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Survival Estimates for Downstream Migrant Yearling Juvenile Salmonids through the Snake and Columbia Rivers Hydropower System, 1966-1980 and 1993-1999 by John G. Williams, Steven G. Smith, and William D. Muir North American Journal of Fisheries Management, Volume 21, pages 310-317, 2001

Abstract

This paper examines average annual survival of juvenile spring-summer chinook salmon Oncorhynchus tshawytscha and steelhead O. mykiss during migration through the hydropower system of the Snake and Columbia rivers from 1966 to 1980 and 1993 to 1999. In each year, survival was estimated from observations of marked fish in a portion of the hydropower system corridor. We expanded these estimates to calculate an annual estimate of survival over the entire system (head of uppermost reservoir to tailrace of lowermost dam). Temporal changes in the hydropower system were compared with trends in estimated survival to evaluate the effects of dams on survival of downstream migrants. When only four dams were in place (1966-1967), estimates of survival through the hydropower system were 32-56%. Four additional dams were constructed between 1968 and 1975. Survival estimates during the 1970s typically were 10-30% for spring-summer chinook salmon, but less than 3% in the drought years of 1973 and 1977. From 1993 to 1999, after structural and operational changes in the hydropower system, survival estimates of spring-summer chinook salmon and steelhead ranged from 31% to 59%. Smolt-to-adult return rates of Snake River wild spring-summer chinook salmon from the middle to late 1960s generally exceeded 4% but decreased during the 1970s. Although survival through the hydropower system in the 1990s is substantially greater than that in the 1970s, adult return rates in the 1990s have remained low. Thus, in the 1990s, the cause of the continuing low adult return rates does not seem to be related to direct mortality of downstream migrant fish within the hydropower system.

Populations of Snake River spring-summer chinook salmon Oncorhynchus tshawytscha and steelhead O. mykiss decreased substantially coincident with construction of hydroelectric dams on the lower Snake and Columbia rivers (Raymond 1988; Williams 1989). Smolt-to-adult return rates of these populations fell from greater than 4% in the mid to late 1960s, when only four dams were in place, to generally less than 2% during the 1970s, after seven or eight dams were in operation (Figure 2 - not shown). When originally constructed, these dams had little or no provision for diverting downstream juvenile migrants past turbines, although they did have fish ladders to provide upstream adult passage. The initial large decrease in adult return rates (early to mid-1970s) coincided with substantially reduced juvenile survival (Raymond 1979) and concurrent high levels of descaling and injuries to fish (Williams and Matthews 1995). Annual survival estimates of spring-summer chinook salmon smolts passing through Little Goose Dam to Ice Harbor Dam from 1970 to 1974 averaged 36% (range, 12-50%). By comparison, estimated survival was nearly 90% to Ice Harbor Dam for fish released from a trap on the lower Salmon River approximately 420 km upstream of Ice Harbor Dam before construction of Little Goose and Lower Monumental dams (Raymond 1979). In an effort to reduce mortality caused by the hydropower system, major changes were made to dams on the Snake and Columbia rivers and their operation between the late 1970s and early 1990s. Changes included increases in flow, removal of debris from forebays at dams, more efficient and continuous turbine operation, installation of "flip-lips" on spillways to decrease atmospheric gas supersaturation, and construction of facilities to bypass juvenile fish away from turbines, followed by modifications to bypass facilities that were found to be inadequate (Williams 1989; Williams and Matthews 1995). Here we synthesize data from 1966 to 1980 and 1993 to 1999 and assess the extent to which changes in dam configurations and operations were related to the survival of migrating juvenile salmon and steelhead.

Survival estimation in the 1990s was made possible by development in the late 1980s to early 1990s of techniques to tag large numbers of fish with passive integrated transponder (PIT) tags and automatically detect them at dams (Prentice et al. 1990a; 1990b). After the development of automatically triggered slide gates to return PIT-tagged fish to the tailrace of dams after they were detected (Marsh et al. 1999) and of statistical techniques to use data from PIT-tagged fish to estimate survival (Skalski et al. 1998), in 1993 the National Marine Fisheries Service (NMFS) began new survival studies on downstream migrant fish to determine whether improvements instituted in the hydropower system had increased smolt survival.

In this paper we extrapolate survival estimates of yearling chinook salmon and steelhead smolts migrating through segments of the Snake and Columbia rivers during earlier (1966-1980) and more recent (1993-1999) periods to estimate survival through the entire hydropower system corridor. We compare survival estimates of downstream juvenile migrants made during the last 33 years. We also contrast the changes in juvenile survival estimates with those of smolt-to-adult return rates. Finally, we discuss the implication of these results to the possible effects of the hydropower system on overall stock performance.

TABLE 1. -- Reach survival estimates of spring-summer chinook salmon and steelhead from the upper dam on the Snake River to a lower dam on the Columbia River from 1966 to 1980. Estimates for 1966-1975 are from Raymond (1979), and those for 1976-1980 are from unpublished NMFS data.
(See Figure 3 - not shown for reaches evaluated each year.) No intermediate estimates are available for 1977.

	Survival from upper Snake River dam to Ice Harbor Dam		Survival from Ice Harbor Dam to lower river dama		Survival from upper Snake River dam to lower river dama
Year	Chinook	Steelhead	Chinook	Steelhead	Chinook	Steelhead
1966			0.63	0.75	0.63	0.75
1967			0.64	0.57	0.64	0.57
1968			0.62	0.60	0.62	0.60
1969	0.75	0.85	0.62	0.42	0.47	0.36
1970	0.33	0.80	0.67	0.48	0.22	0.38
1971	0.48	0.80	0.59b	0.40b	0.28	0.32
1972	0.39	0.60	0.42	0.33	0.16	0.20
1973	0.12	0.27	0.42	0.15	0.05	0.04
1974	0.50	0.78	0.71	0.25	0.36	0.20
1975	0.36	0.74	0.69	0.55	0.25	0.41
1975	0.36	0.74	0.69	0.55	0.25	0.41
1976	0.63	0.72	0.48	0.50	0.30	0.36
1977					0.03	0.02
1978	0.63	0.72	0.48	0.50	0.30	0.36
1979	0.43	0.14	0.72	0.46	0.31	0.06
1980	0.49	0.41	0.74	0.50	0.36	0.21

^a The Dalles Dam, 1966-1975; John Day Dam, 1976-1980.
^b No estimate of survival from Ice Harbor Dam to the lower river dam is from 1968 to 1970 and 1972 to 1975 was used.

Methods

To estimate survival of downstream migrant smolts over the entire hydropower system, we extrapolated previously calculated reach survival estimates to reaches for which estimates were not available. The number of dams in the hydropower system varied throughout the years, as did the segments for which survival was estimated and extrapolated (Figure 3 - not shown).

For 1966-1975, we used the estimates of Raymond (1979); for 1976-1980, we used unpublished NMFS estimates that were based on methodologies similar to those described by Raymond (1979) (Table 1). From 1966 to 1980, NMFS used standardized collection, handling, fish marking, and release methods at upriver and downriver sampling sites (Bentley and Raymond 1968). Collection efficiency estimates were determined throughout the migration season by recoveries at dams from tri-weekly groups of nitrogen freeze-branded smolts released above each dam. Estimates of collection efficiency and survival were based on the release of between 20,550 and 179,417 marked smolts per year (Raymond 1979). Collection efficiency estimates at all dams were derived by use of the same methods. Survival estimates were derived by dividing downstream rates of recovery of marked fish released at an upriver release site by the estimated collection efficiency at the downstream site (Raymond 1979).

For 1993-1999, we used survival estimates from annual PIT-tag survival studies (Iwamoto et al. 1994; Muir et al. 1995; Muir et al. 1996; Smith et al. 1998; Hockersmith et al. 1999; Smith et al. 2000a, 2000b) (Table 2). The annual PIT-tag survival studies used maximum-likelihood procedures to estimate survival to a downstream site from a single release of marked fish at an upstream site. The method requires that two sites downstream of the release site have the capability to detect fish and that the second-to-last site has the capability to return detected fish to the river to continue their migration. The reach over which survival is estimated extends from the point of release to the point at which fish continue their migration after detection at the second-to-last detection site. Skalski et al. (1998) first reported the use of the method for survival estimates of juvenile PIT-tagged fish in the Snake River; however, the method is based on the single-release model presented by Cormack (1964), Jolly (1965), and Seber (1965).

We estimated survival through the entire hydropower system by extrapolating the reach survival estimates (Tables 1, 2) under two different assumptions. In the first, we assumed that the average per-project (one reservoir and one dam) survival for river sections outside the sampled section was equal to that estimated within the appropriate sampled section. This assumption is consistent with results of analyses at Little Goose Dam that found that most mortality occurred from passage through the dam; little was in the reservoir (Muir et al. 1998). For example, the survival estimate in 1969 from Ice Harbor Dam to The Dalles Dam was 0.62 (Raymond 1979). This estimate encompassed three dams and three reservoirs so we es- timated the per-project survival by taking the cube root of the reach survival estimate (0.620.33 5 0.85). For 1966-1980, we extrapolated the per- project survival estimates from Ice Harbor Dam to The Dalles or John Day dams to the lower river section. This expansion better represented survival through the lower dams because the per-project survival through the upper Snake River dams was considerably different (Raymond 1979). Furthermore, in 1966-1968, we used per-project survival estimates of chinook salmon based on three dams, because the estimated survival by Raymond (1979) through that stretch of river in 1969 and 1970 was essentially unchanged after the turbines at John Day Dam came on-line in September 1968.

In the second scenario, we assumed that the average per-kilometer survival for the river section outside the sampled section was equal to that estimated within the sampled section. Extrapolation by distance is justified under the assumption that project mortality is related to reservoir mortality; greater mortality is found in longer reservoirs because travel time is greater. Mechanisms that could result in a distance-survival relationship include increased probability of predation or the effects of cumulative passage stresses on fish (Marmorek and Peters 1998).

To determine whether differences in juvenile survival between 1966 and 1980 and between 1993 and 1999 were related to large changes of flow within the hydropower system, we also examined differences (t-test) in annual mean flow between 10 April and 1 June of each year from 1974 to 1980 (1977 not included because of extremely low flows) and from 1993 to 1999 at Ice Harbor and McNary dams.

TABLE 2. -- Reach survival estimates of spring-summer chinook salmon and steelhead from 1993 to 1999.

	Survival through Lower Granite Reservoir and Dam		Survival from Lower Granite Dam tailrace to tailrace of lower river dam		Survival from Lower Granite Reservoir to tailrace of lower river dam
Year	Chinook	Steelhead	Chinook	Steelhead	Chinook	Steelhead
1993	0.90		0.85a		0.77
1994	0.92	0.90	0.70b	0.77b	0.64	0.69
1995	0.92	0.91	0.72c	0.74c	0.66	0.67
1996		0.94	0.65c	0.69c		0.65
1997			0.65c	0.73c 0.65d		0.47e
1998			0.77c	0.65c 0.77d		0.50e
1999			0.79c 0.70d	0.69c 0.64d	0.56ef	0.44e

^a Little Goose Dam.
^b Lower Monumental Dam.
^c McNary Dam.
^d Tailrace of McNary Dam to tailrace of Bonneville Dam.
^e Survival from tailrace of Lower Granite Dam (not reservoir) to tailrace of lower dam.
^f Based on the product of two nonrounded numbers.

Results

From 1966 to 1968, with only four or five dams in place, extrapolation of per-project survival estimates resulted in estimated survival through the overall system averaging 45%. Survival estimates generally decreased to less than 20% as additional dams were completed in the 1970s (Table 3). Under the low-flow conditions in 1973 and 1977, estimated downstream migrant survival was 1-3% for chinook salmon and less than 1% for steelhead. For 1993-1999, extrapolation of per-project estimates resulted in estimated hydropower system survival ranging from 31% to 59% (Table 4). Although there are differences in specific annual survival estimates between per-project and per kilometer extrapolation (Figure 4 - not shown), both resulted in considerably higher survival estimates for the late 1990s than for the mid to late 1970s, and in some years these estimates exceeded system survival estimates from the 1960s, when only four or five dams and reservoirs existed.

The increased survival estimated in the 1990s compared with that in the mid to late 1970s was not a function of a change in flows. There was no significant difference (P 5 0.83) between the mean daily flow at Ice Harbor Dam from 1974 to 1980 (3,113 m3/s) and the mean daily flow from 1993 to 1999 (3,056 m3/s). Likewise, at McNary Dam, the mean daily flow between the two periods (7,358 and 7,641 m3/s) was not significantly different (P 5 0.79).

TABLE 3. -- Survival estimates of migrating juvenile spring-summer chinook salmon and steelhead from the upper reservoir on the Snake River to the tailrace of Bonneville Dam from 1966 to 1980. Extrapolated survival is based on the annual per-project survival between Ice Harbor Dam and the lower river dam.

	Survival from upper Snake River dam to lower river dam		Extrapolated survival outside sampled reach		Overall system survival
Year	Chinook	Steelhead	Chinook	Steelhead	Chinook	Steelhead
1966	0.63	0.75	0.73a	0.75	0.46	0.56
1967	0.64	0.57	0.74a	0.57	0.47	0.32
1968	0.62	0.60	0.73a	0.71	0.45	0.43
1969	0.47	0.36	0.73	0.56	0.34	0.20
1970	0.22	0.38	0.77	0.61	0.17	0.24b
1971	0.28	0.32	0.71	0.54	0.20	0.17
1972	0.16	0.20	0.56	0.48	0.09	0.09a
1973	0.05	0.04	0.56	0.28	0.03	0.01
1974	0.36	0.20	0.80	0.40	0.28b	0.08
1975	0.25	0.41	0.78	0.67	0.19b	0.27
1976	0.30	0.36	0.33	0.35	0.10	0.13
1977	0.03	0.02	0.12	0.10	< 0.01	< 0.01
1978	0.44	0.30	0.51	0.27	0.23b	0.08
1979	0.31	0.06	0.61	0.31	0.19	0.02
1980	0.36	0.21	0.41	0.13	0.15	0.03

^a Extrapolation based on three dams and reservoirs as survival estimates between Ice Harbor Dam and The Dalles Dam did not change between 1966 and 1970 after completion of John Day Dam in 1968.
^b Based on the product of two nonrounded numbers.

Discussion

Given the marking techniques available at the time, the method of survival estimation used by NMFS in the 1960s and 1970s, as reported by Raymond (1979), was state of the art. Raymond (1979) details how they found no violations of the assumptions necessary for use of the technique. Raymond (National Marine Fisheries Service, unpublished data) did note that any losses of marked fish because of handling would reduce recapture numbers and underestimate collection efficiency at a site. This would not have affected the survival estimates if loss rates at the upstream and downstream sites were equivalent. Williams and Matthews (1995) suggested that greater losses of chinook salmon occurred at the first dam encountered on the Snake River. However, the extent to which differential losses may have biased collection efficiency estimates and thus survival estimates is unknown, but we agree with the assertion of Raymond (1979) that the effect was small. In 1977, for instance, almost no fish (unmarked as well as marked) were collected at The Dalles Dam, which certainly suggested that survival to that point was extremely low. Raymond (1979) did not provide error bounds for survival estimates calculated in the 1960s and 1970s (nor were any associated with the unpublished NMFS estimates from 1976 to 1980); thus we were not able to calculate error bounds for our extrapolations for this period.

The recent NMFS efforts to evaluate survival in the hydropower system have used single-release methods, not because the older methods were inherently biased or provided inaccurate survival estimates, but because improved technology, PIT-tag detectors at dams, and diversion of known individual fish back to the river allow for subsequent detections at downstream sites and the ability to estimate survival probabilities with precision for individual release groups of fish. Furthermore, multiple estimates of survival are now possible within a single season and for different stocks or for fish with different migration histories. Detection of fish occurs automatically at dams and does not require handling of large numbers of fish to recover marked ones. Thus, we contend that differences in estimates of survival reflect improvements in the direct survival of fish that migrate through the hydropower system and not differences in methodology. Furthermore, we believe our extrapolations of the estimates provide the most reasonable estimates of smolt survival through the hydropower system throughout the period.

Although per-kilometer extrapolation of survival estimates for recent years provided slightly lower system survival estimates than did per-project survival extrapolation, these estimates followed the same pattern from 1966 to 1999. The extrapolated survival estimates from 1966 to 1980 compared with those from 1995 to 1999 indicate that hydropower system survival has increased considerably since the 1970s. It is likely that decreased direct mortality resulted from improvements in downstream fish passage conditions at dams between the late 1970s and early 1990s (Williams and Matthews 1995). Moreover, survival estimates were greater in 1995-1999 than in 1993-1994, suggesting that increased survival also resulted from favorable spill conditions, changes in storage reservoir operations, and operation of turbines within 1% of peak efficiency, as mandated by the 1995 National Marine Fisheries Service Biological Opinion for operation of the federal Columbia River power system for endangered Snake River fish (NMFS 1995). There has been relatively high juvenile survival in recent years despite low flows (NMFS 2000a), which exacerbated the negative effects of dams on salmonids in the past. For example, some groups of PIT-tagged fish in early 1993 and 1994 migrated in flows that were nearly as low as those in 1973, yet the survival estimate in the Snake River for those groups was five to six times higher than the 1973 average.

Despite reduced direct mortality to juvenile migrants during recent years, smolt-to-adult returns of wild spring-summer chinook salmon to the Snake River basin have remained considerably below historical levels. Although wild steelhead smolt-to-adult returns increased between 1977 and 1987, reaching nearly 5% in 1987, they decreased to approximately 1% beginning in the late 1980s, levels seen previously only in 1973, 1977, and 1981. Smolt-to-adult returns (Figure 2 - not shown) represent the performance of the stock as a whole (transported and nontransported fish), but data from the 1990s from PIT-tagged fish suggest the smolt-to-adult return rates of nontransported migrants parallel the smolt-to-adult return rates of transported fish (NMFS 2000b). These results, in conjunction with survival estimates of nontransported migrants in the hydropower system, indicate that although the hydropower system contributes to salmonid mortality, it is much lower than in the 1970s, and the hydropower system may no longer represent the most important factor leading to the present low smolt-to-adult survival.

Until uncertainties about delayed effects of the hydropower system on salmonid mortality are resolved, or until dams are removed, it is prudent to consider additional means to improve survival at dams. However, as the system is altered, continued evaluation is required to determine the impacts on both smolt survival and adult returns.

TABLE 4. -- Survival estimates of migrating spring-summer chinook salmon and steelhead from the Lower Granite Dam reservoir to the tailrace of Bonneville Dam from 1993 to 1999. Extrapolated survival is based on the per-project survival within the sampled reach.

	Survival through sampled reach		Extrapolated survival outside sampled reach		Overall system survival
Year	Chinook	Steelhead	Chinook	Steelhead	Chinook	Steelhead
1993	0.77		0.45a		0.34
1994	0.64	0.69	0.48b	0.54b	0.31	0.38e
1995	0.66	0.67	0.78c	0.79c	0.51	0.53
1996	0.65	0.65	0.90d 0.72c	0.77c	0.42	0.50
1997	0.65	0.47	0.90d 0.73c	0.92d	0.43	0.45e
1998	0.77	0.50	0.94d 0.82c	0.90d	0.59	0.45
1999	0.56	0.44	0.94d	0.91d	0.53	0.40

^aTailrace of Little Goose Dam to tailrace of Bonneville Dam.
^bTailrace of Lower Monumental Dam to tailrace of Bonneville Dam.
^cTailrace of McNary Dam to tailrace of Bonneville Dam.
^dLower Granite Reservoir to tailrace of Lower Granite Dam.
^eBased on the product of two nonrounded numbers.

Acknowledgements

We thank the many staff, both past and present, of the Northwest Fisheries Science Center who conducted the fish handling, marking, and recovery operations on which these analyses were based. The manuscript was helped greatly by suggestions of Rich Zabel, Phil Levin, Peter Kareiva, and anonymous reviewers.

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Related Pages:
Count the Fish by Government Accounting Office, GAO-02-612, Salmon and Steelhead Recovery Efforts