FY 2003 Upper Snake proposal 33001

Additional documents

33001 Narrative Narrative
33001 Powerpoint Presentation Powerpoint Presentation
33001 Sponsor Response to the ISRP Response

Section 1. Administrative

Proposal titleAssessment of genetic population structure and risk of introgression and hybridization to native trout in the Mid and Upper Snake River Provinces
Proposal ID33001
OrganizationIdaho Department of Fish and Game, Idaho Office of Species Conservation and University of Idaho (IDFG/IOSC)
Proposal contact person or principal investigator
NameMatthew Campbell
Mailing address1800 Trout Rd. Eagle, ID 83616
Phone / email2089394114 / mcampbel@idfg.state.id.us
Manager authorizing this projectSteve Yundt
Review cycleUpper Snake
Province / SubbasinUpper Snake / Upper Snake
Short descriptionDetect and quantify levels of hatchery produced O. mykiss introgression within, and assess genetic diversity and genetic population structure of native Yellowstone cutthroat trout and redband trout in the Middle and Upper Snake River Provinces.
Target speciesYellowstone cutthroat and redband trout
Project location
43.64 -116.87 Entire middle Snake province.
43.35 -112.64 Entire upper Snake province.
Reasonable and Prudent Alternatives (RPAs)


RPA 184 (

Relevant RPAs based on NMFS/BPA review:

Reviewing agencyAction #BiOp AgencyDescription

Section 2. Past accomplishments


Section 3. Relationships to other projects

Project IDTitleDescription
199800200 Snake River Native Salmonid Assessment This project will provide population information to prioritize populations/sample locations for further genetic study. This project will also provide non-lethally collected fin tissue for genetic analysis.
199500600 Shoshone-Bannock/Shoshone Paiute Joint Culture Facility This project will share genetic results to allow a complete and comprehensive analysis of genetic population structure of redband trout populations throughout the Middle and Upper Snake River Provinces.

Section 4. Budget for Planning and Design phase

Task-based budget
ObjectiveTaskDuration in FYsEstimated 2003 costSubcontractor
Outyear objectives-based budget
ObjectiveStarting FYEnding FYEstimated cost
Outyear budgets for Planning and Design phase

Section 5. Budget for Construction and Implementation phase

Task-based budget
ObjectiveTaskDuration in FYsEstimated 2003 costSubcontractor
Objective 1. Assess the predictive power of Idaho’s Historical Stocking Database in quantifying hybridization and introgression levels, and identify and prioritize non-introgressed populations for additional genetic work. Task 1. Conduct mitochondrial DNA (mtDNA) and nuclear DNA (nDNA) intron Restriction Fragment Length Polymorphism (RFLP) analysis to quantify levels of rainbow trout hybridization and introgression. 1 $159,921
Task 2. Compare stocking variables with observed rates of introgression. 1 $68,537
Outyear objectives-based budget
ObjectiveStarting FYEnding FYEstimated cost
Objective 2. Determine genetic population structure of native Yellowstone cutthroat trout populations and redband trout populations within the Middle and Upper Snake River Sub-Basins. 2004 2005 $484,696
Outyear budgets for Construction and Implementation phase
FY 2004FY 2005

Section 6. Budget for Operations and Maintenance phase

Task-based budget
ObjectiveTaskDuration in FYsEstimated 2003 costSubcontractor
Outyear objectives-based budget
ObjectiveStarting FYEnding FYEstimated cost
Outyear budgets for Operations and Maintenance phase

Section 7. Budget for Monitoring and Evaluation phase

Task-based budget
ObjectiveTaskDuration in FYsEstimated 2003 costSubcontractor
Outyear objectives-based budget
ObjectiveStarting FYEnding FYEstimated cost
Outyear budgets for Monitoring and Evaluation phase

Section 8. Estimated budget summary

Itemized budget
ItemNoteFY 2003 cost
Personnel FTE: Full time research biologist, Part-time lab technician $55,385
Fringe 33.00% for biologist, 41.60% for lab tech. $19,642
Supplies Genetic supplies (chemicals, tips, gloves) and Genetic consulting (Dr. Matt Powell, UofI, 2 months) $93,500
Travel Professional Meetings $1,000
Indirect $35,431
Capital $23,500
PIT tags $0
Subcontractor $0
Other $0
Total estimated budget
Total FY 2003 cost$228,458
Amount anticipated from previously committed BPA funds$0
Total FY 2003 budget request$228,458
FY 2003 forecast from 2002$0
% change from forecast0.0%
Cost sharing
OrganizationItem or service providedAmountCash or in-kind
Other budget explanation

Reviews and recommendations

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

Fundable only if response is adequate
Mar 1, 2002


A response is needed. This proposal would subsume and expand the genetic analysis task of the ongoing proposal 199800200. This proposal is scientifically sound but a response is needed on management applicability and plans. Reviewers' major concern for the project (and for 199800200) centers on how the data will be used to define conservation management units. The proposal primarily describes management at the population level, rather than aggregates of populations that would embrace watersheds or metapopulations.

The project proposes to examine redband and Yellowstone cutthroat trout (YCT) throughout the Upper and Middle Snake provinces, yet sampling and collections appear to be confined to Idaho only (admittedly, the bulk of the geography in the two provinces). The project will be stronger with respect to the provinces and the FWP if it is expanded to cover the entire Upper and Middle Snake provinces. The response should describe the extent to which analysis of trout collected from states adjoining Idaho will be included. If this project were funded and completed, it would generate a valuable geographical-based genetic dataset for redband and YCT populations.

The response (perhaps in collaboration with project 199800200) should provide more detail on how conservation units will be designated (describe criteria and process) and how they might be managed. Project sponsors should describe how the anticipated genetic, abundance, life history, and habitat data will be used to identify conservation management units and provide some idea of how these units could be linked together into a protection and recovery plan for Yellowstone cutthroat trout or redband trout in the upper Snake River system. Would the data be used to identify core or source populations from which recovery actions could be expanded or would sets of populations be protected in refuge-type units such as subbasin level watersheds that might be managed under special or restrictive regulations?

As long as inland trout management continues to focus on population level management, state and federal resource management agencies will remain vulnerable to an endless series of listing petition for inland trout species. Only by defining and subsequently managing conservation units at ecological scales above the population level (e.g., watershed, subwatershed, or metapopulation), will management agencies have any protection against future listing petitions, and any real chance of rebuilding and restoring redband and Yellowstone cutthroat trout populations.

Budget summaries do not show any cost sharing. Why is there no cost-sharing?

High Priority
May 17, 2002


This project would utilize samples that have already been collected. Information from this study is essential for the development of the Yellowstone cutthroat plan. Although the CBFWA believes the proposed work should be categorized as a "High Priority" since management efforts would benefit from the activities, the CBFWA identified four issues that need to be addressed.

First, although the proposed genetic techniques are technically valid, the CBFWA suggests that using existing fin clip samples to determine population structure can be problematic due to collection design (e.g., samples need to be collected over a large area of stream and samples need to represent various age classes). Typically no more than 10 fish per 100m section of stream should be collected. In addition, lengths and sometime weights need to be collected as well. This is to ensure that adults make up the majority of samples. If only juveniles are collected from a short section of stream, in essence siblings could make up the entire sample, thus providing inaccurate population structure makeup. Samples and sample locations need to be geo-referenced. In addition, samples need to be archived for future use. This and other resident fish genetic projects need to be coordinated among all labs to determine which loci are used and to ensure that methods and techniques are the same.

Second, regarding management applications of resultant genetic data, notably lacking from the discussion is the need or potential to replace the stocking of nonnative rainbow trout with progeny from broodstock developed from pure populations of Yellowstone cutthroat trout or redband. In previous reviews the ISRP has indicated that, if a management decision is made to continue stocking fish to augment fisheries in waters inhabitable to native fishes, the brood stock source for such stocking should be from the native fishes. The proposal suggests that Idaho's stocking database may be useful in predicting hybridization and introgression levels and therefore a good predictor of genetic risks to resident trout populations from historical rainbow trout stocking. Using an historical stocking model as a guide to suggest where it may be "safe" to stock non-native rainbow trout, especially where unimpeded access (connectivity) is involved, appears to be playing with fire. Changing environmental conditions could render historic stocking/introgression risk assumptions/relationships invalid. A more comprehensive policy of using progeny from native broodstock for stocking purposes would be less risky.

Third, per the ISRP's comments, the sponsors have modified, through the "fix-it loop", their proposal to include the analysis of redband trout from Oregon waters. Although the proposal sponsors include a personal communication reference (BPT personnel) with respect to the allocation of samples from Malheur Subbasin waters, the CBFWA has identified an oversight. The Statement of Work that the BPT has submitted to BPA for Project 199701900 provides for the collection of samples (i.e., fin samples) and genetic analysis of salmonid species, which includes redband trout, from the locations identified in the revised Proposal 33001. The CBFWA suggests that the BPT should make available, if requested by the sponsors of Proposal 33001, the results from the genetic analyses (techniques used in Project 199701900 are the same as those proposed in 33001) that have and will be obtained through Project 199701900. The CBFWA believes the allocation of funds to Proposal 33001 for the analysis of samples from Oregon would result in unnecessary duplicative efforts in a province where only $500,000 is available for new work. The CBFWA suggests that funding the Oregon portion of the Proposal 33001 would create a duplication of effort and entail an inefficient use of resources. In addition, the CBFWA expressed concern relative to the lack of coordination with the ODFW's staff, specifically their geneticist. Given the CBFWA concerns about duplicative efforts, the geneticists from ODFW, IDFG and MDFWG should meet to coordinate their efforts.

Jun 7, 2002


Fundable; likely to have strong benefits to the fisheries program. The response addresses the ISRP concerns in a thoughtful and thorough manner. It details how Conservation Management Units may be identified and provides examples of how differing genetic results would lead to different management units and actions. It also provides examples of sample collections outside of Idaho, but only inferentially suggests that these samples constitute adequate sampling of native trout populations in the Middle and Upper Snake provinces.

The technical review comments from CBFWA were thoughtful and should be considered by the project sponsors before project implementation.

Jul 23, 2002


Do not recommend. The discussions and agreements among responsible entities, as called for in the Council's 1995 F&W Program have not yet taken place. Findings on Section 10.5B. As BPA commented in 1995, FWL Program amendments, it may not be an FCRPS responsibility to mitigate above Hells Canyon Dam if not affected by the construction or operation of Black Canyon, Anderson Ranch, Boise Diversion, Minidoka, or Palisades reservoirs.
Do Not Fund
Oct 30, 2002