INTRODUCTIONChinook salmon (Oncorhynchus tshawytscha) are native to the Snake River, the largest tributary of the Columbia River. In the Snake River Basin, three races (spring-, summer-, and fall-run fish) are recognized based on time of entry of adults into fresh water. Historically, chinook salmon were abundant throughout most of the large, complex Snake River drainage. From the latter 1800s until the present, a variety of factors have led to the current depressed status of these populations. This situation prompted Oregon Trout, Oregon Natural Resources Council, Northwest Environmental Defense Center, American Rivers, and the Idaho and Oregon Chapters of the American Fisheries Society to petition the National Marine Fisheries Service (NMFS) to list each of the races of Snake River chinook salmon as threatened or endangered "species" under the U.S. Endangered Species Act (ESA) of 1973 as amended (U.S.C. 1531 et seq.). This report summarizes a review of the status of Snake River fall chinook salmon conducted by the NMFS Northwest Region Biological Review Team (BRT). The status of spring and summer chinook salmon from the Snake River is reviewed elsewhere (Matthews and Waples 1991).
KEY QUESTIONS IN ESA EVALUATIONS
Two key questions must be addressed in determining whether a listing under the ESA is warranted:
The "Species" QuestionAs amended in 1978, the ESA allows listing of "distinct population segments" of vertebrates as well as named species and subspecies. However, the Act provides no guidance for determining what constitutes a distinct population, and the resulting ambiguity has led to use of a variety of criteria in listing decisions over the past decade. To clarify the issue for Pacific salmon, NMFS published an interim policy describing how the agency will apply the definition of "species" in the Act to anadromous salmonid species (Federal Register Docket No. 910248-1048; 13 March 1991). A more detailed description of this topic appears in the NMFS "Definition of Species" paper (Waples 1991). The NMFS policy stipulates that a salmon population (or group of populations) will be considered "distinct" for purposes of the Act if it represents an evolutionarily significant unit (ESU) of the biological species. An ESU is defined as a population that (a) is reproductively isolated from conspecific populations and (b) represents an important component in the evolutionary legacy of the species. Types of information that can be useful in determining the degree of reproductive isolation include incidence of straying, rates of recolonization, degree of genetic differentiation, and the existence of barriers to migration. Insight into evolutionary significance can be provided by data on phenotypic and protein or DNA characters; life-history characteristics; habitat differences; and the effects of stock transfers or supplementation efforts. For ESA evaluations of Snake River chinook salmon, we also must consider races of fish that have traditionally been differentiated on the basis of run-timing. Following the framework of the "Definition of Species" paper, we must first determine whether spring-, summer-, and fall-run chinook salmon in the Snake River are separate, reproductively isolated groups. Those groups that are reproductively isolated from groups with other run-times should be considered separately for ESA purposes; fish of different run-times for which reproductive isolation cannot be established should be considered as a unit.
Thresholds for Threatened or Endangered StatusNeither the National Marine Fisheries Service nor the U.S. Fish and Wildlife Service (USFWS), which share authority for administering the ESA, has an official policy regarding thresholds for considering ESA "species" as threatened or endangered. The Northwest Region of NMFS has recently published a paper on this topic (Thompson 1991). Written comments received by NMFS and extensive discussions in ESA Technical Committee meetings stressed the importance of incorporating the concepts of Population Viability Analysis (PVA) into threshold considerations. However, the field is rapidly evolving and a definitive policy position on this issue is not expected in the near future. Furthermore, most of the PVA models developed to date require substantial life-history information that often will not be available for Pacific salmon populations. Therefore, instead of using a single, numerical threshold value, we used a variety of information in evaluating the level of risk faced by an ESU. Important factors considered included 1) absolute numbers of fish and their spatial and temporal distribution; 2) current abundance in relation to historical abundance and current carrying capacity of the habitat; 3) trends in abundance, based on indices such as dam or redd counts or on estimates of spawner-recruit ratios; 4) natural and human-influenced factors that cause variability in survival and abundance; 5) possible threats to genetic integrity (e.g., from strays or outplants from hatchery programs); and 6) recent events (e.g., a drought or improvements in main-stem passage) that have predictable short-term consequences for abundance of the ESU. In addition, until a more comprehensive PVA model becomes available for Pacific salmon, we used the stochastic extinction model of Dennis et al. (1991) to provide some idea of the likely status of the population in the future. This model is useful for identifying outcomes that are likely if no protective measures are taken because it assumes that future fluctuations in population abundance are determined by parameters of the population measured in the recent past.
Hatchery Fish and Wild FishBecause most of the effort in the last decade directed toward restoring Snake River fall chinook salmon focused on brood-stock development at Lyons Ferry Hatchery (Fig. 1), the role of hatchery fish also needs to be addressed in this status review. NMFS policy stipulates that in determining whether a population is "distinct" for purposes of the ESA, attention should focus on "wild" fish, which are defined as progeny of naturally-spawning fish (Waples 1991).1 This approach directs attention to fish that spend their entire life cycle in natural habitat and is consistent with the mandate of the Act to conserve threatened and endangered species in their native ecosystems. Implicit in this approach is the recognition that fish hatcheries are not a substitute for natural ecosystems. The decision to focus on wild fish is based entirely on ecosystem considerations; the question of the relative merits of hatchery vs. wild fish is a separate issue. Fish are not excluded from ESA consideration simply because some of their direct ancestors may have spent time in a fish hatchery, nor does identifying a group of fish as "wild" as defined here automatically mean that they are part of an ESU. Once the wild component of a population has been identified, the next step is to determine whether this population component is "distinct" for purposes of the ESA. In making this determination, we used guidelines in the NMFS "Definition of Species" paper (Waples 1991). We considered factors outlined in Section IIIC (Effects of supplementation and other human activities) to determine the extent to which artificial propagation may have affected the wild fish, through either direct supplementation or straying of hatchery fish. Thus, fish meeting the definition of "wild" adopted here may subsequently be excluded from ESA considerations for other reasons. Threshold determinations also will focus on wild fish, on the premise that an ESU is not healthy unless a viable population exists in the natural habitat. In developing recovery plans for "species" listed as threatened or endangered, the use of artificial propagation may be considered. If an existing hatchery is associated with the listed "species," an important question to address in formulating a recovery plan is whether the hatchery population is similar enough to the wild population that it can be considered part of the ESU. Factors to consider in this regard include origin of donor stock(s), brood-stock practices, evidence for domestication or artificial selection, population size, and the number of generations the stock has been cultured. In general, hatchery populations that have been substantially changed as a result of these factors should not be considered part of the ESU.
SUMMARY OF BIOLOGICAL AND ENVIRONMENTAL INFORMATION
Life History CharacteristicsChinook salmon have a diversity of juvenile and adult life history strategies that have been used to characterize and categorize different populations. One approach, commonly used in Alaska and Canada, is to differentiate between populations with "ocean" or "stream" juvenile life-history patterns (Healey 1983; Taylor 1989). "Ocean" type fish migrate to sea as subyearlings, whereas "stream" type fish spend an additional year (occasionally more) in fresh water before outmigration. "Stream" type chinook salmon predominate in colder latitudes (Alaska and northern British Columbia) and higher elevations (e.g., the upper Fraser River and in some Columbia River tributaries), and "ocean" type fish are more common in warmer areas (coastal areas from Vancouver Island south, the Lower Fraser River, and the Klamath and Sacramento Rivers). In most other areas, there is a strong tendency for one or the other of the life-history strategies to predominate; the Columbia River Basin is notable in that each life-history strategy is represented by numerous runs. In the United States, chinook salmon are typically characterized as "spring-", "summer-", or "fall-run" according to the time adults enter fresh water to begin the spawning migration (a "winter" run is also recognized in the Sacramento River). In general, "spring" chinook salmon are "stream" type fish and "fall" (and "winter") chinook salmon are "ocean" type fish. Populations identified as "summer" chinook salmon have "ocean" type life-history patterns in some areas and "stream" type life-histories in others. In the Columbia River Basin, adult chinook salmon migrating upstream past Bonneville Dam (Fig. 1) from March-May, June-July, and August-October are categorized as spring-, summer-, and fall-run fish, respectively (Burner 1951). Spring chinook salmon occur in tributaries of the lower, mid-, and upper Columbia River2 and in the upper Snake River Basin, and summer chinook salmon are found in the upper Columbia and Snake Rivers. Fall chinook salmon in the Columbia River Basin can be divided into two physiologically distinct types: "tules" and "upriver brights." Tules, which are confined to the lower river tributaries (generally, those below Bonneville Dam), are sexually mature when they enter fresh water as adults, as indicated by their dark coloration. In contrast, fall-run fish destined to spawn in upriver areas are known as "brights" because they mature more slowly (having a greater distance to travel upriver before spawning) and therefore retain their silvery oceanic coloration well into their freshwater migration. Upriver brights are highly prized in river fisheries because their flesh is of high quality. Bright runs are found in the upper Columbia and Snake Rivers and in the Deschutes River in Oregon (Fig. 1). The most abundant remaining naturally-spawning bright runs are found in the Hanford Reach of the Columbia River (an 84-km stretch from near Richland, Washington to Priest Rapids Dam), the last free-flowing stretch of the river between Bonneville Dam and the Canadian border (Swan 1989). In the Snake River, habitat utilized by fall chinook salmon for spawning and early juvenile rearing is very different from that utilized by spring- and summer-run fish (Chapman et al. 1991). The latter two forms spawn and rear in small, high elevation streams, whereas fall chinook salmon use main-stem areas or the lower parts of major tributaries (Fig. 2). Juvenile behavior also distinguishes Snake River fall chinook salmon (which move seaward slowly as subyearlings) from spring- and summer-run fish (which migrate swiftly to sea as yearling smolts) (Schreck et al. 1986; Chapman et al. 1991). Adult Snake River fall chinook salmon enter the Columbia River in July and August and reach the mouth of the Snake River from the middle of August through October. Spawning occurs in the main stem and in the lower reaches of large tributaries in October and November (NWPPC 1989; Bugert et al. 1990). Based on what is known of upper Columbia River fall chinook salmon, juveniles in the Snake River presumably emerge from the gravel in March and April, and downstream migration usually begins within several weeks of emergence (Chapman et al. 1991). Trapping studies conducted in 1954 and 1955 showed that juveniles moving through the lower Snake River in March and April were less than 50 mm in length, whereas those migrating in May and June were 60 to 80 mm (Chapman et al. 1991). Bell (1959, 1961) found that peak fry migration in the Brownlee-Oxbow Dam reach of the Snake River occurred from April through the middle of May. Little information is available to determine the extent to which fall chinook salmon rear for extended periods in the Snake River. Juveniles have been found at Lower Granite Dam and in the reservoir behind the dam through June (Raymond and Sims 1980; Bennett et al. 1990). However, elevated water temperatures are thought to preclude rearing of fall chinook salmon in the Snake River after early to mid-July (Van Hyning 1968; Chapman et al. 1991; Mundy 1991). The preferred temperature range for chinook salmon has been variously described as 54-57°F (12.2-13.9°C; Brett 1952), 50-60°F (10-15.6°C; Burrows 1963), or 13-18°C (Theurer et al. 1985). Summer temperatures in the Snake River substantially exceed the upper limits of this range (see Environmental Features section, below). Rich (1922) studied the downstream migration of chinook salmon in the lower Columbia River and concluded that fry were present from June to October. Fall chinook salmon fry were found to be abundant in May and June (Reimers 1964). Van Hyning (1968) reported that chinook salmon fry tend to linger in the lower Columbia River and may spend a considerable portion of their first year in the estuary. Adults return to the Snake River at ages 2-5, with age 4 the most common age at spawning (Chapman et al. 1991).
Past and Present Distribution and AbundanceHistorically, the Columbia River Basin produced more chinook salmon than any other river system in the world (Van Hyning 1973). Fall chinook salmon were widely distributed throughout the Snake River and many of its major tributaries, from its confluence with the Columbia River upstream 990 km to Shoshone Falls, Idaho (Columbia Basin Interagency Committee 1957; Haas 1965; Fulton 1968; Van Hyning 1968; Lavier 1976; see Fig. 2). Evermann (1896) reported that "we were not able to learn that salmon reached the foot of Shoshone Falls although it is very probable that they do so." Limited information is available from which to estimate the abundance of Snake River fall chinook salmon during the 1800s and early 1900s. Craig and Hacker (1950) estimated that prior to the arrival of white settlers, 50,000 native Americans from the Columbia River tribes may have harvested an average of 18 million pounds of Pacific salmon (Oncorhynchus spp.) and steelhead (O. mykiss) annually. A large proportion of the catch was thought to be fall chinook salmon because these fish were present during low flow conditions that favored harvest. Evermann (1896) reported that the spawning grounds of chinook salmon in the Snake River between Huntington [River Kilometer (RKm) 527] and Auger Falls (RKm 977) were the most important in Idaho, and that more salmon fishing for commercial purposes occurred there than in any other area in the state. According to one account cited in Evermann (1896), "salmon are most abundant about October 10, and are ripe when they first come. The smallest weigh about 5 pounds and the largest probably 60 pounds. Last year I caught about 6 tons, which I sold at 3 cents a pound." Prior to the 1960s, the Snake River was considered the most important drainage in the Columbia River system for the production of anadromous fishes. Approximately half of the fish returning to areas above McNary Dam were destined for the Snake River Basin (Bureau of Commercial Fisheries and Bureau of Sport Fisheries and Wildlife 1964). The construction of 12 dams on the main-stem Snake River (Fig. 1) substantially reduced the distribution and abundance of Snake River fall chinook salmon (Irving and Bjornn 1981a). Fish passage facilities proved unsuccessful at several projects, and spawning habitats, particularly areas most frequently utilized by fall chinook salmon, were eliminated with the formation of reservoirs. The construction of Swan Falls Dam (1901; RKm 734) obstructed passage of adults and rendered 256 km of main-stem habitat inaccessible to fall chinook salmon (Parkhurst 1950). During the early 1900s, the Fish Commission of Oregon placed a weir in the Snake River downstream from Swan Falls Dam near Ontario, Oregon (RKm 599), to collect fall chinook salmon brood stock for hatchery production. Although only a portion of the fall chinook salmon run was intercepted, more than 20 million eggs (a minimum of 4,000 females) were taken in a single year (Parkhurst 1950). This provides some indication of the distribution and large number of fall chinook salmon migrating into the upper reaches of the Snake River during this period. Snake River fall chinook salmon remained relatively stable in abundance through the first part of this century, but declined substantially thereafter. Following the decline of Columbia River spring and summer chinook salmon during the late 1800s, fall chinook salmon constituted the major commercial fisheries, with annual catches ranging from 3 million to nearly 9 million kg (Table 1). Irving and Bjornn (1981b) estimated that the mean number of fall chinook salmon returning to the Snake River declined from 72,000 in the period 1938-49 to 29,000 during the 1950s. Fall chinook salmon escapement reflected in spawning ground surveys also declined during this period. In spite of this significant decline in abundance, the Snake River remained the most important natural production area for fall chinook salmon in the Columbia River Basin through the 1950s (Fulton 1968). The upper reaches of the main-stem Snake River were the primary areas utilized by fall chinook salmon (Fig. 2), with only limited spawning activity reported downstream from RKm 439. The construction of Brownlee Dam (1958; RKm 459), Oxbow Dam (1961; RKm 439), and Hells Canyon Dam (1967; RKm 397) eliminated the primary production areas of Snake River fall chinook salmon. Habitat was further reduced with the construction of four additional dams on the lower Snake River: Ice Harbor Dam (1961; RKm 16), Lower Monumental Dam (1969; RKm 67), Little Goose Dam (1970; RKm 113), and Lower Granite Dam (1975; RKm 173). Apart from the possibility of deep-water spawning (discussed below) in lower areas of the river, the main-stem Snake River from the upper limit of the Lower Granite Dam reservoir to Hells Canyon Dam (approximately 165 km) and the lower reaches of the Imnaha, Grande Ronde, Clearwater, and Tucannon Rivers are the only remaining areas available to fall chinook salmon in the Snake River Basin. Returns of adult fall chinook salmon to the Snake River have declined to very small numbers in recent years. Yearly adult counts at the uppermost Snake River main-stem project affording fish passage averaged 12,720 from 1964 through 1968, 3,416 from 1969 through 1974, and 610 from 1975 through 1980 (Table 2). Counts through 1980 presumably represent wild fish. The first hatchery-reared Snake River fall chinook salmon returned to the Snake River in 1981 (Busack 1991b), and since then, counts of adults at lower Snake River dams reflect a mixture of hatchery and natural production. Estimates of the abundance of naturally-produced Snake River fall chinook salmon over the last decade are discussed in the section on artificial propagation (below).
StrayingSalmon and steelhead that return to spawn in areas other than their natal stream are considered strays. Tagging data suggest that the natural rate of straying of fall chinook salmon into the Snake River is very low. In 1981, over 200,000 juvenile fall chinook salmon from the upper Columbia River were fitted with coded-wire tags (CWTs), and over the next 4 years adult returns were monitored in all Columbia River Basin hatcheries as well as on fall chinook salmon spawning grounds (McIsaac and Quinn 1988). All of the several hundred recoveries of tagged upper Columbia River fish occurred on the natal spawning grounds, upstream from the spawning grounds, or in gill-net fisheries that intercept fish migrating up the Columbia River. This result is consistent with the very low incidence of tagged upper Columbia River fall chinook salmon appearing in Lyons Ferry Hatchery brood stock; since the hatchery (situated near the upstream end of Lower Monumental Dam reservoir, 79 km from Ice Harbor Dam) opened in 1984, only three such tags have been recovered from fish that were collected at Ice Harbor Dam or swam voluntarily into the hatchery (Busack 1991b). There is growing evidence, however, that hatchery fish of Columbia River origin have strayed into the Snake River in the past few years . This topic is discussed in the next section.
Artificial PropagationAvailable information indicates that the few attempts at artificial propagation of fall chinook salmon in the Snake River prior to 1976 were of short duration and had little effect. As noted above, fall chinook salmon eggs were collected during the early 1900s in the upper Snake River near Ontario, Oregon, for hatchery production. The destination of resulting progeny and the duration of this effort are uncertain. In the early 1960s, attempts were made to maintain natural production of fall chinook salmon in habitats above Oxbow Dam on the main-stem Snake River. A stream channel and facilities for incubating up to 5 million eggs annually were first used at Oxbow Dam in 1961 (Welsh et al. 1965). Fall chinook salmon were trapped on site and eyed eggs deposited in the stream channel or transferred to other locations. In 1961, 1,839 adult fall chinook salmon were collected, but only 701 survived to spawning. Although efforts were made to maintain fall chinook salmon production in the upper Snake River, fish passage facilities at these projects proved to be inadequate (Van Hyning 1968). Fall chinook salmon escapement declined dramatically (Table 3), and further attempts to maintain this population were discontinued. Fall chinook salmon were not transported above Oxbow Dam after 1962. The Clearwater River was the focus of the other major artificial propagation effort involving Snake River fall chinook salmon prior to the 1970s. Native fall chinook salmon in the Clearwater River were virtually or totally eliminated following the construction of Lewiston Dam in 1929 (Columbia Basin Interagency Committee 1957). The Clearwater was again accessible to fall chinook salmon in 1939 when the original fishway was remodeled and two new fishways constructed. Transfers of eyed eggs by the Idaho Department of Fish and Game from 1948 through 1955 represent the first efforts to reestablish fall chinook salmon in this drainage (Bureau of Commercial Fisheries and Bureau of Sport Fisheries and Wildlife 1964). The origin and extent of these early transfers are uncertain. Egg transfers from 1960 through 1967 ranged from 400,000 to nearly 1.6 million annually and originated primarily from adult fall chinook salmon trapped at Oxbow Dam. Approximately 250,000 of the 1.46 million eyed eggs collected at Oxbow in 1961 were transferred to the Clearwater River; in 1962, 424 females produced 1.9 million eggs that survived to the eyed stage, and 400,000 of these were transferred to the Clearwater River. Egg transfers to the Clearwater River were terminated in 1968, and adult returns thereafter declined to just a few individuals (Irving and Bjornn 1980). Approximately 500,000 eggs from Spring Creek National Fish Hatchery (NFH) (on the lower Columbia River) were planted in the Clearwater River in 1960. This instance, and a single transfer of juvenile fall chinook salmon from Spring Creek NFH to below Hells Canyon Dam in 1970, represent the only recorded introductions of nonindigenous fall chinook salmon into the Snake River Basin. To offset losses of anadromous fish resulting from the construction and operation of Ice Harbor, Lower Monumental, Little Goose, and Lower Granite Dams, the Lower Snake River Compensation Plan (LSRCP) was authorized under the Water Resources Development Act of 1976 (Public Law 94-587). Federal and state resource agencies collaborated to estimate impacts on fish stocks and develop compensation measures. Hatchery facilities designed to produce 18,300 adult fall chinook salmon returning to the project area were determined necessary to compensate for downstream migrant passage mortality and loss of spawning habitat. The production potential of the remaining free-flowing reach of the Snake River was estimated to be more than 13,000 adults (Herrig 1990). During the planning and design of LSRCP production facilities, substantial declines in fall chinook salmon returns prompted the initiation of an egg bank program to ensure that brood stock of Snake River origin would be available when these facilities became operational. The egg bank program utilized several facilities in the Columbia River Basin in a "spread the risk" philosophy. A primary objective of the egg bank program was to maintain the genetic integrity of the Snake River fall chinook salmon population (Bugert and Hopley 1989). Adults for the egg bank program were first captured in 1976 at Little Goose Dam and raised at Bonneville Fish Hatchery. Resulting progeny, which had their ventral fin clipped so they could be identified if they returned as adults, were released in the Kalama River, a tributary of the lower Columbia River (Bugert and Hopley 1989). A release site in the lower river was selected so that juveniles and adults would not have to negotiate dams on the Columbia and Snake Rivers. From 1977 to 1984, Snake River fall chinook salmon brood stock were trapped at Ice Harbor Dam (Table 4). Eggs were transferred to Kalama Falls Hatchery (Fig. 1) from 1977 through 1983, and adults returning to this hatchery from 1979 to 1986 contributed to the LSRCP egg bank program. In 1978, because of concerns that a single hatchery operation was vulnerable to disease outbreak, a parallel operation was initiated by USFWS at Hagerman NFH, near Twin Falls, Idaho at RKm 944 on the Snake River (Fig. 1). The first releases of juvenile fall chinook salmon into the Snake River under the LSRCP were in 1979 (from the 1978 brood at Hagerman NFH). These releases continued through 1985 and ranged from approximately 45,000 to 475,000 fish (Herrig 1990). Adult returns to the Snake River from these releases began in 1981 and ranged from 0.01 to 0.24% (Bugert and Hopley 1989). All brood-stock operations for Snake River fall chinook salmon were transferred to Lyons Ferry Hatchery following its completion in 1984. Annual releases of juveniles from Lyons Ferry Hatchery have fluctuated from approximately 380,000 to more that 4.5 million fish. The first adults from Lyons Ferry releases returned in 1987 (Herrig 1990). Although available evidence indicates that efforts to maintain the genetic integrity of the Snake River fall chinook salmon population through the generation or so that fish were transferred to the lower Columbia River were successful (Seidel et al. 1988; Busack 1991b), the goal of enhancing natural production has been more elusive. Presumably at least in part as a result of the hatchery program, adult returns to Ice Harbor Dam have increased from low numbers observed in the late 1970s and early 1980s. However, a similar increase has not occurred in the count at Lower Granite Dam, which provides a better indication of the abundance of naturally-spawning fish. The total count has remained under 1,000 fish since 1975, and the count for 1990 was the lowest on record (Table 5). Furthermore, in recent years, stray Columbia River fish of hatchery origin have appeared in alarming numbers in the Lyons Ferry Hatchery brood stock (Table 6). Most of the strays are part of the Bonneville egg bank program for upper Columbia River fall chinook salmon. Adults for brood stock are collected from fish that migrate over Bonneville Dam in the time period designated for fall-run fish (i.e., after 1 August). Releases occur at various sites in the Columbia River, including the Umatilla River. Seasonal dewatering of the Umatilla River for irrigation eradicated native chinook salmon runs, and releases of Bonneville stock fall chinook salmon which began in 1983 are intended to help reestablish a Umatilla run (Howell et al. 1985). Unfortunately, poor acclimation of juveniles prior to release and lack of sufficient water for spawning in the fall apparently contribute to an increased rate of straying in these fish (Chapman et al. 1991). Based on analysis of CWT-fish spawned at Lyons Ferry Hatchery, Cooney (in Busack 1991a) estimated that strays from the Columbia River made up 4% of the adults in 1987, 18% in 1988, and 39% in 1989 (Table 6), and Bugert et al. (1990) estimated that strays made up approximately 25% of the adults at Lyons Ferry Hatchery in 1990. The majority of strays were from releases into the Umatilla River. Progeny from brood years prior to 1989, which sustained straying rates of up to 18%, had already been released from Lyons Ferry Hatchery before the problem was realized. Only a portion of these fish were marked, so there is no way to identify all returning adults resulting from these broods. However, following the discovery of the magnitude of straying (Roler 1990), the Washington Department of Fisheries (WDF) initiated measures to reduce the effects of these strays on the genetic integrity of Lyons Ferry Hatchery brood stock (Busack 1991b). All juvenile progeny from adults spawned in 1989 were marked prior to release, so this entire year class can be prevented from making any future genetic contribution to the hatchery brood stock. In addition, gametes from adults returning in 1990 were not mixed until CWTs (if any) were read and the hatchery of origin determined. This resulted in segregation of three groups of adults for spawning: A-fish carrying CWTs indicating a Lyons Ferry Hatchery origin; B-fish carrying CWTs from other hatcheries (known strays); and C-untagged fish (a mixture of wild fish, untagged strays, and untagged Lyons Ferry Hatchery fish). Only progeny from group A will be allowed to contribute to future generations in Lyons Ferry Hatchery (Busack 1991b). Thus, there is an opportunity to reduce or eliminate the effects of straying into Lyons Ferry Hatchery for the 2 years (1989, 1990) with the highest incidence of straying. The discovery that upper Columbia River hatchery fish are straying into the Snake River in substantial numbers raised concern that some of these fish may also stray onto spawning grounds in the Snake River. To evaluate this possibility, biologists from WDF and the Oregon Department of Fish and Wildlife (ODFW) attempted to estimate the number of hatchery fish that passed Lower Granite Dam in 1990; the number of wild fish could then be estimated by subtraction from the total adult count. The method depends on screening CWT fish at the dam and determining the hatchery of origin. However, two factors complicate this process: 1) not all hatchery fish are marked, and the proportion of marked fish varies considerably among hatcheries [e.g., from an average of about 55% in Lyons Ferry Hatchery (Bugert et al. 1990) to generally less than 10% for the Umatilla program), and 2) CWT fish were not screened at Lower Granite Dam until 1990. The standard approach to the first problem is to "expand" the number of observed tag recoveries to account for untagged fish from the same locality. This amounts to estimating the total contribution from a hatchery by dividing the number of observed recoveries by the fraction tagged. There are intrinsic statistical difficulties in computing the standard errors for the resulting estimates, but the errors are generally thought to be large, particularly if the tagging rate is low. To address the second factor, ODFW (1991b) and WDF (Busack 1991a) estimated the number of hatchery fish at Lower Granite Dam in previous years by assuming that strays from each hatchery reached the dam in the same proportions they were represented in the brood stock at Lyons Ferry hatchery for that year. Clearly, there is an additional degree of uncertainty associated with this estimation procedure. Estimates of hatchery and wild fish reaching Lower Granite Dam based on these methods are shown in Table 5 and Figure 3. Several points are worth noting. First, an appreciable fraction (about 20-80%) of the total fish reaching the dam each year since 1983 is estimated to have been of hatchery origin. Second, after subtracting the estimated number of hatchery fish from the total, the estimated number of wild fish shows a pronounced downward trend in the past decade. Third, the estimated percentage of hatchery fish at Lower Granite Dam in 1990 (77%) was the highest to date, and the estimated number of wild fish the lowest. In fact, the 78 estimated wild fish in 1990 are only 31% of the next lowest estimate (253 in 1987). In addition to the natural spawning areas upstream from Lower Granite Dam, there are two additional locations in the Snake River where wild Snake River fall chinook salmon may spawn in limited numbers. The first area is in the lower Tucannon River, where fall-spawning fish have been found in recent years (Bugert 1991). The ancestry of these fish is uncertain. The second area is in the tailraces of the lower Snake River dams. Although there is no documented evidence of spawning near the dams, several lines of evidence suggest this may be the case. Fall chinook salmon are known to utilize deep-water spawning areas in the upper Columbia River (Swan 1989), and this may be true in the Snake River as well. A preliminary analysis indicates that about 75-80 km of habitat between the mouth of the Snake River and the mouth of the Clearwater River is potentially suitable for deep-water fall chinook salmon spawning (G. Swan3). Furthermore, a substantial fraction of fall chinook salmon counted at Ice Harbor Dam each year do not reach Lower Granite Dam (Table 2). Although other explanations cannot be ruled out, one hypothesis is that many of these unaccounted for fish spawn in the interdam areas. Whether the deep-water spawning, if it occurs, involves hatchery or wild fish (or a mixture of both) is unknown. The high numbers of hatchery fish at Lower Granite Dam are a concern for several reasons. Every fish of hatchery origin represents one less wild fish in the total count, and discounting the hatchery contribution makes the status of the wild population appear more precarious than was thought to be the case only a year ago. There are also concerns that possible hybridization of hatchery strays may reduce fitness of native fish; this may occur if domestication selection has favored genotypes that are adapted to the hatchery environment but not to surviving in the wild. In the case of Snake River fall chinook salmon, however, artificial propagation has been a relatively recent enterprise, so cumulative genetic changes associated with artificial propagation may be limited. Wild fish are also incorporated into the brood stock each year, and this should reduce divergence from the wild population. Release of subyearling fish may also help to minimize the differences in mortality patterns between hatchery and wild populations that can lead to genetic change (Waples in press). A greater concern for the status of the wild population than the numbers of stray hatchery fish is the origin of those strays. As shown in Table 5, 1987 and 1988 were the first years in which hatchery strays of upper Columbia River origin are thought to have appeared at Lower Granite Dam in any number (an estimated 6-9% of the total). In each of the last 2 years, about one-quarter of the fish passing Lower Granite Dam are thought to have originated from hatcheries using upper Columbia River fall chinook salmon. That hatchery fish appear at Lower Granite Dam does not prove they reach the spawning grounds upstream from the dam, nor does it indicate the degree of reproductive success of strays that do reach the spawning grounds. Unless the strays produce viable offspring that themselves survive to reproduce, they will have no permanent genetic impact on the native population. There is evidence from other studies of Pacific salmon and steelhead that suggests hatchery-reared fish may have less reproductive success in natural habitat than do wild fish (Reisenbichler and McIntyre 1977; Chilcote et al. 1986; Fleming and Gross 1989; Leider et al. 1990). This may be particularly true for hatchery fish (e.g., strays or transplants) that are not spawning in their native habitat. In a recent review, Hindar et al. (in press) cited salmonid studies showing that, in some cases, repeated hatchery releases over a period of years have had no detectable genetic effect on the resident population. However, other scenarios, involving hybridization with or replacement of the resident population with massive outplantings, have also been documented. This diversity of outcomes illustrates the principle that the genetic consequences of straying, supplementation, and stock transfers of Pacific salmon are largely unpredictable. In an attempt to evaluate the extent to which genetic characteristics of wild Snake River fall chinook salmon may have been affected by upper Columbia River strays, WDF collected postspawning adults from the spawning grounds in 1990. Unfortunately, only 18 carcasses were recovered-too small a sample for meaningful analysis using protein electrophoresis. However, estimates based on CWT data and scale pattern analysis (which can identify fish that were released from hatcheries as yearlings, in contrast to the subyearling pattern typical of wild fish) indicate that at least three-quarters of the fish collected on spawning grounds were hatchery fish, including two carrying tags indicating releases from the Umatilla River (Bugert 1991). The present status of the wild Snake River fall chinook salmon population is thus in some doubt. The appearance of a substantial fraction of hatchery strays on spawning grounds is alarming. However, the sample size was small, and all of the spawners collected in 1990 were taken from areas in the first 15 km of the 165 km of remaining spawning habitat (ODFW 1991a). The distribution of hatchery and wild fish at more remote spawning areas is unknown. Furthermore, the genetic effects strays may have had on the wild population have not been determined.
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