Return to Proposal Finder FY 2000 Proposal 198909600

Proposal Table of Contents

Additional Documents

Section 1. General Administrative information
Section 2. Past accomplishments
Section 3. Relationships to other projects
Section 4. Objectives, tasks and schedules
Section 5. Budget
Section 6. References
Section 7. Abstract

Reviews and Recommendations
Title Type File Size File Date

Section 1. General Administrative Information

Title of Project Proposal Monitor and Evaluate Genetic Characteristics of Supplemented Salmon & Stlhd
BPA Project Proposal Number 198909600
Business name of agency, institution,
or organization requesting funding
National Marine Fisheries Service, Conservation Biology Division
Business acronym (if appropriate) NMFS

Proposal contact person or principal investigator

Name Robin S. Waples and Paul Moran
Mailing Address 2725 Montlake Blvd. East
City, State, Zip Seattle, WA 98112-2097
Phone 2068603254
Fax 2068603267
Manager of program authorizing this project
Review Cycle FY 2000
Province Columbia Plateau
Subbasin Tucannon
Short Description Monitor changes over time in genetic characteristics of hatchery, natural (supplemented), and wild (unsupplemented) populations of Snake River spring/summer chinook salmon and steelhead. Estimate reproductive success. Use results to help evaluate effect
Target Species Chinook salmon (Oncorhynchus tshawytscha) and steelhead (O. mykiss)

Project Location

[No information]

Reasonable and Prudent Alternatives (RPAs)

Sponsor-Reported Relevant RPAs

Sponsor listed no RPAs for this project proposal

Relevant RPAs based upon NMFS & BPA Review

NMFS and BPA did not associate any reasonable and prudent alternatives with this project proposal

NPPC Program Measure Number(s) which this project addresses: 4.1A.2, 4.1D, 7.2A.1, 7.2A.2, 7.2A.6, 7.3B.2 7.4D.1, 7.4L.1, 7.5B.1, 8.4A.1
FWS/NMFS Biological Opinion Number(s) which this project addresses: Conservation Recommendation #3 from the “Biological Opinion for 1995 to 1998 Hatchery Operations in the Columbia River Basin” (April 5, 1995) stipulates that “The action agencies should conduct monitoring and evaluation studies for hatchery programs. This should assist NMFS in evaluating the effects of hatchery programs on listed and unlisted natural fish.” Consultation #383  Biological Opinion on 19951998 Hatchery Operations in the Columbia River Basin. Issued 4/5/95 Expires 12/31/98. This BO addresses Lookingglass straying issue in Grande Ronde basin. Direct take permits (and associated Biological Opinions) that call for genetic monitoring of populations included in this study: Permit 847expired June 30, 1998. Will be replaced by Permit 1128. Comment Period ended 4/23/98. Waiting for Section 7 consultation. Permit 919expires December 31, 1998. Will be replaced by Permit 1179. Comment Period ends 12/17/98. Permit 921expires December 31, 1998. Will be replaced by Permit 1179. Comment Period ends 12/17/98. Permit 1011expires December 31, 2000. Currently processing Mod 2. Comment Period ended 5/26/98. Waiting for Section 7 consultation.
Other Planning Document References NMFS Snake River Salmon Recovery Plan: Tasks 4.1b, 4.3a; priority 1. Wy Kan Ush Me Wa Kush Wit: Monitoring, Types of Monitoring, level 2., Implementation and Coordination, benefits 2., 4.; Hypothesis 11, Stock-specific Harvest Management Concerns, Recommended Actions/Tests, points 1 and 2.

CBFWA-Generated Information

Database Administrator notes on the history of this proposal form: None
Type of Project (assigned by CBFWA Analysts): anadromous

Section 2. Past Accomplishments

Year Accomplishment
1989 Tissue samples taken for genetic monitoring and logged into the collection at NWFSC represent a major component of the largest tissue repository available for Pacific salmon (>18,000 samples)
1991 High levels of genetic variability documented within and among Snake River chinook salmon and steelhead populations. This variability shown to be stable through time.
1991 Allozyme data supported distinctiveness of Dworshak Hatchery steelhead. Distinctiveness appeared to be ancestral.
1991 Estimation of Nm and the critical ratio of Nb/N
1996 Allozyme data played a critical role in the US v. Oregon dispute resolution
1995 New restriction site markers developed for nuclear DNA loci. >95 primer pairs have been made for introns, 3' & 5' untranslated regions, random clones, and other noncoding sequences.
1995 Groups of microsatellite markers (multiplex sets) developed and implemented in both chinook salmon and steelhead, permitting rapid and efficient genotyping. >90 microsatellite primer pairs made.
1996 DNA markers (nonlethally analyzed) provided information on the relative distinctiveness of NE Oregon spring chinook salmon captive brood stock collections as compared to the Rapid River stock spawned at Lookingglass hatchery
1998 DNA data helped evaluate potential distinctiveness of marked and unmarked fish returning to the trap at the Rapid River Hatchery
1998 Developed an analytical solution for the Phelps/Allendorf effect, a common sampling problem associated with the collection of juveniles when population sizes are small
1996 Technological developments in the rapid assay of single nucleotide polymorphisms (SNPs)
1998 Development of DNA extraction and genotyping of historic scale samples

Section 3. Relationships to Other Projects

Project ID Title Description Umbrella
Early life history Grande Ronde chinook We coordinate genetic sampling with sampling from this study. No
Performance/stock productivity impacts of supplementation We have shared steelhead samples from this study and we provide NBS results of our genetic analyses for some of their study streams. No
Idaho natural production and evaluation, Intensive monitoring subproject; I We coordinate genetic sampling with sampling from these studies. No
Steelhead Supplementation Studies In Idaho Rivers We coordinate genetic sampling with collections for this program. No
Grande Ronde sp. chinook captive broodstock program We coordinate genetic sampling with collections for this program. No
Grande Ronde sp. chinook captive broodstock O&M M&E We coordinate genetic sampling with collections for this program. No
NE Oregon outplanting facilities plan Sampling will be coordinated with this program. No
NE Oregon outplanting facilities plan Sampling will be coordinated with this program. No
NE Oregon sp. chinook hatchery planning We coordinate genetic sampling with this program. No
Smolt monitoring by Fish Passage Center Sampling will be coordinated with this program. No
Manchester captive broodstock O&M We coordinate genetic sampling with this program. No

Section 4. Objectives, Tasks and Schedules

Objectives and Tasks

Objective Task
1. Collect samples a. Consult comanagers and conduct preseason evaluations of previous year escapements to identify optimal sampling strategy
1. b. Coordinate sampling efforts to maximum extent possible with other ongoing projects
1. c. Collect samples from hatchery, natural, and wild populations
2. Conduct genetic analyses a. Perform allozyme and DNA analyses
2. b. Perform quality control tests on preliminary data
3. Measure levels of genetic variability in each population a. Quantify percent polymorphic loci, heterozygosity, number of alleles per locus
3. b. Compare values in hatchery, natural, and wild populations
3. c. Evaluate pattern of change in genetic variability over time
4. Estimate effective population size (Ne) and the ratio Ne/N for each population a. Compute F, a measure of temporal change in allele frequency
4. b. Compute r2, a measure of gametic disequilibrium
4. c. Use temporal and disequilibrium methods to obtain a combined estimate of Ne for each population
4. d. Estimate total population size (N) based on redd counts, spawner surveys, or population enumeration
4. e. Compute ratio Ne/N
5. Evaluate population genetic structure of natural and wild populations a. Compute indices of genetic differentiation among natural and wild populations
5. b. Perform hierarchical gene diversity analyses to partition genetic differences into various components
5. c. Estimate levels of gene flow among populations based on genetic data
6. Evaluate genetic effects of supplementation on target and non-target populations a. Compute indices of genetic differentiation between hatchery and natural and hatchery and wild populations
6. b. Compare patterns of genetic change over time in hatchery populations with those in natural and wild populations
6. c. Compare recent genetic data for Grande Ronde populations with historic (pre-supplementation) data obtained from DNA analysis of archived scales
6. d. Estimate reproductive success of hatchery and natural origin steelhead spawning above the weir in Little Sheep Cr. (Imnaha R.)
7. Evaluate effectiveness of genetic monitoring a. Quantify genetic differences between hatchery, natural, and wild populations
7. b. Quantify sources of noise in analysis (sampling error, genetic drift)
7. c. In light of a) and b), evaluate combined power of genetic markers (allozymes + DNA) to provide monitoring and evaluation information that is useful for an adaptive management approach to supplementation.

Objective Schedules and Costs

Objective Start Date End Date Measurable Biological Objectives Milestone FY 2000 Cost %
1 08/01/89 09/09/98 Tissue samples logged in the NWFSC collection. 10 years of intensive multibasin genetic monitoring samples. 10 subsequent years of pedigreed steelhead samples along with abbreviated genetic monitoring samples. Each year of successful sampling represents a milestone 10.0%
2 12/01/89 06/10/98 Genotypic data obtained for various numbers and types of loci across subsets of samples. Successful verification of genotypes and standardization with other studies 50.0%
3 03/01/90 09/10/98 Comparisons of genetic variability among populations at various spatial and temporal scales. Publication of results in peer reviewed literature, progress reports, interagency memos 5.0%
4 06/01/90 09/10/98 Estimates of Ne/N for hatchery and natural populations. Tests of various methods published in peer reviewed literature, reports, and memos 5.0%
5 03/01/90 09/10/98 Estimates of the hierarchical distribution of genetic variation Publication of results in peer reviewed literature, reports, and memos 5.0%
6 03/01/90 09/10/98 Documentation of particular genetic changes associated with specific artificial propagation programs and a better understanding of the general factors that lead to different outcomes. Publication of results in peer reviewed literature, reports, and memos 15.0%
7 03/01/98 03/10/98 Generate specific guidelines for effective genetic monitoring research with consideration of statistical power and capability to provide practical management information Published characterization of genetic differences between hatchery and natural populations, examination of accuracy and precision, final presentation of information obtained framed in the context of specific management problems 10.0%

Section 5. Estimated Budget Summary

Itemized Budget

Item Note FY 2000 Cost
Personnel $ 78,300
Fringe $ 18,200
Supplies $ 63,000
Operating $ 5,000
Travel $ 7,300
Indirect $ 44,000
Other Lab help $ 22,500
Subcontractor Field sampling, service, disposal $ 11,000
Total Itemized Budget $249,300

Total estimated budget

Total FY 2000 project cost $249,300
Amount anticipated from previously committed BPA Funds $ 0
Total FY 2000 budget request $249,300
FY 2000 forecast from 1999 $ 0
% change from forecast 0.0%

Reason for change in estimated budget

Not applicable

Reason for change in scope

Not applicable

Cost Sharing

Not applicable

Outyear Budget Totals

2001 2002 2003 2004
All Phases $250,000 $250,000 $250,000 $250,000
Total Outyear Budgets $250,000 $250,000 $250,000 $250,000

Other Budget Explanation

Schedule Constraints: The major potential constraint in this study is the availability of parr for sampling from wild and natural populations. This was not a problem in 1989-94, but in 1995 and 1996 lethal collections of spring/summer chinook salmon for allozymes were suspended because of record low returns of adults in 1994 and 1995. In those years, we placed more emphasis on nonlethal fin clips for DNA analysis and continued to sample from hatchery populations as feasible. Lethal samples from natural populations in 1997 were restricted to three collections on the South Fork Salmon River. Larger adult returns in 1997 provided for lethal sampling of juveniles from most study sites in the Summer of 1998. Sampling in 1999 should also be feasible without undue risk to wild/natural populations, but the abundance of parr in subsequent years is more uncertain. Appropriate levels, types, and methods of sampling will continue to be determined in consultation with state agency biologists, and through the process of securing state and federal ESA collection permits. Because of uncertainty regarding obtaining lethal samples for allozyme analysis, more of our work in the future will rely on nondestructive DNA analysis. Sample availability will become less constraining as the emphasis of our research shifts increasingly from allozyme to DNA methods in this phase of the study. In this phase of the study, allozyme samples are likely to be taken only every 3-5 years from the wild and natural populations that were formerly sampled approximately every year. The other extreme, that of too many returning adults, could complicate the Little Sheep Creek reproductive success component of the study. Excessive numbers of adults returning to the weir (e.g., 1000 or more) could delay completion of genotyping and increase materials costs (because all potential parents must be typed). Because the samples can be safely stored, some delay in processing them would not seriously compromise the success of the proposed study.

Section 6. References

Reference Watershed?
Aebersold, P. B., G. A. Winans, D. J. Teel, G. B. Milner, and F. M. Utter. 1987. Manual for starch gel electrophoresis: A method for the detection of genetic variation. NOAA Tech. Rep. 61:1-19. No
Allendorf, F. W., and N. Ryman. 1987. Genetic management of hatchery stocks. In N. Ryman and F. Utter (eds), Population Genetics and Fishery Management, p. 141159. Univ. Washington Press, Seattle. No
Busby, P. J., T. C. Wainwright, G. J. Bryant, L. Lierheimer, R. S. Waples, F. W. Waknitz, and I. V. Lagomarsino. 1996. Status review of west coast steelhead from Washington, Idaho, Oregon, and California. U.S. Dep. Commer., NOAA Tech. Memo. NMFSNWFSC No
Emlen, J. M. 1991. Heterosis and outbreeding depression: a multi-locus model and an application to salmon production. Fish. Res. 12:187-212 No
Fraidenburg, M. E., and R. H. Lincoln. 1985. Wild chinook salmon management: an international conservation challenge. N. Am. J. Fish. Manage. 5:311329. No
Glass, B., and C. C. Li. 1953. The dynamics of racial intermixture--an analysis based on the American Negro. Am. J. Hum. Genet. 7:368-385. No
Grant, S. W. (editor). 1997. Genetic effects of straying of non-native hatchery fish into natural populations: Proceedings of the workshop. U.S. Dep. Commer., NOAA Tech. Memo. NMFS-NWFSC-30, 130 p. No
Hill, W. G. 1981. Estimation of effective population size from data on linkage disequilibrium. Genet. Res. (Cambridge) 38: 209216. No
Hindar, K., N. Ryman, and F. Utter. 1991. Genetic effects of cultured fish on natural fish populations. Can. J. Fish. Aquat. Sci. 48:945-957. No
Kincaid, H. L. 1983. Inbreeding in fish populations used for aquaculture. Aquaculture 33:215227. No
Krimbas, C. B. and S. Tsakas. 1971. The genetics of Dacus oleae. V. Changes of esterase polymorphism in a natural population following insecticide controlselection or drift? Evolution 25:454460. No
Lewontin, R. C., and J. Krakauer. 1973. Distribution of gene frequency as a test of the theory of the selective neutrality of protein polymorphisms. Genetics 74:175195. No
Marshall, T.C., J. Slate, L. Kruuk, and J. M. Pemberton. 1998. Statistical confidence for likelihoodbased paternity inference in natural populations. Molec. Ecol. 7: 639655. No
Matthews, G. M., and R. S. Waples. 1991. Status review for Snake River spring and summer chinook salmon. U.S. Dep. Commer., NOAA Tech. Memo. NMFS F/NWC-200, 75 p. No
Miller, W. H., T. C. Coley, H. L. Burge, and T. T. Kisanuki. 1990. Analysis of past and present salmon and steelhead supplementation. Part I. Report to Bonneville Power Administration, Project 88-100. No
Milner, G. B., D. J. Teel, F. M. Utter, and C. L. Burley. 1981. Columbia River stock identification study: validation of method. Ann. Rep. Res. NOAA, Northwest and Alaska Fisheries Center, Seattle, Washington, 35 p. No
Moran, P., D. A. Dightman, L. K. Park. 1998. Nonelectrophoretic genotyping using allele-specific PCR and a dsDNA-specific dye. Biotechniques 24:206-212. No
Moran, P., D. A. Dightman, R. S. Waples, and L. K. Park. 1997. PCR-RFLP analysis reveals substantial population-level variation in the introns of Pacific salmon (Oncorhynchus spp.). Mol. Mar. Biol. Biotechnol. 6:318-330. No
Myers, J. M., R. G. Kope, G. J. Bryant, D. Teel, L. J. Lierheimer, T. C. Wainwright, W. S. Grant, F. W. Waknitz, K. Neely, S. T. Lindley, and R. S. Waples. 1998. Status review of chinook salmon from Washington, Idaho, Oregon, and California. U.S. Dep. No
National Research Council (NRC). 1996. Upstream: Salmon and society in the Pacific Northwest. National Academy Press, Washington, D.C. No
Nehlsen, W., J. E. Williams, and J. A. Lichatowich. 1991. Pacific salmon at the crossroads: stocks at risk from California, Oregon, Idaho, and Washington. Fisheries 16(2):4-21. No
Nei, M. and F. Tajima. 1981. Genetic drift and estimation of effective population size. Genetics 98:625640. No
Olsen, J. B., J.K. Wenberg, and P. Bentzen. 1996. Semiautomated multilocus genotyping of Pacific salmon (Oncorhynchus spp.) using microsatellites. Mol. Mar. Biol. Biotechnol. 5:259-272. No
Park, L. K. and P. Moran. 1994. Developments in molecular genetic techniques in fisheries. In, G. R. Carvalho and T. J. Pitcher (eds.), Molecular genetics in fisheries, Rev. Fish Biol. Fisheries. 4:272-299. No
Park, L. K., P. Moran, and D. Nickerson. 1994. Application of the oligonucleotide ligation assay to the study of chinook salmon populations in the Snake River. In L. K. Park, P. Moran, and R. S. Waples (eds), Applications of DNA technology to the mana No
Thompson, E. A. 1973. The Icelandic admixture problem. Ann. Hum. Genet. 37:69-80. No
Utter, F., P. Aebersold, and G. Winans. 1987. Interpreting genetic variation detected by electrophoresis. In N. Ryman and F. Utter (editors). Population Genetics and Fishery Management, p. 21-45. University of Washington Press, Seattle. No
Waples, R. S. 1988. Estimation of allele frequencies at isoloci. Genetics 118:371-384. No
Waples, R. S. 1989. A generalized method for estimating effective population size from temporal changes in allele frequency. Genetics 121:379-391. No
Waples, R. S. 1990. Conservation genetics of Pacific salmon. III. Estimating effective population size. J. Heredity 81:277-289. No
Waples, R. S. 1991. Genetic methods for estimating the effective size of cetacean populations. Rep. int. Whal. Comm. (special issue 13):279-300. No
Waples, R. S., and P. E. Smouse. 1990. Evaluation of gametic disequilibrium analysis as a means of identifying mixtures of salmon populations. American Fisheries Society Symposium 7:439-458. No

Section 7. Abstract


Reviews and Recommendations

This information was not provided on the original proposals, but was generated during the review process.

ISRP Preliminary Review , ISRP 99-2 Recommendation:
Jun 15, 1999
[There are no budget numbers associated with this review.]
Recommendation: Fund. OK for a multi-year review cycle, do not need to review annually, however the ISRP would like to see it coordinated with the other supplementation studies and projects and would like to see the results of this study implemented in the supplementation projects.

Comments: This is an excellent, well-written proposal. Summary statements of findings were provided showing significant progress. Several papers based on the results have been published in peer review journals, which indicate acceptance of the work by the scientific community. The study continues to make an important contribution to the understanding of the genetic structure of Columbia River anadromous salmonids.

Nevertheless, proposed uses of the data regarding genetic structure obtained in this study and in Project 900550 are not clear. Important questions remain concerning methods and strategies for protecting gene diversity in the Snake River basin, as well as identifying the amounts of diversity that need protection to ensure the future of these species. Use of resources to continually update databases with more refined information may not provide useful input for such questions, and may only provide an excuse for failing to make long overdue decisions to protect these resources.

Benefits: The project could be the basis of a conservation program, based on the present knowledge, to identify and protect gene diversity in the basin's fishes. Data from the present study can then be used to provide a continuing "test" of the program to identify deficiencies. Short of that, the project is not likely to provide any significant benefit for the fish.

CBFWA: Nonwatershed Technical Group Comments Recommendation:
Aug 20, 1999
[There are no budget numbers associated with this review.]
Technical Criteria 1: Met? Yes -

Programmatic Criteria 2: Met? No - Some objectives not clearly defined

Milestone Criteria 3: Met? No - 10 year project now a 20 year project?

Resource Criteria 4: Met? Yes -

CBFWA: Subregional Team Comments Recommendation:
Aug 20, 1999
[There are no budget numbers associated with this review.]
Drop, but fund Little Sheep Cr. Work under ESA StS placeholder. Low priority objectives were reduced or eliminated. Objectives and costs were moved to a more appropriate project. This work should be considered under an alternate funding source (NMFS) and not the BPA direct FWP budget.

CBFWA Funding Recommendation Recommendation:
Aug 20, 1999

NWPPC Funding Recommendation , NWPPC 2000-6 Recommendation:
Mar 1, 2000
[Decision made in 9-22-99 Council Meeting]

NW Power and Conservation Council's FY 2006 Project Funding Review Funding category:
May 2005
FY05 NPCC Start of Year:
FY06 NPCC Staff Preliminary:
FY06 NPCC July Draft Start of Year:
Sponsor (NOAA Fisheries) Comments (Go to Original on NPCC Website):

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