FY 2000 proposal 198909600

Additional documents

TitleType
198909600 Narrative Narrative

Section 1. Administrative

Proposal titleMonitor and Evaluate Genetic Characteristics of Supplemented Salmon & Stlhd
Proposal ID198909600
OrganizationNational Marine Fisheries Service, Conservation Biology Division (NMFS)
Proposal contact person or principal investigator
NameRobin S. Waples and Paul Moran
Mailing address2725 Montlake Blvd. East Seattle, WA 98112-2097
Phone / email2068603254 / robin.waples@noaa.gov
Manager authorizing this project
Review cycleFY 2000
Province / SubbasinColumbia Plateau / Tucannon
Short descriptionMonitor 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 speciesChinook salmon (Oncorhynchus tshawytscha) and steelhead (O. mykiss)
Project location
LatitudeLongitudeDescription
Reasonable and Prudent Alternatives (RPAs)

Sponsor-reported:

RPA

Relevant RPAs based on NMFS/BPA review:

Reviewing agencyAction #BiOp AgencyDescription

Section 2. Past accomplishments

YearAccomplishment
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 IDTitleDescription
Early life history Grande Ronde chinook We coordinate genetic sampling with sampling from this study.
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.
Idaho natural production and evaluation, Intensive monitoring subproject; I We coordinate genetic sampling with sampling from these studies.
Steelhead Supplementation Studies In Idaho Rivers We coordinate genetic sampling with collections for this program.
Grande Ronde sp. chinook captive broodstock program We coordinate genetic sampling with collections for this program.
Grande Ronde sp. chinook captive broodstock O&M M&E We coordinate genetic sampling with collections for this program.
NE Oregon outplanting facilities plan Sampling will be coordinated with this program.
NE Oregon outplanting facilities plan Sampling will be coordinated with this program.
NE Oregon sp. chinook hatchery planning We coordinate genetic sampling with this program.
Smolt monitoring by Fish Passage Center Sampling will be coordinated with this program.
Manchester captive broodstock O&M We coordinate genetic sampling with this program.

Section 4. Budget for Planning and Design phase

Task-based budget
ObjectiveTaskDuration in FYsEstimated 2000 costSubcontractor
Outyear objectives-based budget
ObjectiveStarting FYEnding FYEstimated cost
Outyear budgets for Planning and Design phase

Section 5. Budget for Construction and Implementation phase

Task-based budget
ObjectiveTaskDuration in FYsEstimated 2000 costSubcontractor
Outyear objectives-based budget
ObjectiveStarting FYEnding FYEstimated cost
Outyear budgets for Construction and Implementation phase

Section 6. Budget for Operations and Maintenance phase

Task-based budget
ObjectiveTaskDuration in FYsEstimated 2000 costSubcontractor
Outyear objectives-based budget
ObjectiveStarting FYEnding FYEstimated cost
Outyear budgets for Operations and Maintenance phase

Section 7. Budget for Monitoring and Evaluation phase

Task-based budget
ObjectiveTaskDuration in FYsEstimated 2000 costSubcontractor
Outyear objectives-based budget
ObjectiveStarting FYEnding FYEstimated cost
Outyear budgets for Monitoring and Evaluation phase

Section 8. Estimated budget summary

Itemized budget
ItemNoteFY 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
$249,300
Total estimated budget
Total FY 2000 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 forecast0.0%
Cost sharing
OrganizationItem or service providedAmountCash or in-kind
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.


Reviews and recommendations

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

Recommendation:
Fund
Date:
Jun 15, 1999

Comment:

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.


Recommendation:
Fund
Date:
Aug 20, 1999

Comment:


Recommendation:
Date:
Aug 20, 1999

Comment:

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 -


Recommendation:
Date:
Aug 20, 1999

Comment:

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.
Recommendation:
Fund
Date:
Mar 1, 2000

Comment:

[Decision made in 9-22-99 Council Meeting]
REVIEW:
NW Power and Conservation Council's FY 2006 Project Funding Review
Funding category:
expense
Date:
May 2005
FY05 NPCC start of year:FY06 NPCC staff preliminary:FY06 NPCC July draft start of year:
$460,500 $460,500 $460,500

Sponsor comments: See comment at Council's website