Beginning in 1993, the National Marine Fisheries Service (NMFS) and the University of Washington (UW) began research to determine survival and travel-time characteristics of wild and hatchery-reared spring/summer Chinook salmon and hatchery steelhead migrating through Snake River dams and reservoirs (Muir et al. 2001a, 2001b; Skalski et al. 1998, Smith et al. 2002, Williams et al. 2001).  This research was expanded in 1995 to include Snake River fall Chinook salmon (Smith et al. 2003).  The initial goals of this research program were to 1) field test and evaluate the single-release, modified single-release, and paired-release Models for the estimation of reach and project survival, 2) provide annual estimates of reach and project survival with known precision, and 3) explore relationships among fish travel time, fish survival, and environmental conditions.  The first goal was addressed in detail during the first 5 years of research.   Presently, we continue to work on the second and third goals.   Additionally, we are now evaluating adult returns of PIT-tagged fish to further understand the relationships among juvenile survival, travel time, migration timing, and other factors, such as numbers of bypasses or passage routes, that juveniles encountered during their downstream migration to look for correlations with adult survival (Williams et al. 2005).  We also continue to evaluate violation of survival model assumptions, a necessary step in producing unbiased survival estimates.
In 2006, we plan to continue providing reach survival estimates through Snake and Columbia River dams and reservoirs throughout the yearling Chinook salmon and steelhead migrations.  Survival estimates will be made as far downstream as possible depending on numbers of fish PIT-tagged and released from other studies, spill levels which affect detection rates, and whether the PIT tag detection system in the Bonneville Dam Powerhouse II corner collector is functional.  For reaches where survival cannot be estimated, available estimates will be extrapolated to provide an estimate through the entire hydropower system.  At Lower Granite Dam, we will PIT tag and release up to 20,000 wild yearling Chinook salmon, 20,000 wild steelhead, and 20,000 hatchery steelhead, depending on their availability.  To reduce handling, we will rely on releases of PIT-tagged yearling Chinook salmon from hatcheries to estimate their survival through the Snake and Columbia Rivers.  We will not PIT tag Snake River hatchery subyearling fall Chinook salmon in 2006 as sufficient numbers will be released by other researchers for transportation evaluation.
If suitable fish can be found, we will PIT tag and release hatchery yearling Chinook salmon with and without bacterial kidney disease (BKD) (14,000 total) to determine the effects of reduced fitness on detection probability and travel time.  One of the assumptions necessary for unbiased estimation of survival for smolts migrating through the hydropower system is that "all fish in a release group have equal survival and detection probabilities" (Skalski et al. 1998).  Recent evidence suggests this assumption may be violated.  For example, Zabel et al. (In press) reported that between 1999 and 2001, yearling Chinook salmon and steelhead previously detected at a Snake River dam were more likely to be detected again at downstream dams.  Fish health could also potentially affect detection probability and needs to be evaluated.  If fish with reduced fitness are more likely to enter bypass systems, this would contribute to the observed lower adult returns for fish that are bypassed multiple times and to differential delayed mortality of transported fish (Sanford and Smith 2002).  Reduced fitness could be caused by disease, culling of weaker hatchery fish, or injuries incurred during migration.  Bacterial kidney disease infection rates are high (but with low infection levels in individual fish) in spring/summer Chinook salmon stocks throughout the Columbia River basin (Williams 2001) and could result in reduced fitness and increased collection rates of infected smolts passing dams.  This hypothesis is supported by the findings of Elliot and Pascho (1991), who observed that guided yearling Chinook salmon tended to have higher ELISA values for BKD than unguided ones at Lower Granite Dam.  Furthermore, adult returns from transport studies in recent years have shown the benefits from transportation to vary throughout the migration season with the early migrants typically having poor returns for both transport and inriver groups.  If weaker/sicker fish arrive at the collector dams first, this could help explain these results.
During 2006, this study will also be partially supporting the PIT tag trawl effort in the Columbia River estuary in a cost sharing agreement with the U. S. Army Corps of Engineers (COE).  The data the PIT tag trawl provides is needed to estimate survival through the final reach of the hydropower system, from John Day to Bonneville Dam tailrace.  Details for this part of the study can be found in the PIT tag trawl proposal to the COE.  

REFERENCES

Elliot, D. G., R. J. Pascho.  1991.  Juvenile fish transportation: Impact of bacterial kidney disease on survival of spring/summer Chinook salmon stocks.  1989 Annual Report to U.S. Army Corps of Engineers, Walla Walla District, Contract No. E86880047, 203 pp.

Muir, W. D., S. G. Smith, J. G. Williams, E. E. Hockersmith, and J. R. Skalski.  2001(a).  Survival estimates for PIT-tagged migrant juvenile Chinook salmon and steelhead in the lower Snake River, 1993-1998.  N. Am. J. Fish. Manage. 21:1-14.

Muir, W. D.,S. G. Smith, J. G. Williams, and B. P. Sandford  2001(b).  Survival of juvenile salmonids passing through bypass systems, turbines, and spillways with and without flow defectors at Snake River dams.  N. Am. J. Fish. Manage. 21:135-146.

Sanford, B. P., and S. G. Smith.  2002.  Estimation of smolt-to-adult return percentages for Snake River Basin anadromous salmonids, 1990-1997.  Journal of Agricultural, Biological, and Environmental Statistics 7:243-263.

Skalski, J. R., S. G. Smith, R. N. Iwamoto, J. G. Williams, and A. Hoffmann. 1998.  Use of passive integrated transponder tags to estimate survival of migrant juvenile salmonids in the Snake and Columbia rivers.  Can. J. Fish. Aquat. Sci. 55:1484-1493.

Smith, S. G., W. D. Muir,  E. E. Hockersmith, W. Zabel, R. J. Graves, C. V. Ross, W. P. Conner, and B. D. Arnsberg.  2003.  Influence of river conditions on survival and travel time of Snake River subyearling fall Chinook salmon.  N. Am. J. Fish. Manage. 23:939-961.


Smith, S. G., W. D. Muir, J. G. Williams, and J. R. Skalski.   2002.  Factors associated with travel time and survival of migrant yearling Chinook salmon and steelhead in the lower Snake River.  N. Am. J. Fish. Manage. 22:385-405.

Williams, J. G.  2001.  Potential impact of Renibacterium salmoninarum on adult returns of Snake River spring/summer Chinook salmon.  Bull. Natl. Res. Inst. Aquacult. Suppl. 5:55-59.

Williams, J. G., S. G. Smith, and W. D. Muir.  2001.  Survival estimates for downstream
migrant yearling juvenile salmonids through the Snake and Columbia River hydropower system, 1966-1980 and 1993-1999.  N. Am. J. Fish. Manage. 21:42-49.

Williams, J. G., S. G. Smith, R. W. Zabel, W. D. Muir, M. D. Scheuerell, B. P. Sandford, D. M. Marsh, R. McNatt, and S. Achord.  2005.  Effects of the federal Columbia River power system on salmon populations.  NOAA Technical Memorandum, NMFS-NWFSC-63.

Zabel, R. W., T. Wagner, J. L. Congleton, S. G. Smith, and J. W. Williams.  In press.  Incorporating individual traits into capture-recapture models to estimate population survival and selection coefficients for migrating salmon.  Ecological Applications.