William D. Muir

Survival of juvenile salmonids passing through bypass systems, turbines, and spillways with and without flow deflectors at Snake River dams

Abstract Using yearling chinook salmon Oncorhynchus tshawytscha and steelhead O. mykiss tagged with passive integrated transponders (PITs), we estimated passage survival through bypass systems, turbines, and spill bays with and without flow deflectors at Snake River dams relative to survival of fish released into the tailrace below the dam. Actively migrating fish were collected and marked with PIT tags at Snake River dam smolt collection facilities. Groups of tagged fish were then released through hoses into different passage routes; releases were coincident with a tailrace release approximately 1–2 km below the dam. Relative survival was estimated by the use of tag–recapture models for paired releases from detections of individual PIT-tagged fish at juvenile collection or detection facilities at downstream dams. Detection sites included Little Goose, Lower Monumental, McNary, John Day, and Bonneville dams, depending on the release location and year. Standard errors of relative survival probability estim...

Survival Estimates for Downstream Migrant Yearling Juvenile Salmonids through the Snake and Columbia Rivers Hydropower System, 1966–1980 and 1993–1999

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...

Factors Associated with Travel Time and Survival of Migrant Yearling Chinook Salmon and Steelhead in the Lower Snake River

Abstract Simple and multiple linear regressions were used to evaluate factors associated with travel time and survival of yearling chinook salmon Oncorhynchus tshawytscha and steelhead O. mykiss migrating in the lower Snake River. Factors were release date and environmental variables measuring river discharge (flow), water temperature, and the percentage of total flow passed over spillways at dams. Data were collected from migrant salmonids tagged with passive integrated transponder (PIT) tags from 1995 through 1999. The greatest distance over which survival could be estimated during all 5 years was from the Lower Granite Dam tailrace to the McNary Dam tailrace (225 river km encompassing four dams and reservoirs). Release groups consisted of PIT-tagged fish leaving Lower Granite Dam daily. Data from more than 451,000 PIT-tagged yearling chinook salmon and 204,000 PIT-tagged steelhead were analyzed. For each daily group, indices of exposure to environmental factors were calculated as the average value for ...

Influence of River Conditions on Survival and Travel Time of Snake River Subyearling Fall Chinook Salmon

Abstract From 1995 to 2000, subyearling fall chinook salmon Oncorhynchus tshawytscha reared at Lyons Ferry Hatchery were PIT-tagged at the hatchery, trucked upstream, acclimated, and released into free-flowing sections of the Snake River weekly from early June to mid-July. We estimated survival probabilities and travel time through the lower Snake River and detection probabilities at dams for each weekly release group. The average median time between release and arrival at Lower Granite Dam was 43.5 d. For each group, we split this time into two nearly equal (on average) periods: one when most fish in the group were rearing and one when most fish had apparently begun active seaward migration. The estimated survival for hatchery fish from release to the tailrace of Lower Granite Dam decreased with release date each year. The estimated survival through this reach was significantly correlated with three environmental variables: survival decreased as discharge (“flow”) decreased, as water transparency increas...

Post-Hydropower System Delayed Mortality of Transported Snake River Stream-Type Chinook Salmon: Unraveling the Mystery

Abstract Past research indicates that on an annual basis, smolts of stream-type Chinook salmon Oncorhynchus tshawytscha collected at Snake River dams and transported by barge to below Bonneville Dam have greater post-hydropower system mortality than smolts that migrate in-river. To date, this difference has most commonly been attributed to stress from collection and transportation, leading to decreased disease resistance or predator avoidance ability. Using both hatchery and wild passive integrated transponder (PIT) tagged Chinook salmon, we explored two mechanisms that either separately or jointly contributed to an alternative explanation: Altered timing of ocean entry and lost growth opportunity leading to size-selective predation. Based on weekly estimates of in-river survival and adult return rates of smolts that were transported or that migrated in-river between Lower Granite and Bonneville dams, we found greater post-hydropower system mortality for smolts transported early in the season but greater ...

Survival Estimates for the Passage of Juvenile Salmonids through Snake and Columbia River Dams and Reservoirs, 1998 Annual Report.

This report provides reach survival and travel time estimates for PIT-tagged hatchery and wild juvenile steelhead and yearling chinook salmon in the Snake and Columbia Rivers during 1998. Estimates of post-detection bypass survival for yearling chinook salmon at McNary Dam are also reported. Results are reported primarily in the form of data tables and figures with minimal description of methods and analysis. Detailed information on the methodology and statistical models used for this report is provided in five previous annual reports on this study, which are cited here.

Fall Chinook Salmon Survival and Supplementation Studies in the Snake River and Lower Snake River Reservoirs, 1997 Annual Report.

In 1997, the National Marine Fisheries Service, the U.S. Fish and Wildlife Service, and the Nez Perce Tribe completed the third year of research to investigate migrational characteristics of subyearling fall chinook salmon in the Snake River Basin.

Survival Estimates for the Passage of Spring-Migrating Juvenile Salmonids through Snake and Columbia River Dams and Reservoirs, 2003-2004 Annual Report.

For juvenile chinook salmon Oncorhynchus tshawytscha, sockeye salmon O. nerka, and steelhead O. mykiss that migrate through reservoirs, hydroelectric projects, and free-flowing sections of the Snake and Columbia Rivers, survival estimates are essential to develop effective strategies for recovering depressed stocks. Many management strategies were based on estimates of system survival (Raymond 1979; Sims and Ossiander 1981) derived in a river system considerably different from todays (Williams and Matthews 1995; Williams et al. 2001). Knowledge of the magnitude, locations, and causes of smolt mortality under present passage conditions, and under conditions projected for the future, are necessary to develop strategies that will optimize smolt survival during migration. From 1993 through 2002, the National Marine Fisheries Service (NMFS) and the University of Washington (UW) demonstrated the feasibility of using three statistical models to estimate survival of PIT-tagged (Prentice et al. 1990a) juvenile salmonids passing through Snake River dams and reservoirs (Iwamoto et al. 1994; Muir et al. 1995, 1996, 2001a, 2003; Smith et al. 1998, 2000a,b; Hockersmith et al. 1999; Zabel et al. 2001, 2002). Evaluation of assumptions for these models indicated that all were generally satisfied, and accurate and precise survival estimates were obtained. In 2003, NMFS and UW completed the eleventh year of the study. Flow levels during the early portion of the 2003 spring migration were similar to 2002, and only slightly higher than in the drought conditions during 2001. However, flow levels were much greater during the later part of the migration in 2003. Spill levels were similar to 2002, much higher than in 2001. Research objectives were to: (1) estimate reach survival and travel time in the Snake and Columbia Rivers throughout the yearling chinook salmon and steelhead migrations; (2) evaluate relationships between survival estimates and migration conditions; and (3) evaluate the performance of the survival-estimation models under prevailing operational and environmental conditions. Additionally, as adult return information becomes available, as part of this study we will evaluate relationships between juvenile survival and subsequent adult returns for fish with different juvenile migration histories.