Independent Scientific Review Panel

for the Northwest Power and Conservation Council

851 SW 6th Avenue, Suite 1100

Portland, Oregon 97204

isrp@nwcouncil.org

Review of Fiscal Year 2004 Pre-proposals

for the

United States Army Corps of Engineers’

Anadromous Fish Evaluation Program

(AFEP Review Part I. FY04 Pre-proposal Review)

Charles C. Coutant

Susan Hanna

Nancy Huntly

William Liss 

Lyman McDonald

Brian Riddell

William Smoker

Richard Whitney

Richard N. Williams

John D. McIntyre, PRG

Tom Poe, PRG

Erik Merrill, Staff

October 15, 2003

ISRP 2003-14
ISRP 2003-14 AFEP Part I. FY04 Pre-proposal Review

i

ISRP Review of Fiscal Year 2004 Pre-proposals for the US Army 

Corps of Engineers’ Anadromous Fish Evaluation Program

Contents

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

Review Questions ..................................................................................................................................3

ISRP Comments on Individual Pre-proposals.......................................................................................5

Estuary Proposals...................................................................................................................................5

1. A study to estimate salmonid survival through the Columbia River estuary using acoustic tags................................5

2. Estuarine habitat and juvenile salmon-current and historic linkages in the lower Columbia River and estuary.......6

3. Evaluation of the relationship among time of ocean entry, physical, and biological characteristics of the estuary 

and plume environment and adult return rates...........................................................................................................................8

4. Evaluating cumulative ecosystem response to restoration projects in the Columbia River estuary ............................8

5. Evaluating long-term and cumulative changes in the lower Columbia River estuary..................................................10

General comments on the statement of need for research concerning “Evaluation of adult salmon habitat use in the 

Columbia River estuary and plume” and competing pre-proposals 6, 7, and 8:..............................................................10

6. Evaluation of adult salmon habitat use in the Columbia River estuary and plume ......................................................11

7. Adult salmon use of the Columbia River estuary and plume ...........................................................................................12

8. Adult salmon use of the Columbia River estuary and plume ...........................................................................................13

Fish Survival Studies...........................................................................................................................14

The Dalles Dam.................................................................................................................................................................................14

9. Evaluation of direct survival at The Dalles Spillway (no proposal)................................................................................14

10. Detection of changes in escape behavior among salmon smolts following passage down The Dalles Spillway..14

11. Characterization of The Dalles Dam spillway environment...........................................................................................15

12. Estimate the survival of migrant juvenile salmonids through The Dalles Dam using Radio Telemetry: 2004 

evaluations.....................................................................................................................................................................................15

13. Estimate fish, spill and sluiceway passage efficiencies of radio-tagged juvenile salmonids at The Dalles Dam in 

2004.................................................................................................................................................................................................16

14. Relative significance of predation by smallmouth bass on juvenile salmonids in the tailrace of The Dalles Dam

..........................................................................................................................................................................................................17

Bonneville Dam.................................................................................................................................................................................18

15. Movement, distribution, and passage behavior of Radio-Tagged juvenile salmonids at Bonneville Dam 

associated with FPE and survival tests......................................................................................................................................18

16. Estimating the survival of migrant juvenile salmonids through Bonneville Dam using Radio Telemetry: 2004 

evaluations.....................................................................................................................................................................................18

17. Hydroacoustic evaluation of juvenile salmonid fish passage efficiency at Bonneville Dam in 2004 .....................18

John Day Dam....................................................................................................................................................................................18

18. Estimate the survival of migrant juvenile salmonids passing through John Day Dam using Radio Telemetry; 

2004 evaluations...........................................................................................................................................................................18

19. Monitor tailrace egress at juvenile bypass system outfall under test discharge levels at John Day Dam...............19

20. Estimate the fish, spill and juvenile bypass passage efficiencies, spill effectiveness and forebay residence times 

of radio-tagged juvenile salmonids relative to spill test at John Day Dam in 2004..........................................................20

Lower Snake River Dams ................................................................................................................................................................21

21. Hydroacoustic evaluation of fish passage at Ice Harbor Dam........................................................................................21

General Comments on Ice Harbor proposals 21, 23, 24, 25:...............................................................................................22

22. Hydroacoustic evaluation of fish passage at Lower Monumental Dam.......................................................................24

23. Direct injury/ survival of juvenile chinook salmon passing through the spillway at Ice Harbor Dam...................24

24. Fish Passage and Survival at Lower Snake River and McNary dams ..........................................................................25

25. Survival and migration behavior of sub-yearling juvenile Chinook salmon at Ice Harbor and Lower 

Monumental Dams, 2004 ............................................................................................................................................................26

Comments on the relative merits of proposals 24 and 25 (26):............................................................................................28
ISRP 2003-14 AFEP Part I. FY04 Pre-proposal Review

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26. Survival and migration behavior of juvenile salmonids at McNary Dam, 2004.........................................................29

27. Evaluation of juvenile salmonid condition in McNary Dam gatewells with prototype vertical barrier screens 

under various turbine operating conditions..............................................................................................................................30

Surface Bypass.....................................................................................................................................30

Lower Granite Dam...........................................................................................................................................................................30

28. Migrational characteristics of juvenile sub-yearling salmon in the forebay of Lower Granite Dam relative to 

removable spillway weir tests, 2004..........................................................................................................................................30

The Dalles Dam.................................................................................................................................................................................31

29. Fish passage studies for surface flow bypass development at The Dalles Dam..........................................................31

30. Distribution and movement of fish and flow upstream of The Dalles Dam and implications for Surface-flow 

bypass..............................................................................................................................................................................................32

31. Three-dimensional behavior and passage of juvenile salmonids at The Dalles Dam, 2004 .....................................33

Adult Studies.......................................................................................................................................34

32. Evaluation of adult salmon and steelhead migrations past dams, through reservoirs, and into tributaries in the 

lower Columbia River-2004........................................................................................................................................................34

33. Professional Services: Research and Monitoring Involving Radio Telemetry of Adult Salmon and Adult 

Lamprey Throughout the Watersheds of the Walla Walla District [Salmon and adult lamprey throughout the 

watersheds of Walla Walla District]..........................................................................................................................................34

34. An evaluation of abundance, downstream passage behavior and return rates from steelhead kelts passing Lower 

Columbia River dams; including a post construction evaluation of modifications to The Dalles Dam spillway and 

the Bonneville powerhouse II corner collector........................................................................................................................35

35. Evaluation of an instream pit detection system to monitor adult salmon and steelhead homing and straying 

behavior..........................................................................................................................................................................................35

Lamprey ..............................................................................................................................................................................................36

36. Evaluation of adult salmon, steelhead, and lamprey migrations past dams, through reservoir in the lower 

Columbia River, and into tributaries .........................................................................................................................................36

Bypass Studies.....................................................................................................................................36

37. DIDSON technology development and fish behavior research related to fish passage at Columbia Basin dams 36

38. Studies to establish biological design criteria for fish passage facilities: High velocity flume development 2004

..........................................................................................................................................................................................................37

39. Development and evaluation of full-flow PIT-tag interrogation systems for Bonneville and John Day Dams ....37

40. Evaluation of modified vertical barrier screens and extended-length submersible bar screens at John Day Dam

..........................................................................................................................................................................................................37

41. Evaluation of gatewell modifications at Bonneville second powerhouse using an integrated approach................38

Transportation Studies.........................................................................................................................38

42. A study to compare SARs of in river migrating versus transported anadromous salmonids....................................38

43. A study to evaluate the effects of transporting spring/summer Chinook salmon in the presence of steelhead 

smolts..............................................................................................................................................................................................39

44. Electronic recovery of ISO-PIT tags from piscivorous bird colonies in the Columbia River Basin .......................39

45. Sampling PIT-tagged juvenile salmonids migrating in the Columbia River estuary .................................................40

46. Evaluation of post-release losses and barging strategies that minimize post-release mortality and determination 

of the benefits of early spring transport from the Snake River.............................................................................................40

47. Evaluation of post-release losses and barging strategies that minimize post-release mortality ...............................41

48. Water temperature effects on juvenile fall chinook salmon survival at the hydroprojects........................................41

49. Use of a gene chip to study the effects of transportation procedures on juvenile salmonids....................................41

Bull Trout Study..................................................................................................................................42

50. Swimming performance of bull trout..................................................................................................................................42

White Sturgeon Study..........................................................................................................................43

51. Behavior of white sturgeon near hydroprojects and fishways........................................................................................43

Avian Predation in the Mid-Columbia ................................................................................................43

52. Avian predation on juvenile salmonids in the McNary Pool, Columbia River. ..........................................................43
ISRP 2003-14 AFEP Part I. FY04 Pre-proposal Review

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ISRP Review of Fiscal Year 2004 Pre-proposals for the US Army 

Corps of Engineers’ Anadromous Fish Evaluation Program

Introduction

In 1998, the U.S. Congress’ Senate-House conference report on the Fiscal Year 1999 Energy and 

Water Development Appropriations bill directed the Independent Scientific Review Panel to review 

the fish and wildlife projects, programs, or measures included in federal agency budgets that are 

reimbursed by the Bonneville Power Administration (Bonneville’s “reimbursable” program). The 

ISRP is to use the same standards and make recommendations as in its review of the projects 

proposed to implement the Northwest Power and Conservation Council’s Columbia River Basin Fish 

and Wildlife Program. Pursuant to the conference report, in June 2003, the Council requested the 

ISRP to focus its Fiscal Year 2004 reimbursable review effort on the United States Army Corps of 

Engineers’ Anadromous Fish Evaluation Program (AFEP), which is one component of Bonneville’s 

“reimbursable” program. 

The AFEP’s main purpose is to produce scientific information to assist the Corps in making 

engineering, design, and operations decisions for the eight mainstem Columbia and Snake River 

hydroelectric projects to provide safe, efficient passage of fish through the mainstem migration 

corridor. Funding for the AFEP is appropriated by Congress, expended by the Corps, and reimbursed 

by Bonneville. Unlike projects directly funded through the Columbia River Basin Fish and Wildlife 

Program, AFEP projects have not undergone ISRP review; consequently, this review provides the 

opportunity to ensure that AFEP proposals receive a similar level of scrutiny for scientific soundness 

as Fish and Wildlife Program proposals.

This is the first of two reports pertaining to the ISRP’s review. In this report, the ISRP provides 

comments on each of the 52 pre-proposals submitted to meet the research needs for the AFEP in 

Fiscal Year 2004. The report is intended to aid the Corps in selecting among pre-proposals and assist 

the project sponsors in drafting final proposals. However, the ISRP comments are limited because 

the pre-proposals did not provide enough information for a complete technical review. The Council’s 

request specified that the ISRP’s technical review be at a pilot scale and the ISRP focus on subsets of 

AFEP proposals covering the estuary and fish survival at the Columbia River federal hydroelectric 

projects (project survival). In consultation with Council and Corps staff, the ISRP further defined the 

subset of project survival proposals as those for the John Day, Ice Harbor, and The Dalles dams. 

Consequently, the ISRP assigned at least three reviewers to examine the highlighted subsets of 

proposals. One reviewer, but usually two or more, also reviewed the other proposals so that the 

ISRP could grasp the full extent of the AFEP. 

The review steps to this stage that have included an ISRP or Peer Review Group member are: 

1) participation in an AFEP overview presentation from the Corps, 

2) observation of Corps’ meetings where one-page statements of needs were developed, 

3) observation of Study Review Work Group and System Configuration Team meetings for 

prioritizing statements of needs and proposed studies, 

4) review of pre-proposals in relation to the statements of needs, 

5) participation in the Corps’ AFEP pre-proposals presentation and discussion meeting, and 

6) discussion of the pre-proposals with the full ISRP to draft consensus comments.
ISRP 2003-14 AFEP Part I. FY04 Pre-proposal Review

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The ISRP’s pre-proposal review is intended to engage the ISRP in the Corps’ project selection 

process so that the ISRP can gather sufficient information to make project specific and programmatic 

assessments on the substance, scale, scope, and process of the AFEP, and to compare the AFEP with 

the Council’s Fish and Wildlife Program. The timing of the ISRP’s pre-proposal reviews was 

selected to be least disruptive of the Corps’ normal, annual cycle of selecting AFEP projects. The 

AFEP schedule and process of setting priorities and selecting projects are significantly different 

from that of the Fish and Wildlife Program. 

The ISRP will observe several important remaining steps in the AFEP process before its review is 

finished. These include the Corps’ selection of pre-proposals for implementation or further 

consideration, the development of pre-proposals into statements of work, and the reporting of study 

results at the annual AFEP research workshop. In recognition of these remaining steps, the ISRP 

defers making overall programmatic comments and final recommendations on projects until the 

review is complete. The ISRP will issue a second report by mid-January 2004 that will provide 

programmatic comments and recommendations on the Anadromous Fish Evaluation Program and 

project selection process as a whole, and will specifically address the questions described in the 

section below.

One issue the ISRP intends to fully address in its final report is how to best incorporate scientific 

peer review in the Corps’ process. Most of the pre-proposals reviewed by the ISRP are not well 

enough developed to be amenable to scientific review and, as written, do not meet ISRP criteria for 

scientific soundness. Detail on research methods and study variables is particularly lacking in the 

pre-proposals. For some pre-proposals this lack of detail is because the researchers are analyzing 

2003 data, and/or 2004 hydro-operation plans are not finalized. These proposals (e.g. #s 13, 18, 20, 

21, 22, 23, 24, 25, 28, etc) contain statements indicating that the 2004 study designs will not be 

finalized until: “the final set of objectives and hypotheses has been selected”, “2003 data are 

completed”, or “until the operational test designs are determined after further discussion this fall”. It 

is understandable that study designs and objectives should be largely based on the most up-to-date 

data, but the specification of the variables to be tested for effects on survival is essential for the 

development of a complete, appropriate study plan. The variables chosen for analysis are significant 

determinants of whether the project will significantly contribute to problem solving, and these 

variables should be subject to review. Conducting a meaningful technical review without a detailed 

study design is not possible.

Other pre-proposals are not as constrained by hydro-operations or past years’ data (e.g. estuary or 

avian predation pre-proposals) but still do not provide details that should (and could) be provided to 

enable scientific review and comparison between competing proposals. 

To support a thorough and efficient scientific review, detail on project background and relation to 

passage problems should be documented and provided along with fully developed proposals. In the 

next stage of the review, the ISRP will review final study designs or statements of work for many of 

these proposals. Project details adequate to support scientific review may be provided at this stage. 

As the ISRP drafts its programmatic report it will address the questions below with specific attention 

given to whether the AFEP project development and funding process is sequenced so that an ISRP or 

other independent review can usefully influence the development of proposals, inform policy 

decisions surrounding the proposals, and ensure program accountability.
ISRP 2003-14 AFEP Part I. FY04 Pre-proposal Review

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Review Questions 

The Council posed the following technical, process, and programmatic questions to the ISRP. These 

will be fully addressed in the ISRP’s second report. Although most of the ISRP comments on the 

pre-proposals do not specifically identify the ISRP’s technical review criteria and questions, 

reviewers considered these criteria and questions as they drafted comments on individual preproposals. 

 

Project Specific Technical Review

As specified in the Appropriations language, the ISRP is to review the subset of proposals in regard 

to whether they: 

i. are based on sound science principles; 

ii. benefit fish and wildlife; 

iii. have clearly defined objectives and outcomes; and 

iv. have provisions for monitoring and evaluation of results.

Specifically, the ISRP review of the subset of AFEP proposals should address the following 

questions:

1. Are the research objectives for each of the technical areas appropriate for the current level of 

scientific knowledge and need?

2. Are the research objectives from which research proposals are being developed clearly identified? 

3. Are the experimental/study designs of the preliminary proposals scientifically sound (do they 

include a power analysis, identify appropriate surrogate stocks, demonstrate rigorous methodology, 

explain logistical constraints)?

4. Do the final proposals adequately address the research objectives?

 

5. For ongoing projects, was the research conducted as designed? If problems arose, were the 

changes in the study adequate to address the problem?

6. Is the data analysis appropriate for the study as conducted?

7. Does the information provided support a decision related to design, operation, construction, or 

configuration of the hydrosystem?

In sum, 1) do the estuary and project/in-river survival projects meet the objectives of the AFEP, as 

described in the statements of need, in a scientifically sound manner, and 2) will the data generated 

by the estuary and project/in-river survival projects inform the analyses of critical 

questions/uncertainties in the Columbia River Basin; i.e., are the right data being collected?

Process 

1. Is the AFEP proposal selection process adequate to ensure independent scientific peer review? If

not, how can it be improved to allow for review?

2. Given basic differences and legal requirements in the programs, is the AFEP project solicitation 

and selection process as open, competitive, and rigorous as that of the Fish and Wildlife Program?
ISRP 2003-14 AFEP Part I. FY04 Pre-proposal Review

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3. Are there opportunities to make the AFEP and Fish and Wildlife Program processes more 

consistent to allow for ready comparisons between programs for such efforts as identifying research 

gaps? 

4. Are there opportunities for further coordination - standard proposal forms, review criteria, etc?

Programmatic 

1. Section 4(h)(11)(A) of the Northwest Power Act calls for the Corps and other Federal agencies 

responsible for managing, operating, or regulating Columbia River Basin hydroelectric facilities to 

take into account at each relevant stage of decisionmaking processes to the fullest extent practicable, 

the program adopted by the Council: 

a) Are the general strategies from the Council’s 2000 Fish and Wildlife Program, pages 25-

30, being addressed in the AFEP?

b) Although recently released, the Council’s 2003 Mainstem Amendments calls for an 

experimental approach to improving fish passage, to what extent is the AFEP currently 

implementing these experiments?

2. To the extent that the AFEP is informed or driven by the Endangered Species Act (BiOp), the 

Clean Water Act, and the Northwest Power Act, is the program integrated and sequenced in a 

scientifically sound manner? Is a broad/integrative context provided by the AFEP? Is the AFEP 

supported by a planning framework or document?

3. How is the information gathered by the AFEP used to inform future research needs and an 

immediate policy decisions?

4. With the information gained in this review and the provincial reviews, are there key uncertainties 

or research gaps related to the operation of the hydroelectric projects that do not appear to be 

adequately addressed in the Columbia River Basin by AFEP, the Fish and Wildlife Program, or the 

mid-Columbia Public Utility Districts’ passage programs? What are the reasons for the uncertainties 

or gaps? Are there alternatives not currently provided within the AFEP research objectives? These 

should be described in detail.

 

5. How are costs integrated in the project selection process? How does the Corps make decisions on

how to most economically and effectively provide safe passage for fish through the hydropower 

system?
ISRP 2003-14 AFEP Part I. FY04 Pre-proposal Review

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ISRP Comments on Individual Pre-proposals 

Estuary Proposals

1. A study to estimate salmonid survival through the Columbia River estuary using 

acoustic tags

Study Code: EST-P-01 Agency/Author: NMFS, PNNL / McComas, Carlson

ISRP Comments:

This is a clearly written proposal to conduct the fourth year of design and feasibility testing of 

tagging and acoustical detection. FY04 would be the final year in the development phase of the 

project, after which full-scale implementation would begin. The project is ambitious but the potential 

benefits are substantial. The tagging and detection techniques being developed are proposed to 

answer questions pertaining to estimation of delayed mortality between Bonneville Dam and the 

mouth of the Columbia River, the characterization of smolt use of the estuary, the effect of estuarine 

restoration actions on habitat selection and survival, and the variation in smolt behavior in the 

estuary over time. The development and testing has proceeded logically in a step-by step fashion 

with each step further advancing the technology. 

The proposal presents a careful and thorough summary of work done to date, the rationale for that 

work, lessons learned, and modifications made. The objectives are measurable and are reasonable in 

relation to the overall goal. The approach described under each objective appears complete and 

reasonable. The discussion of FY05 fish requirements recognizes that sample size will depend on 

information generated during FY04. It is implied, but not stated in detail, that in FY05 and beyond, 

sample sizes and analytical approaches will be shaped to explicitly address the management 

questions regarding delayed mortality, estuary use, etc. This is a significant technical question that 

must be more explicitly addressed in future proposals.

The questions identified during review included:

1. Can a tag small enough for use in subyearling fall chinook can be developed? This is a crucial 

uncertainty because empirical studies to date suggest that juvenile fall chinook tend to spend more 

time in the estuary feeding and rearing than do spring chinook juveniles. Furthermore mortality 

resulting from tagging will need to be determined. The proposal refers to holding fish to test for 

tagging mortality, but such tests cannot address issues of stress levels or predation after releases. Is 

it possible to develop a test to directly monitor these issues?

2. Pertaining to tag size, the proposal indicates that the tag size fits the median sized sub-yearling. 

Is this an adequate representation of wild fall chinook to address the proposal’s objectives? The 

panel recognizes the challenges of studying the smaller sized fish, but is there a complementary 

study that could be designed to address this concern? This issue also relates to concerns for 

differences in the survival and habitat uses of hatchery and wild juveniles.

3. Related to point (2), how does this project relate to project EST-P-02 that proposes to assess 

salmonid habitat use within the estuary? Is there duplication of proposed effort? What is the acoustic 

assessment likely to reveal that will not be shown in EST-P-02?

4. In general, more thought needs to be given to whether it is feasible for the tagging and detection 

technology to achieve the objectives of determining survival estimation and estuarine behavior. For 

example, although the techniques are potentially useful for measuring delayed mortality, is it 

feasible logistically to determine delayed mortality? It seems that the experimental design may need 
ISRP 2003-14 AFEP Part I. FY04 Pre-proposal Review

6

to involve measurement of in-river survival of a group of acoustically tagged Snake River fish above 

Bonneville and below Bonneville. The estimates below Bonneville will need to be compared to 

survival estimates of an acoustically tagged group released below Bonneville to determine if the 

survival of this group is higher than the survival of tagged Snake River fish. The tag requirements of 

such an experiment could be substantial. 

In terms of the committee’s ability to conduct a peer review of this proposal, the generally 

descriptive nature of the proposal limits any scientific review. There are goals and objectives 

presented and methods described very generally, but after three years of work, what are the results 

to-date? For scientific review, more detail on methods, samples sizes, and analyses proposed is 

needed. 

2. Estuarine habitat and juvenile salmon-current and historic linkages in the lower 

Columbia River and estuary

Study Code: EST-P-00-1 Agency/Author: NMFS / Bottom, Ed Casillas

ISRP Comments:

This proposal has been reviewed and considered by members of the panel several times. 

Consequently, our comments relate to this proposal specifically and to our continued thinking about 

estuary studies and estuary restoration programs generally. We have attempted to separate these 

comments.

The panel continues to support this much needed research and believes that the study will contribute 

significantly to understanding the role of estuarine conditions in salmon growth and survival. The 

investigators are very well qualified and have an excellent track record of achievements in Columbia 

River estuary science. However, the proposal doesn’t make direct reference to FCRPS RPAs.

This ongoing project is large and complicated, but the proposal is very general. Given the scope of 

activities and past research, this proposal would have benefited from a global perspective on what is 

being learned and how that knowledge will be applied. This proposal is lengthy and contains a large 

number of tasks to support the three objectives. But it is frequently difficult for the reviewer to keep 

in mind the knowledge the proposal is intended to generate, and how that knowledge will translate 

into achieving the goal of protection and restoration priorities for the Columbia River estuary. 

This proposal would be enhanced by more specificity about assumptions, approaches, and how the 

research links to problem solving in the Columbia River Estuary. Despite a large number of tasks 

and subtasks, the overall tone of the proposal is very general. For example, under Sub-task 1.2, point 

2. FY 2004, refers to assessing whether “the existing monitoring design adequately depicts trends in 

salmon life-history and genetic diversity throughout the lower estuary”, but what would these be 

assessed against and what criteria would be used to assess the need to change? How would 

researches know whether the existing monitoring design will adequately depict trends in salmon life 

history and diversity? Under Subtask 3.1.b., progress to date is described as “Selected data sets have 

been chosen for analysis and hypotheses have been derived,” without any detail as to what they are. 

In the summaries of progress to date, the emphasis is on what has been done, but few specifics are 

provided about what has been learned. Specifics are also lacking in methods to be used for proposed 

work, particularly in the tasks to be completed in FY04. 
ISRP 2003-14 AFEP Part I. FY04 Pre-proposal Review

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Issues that were identified by the reviewers include:

a) Emphasis is placed on establishing historic conditions. Some clarification could be provided as to 

the relevance of historic conditions, would historical conditions actually be appropriate or achievable 

under current environmental conditions? What does it mean to reconstruct historical habitat? Does 

“historical” mean at a single point in time or at different points in time? It seems that the relevance 

of “historic” is to establish a baseline against which current conditions can be compared. But most 

useful to the policy environment is to understand those attributes of historic habitat that are key, 

those that may or may not have been duplicated or at least substituted in the process of change over 

time, and those that are attainable now. The emphasis on “historic” seems to risk becoming too 

simplistic to be useful. 

b) The investigators propose that emergent marshes, a scrub/shrub wetlands, and forested wetlands 

represent different stages of estuarine plant succession. How well established is this supposition? 

Whether these vegetation types represent successional stages or different plant community types that 

have developed in locations with different environmental conditions may be relevant to predictions 

for long term habitat change and so influence restoration protocols.

c) Of particular concern is an apparent assumption that the expression of life history diversity (in a 

genetic sense) has been reduced through modification of the estuary (amongst other impacts in the 

upper Basin). Impacts of estuary changes are certainly likely for fall chinook and chum salmon given 

their smaller size during juvenile migration, but how would the loss of genetic variation in life 

history types be differentiated from difference in the availability of habitat types? This seems to be 

analogous to the long-standing debate in ecology concerning habitat occupancy versus habitat 

preferences. We do not see that the absence of certain habitat types leads to the assumption that 

there has been a corresponding loss of genetic variation for use of this habitat. Plasticity in habitat 

use may be a true life history strategy for salmonids that use complex environments as opposed to 

specific adaptations to certain habitats. We may be over simplifying what the authors’ intended in 

this proposal, but we would recommend research into the genetic nature of these “life history” types 

before concluding that changes in habitat have selected against types of fall chinook and chum. 

Even if it is correct, as recent analyses imply, that temporal and spatial patterns of estuarine rearing 

by juvenile salmon have been simplified, does this necessarily lead to a reduction in diversity of 

salmon life histories? Or to a reduction of resilience and productivity? What degree of adaptation to 

simplified habitats could have taken place?

For the authors’ consideration, other specific questions that were identified include:

1. How long-term does monitoring have to be to establish a trend that will associate variations 

in abundance and life-histories with changes in biological and physical conditions? 

2. How many long-term indicator sites will be established, and how will these be determined? 

What will be the effect on establishing trends of changing site locations (i.e. how can you 

establish trends if sampling locations and protocols evolve throughout the course of the 

study)?

3. If existing uses of habitat are being documented, how do you learn about potentially 

beneficial habitat that may be currently non-existent? How do you learn about what is not 

there, and how do you learn about the extent to which salmon have been able to adapt to the 

loss of habitat types?

4. How do you establish historic uses of different habitat types? Do you infer salmonid presence 

and productivity from habitat existence?
ISRP 2003-14 AFEP Part I. FY04 Pre-proposal Review

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5. Throughout, the focus of the work is to establish correlations. But the intent of the project is 

to extend these correlations to predicted responses to change. How will causality be derived 

from correlation? It is asserted that the development of empirical associations between 

habitat variables and salmon productivity will allow prediction of responses of juvenile 

salmon to past or future changes, but this remains to be demonstrated.

6. How many different habitat types are there in the Columbia River Estuary and are all being 

studied by this project? How are “representative” habitat types determined? Are habitats 

distinguished at the landscape scale, or does this scale aggregate over several types of 

habitat? 

3. Evaluation of the relationship among time of ocean entry, physical, and biological 

characteristics of the estuary and plume environment and adult return rates

Study Code: EST-02-03 Agency/Author: NMFS / Muir

ISRP Comments: 

This proposal is clearly written. The objectives and relevance to the FCRPS are clear. It is useful to 

have lower Columbia River releases so that upriver factors do not confound the analysis. 

A key uncertainty, and a key question for the researchers, is whether it is reasonable to expect to 

observe enough variation in estuary and nearshore environment in the two-month period to be able 

to detect differences in SARs. The ability to detect association of estuary biological and physical 

factors with variation in SARs hinges on there being enough variation in these factors during the 2-

month release period. How much variation is it reasonable to expect in this short period? Ocean 

conditions, even in the nearshore, are not likely to vary a great deal in that time period. What will the 

researchers do if there is not enough variation within the release period? 

The complexity of proposed actions requires much more detail on methods to provide an adequate 

scientific review. The statistical analysis seems simplistic. Is a time series analysis needed if data 

from multiple years are going to be used in the regression? Are more sophisticated survival models 

required? Are the explanatory variables likely to be sufficiently independent to permit a meaningful 

analysis?

4. Evaluating cumulative ecosystem response to restoration projects in the Columbia 

River estuary

Study Code: EST-04-P-New2 Agency/Author: PNNL, NMFS / Thom, Roegner

ISRP Comments:

The AFEP research goal for this topic is to provide objective methods to predict and evaluate the 

cumulative response of ecosystem functions to restoration actions in the Lower Columbia River 

Estuary. The emphasis of the AFEP research summary is on measurement. The research summary 

lists six objectives: to develop (1) the empirical basis for cumulative assessment methodology; (2) a 

set of metrics to evaluate cumulative effects of restoration; (3) a framework for predicting 

cumulative effects of individual projects; (4) field evaluations for measuring ecosystem response to 

restoration projects; (5) a data acquisition and management system for evaluation; and (6) an 

adaptive management system.

The overall goal of proposal EST-04-P-New2 is to develop an estuarine monitoring system. The 

focus of the proposal is to develop methods to assess, monitor and quantitatively evaluate the 
ISRP 2003-14 AFEP Part I. FY04 Pre-proposal Review

9

cumulative effect of Columbia River Estuary salmon habitat restoration actions. The proposal is 

explicit about its underlying assumptions, which seem reasonable in that they emphasize 

standardization of data and methods, identification and assessment of key attributes, the use of an 

overarching framework, and adaptive management based on what is learned from monitoring. 

However, the proposal provides little substantive detail as to how the research goal would be 

accomplished. To achieve project goals the proposal needs more thoughtful and thorough 

development. As written, reasonable assurance of project success is not evident because the proposal 

lacks sufficient detail about methods and implementation. Some components sound like a proposal 

to develop a proposal. 

Most of the proposed work is literature review intended to aid development of methodology. The 

investigators provide little insight into the form of the cumulative assessment methodology, the 

possible ecosystem scale metrics and how they would relate to salmon restoration, and the model for 

predicting cumulative effects on major ecosystem functions, whatever these functions may be. 

Objective 2, which entails all of the above, is supposed to be completed in one year. This timeframe 

seems highly unrealistic.

The proposal should describe experimental design and sampling protocols, or at least discuss the 

major issues related to experimental design, instead of saying that a statistician will be consulted on 

experimental design.

Specific questions and comments:

1. One of the purposes of monitoring is to assess the extent to which goals are being achieved. 

Are there goals for the Columbia River Estuary? If so, they should be explicitly stated in the 

proposal. 

2. It may be overly optimistic to assume that a one-day meeting for Columbia River Estuary 

projects will allow the description of existing monitoring protocols. Will the project PIs also 

be consulted in the development of assessment methodology and metrics? How will buy-in 

for these be achieved?

3. Task 2.3. describes a “semi-quantified conceptual model.” More clarification of the structure 

and function of this model is needed.

4. How will investigators determine whether tasks 2.1 – 2.4 indicate the need for field testing? 

Field-testing methods would not seem to be optional. 

5. It is unclear how the ecosystem perspective for monitoring would be developed. The 

proposal should provide more detail as to how concepts such as functionality, habitat 

suitability and natural state would be measured. What are the appropriate ecosystem metrics? 

Do they focus on fitness of salmonid populations and suitability of salmonid habitat or are 

they broader? What data exist to serve as a baseline? 

The proposal leaves issues related to implementation largely unaddressed. The project will attempt 

to develop methods that apply at a cross-project scale without the authority to enforce them or to 

adaptively manage. The project must therefore rely on voluntary coordination and incentives to 

cooperate. More attention should be given as to how to achieve this, combined with a realistic 
ISRP 2003-14 AFEP Part I. FY04 Pre-proposal Review

10

assessment of the incentives and disincentives for projects to cooperate. Detail should be provided as 

to how standardized monitoring protocols can be implemented across projects. Would projectspecific monitoring be subsumed and funded under this framework approach for the Columbia River 

Estuary? The proposal lacks evidence of the agency and regional commitment that would be 

required to ensure success. 

Finally, the proposal should firmly establish the qualifications of the investigators to undertake this 

project. The proposal lists good participants but, as written, it creates the impression that the 

investigators do not have extensive knowledge in the estuary and do not fully appreciate the 

difficulty, the required coordination, or the time required to accomplish project objectives. 

Additionally, the proposal does not display an awareness of the considerable amount of ongoing 

efforts to develop monitoring and evaluation programs for the upper river.

5. Evaluating long-term and cumulative changes in the lower Columbia River estuary

Study Code: EST-04-New5 Agency/Author: USGS / Petersen

ISRP Comments: 

The proposed work will use sediment cores to document historical changes (at a decadal scale) in 

ecosystem structure and processes in the Columbia River estuary and relate these changes to human 

activities (e.g., dam construction) and natural environmental variation (e.g. regime shifts). This 

project would develop indicators of change in aquatic community condition. These metrics would

relate to primary production, diversity, contaminants, and availability of organic material over time. 

The investigators have conducted a preliminary study on selected cores from the estuary that 

suggests that the proposed approach is feasible. 

The investigators, however, need to provide more detail about how this work will relate directly to 

estuary restoration. The key question would be whether measurements of sediment attributes provide 

the appropriate indicators of habitat or aquatic community health. How would the link be made 

between variables of interest to paleoecologists and current indicators of ecosystem health? The 

proposal needs much more detail as to how it would apply the core sample data to answer current 

restoration questions, and how it would tie in with other projects that also are looking at historical 

conditions and their relation to the present, such as the work by Bottom and Casillas. Additionally, 

to accurately document historical changes requires that the cores be taken from sites that are neither 

depositional nor erosional. How will the investigators ensure that sample sites meet this criterion?

General comments on the statement of need for research concerning “Evaluation of 

adult salmon habitat use in the Columbia River estuary and plume” and competing 

pre-proposals 6, 7, and 8: 

The ISRP questioned the priority of this statement of need, but these preliminary studies could be 

used to assess whether an issue related to adult mortality exists. Each of these proposals is very 

preliminary and could not comment on the stated tasks of associating adult habitat use to changes in 

flow and the Federal Power System. None of the three proposals reviewed contained enough 

information to allow scientific review and ranking, and all demonstrated very rudimentary 

knowledge of salmon physiology and movement in estuaries. What is the evidence that a problem 

exists? The proposals are clearly intended to be at a pilot level to test the methodologies, but none 

showed sufficient depth of planning to separate one proposal from the others. However, the Brown 
ISRP 2003-14 AFEP Part I. FY04 Pre-proposal Review

11

and Geist proposal refers to technologies that are still developmental and may not be available for 

this work plan.

These pilot studies involve the study of adult spring chinook use of the estua ry under spring flow 

and climatic conditions. These conditions may not be the most representative under which to test for 

impacts of hydrosystem flows and the estuary on adult salmon. The panel was surprised that none of 

the proposals considered the known changes to flow regimes and their relation to possible impacts 

on adult salmon migrations and survival. Further, is the primary interest in assessing survival 

through the estuary and lower river, or the use of habitats during this movement? The latter could be 

much more difficult to asses and may vary between years depending on the flow regime and 

temperatures. The Panel would have benefited from a more explicit statement of the information 

needs and why this is considered an issue.

The ISRP was also struck that none of the proposals indicate any effort to contact the fishers who 

have a long history of working in the estuary and an appreciation for how salmon use the estuarine 

environment. 

6. Evaluation of adult salmon habitat use in the Columbia River estuary and plume

Study Code: EST-04-New4 Agency/Author: U of I, OSU / Peery, Schreck

ISRP Comments:

The goal of this project is to develop detailed information on the distribution and use of the 

Columbia River plume and estuary by adult salmonids. It has objectives to determine macro-scale 

and micro-scale use of the estuary by adult salmon migrants, and to assess the need for further 

evaluation. The proposal would collect information on the temporal and spatial patterns of habitat 

uses (the micro-scale) in the estuary (no comments related to the plume?) and use this to determine 

the potential impacts on adult salmon of operations in the Federal Power System. However, at the 

level of detail presented in this proposal, it is not possible to comment on the likelihood of such a 

study. Clearly, at the level contained in this text, the objectives could not be met, but each of the 

proposals is obviously written at a pilot or exploratory level. This proposal, however, refers to 

“monitoring to determine patterns of microhabitat use” which implies a longer-term commitment 

and could become very costly. Before such an objective is supported, a real problem should be 

identified and a full monitoring design presented. This proposal is also differentiated from the other 

two in referring to a Merwin trap to capture and sample fish. This could be a very useful study in 

itself and may merit consideration as an experimental sampling tool that would allow live capture 

and release of salmon.

To relate adult use of the estuary to flow variations, researchers will have to associate fish location 

with actual flow rates and depth of water, etc. The proposal does not comment on the accuracy of 

fish location based on the detection methods. Even the discussion of the mobile tracking brings into 

question how to relate to position of the fish and GPS? The detection range of a tag could be several 

hundred meters, but small errors in distance could imply very different habitats in the flow channel 

for example.

The proposal is not clear on where the sampled fish would be captured. If capture is in the estuary, 

then there will likely be concerns for mortality of tagged fish since they will be acclimating to 

freshwater and susceptible to stress of handling. If an objective of the study is to assess habitat use 
ISRP 2003-14 AFEP Part I. FY04 Pre-proposal Review

12

and survival of adults, then there should clearly be consideration of how to assess tagging related 

mortality.

The very general nature of this proposal resulted in numerous questions being listed by the panel: 

1. What methods of mobile tracking would be used?

2. What methods of fish sampling and collection would be used?

3. What protections would be in place for ESA listed fish?

4. What statistical analysis will establish patterns of use?

5. Why is the timing and scope of year 1 sampling different from subsequent years? Are there 

methodological issues to be worked out in a pilot?

6. How will the subsample (to determine microhabitat use) be chosen? What is its size?

7. How will the assessment of residency, survival, and habitat use be done from the data 

collected?

8. How will the linkages between estuary use and survival and operation of the hydrosystem be 

analyzed?

9. What would determine whether multiple years of data would be needed?

See general comments on pre-proposals 6, 7, and 8 above.

7. Adult salmon use of the Columbia River estuary and plume

Study Code: EST-P-04-New1 Agency/Author: NMFS, WDFW, OSU / Burke, Ashbrook, 

Schreck

ISRP Comments:

The objectives in this proposal are those specified in the request for proposals, but the tasks 

discussed under each objective are quite poorly written. The tasks appear to describe work that has 

already been done, information that is already known, or work not directly relevant to the objective. 

For example, objective 1 is to determine the best technique for capturing, tagging, and tracking 

salmon. Methods described under objective 1, however, describe only one method for doing this and 

it is not clear where the sampling will occur and if the same methods would be used in the plume 

environment. (Collection of adults in Cathlamet Bay would not seem to meet the basic intent to 

study use of the estuary by adults.) 

Under Objective 2, does monitoring “survey operations” imply a different sampling method? A 

similar problem exists with objective 3, that obviously is based on information not presented in the 

proposal and therefore cannot allow for review. Objective 2, to evaluate cost-effectiveness of 

monitoring tributaries vs. known-source fish, does not contain any evaluation of cost-effectiveness 

but rather focuses on how they will determine fate of the fish. But further, the fate of the fish is 

incomplete. If a fish was from above Bonneville but strayed, that has a very different interpretation 

than if it did not survive. If the objective of these proposals is to examine the survival rate of adults 

and their use of the estuary habitats, presumably the objective implies knowing the fate of each 

tagged fish. This limitation also negates the last statement under Objective 4 that all possible fates 

of fish can be either estimated or measured directly. Objective 5 will only be examined at a very 

cursory level since the resolution of habitat definition and use will apparently be defined by the 

positions of the detection arrays.

An important issue related to our comments on tagging mortality (under proposal 6) is addressed 

under Biological Effects in this proposal. These authors suggest that there will be little to no 
ISRP 2003-14 AFEP Part I. FY04 Pre-proposal Review

13

morality from sampling and they provide a citation to Matter and Sandford (2003). Unfortunately, 

the citation in the References is incomplete, so the basis for their statement cannot be examined. We 

remained concerned that this issue be carefully considered in these studies.

Although the three pre-proposals for work with adults in the estuary did not provide adequate 

information to make a definitive ranking, this pre-proposal, with the qualifications of its researchers 

and available equipment, provides the highest likelihood of producing useful information during an 

initial pilot study. However, given the number of concerns noted above, the ISRP would recommend 

a much more thorough proposal be prepared before funding. See general comments on pre-proposals 

6, 7, and 8 above.

8. Adult salmon use of the Columbia River estuary and plume

Study Code: EST-P-04-New3 Agency/Author: PNNL / Brown

ISRP Comments:

Objectives of this proposal are the same as for proposals 6 and 7. However, the background section 

(III A.) leads to some confusion regarding how it relates to the objectives. In particular, the last two 

paragraphs seem to pertain to juveniles and not adult use of the estuary, although their extension to 

adults is possible. The panel disagreed with the comment regarding extended delays in the estuary 

being common. The comment about late-run Tules may relate to the origin of these fish as opposed 

to a general feature of salmon in estuaries. In other large rivers such as the Fraser River, holding in 

the estuary is definitely the exception and not the rule. Only one stock of sockeye salmon is actually

known to hold in the estuary at all. However, salmon may move on tidal currents for a few days as 

they acclimate to the freshwater environments.

The proposal is very short on detail about how the objectives would be accomplished. “Several 

methods will be assessed” for capturing listed salmon means only that commercial and recreational 

catch will be used. How will the catch be sampled? What information will be collected? How will 

the data be analyzed? The proposal only states “extensive notes will be taken” and capture and 

handling techniques “will be recorded.” 

Unlike proposal 7, various options for fish tracking are considered, but these are only described as 

options, without an indication as to which will actually be tested. Cost effectiveness evaluation is 

directly addressed, but a measure of “effectiveness” is not described. For example, would it be more 

cost effective to put receivers at each downstream tributary or would it be better to only use fish of 

known source upriver (detect PIT tags or DNA sampling)? The answer to this question depends in 

large part on the sample size needed to meet the project objectives, i.e., precision about mortality 

rate, does the study intend to examine mortality rate differences between stocks, etc. The proposal 

seems to take a more analytical approach to the objectives than does #7, but it too is quite vague in 

methodological detail.

The panel must emphasize though that this proposal’s reference to new acoustic transmitter tags are 

not fully developed, and it is our understanding that the detectors have not been developed to the 

point of application and deployment. This concern is most clearly expressed in section D that states 

that “Battelle currently has much of the gear”, and that telemetry gear “will largely be covered” by 

other projects. Compared with existing capabilities and experience in proposal 7, these added risks 

are necessary. See general comments on pre-proposals 6, 7, and 8 above.
ISRP 2003-14 AFEP Part I. FY04 Pre-proposal Review

14

Fish Survival Studies

The Dalles Dam

9. Evaluation of direct survival at The Dalles Spillway (no proposal)

Study Code: SPE-P-00-8

Agency/Author: COE / Mike Langeslay COE Lead: Langeslay

ISRP Comments:

No proposal was available so Mike Langeslay of the COE gave a brief description of the study 

design, which was a balloon tag study. As more flow (18 or 21 kcfs) will be put through fewer spill 

bays (2, 4, and 6), the COE and regional fish managers want to know what the direct survival and 

injury levels are under these spill conditions. The study will be done in the spring using yearling 

spring chinook. This study has high priority, because survival studies at The Dalles Dam have shown 

relatively low survival for juvenile salmonids passing the spillway, particularly through the more 

southern spill bays. It is unknown whether increasing spill through the more northern spill bays and 

decreasing spill at the south spill bays will prove a safer passage route for smolts.

10. Detection of changes in escape behavior among salmon smolts following passage 

down The Dalles Spillway

Study Code: SPE-P-00-8 Agency/Author: Oak Ridge National Laboratory / Glenn Cada 

(Langeslay presented) 

ISRP Comments: 

The proposal provided for review is a one-page preliminary proposal. A comment made during the 

review meeting indicated that the authors could offer a more complete proposal if requested. In the 

background section the authors indicate that the significance of sub-lethal stressors (i.e. turbulence) 

related to indirect mortality/predation has not been studied. However, studies have been published

on this subject (see Mesa 1994, TAFS). Also, there is a considerable body of literature published on 

fast-start performance, startle-response, and mechanisms affecting predator avoidance response 

times (e.g. P. Webb published several such papers in the 1970s and 1980s, Harper and Blake 1990, 

Sigismondi and Weber 1988). Some of these should be included in the background to give a firm 

basis for this line of research. 

In the background section the authors say that there is a need to quantify indirect mortality so the full 

consequences of passage through a hydroelectric dam can be assessed. However, there is no 

description in the proposal of how they will quantify indirect mortality with this technique. It is 

proposed to conduct this study in conjunction with a balloon tag study. However, no reference is 

given to that other study, as a result of which, it is difficult to evaluate this one. In fact, it appears 

that the Hi-Z Turbine tag study mentioned may only be hypothetical. No information is provided on 

the numbers of fish expected to be included in the study, nor on the species of interest. 

Based on the brief description of how they will apply the escape behavior technique at The Dalles 

Dam (TDA), it appears that they will receive balloon tagged fish just after recovery from passing 

through the spillway (about 5 min), then film the behavioral response to a “startling stimulus” in a 

holding tank on a boat in the tailrace or at a shore facility and compare passed fish response to 
ISRP 2003-14 AFEP Part I. FY04 Pre-proposal Review

15

control fish response. The instability of a boat in the tailrace would probably be too difficult for 

filming. Using a balloon tagged fish (plus a radio tag attached) for behavioral response studies may 

not produce useful or valid data due to possible tag effects, excessive handling in removal of tags, 

and holding time prior to initiation of filming. As it stands, the proposed study does not address a 

research objective of significance for the current level of scientific knowledge and need in the basin. 

Further, it would not provide information needed for a decision on spillway design or operation, and 

no mention is made of such a possibility.

11. Characterization of The Dalles Dam spillway environment

Study Code: SPE-P-00-8 Agency/Author: PNNL / Tom Carlson, Marshall Richmond

ISRP Comments:

This was a very complete and well prepared pre-proposal. The review of literature and background 

provided in this proposal is very helpful in putting the other proposals for The Dalles Dam (TDA) 

tailrace studies in context and understanding their objectives. A minor complaint is that the Project 

Summary Section is too long and could be streamlined by condensing from about six to two pages. 

It is not clear from the outset that the goals and objectives are for a multi-year study (not just 2004), 

particularly since the Anticipated Duration (on the cover page) is given as January 2004 –December 

2004. This is confusing to reviewers. The authors need to include references providing details 

regarding the major techniques (i.e. sensor fish and the CFD model) to be used for characterizing 

The Dalles Dam spillway environment. Starting on page 3 or 4, when sensor fish are first mentioned, 

references should be added which document the development and testing of this new innovative tool. 

There is also a list of uses of the sensor fish on page 4 but references/reports are not cited. 

References for the CFD model, pages 4 and 5, also need to be provided. A comment made during the 

review meeting indicated the Department of Energy did have peer-reviewed documents describing 

sensor fish and CFD model development.

The underwater collision experiments will provide some useful data to assist in understanding how 

and why certain injuries occur in turbulent environments at hydroelectric projects, but the authors 

did not adequately describe the experimental apparatus that will be used (top of page 16). This 

apparatus needs to be described or a good reference added which does so. This section would also 

benefit the reviewers by including a brief review of the literature dealing with underwater collisions 

of fish with physical structures. 

The section on “Expected results and applicability” is well done. This is a useful method of 

foreseeing possible shortcomings in the design or possible adjustments to obtain more information 

with little additional effort, and to foresee what applications might or might not be made in the 

process of deciding on management options.

12. Estimate the survival of migrant juvenile salmonids through The Dalles Dam 

using Radio Telemetry: 2004 evaluations

Study Code: SPE-P-00-8 Agency/Author: USGS / Tim Counihan

ISRP Comments:

This is a relatively well-prepared proposal to the extent that 2004 operational plans or treatments are 

still undetermined. Not having the 2000-2002 survival studies reports or results to date available (i.e. 

results are only generally described in the Current Status Section) as a basis for review is a problem, 
ISRP 2003-14 AFEP Part I. FY04 Pre-proposal Review

16

because previous years results would obviously show the necessity for continuing on the same track 

or altering the study design. Adding a Table summarizing survival results to date, as in the project 

proposal for study #13 (SPE-P-00-17), would be helpful. 

As stated in this report’s introduction, a major concern with this pre-proposal, as well as with many 

other pre-proposals reviewed (e.g. #s 13, 18, 20, 21, 22, 23, 24, and 25), is that these proposals 

contain statements that indicate that the ’04 study designs will be not be finalized until: “the final set 

of objectives and hypotheses has been selected.” (by regional managers?), “2003 data are 

completed”, or “until the operational test designs are determined after further discussion this fall”. It 

is understandable that decisions for study designs and objectives should be largely based on the most 

up-to-date data. However, with incomplete study designs/proposals in hand it is impossible for 

reviewers to do a meaningful technical review.

It appears that this proposal is closely linked to the following one (#13). In fact, this proposal uses 

the tagged fish from that study to generate the survival estimates. This linkage should be stated more 

explicitly. Better yet, they could be combined or an umbrella proposal done for studies that are 

closely linked. On page 5 reference is made to personal communications from Adams and 

Hockersmith to the effect that the method of estimating survival by passage route using radio tagged 

fish in both the Snake River and mid-Columbia River gives comparable “trends” in results. It would 

be more convincing had references been cited to Shane Bickford at Douglas PUD. 

In the last paragraph on page 6 and again in the last paragraph on page 10, the authors indicate that 

survival of fish passing through the north spillbays was less than for fish passing via the south 

spillbays. Don’t results to date show higher survival through the north spillbays, as opposed to the 

south spillbays? 

The proposal, on page 13 to use drogues to evaluate egress by juvenile salmonids, depends upon an 

assumption that fish are carried as passive objects in flowing water. This may not be true. Salmonids 

have a well-developed sensory system for detecting flow and are able to modify their positions and 

orientations in flowing water. This may give information on a “worst case scenario”, but may not be 

realistic, considering fish behavioral responses. The proposal is heavy on statistical aspects (from 

assumptions to calculations) but light on other methods such as the exact nature of the telemetry 

tags, locations and numbers of antennae and receivers, the vendor for the tags and receiving 

equipment, etc. The proposal presumes knowledge of the telemetry system that may not be 

warranted for many reviewers.

13. Estimate fish, spill and sluiceway passage efficiencies of radio-tagged juvenile 

salmonids at The Dalles Dam in 2004

Study Code: SBE-P-00-17 Agency/Author: USGS / John Beeman, Alec Maule

ISRP Comments:

The objectives are clearly defined and well justified. The use of the summary table of metrics from 

previous years studies was very useful to have giving a better context for proposed study. This type 

of table should be required in proposals for all ongoing projects that have several years of results to 

report. The FPEs for 2002 (incorrectly labeled 2003 in the proposal, but clarified at the proposal 

meeting) are quite low and may indicate very low survival for 2003 (yet to be completed). Was 

anything different in dam operations this year? On page 6 in paragraph 2 there is a brief mention of 

a proposed pilot study to determine detection rates of radio tagged juvenile sockeye salmon. What is 
ISRP 2003-14 AFEP Part I. FY04 Pre-proposal Review

17

the purpose and rationale for this? As this is a new element for the ongoing study, this should be 

treated with much more detail, maybe as a separate study objective. 

This ongoing proposal expectedly lacks the detail of a new study proposal (the project sponsors can 

cite previous years reports). However, in the methods section the project sponsors totally skip over 

the task and activity of tagging the fish including: type of tag and details, tagging technique (gastric 

or surgical?), description of juveniles to be tagged, and collection and holding techniques. 

14. Relative significance of predation by smallmouth bass on juvenile salmonids in 

the tailrace of The Dalles Dam

Study Code: SPE-P-04-New Agency/Author: USGS / Theresa Liedtke, Jim Petersen, 

Matthew Mason

ISRP Comments:

Objective 1 seems to be important to pursue because of the relatively high rate of indirect mortality 

documented in The Dalles Dam (TDA) tailrace. It is also a worthwhile idea of trying a method that 

will identify the location where predation occurs because sampling of predatory fish in their holding 

areas may lead to a false impression as to the degree of predation, as a result of bias in the sample. 

A problem was noted in the statement that “We do not propose to make highly rigorous estimates, 

but rather will make estimates that are comparable between predator species and will answer a 

question such as, ‘Is the loss due to smallmouth bass twice (half) the loss due to northern 

pikeminnow?’’ It seems that the primary determinant in precision of the estimate will be the 

population estimates. Applying an appropriate number of tags and exerting an appropriate sampling 

effort should produce estimates that can be more precise than the objective specified, which seems 

quite loose. A more useful approach here might be one like proposal #11 adopted, imagine possible 

outcomes and possible applications. The context here is one of trying to account for losses of 

juvenile salmonids using the spillway as a route of passage at The Dalles. The estimate of interest is 

the portion of losses in the spillway that can be accounted for as due to smallmouth bass predation. 

Therefore, the beginning point should be a statement of those spillway losses (already given in other 

proposals), then move to description of a method to estimate the fraction due to predation (maybe 

both pikeminnow and bass). The precision needs to be sufficient to be able to compare with the total 

number. 

How will sufficient numbers of smallmouth bass and northern pikeminnow be collected to make 

reasonable estimates of population size, especially when you are stratifying sampling by habitat? 

The project sponsors have sampled here before and should have some data to set minimum sample 

sizes. 

The EMG methodology is an innovative approach that, if successful, could be applied towards 

numerous predator-prey questions. The EMG telemetry approach may be a viable approach for 

determining the exact time a predator fed, but if applied to the field there is no description of how 

the specific location of the event would be determined. It would help if the authors could add an 

Activity 2.2.4 (page 9), which would indicate that if Activities 2.2.2 and 2.2.3 were successful, then 

a procedure to determine specific locations of events in TDA tailrace would be initiated. There is no 

schedule for Task 2.2.
ISRP 2003-14 AFEP Part I. FY04 Pre-proposal Review

18

Bonneville Dam

15. Movement, distribution, and passage behavior of Radio-Tagged juvenile 

salmonids at Bonneville Dam associated with FPE and survival tests

Study Code: SBE-P-00-7 Agency/Author: USGS / Adams

ISRP Comments:

Many of the comments made on proposal 13 apply to this proposal as well. This proposal could be 

combined with the next one, #16, or an umbrella proposal could be done for Bonneville describing 

how these proposed studies are linked (plus other overlapping studies which may be gathering data 

on the same metrics but with different methods, such as hydroacoustics). The background is well 

done and the objectives clearly defined and justified. There is sufficient summary data from previous 

years in the Current Status Section of the proposal to build the logic for continuing to gather the 

same passage metrics in ’04, add FGE, and focus on passage efficiency and survival through the new 

corner collector at B2.

16. Estimating the survival of migrant juvenile salmonids through Bonneville Dam 

using Radio Telemetry: 2004 evaluations

Study Code: SPE-P-02-1 Agency/Author: USGS / Counihan

ISRP Comments: 

See comments on the survival proposal for The Dalles Dam (#12).

17. Hydroacoustic evaluation of juvenile salmonid fish passage efficiency at 

Bonneville Dam in 2004

Study Code: SBE-P-00-7 Agency/Author: PNNL / Gene Ploskey

ISRP Comments:

This is a very complete and well-done proposal. The overlap of hydroacoustic and radio telemetry is

beneficial and complementary, as long as the studies are well coordinated and the data are 

integrated. This is a key evaluation tool of the new corner collector at B2 and the designed coverage 

in this area with multiple tools is more than adequate. The only drawback is the seasonal limitation 

of stopping at July 15 because of the juvenile shad emigration, but radio telemetry can help fill in 

this void.

John Day Dam

18. Estimate the survival of migrant juvenile salmonids passing through John Day 

Dam using Radio Telemetry; 2004 evaluations

Study Code: SPE-P-00-7 Agency/Author: USGS / Counihan

ISRP Comments: 

Reviewers are hampered by a lack of sufficient detail on the questions to be addressed by these 

studies at John Day Dam (numbers 18, 19 and 20). It may be said that the methodologies are well 

described in 18 and 20, but hard to evaluate without a complete description of the overall study 

design. Objectives are well stated, but qualified by a statement, such as in Proposal 18, that the study 
ISRP 2003-14 AFEP Part I. FY04 Pre-proposal Review

19

design cannot be set/finalized until the “final set of objectives and hypotheses [are] selected” (by the 

regional managers?).

These proposals, numbers 18, 19, and 20 need to be considered in the context of: 1) a statement of 

the overall problem to be addressed along with 2) sufficient background information for the 

reviewers to understand what progress has been made, 3) explanation of how each proposal fits into 

the overall problem, and 4) a description of the line of investigation that has been and now is being 

pursued. After reviewing all three proposals it is perhaps possible to piece together what may be 

some of the necessary information. Proposal 20 is the most helpful because it provides some of the 

factual background information necessary to evaluate whether the steps taken to date are 

scientifically sound or not (one of the charges to the ISRP). 

Reviewers may deduce that two ideas regarding application of spill are being tested at John Day 

Dam, either or both of which might increase the effectiveness of spill as a passage alternative for 

juvenile salmonids. Since no improvements are specified at other passage routes, it appears that the 

study is based on a premise that increasing spill effectiveness will improve fish passage efficiency 

(FPE) and thus improve total survival of juveniles passing the project. However, it appears that there 

is a question about whether the method used to increase spill effectiveness might adversely affect 

survival in spill (proposal 18), whether routes of egress might be affected (proposal 19), in addition 

to the basic question about effectiveness of spill under the various spill scenarios being tested 

(proposal 20).

It appears that one idea being tested to date requires measurement of effects of spreading spill over a 

daily 24-hour period versus a 12-hour period at night, and the other test has to do with measuring the 

effectiveness of different amounts of spill (relative to total river flow), and (it appears) combinations 

of spill amount in the daytime versus nighttime (interaction effects?). These require measurement of 

the numbers of fish that choose spill as a passage route under the test conditions, and require 

measurement of the numbers of fish that choose other passage routes under each spill scenario, in 

order to arrive at estimates of FPE as in proposal 20. Survival would be measured in proposal 18 and 

egress in proposal 19.

A fully informed review might affect the decision about what spill combinations should be tested 

next, or what sequence of spills should be used next in the tests, as well as suggestions on a 

statistically sound study design that might more efficiently measure interaction effects.

19. Monitor tailrace egress at juvenile bypass system outfall under test discharge 

levels at John Day Dam

Study Code: SPE-P-00-7 Agency/Author: USGS / Liedtke

ISRP Comments: 

See comments under proposal 18. This is another ongoing study pre-proposal that suffers from the 

fact that it was prepared prior to analysis of 2003 data. This is an ongoing study, since 2000, but we 

don’t find any reports cited giving results of those studies. Results from previous research are 

required to determine if the research was conducted as designed and is producing the necessary data 

to effectively address the objectives. As with many of the ongoing studies, the methodology 

(descriptions of Tasks and Activities) is lacking in sufficient detail (e.g. description of fish to be 

tagged, radio tag description, type of tag insertion – gastric or surgical, holding protocols, set up of 
ISRP 2003-14 AFEP Part I. FY04 Pre-proposal Review

20

fixed receiving equipment, boat tracking protocols, etc). At least citations of more detailed 

descriptions of the protocols and equipment in previous reports or proposals should be included.

20. Estimate the fish, spill and juvenile bypass passage efficiencies, spill effectiveness 

and forebay residence times of radio-tagged juvenile salmonids relative to spill test at 

John Day Dam in 2004

Study Code: SPE-P-00-7 Agency/Author: USGS / Beeman

ISRP Comments: 

See comments under Proposal 18. The proposal says that spill efficiency and spill effectiveness are 

collectively referred to as SPE in this proposal (p. 3, paragraph 3). This does not appear to be helpful 

from the reviewer’s perspective. It simply introduces another set of initials and does not clarify the 

issue. It merely stirs together some parameters that are best viewed separately. The proposal also 

says Hansel estimated spill effectiveness as ranging from 1.1:1 to 2.4:1. Such a statement 

perpetuates an assumption that the relationship is linear. Whitney et al, 19971 reported that studies to 

that time had shown that the relationship is not linear. It would not be expected to be linear, based on 

expected behavior of salmonid smolts. Also, it appears that there may have been some transposition 

of numerator and denominator in the parameter for spill effectiveness, which logically ought to 

reflect the percentage of fish diverted in spill relative to the percentage of flow occurring as spill (not 

the inverse). Otherwise, one will obtain a very large whole number in cases where spill accomplishes 

little or nothing, when what is needed is a parameter that will reflect a percentage of fish passed in 

spill at various levels of spill relative to total flow. The resulting parameter will range from 0 to 

100% in the extremes. See Gary Johnson proposal SBE-P-00-17, footnote on page 2.

It is evident that the difference in FPE shown in Table 1, and referred to on page 4 as differences 

between years (with a note to the reader to check the different treatments between years) is actually 

due to treatments and not annual differences. The conclusion should have been clearly stated – that 

for chinook, when daytime spill is 30% of river flow and nighttime spill is at least 45%, FPE is 

higher with 24-hour spill than with12-hour spill. Increasing nighttime spill to 53% did not increase 

FPE. Providing 30% spill day and night did not improve FPE over the strategy of providing 54% 

nighttime spill for 12 hours with no daytime spill.

The spill treatment levels to be tested in 2004 are crucial to the design and therefore the evaluation 

of this proposal and the ones associated with it. Page 5 indicates the spill levels to be tested have not 

yet been decided. Information is given on page 6 as to the sample sizes of detected radio tagged fish 

required for two levels of precision. The levels of spill chosen for comparison may or may not 

conform to the ability of the study design to detect differences. 

It appears from Table 1 that daytime spill is quite effective for subyearling chinook. That being the 

case, a useful test would be something less than 30% daytime spill and less than 50% nighttime. 

Since the timing of migration of yearling chinook and steelhead is earlier than subyearling chinook, 

it ought to be useful to design a study that focuses on the spring period separately from the summer 

period when subyearlings are most abundant. That being the case, a spring study might test spills of 

30/30 versus 0/45 (ala 2002 test) to verify the results of the 2002 test. A summer study might test 

spills of 40/30 versus 30/40. A worthwhile, much needed study.

 

1 www.nwcouncil.org/library/1997/97-15.htm
ISRP 2003-14 AFEP Part I. FY04 Pre-proposal Review

21

Lower Snake River Dams

21. Hydroacoustic evaluation of fish passage at Ice Harbor Dam

Study Code: SPE-W-04-1 Agency/Author: COE / Smith

ISRP Comments: 

The ISRP received a cursory document for review, which the presentation characterized as a general 

scope of work prepared by the Corps, and not a true proposal. Thus, its status is ambiguous and 

difficult to review.

The study would use hydroacoustic techniques to determine the relative numbers of downstreammoving fish that pass through each passage route of Ice Harbor Dam (the proposal states spillway, 

turbines, and fish bypass in some places but only spillway and turbines in other places).

This proposal relates to the “Study Summary” of the same Study Code (SPE-W-04-1) entitled “Inriver fish passage and survival at Ice Harbor Dam”, which indicated performance between FY 2000 

and FY 2006 (apparently a continuing study, as was confirmed at the presentation). The summary is 

oriented primarily toward survival studies, although it states that “Fish behavior and horizontal 

distribution of both spring and summer migrants is also needed for decisions related to RSW 

placement.” The only Multi-Year Plan that seems to fit this proposal is “Ice Harbor 

Survival/Efficiency Study” updated June 30, 2003, which shows a performance period from FY 

2003 to FY 2006. The Multi-Year Plan does not include hydroacoustics studies, however, which is 

the topic of this proposal. Thus, there is an incomplete and ambiguous definition of need in the 

Corp’s justification documents. However, the ISRP understands that the SRWG is working on a 

study plan for Ice Harbor.

There is insufficient information in the proposal, Study Summary, or Multi-Year Plan to determine 

whether the proposed work is based on “sound science principles.” There is no justification for the 

work, and the proposal is written as a task order with specific contractual details. Insufficient 

background and context is given to evaluate the current level of knowledge and need for the work. 

Thus, it is impossible to judge the appropriateness of the objectives. 

Sufficient information and justification is not given to determine if the study design is scientifically 

sound or to establish whether there will be any “benefit to fish” (other than the statement that the 

Corps wants to increase survival), although such benefit can be imagined. There was no attempt to 

relate the study to that Corps’ goal. The four objectives and outcomes in the proposal are vague and 

unclear and are not clearly related to the eight objectives listed in the Study Summary. Tasks are not 

discussed in relation to objectives. 

The use of hydroacoustics is not justified, especially considering that the Multi-Year Plan included 

just radiotelemetry and use of PIT tags and the Study Summary is oriented mainly toward survival 

(which hydroacoustics will not provide). The proposal does not demonstrate that the Corps is getting 

what is needed with the hydroacoustic technique, although the technique is standardized and used 

often in Corps’ projects. There is some redundancy with telemetry techniques; the differences in 

information should to be presented. Hydroacoustics gives an amalgam of all fish. Because it is 

difficult to distinguish species with hydroacoustics, does the fyke net study provide enough ground 

truth for species identification? Is one abundant species driving the findings? Is it sufficient to track 

hatchery releases by the detailed hatchery release schedule? At downstream dams, the studies are 

stopped on July 15 because of shad, so later migrants are not monitored via hydroacoustics. Is this a 
ISRP 2003-14 AFEP Part I. FY04 Pre-proposal Review

22

problem at Ice Harbor? Radio telemetry, on the other hand, is limited by size (and whether mostly 

hatchery fish are tagged). This technique may be particularly biased against certain stocks such as 

those from downstream tributaries where migrants tend to be smaller, a deficiency that could be 

evaluated using data from hydroacoustics. In this, or perhaps another, proposal the relative values of 

hydroacoustic and telemetry information might be presented. 

These are probably important data to collect. However, the “proposal” is clearly a cut-and-paste 

from a prior year task order (without even changing some of the dates). As such it has no 

scientific/technical value for review. It might more appropriately be a task in a larger proposal on 

fish passage at Ice Harbor. 

Specific Comments 

1. Is this a recent version of Proposal 23 (see general comments, below)?

2. Objective a. is to monitor fish passage at two operational configurations at Ice Harbor 

Dam. Either in a COE RFP or in this proposal, the basis for this objective should be 

described. It seems that data must exist as a basis for some hypothesis that comparing fish 

passage under these two configurations will show some effect.

3. Statement d. doesn’t seem to be an objective.

4. Task 2.1.1.a – What basis is used to eliminate bays?

5. Task 2.1.1.c – Statement is not clear.

6. Task 2.1.1.d – What is the precision of estimates at Ice Harbor and on what is it based?

7. 2.1.2 – Second sentence is not clear.

8. 2.1.3 second paragraph – What information will they provide?

9. What is the error associated with the technology in applications such as proposed?

10. QA/QC. b. These methods should be included in the proposal.

11. How will you “truth” the data being obtained as to species and sizes?

12. Are survival experiments to be repeated several years in sequence with all conditions 

held constant (at least conditions that can be held constant)?

General Comments on Ice Harbor proposals 21, 23, 24, 25: 

The Ice Harbor proposals (Corps #s 21,23), USGS #25, and NMFS #24) are responses to a common 

RFP (Study Summary) implying that the COE has asked for proposals to meet specific information 

needs. The same specific Corps’ Study Summary is listed, and by implication the same Multi-Year 

Plan. However, both the summary and plan are short in length and amount of information, so 

tracking this defined need, and the abilities of the proposals to meet those needs, is difficult. 

Proposals # 21 and 23 appear to be outlines of study proposals similar to RFPs prepared by the 

Corps, which they then distribute to potential contractors. As they are now, each of these preproposals is incomplete. For example, the background sections lack references to previous studies 

and fail to identify pertinent passage or survival issues; there is no justification or rationale for 

objectives; study tests and treatments have not been determined; and detailed methodologies are 

lacking.

This group of proposals has considerable overlap. The general thrust of the proposals is to monitor 

where migrants “pass” the dam or dams, and their survival in passage. Understanding the context of 

the several proposals seems important. We learned during the presentations that proposals 21 and 23 

are open-ended placeholders by the Corps for someone’s (unidentified) funded project, whereas 

proposals 24 and 25 are competing proposals for the same work. 
ISRP 2003-14 AFEP Part I. FY04 Pre-proposal Review

23

With incomplete information about the Corp’s needs, one can only speculate about the relationships 

among these proposals in terms of both the techniques and species to be tested. Proposal 23 may be 

an earlier version of the Study Summary. Proposal 21 is to use hydroacoustic monitoring (chinook 

salmon mentioned in Proposal 23) of downstream migrant passage routes at Ice Harbor and Lower 

Monumental dams. The other proposals emphasize survival estimation. Proposal 25 is to use subyearling chinook salmon (hatchery) and radio-telemetry at both Ice Harbor and Lower Monumental 

dams to describe migration path and survival in passage. Proposal #24 has similar objectives (now 

understood to be competing). It is a proposal to conduct experiments at Lower Monumental, Ice 

Harbor, and McNary dams using yearling and sub-yearling chinook salmon, and yearling steelhead 

captured in upstream traps. The fish will be fitted with radio and PIT tags prior to release at sites 

upstream and downstream of these dams. Projects 24 and 25 intend to estimate survival in each 

passage route. Unless there is some suspicion that the radio-telemetry projects will not get accurate 

estimates of migration route choices, and that this deficiency can be overcome with hydro-acoustics, 

the latter seems to be redundant. A choice between Project 24 and 25 seems to depend on how well 

they each responded to the RFP (Study Summary). The Study Summary did not call for applications 

of all these technologies to compare results and the Multi-Year Plan does not even mention 

hydroacoustics (but calls for radiotelemetry and PIT-tags). The Corps does not seem to desire 

information that requires application and comparison of technologies, suggesting that this difference 

among proposals merely reflects each proponent’s favorite technique.

At least some of these projects are to continue work in progress, which makes comparison with new 

proposals difficult. Project 24 is based on Corps-funded work from several previous years, and it 

asks for support to continue another year. Project 21/23 also seems to be a request to continue, and 

the USGS proposal 25 appears to be new (although not designated as such). Project 21 intends to 

estimate how many fish during the smolt migration pass via each possible passage. All of the 

proposed work, absent crippling problems with river conditions or sample size, will help to 

characterize results for the specific fish they use and for the dam-river conditions during the tests in 

2004. 

There seems to be a need for closer collaboration among these projects if they are to be conducted 

concurrently. The proposals have several similar objectives, potentially conflicting techniques, and 

may interfere. Efficiencies may exist by combining equipment and personnel, and sharing similar 

objectives. 

The proposals were prepared absent complete information concerning expected operating conditions 

at Ice Harbor Dam, sources of fish, and numbers of fish. If the number of fish required by the power 

analyses cannot be obtained, will the projects be terminated? If they proceed with insufficient 

numbers of fish, will the results be useful to the fisheries managers?
ISRP 2003-14 AFEP Part I. FY04 Pre-proposal Review

24

22. Hydroacoustic evaluation of fish passage at Lower Monumental Dam

Study Code: SPE-W-04-4 Agency/Author: COE / Smith

ISRP Comments:

The presentation characterized this “pre-proposal” as a general scope of work prepared by the Corps, 

and not a true proposal. Thus, its status is ambiguous and difficult to review. It is an almost exact 

copy of Proposal 21 on Ice Harbor Dam, to the extent that the name Ice Harbor remains in the text. 

The study would use hydroacoustic techniques to determine the relative numbers of downstreammoving fish that pass through each passage route of Lower Monumental dam (the proposal states 

spillway, turbines, and fish bypass in some places but only spillway and turbines in other places).

This proposal relates to the “Study Summary” of the same Study Code (SPE-W-04-4) entitled “Inriver fish passage and survival at Lower Monumental Dam”, which indicated performance between 

FY 2004 and FY 2006. The summary is oriented primarily toward survival studies. The only MultiYear Plan that seems to fit this proposal is “Lower Monumental Survival/Efficiency Study” updated 

June 30, 2003, which shows a performance period from FY 2003 to FY 2006. The Multi-Year Plan 

does not include hydroacoustics studies, however, which is the topic of this proposal. Thus, there is 

an incomplete and ambiguous definition of need in the Corp’s justification documents. However, the 

ISRP understands that the SRWG is working on a study plan for Ice Harbor, which may extend to 

Lower Monumental.

At item e. in the list of data requirements, the government should have specified the level of 

precision desired, i.e. “95% confidence intervals with a permissible range of X% of the point 

estimate.” 95% C.I. alone is not sufficient, when the range might be from 0 to 100%.

No details are given on the methods (calculations) to be used in expanding the hydroacoustic counts 

into estimates of fish numbers.

See comments on the nearly identical Proposal 21. 

23. Direct injury/ survival of juvenile chinook salmon passing through the spillway at 

Ice Harbor Dam

Study Code: SPE-W-04-1 Agency/Author: COE / Smith

ISRP Comments:

The presentation characterized this “pre-proposal” as a general scope of work prepared by the Corps, 

and not a true proposal. Thus, its status is ambiguous and difficult to review. Much of what is to be 

done has yet to be determined (sources of fish, which spillways, which spill levels, etc.).

This proposal (really a brief statement of work) would use unspecified technologies to estimate 

direct injury to fish passing through Ice Harbor Dam under two operating conditions yet to be 

specified. This proposal relates to the “Study Summary” of the same Study Code (SPE-W-04-1) 

entitled “In-river fish passage and survival at Ice Harbor Dam”, which indicated performance 

between FY 2000 and FY 2006 (apparently a continuing study, as was confirmed at the 

presentation). The summary is oriented primarily toward survival studies, which is the subject of this 

“proposal.” The only Multi-Year Plan that seems to fit this proposal is “Ice Harbor 

Survival/Efficiency Study” updated June 30, 2003, which shows a performance period from FY 
ISRP 2003-14 AFEP Part I. FY04 Pre-proposal Review

25

2003 to FY 2006. This “proposal” appears to be an early draft of the Study Summary. The ISRP 

understands that the SRWG is working on a study plan for Ice Harbor.

There are no methods given, so it is impossible to judge whether the work would be based on sound 

science principles. There is a presumed benefit to fish from determining the current survival in 

spillways, but this is not discussed. The single objective of determining direct injury and survival is 

clearly stated. No information on data analysis is presented and no relationship is drawn between this 

data collection and any decision.

See general comments about proposals 21, 23, 24, and 25 under Proposal 21. 

24. Fish Passage and Survival at Lower Snake River and McNary dams

Study Code: SPE-W-04-1 Agency/Author: NMFS / Eppard

ISRP Comments:

This is a relatively complete proposal. However, this evaluation recognizes that some operational 

features of the study (mainly spill regimes at all dams and turbine operating features at McNary) are 

incomplete pending decisions about operation of the hydropower system in 2004. Study details 

sufficient to make a determination whether this proposal or Proposal 25 is better are not provided in 

the proposal (although this proposal extends its work to McNary). The proposal says they will “... 

estimate relative survival... under existing operations at Ice Harbor Dam”, and further on “under 

existing operations at McNary Dam.” The ISRP has two questions: 1) What are the “existing 

operations”, and 2) Is there a basic problem that lies behind the objectives to measure survival 

“under existing operations”, i.e. are operations likely to vary, and thus affect relative survivals? If so, 

then the ISRP would need to review a more complete study plan.

This proposal would use radio-telemetry (primarily) and PIT-tag technologies to determine and 

evaluate route selection, passage timing and survival of juvenile salmonids passing Lower 

Monumental, Ice Harbor, and McNary dams under operational and experimental conditions yet to be 

determined by the Corps. This proposal relates to several study summaries: SPE-W-04-1, “In-river 

fish passage and survival at Ice Harbor Dam”, which indicated performance between FY 2000 and 

FY 2006 (apparently a continuing study, as was confirmed at the presentation); SPE-W-04-1, “Inriver fish passage and survival at Lower Monumental Dam” (FY04-06; apparently a new study 

although not designated as such); and OTS-W-04-1 (New), “Research to establish new turbine 

operating guidelines at McNary Dam”. The first two summaries are oriented primarily toward route 

of passage and survival studies, which is the subject of this proposal. The third Study Summary is 

related to determining survival under different operating conditions of McNary Dam turbines. The 

Multi-Year Plans that seem to fit this proposal are “Ice Harbor Survival/Efficiency Study”, which 

shows a performance period from FY 2003 to FY 2006, “Lower Monumental Survival/Efficiency 

Study” (2003-2006), and “McNary Survival/Efficiency Study” (2004-2006). All one-page multi-year 

plans were updated June 30, 2003. These “plans” give little planning, however, the ISRP 

understands that the SRWG is working on a study plan for Ice Harbor.

The proposal provides useful information directly and by reference to indicate that the work will be 

based on sound scientific principles. There is an overall goal and several objectives, all of which 

focus on evaluation of components of the overall goal. It might have been stated that the real 

objective is to have highly effective fish passage. There is sufficiently clear reference to Biological 

Opinion decisions to infer a benefit for fish of obtaining this information. There are clearly defined 
ISRP 2003-14 AFEP Part I. FY04 Pre-proposal Review

26

objectives with evaluation of collected data as the outcome. The planned data analyses are not given 

in detail, but prior successful work is referenced liberally. This is a monitoring study with evaluation

as the main objective. This seems adequate for this brief proposal format.

The reviewers liked the double tagging method proposed in this study (radiotelemetry and PIT tags). 

Side-by-side comparisons of passage estimates using the two technologies are needed to resolve 

some uncertainties raised by previous studies.

Detailed Comments: 

1. Objective 1 is limited to “existing operations at Lower Monumental Dam.” Shouldn’t it 

also be limited to the stock, brood, size/condition of fish used, and for the dates of the 

experiment? Reviewers had the same comment for other objectives.

2. Objective 6 – Isn’t there an inconsistency here? All other objectives are to be conducted 

under existing operating conditions, but this objective requires manipulation of the operating 

configuration. Is this proposed as an optional objective assuming that the Corps can provide 

two spill conditions for comparison? 

3. It would have been helpful to reviewers to add brief comments on page 5 to explain 

application of both radio and PIT tags.

4. Page 5 – When “regrouped” are their numbers to be supplemented when needed? If so, 

what is the assurance that all fish will perform comparably?

5. Page 6 – last sentence – What are “reasonably precise estimates?” Shouldn’t sample sizes 

be set based on a desired precision? If that sample size cannot be obtained, managers have to 

consider whether it is worth proceeding.

6. Critical Limitations: What is being done/proposed to ensure that these limitations do not 

preclude completion of a successful project? How will survival be estimated? How are 

assumptions associated with survival estimation being verified? Is interference from other 

telemetry projects likely and, if so, how will it be eliminated? If the assumptions cannot be 

verified, are the data to be produced useful to action agencies?

Also, see general comments on proposals 21, 23, 24, and 25 under Proposal 21. 

25. Survival and migration behavior of sub-yearling juvenile Chinook salmon at Ice 

Harbor and Lower Monumental Dams, 2004

Study Code: SPE-W-04-1 Agency/Author: USGS / Adams

ISRP Comments:

This is a preliminary proposal, pending more details on the study design (e.g., spill experimental 

design from the Corps). The proposal needs more detail to be amenable to an ISRP technical review. 

Insufficient information is presented to adequately compare this proposal with Proposal 24 

(apparently competing proposals), especially since the scopes are quite different. 

This proposal would use radiotelemetry to establish the migration routes and survival of just juvenile 

sub-yearling Chinook salmon at Lower Monumental and Ice Harbor dams. It is in direct response to 

two of the Corps’ Study Summaries: SPE-W-04-1, “In-river fish passage and survival at Ice Harbor 

Dam”, which indicated performance between FY 2000 and FY 2006 (apparently a continuing study, 

as was confirmed at the presentation); and SPE-W-04-1, “In-river fish passage and survival at Lower 

Monumental Dam” (FY04-06; apparently a new study although not designated as such). The MultiYear Plans that seem to fit this proposal are “Ice Harbor Survival/Efficiency Study”, which shows a 
ISRP 2003-14 AFEP Part I. FY04 Pre-proposal Review

27

performance period from FY 2003 to FY 2006, and “Lower Monumental Survival/Efficiency Study” 

(2003-2006). The full context of past and proposed work is not clear from either the Corps’ 

documents or this proposal. The ISRP understands that the SCT is working on a more detailed study 

plan for Ice Harbor.

No specific study design has been proposed for this evaluation, according to the authors. The 

proposal is developed around an assumption that there will be two treatments at Ice Harbor Dam 

during the summer, and two at Lower Monumental. Apparently the “treatments” to which this refers 

are spill levels that may be tested. The ISRP is asked to review the proposal on the basis of this 

assumption, and an assumption that the expected differences in passage can be detected within the 

limits of the system described on pages 7, 8., and 13. The ISRP review is contingent on this 

assumption being met. The background information tells the reader that little work on this subject 

has been conducted during the summer outmigration. 

On page 12 reference is made to studies by Muir et al., 1995, and Eppard et al., 2002, that produced 

estimates of survival using PIT tag technology, but says that no radio-telemetry investigation has 

been undertaken during the summer. What differences in information are to be expected from these 

two techniques? Are both methods needed? Are the estimates comparable? It seems that some 

further justification is needed, not simply that it is a different technique.

Reviewers objected to some of the cut-and-paste redundancy, but the objectives and tasks are clearly 

laid out. Discussion of assumptions is excellent. These are experienced telemetry researchers and 

they should be able to produce very useful results on both passage routes and survival. 

Detailed Comments: 

1. It would help reviewers if the introductory material included some review of what is 

known about passage at these dams. It is suggested that recent studies of sub-yearling 

passage have not been conducted, but results from earlier studies and those on yearlings 

might be instructive to include here.

2. The goals are far too broad for what is proposed by implying they will describe relations 

between fish performance and spill, powerhouse operations, varying flows, pool levels, 

turbine operations, and spill volumes. The results are in fact likely to reflect only conditions 

at the time of testing and the specific fish used in the test. 

3. To what does the statement “relative survival” apply in the third goal statement?

4. Won’t the source of fish and their characteristics influence the results?

5. Isn’t Objective 1 overstated because a range of conditions will not be studied?

6. The two operating configurations to be tested have not been selected. What is the basis on 

which the selection will be made? Does the existing information suggest a hypothesis that is 

to be tested by use of these two configurations? Knowing answers to these questions is 

important for a number of reasons. The study plan would probably differ, plus the study 

design might benefit by inclusion of a more efficient rigorous statistical design. The very 

choice of spill levels to be tested might benefit by review that could make that kind of 

suggestion. There is a need to make a more direct connection between past, present, and 

future levels of spill – or other variables to be included in the study plan. A good plan should 

specify alternatives to be tested that build upon outcomes of past and current results. See 

PNNL proposal 11, which discusses expected results and applicability.

7. Are there to be two operating configurations at both Ice Harbor and Lower Monumental? 

If so, will they be separate in time? 
ISRP 2003-14 AFEP Part I. FY04 Pre-proposal Review

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8. Page 5 - If only 36% of steelhead were traveling in the upper 12 ft of the reservoir, how 

can researchers conclude “... that flow nets near the surface may be more effective for 

passing juvenile salmonids”?

9. Page 6 – What are the data that led to a conclusion that “... the MITAS system has 

enhanced our ability to determine the approach paths and routes of passage relative to spill 

conditions and surface bypass tests.”

10. Page 9, Activity 1.1.1 and Activity 1.1.2 – Isn’t the best possible configuration 

determined at each installation site? The technology is put forth here as a means to gather 

the data described in the goals and objectives, but it now reads as though its applicability has 

to be determined. If the technology needs to be proved, a separate proposal is needed with 

that as a goal.

11. How will researchers eliminate the possibility that a tagged fish may respond differently 

to passage challenge than does an untagged fish?

12. The “dead fish release” procedure is somewhat unclear. A dead fish has an identifying 

coded tag but will just drift with currents, correct?

13. Task 1.6, Activity 1.6.1 – Include a brief statement of results (e.g., any significant 

problems?). What does “relatively small” mean? Under Schedule: What will be the basis for 

this decision?

14. Objective 2 text: Fish from Lower Monumental release: How will these fish be 

accounted for in the Ice Harbor experiment? Is there any chance that successful Lower 

Monumental migrants will be more successful in passing Ice Harbor because of their success 

at Lower Monumental? Wouldn’t that confound any results if supplemental fish were 

required for Ice Harbor test?

15. Task 1.5.1 – This again sounds like the technology may need further development before 

the proposal can proceed with confidence that the goals and objectives can be met.

16. Pages 17-19: Given that survival is a highly contentious issue, shouldn’t actions be taken 

to test whether or not the listed assumptions are appropriate? If the assumptions are not 

verified, are the data to be produced any better than no new data?

17. Page 20, Impacts to other researchers: How much reduction of multiple signal collisions 

and unwanted detection was produced? 

Comments on the relative merits of proposals 24 and 25 (26): 

The scopes of the two studies are different. Proposal 24 (NMFS) is broader, for it plans to study 

McNary Dam as well as Ice Harbor and Lower Monumental, river-run hatchery yearling chinook 

salmon as well as sub-yearling chinook, and use PIT tags as well as telemetry for Ice Harbor. It also 

intends to address the issue of different turbine operations at McNary. Proposal 25 would focus on 

just subyearlings at only Lower Monumental and Ice Harbor. Depending on funding, Proposal 24 

may be overstretching (and thus do a poorer job by attempting to cover too much) but Proposal 25 

may be too limited in scope for the Corps’ needs. Both studies are well formulated to the extent that 

it might be possible to develop a proposal with uncertain experimental treatments to be determined 

by the Corps. However, the Corps should recognize that adequate peer review might contribute 

meaningfully to design of an experiment that would specify the experimental treatments and thereby 

most efficiently address the questions or problems under study.

An attempt to compare these two proposals brings out the fact that planning for such research on the 

Lower Snake River dams and McNary needs to be improved. The planning lacks sufficient 

emphasis on long-range applicability of alternative outcomes of studies. Although both proposals 

nominally respond to the same Corps requests (Study Summaries and Multi-Year Plans), the “one-
ISRP 2003-14 AFEP Part I. FY04 Pre-proposal Review

29

pagers” and the one-page “plans” lack specificity on the Corps’ intent so that quite distinct scopes 

are proposed. In both cases, the operational features to be compared are not known (not yet 

established by the Corps) so that any semblance of hypothesis formation and experimental design is 

impossible. Such details should not be left to the last minute, or the research will suffer. Only when 

it is clear what is wanted and why, can reviewers decide whether one proposal or the other has a 

better chance of success.

Pre-proposal 26 appears to be the McNary portion of pre-proposal 25, which would make the more 

logical comparison to be between pre-proposal 24 and the combination of pre-proposals 25 and 26.

26. Survival and migration behavior of juvenile salmonids at McNary Dam, 2004

Study Code: OTS-W-04-1 (NEW) Agency/Author: USGS / Perry

ISRP Comments: 

This project would use radiotelemetry to evaluate passage and survival of both yearlings (chinook 

and steelhead) and underyearlings (chinook) at McNary Dam, including evaluation of alternative 

turbine operating modes (to compare survival at operation slightly off peak efficiencies). It responds 

to a new Study Code (OTS-W-04-1) and the Study Summary of the same number. The most relevant 

Multi-Year Plan is “McNary Survival/Efficiency Study” although that one-page plan does not 

mention studies of turbine operating efficiency. The ISRP was told the study is directed at a longterm McNary modernization project, which is fitting new turbines. The set of one-pagers and the 

proposal do not do a sufficient job of explaining the broader context, however. 

Furthermore, two objectives (3 and 4) of this proposed study are to estimate survival of juvenile 

salmonids in passing through turbines at McNary Dam when operated other than within 1% 

efficiency. The proposal goes to lengths to estimate sample sizes of fish required, but tells the 

reviewer nothing about what efficiency levels are planned to be tested. The reviewer is left with no 

basis for determining the likelihood of success of this study, or potential applicability of results. See 

ISRP comments under proposal 18 (pertaining to the set for proposals 18, 19, and 20) for details that 

are needed.

This proposal is roughly equivalent to the McNary portion of NMFS’ Proposal 24, which lumped the 

Lower Monumental, Ice Harbor, and McNary work in one proposal. It is apparently the USGS’s 

answer to OTS-W-04-1 but in a separate proposal. The proposal adapts the Lower Monumental/Ice 

Harbor proposed methods to the McNary location. The details of the Corps’ study plan are not 

available, so the proposal lays out what it can without those details. 

To the extent possible with incomplete plans by the Corps, this is a well-written proposal by a group 

that is well qualified to do the work. However, as the ISRP stated in the review a similar proposal in 

the Council’s Fish and Wildlife Program Mainstem/Systemwide project selection process (see 

proposal 350232), the ISRP does not feel that it is appropriate to include the cost of this study in the 

fisheries budget because the expected benefits to fish survival are miniscule. As Dr. John Skalski 

responded to our question during the oral presentation by Dalip Mathur at that time, when one 

considers the fish guidance efficiency of the turbine intake screens and the implementation of the 

spill program, the proportion of fish approaching the project that end up passing through the turbines 

 

2 www.cbfwa.org/cfsite/ResultProposal.cfm?PPID=SW2003000035023
ISRP 2003-14 AFEP Part I. FY04 Pre-proposal Review

30

is very small, so any improvement in total survival of fish passing the project that might be expected 

from changes in turbine efficiency would be extremely small. 

27. Evaluation of juvenile salmonid condition in McNary Dam gatewells with 

prototype vertical barrier screens under various turbine operating conditions

Study Code: OTS-W-04-1 (NEW) Agency/Author: NMFS / Absolon

ISRP Comments: 

This is a minimal proposal for fairly straightforward work, which is described but with little 

background and justification. 

This study would characterize and compare the physical damages, if any, to samples of yearling 

chinook, steelhead and sockeye and underyearling chinook in gatewells and the fish bypass system 

of McNary Dam in two tests: (1) new vs existing vertical barrier screens (VBS) (at high turbine flow 

rates) and (2) three turbine flow rates representing peak turbine efficiency, best turbine geometry, 

and maximum turbine discharge. Fish would be obtained from gatewells, PIT-tagged, and returned 

to the gatewells and sampled in the juvenile fish facility of the fish bypass system and subsequently 

downriver in the Smolt Monitoring Program.

The study responds to Study Summary OTS-W-04-1 (New). The summary calls specifically for 

evaluations of gatewell conditions for these fish species/ life stages (presumably meaning fish 

condition in the gatewells). The relevant Multi-Year Plan is “McNary Survival/Efficiency Study”. 

Although brevity obscures many details of methods, the numbers of fish needed for statistically 

meaningful results have been determined. 

There is little context provided for the work. Only brief reference is made to results of prior year’s 

studies, which are mentioned in the Summary. 

Surface Bypass

Lower Granite Dam 

28. Migrational characteristics of juvenile sub-yearling salmon in the forebay of 

Lower Granite Dam relative to removable spillway weir tests, 2004

Study Code: SBE-W-96-1 Agency/Author: USGS / Adams

ISRP Comments: 

This is a well-written, reasonably complete proposal for continuing fish behavior studies at the 

experimental removable spillway weir at Lower Granite Dam. Ample background is provided, 

including results of prior work (except for 2003, which was still being analyzed). Details and 

rationale are included about numbers of fish to be tagged, placement of receivers, experimental 

design (generalized from prior years’ experiences, in absence of Corps’ information), assumptions 

for survival testing, etc. This work and this contractor have yielded important information in the 

past.
ISRP 2003-14 AFEP Part I. FY04 Pre-proposal Review

31

This is a proposal to conduct radio-telemetry studies of subyearling chinook salmon in the forebay of 

Lower Granite Dam during experimental trials of the removable spillway weir by the Corps. Routes 

of passage and behavior in the forebay would be determined using small radio tags and an array of 

fixed antennae on or near the dam. Sufficient fish would be tagged to obtain the statistical 

significance of results. Focus would be on the fish’s selective use of the removable spillway weir. In 

addition, survival would be estimated for passage routes using control releases below the dam and 

the standard Route Specific Survival Model. The proposal responds to Corps’ Summary Code SBEW-96-1, and is a continuation of prior studies (the subyearlings had not yet been studied). Clear 

objectives are listed and discussed, and the relevant specific research need of the Corps’ Summary is 

indicated.

However, the proposal lacks operational details, which are to be provided later by the Corps. On 

page 4 the proposal states, “Because the Corps has not given us a detailed study design, it is difficult 

for us to conduct a rigorous power analysis.” Without knowing the detailed study design it is not 

possible to conduct a rigorous peer review. 

Questions regarding further development of the study design include: 

1) Will the study involve alternating periods with the removable spillway weir in place and 

not in place? 

2) Will the study design involve varying amounts of flow through the removable spillway 

weir? 

3) Will there be combinations of varying flows and removable spillway weir in place and not 

in place?

Such designs deserve scrutiny by a peer review group to help assure that the most efficient study 

design is developed.

The Dalles Dam

29. Fish passage studies for surface flow bypass development at The Dalles Dam

Study Code: SBE-P-00-17 Agency/Author: PNNL / Johnson

ISRP Comments:

This proposal is well developed and thorough. The details on data acquisition and analysis are 

reassuring given that the investigator is familiar with the kinds of problems to be dealt with, knows 

how to collect useable data, and analyze them to produce useful results. The hydroacoustics 

approach (its deployment in the field and its analytical techniques) has been well developed by 

Johnson, Ploskey, and colleagues over the years and is a valuable tool for Columbia River research. 

This is an appropriate application. It would be helpful if the title had the word hydroacoustics in it to 

distinguish it from all the radiotelemetry studies. As noted for Proposal 21, the relative justifications 

of hydroacoustic and telemetry techniques (alone or together) might be presented.

The hydroacoustics passage metrics (fish passage efficiency, spill passage efficiency, spill 

effectiveness, and sluice passage efficiency) overlap with the radio telemetry passage metrics (Study 

# 13). This is a strength in the ’04 program (having independent estimates of the same metrics), as 

long as there is good coordination amongst researchers and integration of study results. It would be 

helpful if the authors included a brief rationale or justification following each objective. It seems that 

this is a format followed in many of the other pre-proposals. On page 7, under the heading 
ISRP 2003-14 AFEP Part I. FY04 Pre-proposal Review

32

“Experimental Design”, we read, “If the comparison of east vs. west sluice passage is implemented 

(Objective 3), then a randomized block experimental design will be necessary...” But what if there is 

a different question asked by the managers? What would be the statistical method of analysis? Under 

the heading “Expected Results and Applicability”, we read, “ The results from this study and others 

will provide the region with information to make decisions regarding long-term smolt protection 

measures at The Dalles Dam”. The statement is inadequate. It provides no understanding of the 

context for this study. What is the problem at The Dalles Dam and how will information from this 

study help with management decisions? 

The proposal anticipates the study lasting through 2007 (p. 10) but there is no indication of the plans 

for years after 2004. At the top of page 10 there is a section titled “Analysis of Fish Movement and 

Hydraulic Data” that relates to the analysis of data obtained by the acoustic camera. It was not found 

in the analysis methods in SBE-P-00-07, where the authors indicated to locate it. Therefore, it is 

probably in some other proposal. The authors should include a brief description (in this section) of 

how these data will be analyzed.

30. Distribution and movement of fish and flow upstream of The Dalles Dam and 

implications for Surface-flow bypass

Study Code: SBE-P-00-17 Agency/Author: PNNL / Faber

ISRP Comments:

This is another case of where the radio telemetry and mobile hydroacoustic studies overlap in the 

study objective to determine the movement and distribution (approach patterns) of smolts as they 

enter into the forebay of The Dalles Dam. Again, this may be a strength in the 2004 program, to have 

independent estimates of movement patterns for the same area, as long as the researchers coordinate 

well and work together in integrating the resultant data. 

In the second paragraph of page 3, the authors indicate that the flow information in the forebay of 

The Dalles Dam will be acquired using acoustic Doppler current profilers and an existing CFD 

model. A description of the existing CFD model or a reference for the model needs to be included in 

the proposal. 

It would be helpful if the authors included a brief rationale or justification for each objective (page 

4). This study proposes to describe the distribution and movements of juvenile salmonids in the 

forebay of The Dalles Dam and is built around the hope that some means can be found to divert fish 

away from the powerhouse and toward the spillway. Whitney et al. 19973 summarizes attempts to 

accomplish this feat. Generally, forebay diversions of that sort have not been successful for a lot of 

reasons. Collection of fish in the forebay for transfer to below the dam has been accomplished in 

several locations, where the numbers of fish and the sizes of the powerhouses (projects) are not as 

large as The Dalles or other mainstem dams, Whitney et al., 1997. It would be good if the authors 

could insert some text in the background describing some of the difficulties faced in attempting to 

divert or guide juvenile fish in a large forebay environment. Possible outcomes of the study should 

be specified, along with a discussion of the possible applications. That would be the place to review 

Whitney et al., 1997. The basis for this study (possible application of a forebay diversion device) is 

highly doubtful, based on much past experience. The information could be useful for other purposes. 

 

3 www.nwcouncil.org/library/1997/97-15.htm
ISRP 2003-14 AFEP Part I. FY04 Pre-proposal Review

33

Fish flux (on page 10)? As this is not a common term, a definition is needed. What is the “ERDC 

portion” mentioned in the budget section? This was not mentioned in the text. 

General comment – It is a novel approach that they will be looking at fish distribution as they 

approach the immediate forebay, not just determine where the fish go through the dam (where they 

are coming from as well as where they are going). Most research is too concentrated on just 

calculating passage routes. The study might even go farther upstream. The integration with 

hydrodynamics is good, although it would be better to get more information than just strain. Some 

predictions of fish presence in the hydraulic regime using Andy Goodwin’s model (reference 

needed) might give a hypothesized fish distribution that could be tested by the empirical data, rather 

than using the model in a strictly retrospective way. This would be a novel “hypothesis testing” 

approach for the Columbia River work. It would have been good to see some data demonstrating that 

placing the sensors at a distance ahead of the boat motor is sufficient to prevent fish avoidance 

during motorized transects (boat motors are noisy underwater even at a distance, as swimmers 

know). It is recommended that the ADCP data collected in the forebay not be time averaged 

immediately, so that the details of turbulence can be retained. 

31. Three-dimensional behavior and passage of juvenile salmonids at The Dalles 

Dam, 2004

Study Code: SBE-P-00-17 Agency/Author: USGS, PNNL / Cash, Faber

ISRP Comments:

The general approach of developing 3-dimensional fish locations and trajectories in the forebay to 

correlate with hydraulic information and the model by Andy Goodwin (better reference for this 

model is needed) is especially good. As in project SBE-P-0017 (#30 above), it would be interesting 

to have Goodwin make some predictions of fish movement using the hydraulic data and test those 

predictions with the empirical data. Relevance to the RPAs should be described, not just the numbers 

provided. Dates on the Activities were wrong (2004 should be 2003 in several places). 

In the rationale section following Objective 1, the authors indicate that a 3-D system would allow us 

to gather continuous data on fish as they move through The Dalles Dam forebay and especially need 

detailed movements in the area 400m upstream of the dam. However, all 3 tasks (1.1, 1.2, and 1.3) 

indicate that the 3-D system will be deployed to monitor juvenile salmonids just upstream of the icetrash sluiceway. Is it correct to assume that Objective 2 is proposing to cover the 400m up river of 

the dam? The areas of the forebay that will be acoustically monitored for tagged fish movements and 

distribution need to be more clearly delineated and described. There are several places where 

statements are made referring to 3-D study results (e.g. “played a critical role in the development of 

the surface bypass concept throughout the Columbia River Basin.” paragraph 3, page 3) without 

giving references to reports or papers backing up these claims. Again, at the top of page 6, the 

authors state that “In 2000, 2001, 2002, and 2003 the use of 3-D systems was fully implemented at 

Lower Granite Dam (USGS) and Bonneville Dam, powerhouse 1 (USGS, Battelle, WES).” but no 

references are given. Are reports documenting results of these numerous studies available, or are 

they still in preparation or review? 

The problem with gastric implantation of tags is not clearly stated, as this was the standard 

procedure in the 1960s and the techniques were well developed for adults (smaller scale would work 

for juveniles). On page 10 it sounded as though collection of ADV and ADCP data was not certain. 

This seems essential to have. Getting the equipment (purchase and deployment) will be a large cost, 
ISRP 2003-14 AFEP Part I. FY04 Pre-proposal Review

34

but the study objectives seem worth it. If there is no equipment yet, how is this classified as a 

continuing project?

Adult Studies

32. Evaluation of adult salmon and steelhead migrations past dams, through 

reservoirs, and into tributaries in the lower Columbia River-2004

Study Code: ADS-00-1 Agency/Author: U of I, NMFS / Peery, Burke

ISRP Comments:

It was helpful to have the title page say that this is a continuation proposal (for most proposals, this 

had to be deciphered from the text). The proposal did not initially give the gist of the past results to 

see the logic of what was being proposed, although some good description was given later in the 

proposal. The methods were not explained in the proposal (statements like “same as last year” do a 

reviewer little good). The methods in the Project Summary did not even tell what kind of tag is used 

(sonic, radio, archival, etc.). There is actua lly good use of past data, although these data seem to 

have accumulated without much evaluation as the study years rolled along. There is only one past 

report cited for this long-continued study (are there others that we are supposed to know about 

already?). The number of fish to be tagged was determined as the minimum number to “fully 

evaluate passage conditions”, but how would the authors know? Would researchers ever “fully” 

evaluate passage conditions? It was not clear whether the work in 1c (page 9) is actually being 

proposed (3-d acoustic tracking and DIDSON acoustic camera). The information provided is not 

sufficient for peer review. Given the apparent lack of reports on previous work, the planned multiyear summaries and model are excellent and much needed, as is the web-based data archive (could 

this be set up and supported by the region like that for PIT tags).

33. Professional Services: Research and Monitoring Involving Radio Telemetry of 

Adult Salmon and Adult Lamprey Throughout the Watersheds of the Walla Walla 

District [Salmon and adult lamprey throughout the watersheds of Walla Walla 

District]

Study Code: ADS-W-00-1 Agency/Author: U of I / Peery

ISRP Comments:

Research and monitoring of adult lamprey is included in the title of this proposal, but nothing 

appears in the proposal regarding lamprey. Is this one linked to proposal #36? This is a relatively 

weak pre-proposal, with proposed 2004 research stated in mostly very general terms in the text at the 

end of each objective or sub-objective description. With the exception of the temperature work 

proposed (Objective 5), which is fairly well detailed, the proposed studies for 2004 need to be 

described in much more detail before an adequate technical review can be done. As stated for the 

previous proposal # 32, it appears that many years of radio telemetry studies on adult salmonids have 

been done, but reports documenting the results are lacking. The information provided is not 

sufficient for peer review.
ISRP 2003-14 AFEP Part I. FY04 Pre-proposal Review

35

34. An evaluation of abundance, downstream passage behavior and return rates from 

steelhead kelts passing Lower Columbia River dams; including a post construction 

evaluation of modifications to The Dalles Dam spillway and the Bonneville 

powerhouse II corner collector

Study Code: ADS-02-6 Agency/Author: COE FFU / Wertheimer

ISRP Comments: 

This is an interesting proposal for an ongoing study that is examining passage of steelhead kelts 

through the Lower Columbia hydrosystem projects. The proposal outlines work proposed for the 

third and final year of the study. It contained quite a bit of information, but not enough to allow a 

thorough scientific or technical review. Because this is the final year of a three-year study, there 

should be a synthesis of data in the proposal. 

Based on the presentation and the small amount of data presented in the proposal, the return rates 

seen so far are poor. It is important that this study be coordinated with USACE and tribal kelt 

studies in the Snake River (centered around Lower Granite Dam) and the Yakima River. 

Information from the Lower Columbia River study could inform the upriver studies. Such 

coordination may already be in place, however, neither the proposal nor the presentation described 

other kelt studies in the Columbia River basin and how they might be linked into a greater 

understanding of present and potential spawning contributions from naturally or artificially 

reconditioned steelhead kelts. For example, information from upriver and lower river studies 

together might show that upriver reconditioning and release of mature fish back into the proximity to 

natal systems results is a measurable and important contribution to upriver steelhead populations, 

while return rates of kelts navigating the hydrosystem (up and down or some combination thereof) 

are too low to justify the activity biologically or economically. 

The proposal did not contain adequate detail to review the data collection methods or proposed 

analytical methods; however, based on the preliminary proposal, reviewers had a concern about 

covariation among data detection points for a single kelt migrating down through the hydrosystem as 

it would be sequentially detected at successive dams. Therefore, the detections would not be 

independent of one another. The proposal did not provide enough detail to determine how the 

project sponsors might address this and other analytical questions. 

35. Evaluation of an instream pit detection system to monitor adult salmon and 

steelhead homing and straying behavior

Study Code: ADS-00-4 Agency/Author: U of I, USFWS / Peery, Zydlewski 

ISRP Comments: 

This project proposes to evaluate the use of instream PIT tag detection technology to monitor fish 

straying (temporary or permanent) using the 23 mm ISO (134kHz) PIT tags that have been used 

successfully in studies such as the USFWS’s steelhead study on Abernathy creek. Consequently, the 

proposed study should more fully describe whether its goals are to revaluate the ISO PIT technology 

or to evaluate temporary versus permanent straying. 

The biggest change proposed in this study from earlier small-scale studies was the proposal to apply 

this technology to much larger systems like the Deschutes, John Day, Klickitat, or Yakima where 

straying has been identified as a problem or potential problem. Unfortunately, neither the proposal 
ISRP 2003-14 AFEP Part I. FY04 Pre-proposal Review

36

nor the presentation presented evidence that application of the ISO PIT technology is feasible in 

river systems as large as the Deschutes. It was unclear from the presentation whether the sponsors 

proposed installing the ISO PIT tag detectors in arrays across the mainstem lower Deschutes (or any 

other major tributary) or whether the application would be primarily in tributaries to these, such as 

Trout Creek in the Deschutes. Other potential detection sites might include locations along the 

banks where steelhead migrate or in fishways, such as the ladder at Sherars Falls on the Deschutes. 

None of this was articulated in the proposal or the presentation and clearly needs to be included in a 

full proposal before a technical review is possible. 

Finally, discussion of potential information and applications needs to be more fully discussed in 

order to warrant investing in this technology at this scale. For all the effort involved, what would 

the region gain using this method over radio-tags other than potential long-term efficiency?

Lamprey

36. Evaluation of adult salmon, steelhead, and lamprey migrations past dams, through 

reservoir in the lower Columbia River, and into tributaries

Study Code: LPS-P-04 New Agency/Author: NMFS, U of I / Moser, Peery

ISRP Comments: 

This research will provide much needed information that should lead to improved passage of 

lampreys at Bonneville Dam and contribute to improvements of lamprey passage at other dams.

The research will test improved designs for bypass structures to allow passage of lampreys through 

the makeup water channels to the forebay at Bonneville Dam. The research also will evaluate 

lamprey behavior in 26 fishway configurations. The investigators should carefully consider whether 

it is necessary to test all of these configurations. Are there certain configurations that theory and past 

experience suggest should be the most likely to improve passage?

Have the authors considered the possibility of simply adding roughness to the bottom of the ladders 

by introducing rocks/boulders of appropriate size to break up the directional flow on a small scale 

and give the lamprey an avenue for transit, along with attachment surfaces they are known to use in 

migrating upstream? 

Bypass Studies

37. DIDSON technology development and fish behavior research related to fish 

passage at Columbia Basin dams

Study Code: BPS, SBE Agency/Author: U of I / Liou

ISRP Comments: 

This is an excellent proposal. The technology may revolutionize research approaches for optimizing 

smolt passage at dams (comparable to the impact of PIT tags). 

This research would develop the use of the DIDSON acoustic camera for relating fish behavior to 

the detailed hydraulics of dam structures, especially fish bypasses. The research would emphasize 

signal-processing technologies to maximize information yield and tests of the strain-velocitypressure hypothesis for fish behavior developed by Goodwin. Unique tagging methods to optimize 
ISRP 2003-14 AFEP Part I. FY04 Pre-proposal Review

37

fish identification by the camera would be explored. Initial studies would be conducted in laboratory 

tank settings where fish, hydraulics, and the placement of the DIDSON camera can be manipulated 

to obtain maximum information. Further research would be conducted in field locations such as the 

Bonneville 2 Corner Collector. 

This is an unsolicited proposal that thoroughly established its need and provided ample information 

to judge its scientific soundness. The work is broadly related to several Study Codes (Study 

Summaries), none of which call specifically for this work. They are BPS-P-00-15, BPS-P-03-NEW, 

SBE-03-1-NEW, SBE-03-NEW, and SBE-P-00-17. This proposal recommends an innovative 

approach to reaching the objectives of all of the cited Study Codes.

38. Studies to establish biological design criteria for fish passage facilities: High 

velocity flume development 2004

Study Code: BPS Agency/Author: NMFS / Gessel

ISRP Comments: 

The pre-proposal is well done with a good background, clearly stated objectives, and a sound 

research design. The major justification for the study is that when juvenile steelhead are transported 

with juvenile chinook, the smaller chinook juveniles are stressed (McCabe et.al., 1979). However, it 

appears that there is no evidence that chinook hauled with steelhead produce fewer adult chinook 

returns than a control. If there is currently no evidence of harm, wouldn’t it be more appropriate to 

find out if the stress to smaller chinook juveniles translates into higher mortalities, before investing 

resources to determine the most effe ctive process for separating juvenile salmonids of different 

sizes? 

39. Development and evaluation of full-flow PIT-tag interrogation systems for 

Bonneville and John Day Dams

Study Code: BPS-P-03-New Agency/Author: NMFS / Prentice

ISRP Comments: 

The PIT-tag interrogation systems for Bonneville and John Day Dams are needed, and the proposal 

seems feasible based upon previous development of the adult PIT tag detections system. The 

investigators are unquestionably the best qualified to do the work. Similar PIT tag development 

work by the NMFS lab is funded through the Fish and Wildlife Program.

(See www.cbfwa.org/files/province/systemwide/projects/198331900n.doc.)

40. Evaluation of modified vertical barrier screens and extended-length submersible 

bar screens at John Day Dam

Study Code: BPS-P-00-15 Agency/Author: NMFS / Brege

ISRP Comments:

This is a reasonable project. The primary question addressed in this study is whether modification of 

the materials used for the vertical barrier screens may affect the injury rate and/or survival of 

subyearlings as they are diverted with the intake screens into the gatewells where they may be 

subject to contact with the vertical barrier screens? The question is good, relevant to needs and the 

design seems adequate, for what seems to be fine tuning of the bypass system at John Day Dam. 
ISRP 2003-14 AFEP Part I. FY04 Pre-proposal Review

38

41. Evaluation of gatewell modifications at Bonneville second powerhouse using an 

integrated approach

Study Code: BPS-P-00-14 Agency/Author: PNNL / Ploskey

ISRP Comments:

This proposal is very well done; among the best of all submissions. The background is highly 

detailed, the objectives clearly stated and justified, and the appropriate data will be collected with 

several complementary methods to adequately address each of the objectives.

Transportation Studies

42. A study to compare SARs of in river migrating versus transported anadromous 

salmonids

Study Code: TPE-W-00-1 Agency/Author: NMFS / Matthews

ISRP Comments: 

This proposal involves two ongoing projects and proposes three new projects that are logical 

extensions of past work. The proposal is well written and clearly differentiates the five activities or 

objectives. This proposal is similar to a proposal to the Mainstem/Systemwide submissions to BPA 

(Project 35047) but we have compared these proposals and each activity in this proposal is supported 

on its own merit.

The objectives or studies in this proposal include:

1. Objective 1: compare SARs of PIT-tagged wild yearling chinook salmon and wild steelhead 

smolts. The proposal is in the Snake River, compares barged versus in-river migrants nondetected at any downstream dam, and is an ongoing study. This proposal involves recovery 

of adults only and analysis.

2. Objective 2: compare SARs of PIT-tagged hatchery-reared sub-yearling chinook salmon. The 

proposal would be in the Snake River, compare barged versus two other release groups, and 

is a new study. The two releases are late spring and fall. Costs also include recovery of past 

tag releases and analysis.

3. Objective 3: compare SARs of PIT-tagged hatchery-reared yearling chinook salmon and 

steelhead smolts from the upper Columbia River, and compare barged versus smolts bypassed in a full-flow pipe. Continuation of an initial study conducted in 2003. Samples sizes 

for this objective are very large and, therefore, likely to very expensive. 

4. Objective 4: compare SARs of subyearling chinook PIT-tagged and transported from 

McNary Dam to below Bonneville with in-river migrants released into the McNary tailrace. 

Study involves upper Columbia River subyearlings previously tagged at McNary collection 

facility. This proposal involves recovery of adults only and analysis.

5. Objective 5: compare SARs of PIT-tagged wild yearling chinook that are transported under 

“current” conditions versus a proposed delayed barging scheme. A new proposal to be 

conducted in the Snake River as a pilot year in 2004. The objective is to delay release of 

early transported smolts in an effort to increase their marine survival rate. 
ISRP 2003-14 AFEP Part I. FY04 Pre-proposal Review

39

Of the new proposals, the upper Columbia study with yearling chinook and steelhead is likely to be 

very expensive (if this is an issue) given the sample sizes presented in the proposal. The calcula tions 

are based on reasonable assumptions but the supporting agency may wish to review the costs for that 

one project. 

43. A study to evaluate the effects of transporting spring/summer Chinook salmon in 

the presence of steelhead smolts

Study Code: TPE-W-04-06 Agency/Author: NMFS / Gilbreath

ISRP Comments:

This study is linked to #38 and answers some of the above questions on proposal # 38. The studies 

proposed in this one should be completed prior to initiating #38. This is a well-designed study. The 

only concern is that the sample size of the marked groups may not be large enough to estimate smolt 

to adult return rates (given variation in adult returns to Lower Granite).

44. Electronic recovery of ISO-PIT tags from piscivorous bird colonies in the 

Columbia River Basin

Study Code: BPS-00-11 Agency/Author: NMFS / Ryan

ISRP Comments: 

This proposal is for the continuation of an important PIT-tag detection program begun in 1998, and 

with two notable additions proposed. Four objectives are presented including: detection of PIT tags 

on piscivorous bird colonies in the Basin (ongoing objective), use of the detections to assess 

vulnerability of salmonid groups to predation (ongoing), comparing vulnerability of salmonids 

released into the estuary versus those detected at Bonneville Dam (new), and estimation PIT-tag 

detection efficiency at the various colonies (ongoing or new was not stated in the proposal). The 

latter objective is based on some past sampling and is a good test of the sampling program, however, 

the basis of the sample sizes and past results were not presented.

The suggested application of PIT tags to downstream salmon population is also a reasonable addition 

to the project, but again the justification for sites selected and sample sizes of tags were not 

presented.

The ISRP has two comments on data analysis in this proposal. The section on analysis was very 

brief and would obviously be inadequate for any peer review. However, our comments were:

1) once a measure of tag detection at a colony is estimated, how is it incorporated into the 

estimation of predation mortality? PIT tags are individual markers but are applied to groups 

of fishes (possible at a hatchery or one day at a collection facility), is the mortality rate on a 

“group” of tags increased by the rate of non-detection?

2) the data analysis section refers to comparing detections to total releases, but the 

probability of an individual being killed will be related to the previous mortalities (i.e., IT-tag 

removals) on a group of tags. This section of the report is so condensed as to seem 

misleading.

Given the demonstrated losses of PIT tags to piscivorous birds, this proposal is clearly an important 

project to continue. However, the expansion of these recoveries to predation mortality rates is an 
ISRP 2003-14 AFEP Part I. FY04 Pre-proposal Review

40

important step in partitioning downstream mortalities from marine mortality rates, and merits much 

more explanation than included in this proposal.

45. Sampling PIT-tagged juvenile salmonids migrating in the Columbia River estuary

Study Code: BPS-00-9 Agency/Author: NMFS / Ledgerwood

ISRP Comments:

This proposal is for the continuation of a novel and essential recovery program for PIT-tagged 

salmonids from upstream of the Columbia River estuary. Since 1995, these researchers have been 

developing trawls and, now other net configurations, to detect PIT-tagged salmonids pass through 

these nets and released without any handling. The detection efficiency has been gradually improved 

to the point that an estimated 2% of the PITs passing Bonneville Dam were detected in 2003. This 

proposal would continue to examine detection efficiencies, develop a new sampling configuration 

for a nearshore sampling system, and would extend the sampling period through the summer to 

beginning recovery of sub-yearling PIT tags. These detections are essential to any estimate of 

survival of PIT-tagged salmonids to the Bonneville Dam, and can be complementary to the bird 

predation studies that recovery PITs in the lower river colonies.

The proposal is very clearly written, and methods and data analysis well described. The proposal 

presents the possibility of using trawls in the lower estuary to also assess survival in the estuary, 

duration of passage or use, etc. This possibility is interesting but the amount of time a trawl may 

function in the lower estuary may be a limiting factor.

46. Evaluation of post-release losses and barging strategies that minimize post-release 

mortality and determination of the benefits of early spring transport from the Snake 

River

Study Code: TPE-W-00-2 Agency/Author: OSU / Schreck 

ISRP Comments: 

This proposal includes an objective to continue evaluation of post-release losses and barging 

strategies that minimize post-release mortality (Objective 1) and a new project to determine the 

effects of early spring transport from the Snake River (Objective 1b.).

The proposal provides an in-depth description of the project and past results. The proposal is 

generally well written, with the exception that the description of the new objective was confusing. 

Our understanding to that task is that it will assess why spring chinook that are barged during the 

early portion of the emigration from the Snake River have survivals very similar to the run-of-theriver spring chinook (i.e., no benefit from barging). Assuming our interpretation is correct, the 

description of the method proposed, page 18, is very limited. The fish would be tracked using 

radiotelemetry but the total sample size is only 150 fish (3 days x 50 fish). What is the basis of these 

samples and what level of comparison can be made using this sample size?

However, the majority of the proposal is a continuation of studies involving radiotelemetry and 

acoustic tags to study survival and migration of spring chinook from Bonneville through the estuary 

and into the coastal nearshore waters. The committee continues to strongly support these 

technologies to provide insight into the locations and timing of mortalities during this downstream 

phase. The expansion of the acoustic arrays into the nearshore ocean is a welcomed addition. 
ISRP 2003-14 AFEP Part I. FY04 Pre-proposal Review

41

47. Evaluation of post-release losses and barging strategies that minimize post-release 

mortality

Study Code: TPE-W-00-2 Agency/Author: OSU / Schreck

ISRP Comments:

The ISRP assumes that this study code refers to the proposal TPE-W-00-2, Objective 2. This one 

page of ideas, however, does not constitute a proposal. But, both of the tasks identified by Dr. 

Schreck could be valid points for investigation. There does, however, seem to be an obvious 

sequence to the studies. We would definitely support investigating the second task (task b) first. 

The laboratory studies could be well controlled and would eliminate the uncertainty associated with 

releasing the smolts into estuarine conditions, as identified in the proposal. 

Study plans to address the first task could also be further developed. It would seem apparent that 

large numbers of the smolts released should have been PIT-tagged so that smolt-to-adult survival 

rates can be estimated and compared to alternative treatments. But depending on the hypotheses to 

be tested, a decision may be to use radio-tags for examining bird predation or acoustic tags to 

provide more direct measures of emigration timing, routes of passage, etc. 

If requested for comment, the ISRP would be unlikely to support the change in use of barges etc. that 

would be required to study task (a). However, task (b) could apparently be added to other projects 

and would be a very logical study to undertake in support of task (a) if it was to be considered in the 

future.

48. Water temperature effects on juvenile fall chinook salmon survival at the 

hydroprojects

Study Code: TPE-W-04-03 New Agency/Author: OSU / Schreck

ISRP Comments:

This proposal is a very brief one-page concept proposal that does not provide enough information for 

technical review. The goals of determining the effects of elevated water temperatures on juvenile fall 

chinook during in-river migration and providing quality control for tagging studies may be quite 

important. However, there is only some limited anecdotal data given to indicate poor survival of fall 

chinook juveniles at a holding facility at Lower Granite Dam in 2003. The justification for this type 

of study needs to be fully developed and a detailed study design given that will provide data to 

address the study questions/objectives. 

49. Use of a gene chip to study the effects of transportation procedures on juvenile 

salmonids

Study Code: TPE-W-04-6 New Agency/Author: OSU / Schreck

ISRP Comments: 

This one-page proposal proposes to examine the effect of transportation procedures on various 

physiological components using gene chip/array technology. The proposal notes that the technique 

allows assay of 100s-1000s of parameters by examining the genes that are turned on or off following 

a particular experience. The proposal also notes that the technique has been successfully applied in 

medial and mammalian research, although no detail or examples were provided on how the research 
ISRP 2003-14 AFEP Part I. FY04 Pre-proposal Review

42

was applied and what kind of questions it was used to answer. At this point, the technique is untried 

in fisheries. 

It is impossible to review the proposed work given the lack of detail provided in the pre-proposal. 

Prior to supporting what is clearly a research and development effort, it seems prudent to review a 

full proposal that includes an extensive literature cited section and examples of applied results to 

resource management questions from the gene chip/array technology. Given the strong applied and 

implementation focus of the AFEP, the program’s responsibility to fledgling research and 

development efforts such as this proposal is unclear. This is a policy and administrative level 

question, rather than a scientific one. 

Bull Trout Study

50. Swimming performance of bull trout

Study Code: BT-P-04-New Agency/Author: USGS, USFWS / Mesa, Zydlewski

ISRP Comments: 

This project seems to have the cart before the horse. They need to first demonstrate that some 

problems exist. This proposal is based on a presumption that bull trout are relatively poor 

swimmers. The more appropriate experiment is to test whether or not bull trout find migration 

challenges overwhelming. If that is demonstrated, alternative explanations including swimming 

performance become worthy of consideration. 

Specific Comments:

1. Assuming swimming performance is a problem for bull trout confronting migration 

challenges, is it realistic to assume that the conditions proposed here for study will provide 

any real comparability to those confronting a migrating bull trout?

2. Holding mixed sizes of bull trout in a single tank will result in fewer fish upon arrival than 

you had when you left. How will you account for any difference that may be associated with 

the time a fish is held in the tank?

3. Are there plans to account for any StressCoat and stock effect?

4. Page 6. What is “fully characterize the swimming performance?”

5. You plan to use fish captured in 2002, 2003, and 2004. Presumably, many of these fish have 

been held under culture conditions and have lost much of their physical fitness. If so, will 

the results of the proposed tests be accurate? 

6. Page 8 – Two size categories are proposed: 10-24 cm and 25-40 cm. These are very broad 

ranges – some fish in the small category could be twice as large as other fish in the same 

category. Will this provide any meaningful relationship to size?

7. Objective 2 will be done with fish from Objective 1. Wouldn’t it be more appropriate to use 

fish that had not been stressed in previous tests?

8. You reported that the chambers are not available. Have you tested the apparatus so that you 

are confident that the “erratic behavior” that caused previous failures will not occur here too?

9. Page 9 – You propose to complete three trials for each fish, and based on the results make a 

decision as to whether or not you can combine the results. Have you now confirmed this 

approach with a statistician? How does this proposed experiment and analysis relate to 

potential problems for bull trout at dams?

10. You are proposing to do the blood work on 8-10 fish. Given the variance reported for these 

kinds of data, will the sample provide useful information?
ISRP 2003-14 AFEP Part I. FY04 Pre-proposal Review

43

White Sturgeon Study

51. Behavior of white sturgeon near hydroprojects and fishways

Study Code: WTS-04-New Agency/Author: USGS, NMFS, U of I / Parsley, Moser, Peery

ISRP Comments: 

This is a well written, technically sound proposal for needed work on a principal resident species 

that is impacted by the dams. 

This proposal would tag adult and sub-adult white sturgeon with radio or acoustic tags and 

determine their location and behavior in tailwaters, near fish ladder entrances, in fish ladders, and in 

the forebays of Lower Columbia River dams, particularly The Dalles. The objective is to learn why 

sturgeon generally fail to use fish ladders and thus are blocked by dams. White sturgeon do pass 

through The Dalles Dam; the research would seek something particularly suitable about the 

configuration at that project. The telemetry would use existing receivers placed at the dams for other 

research, especially adult salmonid behavior studies (although some new receivers would be placed 

especially for sturgeon, e.g., in fish ladders). The proposal is responsive to the “one-pager” ADS-04-

NEW, and to the Council’s Program requirement to mitigate resident species impacted by the 

hydrosystem. There is no Corps Multi-Year Plan that is applicable. 

The ISRP was told that this work is regularly proposed and not funded, but the ISRP believes work 

on this problem is justified. The background section explained the rationale for the work especially 

well.

Avian Predation in the Mid-Columbia

52. Avian predation on juvenile salmonids in the McNary Pool, Columbia River.

Study Code: Not Applicable Agency/Author: D. Roby and K. Collis

ISRP Comments:

This proposal consists of two pages but does present a case for the development of a more 

comprehensive proposal. The authors present recent results of avian predation impacts in the 

McNary Dam area that were comparable to the predation impacts at Rice Island. Predation in these 

freshwater pools may even increase given water clarity and if growth of the colonies continues. The 

authors also suggest that management of the colonies in the lower river could result in relocation of 

the birds to these more interior colonies. The tasks outlined in the proposal are reasonable and 

follow, although there was not enough description of the vulnerability studies (task 4) for us to 

assess the method. 

Given the past productivity of the authors and their successful completion of studies in the estuary, it 

would seem prudent to request a more comprehensive proposal be developed. 

The proposal presents an interesting question concerning total avian predation pressures in the 

Columbia Basin. Given the results of studies in the estuary and then the results presented in this preproposal, what is the possible range of total predation on salmonids and what portion of the juveniles 

could this represent. In some years, large numbers of deaths may be a relatively small portion of the 
ISRP 2003-14 AFEP Part I. FY04 Pre-proposal Review

44

total emigration. However, in years with low flow or poor returns, the avian predation could present 

a major portion of the emigrants and should be accounted for in other planning exercises (e.g., 

harvest planning). The ISRP suggests that the Basin may want to investigate this range of impacts

and develop a scoping paper of the potential effects and how to respond to them.

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