Independent Scientific Review Panel

for the Northwest Power Planning Council

851 SW 6th Avenue, Suite 1100

Portland, Oregon 97204

isrp@nwppc.org

Review of Proposals Submitted in Response to 

Bonneville Power Administration’s March 14, 2003 

Request for Studies for Reasonable and Prudent Alternative 

Actions 182 and 184 of the 2000 Federal Columbia River 

Power System Biological Opinion

(ISRP Review of RFS Proposals)

Susan Hanna

Nancy Huntly

William Liss 

Lyman McDonald

Brian Riddell

William Smoker

Richard N. Williams

Jack Griffith, PRG

Eric Loudenslager, ISAB-PRG

ISRP 2003-7

April 25, 2003
ISRP 2003-7 RME RFS Proposal Review

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ISRP Review of RFS Proposals

Contents

Introduction................................................................................................................................... 1

Action 184: Synthesis of Existing Analytical Approaches, or Development of a New 

Analytical Approach, for Determining the Effects of Hatchery Reforms on Extinction Risk 

and Recovery ................................................................................................................................. 2

Proposal 10: A Tool for Evaluating Risks and Benefits of Reform Actions in Hatchery Programs 

(WDFW)................................................................................................................................3

Proposal 13: Analytical Approach for Determination of Effects of Hatchery Reform on Extinction 

Risk and Recovery of Salmon and Steelhead (CRITFC)............................................................4

Action 184: Reproductive Success of Natural-Origin, Hatchery-Origin, and Reconditioned 

Kelt Steelhead................................................................................................................................ 5

Proposal 4: Reproductive Success of Natural-Origin, Endemic Hatchery Origin, and 

Reconditioned Kelt Summer Steelhead in the Tucannon River (WDFW)....................................7

Proposal 5: Assessment of the Reproductive Success of Reconditioned Kelt Steelhead with DNA 

Microarray Technology (Battelle)............................................................................................9

Proposal 9: An Evaluation of the Efficacy of Steelhead Kelt Reconditioning to Address 

Biological Opinion Action 184b: The Reproductive Success of Hatchery-Origin and Wild-Origin 

Repeat Spawners (USGS)......................................................................................................10

Proposal 14: Proposal to Evaluate Reproductive Success of Natural-Origin, Hatchery-Origin, and 

Kelt Steelhead in the Columbia River Basin (CRITFC)...........................................................11

Action 182: Studies to Determine Reproductive Success of Hatchery Spawners ................. 13

Proposal 8: Evaluating the Reproductive Success of Natural- and Hatchery-Origin Columbia 

River Chum Salmon (WDFW) ..............................................................................................15

Proposal 7: Reproductive Success of Hatchery Spawners in the Chinook River, Washington (Sea 

Resources)...........................................................................................................................17

Proposal 15: Natural Reproductive Success and Demographic Effects of Hatchery-Origin 

Steelhead in Abernathy Creek, Washington: Can Newly Developed, Native Broodstocks of 

Steelhead Derived from Captively-Reared Parr Potentially Contribute to Recovery of Naturally 

Spawning Populations? (USFWS) .........................................................................................19

Proposal 2: Evaluation of the Reproductive Success of Wild and Hatchery Steelhead in Natural 

and Hatchery Environments (UW).........................................................................................21

Proposal 6: Relative Reproductive Success of Hatchery-Origin and Wild-Origin Steelhead 

Spawning Naturally in the Hood River (OSU)........................................................................22

Proposal 1: Investigation of the Relative Reproductive Success of Hatchery and Wild Steelhead 

in the Deschutes River Basin (ODFW)...................................................................................24

Proposal 3: Pedigree Approach to Determine Reproductive Success of Natural and Hatchery 

Origin Spring/Summer Chinook Salmon Spawners in Johnson Creek, Idaho (NPT)..................27

Proposal 11: Comparative Reproductive Success of Wild and Hatchery Origin Spring/Summer 

Chinook Salmon that Spawn Naturally in the Pahsimeroi and Upper Salmon Rivers (IDFG) .....30

Proposal 12: Evaluating the Relative Reproductive Success of Natural- and Hatchery-Origin 

Snake River Fall Chinook Spawners Upstream of Lower Granite Dam (WDFW)......................32

Table of Proposals....................................................................................................................... 34
ISRP 2003-7 RME RFS Proposal Review

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ISRP Review of RFS Proposals

Introduction

This is the third in a series of 2003 ISRP reviews associated with NOAA Fisheries and the Federal 

Columbia River Power System Action Agencies’ (Bonneville Power Administration, Corps of 

Engineers, and Bureau of Reclamation) Research, Monitoring, and Evaluation (RME) effort. At the 

request of the Council and BPA, the ISRP reviewed 15 proposals submitted in response to 

Bonneville Power Administration’s March 14, 2003 Request for Studies (RFS) intended to address 

research, monitoring, and evaluation requirements under Reasonable and Prudent Alternative (RPA) 

Actions 182 and 184 of the NOAA Fisheries’ 2000 Biological Opinion (BiOp) on the Operation of 

the Federal Columbia River Power System (FCRPS). The Request for Studies (RFS) was needed to 

fill research needs for the BiOp that are not actively being addressed through the Bonneville Power 

Administration’s current implementation program. 

The RFS covered the following three topics relevant to the Reasonable and Prudent Alternative 

Actions:

1) Action #184: Synthesis of Existing Analytical Approaches, or Development of a New Analytical 

Approach, for Determining the Effects of Hatchery Reforms on Extinction Risk and Recovery (2 

proposals received); 

2) Action#184: Reproductive Success of Natural-Origin, Hatchery-Origin, and Reconditioned Kelt 

Steelhead (4 proposals); 

3) Action #182: Studies to Determine Reproductive Success of Hatchery Spawners (9 proposals).

The development of the RFS included input from the ISRP. In a February 28, 2003 memo to the 

Council, the ISRP provided a review of the RME group’s draft Request for Studies (Requests for 

Proposals initially) to address RME gaps for FCRPS BiOp Actions 182, 184, and 195 (Extra 

Mortality); see www.nwcouncil.org/library/isrp/isrp2003-4.htm. The RME group considered the 

ISRP review, revisited the RFSs, dropped the Extra Mortality RFS (RPA 195), refined the hatchery 

related RFSs (RPAs 182 and 184), and released the Request for Studies on March 14. On April 14th, 

the ISRP received 15 proposals for immediate review. 

Although this review was on a quick timeline (9 business days), a majority of ISRP members and 

two Peer Review Group members participated in the review, shared comments, discussed the 

proposals in detail, and reached the recommendations in the report by consensus. As with all ISRP 

proposal reviews, the ISRP reviewed the proposals in the context of the Council’s program and in 

regard to whether they:

1. are based on sound science principles; 

2. benefit fish and wildlife; 

3. have clearly defined objectives and outcomes; and 

4. have provisions for monitoring and evaluation of results.

In addition to the standard ISRP criteria, the ISRP reviewed each proposal according to the specific 

criteria and questions provided in the RFS. In this report, ISRP recommendations and comments are 

provided for each proposal and grouped by the three RFSs. The ISRP provides general comments on 

the three sets of proposals at the beginning of each RFS section. 

Given the aggressive schedule for the Council to consider the proposals and ISRP recommendations 

at the May Council meeting and for Bonneville to announce a decision on the proposals by May 9th, 
ISRP 2003-7 RME RFS Proposal Review

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the ISRP began this review with the assumption that a response loop was not part of the review 

process and intended to provide clear recommendations on which proposals best addressed the 

Reasonable and Prudent Alternative Actions as described in the RFS. However, when ISRP 

reviewers shared and discussed comments, several issues arose that justify the need for the Council 

and Bonneville to consider a response/revision loop for this set of proposals. The proposals: 1) are 

designed to meet requirements of the BiOp but did not address all the questions contained in the 

RFS; 2) were of similar quality to proposals in the provincial reviews that the ISRP would have 

recommended “a response is needed” before making a final recommendation; and 3) are competing 

for funds with proposals submitted for the Mainstem/Systemwide and should be equally technically 

justified. If requested, the ISRP is available to review any revisions to the proposals submitted for 

the RFSs to ensure that they fully address the gaps identified for the BiOp.

Because of the short timeframe provided for project sponsors to draft proposals, the ISRP was not 

surprised that proposal revisions are warranted. The importance and complexities of the RME effort 

warrant a schedule that provides adequate time for project sponsors to fully develop their ideas and 

methods, and for reviewers and decision-makers to fully consider the proposals in the context of the 

Fish and Wildlife Program and BiOp. As a general rule, the ISRP hopes this is the last solicitation 

and review process scheduled over such a short time period. 

Despite our continued concerns about schedules, the ISRP notes that Bonneville and the Council 

have made significant progress to formalize the ISRP’s role. In fact, the ISRP’s understanding of the 

decision on the revised Mainstem/Systemwide proposals is that the Council, Bonneville, and NOAA 

Fisheries were very responsive to the ISRP’s project specific and programmatic recommendations. 

We look forward to a continued role in this process and in assisting the Independent Scientific 

Advisory Board in its likely review of the RME Framework document. This regional effort to 

establish a scientifically sound, cost-effective, and long-term RME plan for the Columbia River 

Basin is an endeavor of paramount importance.

FCRPS BIOP Action #184: Synthesis of Existing Analytical Approaches, 

or Development of a New Analytical Approach, for Determining the 

Effects of Hatchery Reforms on Extinction Risk and Recovery

This RFS solicited for proposals from qualified individuals or groups to develop a standardized 

analytical approach for synthesizing the results and detecting the effects at the population and ESU 

levels of a myriad of hatchery reforms in terms of their effects on extinction risk and recovery at the 

population and Evolutionarily Significant Unit (ESU) levels, consistent with the purposes of Action 

184. Specifically the solicitation calls for studies to determine the efficacy of hatchery reforms in 

reducing extinction risks and/or contributing to recovery goals. RPA Action 184 calls for research to 

assess: (1) the efficacy of hatchery reforms in reducing extinction risk, and (2) the efficacy of 

conservation hatchery activities in contributing to recovery. This RFS is focused on the first of these 

two topics. The cost for a 9-month project to fulfill this RFS was estimated to be from $100,000 to 

$150,000. Two proposals were received in response to this RFS. 

The ISRP was surprised at the content and approach of these two proposals, and that there were only 

two proposals received. We wonder if the short timeline on the call worked against both broader 

response and more in-depth attempts to truly synthesize data at large scales. The RFS emphasized 

that latter point, yet neither proposal adequately addressed the issue of large-scale synthetic 
ISRP 2003-7 RME RFS Proposal Review

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analytical tools and approaches. However, the problem appears to be that what truly is needed is 

data. The ISRP pointed out the potential lack of data in our preliminary review of the requests for 

studies and both proposals confirm our evaluation. We can recommend proposal #10 for 

development of an evaluation model based on expert opinion (specific review comments included 

below) as a stopgap measure in the short term. In the long term, only collection of better monitoring 

data as proposed in some of the other proposals in this solicitation, and as will be identified in the 

course of development of an expert system, will allow detection of the effects at the population and 

ESU levels of a myriad of hatchery reforms in terms of their effects on extinction risk and/or 

recovery.

Proposal 10: A Tool for Evaluating Risks and Benefits of Reform Actions in Hatchery 

Programs (WDFW)

ISRP Recommendation: 

Fundable at low priority subject to addressing minor criticisms below. 

We can recommend proposal #10 for development of an evaluation model based on expert opinion 

as a stopgap measure in the short term. In the long run, only collection of better monitoring data as 

proposed in some of the other proposals to satisfy RPA Actions #184 and #182, and as will be 

identified in the course of development of an expert system, will allow detection of the effects at the 

population and ESU levels of a myriad of hatchery reforms in terms of their effects on extinction 

risk and/or recovery. Overall, the proposal is weak in directly addressing needs described in the 

RFS.

Direct answers to RFS questions.

· Would the study result in the development of a standardized analytical approach for 

synthesizing the results and detecting the effects at the population and ESU levels of a 

myriad of hatchery reforms in terms of their effects on extinction risk and/or recovery?

The proposed approach is standardized but derived data will be mainly qualitative 

(subjectively determined by expert opinion) and in this sense, not strictly quantitative and 

analytical. The ability to apply the approach to a given hatchery and hence compare the 

different hatchery reforms in terms of effects on extinction risk and/or recovery at the 

population or ESU levels will vary with the data available. Fewer data means more reliance 

on expert opinion. 

· Will the study provide documentation and/or explanatory text for the analytical approach 

sufficient to allow other entities to readily use it to evaluate potential effectiveness of 

hatchery reform measures?

Yes and no. Others will be able to use the method, but use will depend on the availability of 

data and experts. It is likely that the work would provide documentation and explana tory text 

sufficient to support use by others, as the main players in the proposed effort have a track 

record of making information and approaches available to others. However, the outcome will 

be an expert system subject to continuous restructuring as new empirical information comes 

available or it would simply freeze today’s admittedly inadequate information as to outcomes 

of new approaches (reform). This would seem to make the project continuing, rather than a 
ISRP 2003-7 RME RFS Proposal Review

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nine-month project with a clear useful end-product. The funding agency should carefully 

consider whether or not they wish to start what may turn out to be a 10-12 year project.

Primary Review Comments and Questions for Improvement of the Proposal

The authors recognize that, too few data are available to provide case-specific assessments. They 

propose an expert system approach that can use whatever data exist from ongoing processes, such as 

HGMPs, the APRE databases, and EDT analyses, to qualitatively assess risks and benefits. We agree 

that an expert system such as proposed is probably the only way to provide qualitative risk 

assessments of hatchery practices. The alternative is to wait 10-12 years for the completion of 

rigorous studies on the reproductive success of hatchery and wild fish to obtain more quantitative 

assessments.

The proposed approach is founded on the principles of probabilistic risk assessment and attempts to 

estimate risk as a function of the subjective probability that different events might occur and their 

possible consequences. The principal investigators propose to use “expert opinion” to derive lists of 

hazards, weighting factors for hazards, variables contributing to risk, and distributions of potential 

consequences. However, the proposal continues to use the term “risk” in other ways. To further 

confuse the terminology, it uses “hazards” interchangeably with “risks”. It refers to “risk-benefit” 

analysis without explicitly addressing benefits. These issues and definitions should be addressed and 

made clear before the project is funded.

It is an act of faith to assume that a consensus model based on expert opinion will in fact be a good 

model. The proposal should include methods for evaluating the quality of the resulting consensus 

model before funding. An itemized budget should be provided.

Proposal 13: Analytical Approach for Determination of Effects of Hatchery Reform on 

Extinction Risk and Recovery of Salmon and Steelhead (CRITFC)

ISRP Recommendation: Not Fundable. Unfortunately, the region lacks the data needed to 

successfully implement this project. The work would seem to require information that could only be 

gathered with a longer-term and larger-scale study than is described or that fits the 9-month 

timeframe specified in the RFS. 

Direct answers to RFS questions.

· Would the study result in the development of a standardized analytical approach for 

synthesizing the results and detecting the effects at the population and ESU levels of a 

myriad of hatchery reforms in terms of their effects on extinction risk and/or recovery?

Unfortunately no, because of the region lacks adequate data. 

· Will the study provide documentation and/or explanatory text for the analytical approach 

sufficient to allow other entities to readily use it to evaluate potential effectiveness of 

hatchery reform measures? 

 Unfortunately no, because the region lacks adequate data. 
ISRP 2003-7 RME RFS Proposal Review

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Primary Review Comments and Questions for Improvement of the Proposal

The proposal should have a more clear and definite statement of tasks and methods to accomplish 

the tasks and objectives.

This proposal would take a synthetic approach to assessing the effect of hatchery reforms on risks 

for wild salmonids. It provides an extensive literature review of the issues related to reproductive 

success, artificial propagation, conservation goals, risks of hatchery operations, and biological 

impairment from hatchery wild interbreeding. The idea is to link hatchery practices with variation in 

traits that determine fitness. The idea of developing a statistical framework to assess these linkages 

and to use this framework to guide hatchery practices seems like a good one. Unfortunately, 

empirical work and data would need to be greatly expanded to relate the proposed genetic approach 

to indexing outcomes of hatchery practices to an assessment of risk at the population or ESA level.

The proposal fails to provide convincing linkage of the small-scale and local measures that will be 

taken to population- or ESA-level demographic responses. The proposal assumes that simple gene 

expression, as indexed with arbitrary microarray analyses, will translate simply into population-level 

fitness and thus can be used to assess risk resulting from hatchery protocols. This is an untested 

assertion and cannot be assumed to be correct. The proposal needs a strong way to test this 

assumption.

The short section on their statistical model was unclear on what dependent variables are to be 

modeled, what independent variables are to be included, and where the data will come from. 

Examples of the computation conducted on an example using real data (or hypothetical data) would 

have been helpful. 

FCRPS BiOp RPA Action#184: Reproductive Success of Natural-Origin, 

Hatchery-Origin, and Reconditioned Kelt Steelhead

Background

This RFS solicited for a study of the relative reproductive success of reconditioned steelhead kelts to 

provide information critical for evaluating the potential benefits of enhancing iteroparity. 

Specifically, the study would determine the relative reproductive success of reconditioned steelhead 

kelts spawning in the wild compared to natural-origin adults, hatchery-origin adults, and cross 

matings of these three variants, in one or more populations. The study should be directly applicable 

to one or more of the following listed ESUs: Upper Columbia, Mid-Columbia, and Snake River 

steelhead. The cost for a study at the general desired level of effort was estimated at $400,000 to 

$650,000 per year. 

ISRP General Recommendation

If any of these proposals are funded they need to address all the questions posed in the RFS. In their 

present forms, none of the four proposals adequately addressed all the questions posed in the RFS. 

In the group of proposals, several points are blurred together. With regard to reproductive success of

kelts, reviewers and proposers seem concerned about the genetic fitness issues associated with reintroducing the iteroparous life history trait back into the natural populations. The tool suggested for 

these studies is DNA pedigree analysis using microsatellite DNA or microarray DNA so that the 
ISRP 2003-7 RME RFS Proposal Review

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reproductive success of kelts, hatchery, and wild fish can be compared in the next generation. These 

are tools that identify genetic differences between individuals. It is unclear in these studies whether 

the analysis is intended to simply be a means to study the relative reproductive success or is it also 

intended to imply genetic changes in the population (i.e., long-term changes in the genetic fitness of 

the population)?

There are three aspects of kelt reconditioning that merit study:

1) The physiological reconditioning of the fish and the quality of the gametes produced (egg 

number, size, quality) and the timing of maturity (is it coincident with the wild?) ...i.e., the 

phenotypic expression of maturity

2) Whether there are genotype x environment interactions in the reconditioning of kelts that 

may lead to a non-random contribution of genetic material in the next generation? ... this 

may occur also in Nature (are certain genotypes more likely to be repeat spawners) or may 

reflect the “domestication” concerns resulting from reconditioning in an artificial 

environment.

3) What are the longer term genetic effects of re-introducing repeat spawning into depressed 

populations ... is the demographic boost balanced by changes in the genetically effective 

population size?

One proposal (RFS# 009) considers point one only (described as phase 1), one is primarily a 

methods proposal (RFS# 005) that could actually allow future research to more fully define 

“genotypes” and consideration of points two and three, and two of the proposals (RFS# 004, 014) 

use genetic analyses to compare spawning success of kelts, hatchery, and wild fish. 

Unfortunately, what is not explicitly discussed in any of the proposals is that variation in spawning 

success could be explained due to point 1 and/or could have a genetic component (i.e., aspects of 

points 2 and 3). An important point to consider is that variation in reproductive success (even 

measured to the adult stage) is not adequate evidence of differences in reproductive fitness – in the 

true genetic sense. None of the proposals explicitly and adequately discussed issues of genetic risk 

in the populations that are to be augmented by the introduction of kelts. It is unfortunate that we do 

not see a more thoughtful consideration of these points in any of the proposals. 

With respect to assessing fitness effects, there are three points to consider further:

1. Measuring immediate spawning success is not a sufficient assessment of reproductive fitness 

of kelts.

2. Assessing reproductive fitness and genetic effects of this life history trait is inherently long 

term and will not be answered in the next 3-5 years. It will require much longer 

commitments and funding to answer this question. 

3. At present, we may not have adequate genetic tools to study the genetic basis of this trait. 

An assessment of the genetic risk associated with kelt reconditioning could generated by monitoring 

the pedigree of steelhead that become successfully reconditioned spawners, and whether they 

represent a subset of the lineages in a population or are a random sample of the population (a test of 

point 2). But other than a genetic basis for differential success of certain kelts, what other genetic 

concerns would there be? Remember that a kelt has already been successful to the extent that it 
ISRP 2003-7 RME RFS Proposal Review

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survived to maturity and spawned, most are female so that successful mating is very likely 

(assuming that the timing is correct and eggs are viable), and spawning likely occurs after 1 to 2 

years of conditioning and should avoid mating with immediate siblings etc.

Proposal 4: Reproductive Success of Natural-Origin, Endemic Hatchery Origin, and 

Reconditioned Kelt Summer Steelhead in the Tucannon River (WDFW) 

ESU: Snake River Steelhead

ISRP Recommendation: Fundable at medium priority, contingent on adequate response to 

unaddressed RFS questions and ISRP concerns. Many of the RFS questions were not addressed. 

Priority for the project would be higher if a smolt trap was available for this project, and evidence 

existed that the process of reconditioning kelts had been successfully undertaken.

ISRP Review Comments: 

The Tucannon situation is directly applicable to a listed ESU and presents an important opportunity 

for satisfying the requirements of the RFP even given the difficult sampling problem of finding 

offspring of wild fish with which to estimate reproductive success. The project geneticist is well 

qualified. However, the questions about genetic consequences in the RFP aren’t addressed in the 

proposal. The proposal does not describe a plan to answer the questions or address the potential 

long-term genetic risk of kelt reconditioning. A smolt trap would be a better approach, although they 

are already likely getting some of their sampling with ongoing monitoring via electrofishing. 

The proposal is not thoroughly written, is a bit disorganized, and seems to place little emphasis on 

examining possible risks of kelt reconditioning. “After spawning, fish will be PIT tagged for unique 

identification and transported to a 20’ circular rearing tank at LFH, and the reconditioning process 

will begin.” Shouldn’t the fish be marked and identified earlier so that fitness of their offspring 

reared in the hatchery can be compare to the offspring produced from the reconditioned adults? 

Maybe they are doing this but it is not clear. Will each individual female be incubated separately at 

LFH the first year so that results can be compared to results after reconditioning.

Are tissue samples needed from both the juveniles (Task 2b) and smolts (Task 2c- costs are not 

included because the trap is proposed in another study and may or may not be funded) if the smolt 

trap is funded. Which is best?

“Task 2d. Collect DNA tissues from all natural origin returning adults at the TFH adult trap from 

study year fish to conduct pedigree analysis from adult to adult.” Shouldn’t they also collect DNA 

tissues from hatchery produced adults that are allowed to spawn naturally? 

Following fitness of the various crosses to F2 and F3 is not mentioned. Are control streams needed 

to follow fitness over time without hatchery and reconditioned steelhead?

RFS Review Criteria: 

• Will the study determine the relative reproductive success of reconditioned steelhead kelts 

spawning in the wild compared to natural-origin adults, hatchery-origin adults, and cross 

matings of these three variants, in one or more populations?

Yes, in the Tucannon River population of steelhead, if successful in each of several components—

reconditioning kelts, sampling offspring successfully (will a representative sample of natural-origin 

parr be obtained from eight ‘Index Sites’ in the Tucannon R? How will additional sites be chosen? 
ISRP 2003-7 RME RFS Proposal Review

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The proposal is a bit vague. For example, on whether or not funds have been inc luded for DNA 

tissue analysis from the parents of the hatchery origin adults – or, is this a good idea? 

• Does the proposal employ the use of microsatellite DNA analysis in order to ascertain the 

pedigree of resulting progeny and subsequent returning adult steelhead. If not does the method 

proposed provide quantification of reproductive success of equal of better power than 

microsatellite DNA analysis?

Yes 

• Does the study include analysis of the potential genetic consequences of repeat-spawning 

steelhead on small populations?

Not included in this proposal. 

Other research topics, which should be addressed in the proposed study if possible, include: 

• How increasing iteroparity might increase inbreeding in the target population, 

particularly if it is small?

Not in the proposal. 

• How reconditioning kelts might increase domestication selection in the target 

population? 

Not addressed well in the proposal. 

• How the reconditioning program might alter age structure and life history structure in 

the target population. 

Not addressed well in the proposal. 

• Does the research site(s) offer the ability to capture and sample sufficient outmigrating offspring 

and all, or nearly all, returning adult steelhead. 

Yes for adults, but not for outmigrating smolts unless the smolt trap is funded in a chinook study. 

Electrofishing for juveniles might not give adequate sample size and might not be completed. Smolt 

monitoring might be less than ideal unless a new trap is installed. 

• Is the proposed study directly applicable to one or more of the following listed ESUs: Upper 

Columbia, Mid-Columbia, and Snake River steelhead.

Yes. 

• Cost-effectiveness (e.g., the ability to take advantage of existing fish production, research, 

monitoring or evaluation activities) will be an important consideration in the proposal selection 

process. 

Potentially highly efficient by adding marginal effort to other projects. Budget seems sketchy but 

suggests large effort devoted here. ~$140K (only adult sampling and without juvenile sampling) and 

~$260K (with juvenile sampling) seems reasonable. Would the $140K include funds for sampling 

smolts if the smolt trap is approved? 
ISRP 2003-7 RME RFS Proposal Review

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Proposal 5: Assessment of the Reproductive Success of Reconditioned Kelt 

Steelhead with DNA Microarray Technology (Battelle) 

ESU: Mid-Columbia River Steelhead

ISRP Recommendation: Do not fund. No revision requested. This is not tied directly enough to the 

Kelt RFS. 

The ISRP notes however that this is a very well written and technically qualified proposal that may 

produce an important technique (microarray analysis) in the genetic studies of steelhead and other 

fishes. The proposal did outline an interaction with the kelt reconditioning study in the Yakima 

basin, included a proof of principle of this technique by comparing it directly with DNA microsatellite studies, and a goal to transfer this technology to regional laboratories. New tools that could 

allow researchers to more finely resolve genetic variation between individuals and populations will 

continue to be important, but this tool may not be necessary or available in the timeframe to address 

these RPA issues associated with reproductive success. 

RFS Review Criteria: 

• Will the study determine the relative reproductive success of reconditioned steelhead kelts 

spawning in the wild compared to natural-origin adults, hatchery-origin adults, and cross 

matings of these three variants, in one or more populations?

Yes, but measurement of the fitness of the various groups is not discussed in detail. 

• Does the proposal employ the use of microsatellite DNA analysis in order to ascertain the 

pedigree of resulting progeny and subsequent returning adult steelhead. If not does the method 

proposed provide quantification of reproductive success of equal of better power than 

microsatellite DNA analysis?

They propose to further develop and test DNA Microarray Technology. Are these the same? Is the 

DNA microarray technology needed? 

• Does the study include analysis of the potential genetic consequences of repeat-spawning 

steelhead on small populations?

Not explicitly, although perhaps implied by cooperation with the Yakima Fisheries Projects.

Other research topics, which should be addressed in the proposed study if possible, include: 

• How increasing iteroparity might increase inbreeding in the target population, 

particularly if it is small?

Not explicitly, although perhaps implied by cooperation with the Yakima Fisheries Projects.

• How reconditioning kelts might increase domestication selection in the target 

population? 

Not explicitly, although perhaps implied by cooperation with the Yakima Fisheries Projects.

• How the reconditioning program might alter age structure and life history structure in 

the target population. 

Not explicitly, although perhaps implied by cooperation with the Yakima Fisheries Projects.
ISRP 2003-7 RME RFS Proposal Review

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• Does the research site(s) offer the ability to capture and sample sufficient outmigrating offspring 

and all, or nearly all, returning adult steelhead. 

Not explicitly, although perhaps implied by cooperation with the Yakima Fisheries Projects.

• Is the proposed study directly applicable to one or more of the following listed ESUs: Upper 

Columbia, Mid-Columbia, and Snake River steelhead. 

Marginally. 

Cost-effectiveness (e.g., the ability to take advantage of existing fish production, research, 

monitoring or evaluation activities) will be an important consideration in the proposal selection 

process. 

No. At $462k/year over 4 years or $1.848 million total it is on the top end. 

Proposal 9: An Evaluation of the Efficacy of Steelhead Kelt Reconditioning to 

Address Biological Opinion Action 184b: The Reproductive Success of HatcheryOrigin and Wild-Origin Repeat Spawners (USGS) 

ESU: Lower Columbia River Steelhead

ISRP Recommendation: Qualified fundable for phase 1, contingent on adequate response to 

unaddressed RFS questions and ISRP concerns. This proposal is of the lowest priority of the three 

reconditioning (#4, #9, and #14) proposals because it does not have as direct application to the 

ESUs. 

A strength of this proposal is that it looks at the early lifestage of the steelhead. They are proposing 

in Phase I to see if kelts can be reconditioned and produce offspring approximately equal to a virgin 

spawner in a controlled environment. Phase II will only be conducted if Phase I is successful. 

Methods for design or analysis of Phase II are not given. The very brief discussion of work to 

potentially follow Phase I and II may be the most unique part of the study, namely comparison of the 

reproductive viability of gametes and progeny from reconditioned spawners (i.e., those retained in a 

hatchery environment) relative to naturally returning repeat spawners. Reviewers also assessed a 

lower rank to this investigation as it may not constitute an adequate test of gamete viability when 

tested only within the controlled environments. Reproductive success may be as much a function of 

spawning behavior, synchrony of gamete development, and local stresses, which cannot be naturally 

controlled in the laboratory environment. 

Following fitness of the various crosses to F2 and F3 is not mentioned. Are control streams needed 

to follow fitness over time without hatchery and reconditioned steelhead?

Why pool milt—is intent to examine variability of potency? H s W?

RFS Review Criteria: 

• Will the study determine the relative reproductive success of reconditioned steelhead kelts 

spawning in the wild compared to natural-origin adults, hatchery-origin adults, and cross 

matings of these three variants, in one or more populations? 

Yes, if Phase I to recondition kelts seems to be working. Directly studies components of fertility of 

reconditioned kelts; studies reproductive success as well at maturity of offspring. 
ISRP 2003-7 RME RFS Proposal Review

11

• Does the proposal employ the use of microsatellite DNA analysis in order to ascertain the 

pedigree of resulting progeny and subsequent returning adult steelhead. If not does the method 

proposed provide quantification of reproductive success of equal of better power than 

microsatellite DNA analysis? 

Yes. 

• Does the study include analysis of the potential genetic consequences of repeat-spawning 

steelhead on small populations?

No. 

Other research topics, which should be addressed in the proposed study if possible, include: 

• How increasing iteroparity might increase inbreeding in the target population, 

particularly if it is small?

No. It describes effect qualitatively, doesn’t propose to study immediately.

• How reconditioning kelts might increase domestication selection in the target 

population? And

• How the reconditioning program might alter age structure and life history structure in 

the target population. 

No. 

• Does the research site(s) offer the ability to capture and sample sufficient outmigrating offspring 

and all, or nearly all, returning adult steelhead. 

Yes, apparently. 

• Is the proposed study directly applicable to one or more of the following listed ESUs: Upper 

Columbia, Mid-Columbia, and Snake River steelhead. 

No 

• Cost-effectiveness (e.g., the ability to take advantage of existing fish production, research, 

monitoring or evaluation activities) will be an important consideration in the proposal selection 

process.

Yes, at ~$160 to $300 the budget is in line with others. 

Proposal 14: Proposal to Evaluate Reproductive Success of Natural-Origin, 

Hatchery-Origin, and Kelt Steelhead in the Columbia River Basin (CRITFC)

ESU: Multiple candidate ESUs

ISRP Recommendation: Fundable, contingent on adequate response to unaddressed RFS questions 

and ISRP concerns. This proposal received the highest ranking of the four proposals submitted for 

the RFS because it offers the most comprehensive application to the priority ESUs listed in the RFS. 

However, the proposal needs to be scaled back. 

They propose to apply kelt reconditioning methods developed by project 2000-017 with geographic 

replication for evaluation of fitness of various crosses across all ESUs of interest in the Request for 

Studies. Replication over space is highly desirable, however it is unclear if they are replicating each 

stream in time. They mention following the 2004 spawning class for reproductive success, but what 
ISRP 2003-7 RME RFS Proposal Review

12

about 2005 and beyond. Resident trout are included, a study component mentioned in many of the 

proposals.

The theoretical risk associated with the kelt reconditioning projects is of increasing inbreeding by 

using the reconditioned kelts in a small population. The implicit argument is a demographic boost is 

needed to a greater extent than the potential risk of inbreeding depression. The CRITFC kelt 

proposals seem be overly optimistic about the potential benefits of kelt reconditioning. The streams 

chosen are primarily upstream of many dams and will likely need to be continually propped up as 

the kelts will likely not naturally be successful given the migratory conditions. This proposal would 

start a fairly aggressive program before the benefits and risks are determined. The proposal seems to 

place little emphasis on examining possible risks of kelt reconditioning. Consequently, we 

recommend that the number of streams need to be scaled-back to less than five to reflect the fact that 

this a research project. This seems to be an effort to drastically expand the implementation of kelt 

reconditioning, without first evaluating the possible undesirable consequences, as called for in the 

RFP. 

Following fitness of the various crosses to F2 and F3 is not mentioned. Are control streams needed 

to follow fitness over time without hatchery and reconditioned steelhead? The study should pay 

more attention to gamete quality. Where are the controls in the study?

RFS Review Criteria: 

• Will the study determine the relative reproductive success of reconditioned steelhead kelts 

spawning in the wild compared to natural-origin adults, hatchery-origin adults, and cross 

matings of these three variants, in one or more populations?

Yes, with replications. Cross matings are not mentioned, but we assume they would be studied. 

• Does the proposal employ the use of microsatellite DNA analysis in order to ascertain the 

pedigree of resulting progeny and subsequent returning adult steelhead. If not does the method 

proposed provide quantification of reproductive success of equal of better power than 

microsatellite DNA analysis?

Yes. 

• Does the study include analysis of the potential genetic consequences of repeat-spawning 

steelhead on small populations?

No. Not specifically addressed.

Other research topics, which should be addressed in the proposed study if possible, include: 

• How increasing iteroparity might increase inbreeding in the target population, 

particularly if it is small? 

Not specifically addressed.

• How reconditioning kelts might increase domestication selection in the target 

population? And

Not specifically addressed. 

• How the reconditioning program might alter age structure and life history structure in 

the target population.

Not specifically addressed.
ISRP 2003-7 RME RFS Proposal Review

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• Does the research site(s) offer the ability to capture and sample sufficient outmigrating offspring 

and all, or nearly all, returning adult steelhead.

This is a criterion for site selection.

• Is the proposed study directly applicable to one or more of the following listed ESUs: Upper 

Columbia, Mid-Columbia, and Snake River steelhead. 

Yes, in all three.

• Cost-effectiveness (e.g., the ability to take advantage of existing fish production, research, 

monitoring or evaluation activities) will be an important consideration in the proposal selection 

process.

No, at ~$1,017K for year one, this is one of the more expensive proposals. However, the study allows for 

replication in 5 streams, or about $200K per stream, the standard budget.

Action 182: Studies to Determine Reproductive Success of Hatchery 

Spawners

Background

This RFS sought proposals from qualified individuals or groups to conduct scientifically sound 

studies that focus on the biological question(s) to determine relative reproductive success of naturalorigin and wild-spawning hatchery-origin anadromous salmonids in the Columbia Basin. Studies 

must be designed to directly estimate the reproductive success of both hatchery-origin and naturalorigin fish spawning naturally in the same population. These studies are needed to address scientific 

uncertainties outlined in Reasonable and Prudent Alternative (RPA) Action 182. Determining the 

reproductive success of natural-origin and hatchery-origin fish addresses critical uncertainties 

regarding population status assessment and recovery planning. 

The RFS sought studies directly applicable to one or more of the following listed ESUs (for which 

there are currently no reproductive success studies underway): Upper Columbia steelhead, MidColumbia steelhead, Snake River fall chinook, and Columbia River chum. Proposals were received 

for all of those listed ESUs except Upper Columbia steelhead. Studies not occurring in those ESUs, 

but with clear applicability to those ESUs will also be considered. Several studies with general 

applicability to steelhead and spring/summer chinook were received. Cost for a reproductive 

effectiveness study at the general desired level of effort was anticipated to be $200,000 to $300,000 

per year. Implementation of four studies was the intent of this solicitation, but this number could 

vary, based on the final negotiated costs of the selected proposals. Nine proposals were received 

addressing this RFS.

ISRP General Comments on the Request for Studies for RPA 182 

The RME group has not clearly differentiated the contribution that reproductive success evaluations 

of hatchery-origin and natural-origin salmon and steelhead when spawning naturally make to 

fulfilling RPA 182 vs. 184. Based on the background documents, the ISRP’s understanding is that 

RPA 182 addresses the problem of calculating lambda for BiOp check-ins in 2005 and 2008 for 

populations composed of both hatchery- and natural-origin adults. As the reproductive success of 

the hatchery-origin adults increases, the ESA status of the population may deteriorate because the 

population is being supported (replaced?) by hatchery fish. In the RFS for 182 the RME group gives 

priority to state-of-the-art hatchery programs. It is not clear why this should be a priority. The ISRP 
ISRP 2003-7 RME RFS Proposal Review

14

believes an important priority should be conducting these assessments with those ESUs and 

populations where hatchery strays are perceived to be a problem for the ESA assessments. In 

evaluation of these proposals for funding, the ISRP recommends that the funding agencies consider 

those that test the reproductive success of hatchery-origin adults that are creating the uncertainty, not 

necessarily selecting a subset of the state-of-the-art artificial production programs within the basin. 

Parts of the RFS and some of the projects read more like they are evaluating whether hatchery fish 

can make a contribution to recovery. This is covered under RPA 184. The reproductive success 

evaluations can make meaningful contributions to both of these RPAs.

These issues need to be considered in deciding which projects are likely to provide the information 

required to fulfill the RPA 182 and 184 uncertainties. As examples, Proposal 1, an investigation of 

the reproductive success of hatchery-origin adults in the Deschutes River Basin, does not evaluate 

"state-of-the-art" fish culture operations. However, it is evaluating hatchery-origin adult strays from 

variable unknown sources that create the dilemma for the ESA calculations of lambda. Other 

projects are evaluating hatchery-origin adults that are part of reintroduction programs. These 

projects appear directed at the question of what contribution hatchery-origin adults can make to 

recovery, rather than developing the data to adjust the calculation of lambda.

Comments Applicable to the Set of Proposals

For the entire suite of projects to fulfill the RPA, the ISRP believes that it is necessary to consider 

whether the "natural" fish inhabiting an assessment stream are representative of "wild" fish. The 

ISRP is concerned about interpreting studies where the extant population has a long history potential 

interbreeding with hatchery fish. Has the hatchery component been a part of the population for so 

long that there is little difference between the hatchery and wild? Assessments of reproductive 

success in control or reference streams with little past hatchery influence may be helpful in sorting 

out the effects of past interbreeding between hatchery and natural fish. A related issue is that 

principal investigators of proposals in this section should address how the results will be interpreted 

if the progeny of HxH, HxW, and WxW crosses have equal fitness in the F2 and F3 generation. 

That is, should one conclude that the genetics of the WxW crosses are so similar to the hatchery 

crosses that no difference in fitness can be determined, or should one conclude that supplementation 

and/or straying is working perfectly? It is not clear to the ISRP that available data will be able to 

distinguish between these two conclusions. That is, is it enough just to compare fitness of HxW and 

HxH crosses with fitness of WxW in the same stream when the fitness of the WxW may be changing 

because of the supplementation or straying? We note that this question should be asked of all 

proposals submitted in response to the RFS covering RPA #182.

A general weakness of the proposals is that most do not include “control” streams or reaches where 

only WxW crosses are allowed and fitness compare to the HxH, HxW, and WxW crosses in the 

treatment streams. Funding priority should be given to those proposals that are likely to yield 

meaningful comparisons with “control/reference” conditions.

The RFS requested that proposals address the likely effect of any difference in reproductive success 

of hatchery and wild fish, in terms of population growth, population recovery, and genetic 

diversity/fitness in subsequent generations according to the Viable Salmonid Population (VSP) 

criteria. Control streams or some other means of assessing effects of out of basin factors on 

population growth rate and other demographic parameters would be crucial in determining the 

robustness of inferences about population-level impacts. 
ISRP 2003-7 RME RFS Proposal Review

15

In general the proposals do not do a good job of assessing the potential effects of resident trout on 

the results of the steelhead studies. How will the principal investigators evaluate differences in 

reproductive success of the various crosses if there is substantial interaction and interbreeding with 

resident trout?

Finally, there are significant data management issues involved in genetic testing, in the sampling 

protocols, and in the sheer magnitude of data to keep track of in these proposals. Without adequate 

quality assurance and control, researchers could make subjective decisions that could substantially 

affect their outcomes. Thus, quality assurances and control plans should be built into the proposals. 

Addressing QA/QC should involve plans regionally as well as for individual projects.

Proposal 8: Evaluating the Reproductive Success of Natural- and Hatchery-Origin 

Columbia River Chum Salmon (WDFW)

ESU: Columbia River Chum

ISRP Recommendation: Fundable contingent on an adequate response to ISRP questions and 

comments. This proposal is a technically sound investigation, in a “semi controlled spawning 

habitat” mesocosm, of reproductive success of hatchery-bred and natural origin chum salmon from 

the Grays River. It will enable researchers to study in detail morphological and behavioral 

components of fitness of spawning chum salmon and potentially to understand related differences of 

reproductive success, measured at both fry and adult life stages, between hatchery-origin and 

natural-origin spawners. The origins of individual parents of the first filial generation would be 

identifiable from dissected otoliths after spawning and they would be associated with their offspring 

by their msDNA genotypes. The lineages of later generations would be identifiable by msDNA 

parentage analysis. It is not clear to reviewers why a direct study of reproductive success in the 

Gray’s River or a weir-controlled tributary of the River would not be more directly applicable to 

questions about the relative fitness of hatchery-origin chum salmon and of their offspring. Will 

salmon in a gravel-filled trough exhibit the same array of behaviors that they would in their native 

habitat? Would a direct study be infeasible? 

The proposers report that first-generation returns to the supplementation hatchery on the Grays River 

last year (2002?) may have comprised the largest spawning population ever observed in the river but 

that otoliths recovered from spent fish have not been examined and it is not known whether salmon 

produced by the hatchery contributed substantially to the spawning population. What proportion of 

Grays River spawners in 2002 were produced by the hatchery? (Surely a small sample of otoliths 

could readily be examined.)

Assuming that a substantial portion of the Grays River spawners will have been produced from the 

hatchery, the proposers establish the purpose of their research as discovering whether these hatchery 

origin spawners are reproductively successful, as successful as wild-origin fish. That is, the rationale 

for hatchery supplementation depends on the reproductive success of the hatchery-origin spawners 

without cost to the fitness of the natural-origin component of the population. They point out that the 

Grays River population is the only Columbia River population with a supplementation hatchery 

component, thus it offers the only opportunity for comparative study of reproductive success in 

hatchery- and natural-origin chum salmon. Reviewers ask whether a more appropriate reference 

would be the reproductive success of natural-origin chum salmon in the absence of hatchery-origin 

salmon; could research in a ‘semi controlled’ spawning habitat such as that proposed at Beaver 

Creek be designed to provide such a comparison? Could comparisons of reproductive success 

between hatchery-origin rich and natural-origin rich tributaries of the Grays River provide such 
ISRP 2003-7 RME RFS Proposal Review

16

comparisons? It concerns the ISRP that the proposed research in a ‘semi controlled’ habitat will not 

be able to control the proportion of hatchery origin (HOR) and natural origin (NOR) spawners 

except by choosing the tributary of the Grays River where the spawners are collected (Crazy 

Johnson Creek is believed to be rich in natural origin spawners, West Fork in hatchery origin 

spawners.) What evidence is there (if no otoliths have been examined) that this spawner-selection 

protocol will provide adequate experimental contrast between the lineages? Without control over the 

proportions of HOR- and NOR-spawners, will the proposed research detect any frequency-of-HORs 

effect on the reproductive success of HOR and NOR spawners?

The proposed research is expensive, but it is the only proposed research in the ESU.

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 – assuming that enough salmon survive to be counted and that adequate numbers of HO 

and NO parents are incorporated in the initial spawning.

• 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 – a strength of the proposed research is that behavioral and morphological components 

of reproductive success of individual spawners will be observed. 

• 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?

The project has the potential to address whether the population grows and how genetic 

diversity and fitness are affected by hatchery origin spawners, but the proposal does not 

address the question directly.

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;

Yes—it is the only proposed study of reproductive success in the Columbia River chum 

ESU.

• 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
ISRP 2003-7 RME RFS Proposal Review

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hatchery spawners persists in subsequent generations (beyond F2);

Yes 

• The degree to which proposals may provide information more broadly applicable to

multiple species/ESUs identified above;

More to the point— reproductive comparisons from smolt species may not be pertinent to 

chum, a fry-emigrating species, so it is arguably important to compare reproductive success 

in chum salmon.

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

Yes - the potential is here.

• Overall cost effectiveness

Highest cost of all the proposals in this set.

Proposal 7: Reproductive Success of Hatchery Spawners in the Chinook River, 

Washington (Sea Resources)

ESU: Lower Columbia River Coho

ISRP Recommendation: Fundable contingent on an adequate response to ISRP questions and 

comments. The research would compare reproductive success of hatchery-origin and natural-origin 

spawners that are both derived from a conventional hatchery program. Because it does not contrast 

reproductive success of hatchery and natural origin fish in one of the listed ESU's the proposed 

research would not strictly meet the criteria in the RFS. However, the questions the project would 

address are significant and address important uncertainties for listed ESU’s of other species. The 

results would be directly applicable to the Lower Columbia River Southwest Washington coho ESU 

which are a candidate for listing under the Endangered Species Act and which the recent report by 

the Biological Review Team categorized as endangered.

Models of how interbreeding with hatchery-origin fish may reduce fitness of natural-origin fish 

aren’t developed and the research isn’t proposed in context of such models. The hypotheses stated in 

objectives 2 and 3 are simplistic statistical hypotheses. Mechanistic hypotheses posing possible 

causal relationships would be more useful and more interesting. For example, what phenotypic traits 

would be expected from each type of cross, how would they affect fitness, and why would they be 

expected. If these kinds of hypotheses are not proposed, the applicants should explain why.

In objective 2 the applicants propose to estimate fry and parr survival. How would this be 

accomplished? If egg-fry survival is to be estimated, how will spawner density and egg production 

from each type of cross be determined? If the purpose is only to estimate fry produced by each type 

of cross (fry/spawner), the number of spawners must be determined. How will this determination be 

made?

“After the third year of the project, we will be able to assign parentage to the adults returning to the 

weir” –How will strays into the Chinook River be accounted for? Will there be substantial numbers 

of unidentifiable coho? Will they be prohibited from entering the River?
ISRP 2003-7 RME RFS Proposal Review

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In general the methods for several of the sub-objectives of objective three are not well explained. For 

example, how will heritability be estimated (objective a4), why is heritability an important 

parameter, how will objective a6 be accomplished, what are the direct and indirect methods 

proposed in objective a7? Objective 3, task a3 contains two different parts -- determining whether 

random mating occurs and determining whether the different crosses have offspring with similar 

survival rates. The two Parts of the objective should be dealt with separately. The methods for 

accomplishing objective a10, which apparently attempts to address evaluation criterion 3, need to be 

explained in far greater detail.

The methods call for collection and genotyping of “Approximately 2000 offspring produced by each 

set of potential parents”; the number of potential parents apparently numbers in the hundreds and the 

number of sets of parents would be very large, so this would be in aggregate an intractable task. 

Is this a suitable site for this study if the planned estuary restoration projects (e.g. removal of 

tidegates) are implemented? How would this impact the study design?

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

• 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 – there would be evaluations of reproductive success at several life stages.

• 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?

The project has the potential to address whether the population grows and how genetic 

diversity and fitness are affected by hatchery origin spawners, but the proposal does not 

address the question directly. 

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;
ISRP 2003-7 RME RFS Proposal Review

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No, but the results would be directly applicable to the Lower Columbia River Southwest 

Washington coho ESU which are a Candidate for listing under the Endangered Species Act 

and which the recent report by the Biological Review Team categorized as endangered and 

the project would address are significant and address important uncertainties for other listed 

ESU’s

• 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 could be extended.

• The degree to which proposals may provide information more broadly applicable to 

multiple species/ESUs identified above;

Yes, but the proposal does not respond explicitly to this question.

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

Yes – the project could commit to a long term study.

• Overall cost effectiveness

Relatively inexpensive compared to other proposed projects, benefits from collaboration of 

different groups and from other related projects.

Proposal 15: Natural Reproductive Success and Demographic Effects of HatcheryOrigin Steelhead in Abernathy Creek, Washington: Can Newly Developed, Native 

Broodstocks of Steelhead Derived from Captively-Reared Parr Potentially Contribute 

to Recovery of Naturally Spawning Populations? (USFWS)

ESU: Southwest Washington Steelhead

ISRP Recommendation: Fundable, contingent on an adequate response to the ISRP’s questions. 

The proposed research (favorably reviewed by ISRP after submission in three earlier contexts) 

would investigate a novel method for developing native broodstocks of steelhead as required by the 

NMFS BiOp on Artificial Propagation, i.e. rearing captured parr to maturity as a source of 

broodstock rather than taking eggs from mature native fish. Thus, even though the research is not 

directly on one of the listed ESU’s, its results will be directly applicable to recovery of listed 

steelhead. It is noteworthy that, unlike other research on the reproductive success of hatchery origin 

(HOR) and natural origin (NOR) salmon, in this study the productivity of natural origin fish will be 

observed in control streams, without the presence of hatchery origin fish; most of the other projects 

would compare reproductive success of natural origin and hatchery origin fish, but only in the 

presence of each other. The Deschutes River study, proposal 1, also has controls. 

Questions arising in the present review include one concerning the putatively native fish in 

Abernathy Creek—how influenced has this population been by hatchery production in the past, from 

other populations? Secondly—how will straying of steelhead into the control streams influence their 

comparison of productivity in the supplemented Abernathy Creek population to productivity in the 
ISRP 2003-7 RME RFS Proposal Review

20

control streams? Is there inter-breeding with resident trout and if so, how is it accounted for in the 

analyses?

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 

• 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 – the research would evaluate reproductive success, survival of offspring, during the 

freshwater phase of the life history, as smolts emigrating from Abernathy Creek, and as 

mature adults. Mechanistic hypotheses relating parentage of fish to survival at sequential life 

stages aren’t addressed explicitly in the proposal, but are implicit and will be susceptible to 

testing with the data gathered.

• 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?

The project has the potential to address whether the population grows and how genetic 

diversity and fitness are affected by hatchery origin spawners, but the proposal does not 

address the question directly.

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;

Yes – this study will not occur in a listed ESU but is designed to produce results applicable to 

listed ESU’s.

• 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 - study design will allow determination of whether statistically significant differences in 

reproductive success exist between NOR and HOR in generations beyond F1 (to F3). It 

contains a good selection of treatment and control sites. 

• The degree to which proposals may provide information more broadly applicable to 

multiple species/ESUs identified above;
ISRP 2003-7 RME RFS Proposal Review

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Yes - the rationale is that this is a model system for developing supplementation strategies 

for upper and mid Columbia steelhead. 

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

Yes 

• Overall cost effectiveness

The proposed research would build on and the requested funds would be leveraged by other 

ongoing work. Methods are well established and reliable.

Proposal 2: Evaluation of the Reproductive Success of Wild and Hatchery Steelhead 

in Natural and Hatchery Environments (UW)

ESU: Out of Basin Steelhead

ISRP Recommendation: Fundable, a high quality proposal, but it does not specifically address 

RPA 182 and some questions in the RFS. The study is investigating the natural spawning success of 

an imported, highly domesticated, steelhead stock and to that extent addresses questions posed by 

RPA 182. In Forks Creek a decision was made to exclude all future hatchery-origin adults access to 

the natural spawning grounds after they had access for two return years. Preliminary studies have 

examined the spawning by these hatchery-origin adults. The current request is to follow the 

trajectory of hatchery and hatchery x wild lines to examine their fate. Even though the situation is 

not an ideal model of a supplementation program, understanding the uncertainty addressed here is 

important for the basin. 

This study is different from most of the others because it is investigating pedigrees both inside and 

outside the hatchery. This adds a dimension that potentially could contribute to understanding the 

consequences of selection differences between the hatchery environment and the natural 

environment. It is a fascinating study, with considerable overarching policy implications from the 

results. It is less clear how the results will assist in parameterizing the extinction risk models used in 

recovery planning. 

Is there inter-breeding with resident trout and if so, how is it accounted for in the analyses?

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 

• 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?
ISRP 2003-7 RME RFS Proposal Review

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Yes

• 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?

Not easily - It is not clear how the results will assist in parameterizing the extinction risk 

models used in recovery planning because the hatchery origin fish in this study are not 

native, have inherently maladaptive life history traits in the receiving environment, and have 

been subject to artificial culture and selection. 

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 site and ESU fall outside of the Columbia basin – the studies conclusions would be 

applicable to situations in which the HO population is not native or locally adapted to the 

watershed of the hatchery of concern. 

• 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 degree to which proposals may provide information more broadly applicable to 

multiple species/ESUs identified above;

Yes

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

Yes

• Overall cost effectiveness

Good

Proposal 6: Relative Reproductive Success of Hatchery-Origin and Wild-Origin 

Steelhead Spawning Naturally in the Hood River (OSU)

ESU: Lower Columbia River Steelhead

ISRP Recommendation:
ISRP 2003-7 RME RFS Proposal Review

23

Fundable, high rank. If selected for funding the principal investigator should respond to the general 

ISRP comments in the contracting process. The ISRP ranks this proposal high even though it is not 

one of the priority ESUs. Preliminary data exist, the information is applicable to other locations, and 

useful results can be obtained on the fitness of F2 and F3 progeny relatively quickly. 

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, these questions can be answered by the proposed research. 

• 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, these questions can be answered by the proposed research. 

• 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?

Yes, this question can be answered by the proposed research. 

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 addresses the Lower Columbia River steelhead ESU and results should be 

applicable to the Mid-Columbia steelhead ESU, and other locations.

• 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 degree to which proposals may provide information more broadly applicable to 

multiple species/ESUs identified above;

Yes.

• Potential to commit to a long-term study (beyond F2); and
ISRP 2003-7 RME RFS Proposal Review

24

Yes.

• Overall cost effectiveness

At approximately $215K to $270K per year the costs seem to be in line with other proposals.

General comments and evaluation.

The study contrasts "state of the art" supplementation derived hatchery-origin adults and 

conventional hatchery-origin adults with natural-origin adults for both winter and summer runs. The 

study has considerable data already analyzed. The contrasts are sequential, not contemporaneous. 

The same stock in the same stream is being evaluated. Reproductive success of the entire population 

over several generations is possible because of sampling at Powerdale Dam. There will be direct 

estimates of reproductive contribution.

This study will evaluate reproductive performance of all the potential parents to a steelhead 

population over nearly two decades. The selection of loci is finished and preliminary analyses from 

selected years are included in the proposal. The project uses one of the better managed and 

monitored supplementation projects. Since this is a retrospective reconstruction of two decades of 

pedigrees the timeline to completion should be shorter than for those projects that must rely on 

future returns. 

The principal investigator should outline an approach for investigating possible causes of difference 

in reproductive success. The ISRP notes that the cause of differences will not be evaluated, nor will 

the analysis partition survival to different life-stages. 

Is there a possible “control” stream with only WxW crosses? 

The methods are a little vague, but the preliminary analyses have been conducted and the ISRP 

judges that this is probably not a problem. 

Is there inter-breeding with resident trout and if so, how is it accounted for in the analyses?

Proposal 1: Investigation of the Relative Reproductive Success of Hatchery and Wild 

Steelhead in the Deschutes River Basin (ODFW)

ESU: Mid-Columbia River Steelhead

ISRP Recommendation: Qualified fundable. The study should be implemented in phases (see below 

for recommendations) given adequate response to reviewer’s questions and comments. The study 

is important and addresses RPA 182, but does not directly address the requirements of the RFS. 

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?
ISRP 2003-7 RME RFS Proposal Review

25

The evaluation is designed to test for significant differences in reproductive success between 

natural-origin and hatchery-origin steelhead. The evaluation does not include a design to 

extend to the F2 adult returns, but could be easily modified to include F2 adult returns. 

• 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?

Two life-stages, egg-to-smolt and smolt-to-adult, will be evaluated along with contrasts of 

life-history characters between adjacent treatment and reference streams. The sponsors 

indicate they will estimate the heritability of life-history characters. This will be less 

informative than establishing phenotypic and genetic correlation's between "traits" and 

"fitness". 

• 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?

The study would contribute data important to parameterizing the extinction risk models used 

by NOAA-Fisheries.

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 Mid-Columbia steelhead.
ISRP 2003-7 RME RFS Proposal Review

26

• 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);

This is not included in the proposal but could be addressed.

• The degree to which proposals may provide information more broadly applicable to 

multiple species/ESUs identified above;

Good for steelhead above Bonneville.

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

Good. 

• Overall cost effectiveness.

Maybe a little on the expensive side, but there are more startup costs in this one. $400K the 

first year and $300 each year after does not seem to be too much out of line with the other 

proposals.

General comments and evaluation.

This well-written proposal addresses the potentially important problem of effects of hatchery 

straying on naturally spawning steelhead in the Deschutes subbasin. However, the primary 

weakness of this study is unknown implementation conditions in the two creeks. The applicants 

should first document the incidence of straying in each stream and the degree of genetic difference 

between naturally spawning adults and hatchery strays. Both streams appear to have had an 

extensive history of stray hatchery fish spawning with “wild” steelhead. If genetic introgression has 

been extensive the genetic makeup of “hatchery” strays and “wild” spawners may be similar, 

reducing the ability of the researchers to detect genetic differences between progeny of strays and 

“wild” fish. Also, the abundance of adults and juveniles should be evaluated because parentage 

assignments will be made on a sample of juveniles, and all adults once they start returning. It is not 

clear whether the abundance of juveniles will be sufficient to sample contributions from the 

spawning adults. Future funding should be contingent upon the results of the preliminary work. 

The project evaluates "stray" hatchery-origin adults spawning in the wild rather than individuals 

from "state of the art" hatchery programs and for this reason does not seem to directly respond to the 

requirements of the RFS. It does respond to RPA #182. The focus of the proposal is on assessing 

the effect of stray hatchery fish, period. It seems that the study plan should also somehow 

incorporate the local Round Butte or Warm Springs hatchery fish. As it stands, this study may do a 

great job of evaluating the consequences of hatchery strays, but ignores some of the large issues that 

need to be addressed.

This would be a fascinating study to see what would happen to fitness of later generations when you 

cut the hatchery strays off from the control stream. 
ISRP 2003-7 RME RFS Proposal Review

27

The experimental approach does not permit evaluating the "same stock in the same stream", since 

the strays are not necessarily from the same Mid-Columbia ESU and could change from year to year. 

Use of a “control” stream is a MAJOR plus for the study. Most of the proposals do not have 

adequate control streams in the study design. Bakeoven and Buck Hollow creeks are probably good 

choices because they are relative warm on the east side of the Deschutes and may represent extreme 

environmental conditions to which wild steelhead are adapted.

The principal investigator proposes to consider inter breeding with resident rainbows. The proposal 

does not carefully describe how the principal investigator would evaluate differences in reproductive 

success if they find large effects of resident fish (no testable hypotheses) but other proposals did not 

do that, either. 

Proposal 3: Pedigree Approach to Determine Reproductive Success of Natural and 

Hatchery Origin Spring/Summer Chinook Salmon Spawners in Johnson Creek, Idaho 

(NPT)

ESU: Snake River Spring/Summer Chinook

ISRP Recommendation:

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.
ISRP 2003-7 RME RFS Proposal Review

28

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 
ISRP 2003-7 RME RFS Proposal Review

29

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 outof-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 coinvestigator 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.
ISRP 2003-7 RME RFS Proposal Review

30

Proposal 11: Comparative Reproductive Success of Wild and Hatchery Origin 

Spring/Summer Chinook Salmon that Spawn Naturally in the Pahsimeroi and Upper 

Salmon Rivers (IDFG)

ESU: Snake River Spring/Summer Chinook

ISRP Recommendation: Fundable contingent upon adequate response to the ISRP’s questions and 

comments. This proposal is of low rank. The proposal is responsive to two of the three evaluation 

criteria posed in the RFS. It appears to duplicate other studies in this ESU. The ESU is not one of the 

four listed ESUs. The applicants are unsure as to whether their results will be applicable to the ESUs 

specified in the additional criteria in the RFS. The work will not extend beyond the F2 generation. 

The proposal should be strengthened by the addition of control streams. 

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

• 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?

The applicants propose to sample multiple juvenile life stages and the study has the potential 

to detect allelic and genotypic changes for juveniles. 

• 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?

No

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;

This is not one of the four priority ESUs listed in the RFS, but the work would have 

application to other spring/summer chinook populations. 
ISRP 2003-7 RME RFS Proposal Review

31

• 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);

The applicants did not propose to extend the study beyond the F2 generation.

• The degree to which proposals may provide information more broadly applicable to 

multiple species/ESUs identified above;

The applicants are unsure as to whether their results will be applicable to the ESUs specified 

in the additional criteria in the RFS.

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

The applicants did not propose to extend the study beyond the F2 generation.

• Overall cost effectiveness

The costs seem reasonable and are in line with other proposals

The applicants propose to compare reproductive success of wild and hatchery origin fish in two 

Idaho rivers. The work builds on research and data collection undertaken by the Idaho 

Supplementation Study.

The proposal is a least partially responsive to two of the three evaluation criteria posed in the RFS. 

As acknowledged by the applicants, the proposed work does not address possible causes for 

differences in reproductive success between hatchery and wild salmon. The proposal also does not 

address differences in demographic parameters recommended by VSP. The applicants are unsure as 

to whether their results will be applicable to the ESUs specified in the additional criteria of the RFS. 

Releases of hatchery adults will cease in 2007 and consequently the research will not assess effects 

beyond the F2 generation. The budget seems reasonable for the work proposed.

Adding “control” streams from the ISS to the study and extension to evaluate fitness of F2 and F3 

progeny would be beneficial. This study would add significant value to the interpretation of 

information from the ISS. Potential useful and unique results could be obtained, but the applicants 

did not emphasize the extra benefit that this project would add that the others do not have. Namely, 

what happens to the productivity of F2 and F3 progeny in wild by wild crosses after supplementation 

is stopped for both supplemented and control streams? That is, when supplementation is stopped, 

how does the reproduction (fitness) of WxW crosses compare with reproduction of WxW crosses on 

formerly supplemented streams at the F2 and F3 levels? 
ISRP 2003-7 RME RFS Proposal Review

32

Proposal 12: Evaluating the Relative Reproductive Success of Natural- and HatcheryOrigin Snake River Fall Chinook Spawners Upstream of Lower Granite Dam (WDFW)

ESU: Snake River Fall Chinook

ISRP Recommendation: Qualified funding of Phase 1, pending adequate revision. Genetic 

divergence should be demonstrated and the utility of the mixture analysis approach should be 

convincingly demonstrated. Do not fund Phase 2 at this point, pending successful demonstration of 

the approach. The applicants do not address evaluation criteria two and three in the RFS. This limits 

the utility and applicability of the research. The work is in a priority ESU and the project could be 

done in a relatively short time because the tissue samples are already collected. 

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

• 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?

No 

• 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?

No

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 thefollowing listed 

ESUs (for which there are currently no reproductive successstudies underway): Upper 

Columbia steelhead, Mid-Columbia steelhead; SnakeRiver fall chinook; and Columbia River 

chum. Studies not occurring in those ESUs, but with clear applicability to those ESUs will 

also be considered;

The Snake River fall chinook ESU is involved.

• 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);

No 
ISRP 2003-7 RME RFS Proposal Review

33

• The degree to which proposals may provide information more broadly applicable to 

multiple species/ESUs identified above;

The analytical approach could be applicable to other situations where a pedigree analysis is 

unsuitable. 

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

Yes

• Overall cost effectiveness

Costs are in line with other studies. 

The proposal is to conduct a pilot study to determine if genetic divergence among natural and 

hatchery origin Snake River fall Chinook salmon is sufficient to estimate differences in relative 

reproductive success. The proposal does not adequately address any of the evaluation criteria in the 

RFS. It is, however, the only proposal directed at Snake River fall Chinook.

The project evaluates the contribution of reproduction by state of the art hatchery production and 

"stray" hatchery-origin with natural-origin adults. The same stock (primarily) in the same river 

system is being contrasted. A mixture analysis, rather than a direct pedigree analysis, will be 

evaluated, because the sampling conditions preclude the direct pedigree approach. However, a more 

thorough explanation of why pedigree data cannot be collected is needed.

The proposal does not describe how the applicants will know if the observed genetic divergence is 

adequate to estimate differences in relative reproductive success. Based on the success of the pilot 

study, the applicants propose to estimate relative reproductive success of hatchery and natural origin 

spawners, but they do not provide any details as to how they will accomplish this estimation. Phase 2 

of the proposed work is dependent upon successfully finding genetic divergence and will continue

the as yet unexplained estimation of reproductive success from 2004 to 2008 for the F2 generation.

Not all of the important Columbia basin salmon ESU's will be amenable to a pedigree analysis 

because of logistical constraints on trapping adults and juveniles. This proposal approaches this 

difficult circumstance by exploring mixture analysis as an alternative (assignment of individuals to a 

group rather than to specific parents). Since the biological material (fin clips etc) is already 

collected for a retrospective reconstruction of the mixtures, an answer to whether or not the approach 

will be fruitful should not take long. On the basis that this is one of the more precariously situated 

ESU's, the analytical approach is worth pursuing, and the initial investigation will be retrospective.
ISRP 2003-7 RME RFS Proposal Review

34

Table of Proposals

Project ISRP Recommendation Page

Action 184: Synthesis of Existing Analytical Approaches, or Development of a New 

Analytical Approach, for Determining the Effects of Hatchery Reforms on Extinction 

Risk and Recovery

2

Proposal 10: A Tool for Evaluating Risks and Benefits 

of Reform Actions in Hatchery Programs (WDFW)

Fundable at low priority subject to addressing minor 

criticisms. 

3

Proposal 13: Analytical Approach for Determination 

of Effects of Hatchery Reform on Extinction Risk and 

Recovery of Salmon and Steelhead (CRITFC)

Not Fundable 4

Action 184: Reproductive Success of Natural-Origin, Hatchery-Origin, and 

Reconditioned Kelt Steelhead

5

Proposal 4: Reproductive Success of Natural-Origin, 

Endemic Hatchery Origin, and Reconditioned Kelt 

Summer Steelhead in the Tucannon River (WDFW)

Fundable at medium priority, contingent on adequate 

response to unaddressed RFS questions and ISRP 

concerns. RFS identified ESU -- Snake River Steelhead.

7

Proposal 5: Assessment of the Reproductive Success 

of Reconditioned Kelt Steelhead with DNA Microarray 

Technology (Battelle)

Do not fund. No revision requested. This is not tied 

directly enough to the Kelt RFS. 

9

Proposal 9: An Evaluation of the Efficacy of Steelhead 

Kelt Reconditioning to Address Biological Opinion 

Action 184b: The Reproductive Success of HatcheryOrigin and Wild-Origin Repeat Spawners (USGS)

Qualified fundable for phase 1, contingent on adequate 

response to unaddressed RFS questions and ISRP 

concerns. This proposal is of the lowest priority of the 

three reconditioning (#4, #9, and #14) proposals because 

it does not have as direct application to the ESUs. Lower 

Columbia River Steelhead

10

Proposal 14: Proposal to Evaluate Reproductive 

Success of Natural-Origin, Hatchery-Origin, and Kelt 

Steelhead in the Columbia River Basin (CRITFC)

Fundable, contingent on adequate response to 

unaddressed RFS questions and ISRP concerns. This 

proposal received the highest ranking of the four 

proposals submitted for the RFS because it offers the 

most comprehensive application to the priority ESUs 

listed in the RFS (Multiple Candidate Steelhead ESUs). 

However, the proposal needs to be scaled back. 

11
ISRP 2003-7 RME RFS Proposal Review

35

Project ISRP Recommendation Page

Action 182: Studies to Determine Reproductive Success of Hatchery Spawners 13

Proposal 8: Evaluating the Reproductive Success of 

Natural- and Hatchery-Origin Columbia River Chum 

Salmon (WDFW)

Fundable contingent on an adequate response to ISRP 

questions and comments. RFS identified ESU --

Columbia River Chum.

15

Proposal 7: Reproductive Success of Hatchery 

Spawners in the Chinook River, Washington (Sea 

Resources)

Fundable contingent on an adequate response to ISRP 

questions and comments. Not RFS identified ESU --

Lower Columbia River Coho.

17

Proposal 15: Natural Reproductive Success and 

Demographic Effects of Hatchery-Origin Steelhead in 

Abernathy Creek, Washington: Can Newly Developed, 

Native Broodstocks of Steelhead Derived from 

Captively-Reared Parr Potentially Contribute to 

Recovery of Naturally Spawning Populations? 

(USFWS)

Fundable contingent on an adequate response to ISRP 

questions and comments. Not RFS identified ESU --

Southwest Washington Steelhead.

19

Proposal 2: Evaluation of the Reproductive Success of 

Wild and Hatchery Steelhead in Natural and Hatchery 

Environments (UW)

Fundable, a high quality proposal, but does not 

specifically address the RPA 182 and some questions in 

the RFS. Not RFS identified ESU -- Out of Basin 

Steelhead.

21

Proposal 6: Relative Reproductive Success of 

Hatchery-Origin and Wild-Origin Steelhead Spawning 

Naturally in the Hood River (OSU)

Fundable, high rank. If selected for funding the principal 

investigator should respond to the general ISRP 

comments in the contracting process. Ranked high even 

though it is not one of the RFS identified ESUs -- Lower 

Columbia River Steelhead.

23

Proposal 1: Investigation of the Relative Reproductive 

Success of Hatchery and Wild Steelhead in the 

Deschutes River Basin (ODFW)

Qualified fundable. The study should be implemented in 

phases given adequate response to reviewer’s questions 

and comments. The study is important and addresses 

RPA 182, but does not directly address the requirements 

of the RFS. RFS identified ESU -- Mid-Columbia River 

Steelhead.

25

Proposal 3: Pedigree Approach to Determine 

Reproductive Success of Natural and Hatchery Origin 

Spring/Summer Chinook Salmon Spawners in Johnson 

Creek, Idaho (NPT)

Fundable in part for Objectives 1 and 2, contingent upon 

adequate response to the ISRP’s questions. Objectives 3 

and 4 require major revision as to how they will be 

accomplished. Low priority. Not RFS identified ESU --

Snake River Spring/Summer Chinook.

27

Proposal 11: Comparative Reproductive Success of 

Wild and Hatchery Origin Spring/Summer Chinook 

Salmon that Spawn Naturally in the Pahsimeroi and 

Upper Salmon Rivers (IDFG)

Fundable contingent upon adequate response to the 

ISRP’s questions and comments. Low rank. Not RFS 

identified ESU -- Snake River Spring/Summer Chinook.

30

Proposal 12: Evaluating the Relative Reproductive 

Success of Natural- and Hatchery-Origin Snake River 

Fall Chinook Spawners Upstream of Lower Granite 

Dam (WDFW)

Qualified funding of Phase 1, pending adequate revision. 

Do not fund Phase 2 at this point, pending successful 

demonstration of the approach. RFS identified ESU --

Snake River Fall Chinook.

32
ISRP 2003-7 RME RFS Proposal Review

36

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