FY 2003 Request for Studies proposal 200305300
Contents
Section 1. General administrative information
Section 2. Past accomplishments
Section 3. Relationships to other projects
Section 4. Budgets for planning/design phase
Section 5. Budgets for construction/implementation phase
Section 6. Budgets for operations/maintenance phase
Section 7. Budgets for monitoring/evaluation phase
Section 8. Budget summary
Reviews and Recommendations
Additional documents
| Title | Type |
|---|---|
| 200305300 Narrative, Request for Studies Proposal, "Assessment of the Reproductive Success of Reconditioned Kelt Steelhead with DNA Microarray Technology" | Narrative |
Section 1. Administrative
| Proposal title | Assessment of the Reproductive Success of Reconditioned Kelt Steelhead with DNA Microarray Technology |
| Proposal ID | 200305300 |
| Organization | Battelle (Battelle) |
| Proposal contact person or principal investigator | |
| Name | Craig McKinstry |
| Mailing address | 902 Battelle Blvd., P.O. Box 999, MSIN K5-12 Richland, WA 99352 |
| Phone / email | 5093756470 / craig.mckinstry@pnl.gov |
| Manager authorizing this project | Craig McKinstry |
| Review cycle | FY 2003 Request for Studies |
| Province / Subbasin | Mainstem/Systemwide / Systemwide |
| Short description | Our goal is to adapt DNA microarray fingerprinting techno logy and statistical sampling, estimation and analysis methods to link steelhead progeny in the F2 generation to their parents in the F1generation, where the F1 generation is comprised of both fi |
| Target species | Steelhead |
Project location
| Latitude | Longitude | Description |
|---|---|---|
| 46.2537 | -119.2269 | Yakima River |
Reasonable and Prudent Alternatives (RPAs)
Sponsor-reported:
| RPA |
|---|
| 184 |
Relevant RPAs based on NMFS/BPA review:
| Reviewing agency | Action # | BiOp Agency | Description |
|---|
Section 2. Past accomplishments
| Year | Accomplishment |
|---|
Section 3. Relationships to other projects
| Project ID | Title | Description |
|---|
Section 4. Budget for Planning and Design phase
Task-based budget
| Objective | Task | Duration in FYs | Estimated 2003 cost | Subcontractor |
|---|
Outyear objectives-based budget
| Objective | Starting FY | Ending FY | Estimated cost |
|---|
Outyear budgets for Planning and Design phase
Section 5. Budget for Construction and Implementation phase
Task-based budget
| Objective | Task | Duration in FYs | Estimated 2003 cost | Subcontractor |
|---|
Outyear objectives-based budget
| Objective | Starting FY | Ending FY | Estimated cost |
|---|
Outyear budgets for Construction and Implementation phase
Section 6. Budget for Operations and Maintenance phase
Task-based budget
| Objective | Task | Duration in FYs | Estimated 2003 cost | Subcontractor |
|---|
Outyear objectives-based budget
| Objective | Starting FY | Ending FY | Estimated cost |
|---|
Outyear budgets for Operations and Maintenance phase
Section 7. Budget for Monitoring and Evaluation phase
Task-based budget
| Objective | Task | Duration in FYs | Estimated 2003 cost | Subcontractor |
|---|
Outyear objectives-based budget
| Objective | Starting FY | Ending FY | Estimated cost |
|---|
Outyear budgets for Monitoring and Evaluation phase
Section 8. Estimated budget summary
Itemized budget
| Item | Note | FY 2003 cost |
|---|---|---|
| Other | Expenses not itemized | $462,000 |
| $462,000 | ||
Total estimated budget
| Total FY 2003 cost | $462,000 |
| Amount anticipated from previously committed BPA funds | $0 |
| Total FY 2003 budget request | $462,000 |
| FY 2003 forecast from 2002 | $0 |
| % change from forecast | 0.0% |
Cost sharing
| Organization | Item or service provided | Amount | Cash or in-kind |
|---|
Reviews and recommendations
This information was not provided on the original proposals, but was generated during the review process.
Comment:
Do not fund. No revision requested. This is not tied directly enough to the Kelt RFS.The ISRP notes however that this is a very well written and technically qualified proposal that may produce an important technique (microarray analysis) in the genetic studies of steelhead and other fishes. The proposal did outline an interaction with the kelt reconditioning study in the Yakima basin, included a proof of principle of this technique by comparing it directly with DNA micro-satellite studies, and a goal to transfer this technology to regional laboratories. New tools that could allow researchers to more finely resolve genetic variation between individuals and populations will continue to be important, but this tool may not be necessary or available in the timeframe to address these RPA issues associated with reproductive success.
RFS Review Criteria:
Will the study determine the relative reproductive success of reconditioned steelhead kelts spawning in the wild compared to natural-origin adults, hatchery-origin adults, and cross matings of these three variants, in one or more populations?
Yes, but measurement of the fitness of the various groups is not discussed in detail.
Does the proposal employ the use of microsatellite DNA analysis in order to ascertain the pedigree of resulting progeny and subsequent returning adult steelhead. If not does the method proposed provide quantification of reproductive success of equal of better power than microsatellite DNA analysis?
They propose to further develop and test DNA Microarray Technology. Are these the same? Is the DNA microarray technology needed?
Does the study include analysis of the potential genetic consequences of repeat-spawning steelhead on small populations?
Not explicitly, although perhaps implied by cooperation with the Yakima Fisheries Projects.
Other research topics, which should be addressed in the proposed study if possible, include:
Not explicitly, although perhaps implied by cooperation with the Yakima Fisheries Projects.
- How reconditioning kelts might increase domestication selection in the target population?
- How the reconditioning program might alter age structure and life history structure in the target population.
- • Does the research site(s) offer the ability to capture and sample sufficient outmigrating offspring and all, or nearly all, returning adult steelhead.
-
Not explicitly, although perhaps implied by cooperation with the Yakima Fisheries Projects.
- • Is the proposed study directly applicable to one or more of the following listed ESUs: Upper Columbia, Mid-Columbia, and Snake River steelhead.
Cost-effectiveness (e.g., the ability to take advantage of existing fish production, research, monitoring or evaluation activities) will be an important consideration in the proposal selection process.
No. At $462k/year over 4 years or $1.848 million total it is on the top end.
Comment:
Fundable, high rank. If selected for funding the principal investigator should respond to the general ISRP comments in the contracting process. The ISRP ranks this proposal high even though it is not one of the priority ESUs. Preliminary data exist, the information is applicable to other locations, and useful results can be obtained on the fitness of F2 and F3 progeny relatively quickly.Does the study address the following RFS questions:
Are there statistically significant differences in reproductive success between natural-origin and hatchery-origin fish when measured at the second generation (F2)? Do F1 progeny with HxW parents differ from F1 progeny with HxH parents in the production of F2 progeny?
Yes, these questions can be answered by the proposed research.
What are possible hypotheses to explain this difference? For example, can the difference be attributed to reduced genetic fitness of hatchery-origin compared to natural-origin fish? Are differences more significant during any specific life history stages?
Yes, these questions can be answered by the proposed research.
What is the likely effect of any difference, in terms of population growth, population recovery, and genetic diversity/fitness in subsequent generations according to the Viable Salmonid Population (VSP) criteria?
Yes, this question can be answered by the proposed research.
Does the proposal address the additional criteria for selecting among well-designed and responsive proposals include:
The degree to which studies are directly applicable to one or more of the following listed ESUs (for which there are currently no reproductive success studies underway): Upper Columbia steelhead, Mid-Columbia steelhead; Snake River fall chinook; and Columbia River chum. Studies not occurring in those ESUs, but with clear applicability to those ESUs will also be considered;
The study addresses the Lower Columbia River steelhead ESU and results should be applicable to the Mid-Columbia steelhead ESU, and other locations.
The degree to which the study is designed (or is capable of being extended) to address whether and to what extent any difference in reproductive success of hatchery spawners persists in subsequent generations (beyond F2);
Yes.
The degree to which proposals may provide information more broadly applicable to multiple species/ESUs identified above;
Yes.
Potential to commit to a long-term study (beyond F2); and
Yes.
Overall cost effectiveness
At approximately $215K to $270K per year the costs seem to be in line with other proposals.
General comments and evaluation.
The study contrasts "state of the art" supplementation derived hatchery-origin adults and conventional hatchery-origin adults with natural-origin adults for both winter and summer runs. The study has considerable data already analyzed. The contrasts are sequential, not contemporaneous. The same stock in the same stream is being evaluated. Reproductive success of the entire population over several generations is possible because of sampling at Powerdale Dam. There will be direct estimates of reproductive contribution.
This study will evaluate reproductive performance of all the potential parents to a steelhead population over nearly two decades. The selection of loci is finished and preliminary analyses from selected years are included in the proposal. The project uses one of the better managed and monitored supplementation projects. Since this is a retrospective reconstruction of two decades of pedigrees the timeline to completion should be shorter than for those projects that must rely on future returns.
The principal investigator should outline an approach for investigating possible causes of difference in reproductive success. The ISRP notes that the cause of differences will not be evaluated, nor will the analysis partition survival to different life-stages.
Is there a possible “control” stream with only WxW crosses?
The methods are a little vague, but the preliminary analyses have been conducted and the ISRP judges that this is probably not a problem.
Is there inter-breeding with resident trout and if so, how is it accounted for in the analyses?
Comment:
Comment:
Comment:
Do not fund. A response was not requested. This is not tied directly enough to the Kelt RFS.The ISRP notes however that this is a very well written and technically qualified proposal that may produce an important technique (microarray analysis) in the genetic studies of steelhead and other fishes. The proposal did outline an interaction with the kelt reconditioning study in the Yakima basin, included a proof of principle of this technique by comparing it directly with DNA micro-satellite studies, and a goal to transfer this technology to regional laboratories. New tools that could allow researchers to more finely resolve genetic variation between individuals and populations will continue to be important, but this tool may not be necessary or available in the timeframe to address these RPA issues associated with reproductive success.