FY 2003 Request for Studies proposal 200306000

Section 1. Administrative

Project location

Reasonable and Prudent Alternatives (RPAs)

Section 2. Past accomplishments

Section 3. Relationships to other projects

Section 4. Budget for Planning and Design phase

Task-based budget

Outyear objectives-based budget

Outyear budgets for Planning and Design phase

Section 5. Budget for Construction and Implementation phase

Task-based budget

Outyear objectives-based budget

Outyear budgets for Construction and Implementation phase

Section 6. Budget for Operations and Maintenance phase

Task-based budget

Outyear objectives-based budget

Outyear budgets for Operations and Maintenance phase

Section 7. Budget for Monitoring and Evaluation phase

Task-based budget

Outyear objectives-based budget

Outyear budgets for Monitoring and Evaluation phase

Section 8. Estimated budget summary

Itemized budget

Total estimated budget

Cost sharing

Reviews and recommendations

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

Comment:

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

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?

No

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?

No

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 thefollowing listed ESUs (for which there are currently no reproductive successstudies underway): Upper Columbia steelhead, Mid-Columbia steelhead; SnakeRiver fall chinook; and Columbia River chum. Studies not occurring in those ESUs, but with clear applicability to those ESUs will also be considered;

The Snake River fall chinook ESU is involved.

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);

No

The degree to which proposals may provide information more broadly applicable to multiple species/ESUs identified above;

The analytical approach could be applicable to other situations where a pedigree analysis is unsuitable.

Potential to commit to a long-term study (beyond F2);

Yes

Overall cost effectiveness

Costs are in line with other studies.

The proposal is to conduct a pilot study to determine if genetic divergence among natural and hatchery origin Snake River fall Chinook salmon is sufficient to estimate differences in relative reproductive success. The proposal does not adequately address any of the evaluation criteria in the RFS. It is, however, the only proposal directed at Snake River fall Chinook.

The project evaluates the contribution of reproduction by state of the art hatchery production and "stray" hatchery-origin with natural-origin adults. The same stock (primarily) in the same river system is being contrasted. A mixture analysis, rather than a direct pedigree analysis, will be evaluated, because the sampling conditions preclude the direct pedigree approach. However, a more thorough explanation of why pedigree data cannot be collected is needed.

The proposal does not describe how the applicants will know if the observed genetic divergence is adequate to estimate differences in relative reproductive success. Based on the success of the pilot study, the applicants propose to estimate relative reproductive success of hatchery and natural origin spawners, but they do not provide any details as to how they will accomplish this estimation. Phase 2 of the proposed work is dependent upon successfully finding genetic divergence and will continue the as yet unexplained estimation of reproductive success from 2004 to 2008 for the F2 generation.

Not all of the important Columbia basin salmon ESU's will be amenable to a pedigree analysis because of logistical constraints on trapping adults and juveniles. This proposal approaches this difficult circumstance by exploring mixture analysis as an alternative (assignment of individuals to a group rather than to specific parents). Since the biological material (fin clips etc) is already collected for a retrospective reconstruction of the mixtures, an answer to whether or not the approach will be fruitful should not take long. On the basis that this is one of the more precariously situated ESU's, the analytical approach is worth pursuing, and the initial investigation will be retrospective.

Comment:

Comment:

Comment:

The proponents essentially agree with the ISRP evaluation to fund phase 1 and elaborate on that agreement in their responses. The authors’ explanation of why to select the mixture model versus a pedigree analysis is appropriate; they explained in adequate detail why pedigree analysis is not feasible. This is clearly a preliminary study to see if the LGD sampling of adults can be matched with progeny to detect a difference. This is a logical first step, and needed before any commitment can be made to later phases (and meeting the listed criteria). It is a good example of using what we have to good advantage (including historical samples already in hand). It was also clear that other ISRP concerns cannot be addressed until their Phase 1 is complete.

The major difference between this proposal (other than it is the only one on Fall chinook) and others is that an admixture model would be used to estimate spawning success as opposed to the more detailed pedigree or parentage models. The history of using such models is that they can be very accurate but need to have good baseline data. The data should be adequate for the use in this proposal, but those tests should be conducted and verified (i.e., using blind tests using fish from known origins). Based on the accuracy of the blind tests and the estimates of precision, sample sizes can be determined for numbers of adults and juveniles.

This may be a useful application of the mixture model and does not require the sample sizes for parentage analysis. The staff managing the data has extensive experience in managing large databases (e.g., the coastwide electrophoretic databases for chinook and coho salmon, and steelhead).

Bottom line, the ISRP supports Phase I based on good responses to our questions. The issue of Phase II, however, should consider when a decision would have to be made on the utility of these results. If Phase II is to proceed, pending results, then a timeframe should be established for decisions and these funds likely protected until a decision not to proceed is made.

Comment:

Sponsor comments: See comment at Council's website