FY 2003 Mainstem/Systemwide proposal 200307500

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

Other budget explanation

This budget does not include cost of living allowances nor inflation.

Reviews and recommendations

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

Comment:

The ISRP agrees with the importance of studies like this and strongly supports the integration of genetic methods in this study, however there are aspects of the design that should be reconsidered:

1. The selection of 6 hatchery stocks and 3 treatments receives little justification. In the initial years of these studies the number of stocks could be limited (see comments in b) and pre-study tests of the treatments could be conducted before assuming that these treatments will result in the "stress" expected, or that the stress does not simply kill all the fish. What preliminary studies have been conducted?
2. We are uncertain about a number of aspects of the proposed half-sib breeding design.
1. Half-sib designs assume all males are independent; therefore, at least twice the number of males as females are needed.
2. The design as described cannot directly estimate GxE interactions. For Task 2a, how do you expect to partition the GxE effect?
3. There will likely be maternal effects that cannot be accounted for and there is no treatment replication within stock x family x treatment (i.e., no rearing container controls). Revising the design is likely to require more rearing containers and/or dropping some stocks to provide more containers.
3. What is the value of maintaining the run-timing component within stocks?
4. The budget implies three years of study but the text does not make any such reference (other than a reference to using rainbow trout later). What is the expected duration of these studies?
5. Reliance on early development traits may not be appropriate. Phenotypic traits with strong relations to fitness (such as egg survival) may have very limited genetic variation. In which case, the outcome of this study may relate more to these specific traits than to a general feature of adaptive genetic variation. To minimize such a risk, it may be advisable to maintain the progeny during early growth stages and examine additional traits less associated with immediate survival.
6. There are issues in measuring GxE. First, the genotype being referred to is actually the family that will be composed of multiple genotypes. Here is where the real value of the molecular genetic studies could be used, but this aspect is not highlighted in the proposal. Second, if quantitative genetic methods are to be used to assess GxE interactions then there are specific breeding studies in multiple environments that can be used to estimate the interaction. Coupling these with the molecular genetic work could be a very original piece of research!
7. Task 4 seems to imply that the results of these detailed studies will be compared with the production history of the source hatcheries. The inherent assumption that past production history would relate to present genetic composition is weak and we question the utility of this part of the study.
8. A final point for clarification is the authors' use of 'drift'. On page 9 Section 9, in the section on Genetic analysis of chinook salmon, the authors state "Differential success among family lines to environmental challenges will also be assessed by examining for changes in offspring genotype from that of the parents. Equalized familial representation across treatments will allow for the removal of variance associated with familial lines and variance due to drift." It is not clear how these statements relate to the methods to be used and how genetic (presumably) drift relates to these analyses. Unless survival is very poor and/or highly variable between families, why does drift receive the profile it does in the proposal and why would equal family size control it? The proposal should clarify who is actually conducting this research and the references cited in Section 2 should be completed.

Action Agency/NMFS RME Group Comments:

HARVEST AND HATCHERY SUBGROUP -- Address critical element of RPA? No. More relevant to RPA 179. The proposal does not attempt to address hatchery/wild reproductive success in RPA 182. With respect to RPA 184, it neither addresses the topic of hatchery reform, nor address whether conservation hatcheries contribute to recovery. Too far removed from practical application and not adequately linked to specific reform under RPA 184.

Opposing view. Relevant to RPA 184. Will examine genotype-environment interactions and will attempt to determine if incubation performance of a stock is related to life history performance and if incubation success could be used as a predictor of expected performance through the adult stage. Results of study may provide guidance in identifying and prioritizing populations for conservation activities.

Scope? [ESU's covered, Transferability, Species covered] Would address listed chinook. Results not transferable between species, ESUs, or populations, due to site- specific artificial selection regimes at experimental location.

Study design adequate, as is, or as may be modified?

No comment at this time.

ISRP Remarks on RME Group Comments:

The ISRP generally agrees with the RME group comments, siding more with the 'opposing view' but having concern about the study design.

Comment:

Comment:

The authors considered each of the ISRP's preliminary review comments and have strengthened their proposal. Project sponsors propose to change the breeding design to a factorial design capable of estimating interactive effects, and discuss the changes this will entail within the available facilities. The duration of the project has been shortened. The basic notion here that variation of survival during embryogenesis among families would be related to variation of other fitness traits in later development is still a concern, but we understand the notion that variation of development time may be an important component of adaptation to local environments by chinook in the basin and that this study of high altitude and low altitude spawning populations might elucidate an important mechanism of adaptation.

No doubt the region will learn from this investigation, but we continue to wonder if more could be learned with the inclusion of molecular data. If the genotype of each individual can be assessed (presumably across families and stock), a more direct test of genotype x environment interactions would seem to be to relate "type" to performance -- more of a regression analysis (common in quantitative genetic studies for GxE).

Comment:

Comments
The proposal will attempt to assess the quantitative genetic basis to phenotypic variation in life history traits through a study (using a half-sib breeding design) to assess Genotype x Environment interactions in traits associated with early development. However, there are some concerns about the experimental design. The design as described cannot directly estimate Genotypic x Environment interactions. Focusing on fitness traits associated with early life, e.g., egg to fry survival, assumes that there is a sufficiently variable genetic component to this trait, which may not be the case. There may be other phenotypic traits that would better demonstrate adaptive variation. Finally, the relevance of genetic drift to this experiment seems overstated in this proposal.

Already ESA Required?
No

Biop?
Yes

Comment:

Comments: