FY 2003 Request for Studies proposal 200305100

Section 1. Administrative

Proposal titlePedigree Approach to Determine Reproductive Success of Natural and Hatchery Origin Spring/Summer Chinook Salmon Spawners in Johnson Creek, Idaho
Proposal ID200305100
OrganizationNez Perce Tribe (NPT)
Proposal contact person or principal investigator
NameRick Orme
Mailing addressP.O. Box 1942, 125 S. Mission McCall, Idaho
Phone / email2086345290 / RickO@nezperce.org
Manager authorizing this projectRick Orme
Review cycleFY 2003 Request for Studies
Province / SubbasinMountain Snake / Salmon
Short descriptionWe propose to address RPA 182 using microsatellite based parentage assignment and exclusion analyses to test for survival, productivity, and behavioral differences by life stage (parr, presmolt, smolt, and adult) for all possible crosses of naturally spaw
Target speciesSpring/Summer Chinook
Project location
44.9625 -115.5008 Johnson Creek
Reasonable and Prudent Alternatives (RPAs)



Relevant RPAs based on NMFS/BPA review:

Reviewing agencyAction #BiOp AgencyDescription

Section 2. Past accomplishments


Section 3. Relationships to other projects

Project IDTitleDescription

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
Outyear objectives-based budget
ObjectiveStarting FYEnding FYEstimated cost
Outyear budgets for Construction and Implementation phase

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
Supplies $168,500
Overhead $27,000
Personnel $110,000
Total estimated budget
Total FY 2003 cost$305,500
Amount anticipated from previously committed BPA funds$0
Total FY 2003 budget request$305,500
FY 2003 forecast from 2002$0
% change from forecast0.0%
Cost sharing
OrganizationItem or service providedAmountCash or in-kind
JCAPE $16,000 cash

Reviews and recommendations

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

Fundable if response is adequate
Apr 25, 2003


Fundable in part for Objectives 1 and 2, contingent upon adequate response to the ISRP’s questions and comments. Objectives 3 and 4 require major revision as to how they will be accomplished. Regardless this proposal is low priority. It appears to duplicate other studies in this ESU. This ESU is not one of the four priority ESUs listed in the RFS, but the proposal could have application to other spring/summer chinook populations.

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, with inferences to F3 progeny during the course of the study.

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?

Yes. They have the ability to look at survival during different life stages and periods of migration.

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?

We believe so, but this aspect of the research is poorly addressed.

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

The study involves spring/summer chinook in Johnson Creek, East Fork of South Fork of Salmon River. The ESU is not one of the above four, but the study should be of interest. Johnson Creek is in an ESU listed as threatened under the ESA.

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);

Yes. The study will address both F2 and F3 generations.

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

The study is of interest to spring/summer chinook in other ESUs.

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

The study will carry through three complete F3 brood years.

Overall cost effectiveness

The cost for this eight-year study seems reasonable.

This proposal seeks to address elements of each of the three major criteria posed in the RFS. In addition the proposal attempts to address several of the additional criteria including evaluation of reproductive success beyond the F2 generation and the potential to commit to longer-term studies. It does not specifically address the ESU’s listed in the additional criteria but may be applicable to them. The study proposes to evaluate reproductive success of hatchery and wild spring/summer chinook spawners in Johnson Creek, Idaho. A supplementation project was begun in Johnson Creek in 1998. Facilities for collecting adults and juveniles have been established. Apparently genetic and demographic data were obtained from wild x wild crosses prior to the first return of supplemented adults in 2001. The study dovetails with ongoing trapping and monitoring at Johnson Creek. The applicants provide better than average detail regarding the approach to evaluate possible differences in reproductive success.

The applicants seem to have reached the conclusion that supplementation has had or will have a positive effect on adult returns and genetic diversity without full analysis of current and future data. On page 2, apparently as a result of comparing adult returns in 2001 and 2002 to returns in previous years, the conclusions is drawn that “ the supplementation effort has succeeded in increasing adult returns to Johnson Creek.” Similarly, on page 11-12, the statement is made that “ the model can be used to determine the optimal number of supplementation fish that could spawn with wild fish to maximize genetic diversity or effective population size.” The assumption here appears to be that supplementation will indeed enhance genetic diversity of the population. The applicants have not provided concrete evidence that supplementation has been successful in Johnson Creek in part because they have failed to account for increases in population size that could have occurred as a result of changes in out-of-basin factors such as ocean conditions and to provide information on the relative contribution of wild and supplemented adult to population growth. The failure to address out-of-basin factors pervades the proposed demographic analysis.

Genetic aspects of the study:

  1. How valid is the assumption of random mating between wild and supplemented adults. A justification for this assumption is needed, especially in light of research by investigators such as Fleming and Gross that demonstrated differences in reproductive behavior between wild and hatchery spawners.
  2. Will the effects of crosses of different sexes of fish with wild and hatchery origins (e.g., wild male x hatchery female, hatchery male x wild female) be analyzed. If not, why?
  3. There is little discussion of how the data will be analyzed and tested statistically.
  4. A comparison of changes in fitness of WxW crosses with changes (or lack of changes) in fitness of WxW crosses in a “control” stream of the ISS would be useful. Is it sufficient just to compare fitness of HxW and HxH crosses with WxW when the fitness of the WxW may be changing because of the supplementation?
  5. The ratio of hatchery to wild spawners was not clear. From the proposal, it appears that all returning supplementation fish are passed above the weir and allowed to spawn, regardless of the number of wild spawners that return. Is this wise, or does it allow a unique look at supplementation?
  6. The applicants propose that the study could be restricted to adult sampling to reduce the cost. This would also put the study results in line with what is possible in some of the other proposals, i.e., fitness as measured by “adult to adult” returns.
  7. Only wild adult chinook salmon are retained for brood stock so this should provide a unique look at the issues of design and success of supplementation projects.
  8. Who will perform the laboratory work?

Demographic aspects of the study:

This aspect of the research is very weak and is described in a cursory manner. The methods for accomplishing objectives three and four, which address demographic aspects of the study, are not clearly and comprehensively discussed, and the problems and assumptions with the proposed approaches are not identified and evaluated. A population ecologist/modeler should be a co-investigator on the proposal and provide the necessary technical expertise for the demographic and model development section of the proposal.

  1. The specific demographic and genetic information available for the population prior to supplementation is not given. It is unclear if and how this information will be used in assessing whether supplementation has changed the demographic parameters of the population.
  2. The applicants propose to develop a model to evaluate the effects of supplementation on demographic parameters. The model is not described in sufficient detail to permit assessment of its adequacy in evaluating supplementation effects. It is unclear exactly what the structure and parameters of the model will be, how the model will be used to compare population demographics of the supplemented and unsupplemented population, how uncertainty will be incorporated, and how out-of-basin factors affecting adult returns and juvenile survival will be accounted for. Are there similar types of models in use today or is this a pioneering effort? The qualifications of the proposed modelers were not given.

Fundable - response required
May 14, 2003


Fundable - response required
May 14, 2003


Not Fundable
Jun 27, 2003


Not fundable, the proposal and response did not provide a compelling rationale for funding this project. While the authors provided extensive comments, too many questions remain.

On page 5, concerning the “conclusions that supplementation has had or will have a positive effect”; reviewers do not follow this answer. The authors’ respond that the adult-to-adult return rate for supplementation fish was twice the wild fish. How do they know this? To estimate these returns would mean that adults are “typed” to origin, further it ignores any information from smolt production. If adult typing is being done already, why is this proposal being submitted again and who is paying for what now?

The interpretation of results, bottom page 7, remains a valid issue but clearly falls into the “explanation” type of data (as ISAB identified in the Supplementation report). The authors acknowledge that they cannot differentiate results without doing the mating studies or observations in the stream (which would require some external mark). The general issue of what needs to be sampled affects most of the remaining points, including the discussion on demographic aspects. While the authors’ acknowledge that not conducting the juvenile sample would reduce costs, they could not answer most of the remaining questions or explain interactions in the stream. They do not seem firm on this issue, one way or the other.

On page 10, question 5 is not really answered. They do need to consider the loading ratio for these studies … what will be done if there is very poor production from the naturally spawning fish?

On page 10, question 8. If the lab currently analyses 4 loci, that is simply not sufficient for parentage analyses. Other proposals responding to the RFS, intended to use 16-20 microsatellite loci for similar analyses, thus providing considerably more analytical power. This low number of loci would have to influence what they can say about analyses-to-date. The number of loci must be increased, as they say in the last sentence of that paragraph.

Reviewers were not very supportive of modeling to “attempt to generate a “control” of demographic parameters that would … if supplementation was not occurring”. Reviewers doubt that this is a worthwhile component of what the RFS funds should cover. If the proposers want to create a model, the first thing reviewers would suggest is for them to develop a flow diagram of effects, interactions, necessary parameters, etc. By doing this, they may at least determine what the minimum information (the critical or vital statistics) necessary is for their study.

The discussion regarding proposed use of Lake Creek as a quasi-control stream was highly redundant and not clearly presented. The same comments from the initial ISRP review about the brevity of information provided for Objectives 3 & 4 still apply. The methods for Objective 3 are still quite briefly described, and the model proposed for Objective 4 is not only briefly described, it also sounds potentially uninformative and optional.

The underlying theme of this proposal “to document a success” raised questions of objectivity. Recent ISRP comments on the ISS design may also influence the value of Johnson Creek for this solicitation.