Fy 2007 Innovative Project Solicitation Application of Innovative Acoustic Telemetry Technology to Underpin Statistically-Valid Survival Estimates for Chinook Salmon in the Nearshore Ocean Off the Mouth of the Columbia River

The three ocean arrays will not permit differentiating survival, movement, and detection processes within the near ocean environment. However, if detection probabilities at each array remain constant throughout the season, then changes in movement can be detected. For example, define and to be the probabilities of moving to the north array and being detected there at the times and , respectively. If is constant over these times, then implies more northward movement at time than at time , demonstrating a shift in movement during the season.

A weaker assumption is that detection probabilities at the different arrays remain proportionally constant throughout the season. This assumption states that and remain constant, rather than each of , , and . With this assumption, we can detect changes in relative movement. For example, again define and as above. Also define and to be the probabilities of moving to the south array and being detected there at times and , respectively. Then is an index of north movement relative to south movement at time ; however, this index of movement does not account for different detection probabilities at the north and south arrays. Nevertheless, we can compare this measure to the analogous measure at time and derive a measure of the change in relative north/south movement over time:

.

With constant over time, this measure does not depend on detection probabilities at the arrays. Under a variety of assumption about detection probabilities, the trinomial detection data from the ocean arrays can be analyzed using general linear models to assess homogeneity over time and compare between fish stocks, in-river vs. barged fish, and evaluate relationships with hydrographic and oceanographic conditions.

This study will use opportunistic data from acoustic-tag releases from different locations, each involving a different tag life which will be exhibited downstream of Bonneville. Thus, to properly analyze these data, we will need to perform group adjustments for tag life. We expect there to be no difficulty in attaining the necessary tag-life information from researchers performing the releases.

Successful completion of this study will demonstrate the feasibility of deploying a comprehensive study design capable of estimating absolute mortality through the MCR and subsequent nearshore ocean movement and survival in subsequent years. The tagging results will also provide the necessary information needed to determine sample sizes and detection rates in consummate studies of estuary and near ocean survival and comparison of in-river and transport fish.

Specific information generated by the investigation will include the following:

1. 
   The terminal ocean arrays will extend estimation of survival in-river to the last acoustic array at the mouth of the Columbia River (MCR) (i.e., , Figure 5). That is, this study will provide survival estimates for subyearling and yearling Chinook salmon for the estuary between East Sand Island and the Columbia River bar.
   
2. 
   Comparison of the relative movements north, south, and seaward over time, between fish stocks, and in relation to positions of the Columbia River plume [i.e., ratios and ]. That is, we will examine the horizontal distribution of detections by species at the nodes in the three arrays.
   
3. 
   Indication of whether smolts move out to the open ocean and whether subsequent studies need to maintain arrays at the edge of the continental shelf when attempting to estimate survival through the MCR.
   
4. 
   In the case where barged smolts can be acoustic-tagged, a comparison can be conducted of relative movement patterns between transported and in-river fish through the estuary and nearshore ocean environment.
   
5. 
   Estimation of travel times through the estuary and nearshore ocean environment and comparison between transport and in-river migrants will be conducted. That is, we will estimate the residence time during early ocean entry for the study area 20 km out from the MCR.
   

The final annual report will be the one and only technical report for this innovative project. It will thoroughly document the objectives, scientific background, methods, and results, and explain application of the findings to benefit future projects in the F&W Program that will increase the survival of Columbia River salmonids.

The Project Leader has a PISCES account and substantial experience using this software. Quarterly status reports will be provided as required by BPA. These reports will update the status of progress toward the milestones identified in the scope of work in PISCES.

The Pacific Northwest National Laboratory (PNNL) has stringent project management guidelines and protocols. These include mandatory Project Management Plan, Safety Plan, and Animal Care Protocols. The Project Leader is trained in all of these elements. He has managed numerous scientific investigations for PNNL.

This study will result in new knowledge about the relationship between smolt migration patterns and oceanographic conditions off the mouth of the Columbia River. The results will feed the design of statistically valid studies of smolt survival in the ocean. This project will be monitored and evaluated through 1) the federal research, monitoring and evaluation process and its estuary/ocean subgroup, 2) the Pacific Northwest Aquatic Monitoring Partnership’s estuary group, 3) the USACE’s Anadromous Fish Evaluation Program, and 4) the BPA’s PISCES project tracking system. As appropriate, we will inform managers about the project’s accomplishments through staff briefings and meetings. Also, important findings will be published, and hence monitored, through the scientific peer-review process.

This project will have the advantage of PNNL’s facilities and local infrastructure. Laboratory, storage, and boat maintenance facilities are operated by PNNL at North Bonneville, Richland, and Sequim, WA. PNNL also has offices in Portland, OR. During the field season, the research vessel will be moored at the Port of Ilwaco, where the are quality boat support services.

The research vessel we plan to use is the 31-ft WAC (walk around cabin) SAFE (Secure Around Floatation Equipped; http://www.safeboats.com/default/home.html) boat powered by twin 250 hp Mercury Verado engines (Figure 6). The boat was custom designed and built for PNNL to deploy and recover acoustic telemetry equipment in marine waters around the Columbia River bar. Named the R/V Desdemona, the boat was christened in 2006. As a contingency, we have contacts with local crab fishermen to lease a large fishing vessel, if an additional/larger vessel is warranted.

Figure 6. The R/V Desdemona.

This project will deploy the latest technology for acoustic telemetry, the Juvenile Salmon Acoustic Telemetry System. The advantages of JSATS begin with the tag, which transmits a digitally encoded pulse (as opposed to a simple phase-shifted analog pulse) that includes a CRC message at the end of the encoding to dramatically reduce the number of false positives. False positives cannot be eliminated mathematically and greatly increase data-processing time. The JSATS tags also have a higher source level that other micro tags (150 dB relative to 1 µPascal at 1 m versus about 140 dB) thereby greatly improving signal to noise ratios. The JSATS tags have a longer active battery life than other tags, in spite of having a significantly higher source level than other tags. A JSATS tag can last about 60 days pinging once every 10 s, 45 days pinging once every 7 s, and 30 days pinging once every 5 s. They also have an inactive shelf life of up to 1 year. We also expect fewer and less significant tag effects on small fish than would be expected with non-JSATS tags because JSATS tags are light (0.60 g in air and 0.35 g in water) and have a conformal shape designed to fit within the body cavity of a juvenile salmonid with minimal impact on the animal. Non-JSATS micro tags weigh more than 1 g in air and are cylindrical, which makes them easier to manufacture but harder on smolt endurance and internal organs. For example, the transmitters used in 2006 for BPA study 200311400 reportedly weighed over 3 g in air.

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Clements, S., D. Jepson, M. Karnowski, and C. Schreck. 2005. Optimization of an acoustic telemetry array for detecting transmitter-implanted fish. N. Amer. J. Fish. Manag. 25:429-436.

Cormack, R. M. 1964. Estimates of Survival from the Sighting of Marked Animals. Biometrika 51:429-438.

Emmett, R.L., R.D. Brodeur, and P.M. Orton. 2004. The vertical distribution of juvenile salmon and associated fishes in the Columbia River plume. Fish. Oceanog. 13:392-402.

Emmett, R.L., G.K. Krutzikowsky, and P. Bentley. 2006. Abundance and distribution of pelagic piscivorous fishes in the Columbia River plume during spring/early summer 1998-2003: Relationship to oceanographic conditions, forage fishes,and juvenile salmonids. Progress in Oceanography 68:1-26.

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Independent Scientific Advisory Board (ISAB). 2007. Review of hypotheses and causative factors contributing to latent mortality and their likely relevance to the “below Bonneville” component of the COMPASS model. Northwest Power and Conservation Council, Portland, OR. ISAB 2007-1.

Independent Scientific Review panel (ISRP). 2005. Retrospective report 1997-2005. Northwest Power and Conservation Council, Portland, OR. ISRP 2005-14.

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McMichael, G.A., J.A. Vucelick, T.J. Carlson, G.E. Johnson, and G.R. Ploskey. 2006. Use of acoustic telemetry to assess habitat use of juvenile Chinook salmon and steelhead at the mouth of the Columbia River. Final report of research submitted to the USACE, Portland District. PNNL-15575.

Muir, W.D. and R.L. Emmett. 2004. Evaluation of the relationship among time of ocean entry, physical and biological characteristics of the estuary and plume environment, and adult return rates. Report by the National Marine Fisheries Service for the USACE, Portland District, Portland, OR.

National Marine Fisheries Service. 2004. Biological Opinion on Operation of the Federal Columbia River Power System. Available at www.salmonrecovery.gov/implementation.

Pearcy, W.G. and J.P. Fisher. 1988. Migrations of coho salmon, Onccorhynchus kisutch, during their first summer in the ocean. Fish. Bull. 86:173-195.

Ploskey, G.R., M.A. Weiland, J.S. Hughes, S.R. Zimmerman, R.E. Durham, E.S. Fischer1, J. Kim, L. Townsend, J.R. Skalski, and R.L. McComas. 2006. Acoustic Telemetry Studies of Juvenile Chinook Salmon Survival at the Lower Columbia Projects in 2006. Draft report of research submitted by PNNL to the USACE, Portland District, Portland, OR

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Schreck, C.B., T.P. Stahl, L.E. Davis, D.D. Roby, and B.J. Clemens. 2006. Mortality estimates of juvenile spring-summer Chinook salmon in the lower Columbia River and estuary, 1992-1998: evidence for delayed mortality? Trans. Amer. Fish. Soc. 135:457-475.

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H. Key Personnel

The names, titles, FTE/hours, and duties for the key personnel on this project are contained in the following table. One-page resumes for key personnel are presented after the table.

B.S. Fisheries, University of Washington, 1971

M.S. Fisheries, University of Washington, 1974

Ph.D.Fisheries, University of Washington, 1979

Chief Scientist, Ecology, Energy Technology Directorate, Pacific Northwest National Laboratory

Dr. Carlson has over 30 years of experience in acoustics including fixed location and kinematic hydroacoustics, acoustic telemetry, and the effects of sound on fish and marine mammals. Recent research also includes the effects of changes in pressure during turbine and spill passage on juvenile salmonids and assessment of the effects of exposure to severe turbulence and structure during turbine and spill passage.. Dr. Carlson has been the principle investigator for development of advanced acoustic micro-transmitters and receiving systems for assessment of the migratory behavior and survival of juvenile salmonids during passage through the federal Columbia River hydropower system. Primary expertise is in assessment of the effects of sound on fish health and behavior and the use of sound to assess the behavior and survival of juvenile fish is freshwater, estuarine and marine environments.

Carlson TJ, MA Weiland, and VA Sutton. 2002. "Ultrasonic 3-D Tracking of Fish and Drogues Passing through a Kaplan Turbine Intake at McNary Dam, 1999 & 2000 ." In Fourth Fisheries Bioengineering Symposium, 132nd American Fisheries Society Annual Meeting . PNNL-SA-36990, Pacific Northwest National Laboratory, Richland, WA.

Faber DM, MA Weiland, R Moursund, TJ Carlson, N Adams, and D Rhondorf. 2001. Evaluation of the Fish Passage Effectiveness of the Bonneville I Prototype Surface Collector using Three-Dimensional Ultrasonic Fish Tracking . PNNL-13526, Pacific Northwest National Laboratory, Richland, WA.

Faber, D.M., K. Cash, T.J. Carlson, and S. Zimmerman. 2002. Design of Acoustic 3D Tracking Baseline Arrays for Fish Behavior Studies, PNNL-13925, Pacific Northwest National Laboratory, Richland, WA.

Popper, AN and TJ Carlson. 1998. "Application of Sound and Other Stimuli to Control Fish Behavior," Transactions of the American Fisheries Society, Vol. 127, No. 5, pp. 673–707, - afs.allenpress.com.

Ploskey, G.R., P.N. Johnson, and T.J. Carlson. 2000. "Evaluation of a Low-Frequency Sound-Pressure System for Guiding Juvenile Salmon away from Turbines at Bonneville Dam, Columbia River," North American Journal of Fisheries Management 20(4): 951-967.