A. Abstract and Statement of Innovation s1

Title: Using acoustic telemetry to evaluate the behavior, habitat use, and survival of tagged juvenile salmonids in the John Day Reservoir

A. Abstract and statement of innovation Recently there have been regional discussions regarding the benefits of operating the John Day Reservoir at minimum operating pool to improve the survival of migrating juvenile salmonids. The intent of the proposed operation change is to reduce the travel time and improve the survival of migrating juvenile salmonids through John Day Reservoir. We believe that current acoustic telemetry technologies can be used to better understand the effects of the current and future operations by allowing for the estimation of 1) where specifically in the reservoir migration delay is occurring; 2) where specifically in the reservoir mortality is occurring, and 3) what habitats are being used in specific sections of the reservoir thus providing insight to the relation of delay and mortality to habitat use of the tagged fish. However, alterations and further investigation of the existing experimental designs and model assumptions currently used to assess dam and pool survival are necessary to address the effects of reservoir operations in smaller sections of the reservoir. In this study, we propose to formulate and test design considerations for assessing within reservoir behavior, habitat use, and survival of juvenile salmonids at smaller spatial scales to better understand the effects of current and future reservoir operations. As part of this pilot project, we plan to formulate and test a unique application of acoustic telemetry to assess habitat use of tagged juvenile salmonids by developing boat mounted mobile arrays that will allow for various habitats to be sampled to better understand habitat use.

B. Technical and/or Scientific Background The mainstem Columbia River is an important migration corridor for endangered and threatened salmonids. Considerable resources are being expended to mitigate the effects of the development of the federal hydrosystem on stocks of Pacific salmon. Recently there have been discussions about operating the John Day Reservoir at minimum operating pool (mop) to decrease the travel time and increase the survival of migrating juvenile salmonids. The John Day Reservoir has also been previously considered for drawdown because of its length and long hydraulic retention time compared with other Columbia River and lower Snake River reservoirs. The reservoir provides shoreline-rearing habitat for subyearling Chinook salmon that disperse downstream as fry from the Hanford Reach (Tiffan et al. 2006) and also serves as a migration corridor for emigrating subyearling Chinook salmon (including smolts) and other juvenile anadromous salmonids produced in upstream spawning areas and hatcheries. Thus, considerable attention has been given to the effects of altering the operations for the impoundment. The potential effects of drawdown have been assessed through modeling exercises and the interpretation of changes in various types of habitat and population modeling results (Tiffan et al 2006, U.S. Army Corps of Engineers 1994, Sheer 1999; PNNL and USGS 2000; U.S. Army Corps of Engineers 2000). Despite the assertion that migration occurs through John Day Reservoir, little is known of the specific migration characteristics, survival, and habitat use of migrating juvenile salmonids in this Columbia River impoundment. Conversely, many studies have been conducted over the past two decades to evaluate survival through mainstem dams, reservoirs, and over larger reaches (i.e. multiple reservoirs). Various tagging technologies have been used to mark fish for these evaluations including freeze brands (Laird et al.1975), passive integrated transponder (PIT) tags (Muir et al. 1995, Dawley et al. 1998), radio tags (Counihan 2002, Counihan 2003, Counihan 2006), and more recently acoustic tags. In recent years, large numbers of tagged juvenile salmonids have been released in research efforts to understand the causes of mortality and the effectiveness of mitigation at mainstem Columbia River hydroelectric dams. Reservoir or pool survival, dam survival, and survival through the immediate tailrace areas can be estimated from the experimental design typically associated with these studies. Much effort has and is currently being expended to ensure the adequacy and standardization of the methodology associated with these evaluations (Peven et al. 2005). As per these recommendations, efforts are undertaken to evaluate the adequacy of assumptions associated with statistical models used to estimate survival. For instance, the placement of interrogation arrays downstream of the project of interest is designed such that the probability of detecting dead tagged fish is minimized. To assess the efficacy of these measures dead fish are typically released in the tailrace of the project being evaluated. Interrogations (or the lack of) are then noted and the locations of the arrays are adjusted accordingly. However, no such effort has been undertaken to evaluate this assumption for smaller reservoir reaches. Further, inferences regarding differences in behavior and survival are confounded if the same fish are used to evaluate and compare these characteristics in multiple reservoir reaches. For instance, tag implantation can differentially affect the performance of tagged fish as they migrate downstream and result in biased survival estimates (Peven et al. 2005). Similarly, Hockersmith et al. (1998) noted that survival of radio-tagged salmon was lower than for PIT-tagged fish and that the difference was greater the longer the fish had been tagged.

We believe that existing acoustic telemetry technologies can be adapted and used to better understand the effects of the John Day Reservoir operations by allowing for the estimation of 1) where specifically in the reservoir migration delay is occurring; 2) where specifically in the reservoir mortality is occurring, and 3) what habitats are being used in specific sections of the reservoir, thus providing insight to the relation of delay and mortality to habitat use of tagged fish. However, the experimental design and assumption tests currently used to assess dam and pool survival should be modified to assess the effects of reservoir operations in smaller sections of the reservoir. For instance, the effects of post tagging mortality of tagged fish with respect to time, the specificity of assumption testing typically used to address dam and pool survival and not smaller reservoir sections, and the use of fish released at John Day Dam to infer differences in reservoir sections confound interpretations of the behavior and survival of tagged fish in smaller reservoir sections. In this study, we propose to formulate and test design considerations for assessing reservoir behavior, habitat use, and survival. As part of this pilot project, we also plan to provide insight into a unique application of acoustic telemetry systems to assess habitat use of tagged juvenile salmonids. C. Rationale and Significance the Council’s Fish and Wildlife Program By providing methods to better understand reservoir survival at a smaller spatial scale, we feel that this proposed work is consistent with the overall intent of the Fish and Wildlife Program and other regional efforts to recover endangered and threatened Pacific salmon. More specifically, we feel that the proposed project would provide information and products that would help to better evaluate the effect of implementing the target objectives listed below that are from the Lower Middle Columbia Subbasin Plan (see: p.39).

Tier Rankings* by Geographical Areas Target objective and Associated Key Primary Secondary strategy Finding Improve juvenile passage The construction of the All three dams and conditions at The Dalles, hydropower system turned reservoirs John Day and McNary the river into a series of dams though water reservoirs, which has management actions, greatly extended the including extending juvenile migration period. summer spill Juvenile steelhead migrate through the area throughout the spring and early summer; juvenile coho in the spring; and fall chinook in late spring and late summer. Restore normative Reduced travel time will All three dams and hydrograph will improve survival and reservoirs improve migration subsequent adult returns. conditions. Flow augmentation can increase water velocities. Alternative flood control strategies can helpful recapture the historical timing of flow. Increased spill diverts fish from the turbines and increases survival.

D. Relationships to other projects This project would be conducted with the intent of being fully coordinated with ongoing ACOE Anadromous Fish Evaluation Program funded research in the Snake River, at McNary Dam, and in the mid-Columbia as our ability to interrogate tags from these studies dictates. We anticipate that some, if not all of these studies will be using HTI acoustic telemetry tags. Thus we should be able to interrogate and evaluate the behavior and survival of fish released as part of these studies. During 2007, the USGS released 2000 acoustic tagged yearling Chinook salmon at Lower Granite Dam and 3000 yearling Chinook, 3000 subyearling Chinook, and 1000 steelhead trout at McNary Dam as part of an AFEP funded study. We feel that if similar numbers of fish are released next year then there is great potential to garner more information. For instance, it would be informational to understand how the habitat used by fish released further upstream, say in the Snake River, differs from that by fish released at McNary Dam or directly as part of this study. We are not particularly tied to a particular tag/telemetry system manufacturer but will use a tag that will allow for the most information to be garnered in the limited time duration as stipulated in this proposal solicitation. Further, we know that the HTI tags and telemetry systems will allow us to potentially determine fish position within a particular habitat type in a 3-D context. We would like to determine the usefulness of attaining 3-D positions and/or tracks as we monitor various habitats. If other tags and telemetry systems (i.e., JSAT) will allow for this information to be collected and others are releasing tagged fish using this technology, we would be interested in using the JSAT system. We feel that this research has the potential to provide a link between the AFEP and BPA funded studies. This project could inform AFEP efforts by addressing assumptions that are not addressed as part of their studies and also allow for fiscal efficiencies because of the large numbers of tags typically released as part of the AFEP evaluations of survival at mainstem hydroelectric projects.

E. Proposal objectives, work elements, and methods and monitoring and evaluation While many studies have evaluated the sources of mortality associated with passage through mainstem hydroelectric projects, little is known of where specifically mortality is occurring in the reservoirs. Some studies have evaluated pool survival (survival from the tailrace of the upstream dam to the forebay of the next downstream project), project survival (tailrace of upstream dam to tailrace of downstream dam), and reach survival (e.g., multiple reservoirs). However, studies looking at the behavior and survival through smaller reservoir sections are generally lacking. Understanding specifically where in the reservoirs mortality is greatest could help to direct management efforts to improve survival. For instance, if mortality is greater in one section than another and operating John Day Reservoir at mop differentially affects migration rates through specific reservoir sections, then the expected benefits of the operation may not be as great as anticipated. Similarly, sections with high mortality may have high predator densities or contain habitat types (e.g., Eurasian watermilfoil) where predator encounters are greatest.

As noted previously, the experimental designs commonly used in studies that evaluate mortality associated with dam passage confound the interpretation of behavior and survival through smaller sections. Also, little is known of the transport and probability of detection of dead tagged individuals through shorter reservoir sections since assumption tests used in survival studies through hydroelectric projects evaluate this assumption by releasing fish at the project of interest and not within the reservoir. Detections of dead tagged individuals could bias estimates of survival. Further, it is likely that the effects of tag implantation vary over time and thus, over distance given the directional nature of the seaward migration of anadromous juvenile salmon. Therefore, survival estimates being greater or lesser in one reservoir section than another may be due to tagging effects that are not controlled for in studies where releases are made above or immediately below hydroelectric projects.

In this study, we propose to formulate and test the design of studies that would allow for the estimation of behavior and survival within reservoir sections and allow for valid comparisons to be made between reservoir sections. We propose to test the feasibility of doing this by dividing the John Day Reservoir up into sections based on hydrogeomorphic characteristics and then releasing tagged fish at the upstream end of each section. These fish will then be interrogated at downstream locations and we will be able to generate survival estimates for each section. By making the releases at the upstream end of each section, we hope to remove the potential bias associated with interrogating fish in each section that have had the tag implanted for varying lengths of time and thus reduce the potential for differential tagging effects to be manifested over time (Peven et al 2005). We will then be able to compare the survival and travel time of these tagged fish with that of tagged fish released as part of other studies released from other locations (e.g., mid-Columbia, Snake, McNary Dam). The comparison of the survival of these different tagged fish groups within smaller river sections will provide insight into the adequacy of the existing study design to assess reservoir survival.

Tagged juvenile salmonids, whether tagged with radio or acoustic transmitters have been used to assess survival though dams and reservoirs. However, little is known of what types of habitats these tagged fish use. For instance, it is commonly assumed and has been hypothesized that juvenile subyearling Chinook salmon use shallow water habitats in the John Day Reservoir (Tiffan et al. 2006); do tagged individuals exhibit this behavior? Does the type of habitat used by tagged fish vary within the reservoir? At what depth do tagged fish migrate, do they follow the thalweg? In reservoir sections with lower survival, are there differences in the types of habitats that the tagged fish use? While the full examination of these questions are beyond the scope of this pilot proposal, a better understanding of how tagged fish behave would help managers understand the context of estimates of survival and behavior generated using tagged fish as surrogates for the untagged population. We feel that we can deploy mobile acoustic telemetry arrays to randomly sample across various habitat types in the river section to further assess habitat use. We will have to rely heavily on interrogating the large numbers of fish released as part of other studies to increase our probability of detecting tagged fish in sufficient numbers to provide a meaningful evaluation. Dependent on the successful outcome of this pilot project, we would then propose to deploy the arrays to cover available habitats within each reservoir section and then through the development of the probabilistic sampling design, we would propose methods to assess habitat use differences between reservoir sections.

Work element 1. Set up and deploy arrays that can be used to interrogate tagged fish downstream of each release location used for estimating reservoir section survival.

Acoustic telemetry arrays will be deployed at locations downstream of McNary Dam to interrogate fish released as part of this study. We will establish three reservoir sections that we can evaluate behavior and survival of fish tagged and released as part of this study and also fish released as part of other research being conducted at upstream locations. The minimum design criteria for estimating the survival of fish downstream of each location will be the establishment of two downstream interrogation arrays (Peven et al. 2005).

Task 1.1 Using hydrodynamic model simulations and other habitat information divide the John Day Reservoir into three distinct sections. Task 1.2 Deploy acoustic nodes at a minimum of two locations downstream of the release location to allow for the estimation of survival.

Task 1.3 Test equipment using test tags and establish Quality Assurance Plan for the operation and data processing aspects of the equipment operation.

Work element 2. Formulate and test the experimental design and associated assumptions in the use of acoustic telemetry systems to estimate the survival and travel time of yearling and subyearling Chinook salmon through three sections of the John Day Reservoir.

1) Ho: The survival and travel time of tagged fish released at the upstream end of reservoir sections in John Day Reservoir is the same as for tagged fish released as part of studies at McNary Dam and at other upstream locations for a particular reservoir section.

2) Ho: The survival and travel time of tagged fish is equal through each reservoir section evaluated.

3) Ho: The probability of detecting dead tagged juvenile salmonids at arrays downstream of the release location is zero.

Tagged juvenile yearling and subyearling Chinook salmon will be released at the upstream end of each reservoir section (Figure 1). We plan to release 100 yearling Chinook salmon and 100 subyearling Chinook salmon at the upstream end of each reservoir section (total = 300 yearling and 300 subyearling Chinook salmon), Releases will be made throughout the migration season and will be timed such that the releases will encompass the conditions experienced by run of the river fish. We coarsely estimate that we will be able to produce survival estimates with a standard error of 0.03 (assuming S = 0.90 in each section, capture probability = 0.95 for each telemetry array). Survival will be estimated using the single release survival model (Peven et al. 2005) for fish released as part of this study and for fish released as part of other studies at upstream locations. Travel time through each section will be estimated for each release type (e.g., fish released as part of this study and for fish released as part of other evaluations). We will then evaluate differences in survival of release groupings formulated by release locations.

The assumptions of the single release-recapture model that may be tested are the following:

. McNary Dam

R 2 s λ1 2

λ2 s3

λ3 John Day Dam

John Day Reservoir Survival: Sˆ1* S ˆ 2 * S ˆ 3

Figure 1. Schematic of proposed release and detection location design and estimable survival parameters (S = survival estimate, p = capture probability, and λ = S • p) generated from the proposed release- recapture design using a single release model to estimate migrant juvenile salmonid survival through the John Day Reservoir. Dams are represented by rectangles and ovals represent potential detection arrays. Reservoir survival would be estimated by the product of the survivals for each release group. The variance will be estimated using the Delta Method (Seber 1973). A1. Individuals marked for the study are a representative sample from the population of interest.

A2. Tagging or sampling does not affect survival and capture probabilities. That is, tagged animals have the same probabilities as untagged animals.

A3. All sampling events are “instantaneous.” That is, sampling occurs over a negligible distance relative to the length of the intervals between sampling events.

A4. The fate of each tagged individual is independent of the fate of all others.

A5. All tagged individuals alive at a sampling location have the same probability of surviving until the end of that event.

A6. All tagged individuals alive at a sampling location have the same probability of being detected on that event.

A7. All tags are correctly identified and the status of smolt (i.e., alive or dead) is correctly assessed.

The first assumption (A1) concerns making inferences from the sample to the target population. For example, if inferences are sought for Chinook salmon smolts, then the sample of tagged fish should be drawn from that class of fish. Otherwise, nonstatistical inferences are necessary, justifying the similarity between the target population and the representatives of marked populations. These assumptions could also be violated if smolts selected for tagging were larger on average than the population of smolts in general.

Assumption (A2) again relates to making inferences to the population of interest (i.e., untagged fish). If tagging has a detrimental effect on survival, then survival estimates from the single release-recapture design will tend to be negatively biased (i.e., underestimated).

The third assumption (A3) specifies that mortality is negligible immediately in the vicinity of the sampling stations, so that the estimated mortality is related to the river reaches in question and not during the sampling event. In the case of outmigrating smolts, the time they spend in the vicinity of detection equipment is brief and small, relative to the size of the river reaches in question. This assumption is for sake of mathematical convenience and should be fulfilled by the nature of the outmigration dynamics and deployment of the hydrophone or antenna array in the case of active tags.

The assumption of independence (A4) implies that the survival or death of one smolt has no effect on the fates of others. In the larger river system with tens of thousands of smolts, this is likely true. Furthermore, this assumption is common to all tag analyses with little or no evidence collected to suggest it is not generally true. Nevertheless, violations of assumption (A4) have little effect on the point estimate but might bias the variance estimate with precision being less than calculated.

Assumption (A5) specifies that a smolt’s prior detection history has no effect on subsequent survival. This could be violated if some smolts were self-trained to repeatedly go through turbine or spill routes or alternatively, avoid routes because of prior experience. This occurrence is unlikely and can be assessed from the detection histories of the individual smolts. The lack of handling following initial release of acoustic-tagged or radio-tagged smolts further minimizes the risk that subsequent detections influence survival. Similarly, assumption (A6) could be violated if upstream passage routes taken by the smolts influenced downstream detections. Violation of this assumption is minimized by placing hydrophone or acoustic arrays across the breadth of the river or below the mixing zones for smolts following different passages at the dam. Also, Burnham et al. (1987) Tests 2 and 3 can be used to assess overall goodness-of-fit to single release-recapture assumptions. In particular, whether upstream capture histories affect downstream histories of occurrence.

Assumption (A7) implies that the smolts do not lose their tags and are subsequently misidentified as dead or not captured, nor are dead fish falsely recorded as alive at detection locations. Tag loss and tag failure would tend to result in a negative bias (i.e., underestimation) of smolt survival rates. The possibility of a radio- or acoustic- tag failure will depend on travel time relative to battery life. Dead fish drifting downstream could result in false-positive detections and upwardly biased survival estimates. The passive drift of dead fish bearing active tags is a concern when acoustic or radio tags are used. We expect that a portion of the tagged fish we release will die en route. Since the transmitters in these dead fish can continue to operate, dead fish that continue to be swept downstream toward the next recapture system may be detected if the flow conditions are sufficient to transport them downstream. We propose to assess the probability of this occurring by releasing dead tagged fish at our release locations and then interrogating them at downstream telemetry arrays. We also will mobile track some of these fish to better assess the distance they are transported downstream and the potential for detection at the next array and reservoir section. To account for the variability in the flow conditions that are likely to be encountered, we will make releases throughout the release season.

Task 2.1 Collect yearling and subyearling Chinook salmon to be tagged at the McNary Dam collection facility.

Task 2.2 Tag, hold and release tagged fish.

Task 2.3 Collect, compile and post-process acoustic telemetry data.

Task 2.4 Estimate the travel time for tagged fish passing through each reservoir section.

Task 2.5 Estimate the survival of tagged fish through each reservoir section. Task 2.6 Compare the survival of tagged yearling and subyearling Chinook salmon from the different release groupings through each reservoir section.

Task 2.7 Tag, euthanize, and release dead tagged fish.

Task 2.8 Estimate the probability of detecting dead tagged fish through each section monitored.

Work element 3. Assess the utility of using acoustic telemetry systems to determine the habitat use of tagged yearling and subyearling Chinook salmon. Understanding the habitats used by tagged yearling and subyearling Chinook salmon will help to put the survival and travel times estimated through the various reaches in the proper context and potentially identify causal mechanisms for mortality and migration delays. We acknowledge that inferring that the habitats used by tagged yearling and subyearling Chinook salmon to the untagged population is problematic because of potential behavioral differences between them. However, if tagged fish are to be used to assess survival through reservoir sections, whole reservoirs (already being done), and larger river reaches (ongoing and proposed), understanding the habitat used by tagged fish will provide a better understanding of where and why the mortality is occurring. We feel that we can deploy mobile arrays to assess presence/absence and assess the position of fish in the water column within reservoir sections. We propose to assess the feasibility of doing this by affixing hydrophones to multiple boats mimicking the fixed arrays. The utility of using the mobile array would be to reduce the equipment costs associated with having replicate arrays throughout the reservoir by creating a mobile tracking system that would allow for multiple samples to be collected in various habitat types. We would rely primarily on fish released as part of other studies for this work element. We contend that there is a high likelihood of large numbers of fish being released during the 2008 migration season. During 2007, the USGS released 2000 acoustic tagged yearling Chinook salmon at Lower Granite Dam and 3000 yearling Chinook, 3000 subyearling Chinook, and 1000 steelhead trout at McNary Dam as part of an AFEP funded study. We feel that if similar numbers of fish are released next year then there is great potential to garner more information.

Ho: Habitat use of tagged fish can be determined by setting up fixed and mobile acoustic telemetry arrays in littoral and deep-water habitats.

Task 3.1 Select littoral and main channel monitoring locations in each reservoir section using habitat information housed at USGS Columbia River Research Laboratory.

Task 3.2 Randomly select littoral and main channel sampling locations using geospatially referenced habitat data.

Task 3.3 Establish protocols and logistics for the establishment of mobile acoustic telemetry arrays. Task 3.4 Test mobile acoustic telemetry arrays in selected locations.

Work element 4. Report results in technical reports, peer reviewed publications, and presentations. All work will be summarized and presented in a final technical report, peer reviewed publications, and presentations to professional and public interest groups.

F. Facilities and Equipment The U.S. Geological Survey (USGS) is the primary research arm of the Department of the Interior, which manages nearly one-fifth of all land in the United States. The Columbia River Research Laboratory has conducted research evaluating the survival of yearling and subyearling Chinook salmon and steelhead trout at hydroelectric dams in the Snake and Columbia Rivers since 1999. The Columbia River Research Laboratory has been conducting research on anadromous and resident fisheries in the Columbia River Basin for over 25 years. The laboratory has state of the art computing resources and GIS capabilities, and approximately 30 research vessels deployed throughout the basin.

G. Literature cited Adams, N.S., D.W. Rondorf, S.D. Evans, J.E. Kelly, and R.W. Perry. 1998. Effects of surgically and gastrically implanted radio transmitters on swimming performance and predator avoidance of juvenile Chinook salmon (Oncorhynchus tshawytscha). Canadian Journal of Fisheries and Aquatic Sciences. 55:781-787.

Bickford, S. A. and J. R. Skalski. 2000. Reanalysis and interpretation of 25 years of Snake-Columbia River juvenile salmonid survival studies. North American Journal of Fisheries Management. 20:53-68.

Burnham, K.P., D.R Anderson, G.C. White, C. Brownie, and K.H. Pollock. 1987. Design and analysis methods for fish survival estimates based on release-recapture. American Fisheries Society Monograph No. 5.

Counihan, T. D., J. H. Petersen, and K. J. Felton. 2002. Survival Estimates of migrant Juvenile Salmonids in the Columbia River from John Day Dam through Bonneville Dam using Radio-Telemetry, 2000. Annual report prepared by U. S. Geological Survey, Cook, Washington for the U.S. Army Corps of Engineers, Portland, Oregon.

Counihan, T.D., G.S. Holmberg, C.E. Walker, and J.M. Hardiman. 2003. Survival estimates of migrant juvenile salmonids through The Dalles Dam using radiotelemetry, 2002. Draft Report of Research prepared for the U.S. Army Corps of Engineers, Portland, OR. Counihan, T.D., A.L. Puls, C.E. Walker, J.M. Hardiman, and G.S. Holmberg. 2006. Survival estimates of migrant juvenile salmonids through The Dalles Dam using radiotelemetry, 2004. Draft Report of Research prepared for the U.S. Army Corps of Engineers, Portland, OR.

Dawley, E.M., L.G. Gilbreath, E.P. Nunnallee, and B. P. Sandford. 1998. Survival of juvenile salmon passing through the spillway of The Dalles Dam, 1997. Annual report prepared for the U.S. Army Corps of Engineers, Portland, OR. Contract MIPR E96970020.

Hockersmith E.E, W. D. Muir, S. G. Smith, B. P.Sandford, R. W. Perry, N. S. Adams, and D. W. Rondorf. 2003. Comparison of migration rate and survival between radio-tagged and PIT-tagged migrant yearling Chinook salmon in the Snake and Columbia rivers. North American Journal of Fisheries Management. 23:404–413

Laird L. M., R. J. Roberts, W. M. Shearer, J. F. McArdle. 1975. Freeze branding of juvenile salmon Journal of Fish Biology 7 (2), 167–171.

Muir, W.D., and eleven coauthors. 1995. Survival estimates or the passage of juvenile salmonids through Snake River Dams and reservoirs, 1994. Annual report prepared for the Bonneville Power Administration, Portland, OR and U.S. Army Corps of Engineers, Walla Walla, WA. Contract DE93-29A179-93B101891, Project 93-29. 187 p.

Peven, C., A. Giorgi, J. Skalski, M. Langeslay, A. Grassell, S.G. Smith, T. Counihan, R. Perry, S. Bickford. 2005. Guidelines and recommended protocols for conducting, analyzing, and reporting juvenile salmonid survival studies in the Columbia River basin. Technical Report, U.S. Army Corps of Engineers.

PNNL (Pacific Northwest National Laboratory) and USGS (U.S. Geological Survey). 2000. Assessment of the impacts of development and operations of the Columbia River hydroelectric system on mainstem riverine processes and salmon habitats. Final Report to the Bonneville Power Administration, Project 199800402, Portland, Oregon.

Sheer, M. B. 1999. An assessment of fall Chinook (Oncorhynchus tschawytscha) spawning habitat for present and pre-impoundment river conditions in a section of the John Day Reservoir, Columbia River. Master’s thesis. Oregon State University, Corvallis.

Skalski, J. R., R. Townsend, J. Lady, A.E. Giorgi, J.R. Stevenson, and R.D. McDonald. 2002. Estimating route-specific passage and survival probabilities at a hydroelectric project from smolt radio-telemetry studies. Canadian Journal of Fisheries and Aquatic Sciences. 59:1385-1393.

U.S. Army Corps of Engineers. 1994. Columbia River salmon mitigation analysis system configuration study phase I. Lower Snake Reservoir drawdown. U.S. Army Corps of Engineers, Technical Report Appendix A. U.S. Army Corps of Engineers, Portland, Oregon.

U.S. Army Corps of Engineers. 2000. Salmon recovery through John Day Reservoir: John Day drawdown phase 1 study. U.S. Army Corps of Engineers, Portland, Oregon. H. Key personnel Timothy D. Counihan

U.S. Geological Survey Biological Resources Division Columbia River Research Laboratory 5501-A Cook Underwood Road Cook, Washington 98605 Education: M. S., Wildlife Science, New Mexico State University, 1991 B. S., Biology, Montana State University, 1989

Work Experience 1993-Present Research Fishery Biologist, U.S. Geological Survey, Biological Resources Division, Columbia River Research Laboratory, Cook, WA. Current responsibilities: Current projects include modeling the survival of endangered and threatened juvenile salmonids as they pass through the lower Columbia River dams and working on a multi-agency team to formulate a habitat classification system and habitat and ecological monitoring program for the lower Columbia River. Other research includes research examining the distribution and abundance of Eurasian watermilfoil in relation to the hydraulic characteristics of Bonneville Reservoir, Columbia River with emphasis on the effects of hydrosystem operation on the distribution of this invasive aquatic plant and modeling the potential spread of New Zealand mudsnail in Bonneville Reservoir.

Expertise: Primary areas of expertise include the design and analysis of fish and ichthyoplankton surveys, survival assessment using mark-recapture models, white sturgeon ecology, larval fish ecology, and biometrics.

Publications and Reports

Counihan, T. D. J.M. Hardiman and J.R. Hatten. In preparation. Modelling the influence of channel morphology and reservoir operations on the distribution of Eurasian watermilfoil in an impoundment of the Columbia River. Simenstad, C.A., J.L. Burke, I. R. Waite, T.D. Counihan, and J.R. Hatten. In preparation. Lower Columbia River and Estuary Ecosystem Classification: Phase I. Prepared for Lower Columbia River Estuary Partnership Counihan, T. D., A. I. Miller, and M. J. Parsley. 1999. Indexing the relative abundance of age-0 white sturgeon in an impoundment of the lower Columbia River from highly skewed trawling data. North American Journal of Fisheries Management. Counihan, T. D., and C. N. Frost. 1999. Influence of externally attached transmitters on the swimming performance of juvenile white sturgeon. Transactions of the American Fisheries Society. Counihan, T. D., A. I. Miller, M. G. Mesa, and M. J. Parsely. 1998. The effects of dissolved gas supersaturation on white sturgeon larvae. Transactions of the American Fisheries Society 127:316-322. Jill M. Hardiman

U.S. Geological Survey Biological Resources Division Columbia River Research Laboratory 5501-A Cook Underwood Road Cook, Washington 98605 Education Colorado State University, M.S. Fishery and Wildlife Biology, 2003 University of Puget Sound, B.S. in Biology, 1992

Work Experience Fishery Biologist - USGS/Columbia River Research Laboratory, Cook, WA -3/04 to present  Prepare professional presentations, annual reports, research proposals, and manuscripts  Evaluate juvenile salmonid passage and survival at three hydroelectric facilities on the Lower Columbia River  Investigate hydrodynamic modeling and community dynamics with regard to invasive species in Bonneville Dam reservoir Fishery Biologist IV - Johnson Controls Inc. contract for USGS/Columbia River Research Laboratory - 8/03-3/04  Prepare professional presentations, annual reports, research proposals, and manuscripts  Use SAS to analyze and summarize age frequency data from 14 years of white sturgeon trawl surveys  Prepare Geographic Information Systems (GIS) maps for study design, sampling protocols, presentations, spatial analysis, and reports for Eurasian Watermilfoil surveys Graduate Teaching Assistant/Research Assistant - Colorado State University, Department of Fishery and Wildlife Biology, Fort Collins, CO 8/00-5/03  Conduct limnology surveys for stratified zooplankton tows, temperature, dissolved oxygen and light profiles, conductivity, and Secchi depth measurements  Track zooplankton seasonal densities to determine effects on age-0 kokanee distribution and use in bioenergetics models to determine stomach capacity, feeding rates, and time to satiation  Conduct sampling of age-0 kokanee with hydroacoustics, gill nets, seines and trawls in rivers and reservoirs  Collect benthic, zooplankton, and fish samples for stable isotope analysis Selected Publications Counihan, T. D., J. M. Hardiman, C. E. Walker, A. L. Puls, and G. S. Holmberg. 2005. Survival estimates of migrant juvenile salmonids in the Columbia River through Bonneville Dam using radio-telemetry, 2005. Prepared by the U. S. Geological Survey, Cook, WA for the U. S. Army Corps of Engineers, Portland, OR. Hardiman, J. M., B. M. Johnson, and P. J. Martinez. 2004. Do predators influence distribution of age-0 kokanee in a Colorado reservoir? Transactions of the American Fisheries Society 133:1366-1378. Johnson, B. M. and J. M. Hardiman. 2003. Kokanee in Blue Mesa Reservoir: Causes for their decline and strategies for recovery, Final Report. Fisheries Ecology Laboratory, Department of Fishery and Wildlife Biology, Colorado State University. Prepared for: National Park Service, Gunnison, CO, November 3, 2003. Kenneth M. Cash

U.S. Geological Survey Biological Resources Division Columbia River Research Laboratory 5501-A Cook Underwood Road Cook, Washington 98605 Experience 1997-Present Fishery Biologist, U.S. Geological Survey, Biological Resources Division, Columbia River Research Laboratory, Cook, WA. Current responsibilities: Current projects include research examining the Three- dimensional behavior, passage distribution, tailrace egress and route-specific survival of juvenile salmon and steelhead trout in relation to dam operations and surface passage structures at all four lower Snake River dams and McNary Dam. Other research includes behavior and survival of endangered juvenile salmonids as they pass water diversion structures on the lower Sacramento River. Education: M. S., Wildlife Ecology, Mississippi State University, 1993 B. S., Wildlife and Fisheries Science, South Dakota State University, 1991 Expertise: Primary areas of expertise include the design and analysis of fish behavior studies using acoustic telemetry, radio telemetry, and active hydroacoustics. Publications and Reports

Cash, K.M., D.M. Faber, T.W. Hatton, E.C. Jones, R.J. Magie, N.M. Swyers, R.K. Burns, M.D. Sholtis, S.A. Zimmerman, J.S. Hughes, T.L. Gilbride, N.S. Adams, and D.W. Rondorf. 2005. Three-dimensional behavior and passage of juvenile Salmonids at The Dalles Dam, 2004. Final Report by U.S. Geological Survey and Pacific Northwest National Laboratory to the U.S. Army Corps of Engineers, Contract W66QKZ40278562, Portland, Oregon. Cash, K.M., T.W. Hatton, E.C. Jones, R.J. Magie, N.S. Adams, and D.W. Rondorf. 2005. Three- dimensional fish tracking to evaluate the removable spillway weir at Lower Granite Dam during 2003. Report by U.S. Geological Survey to the U.S. Army Corps of Engineers, Contract W68SBV00104592, Walla Walla, Washington. Cash, K.M., T.W. Hatton, E.C. Jones, R.J. Magie, K.C. Mayer, N.M. Swyers, N.S. Adams, and D.W. Rondorf. 2002. Three-dimensional fish tracking to evaluate the removable spillway weir at Lower Granite Dam during 2002. Report by U.S. Geological Survey to the U.S. Army Corps of Engineers, Contract W68SBV00104592, Walla Walla, Washington. Cash, K. M., N. S. Adams, T. W. Hatton, E. C. Jones, and D.W. Rondorf. 2001. Three-dimensional fish tracking to evaluate the operation of the lower granite surface bypass collector and behavioral guidance structure during 2000. Report to the U.S. Army Corps of Engineers, Contract W68SVB00104592, Walla Walla, Washington. Cash, K.M., 2001. Feasabiltiy of using a 3d acoustic telemetry system at Cabot Station on the Connecticut River, Massachusetts. Report to the USGS, S.O. Conte Laboratory, Turner Falls, Massachusetts. Cash, K.M., D.M. Faber, and D.W. Rondorf. 1998. Smolt Distribution and Water Velocities Base on a Hydroacoustic Survey in the Forebay of Cowlitz Falls Dam, Washington. Pages 15-34 in Adams et al. 1998. Behavior of Juvenile Salmonids at Cowlitz Falls Dam, Washington. Report to Public Utilities District No. 1 of Lewis County. Randle, Washington. Cash, K. M., D. M. Faber, and T.J. Darland. 1998. Distribution of Juvenile Salmonids Detected by point sampling hydroacoustic surveys in the forebay of Lower Granite Dam. Pages 77-116. in Adams et al. 1998. Migrational characteristics of Juvenile spring chinook and steelhead in the forebay of Lower Granite Dam relative to the 1998 surface bypass collector and Behavioral Guidance Structure Tests. Report to the U.S. Army Corps of Engineers, Walla Walla, Washington Christopher E. Walker

U.S. Geological Survey Biological Resources Division Columbia River Research Laboratory 5501-A Cook Underwood Road Cook, Washington 98605 Education Portland State University, M.S. Environmental Sciences/Biology Portland State University, B.S. Environmental Science/Biology

Work Experience United States Geological Survey, BRD, Cook, WA, 5/01-present, Biologist Duties: report and proposal writing, publication writing and review, prepare graphs and charts for reports and presentations, collection and analysis of other biological data, experimental set-up and study design, database management and use of GIS, statistical analysis, analyze samples for chlorophyll a, ID and enumerate phytoplankton, coordinate project with contractors and other agencies Portland State University, Portland, OR, 8/99-4/01, Research Assistant Duties: collecting water samples, macroinvertebrates, and algae, mini-piezometer installation (small wells), took water and biological samples, measured stream habitat parameters (i.e. discharge, morphometry, riparian conditons, instream substrate), analyzed samples for nutrients (ortho-phosphate, NO3+NO2, NH4+, TP, TN), chlorophyll a, ash-free dry mass, identify aquatic macroinvertebrates and algae, statistical analysis using multivariate and univariate approaches for relating biotic communities to environmental variables, report writing, publication writing and review, methods development, prepared graphs and charts for reports and presentations, experimental set- up, data base management, spatial analyses using GIS Department of Environmental Quality, State of Oregon, 6/00-9/00 Field Tech. Duties: conduct water quality, habitat, macroinvertebrate, and fish, included backpack electroshocking, use of other instruments such as GPS, conductivity meter, pH meter, performing DO titrations and Fish measurements/Ids (salmonids) and Macroinvertebrate IDs, stream measurements such as discharge, measurements of riparian conditions, and instream substrate

Selected Publications Walker, C.E., Schrock, R.M., Reilly, T.J., and A.L. Baehr. 2005. A direct immunoassay for detecting diatoms in groundwater as an indicator of the direct influence of surface water. Journal of Applied Phycology 17(1):81-90. Walker, C.E., and Y. Pan. 2005. Changes in Diatom Assemblages Along an Urban-to-Rural Gradient. Hydrobiologia. (in press) Sonoda, K. Yeakley, J.A. Walker, C.E. 2001. Near-stream landuse effects on streamwater nutrient distribution in an urbanizing watershed. Journal of the American Water Resources Association 37(6):1517-1532. Counihan, T.D., Holmberg, G.S., Walker, C.E., and J.M. Hardiman. 2003. Survival Estimates of migrant Juvenile Salmonids in the Columbia River through John Day Dam using Radio- Telemetry, 2003. Prepared by U. S. Geological Survey, Cook, Washington for the U.S. Army Corps of Engineers, Portland, Oregon, contract W66QKZ31005684. Amy L. Puls U.S. Geological Survey Biological Resources Division Columbia River Research Laboratory 5501-A Cook Underwood Road Cook, Washington 98605 Education M.S., Marine Biology, Oregon Institute of Marine Biology, University of Oregon, 2002 B.S., Biology, University of Oregon, 1997

Work Experience Fisheries Biologist - USGS, Columbia River Research Laboratory, Cook, WA, 4/04-present Investigated survival and egress of juvenile salmonids during hydroelectric dam passage on the Columbia River using radio telemetry.  Design and plan experiments examining the behavior and survival of radio-tagged juvenile salmonids at hydroelectric projects  Use SAS to manage, manipulate, and analyze large datasets of fish distribution data  Compose and prepare research proposals, technical presentations, reports and manuscripts  Formulate and implement quality assurance/quality control procedures for data processing Graduate Research; Zooplankton Ecology - Oregon Institute of Marine Biology, Charleston, OR, 1/98 - 3/02 Investigated spatio-temporal variation of abundance for ~20 zooplankton species in relation to physical forcings and larval behavior in the Coos Bay estuary, Oregon. Gained insights into zooplankton transport mechanisms and exchange of zooplankton between the estuary and the ocean.  Developed hypotheses, designed study, and wrote grant proposals  Collected biological data from boats using neuston nets and standard plankton nets; collected physical data using CTD, DO meter, velocity meter, and GPS  2000+ hours spent identifying and enumerating zooplankton Research Assistant - Oregon Institute of Marine Biology, Charleston, OR, 1/98 - 12/00 Investigated physical and biological processes influencing the larval transport and recruitment of Dungeness crabs and other marine invertebrates as part of the Pacific Northwest Coastal Ecosystems Regional Study (PNCERS), a multi-institute, interdisciplinary study.  Collected and preserved 3-5 light trap samples daily  Constructed and maintained light traps  Used dissecting scope to identify and enumerate larvae from samples

Select Publications Puls, A.L. 2002. Transport of zooplankton in South Slough, Oregon. Master's thesis. 96p. University of Oregon,Eugene. Puls, A.L. 2001. Arthropoda: Decapoda. Pages 89-161 in A.L. Shanks, editor. An Identification Guide to the Larval Marine Invertebrates of the Pacific Northwest. Oregon State University Press, Corvallis. Meeuwig, M.H., AL Puls, J.M. Bayer. Provisionally accepted. Survival and tag retention of Pacific lamprey larvae and macrophthalmia marked with coded wire tags. North American Journal of Fisheries Management. Puls, A.L., G.C. Roegner, A.L. Shanks. In prep. Fluxes of invertebrate larvae through South Slough, Oregon