the Independent Scientific Review Panel states:

"I know some people will look at this data [declining salmon runs] and say, it's the ocean's fault. I would say that it's clearly not the ocean's fault. Salmon have survived changing ocean conditions for thousands of years, but the big decline in the runs occurred in recent decades. So you have to ask yourself, what's occurred during that time, -- what's different? And the clear answer is man's impact, -- dams, habitat destruction, overfishing, hatcheries. We can't use the ocean as an excuse to stop our efforts to improve passage, spawning and rearing conditions." (Harrison 1998).
this view was echoed recently by Will Stelle, Jr., Regional Administrator for the National Marine Fisheries Service, in a guest opinion editorial to the Portland Oregonian newspaper:
"Some argue that it's the ocean, and so we should relax and wait until the ocean turns around. Wrong." (Stelle 1998).
The importance of ocean conditions and variability must be kept in proper context. Wide annual and periodic fluctuations in adult returns are common for salmon and steelhead. Prior to the 1970s, strong stock productivity and abundance helped absorb these fluctuations without risk of extinction. Since the 1960s, low stock productivity and abundance resulting from hydropower development leave little room to absorb these natural shifts in ocean conditions, further elevating the risk of extinction.

The PATH process has helped examine the plausibility of estuary and ocean conditions being responsible for the current imperiled status of Snake River salmon (Marmorek and Peters 1996). If estuary/ocean conditions (e.g., nutrients, temperature, forage) and predators (e.g., penniped, avian) are the primary limiting factor, then downriver stocks that exhibit similar life history patterns should also be severely depressed. PATH scientists compared several spring chinook stocks from Snake River tributaries with similar spring chinook stocks from downriver tributaries. These upriver and downriver stocks migrate at similar age, time and size, enter the estuary at similar times, have similar distributions in the ocean, and return as adults at similar age, time and size. The most significant difference in their life cycle is the lower stocks originate above one to three dams, whereas the upriver stocks originate above eight dams. All of these fish should experience similar conditions and predators in the estuary and ocean.

PATH scientists found common effects from ocean conditions for upriver and downriver stocks, but that upriver stocks suffered a significant decline in survival and abundance after the 1960s that was not evident in downriver stocks (Marmorek and Peters 1996; Appendix 2.3; Figure 4). This decline coincided with completion of the lower Snake River dams (Maromorek and Peters 1996; Appendix 2.3; Figure 3). Since that divergence, relative survival of Snake River stocks is typically two to five times lower than the downriver stocks (Appendix 2.3; Figure 5). Only during the mid-1980s did upriver stocks get within 80% of their downriver counterparts, -- these were generally good water years with high flow and spill during smolt migration.

Based on these conclusions, if smolt transportation has compensated for the dams and the estuary and ocean are now the primary factors limiting Idaho salmon and steelhead, then ocean conditions and predators must be selective against Snake River fish, but still unrelated to the hydroelectric system. Available data does not support this line of reasoning (Appendices 3.2, 3.3,

Genetics Perspective to Fitness
Headwater Nutrient Loss
Delayed Mortality Hypotheses
1950s and 1960s Productivity
Ocean and Estuarine Predators
Ocean and In-river Harvest
Smolt Transportation 3.4, 3.5, 3.6, 3.7, 3.9, 3.10, 3.11, 3.12, 3.13). the biological rationale and mechanism that could logically describe how ocean and estuary conditions unrelated to the hydroelectric system would systematically kill two to five times more Snake River fish than similar downriver fish has not been clearly identified. The biological rationale that we are aware of, proposes that elevated disease, hatchery influence and poor genetics in Snake river fish may account for the difference in survival compared to downriver stocks (Marmorek and Peters 1998). We describe in the following section why this hypothesis is not scientifically supportable.

Hatcheries, Disease and Genetics

In their conclusions document, PATH scientist state:

"Preliminary results suggest that artificial propagation of spring/summer chinook has not significantly contributed to declines in wild populations of spring/summer chinook in upstream areas (Snake and upper Columbia rivers) between pre-1970 and post-1974." (Marmorek and Peters 1996)
Hatchery production has increased dramatically in the Snake River Basin since construction of the lower Snake River, Hells Canyon Complex and Dworshak dams (Figure 6). Some claim that this increase in hatchery production is responsible for the decline and continued suppression of wild Snake River salmon and steelhead. The increase in hatchery production is actually in response to the decline in fish numbers, not the cause of this decline.

During this period, the Department and Commission made every effort to ensure increased hatchery production did not adversely affect remaining wild salmon and steelhead populations. This included designating large basins as genetic refuges off limits to hatchery production. These areas include the Middle Fork Salmon (steelhead and chinook), South Fork Salmon (steelhead) and Selway (steelhead) rivers. Numerous other drainages received little or no hatchery outplants. The Department also implemented progressive hatchery practices designed to minimize adverse hatchery impacts and accentuate benefits to natural production (Bowles and Leitzinger 1991; IDFG 1992a; Bowles 1993; IDFG 1994; Bowles 1995).

There is no evidence that fish pathogens associated with hatchery practices are responsible for the decline or continued suppression of Idaho's wild salmon and steelhead (Appendix 3.3). Bacterial kidney disease (BKD) is present in both wild and hatchery chinook, but prevalence and level are low, particularly in wild fish. The highest risk for disease infection and amplification among hatchery and wild fish is associated with the smolt transportation program (Appendix 3.3). Researchers have demonstrated that the stress and close quarters associated with the smolt collection and transportation programs is a primary catalyst for disease outbreak and transmission (Appendix 3.3)

There is no evidence that the genetic makeup of Idaho's wild salmon and steelhead has been altered significantly, or that genetic makeup and associated fitness have been reduced enough to diminish recovery potential (Appendix 3.4) If genetic fitness has been reduced, egg-to-smolt survival should also be reduced. Egg-to-smolt survival has declined only slightly since the dams were completed in the lower Snake River, whereas smolt to adult survival has declined dramatically (Marmorek and Peters 1996; Appendix 3.12). Reduced genetic fitness would also be expressed in reduced resiliency, or the ability of populations to respond when environmental conditions are favorable. Wild Snake River salmon and steelhead populations show resiliency, as demonstrated in strong adult returns associated with good flow and spill conditions in the mid-1980s (Bowles 1993) and 1995.


There is no evidence that harvest limits recovery of Idaho's wild spring/summer chinook salmon (Appendix 3.10). Prior to completion of the lower Snake River dams, cumulative harvest rates typically exceeded 60%, yet wild runs remained stable and strong. Since completion of the lower Snake River dams, average harvest rates for all fisheries have been reduced to less than 10%, yet wild runs continue to decline (Appendix 3.10).

Current harvest rates have more significant impact for wild Snake River B-Run steelhead and fall chinook (Appendix 3.10). Approximately one-third of Idaho's wild B-run steelhead are harvested in tribal fisheries in the Columbia River. Over 50% of Snake River fall chinook are harvested in ocean and lower Columbia River fisheries. Although these losses to harvest are far less than juvenile and adult mortality associated with dam and reservoir passage, it is still an important limitation to recovery (State of Idaho 1997). The Department and Attorney General's Office are regional leaders in advocating harvest restrictions consistent with conservation objectives.

The Commission and State of Idaho strongly support restoring full harvest opportunities to sport, tribal and commercial fisheries.

"Idaho views weak stock constraints as an unfortunate but necessary measure until escapement goals are met. Once again, the best way to reduce weak stock constraints over the long-term is to rebuild runs of wild Snake River steelhead [and fall chinook] by improving mainstem migration conditions and implementing near-term harvest restrictions." (State of Idaho 1997).

Harvestable surpluses are clearly our long-term goal. Harvest must be limited to those fish not essential to future production. The Commission recognizes the need to not overly constrain ocean and lower-river fisheries, but maintains that escapement and genetic diversity within and between populations is a mandatory conservation requirement." (IFG Commission 1996).

The Commission has adopted conservative harvest regulations for in-state fisheries. It has been illegal to harvest wild adult salmon in Idaho since the late-1970s and wild steelhead since the mid-1980s. Idaho has not had a state-wide general chinook fishery for 20 years. Limited fisheries near some hatcheries have occurred infrequently; any wild fish caught were released immediately.
Conclusion on Limiting Factors

This scientific assessment points to the construction and operation of additional mainstem dams in the late 1960s and early 1970s as the primary factor limiting recovery of Idaho's salmon and steelhead. This conclusion has been the official position of the Department, Commission and State of Idaho 1996, IFG Commission 1996; IFG Commission 1997; State of Idaho 1997; State of Idaho 1998). This reassessment has not provided any scientific basis for changing this position; instead the data and recent scientific publications strength the conclusion that the dams are still the primary problem, and support the conclusion that smolt transportation has not fully compensated for the mainstem hydrosystem.

Their Status and Recovery Options
Report to the Director Idaho Fish & Game 5/1/98
Causes of Decline and Factors Limiting Recovery

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