FY07-09 proposal 200725000

Jump to Reviews and Recommendations

Section 1. Administrative

Contacts

Section 2. Locations

Province / subbasin: Mountain Snake / Salmon

Section 3. Focal species

Section 4. Past accomplishments

Section 5. Relationships to other projects

Section 6. Biological objectives

Section 7. Work elements (coming back to this)

Section 8. Budgets

Itemized estimated budget

Total estimated FY 2007-2009 budgets

Cost sharing

Section 9. Project future

Future O&M costs: Little additional O&M would be necessary because juvenile collections would end along with ISS collections, and hatchery personnel will continue to operate weirs for broodstock collection.

Termination date: 12/31/2019
Comments: This date would allow the collection of the last F2 generation adults in late 2017 and then approximately one and a half years for final analyses and publication of peer reviewed articles

Final deliverables: Completion report and one or more peer reviewed publications

Section 10. Narrative and other documents

Reviews and recommendations

ISRP PRELIMINARY REVIEW (Jun 2, 2006)

Recommendation: Response requested

NPCC comments: This proposal was generated in response to the ISRP's recommendation on the ISS to use parentage analysis to partition juvenile Chinook production in ISS streams by natural, supplementation, and general production hatchery parents. Recognizing that the ISRP recommended a parentage analysis for the ISS, this new project should be justified within the context of the larger genetic network in the Columbia River Basin. The response should include evidence of discussion and coordination with ongoing efforts in the Basin. Are the proposed streams sites the best place to do this parentage analysis? Please include in response why these sites were chosen and what advantages they have over other sites? See programmatic comment and provide clear evidence that there is a regional statistical design for this work taking advantage of economies of scale for collection and testing of samples. In response, please include more details of the methods for genetic testing and collection. The Lutch report previously reviewed by the ISRP describes some of the methods, but the methods need to be summarized in the current proposal. If selected for funding, this project should be demonstrated and funded in phases; e.g., this project can be allocated funding based on demonstration of the ability to perform the parentage analysis, and expanded to genotype the full suite of individuals as justified by evidence that the uncertainties can be resolved. For analyses of population change objective see Pearse, D. E. and K. A. Crandall. 2004. Beyond Fst: Analysis of population genetic data for conservation. Conservation Genetics 5:585-602. For both analysis of population change and parentage analysis, the critical element at this point is to collect tissues. This should be recommended at the full-scale project to estimate mating behavior, not just single parent assignments. After a reasonable number of individuals are genotyped, preliminary analyses can be performed to inform the decision as to whether or not to complete genotyping for the entire set of individuals. The project has yet to identify a lab to genotype the fish but that should not be a problem. At this time a lead geneticist is not identified. This needs to happen before the genotyping begins. The budget for the genetics work, about 1 million per year, seems very high. The percentage of funding for the genetic work appears higher than in other similar proposals. Over the past few years, the cost per specimen has been going down. In response, please provide additional justification for the anticipated costs per specimen and for equipment. If the budget includes sot of equipment, what opportunities exist for reducing costs by subcontracting to other labs?

ISRP FINAL REVIEW (Aug 31, 2006)

Recommendation: Fundable

NPCC comments: The sponsor provides a complete reply to the questions raised by the ISRP. The ISRP requested evidence and justifications that the sites selected for an analysis of the relative reproductive performance of general production (hatchery), supplementation (hatchery), and natural-origin salmon were suitable. This response is thorough. The ISRP also requested additional information on the type of analysis the sponsor was going to pursue. The sponsor provided information on the type of genetic marker they intend to employ (the coastwide standard Chinook microsatellite panel) and that either assignment or exclusion methods would be used to identify parents. Sponsor provided a thorough discussion of sample sizes and statistical tests to evaluate assortative mating. The response to the ISRP questions were less satisfying regarding 1) beginning with an initial analysis followed by expanding the investigation to archived and contemporary samples, and 2) identifying a lead geneticist, a genetics lab to perform the genotyping, and an apparently high cost per sample. In response to the ISRP suggestion that the analysis begin with a subset of individual and demonstrate the ability to reasonably make an assessment of relative reproductive success, the sponsors noted that they have been associated with successful studies with Chinook salmon in the Pahsimeroi River and with sockeye salmon in Redfish Lake. The ISRP does not question the feasibility of the methodology working or the ability of the sponsor to execute the work. The query was about whether in this specific instance the estimates of reproductive success will be reasonable and statistically justified. In coho salmon studies in Minter Creek, Washington and steelhead studies in Hood River, Oregon there are an appreciable number of individuals that cannot be assigned to parents. It is unknown whether this represents individuals produced by resident fish or migrants. If this were the case in the ISS streams, extensive effort would not be justified. Nonetheless, the ISRP considers the examples provided sufficient evidence of proof of concept. Finally while the ISRP would prefer that in a project of this magnitude and importance the lead geneticist and lab would have been established before the proposal was accepted, we are satisfied they have a framework for identifying an appropriate lead geneticist and lab.