FY 2003 Mainstem/Systemwide proposal 198909600

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

Reason for change in estimated budget

The budget for this project increases at this time because of the addition of two critically important studies of the reproductive success in wild, conventional and captive broodstock chinook salmon spawning in Lostine River and Catherine Creek. We also propose expansion of the steelhead reproductive success research in Little Sheep Creek to including fitness study of the hatchery broodstock and the recording of digital images of all adults ($15k) for morphometric analysis. We also request a smolt trap in Little Sheep Creek ($115k/year) to provide an additional samping point for evaluating differential parr-to-smolt survival. The volume of samples to be genotyped for this study exceeds the capacity of our current instruments and will reguire an additional ABI 3100 capillary electrophoresis unit ($150k, one-time cost, FY03 only).

Reason for change in scope

We have tracked genetic changes in the Lostine River and Catherine Creek popultions since 1989 and 1990, respectively. We find however, that interpretation of those allele frequency data is complicated by variable returns and highly variable proportions of hatchery spawners. Hatchery fish are certainly contributing to natural production, but the extent to which they are interbreeding with wild fish remains unclear. There is now the opportunity to apply the technology we have already demonstrated in Little Sheep Creek steelhead to these important chinook populations. By creating pedigrees in natural and hatchery populations we will provide specific information regarding the success or failure of supplementation efforts and perhaps also an understanding of the biological reasons for that success or failure.

Cost sharing

Other budget explanation

This budget reflects a major shift in commitment of funds toward DNA-related reseach relative to the allozyme markers that have been the cornerstone of this project since its inception in 1989. In Part 2 we explain our division of effort between DNA and allozymes and between the new pedigree-based research and more traditional allele frequency monitoring. DNA technology has matured to the point that it can fill both its new role in parentage determination and quantitative genetic analysis, as well as an ongoing role in future allele frequency monitoring studies. We propose continuation of limited allozyme sampling over approximately 3-year intervals from at least some locations. This limited sampling will permit continued utility of the substantial Snake River allozyme data set, a virtually unbroken genetic record going back to the late 1980s for many of the most threatened Snake River populations. All other future sampling for this study will employ nonlethal fin clips. Increased costs in this budget cycle result from ambitious expansion of the current pedigree-based research in Little Sheep Creek steelhead and implementation of two new similar studies in chinook salmon (Lostine River and Catherine Creek). We propose continuation and expansion of multibasin allele frequency monitoring with DNA markers because we believe the allele frequency monitoring provides a broader geographic and programatic perspective to genetic monitoring (see Part 2 for detail).

Reviews and recommendations

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

Comment:

Expansion of the budget is explained and justified. It includes both an actual expansion of the data collection and lab analysis to the Lostine River, Catherine Creek, and Little Sheep Creek steelhead, as well as expanding the project to include the development of pedigree analysis and a strategy shift to increasing reliance on microsatellite DNA analysis rather than allozyme analysis. In particular, the latter change is justified and warranted. Shifting to the pedigree/paternity analysis is needed in order to investigate the more subtle effects of hatchery/wild fish interactions through supplementation to which the allozyme results were relatively insensitive. Microsatellite DNA pedigree analysis should be insightful for this purpose. At the same time, continuing the allozyme data collection at a base level is warranted in order to retain continuity of data over time (nearing two decades).

This proposal is well written and the researchers have maintained a very high level of scientific productivity. We would like the project sponsors to consider the following few comments:

1. Our most basic concern is for the scope and size of this one project. The proposal provides very little in terms of numbers of samples taken, capability for timely processing of these samples, and technical basis of the sample sizes. The tier 2 sample sizes seem particularly small, but no basis for the determinations of these samples was provided.
2. Section 9, page 16, Methods states that the captive brood chinook will not be sampled for DNA "because family-specific success data are already available through segregated rearing, marking, and enumeration." It is not evident from this statement whether that family-success is based on breeding programs or a different DNA sampling task? If these fish have not been sampled for DNA and are released into Catherine and Lostine rivers they could not be included in the pedigree analyses. This point should be clarified to ensure there is no oversight.
3. Section 9, page 12 Objective 1 Assumption. The authors suggest only partial sampling of potential parents can be compensated for by increasing samples sizes of offspring or the number of loci used. Increased sample size could improve precision, but we do not see how sample size alone can compensate for unknown parental genotypes? Increasing the number of loci sampled may assist if there are differences detected that are useful, but they also may not. The intention of this comment should be clarified.
4. Two major cost items included were a new ABI 3100 capillary electrophoresis unit ($150k, one-time cost, FY03 only) and the provision of an additional smolt weir in the Imnaha system ($115K). There is essentially no justification for these major expenses, what are the consequences of not funding? Is the smolt trapping coordinated (and agreed) with by others in the basin and why is it essential?

Action Agency/NMFS RME Group Comments:

HARVEST AND HATCHERY SUBGROUP -- Address critical element of RPA? Relevant to both RPAs. The proposal applies to RPA 182, since it includes the study of reproductive success. Little Sheep steelhead portion addresses this RPA well.

The proposal applies to RPA 184, as well. It relates to conservation hatcheries as a recovery tool (and the extent to which it might contribute). Some hatchery reforms are directed at reducing gene flow from hatchery fish to wild fish.

Scope? [ESU's covered, Transferability, Species covered] Target species are chinook salmon and steelhead. It covers most of an ESU and two listed species. Results should be broadly applicable.

Study design adequate, as is, or as may be modified? Regarding Sheep Creek, the data presented at the captive brood workshop showed limited success at assigning parentage, an issue that requires further discussion with investigators. This may be exacerbated for steelhead, where the genetic exchange with resident fish may be fluid, and where precocial and resident males are likely to contribute genetically. In general, good use of techniques available to determine contribution at this time. Incorporates latest genetic technology plus parentage analysis. This may provide the most powerful insight to relative fitness of hatchery vs. wild spawners.

It resembles some of the M&E programs addressing genetic effects from hatcheries - it describes basic genetic metrics (Ne, Fst, etc.), then tracks change over time. Continues long genetic data set, giving this special monitoring/evaluation value. For chinook, good monitoring for supplemented versus unsupplemented areas in the Grande Ronde (although straying into unsupplemented areas has occurred, and will cloud results).

ISRP Remarks on RME Group Comments:

The RME group comments on 198909600 are consistent with the ISRP's review comments. The BPA comments regarding Sheep Creek and the data presented at the captive brood workshop which showed limited success at assigning parentage, may be an issue that requires further consideration by the investigators. As noted in the RME group comments, the issue may be exacerbated for steelhead, where the genetic exchange with resident fish may be fluid, and where precocial and resident males are likely to contribute genetically.

Comment:

Comment:

Comment:

The proposal provided summary statements of findings that showed significant progress over the history of the project. Several papers based on the results have been published in peer-reviewed 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.

Expansion of the budget is explained and justified. It includes both an actual expansion of the data collection and lab analysis to the Lostine River, Catherine Creek, and Little Sheep Creek steelhead, as well as expanding the project to include the development of pedigree analysis and a strategy shift to increasing reliance on microsatellite DNA analysis rather than allozyme analysis. In particular, the latter change is justified and warranted. Shifting to the pedigree/paternity analysis is needed in order to investigate the more subtle effects of hatchery/wild fish interactions through supplementation to which the allozyme results were relatively insensitive. Microsatellite DNA pedigree analysis should be insightful for this purpose. At the same time, continuing the allozyme data collection at a base level is warranted in order to retain continuity of data over time (nearing two decades).

If funded, this project should be coordinated with other monitoring projects to ensure compatibility of objectives, common methods, and protocols. This coordination could be accomplished under the favorably reviewed CBFWA proposal #35033.

Comment:

Comments
NMFS proposal. Inappropriate to comment.

Already ESA Required?
No

Biop?
Yes

Comment:

Comments:

Comment:

Comment:

Sponsor comments: See comment at Council's website