Snake River fall Chinook salmon life history investigations proposal 200203200

FY07-09 proposal 200203200

Section 1. Administrative

Proposal title	Snake River fall Chinook salmon life history investigations
Proposal ID	200203200
Organization	US Geological Survey (USGS) - Cook
Short description	This project investigates the consequences of ocean- and reservoir-type life histories on passage timing, travel rate, survival, and SAR calculations for Snake River fall chinook salmon. Mechanisms and prevalence of these life histories are explored.
Information transfer	Information will be disseminated at regional management forums (e.g., TMT, FPAC, SRWG, ISAB meetings), at professional meetings, in technical reports, and peer-reviewed journal articles. Information will be used to evaluate effectiveness of juvenile transportation, summer spill, and summer flow augmentation.
Proposal contact person or principal investigator

Contacts

Contact	Organization	Email
Form submitter
Kenneth Tiffan	U.S. Geological Survey	[email protected]
All assigned contacts
William Connor	U.S. Fish & Wildlife Service	[email protected]
David Geist	Pacific Northwest National Laboratory	[email protected]
John Skalski	University of Washington	[email protected]
Kenneth Tiffan	U.S. Geological Survey	[email protected]
Kenneth Tiffan	U.S. Geological Survey	[email protected]

Section 2. Locations

Province / subbasin: Mainstem/Systemwide / Systemwide

Latitude	Longitude	Waterbody	Description
46N40'	117W26'	Snake River	Lower Snake River

Section 3. Focal species

primary: Chinook Snake River Fall ESU

Section 4. Past accomplishments

Year	Accomplishments
2005	Documented winter passage occurs at all lower Snake River projects when bypasses are not operated. Publish journal article describing the reservoir-type life history and the significant contribution these fish make to the spawner population.
2004	Documented winter passage at Lower Granite Dam of 64% of radio-tagged fish released in the forebay. 76% of tagged fish passed the dam when the juvenile bypass was not operated.
2003	Installed acoustic telemetry array at Lower Granite Dam to detect winter passage of juvenile fall Chinook. Demonstrated that overwintering fall Chinook can be captured by hook-and-line sampling.
2002	Begin collection of scales from fall chinook spawners at Lower Granite Dam to determine previous juvenile life history.

Section 5. Relationships to other projects

Funding source	Related ID	Related title	Relationship
BPA	198335003	Nez Perce Tribal Hatchery M&E	Project 198335003 provides the early life history information on fall Chinook salmon that are beach seined in the Clearwater River. The Clearwater River produces juvenile fall Chinook salmon that have a high propensity to adopt a reservoir-type life history. We will work with NPT staff of project 198335003 obtain information of fish they PIT tag to better understand why many Clearwater River fish become reservoir-types.
BPA	200202700	Hydrodynamics & Water Quality	The proposed project related to Project 200202700 “Hydraulic characteristics of the lower Snake River during periods of juvenile fall Chinook salmon migration”, which monitored and modeled the complex hydrodynamic and water temperature processes in the lower Snake River from 2002 through 2005, and ended in 2006. This project extends research started under this project by relating the observed hydraulic phenomenon to salmon behavior and survival. Hydraulic phenomenon researched under that project and to be continued (now with direct biological measurements) under this project relate to the biological impacts of cold hypolimnetic releases from Dworshak reservoir on the lower Snake River during periods of flow augmentation, flow reversal of epilimnetic waters in the lower Snake River reservoirs due to wind setup, and direct hydraulic effects of load-following/low total river discharge on the reservoir system.
BPA	199102900	Post-Release Survival of Fall	The proposed project relates to Project 199102900 that has proposed to continue its research, monitoring, and evaluation of emerging issues and measures to recover the Snake River fall Chinook salmon ESU. Staff of project 199102900 has PIT tagged fall Chinook annually since 1991 and its data was used in part to identify the reservoir-type life history described by Connor et al. (2005). Because Ken Tiffan and Billy Connor co-authored the present proposal and are also the sponsors of 199102900, we will be able to effectively coordinate field activities between the two projects to reduce costs. The proposed work to define the mechanisms underlying the ocean-type and reservoir-type life histories will complement the proposed growth and food consumption activities of project 199102900, which will also explore the latter metrics as potential mechanisms of life history selection.
Other: USACE	None	Comparison of acclimated and directly-released Lyons Ferry Hatchery fall chinook subyearlings made upstream of Lower Granite Reservoir	This project relates to the regionally collaborated study initiated in 2005 by Marsh and Connor (2005) and funded by the U.S. Army Corps of Engineers to understand the efficacy of transportation and spill. Our proposed work is relevant because the regional experts have not resolved how they will account for undetected reservoir-type fish in future SAR calculations. The proposed project will address this issue by providing a method to accurately calculate SARs by accounting for the reservoir-type life history and by estimating the number of fish that adopt this life history. This will be made possible in part by tagging and release of 328,000 hatchery fall Chinook salmon used as surrogates for wild fall Chinook salmon that will be funded by the U. S. Army Corps of Engineers. Coordination between our proposed work and the work of Marsh and Connor (2005) will be efficient and cost effective because Billy Connor is a sponsor of both studies.

Section 6. Biological objectives

Biological objectives	Full description	Associated subbasin plan	Strategy
Physical and biological effects on life history	Increase the understanding of how reservoir water temperature, reservoir water velocity, and migration timing affect juvenile fall Chinook salmon behavior, survival, and life history.	None	UPA, Section IV. RM&E Substrategy 1.3, 2.1; Section III. E.; RPA 143
Reservoir life history effects on SARs	Decrease the uncertainty in how the reservoir life history affects estimates of smolt-to-adult return rates of Snake River fall Chinook salmon.	None	NPCC RM&E Plan App. D 2.4, 2.7; Critical Management Uncertainty #4
Spill timing effects on survival of fall chinook	Increase the understanding of when to spill water and transport fish in the Snake River to increase juvenile fall Chinook salmon survival.	None	UPA, Section IV. RM&E Substrategy 1.3, 2.1; Section III.E.; RPA 143

Section 7. Work elements (coming back to this)

Work element name	Work element title	Description	Start date	End date	Est budget
Develop RM&E Methods and Designs	Develop experimental designs	This work element will develop the statistical study plans for the tagging studies each year. Statistical synopses will be developed describing the release-recapture study designs, the parameter estimates, variances and tests of assumptions. The purpose of the synopses is to assure all study objectives can be accomplished validly and efficiency. This element will include sample size and precision calculations. The document will be prepared before the tagging season for peer review and will be converted after the season to part of the methods section of the annual report. The synopsis will also service as a guidance document during the data analyses.	1/1/2007	3/1/2007	$80,812
Biological objectives Physical and biological effects on life history Reservoir life history effects on SARs Spill timing effects on survival of fall chinook			Metrics
Install Fish Monitoring Equipment	Deploy, maintain, and recover radio telemetry, and acoustic telemetry, and PIT tag receiving systems at dams and in river reaches	Acoustic Telemetry - Acoustically tagged fish will be detected using autonomous receiving nodes (Sonic Concepts, Model N201). Each receiving node is a self-contained, battery-powered underwater data logger and hydrophone. Standard lithium batteries provide long-term, continuous operation (30 days) and compact FlashCard technology enables large numbers of records to be stored on the node (up to 2 million tag detections). The receiving nodes are suspended in the water column by a buoy, and are recovered using an acoustic release that frees the buoyed node from its anchor where it can be recovered by boats on the water’s surface. The geodetic position of each node will be recorded at the time of deployment using coordinates obtained through the global positioning system (GPS). The node is capable of receiving tag signals at distances >300 m in freshwater. Thus, a typical configuration will place nodes in a line (defined as an array) across the river/dam on ~200-300 m centers. Our study design proposes 5 fixed-location hydrophone arrays ~5 miles below Lower Granite, Little Goose, Lower Monumental, and Ice Harbor (2 nodes here) dams as shown in Figure 1. Two-dimensional hydrodynamic models (e.g., CE-QUAL-W2) will be used to guide equipment deployment where feasible/practical. Each array will consist of 3 autonomous nodes, for a total of 15 nodes. We will conduct range tests to determine the static range of individual nodes. Mobile range tests will be conducted by towing an umbilical transmitter suspended from a buoy approximately 10 m astern of a vessel navigating slowly away from the recorded location of each node along a straight track. The transmitter will be towed to a distance of at least 300 m from the node. A GPS track with associated time stamps will be used to determine the position (range) along the tracks, and the clocks (node and GPS) will be synched by the time of the first detection of the umbilical transmitter. In addition to range testing, we will also install beacon transmitters within the arrays to serve as system function checks throughout the course of the sampling season. We anticipate that other, on-going studies will be utilizing the autonomous nodes within the lower Snake and Columbia rivers during the duration of our study. These studies are funded by the US Army Corps of Engineers (USACE) as part of the Anadromous Fish Evaluation Program (AFEP). For example, in FY 2006 the following nodes are proposed to be installed in the study area: Lower Monumental Dam and Reservoir, Ice Harbor Reservoir, McNary Reservoir, John Day Reservoir, The Dalles Reservoir, Bonneville Dam and Reservoir, and in the Columbia River estuary below Bonneville Dam. Ideally, we would coordinate with researchers using these nodes in order to obtain the data needed to address the objectives of our study. However, the USACE was not able to guarantee the equipment would be in place at the time of our study. Given the importance of the receiving equipment in accomplishing the objectives of this study, we have gone ahead and prepared budget estimates as if the equipment would not be in place. It should be noted that substantial cost-savings to our proposed project would be realized if the USACE hydrophone arrays are kept in place. We will continue to monitor this situation and will make necessary adjustments in our final budget according to the availability of other equipment. Radio Telemetry - Fixed radio telemetry detection sites will be established at the following 14 locations (Lower Granite Reservoir : Steptoe Canyon, Blyton, Granite Pt, Lower Granite forebay, and Lower Granite tailrace; Little Goose Reservoir: Central Ferry, New York Island, Little Goose forebay, and Little Goose tailrace; Lower Monumental Reservoir: Lyons Ferry, Lower Monumental forebay, and Lower Monumental tailrace; Ice Harbor Reservoir – Ice Harbor forebay and Ice Harbor tailrace). All but two of these sites are currently established and represent a cost savings to this project. Each site will consist of two 6-element Yagi antennas, a Lotek SRX400 receiver, a solar panel, and 12-V battery. The detection range of radio antennas and receivers is sufficient to obtain complete coverage of the reservoir at each location for fish traveling in the top 10 m of the water column by placing a fixed site on each side of the reservoir. We will record the geographic location of each fixed site with a differentially-correct GPS. Receivers will record the date, time, tag frequency and code, and signal strength of detected fish. PIT-tag Systems – PIT-tag detection systems are installed at the four lower Snake River dams and at McNary, John Day, and Bonneville dams on the lower Columbia River. These are maintained by the Pacific States Marine Fisheries Commission, which also maintains the PIT-tag Information System which is the database where PIT-tag release and detection data are stored.	3/1/2007	4/30/2007	$585,869
Biological objectives Physical and biological effects on life history Reservoir life history effects on SARs Spill timing effects on survival of fall chinook			Metrics
Mark/Tag Animals	Collect and tag fish	Acoustic Tagging – A total of 4,000 subyearling fall Chinook salmon will be tagged with an acoustic transmitter that was co-developed by scientists at Battelle and NOAA Fisheries working with Sonic Concepts, Inc. This tag operates at a frequency of 417 kHz which optimizes detections within the acoustically noisy environment of hydropower dams. Currently, the acoustic transmitter weighs ~0.63 g in air and has an excess mass in water of <0.39 g. The minimum length of fish for tagging with the current acoustic transmitter is 95 mm FL. It is expected that by the time this study begins in 2007, the transmitter will be up to 18% smaller which will enable us to tag smaller fish, perhaps as small as 90 mm. The battery life of the current transmitter is 60 days at a 10 s ping rate. The battery life of the smaller transmitter is expected to be about the same. Per the sample size calculation and experimental design (WE 1.1), releases will be made in groups of 100 fish each in the upper end of each reservoir (n=4) over a ten month time period each year. Each release group will be tagged within a 12-h period. The surgical procedures to insert micoacoustic tags will be as follows: Fish will be placed in oxygenated anesthetic buckets prior to surgery. Anesthetic buckets will be prepared using Tricaine Methanesulfonate (MS-222) at a dose of 80 mg/l. After a fish loses equilibrium in the anesthetic tank it will be immediately weighed and measured. The fish will then be placed on the surgery table and given anesthesia through rubber tubing from a gravity fed bucket in the form of MS-222 at a dose of 40 mg/l. This anesthesia will also be oxygenated. With the fish facing ventral side up, a small 5- to 8-mm incision will be made 3 mm from and parallel to the mid-ventral line between the pelvic girdle and anal fin. The microacoustic tag will then be implanted along with a PIT tag. Oxytetracycline will then be injected into the incision at a concentration of 100 mg/ml in an amount of 50 mg/kg body weight. The incision will be sutured immediately following the oxytetracycline injection with two to three stitches. The wound will be treated with an antibacterial ointment. Post-surgery, fish will be placed into a recovery bucket with fresh-oxygenated river water and monitored to ensure they recover equilibrium. Fish will be held in the release tanks 24 h after tagging before they are released. Fish will be visually examined for any appearance of impaired swimming ability or loss of equilibrium. All fish that do not appear to be healthy prior to release will be sacrificed and removed from the release group. Fish for acoustic tagging will be Lyons Ferry Hatchery subyearlings released as surrogates for wild fish early in the season. As fish size increases, wild fish will be obtained from Lower Granite Reservoir as described below or from the bypass facilities for releases in Little Goose, Lower Monumental and Ice Harbor reservoirs. Radio tagging – Subyearling fall Chinook salmon will be implanted with 0.34 g radio transmitters with a 16 cm antenna (Lotek Wireless, Inc.), which is the smallest tag currently available. These coded tags can be programmed for variable life spans. A tag with a burst rate of 8 s will last about 45 d, which is what will be used for summer migrants during this study. Fish collected and tagged in the fall and winter will be tagged with a 2.1 g that will last 139 d at a burst rate of 10 s. Personnel are currently using this tag on Project 200203200 and the tag and fish have performed satisfactorily. During tagging, we will not exceed a tag/body-weight ratio of 5%, which is the accepted norm in the basin. Using this criterion, we will be able to tag 85-90 mm fish in early summer (0.34 g tag), and 150 mm+ fish in the fall and winter (2.1 g tag). Fish will be surgically tagged as described above except the tag antenna will threaded through the fish’s body wall at the posterior end of the body cavity (Adams et al. 1998). Twenty-five subyearlings will be collected monthly (June through February) from the head of Lower Granite Reservoir for radio tagging. Fish will be collected by hook-and-line, purse seine, or two-boat trawl (Rondorf et al. 1990). On Project 2002032, we have demonstrated that fish can be effectively captured by hook-and-line with minimal mortality (Tiffan and Connor 2005; Tiffan et al. 2005a).	5/1/2007	2/28/2010	$5,882,924
Biological objectives Physical and biological effects on life history Reservoir life history effects on SARs Spill timing effects on survival of fall chinook			Metrics Primary R, M, and E Type: Uncertainties Research Focal Area: Hydrosystem
Collect/Generate/Validate Field and Lab Data	Monitor passage of tagged fish at fixed telemetry and PIT systems	The fixed-hydrophone arrays will be downloaded once per month for 12 months. Downloading of the arrays consist of triggering an acoustic release which frees the node from its anchor. The node is then recovered on the surface of the water. Once on board the vessel, the compact flashcard containing the data is removed, downloaded, and then replaced. At the time data are downloaded, the batteries of the node are replaced and any necessary maintenance is performed. The anchor is retrieved by hydraulic winch and the system is redeployed. The geodetic position of each node will be recorded at the time of re-deployment using coordinates obtained through the GPS. Receivers at fixed radio-telemetry detection sites will be downloaded weekly throughout the year. Data will be transferred to cds for storage and subsequent analyses. PIT-tag detection data will be downloaded from the PIT-tag Information System for the time period that PIT-tag detections systems are operated (typically April 1 through October 31 each year).	5/1/2007	5/31/2010	$627,602
Biological objectives Physical and biological effects on life history Reservoir life history effects on SARs Spill timing effects on survival of fall chinook			Metrics Primary R, M, and E Type: Uncertainties Research Focal Area: Hydrosystem
Collect/Generate/Validate Field and Lab Data	Detect RT and AT-tagged fish in reservoirs by mobile tracking	Acoustic Tracking - Mobile tracking of fish tagged with an acoustic transmitter will be accomplished using a Sonic Concepts hydrophone connected to a receiving node and a GPS unit. The hydrophone will be positioned over the side of the boat. Tag codes will be listened for until at least 5 hits per tag are received; we expect this to take about 5 minutes per stop. Our assumption is that stops will be made 2 times every mile (i.e., 10 min per mile). Output from the receiving node consists of the fish tag code, time of detection, and GPS coordinate. Our study design assumes that two crews will independently (but simultaneously) survey each reservoir once per week for 12 months. We assumed that one crew (2 staff, one boat) could survey one reservoir per day. Thus, it would take four days to complete one survey each week for 52 weeks. Radio Tracking – Radio-tagged fish will be mobile tracked concurrent with acoustic mobile tracking to obtain location information between our fixed sites that can be used in migration rate calculations. Each boat will be fitted with a 15-ft mast that will hold a 4-element antenna connected to a receiver. Receivers will be set to scan continuously and record the detection of any active tags (i.e., those whose lifespan has not been exceeded) while acoustic-tagged fish are mobile tracked. If a radio-tagged fish is detected, its general location will be recorded with a GPS.	5/1/2007	4/30/2010	$1,788,023
Biological objectives Physical and biological effects on life history Reservoir life history effects on SARs Spill timing effects on survival of fall chinook			Metrics Primary R, M, and E Type: Uncertainties Research Focal Area: Hydrosystem
Collect/Generate/Validate Field and Lab Data	Determine the number of reservoir-type fish that overwinter in Lower Snake River reservoirs	We will use active hydroacoustic fish stock assessment techniques to determine the number of reservoir-type fish that overwinter in lower Snake River reservoirs. This is proposed as a feasibility test since no information exists on expected variability in fish distribution and abundance that can be used to determine the level of effort needed for this activity. We will initiate field sampling in Lower Granite Reservoir since we know that juvenile fall Chinook salmon overwinter there (Haskell et al. 2004; Connor et al. 2005; Tiffan and Connor 2005; Tiffan et al. 2005a). We will use a HTI echo sounder with a 15º split-beam down-looking transducer and a 30° side-looking transducer deployed from a boat. The side-looking transducer will enable us to better estimate fish abundance near the surface. Transects will be established perpendicular to the flow of the river at an initial spacing of 0.1 km in the forebay and every 1.5 km beginning 5 km above the forebay and extending upstream to the confluence of the Snake and Clearwater rivers. Transects will be navigated using a GPS. Assuming that each transect takes 20 min to navigate about 80 transects will be sampled during a given survey, it will take 3-4 days to completely survey Lower Granite Reservoir. We will conduct surveys once a month from October through March. A critical uncertainty associated with this task is being able to confirm acoustic targets. In the past, this project experimented with the use of a mid-water trawl as a means to capture fish for radio tagging. These activities met with little success, but the fish we did capture were reservoir-type fall Chinook salmon. We will explore the following methods of confirming hydroacoustic targets. First, we will deploy a DIDSON acoustic camera during hydroacoustic surveys to record images of fish. The DIDSON forms near-video quality images using sound (Belcher et al. 2001) similar to ultrasound machines physicians use. Although we will not be able to distinguish species with the DIDSON, we will be able to measure fish sizes to determine if the fish we observe are of similar sizes to those of reservoir-type fish. Second, we will use a purse seine to collect fish observed along hydroacoustic transects. The purse seine measures approximately 229 m x 11m, and is made of 1-2 cm knotless mesh. When the net is pursed, fish can easily be maintained in water and then collected with sanctuary nets. Third, we explore the use of vertical gill nets that will deployed along transects. Nets will be 10 ft wide x 60 ft deep and will be constructed of fine-diameter monofilament to increase the chance of tooth entanglement rather than gill entanglement. Nets will only be fished for 15-min periods to minimize mortality. Captured fish will weighed, measured, and released.	10/1/2007	3/30/2010	$157,116
Biological objectives Physical and biological effects on life history Reservoir life history effects on SARs Spill timing effects on survival of fall chinook			Metrics Primary R, M, and E Type: Uncertainties Research Focal Area: Hydrosystem
Install Fish Monitoring Equipment	Deploy, maintain, and recover fixed hydraulic and temperature monitoring equipment	Two self-contained and bottom-mounted acoustic Doppler current profilers (ADCPs) will be deployed in each reservoir (eight ADCPs total) during the project’s field seasons. Near the forebay BRZ where water depths are deepest, a 600 kHz unit with pressure sensor will be deployed. Near the mid-pool, a 1200kHz unit will be deployed. Data will be collected at a frequency of (at least) every 15 minutes. The ADCPs run on battery packs and will be downloaded and maintained at regular intervals. A vertically spaced array of self-contained temperature loggers (a.k.a. thermistor strings) will be deployed at four locations in each the reservoir (sixteen thermistor strings total). If practical with the AT/RT design, the strings will be placed at coincident locations with the AT/RT monitoring arrays (a.k.a. ‘gates’). Thermistor strings are constructed by using self-contained temperature loggers that are connected together using wire rope and deployed using steel weights, a sub-surface buoy, and a surface buoys (see Cook et al. 2005). Loggers will be spaced at 2 to 3 m vertical intervals in the hypolimnion and an increased vertical resolution of 1 to 2 m in the expected epilimnion and thermocline region. These locations will be based upon observed 2003 and 2004 mid-pool and forebay BRZ data. Data will be collect at a frequency of (at least) every 10 minutes. The temperature loggers will be downloaded and maintained at regular intervals. On two of the thermistor strings in each reservoir (eight total), pressure sensors (SeaBird SBE 39s) will be deployed to record time-series changes in water surface elevation. These loggers will be programmed to collected data at a frequency of (at least) once per minute, which is sufficient to record elevation changes due to load following and large-scale barotropic seiche activity.	3/1/2007	3/30/2010	$956,076
Biological objectives Physical and biological effects on life history Reservoir life history effects on SARs Spill timing effects on survival of fall chinook			Metrics
Collect/Generate/Validate Field and Lab Data	Collect data on hydraulic conditions in lower Snake River	Mobile ADCP and water temperature profile data will be collected to understand how hydraulic/water quality conditions vary between the fixed monitoring stations. Water velocity data will be collected using either a 1200 kHz or 600 kHz boat-mounted ADCP. Real-time differentially corrected GPS and CTD data will be collected concurrently with the ADCP measurements. Data will most likely be collected in conjunction with mobile fish tracking surveys, although hydraulic mobile measurements will be collected at less frequent intervals. Data will be synoptically collected throughout each reservoir at a frequency of approximately once per month, with data collection occurring more frequently during periods of greater hydraulic variability (e.g., spring freshet, onset of thermal stratification, etc) and at less frequent intervals during periods of relatively isothermal water temperature conditions and small hydraulic variations.	3/1/2007	3/30/2010	$57,875
Biological objectives Physical and biological effects on life history Reservoir life history effects on SARs Spill timing effects on survival of fall chinook			Metrics Primary R, M, and E Type: Uncertainties Research Focal Area: Hydrosystem
Analyze/Interpret Data	Integrate acoustic-tag data with river environment data	Battelle has developed software (called TagViz) to integrate acoustic tag information with spatial and temporal information about the river environment (see work elements 1.8 and 1.9). Data are stored in a relational database that supports the industry standard SQL query language, allowing for powerful and flexible analysis of integrated data. The system supports the visualization of raw and derived results in the context of the river and dam environments represented by GIS and, if available, computational fluid dynamics (CFD) model data. Survival, approach, and passage metrics are available as queries of the database. Metrics can be developed for any combination of season, time of day, species, group, route, or treatment. Through the query engine, it is possible to associate those metrics with any aspect of the river environment, such as dam operations. The TagViz System is designed to serve as a data processing and management system with a web-based user interface as the front-end and a relational database as the back-end that gathers all information relevant to the survival studies. It is designed to be a completely extensible, multi-user system with multi-point access. Data processing will begin once the data are collected from the receiving nodes. Data are uploaded from the flash cards to a laptop computer and returned to the office where they are loaded into a Microsoft SQL server (relational database) using a visual basic stand-alone application (Figure 3). Once the data are in the relational database, the data is filtered for tag hits using a set of rules defined in the standard operating procedures (SOP) that will be included in the final study design. All data analysis and processing will follow QA/QC procedures that will be provided in the final study design. This will validate the data for preliminary data analysis. After passing the preliminary data QA/QC test, the data are available in a web-based application for client viewing within 48 hours of data processing (i.e., data download). The web application contains all the data for the current data set for the current project the user has access to. Included in this will be preliminary web reports that will be available on a server within 48 hours of data processing. The preliminary reports will include such information as summarized travel time information and survival rates. TagViz is able to provide visualization of the individual fish tracks. For example, the user may wish to view the tracks of fish that are detected within a particular array at one of the dams. Other customized reports will be provided based on the client needs. The web-based server/system is password protected. These passwords will be provided to the registered users so that they may view preliminary data reports in tabular and visual formats. The database and system administrator must give explicit permission for accessing the data. Data are stored and backed up every day in incremental order and full backup is performed for each system every month. The latest backups are stored in an off-site location and are available within 24 hrs from PNNL Records Management Department.	5/1/2007	4/30/2010	$363,786
Biological objectives Physical and biological effects on life history Reservoir life history effects on SARs Spill timing effects on survival of fall chinook			Metrics Primary R, M, and E Type: Uncertainties Research Focal Area: Hydrosystem
Analyze/Interpret Data	Determine the number of reservoir-type fish that overwinter in Lower Snake River reservoirs	Hydroacoustic data will be analyzed to determine the volume of water sampled along each transect and the number of targets (i.e., fish) observed. The number of fish observed will be corrected using the species composition data collected in purse seines, gill nets, and from DIDSON images so that our fish abundance estimates will represent only juvenile fall Chinook salmon. Using volume sampled and fish abundance information, we will calculate fish density of each transect. We will examine plots of fish abundance for obvious spatial variability. We will compare the mean fish density between the following areas: forebay, forebay to mid reservoir, and mid reservoir to the confluence and sampling periods (i.e., months) using two-way analysis of variance with location and month as the main effects. Finally, we will expand our fish density estimates to the entire reservoir to estimate the population of reservoir-type fish by month. We will do this by expanding the fish density estimate for each transect to the volume of the reservoir that encompasses that transect. For example, if a transect is located at river kilometer 216 and transects are spaced every 1.5 km, then we will multiply the fish density estimate for that transect by the reservoir volume estimated for river kilometer 215.25 to 216.75.	10/1/2007	9/30/2010	$352,500
Biological objectives Physical and biological effects on life history Reservoir life history effects on SARs Spill timing effects on survival of fall chinook			Metrics Primary R, M, and E Type: Uncertainties Research Focal Area: Hydrosystem
Analyze/Interpret Data	Compare juvenile fall Chinook salmon migration behavior (timing, rate, travel direction) to hydraulic data using RT, AT, and PIT data (fixed and mobile)	Under this work element, the fixed and mobile hydraulic data will be processed and verified. This includes checking the dataset for anomalies and converting all data into more useful products that raw logger output files (e.g. GIS maps, common data formats, etc.). Data will be analyzed and interpreted to identify hydraulic phenomenon such as wind setup when the reservoirs are stratified (see Cook et al. 2005) and effects due to load following. The calibrated and validated 2D numerical models of each reservoir (see Cook et al 2005; application of CE-QUAL-W2) will be applied to help determine reservoir conditions in locations between the fixed monitors. These models are capable of simulating load following, wind setup, and the onset/erosion of thermal stratification in the reservoirs. Detection data of all tagged fish will be arranged in sequential order based on time of detection. Data records will be proofed to remove erroneous records (e.g., records with low signal strengths, records that could not possibly have occurred in space and time, etc.) and ensure data quality. Migration rates will be calculated for each tagged fish by first calculating the time between the last detection at a detection site and the time of first detection at the next downstream detections site, or upstream site if a fish makes an upstream excursion. The distance between the detection sites will then be divided by the elapsed time to determine migration rate. Residence times of tagged in each reach (i.e., the area between detection sites) will be summarized by month and examined for seasonal trends. Within a reservoir, mean migration rates will be calculated for each reach and for each month and compared using two-way analysis of variance with reach and month as the main effects. Our expectation is that residence times will be shorter in upstream reaches where velocities are higher than in downstream reaches such as those encompassing forebays. Furthermore, we anticipate that residence times will increase within reaches as the migration season progresses due to decreasing flows. We also expect plots of residence times, particularly those in the forebays, to show when in the outmigration season fish essentially stop directed downstream movement (e.g., residence times >15-20 d). Another way of identifying a decrease in the disposition to migrate is to plot the monthly percent detections of tagged fish remaining in a reservoir, the percent passing a dam, and the percent not detected. Our expectation is that early in the season, the percent of fish passing a dam from a given release group will be high compared to those remaining in a reservoir over the life of their tag, but later in the season, this percentage will drop as some fish adopt a reservoir-type life history. If we assume that mortality affects tag detection probability, then we would also expect the percentage of undetected fish to increase seasonally in the face of greater predation pressure at warmer temperatures. Finally, we will determine the number and timing of fish passing lower Snake River reservoirs during the winter after the bypass have been shut down. Fish behavior information will be combined with hydraulic data to produce synthesized results that link observed fish migration behavior (travel rate, travel time, upriver travel derived from PIT/AT/RT dataset) with the various hydraulic datasets (fixed and mobile ADCP, temperature loggers and numerical modeling). These data will be related both over time and on a river reach-by-reach basis. Specific emphasis will be dedicated to investigating relationships between emigration timing/rate and daily-average river discharge, diel fluctuations in river discharge (e.g., load-following), vertical temperature difference, thermocline depth, wind setup and upstream epilimnetic water movement. Multiple regression models will be developed to examine the relationship between fish migration rates (dependent variable) and water velocities, temperatures, time of year, and fish size (independent variables) within each reach. The same will be done for residence time data. We expect to identify a set physical and biological conditions that can be used to predict when fish begin to adopt a reservoir life history, and how that can be changed through dam operations. Each of our release groups of tagged fish provides essentially a separate test group that can be analyzed to compare outmigration timing, survival, and residualization. A survivorship curve will be constructed that relates presence in the reservoir as a function of time. Parametric (i.e., Weibull) or nonparametric (Kaplan-Meir) survivorship curves will be compared and related to time of release and location of release. Survival analyses using proportional hazard models (i.e., Program SURPH) will be used to relate reservoir survival to ambient conditions such as flow, water temperature, and hydro operations (See Work Element 2.3). These analyses will be based on group covariates. Data from the mobile survey will also be used to relate reservoir survival to individual fish covariates. The survival relationships with fish location and residence time in the reservoir (Work Element 2.1) will be examined using the individual covariate option in Program SURPH. Similarly, the probability of reservoir residualization will also be examined as a function of the individual covariates.	3/1/2008	9/30/2010	$845,857
Biological objectives Physical and biological effects on life history Reservoir life history effects on SARs Spill timing effects on survival of fall chinook			Metrics Primary R, M, and E Type: Uncertainties Research Focal Area: Hydrosystem
Analyze/Interpret Data	Develop method to calculate Lower Granite equivalents for SAR calculations	The release-recapture models will not only provide reach survival estimates, but also information upon which to estimate smolt-to-adult (SAR) ratios and transport-inriver (T/I) ratios. This element will estimate SARs using the alternative tagging data and examine the nature and magnitude of any biases introduced by late winter outmigration or residualization. Program ROSTER (i.e. River-Ocean Survival and Transportation Effects Routine) will analyze the joint smolt-adult data. The program provides estimates of SARs, as well as site-specific and system-wide transport effects. Starting with analytical expressions for SARs and T/I ratios as a function of smolt survival and bypass detection probabilities, the degree of bias anticipated under alternative tag-types and migration scenarios will be calculated. These bias calculations will be used to assess which tagging scenarios can and cannot be used in summer spill and fall Chinook transport experimentation. This work element will also determine whether auxiliary information from acoustic tags could be used to provide bias corrections to the large PIT-tag studies currently used to study transportation effects.	5/1/2008	9/30/2010	$37,720
Biological objectives Physical and biological effects on life history Reservoir life history effects on SARs Spill timing effects on survival of fall chinook			Metrics Primary R, M, and E Type: Uncertainties Research Focal Area: Hydrosystem
Produce Environmental Compliance Documentation	Secure all permits	The following permits will be required to complete this project: list of permits. PNNL will secure animal care approvals from the Lab’s Animal Care Committee. Project 2002032 currently authority to collect and tag ESA-listed Snake River fall Chinook salmon, which is renewed annually.	1/1/2007	12/31/2009	$8,558
Biological objectives Physical and biological effects on life history Reservoir life history effects on SARs Spill timing effects on survival of fall chinook			Metrics
Manage and Administer Projects	Manage project	Each of the principal investigators will be responsible for management of the overall project, as well as their organizational responsibilities. Management activities will include administrative responsibilities required for compliance with BPA program requirements such as metric reporting, financial reporting (accruals), and development of annual statements of work.	1/1/2007	9/30/2009	$78,574
Biological objectives Physical and biological effects on life history Reservoir life history effects on SARs Spill timing effects on survival of fall chinook			Metrics
Coordination	Planning and Coordination	This project will require coordination with a number of agencies and organizations. This includes attendance at up to 4 coordination meetings where we will present data collection plans, work schedules, and findings. Principal investigators will be responsible for coordination among themselves, and also with US Army Corps of Engineers (Walla Walla District), state and federal fisheries management agencies (NOAA, USFWS, WDFW, ODFW), tribes, and fall Chinook salmon coordination groups.	1/1/2007	9/30/2009	$126,883
Biological objectives Physical and biological effects on life history Reservoir life history effects on SARs Spill timing effects on survival of fall chinook			Metrics
Produce/Submit Scientific Findings Report	Prepare quarterly reports	Quarterly reports to BPA’s contracting offices technical representative (COTR) will be prepared by PNNL, USGS, and USFWS. These reports will describe any particularly interesting results obtained during the quarter, any deviations from the scheduled work, a plan for correcting those problems, and a budget analysis.	4/1/2007	1/30/2010	$38,436
Biological objectives Physical and biological effects on life history Reservoir life history effects on SARs Spill timing effects on survival of fall chinook			Metrics
Produce/Submit Scientific Findings Report	Prepare annual reports	Annual reports to BPA’s COTR will be prepared by the PNNL, USGS, and USFWS. Reports will summarize the results obtained that year. Reports will follow standard scientific format and include an executive summary, introduction, methods, results, discussion, recommendation, and literature cited section, as well as tables, figures, and data appendices.	3/1/2008	3/1/2010	$285,539
Biological objectives Physical and biological effects on life history Reservoir life history effects on SARs Spill timing effects on survival of fall chinook			Metrics
Produce/Submit Scientific Findings Report	Prepare project completion report	In the final year of the project (year 4) the principal investigators will prepare a project completion report that summarizes all three years of the project and includes the final year’s annual data. The report will follow standard scientific format and include an executive summary, introduction, methods, results, discussion, recommendations, and literature cited sections, as well as tables, figures and data appendices.	7/1/2010	9/30/2010	$59,065
Biological objectives Physical and biological effects on life history Reservoir life history effects on SARs Spill timing effects on survival of fall chinook			Metrics
Produce/Submit Scientific Findings Report	Write article(s) for submission to peer-reviewed journals	At the completion of this project, and possibly sooner, if warranted by preliminary results, the principal investigators will collaborate to submit paper(s) to peer reviewed scientific journals such as Transactions of the American Fisheries Society, North American Journal of Fisheries Management, and/or other journals as appropriate.	7/1/2010	9/30/2010	$168,752
Biological objectives Physical and biological effects on life history Reservoir life history effects on SARs Spill timing effects on survival of fall chinook			Metrics

Section 8. Budgets

Itemized estimated budget

Item	Note	FY07	FY08	FY09
Personnel	37.83	$875,954	$893,920	$941,854
Fringe Benefits	[blank]	$223,609	$222,116	$228,023
Supplies	4900 acoustic and radio tags annually	$1,845,295	$1,449,073	$1,453,076
Travel	[blank]	$130,165	$130,831	$133,809
Overhead	[blank]	$1,262,697	$1,225,960	$1,266,099
Other	Boat and vehicles	$78,472	$69,526	$71,488
Totals		$4,416,192	$3,991,426	$4,094,349

Total estimated FY 2007-2009 budgets

Total itemized budget:	$12,501,967
Total work element budget:	$12,501,967

Cost sharing

Funding source/org	Item or service provided	FY 07 est value ($)	FY 08 est value ($)	FY 09 est value ($)	Cash or in-kind?	Status
USACE	PIT tags and tagging	$1,200,000	$1,200,000	$1,200,000	In-Kind	Under Development
USGS	Radio telemetry receivers	$250,000	$250,000	$250,000	In-Kind	Confirmed
USGS	Hydroacoustic echosounder	$50,000	$50,000	$50,000	In-Kind	Confirmed
USGS	Hyrdoacoustic transducer	$15,000	$15,000	$15,000	In-Kind	Confirmed
USGS	DIDSON acoustic camera	$75,000	$75,000	$75,000	In-Kind	Confirmed
USGS	2 Boats	$70,000	$70,000	$70,000	In-Kind	Confirmed
USGS	Miscellaneous radio telemetry equipment	$12,000	$12,000	$12,000	In-Kind	Confirmed
Totals		$1,672,000	$1,672,000	$1,672,000

Section 9. Project future

FY 2010 estimated budget: $433,083
FY 2011 estimated budget: $433,083

Comments: Funds needed for completion of final report and publication of journal articles

Future O&M costs:

Termination date: 9/30/2111
Comments:

Final deliverables: Final project completion report; Peer-reviewed journal publications of significant project findings

Section 10. Narrative and other documents

Reviews and recommendations

FY07 budget	FY08 budget	FY09 budget	Total budget	Type	Category	Recommendation
NPCC FINAL FUNDING RECOMMENDATIONS (Oct 23, 2006) [full Council recs]
$1,000,000	$1,000,000	$1,000,000	$3,000,000	Expense	Basinwide	Fund
NPCC DRAFT FUNDING RECOMMENDATIONS (Sep 15, 2006) [full Council recs]
$1,000,000	$1,000,000	$1,000,000	$0		Basinwide

ISRP PRELIMINARY REVIEW (Jun 2, 2006)

Recommendation: Fundable

NPCC comments: This is a good proposal from a team with an established track record of success. The level of funding may be contingent on support from the US Army Corps of Engineers (USACE). The project proposes to obtain primary data that will be essential to refining estimates of smolt-to-adult return rates (SARs), transport, etc for Snake River fall Chinook, particularly the newly recognized reservoir life history, under variable hydrosystem operations. These data and analyses are important to understanding the life history of this Evolutionary Significant Unit (ESU) and to evaluating whether hydrosystem operations can be manipulated to the benefit of the ESU. The technical background is well developed and the research questions are clearly identified. A couple of the acronyms (e.g., TBR) were not identified and may not be familiar to everyone. The reservoir life history in Snake River fall Chinook is an important new development and deserves study. The complications the reservoir life history causes for the estimation of SARs and for evaluating transportation and in-river survival are clearly explained. The project is clearly related to Updated Proposed Actions in the 2004 BiOp, and to the Council's Research Plan. It does not mention any subbasin plans. There is text that establishes the relationship between this project and several others addressing Snake River fall Chinook status and hydrosystem operations. Given that the principal investigators are sometimes the same on these different projects, along with the huge budget increase, it would be helpful if there was a table that clearly identified all the data that was being collected by which project for what hypothesis testing. Trying to keep all of this straight is not easy, and therefore it is difficult to identify unnecessary redundancy in these proposals. They all tend to take credit for contributing the data necessary for our current understanding of Snake River fall Chinook. The history was adequately explained, but without much detail for a project that is requesting so much money (~$4 million per year, much more than in previous years). This was one of the projects that led to a much better understanding of the reservoir life history type, winter behavior and passage through the dams, and various methods of identifying the reservoir-type through scale analysis and genetic markers. Neither the history nor the relationships section differentiates well enough between its work and that of 199102900 (Connor's US Fish and Wildlife Service project). The history section might have gone into more detail about how the results have been used to date in the hydrosystem operations. Clearly defined, measurable objectives are presented with adequately explained hypotheses and timelines. Excellent fish tracking methods are planned -- acoustic, radio, PIT, all related to hydraulics. The explanation of the experimental design, primary data collections and field methods, and analysis are clear. Because the project involves extensive fish marking it is important to include power analyses in determining appropriate sample sizes, and the proposal does a good job of showing how this was done. Procedures for monitoring and evaluation are thoroughly explained. This work will be applicable to studies of the behavior of other species in other regions of the Columbia River Basin. The group has excellent facilities, equipment, and personnel. Much equipment is from Corps projects and will be used simultaneously with their work (cost-saving should be explored to reduce the cost to this project). The proposal describes the different ways information will be disseminated. They also include plans for long-term data and meta-data storage at the Pacific Northwest National Laboratory. This group has a fine record of publication.

ISRP FINAL REVIEW (Aug 31, 2006)

Recommendation: Fundable