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
Genetic Monitoring and Evaluation of Snake River Salmon and Steelhead

BPA project number   8909600

Business name of agency, institution or organization requesting funding

Sponsor type   WA-Federal Agency

Proposal contact person or principal investigator
 NameRobin Waples
 Mailing addressNation Marine Fisheries Service
U.S. Dept of Commerce
2725 Montlake Blvd East
Seattle, WA 98112

BPA technical contact   Tom Vogel, EWN 503/230-5201

Biological opinion ID   None

NWPPC Program number   7.3B.2, 7.3B.5

Short description
Evaluate the genetic consequences of using hatchery fish to supplement natural populations of chinook salmon and steelhead in the Snake River.

Project start year   1989    End year   1999

Start of operation and/or maintenance   

Project development phase   Implementation

Section 2. Narrative

Related projects
Experimental design for this study was coordinated with state and tribal biologists, and we work closely with these groups each year in planning and conducting sampling. To the extent possible, sampling is also coordinated with other studies to minimize disturbance to the natural populations and maximize usefulness of the genetic and biological information collected. The following are the major related projects we have coordinated with for planning, sampling and/or dissemination of results.
Northeast Oregon: Early life history study of Grande Ronde Basin chinook salmon (Project 92-26-1, ODFW); Smolt migration characteristics and parr-to-smolt survival of naturally produced spring chinook salmon in the Grande Ronde and Imnaha river basins (part of Fish Passage Center smolt monitoring program); Evaluation of reestablishing natural production of spring chinook salmon in Lookingglass Creek, Oregon, using a non-endemic hatchery stock (CTUIR and ODFW, funded through LSRCP); Evaluation of the Lower Snake River Compensation Plan in Oregon (ODFW, funded through LSRCP). Idaho: Performance/stock productivity impacts of hatchery supplementation (Project 90 052, NBS); Idaho natural production and evaluation, Intensive monitoring subproject (Project 91 073, IDFG); Idaho supplementation studies (Project 89 098, IDFG); Monitoring the migrations of wild Snake River spring/summer chinook salmon smolts (Project 91-028, NMFS).
In addition, for the past several years we have shared juvenile chinook salmon collected under our study with Drs. Diane Elliot and Ron Pascho of the National Biological Service, who use the samples for analysis of bacterial kidney disease in their study, "Juvenile fish transportation: Impact of bacterial kidney disease on survival of spring/summer chinook salmon stocks," funded by the US Army COE. This collaboration has been temporarily suspended because only fin clips were collected in 1995 but may resume in 1997 if adult returns improve.

Project history
The study began in fall of 1989, and analysis is currently underway for samples from the 7th year of field collections. The basic research plan involves eight different supplementation programs (four each for chinook salmon and steelhead). The experimental desigh calls for yearly samples from hatchery stocks used in outplanting, from a natural population affected by releases from that hatchery, and from a wild population in the same drainage not intended to be affected. Although the central focus of the research has remained unchanged, the sampling design has been somewhat flexible to respond to high priority issues associated with supplementation in the Snake River basin that have arisen since 1989.

In addition to measure 7.3B2 cited above, this study directly addresses program efforts to monitor the potential effects of outplanting on natural gene pools, to maintain genetic integrity of spawning stocks in the Grande Ronde and Imnaha River drainages; and to study the best methods for supplementing wild stocks in the upper Snake and Columbia Rivers. The study also helps fulfill commitments in the Proposed Recovery Plan for Snake River Salmon to initiate genetic monitoring programs for natural populations that may be affected by stray hatchery fish (NMFS 995 Sec. V-4-16) and to implement sound genetic management strategies and carry out monitoring and evaluation for supplementation programs for Snake River spring/summer chinook salmon (Sec. V-4.1.b).

Biological results achieved
This study involves monitoring, evaluation, and research and thus does not directly produce fish or alter habitat. However, because supplementation is viewed as a central component of the Fish and Wildlife Program to restore salmon and steelhead in the Columbia River basin, information (such as is derived from this study) that helps determine the most effective ways of supplementing natural populations will lead directly to enhancement of the resource.

Annual reports and technical papers
Waples, R. S., D. J. Teel, and P. B. Aebersold. 1991. A genetic monitoring and evaluation program for supplemented populations of salmon and steelhead in the Snake River Basin. Annual Report of Research to Bonneville Power Administration, Portland, OR, 50p.

Waples, R. S., O. W. Johnson, P. B. Aebersold, C. K. Shiflett, D. M. VanDoornik, D. J. Teel, and A. E. Cook. 1993. A genetic monitoring and evaluation program for supplemented populations of salmon and steelhead in the Snake River Basin. Annual Report of Research to Bonneville Power Administration, Portland, OR, 179 p.

Utter, F. M., R. S. Waples, and D. J. Teel. 1992. Genetic isolation of previously indistinguishable chinook salmon populations of the Snake and Klamath Rivers: Limitations of negative data. Fish. Bull. (U.S.) 90:770-777.

Park, L. K., P. Moran, and R. S. Waples (editors). 1994. Application of DNA technology to the management of Pacific salmon. Proceedings of the workshop, 22-23 March 1993, Seattle, WA. U.S. Dept. Commerce, NOAA Tech. Memo. NMFS-NWFSC-17, 178 p.

Waples, R. S., and C. Do. 1994. Genetic risk associated with supplementation of Pacific salmonids: Captive broodstock programs. Can. J. Fish. Aquat. Sci. 51 (Suppl. 1):310-329.

PARK, L. K., AND P. MORAN. 1994. Developments in molecular genetic techniques in fisheries. Reviews in Fish and Fisheries Biology 4:272 299.
PARK, L. K., P. MORAN, AND D. DIGHTMAN. 1995. A polymorphism in intron D of the chinook salmon growth hormone 2 gene. Animal Genetics. 2(26):285.
PARK, L. K., P. MORAN, and D. NICKERSON. 1994. Application of the oligonucleotide ligation assay (OLA) to the study of chinook salmon populations from the Snake River. In, L. K. Park, P. Moran and R. S. Waples (eds.). Application of DNA technology to the management of Pacific salmon. U.S. Dep. Commer., NOAA Tech. Memo NMFS NWFSC-17:91-97.
PARK, L. K., P. MORAN, AND D. DIGHTMAN. In press. A chinook salmon PCR-RFLP marker in the p53 locus. Animal Genetics

Management implications
As discussed under "Biological need," a comprehensive monitoring and evaluation program (including but not limited to genetics) is essential for an adaptive management approach to supplementation. Results from this study can also be (and have been) used to address common, practical management questions such as, How similar genetically are the hatchery stock and the targeted natural population(s), and how does this relationship change over time? Is there fine-scale stock structure that may be at risk from certain broodstock collection or release strategies? Are there indications that supplementation is genetically impacting wild populations that were not intended to be affected? Is there evidence for erosion of genetic diversity in hatchery and/or natural populations? What genetic characteristics are found in supplementation programs that are "successful" (as measured by stock production, productivity, or other measures), and what are found in programs that are less successful?

Specific measureable objectives
* Quantify genetic differences/similarities between hatchery and wild/natural populations and how this pattern changes over time.
* Quantify changes over time in levels of genetic variability within populations.
* Estimate effective population size and the ratio Ne/N for each population each year.
* Use genetic data to estimate natural levels of gene flow among geographic subpopulations, which can be compared with levels associated with supplementation.

Testable hypothesis
This study directly addresses a number of testable hypotheses:
* There are no genetic differences among natural populations, except those that can be attributed to sampling error and random year-to-year variation.
* There are no genetic differences between hatchery populations and natural populations they were derived from.
* Populations that have been supplemented show the same magnitude of genetic change over time as unsupplemented populations.
* Populations in which genetic effects of supplementation can be detected show the same patterns of abundance and productivity as unsupplemented populations. [requires collating results with data from other projects].
* Non-target wild populations have not been genetically affected by hatchery strays.
* The relationship between effective population size (Ne) and total population size (N) is the same in hatchery and natural populations.
* The relationship between Ne and N in natural populations is the same in years of high and low escapements.
* Inter-locus variance of F (a measure of allele frequency change over time) is no larger than would be expected if all changes are due to sampling error and genetic drift.
* Current natural populations in the Grande Ronde basin are not more similar to the Rapid River stock from Lookingglass Hatchery than they were historically. [Based on DNA analysis of archived scales.]

Underlying assumptions or critical constraints
Data analysis and interpretation for this study depends on two important assumptions:
* Allozyme variation is largely neutral. Undoubtedly some departures from strict neutrality exist, but substantial departures might bias conclusions drawn from the data. With respect to temporal variation, this assumption can be tested as described above under "testable hypotheses."
* Sampling is random with respect to the entire population. Again, some departures from strict randomness are expected, but non-representative samples can bias results. Collection methods attempt to minimize possibilities of collecting a non-representative sample, but randomness is difficult to guarantee in field collections of juveniles. In some cases, a sample of progeny from a relatively few individuals can be identified by an unusually low estimated Ne/N ratio.

In each basin for each species, the experimental design calls for samples of juveniles from hatchery populations used in supplementation, natural populations targeted for supplementation, and non-target wild populations. Most populations are sampled every year or every other year. Sample collection is coordinated with local state and tribal fishery biologists. Samples are analyzed using protein electrophoresis for over 35 variable gene loci in chinook salmon and over 50 variable loci in steelhead. A subset of the fish in each sample are also examined for a suite of mitochondrial and nuclear DNA markers. DNA data may be taken from fin clips and archived scales as well as whole fish. Other biological information taken from the fish includes length and age for steelhead.
A variety of standard statistical analyses are performed on the data, including indices of genetic variability, tests of conformance to Hardy-Weinberg genotypic proportions, contingency chi square tests, genetic distance, F statistics, and hierarchical gene diversity analysis. In addition, statistical approaches developed here at the Center specifically for use with Pacific salmon are used to analyze data for duplicated gene loci and for estimating effective population size using both temporal changes in allele frequency and gametic disequilibrium.
For samples analyzed during fiscal years 1989-95, samples of 60-100 juveniles per population were collected as fry or parr in late summer or early fall. Because of record low returns of chinook salmon to the Snake River in 1994, parr collections in 1995 (for analysis in FY1996) were modified to avoid sacrificing any individuals. Instead, fin clips for DNA analysis were taken from fish already being collected for other purposes (e.g., PIT-tagging or smolt monitoring).

Brief schedule of activities
Activities in FY1997 will proceed as outlined above, and we will continue to monitor both steelhead and chinook salmon populations to determined appropriate levels of sampling. We expect to restrict sampling of chinook salmon in 1996 to non-lethal fin clips for DNA analysis, as described above. IN FY1998 we hope to resume samples for allozyme analysis if runs return to more abundant levels. The study was initially designed to run for ten years, so FY1999 will be a time for review and evaluation of results obtained through that time.

Biological need
The central tenet of adaptive management is maintaining flexibility to respond to biological indicators of the success or failure of specific management strategies. This flexibility, however, is of little use without an adequate monitoring and evaluation program to provide the basis for making scientifically-based decisions. Supplementation is an experimental strategy that has considerable promise but also many associated uncertainties. The genetic consequences of supplementing natural populations with hatchery reared fish are among the biggest uncertainties, and this issue cannot be addressed without a monitoring program that focusses on genetic markers. This study is thus an essential component of a more comprehensive, cross-disciplinary monitoring and evaluation program for salmon supplementation.

Critical uncertainties
This study addresses several uncertainties of considerable interest to fishery managers throughout the region:
* What are the genetic consequences of supplementing natural populations with hatchery-reared fish?
* How does productivity of populations in which supplementation has a measurable genetic effect compare to those that have not been supplemented, or which have been supplemented without any evidence of a genetic effect?
* What levels of gene flow are associated with straying by non-native hatchery fish into natural spawning areas?
* What is the relationship between total and effective population size in natural and hatchery populations of chinook salmon and steelhead?

Summary of expected outcome
We expect the results from this study to provide the following types of information:
* Population genetic structure of chinook salmon and steelhead in the Snake River basin.
* Effectiveness of supplementation as measured by genetic impacts on target natural populations and non-target wild populations.
* A better understanding of the relationship between effective and total population size in natural and hatchery populations.
* A better understanding of the strengths and weaknesses of using allozymes to monitor salmon and steelhead supplementation.
* An evaluation of the advantages and disadvantages of using DNA markers for monitoring and evaluation of salmon supplementation.

Dependencies/opportunities for cooperation
The major contingency for this project is the continued availability of samples from the natural populations. Comprehensive data for allozyme analyses requires sacrificing fish. As noted above, our sampling strategy for chinook salmon was modified in 1995 (and will be again in 1996) to avoid lethal sampling. Non-lethal DNA sampling, however, is not expected to be affected by these concerns.
Availability of allozyme samples from natural populations depends primarily on the abundance of adults the previous year (or previous 1-3 years for steelhead). Early indications are that 1996 will be a better return year for chinook salmon than 1994 and 1995. Appropriate levels of sampling will be determined in consultation with state agency biologists, and through the process of securing state and federal ESA collection permits.

The only significant source of risk from this study is depletion of the natural population from sampling. In "normal" return years, the level of take is a tiny fraction of the parr population. In years of critically low returns, sampling is a more serious concern, and this risk has been dealt with as described above.

Monitoring activity
Although it also provides opportunities to address basic research issues, a primary focus of this study is monitoring and evaluation. The structure for yearly sampling and analysis provides a built-in framework for regular evaluation of the project results. Published documents describing results from this project or associated work are listed above; results are also disseminated to regional fishery managers more informally through periodic presentations and updates on key issues.
In addition to this regular process, two more comprehensive assessments are planned. In late spring 1996, we will prepare an evaluation of results obtained from the first 6 years of the study. Included in this evaluation will be an assessment of the usefulness of genetic monitoring for supplementation and the best strategies for its implementation. In FY1999, we will review the results for the 10-year period and whether to propose continuing the project and, if so, in what form.

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: 213,300
1991: 433,800
1992: 299,800
1993: 260,000
1994: 248,000
1995: 250,700
Obligation: 0
Authorized: 231,880
Planned: 231,880
1997: 250,000
1998: 250,000
1999: 250,000
2000: 250,000
2001: 250,000

* 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   Snake River

Recommendation    Tier 1 - fund

Recommended funding level   $250,000

BPA 1997 authorized budget (approved start-of-year budget)   $250,000