BPA Fish and Wildlife FY 1997 Proposal

Section 1. Administrative
Section 2. Narrative
Section 3. Budget

see CBFWA and BPA funding recommendations

Section 1. Administrative

Title of project
Epidemiological Survival Method

BPA project number   8910700

Business name of agency, institution or organization requesting funding

Sponsor type   WA-Consultant

Proposal contact person or principal investigator
 NameDr. John Skalski
 Mailing addressColumbia Basin Research, Puget Sound Plaza Building, 1325 Fourth Avenue, Suite 1820, Seattle, WA

BPA technical contact   Pat Poe, EWI 503/230-4043

Biological opinion ID    ND NMFS BO RPA 13f

NWPPC Program number   5.0F.5

Short description
Improve monitoring and evaluation capabilities by developing new and improved measurement tools to estimate juvenile and adult survival. Develop statistical methods for PIT-tag release studies to determine survival rates and behavior of outmigrating smolts. Results of tagging studies are analyzed to extract information on survival relationships useful in improving mitigation.

Project start year   1989    End year   

Start of operation and/or maintenance   

Project development phase   Implementation

Section 2. Narrative

Related projects
Project #9302900 with NMFS/CZES, "Survival estimates for the passage of juvenile salmon and steelhead through Snake River Dams and reservoirs." This BPA project provides direct technical and analysis support of the NMFS field studies of project 9302900. Specifically, this project responds to NMFS requests to enhance survival estimation capabilities incorporated in program SURPH. This project also produces data queries tailored to PITTAGIS to extract PIT-tag information to analyze survival data in various formats covering the multiple river reaches, years of release, and origins of tag releases. These data queries are necessary prerequisites to using the PIT-tag data in survival estimation. This project also responds to community requests to NMFS to investigate alternative ways of analyzing and interpreting the tagging data.

Project history
Both the National Marine Fisheries Service (NMFS) 1995 Biological Opinion and the Northwest Power Planning Council's Fish and Wildlife Program call for reliable monitoring and evaluation of mitigation actions implemented within the Columbia River Basin. With respect to evaluating actions associated with hydropower operations, three performance measures have been repeatedly identified as being instructive; smolt mitigation speed, smolt survival through the hydroelectric complex, and subsequent survival to adulthood.
The primary objectives of this project are:
1. To assess the accuracy and precision of such performance measures.
2. To identify any deficiencies in estimation procedures.
3. To identify or develop analytical approaches to improve the statistical integrity of such estimates.
4. To examine the relationships between these performance measures and a variety of predictor variables that can affect salmon survival, particularly as associated with conditions encountered during their seaward migration.
A major contribution of this project has been the development of statistical theory, software, and analysis package which provides the scientific basis for the ongoing Snake/Columbia River survival studies evaluated by NMFS under Project No. 9302900. These ongoing efforts have produced statistical software (i.e., SURPH) for UNIX- and PC-based computers which are accessible to the Columbia Basin community via internet and the World Wide Web (WWW). Additional products include a comprehensive users manual for SURPH and software for sample size calculations. Specific accomplishments by year follow:
Developed theory to assess survival effects that result from ambient river conditions.
Began software development for statistical analyses, and began statistical theory to assess individual covariate effects on survival.
Demonstrated ability to simultaneously assess ambient effects and individual covariate effects.
Extended computer software to include analysis of group and individual covariate effects. Proposed "strawman" design for development of PIT-tag facilities on Snake/Columbia River. Developed study plan for a Snake River survival study evaluation. 1993:
Completely statistical software development of analysis package--final debugging of computer program, helped facilitate Snake River survival study, and conducted analysis of hatchery survival studies. 1994:
Completed SURPH statistical software and dissemination of a users manual for statistical analysis of data.
Produced a PC version of SURPH software and sample size program to design tag-release studies.

Biological results achieved
This project spearheaded the survival studies currently being conducted on the Snake/Columbia Rivers (1993-1995+). Monte Carlo investigations identified sensitivities of PIT-tag studies to violations of some assumptions and robustness to other assumptions paving the way for field trials. In conjunction with the National Marine Fisheries Service (NMFS), this study has helped to generate new biological understandings of the dynamics of smolt outmigration. These findings include:
1. Information on smolt travel time - survival relationships.
2. Information on river flow/temperature - survival relationships.
3. Comparisons of hatchery and wild chinook and steelhead smolt survival.
4. Comparison of smolt survival across 3 years and 2-4 river reaches.
5. Survival rates of upper Snake River hatchery releases.
6. Baseline survival data for comparison with potential mitigation practices in years to come.
These data have already influenced the choices of mitigation practices that might be attempted in the near future. Other aspects of the project are investigating the estimation of season-wide survival rates for the entire outmigration season.

Annual reports and technical papers
BPA Reports:
DOE/BP-02341-1, October 1993: Skalski, J.R., A. Hoffman, and S.G. Smith. 1993. Development of Survival Relationships Using Concomitant Variables Measured from Individual Smolt Implanted with PIT-tags. 1990-1992 Annual Report prepared for Bonneville Power Administration, Portland, Oregon.
DOE/BP-02341-2, April 1995: Smith, S.G. and J.R. Skalski. 1994. SURPH.1 Manual: Statistical Survival Analysis of Fish and Wildlife Tagging Studies. Computer Software Manual prepared for Bonneville Power Administration, Portland, Oregon.
Other Scientific Reports Produced For Publication:
Skalski, J.R. 1991. Initial "strawman" design for a 1992 Snake River survival study. Bonneville Power Administration, Portland, OR.
Smith, S.G. 1991. Assessing hazards in wild populations using auxiliary variables in tag-release models. Ph.D. dissertation. Univ. of Washington. Seattle, WA.
Hoffmann, A. 1993. Quantifying selection in wild populations using known-fate and mark-recapture designs. Ph.D. dissertation. Univ. of Washington. Seattle, WA.
Hoffmann, A., and J.R. Skalski. 1995. Inferential properties of an individual-based survival model using release-recapture data: Sample size, validity and power. J. Appl. Stat. 22:579-595.
Smith, S.G., and J.R. Skalski. 1995. Assessment of statistical significance of group covariate effects on survival using analysis of deviance of release-recapture data. J. Appl. Ecol. (Accepted).
Skalski, J.R., and S.G. Smith. 1994. Risk assessment in avian toxicology using experimental and epidemiological approaches. In Wildlife toxicology and population modelling: Integrated studies of agroecosystems, pp.467 - 488. Lewis Publishers. Boca Raton, FL.
Skalski, J.R., A. Hoffmann, and S.G. Smith. 1993. Testing the significance of individual-and cohort-level covariates in animal survival studies. EURING 92. In Marked Individuals in the study of bird populations, pp.9 - 28. S.D. Lebreton and P.M. North (Eds.). Birkhauser Verlag. Boston, MA.

Management implications
This BPA project is providing the statistical underpinnings to ongoing smolt survival studies being conducted by NMFS on the Snake/Columbia Rivers. Data generated by these studies are being used to monitor outmigration success, provide baseline information to evaluate future mitigation measures, update Columbia River models (i.e., CRiSP) and investigate river management decisions such as spill programs.

Specific measureable objectives
1996: Expand analytic capabilities to design and analyze smolt survival studies. Developments include nonparametric and parametric confidence interval estimates, estimation schemes for season-wide estimates of smolt survival, and analysis of repeated measurements of smolt traits as juveniles progress downriver. Analyze capture probability information collected in 1993-95 to extract fish guidance efficiency (FGE) and spill efficiency relationships.
1997: Complete research on repeated measures of smolt traits and survival. Continue to support Columbia River survival studies. Investigate alternative approaches to estimate ocean survival rates.
1998: Respond to major user group needs for improve analysis of survival studies. Provide software to routinely test assumptions of survival studies.

Testable hypothesis
Ho: The statistical theory and software developed by this effort will not improve the region's ability to test survival relationships and research hypotheses to address critical uncertainties in the Columbia River Fish and Wildlife Program.

Underlying assumptions or critical constraints
No constraints.

Estimation of smolt and adult survival rates based on maximum likelihood methods, generalized linear models, and analysis of deviance. Confidence interval estimation of survival parameters based on multiple procedures including normal theory, nonparametric bootstrap methods, and profile likelihood techniques.

Brief schedule of activities
1997: Complete research on repeated measures of smolt traits and survival. Continue to support Columbia River survival studies. Investigate alternative approaches to estimate ocean survival rates.
1998: Respond to major user group needs for improve analysis of survival studies. Provide software to routinely test assumptions of survival studies. Develop guidance to design seasonwide survival studies and experiments.

Biological need
Hatchery managers and fisheries managers need to know how alternative rearing practices, water management practices, and mitigation activities affect smolt outmigration success. This project has helped develop survival studies that provide accurate and precise estimates of survival unaffected by uncertainties in FGE, spill and collection efficiency that here to now have confounded other attempts at quantifying smolt survival.

Critical uncertainties

Summary of expected outcome
Publicly accessible and user-friendly statistical software has been developed and is being used to analyze Columbia-Snake River survival studies since 1993. Ongoing efforts are expanding capabilities of extracting information on survival relationships and providing robust point and interval estimates.

Dependencies/opportunities for cooperation
The project has been cooperating with other fisheries agencies Council and other forums to investigate smolt survival processes, including:
1. National Marine Fisheries Service
2. Various state hatchery managers.
3. Council/NMFS ISG/ISAB Expert Panels.
4. PATH groups

Development of reliable statistical methods holds no risk to fisheries stocks

Monitoring activity
The project's contributions and outcomes are measured against the deliverables identified in the contract. BPA and the Principal Investigator will monitor the contract closely to assure that it is providing the deliverables contracted for. Additionally, feedback from users of the products and services will be used to measure the quality of the deliverables. BPA will discuss the value of the tools, services and products produced by this project with users and interested parties and make any products available to all parties. In addition, all technical products and reports produced will be distributed for technical peer review prior to publication.

Section 3. Budget

Data shown are the total of expense and capital obligations by fiscal year. Obligations for any given year may not equal actual expenditures or accruals within the year, due to carryover, pre-funding, capitalization and difference between operating year and BPA fiscal year.

Historic costsFY 1996 budget data*Current and future funding needs
1989: 99,999
1991: 127,871
1992: 130,656
1993: 197,060
1994: 168,011
1995: 164,725
1996: 169,952
Obligation: 169,952
Authorized: 154,018
Planned: 169,952
1997: 150,000
1998: 431,000
1999: 456,000
2000: 486,000

* For most projects, Authorized is the amount recommended by CBFWA and the Council. Planned is amount currently allocated. Contracted is the amount obligated to date of printout.

Funding recommendations

CBFWA funding review group   Mainstem

Recommendation    Tier 1 - fund

Recommended funding level   $150,000

BPA 1997 authorized budget (approved start-of-year budget)   $150,000