Columbia Basin Fish and Wildlife Program Columbia Basin Fish and Wildlife Program
SOW Report
Contract 27839: 1989-098-00 IDAHO SUPPLEMENTATION STUDIES
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Salmon Studies in Idaho Rivers
Province Subbasin %
Mountain Snake Salmon 100.00%
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  • 31540: 1989-098-00 EXP SALMON STUDIES ID RVRS
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Idaho Supplementation Studies (ISS) is a Clearwater River and Salmon River sub-basin wide cooperative research project that is partitioned among four resource management entities for implementation. These include the Idaho Department of Fish and Game, Nez Perce Tribe, Shoshone-Bannock Tribe, and the U.S. Fish and Wildlife Service-Idaho Fishery Resource Office. The Idaho Department of Fish and Game functions as the lead agency with respect to project development, coordination, and implementation. The remaining duties are partitioned among all cooperating agencies, and each is individually contracted through Bonneville Power Administration. This Statement of Work for contract year 2006 (Jan - Dec 2006) includes synthesis of research activities and tasks completed by all cooperating agencies.

Most program activities remain essentially unchanged from last year.  However, one activity will be discontinued, and the information collected in another will be altered slightly to in response to the fact that the program has transitioned between the treatment and evaluation periods.  Task 1.10 (in the previous, objectives based format) will be discontinued.  This task involved the release of differentially marked ISS treatment fish into study streams according to prescribed releases in the study design.  Task 2.6 (in the previous format), which used PIT tag detections to estimate the survival of supplementation pre-smolts and smolts to Lower Granite Dam and to compare these values to the survival of wild/natural emigrants will be changed slightly, as will the number of PIT tags used.  We will continue to collect PIT tag detections at Lower Granite Dam, but will now compare survival between treatment and control streams.  We also plan to PIT tag an additional 5,000 juveniles in the Lemhi and Pahsimeroi rivers to improve the accuracy and precision of survival estimates for age-0 and age-1 emigrants from these systems.  Adequate funds were not available in the FY05 budget to purchase these additional tags, and make our payment on the genetic sequencer.  However, an adequate number of surplus PIT tags from previous years and other BPA funded projects were identified to meet our needs for this year and potentially next year as well.  

The Northwest Power Planning Council (NPPC) has identified supplementation as a high priority to achieve its interim goal of doubling anadromous fish runs in the Columbia Basin (NPPC 1987).  This research relates directly to basin-wide needs and concerns addressed in the Columbia Basin Fish and Wildlife Program (NPPC 1987).  Section 206(b)(1)(D) mandates supplementation research to assess the potential of supplementation to increase natural production. Section 204(D) stresses the importance of evaluating genetic and ecological effects from out planting hatchery fish on natural populations.  The need to address supplementation questions for upriver stocks is specified in Section 703(h)(1).

In relationship to the most recent Columbia River Basin Fish and Wildlife Program objectives the following apply without modification of ISS study objectives: section 7 of the Columbia River Basin Fish and Wildlife Program (NPPC 1994) "calls for immediate efforts to gather data on wild and naturally spawning stocks, review impacts of the existing hatchery system and coordinate supplementation activities."  In an attempt to "develop a clear policy to guide the use of supplementation," section 7.3B.2 specifically outlines the need to "implement the high priority supplementation projects including design, construction, operation, maintenance, monitoring and evaluation."

Idaho Supplementation Studies (ISS) is a statewide cooperative research project spanning both the Clearwater River and Salmon River sub-basins in central Idaho. Due to the large geographic scope and duration of this study, research activities are coordinated and partitioned among Idaho Department of Fish and Game, Nez Perce Tribe, Shoshone-Bannock Tribes, and the U.S. Fish and Wildlife Service.  This project has also coordinated extensively with the Supplementation Technical Work Group (STWG) that identified specific research needs and developed a five-year work plan to integrate supplementation research activities.

The Idaho Department of Fish and Game implements approximately half of the study through a contract with Bonneville Power Administration (BPA), with specific duties partitioned among research and regional management offices. These include project implementation, data transfer and storage, statistical analyses, and cooperative report writing. Cooperating agencies and their respective programs (e.g. hatchery and research) are responsible for monitoring and evaluation of all ISS response measures for their assigned study streams. Results from the annual activities on each study stream are incorporated into the overall ISS program.

The role of supplementation in helping recover declining anadromous stocks in the Columbia Basin is the subject of much debate. Previous supplementation activities have met with little success, although evaluations were not as rigorous nor did they address specific questions relating to supplementation. In addition, such programs used conventional hatchery guidelines rather than focusing on natural production and genetic conservation. We believe supplementation can potentially play an important role in the recovery process for upriver stocks of Chinook salmon (Oncorhynchus tshawytscha), concurrent with improvements in the overriding mainstem factors.  However, past failures and considerable risks associated with supplementation require careful development and evaluation of test supplementation programs prior to basin-wide implementation.

The goal of the Idaho Supplementation Studies Project is to evaluate the usefulness of supplementation as a recovery/restoration strategy for depressed stocks of spring and summer Chinook salmon in Idaho.  The project is a multi-agency effort that encompasses 30 streams throughout the Salmon and Clearwater River basins. Benefits of the ISS study will include helping to define the potential role of Chinook salmon supplementation in managing Idaho's natural spring and summer Chinook salmon populations, and identifying genetic and ecological impacts to existing natural populations. The ISS experimental design is split into three main approaches:

(1) large-scale population production and productivity studies designed to provide Snake River basin-wide inferences, (2) using study streams to evaluate specific supplementation programs, and (3) small-scale studies designed to evaluate specific hypotheses. Approaches (1) and (2) measure population responses to supplementation and are long-term studies. Approach (3) utilizes short-term studies conducted in "controlled" environments to determine specific effects of supplementation, such as competition, dispersal, and behavior. We expect this research to demonstrate the best methods for supplementing existing natural populations of Chinook salmon and re-establishing natural populations in streams where Chinook salmon have become extirpated. The supplementation effects will be monitored and evaluated by comparing juvenile production and survival, fecundity, age structure, and genetic structure and variability in treatment and control streams having similar ecological parameters.

The ISS study was developed in 1989 (Bowles and Leitzinger 1991) and originally outlined a minimum of 15 years of research spanning three Chinook salmon generations. Sampling was initiated in 1991 and implementation began in 1992. ISS uses a multi-phased approach for supplementation, monitoring, and evaluation activities. In Phase I, or broodstock development phase, local adult returns were collected to develop supplementation broodstock. Phase II (treatment phase) uses the returning hatchery adults to supplement natural origin recruits in treatment streams and maintains supplementation broodstocks for juvenile production and release. In Phase III, or evaluation phase, supplementation treatments are terminated and returning adults are allowed to supplement natural production. Monitoring and evaluation of response is continued throughout the duration of the study. Currently, the project is transitioning between Phase II and III.

Transition of the ISS study out of phase II depends on the amount of supplementation occurring in treatment streams.  However, the declining status of Chinook salmon runs in Idaho has compromised the ability to create localized ISS broodstock and also limited the number of supplementation releases per study stream. This change in design parameters was a major concern raised by the Independent Science Review Panel (ISRP) during the last contract renewal process (FY 2002). Since production and productivity response to treatment is the major focus of the research, we invested much effort in 2002 and 2003 on a programmatic review of ISS activities through project year 2001. Much of the review focused on the current level of stream-specific treatment and the measured response in natural production and productivity.

Statistical review of ISS data was accomplished by contracting an independent statistician to complete a statistical treatment of ISS project data. Results of the statistical analysis enabled us to make technical adjustments to certain aspects of the study. First, we extended the treatment phase to achieve at least half of the prescribed treatment through phase II. Locally adapted broodstocks were constructed through brood year 2002, with the last juvenile release occuring in spring 2004. Second, we developed our best data set for evaluating response to treatment, and demonstrated that data compilation among a multi-agency research project was feasible. Third, we provided an evaluation and statistical analysis protocol for treatment and control streams to evaluate effects of supplementation during Phase III of the project, as recommended by ISRP. Summary of this review is available as a BPA technical report (Lutch,, 2003). Within the 2006 Statement of Work, recommendations resulting from this review are reflected in the tasks used to meet research objectives and test specific hypotheses.


We list two study design objectives and associated tasks to address the evaluation of production and productivity response to supplementation. Objective 1 is broad in scope, focusing on a global evaluation of natural production across all study streams. Objective 2 monitors and evaluates productivity at a finer scale, and enables partitioning of evaluation points (e.g. survival) for a sub-set of study streams with greater precision while validating production evaluation. Although a thorough evaluation of supplementation is not possible at this stage of the study, we propose interim data analysis checkpoints be completed annually. Data analysis and products from the first objective are incorporated into Objective 2.

Each ISS cooperator adheres to the two research objectives listed below for the evaluation of the ISS study, performing tasks that enable us to programmatically meet research objectives and test specific hypotheses. Most hypotheses (one, three, four and five) and the associated tasks identify consistent methods for monitoring and evaluation of the ISS study according to the original study design (Bowles and Leitzinger 1991). While a portion of samples required to test hypothesis 2 are already being collected to test hypothesis 4, the two hypotheses should not be confused. Hypothesis 4 addresses the issue of the relative productivity among different parental combinations of natural and supplementation fish. It originates directly from the experimental design and is associated with an existing and ongoing small-scale study in the IDFG portion of the ISS package. In contrast, hypothesis 2 represents a significant change in the scope of the existing project and has been added to address an evolving technical review from the Independent Science Review Panel relative to usefulness of DNA assignment testing to address issues such as the effect of hatchery strays on estimates of natural production. Deliberation among ISS cooperators for the utility of DNA assignment testing will continue as we draft a response to these recommendations. Our response will include estimates of additional funding that will be required to complete the additional field activities and data analyses required to test hypothesis 4.

Study design objectives:
Objective 1: Monitor and evaluate the effects of supplementation on natural production of Chinook salmon by measuring response in adult escapement and numbers of emigrating parr, pre-smolt and smolts in treatment (supplemented) and control (non-supplemented) streams. Test the specific hypotheses listed below by performing tasks associated with each.

H01 The number of adult salmon returning to the Salmon River and Clearwater River basins is similar between supplemented streams (treatment) and control streams (untreated).

Corollary: Rejecting H01 indicates that supplementation either increases or decreases the number of adult salmon returning to treatment streams relative to control streams.

H02 Parental proportions of natural produced and hatchery Chinook salmon are not significantly different among F1 progeny life stages (parr, presmolt and smolt).

Corollary: Rejecting H02 indicates that parental proportions of hatchery and naturally produced Chinook salmon differ among F1 progeny.

H03 Juvenile production measured by estimating abundance of parr, smolt, and pre-smolt Chinook salmon is similar between supplemented streams and control streams.

Corollary: Rejecting H03 indicates that supplementation either increases or decreases juvenile production in treated streams relative to control streams.

Objective 2: Monitor and evaluate changes in natural productivity of target and adjacent populations following supplementation.

H04 There are no significant differences in relative reproductive success of hatchery and natural origin F1 adults from juvenile life stages of the same year class.

Corollary: Rejecting H04 indicates that differences in productivity (e.g. survival) exist between progeny produced from supplementation origin and naturally produced adults.  

H05 Chinook salmon productivity between supplementation streams (treated) and control streams (untreated) is equal.

Corollary: Rejecting H05 indicates that supplementation either positively or negatively affects survival and performance of existing natural populations.

Objective 3: Prepare and submit required reports to BPA, and share information and results of ISS research activities

Objective 4: Maintain ISS coordination among cooperating agencies and manage project activities with respect to implementation of the study design and integration with ongoing projects.

Bowles, E.C., and E.J. Leitzinger.  1991.  Salmon supplementation studies in Idaho rivers.  U.S. Department of Energy, Bonneville Power Administration Contract number DE-B179-89-BPO1466, Portland, Oregon.

Lutch, J., C. Beasley, and K. Steinhorst.  2003.  Evaluation and statistical review of Idaho supplementation studies.  Report to the Bonneville Power Administration, Project number 1989-09800, Portland, Oregon.  

NPPC (Northwest Power Planning Council).  1987.  Columbia river basin fish and wildlife program.  Portland, Oregon
NPPC (Northwest Power Planning Council).  1994.  Columbia river basin fish and wildlife program.  Portland, Oregon.
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* Expenditures data includes accruals and are based on data through 30-Apr-2024.

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Viewing of Work Statement Elements

Deliverable Title WSE Sort Letter, Number, Title Start End Concluded
Joint statement of work A: 119. Produce Cooperative SOW 10/27/2006
Joint annual "brood year" report B: 132. Produce Joint Annual Reports 12/31/2006 12/22/2006
Peer reviewed article(s) C: 183. Produce Peer Reviewed Journal Article(s) 12/31/2006
Program coordination D: 118. Coordinate ISS Program Activities with Cooperationg Agencies 09/01/2006 08/31/2006
Installed sampling infrastructure E: 70. Install Screw Traps and Adult Weirs 07/15/2006 07/15/2006
Redd counts and carcass collections F: 157. Conduct Redd Counts and Carcass Surveys 10/15/2006 10/20/2006
Additional carcass collection G: 157. Additional Carcass Surveys 10/01/2006 11/30/2006
Adult escapement data H: 157. Monitor Adult Escapement into Study Streams 10/01/2006 10/13/2006
Adult DNA samples I: 157. Collect DNA Samples from Adult Chinook Salmon at ISS Wiers 10/15/2006 10/13/2006
Juvenile DNA Samples J: 157. Collect DNA from Juvenile Chinook Salmon as ISS Traps 12/01/2006 12/04/2006
Juvenile movement and migration data K: 157. Operate Juvenile Screw Traps 12/31/2006 12/29/2006
Interagency program data access L: 160. Maintain Project Servers and Databases 12/31/2006 12/22/2006
Survival and escapement data M: 158. Mark Juvenile and Adult Chinook Salmon 11/15/2006 12/29/2006
Survival data N: 159. Manage PIT Tag Files 09/15/2006 09/13/2006
Database O: 159. Upload ISS Juvenile Chinook Salmon Data to Centralized Database 04/30/2006 04/27/2006
Adult production estimate P: 162. Estimate Adult Production in ISS Study Streams 10/31/2006 11/03/2006
Juvenile production estimate Q: 162. Estimate Juvenile Production in ISS Study Streams 10/31/2006 11/10/2006
Reproductive contribution estimate R: 162. Perform Microsatellite Parental Exclusion Tests 12/15/2006 12/22/2006
Juvenile survival estimates S: 162. Estimate Juvenile Survival to Lower Granite Dam 10/31/2006 11/03/2006
ESA compliance T: 165. ESA Take Reporting 12/31/2006 11/01/2006
Provincial Proposals U: 119. Prepare Proposal Package for FY07 Provincial Review 01/15/2006 01/13/2006

Viewing of Implementation Metrics
Viewing of Environmental Metrics Customize

Primary Focal Species Work Statement Elements
Chinook (O. tshawytscha) - Snake River Spring/Summer ESU (Threatened)
  • 1 instance of WE 183 Produce Journal Article
  • 1 instance of WE 70 Install Fish Monitoring Equipment
  • 6 instances of WE 157 Collect/Generate/Validate Field and Lab Data
  • 1 instance of WE 158 Mark/Tag Animals
  • 2 instances of WE 159 Transfer/Consolidate Regionally Standardized Data
  • 4 instances of WE 162 Analyze/Interpret Data

Sort WE ID WE Title NEPA NOAA USFWS NHPA Has Provisions Inadvertent Discovery Completed
A 119 Produce Cooperative SOW
B 132 Produce Joint Annual Reports
C 183 Produce Peer Reviewed Journal Article(s)
D 118 Coordinate ISS Program Activities with Cooperationg Agencies
E 70 Install Screw Traps and Adult Weirs
F 157 Conduct Redd Counts and Carcass Surveys
G 157 Additional Carcass Surveys
H 157 Monitor Adult Escapement into Study Streams
I 157 Collect DNA Samples from Adult Chinook Salmon at ISS Wiers
J 157 Collect DNA from Juvenile Chinook Salmon as ISS Traps
K 157 Operate Juvenile Screw Traps
L 160 Maintain Project Servers and Databases
M 158 Mark Juvenile and Adult Chinook Salmon
N 159 Manage PIT Tag Files
O 159 Upload ISS Juvenile Chinook Salmon Data to Centralized Database
P 162 Estimate Adult Production in ISS Study Streams
Q 162 Estimate Juvenile Production in ISS Study Streams
R 162 Perform Microsatellite Parental Exclusion Tests
S 162 Estimate Juvenile Survival to Lower Granite Dam
T 165 ESA Take Reporting
U 119 Prepare Proposal Package for FY07 Provincial Review
V 185 Periodic Status Reports for BPA