Independent Scientific Review Panel

for the Northwest Power Planning Council

851 SW 6th Avenue, Suite 1100

Portland, Oregon 97204

isrp@nwppc.org

Final Review 

of

Fiscal Year 2003 

Mainstem and Systemwide 

Proposals

ISRP 2002-14

November 5, 2002
Review Team

ISRP

Charles C. Coutant

Susan Hanna

William Liss 

Lyman McDonald

Brian Riddell

William Smoker 

Richard Whitney

Richard N. Williams

with

Daniel Goodman

Peer Review Group

Richard Alldgredge

John Pizzimenti

Staff

Erik Merrill
ISRP 2002-14 Final Mainstem and Systemwide

i

ISRP Final Review of Fiscal Year 2003 Mainstem 

and Systemwide Proposals

Contents

Table of Mainstem and Systemwide Proposals by Project ID......................ii

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

Recommendation Categories .....................................................................2

Programmatic Issues.................................................................................3

Research, Monitoring, and Evaluation.......................................................................... 3

Measure Smolt Survival Directly.................................................................................. 6

Hanford Reach Stranding.............................................................................................. 6

Gas Bubble Disease ...................................................................................................... 7

Conservation Enforcement............................................................................................ 8

NATURES Rearing and Captive Broodstock Research............................................... 8

ISRP Final Comments and Recommendations on Each Proposal............... 10

Wildlife ....................................................................................................................... 10

White Sturgeon ........................................................................................................... 11

Lamprey...................................................................................................................... 16

Bull Trout .................................................................................................................... 19

Avian and Fish Predation on Juvenile Salmonids....................................................... 20

Estuary/Plume and Lower Columbia .......................................................................... 24

Artificial Production Related Projects ........................................................................ 33

Mainstem Habitat........................................................................................................ 50

Water Quality: Gas Bubble, Temperature, and Contaminants................................... 54

Juvenile and Adult Fish Passage ................................................................................. 62

Data Management ....................................................................................................... 73

Monitoring and Evaluation: Systemwide and Habitat Action Effectiveness.............. 78

Harvest........................................................................................................................ 84

Coded Wire Tag Monitoring Program........................................................................ 91

Conservation Enforcement.......................................................................................... 95

Fish and Wildlife Program Coordination, Analysis, and Communication................. 99

 Index of Proposals by Project ID................................................105
ISRP 2002-14 Final Mainstem and Systemwide

ii

Table of Mainstem and Systemwide Proposals by Project ID

ProjectID Title Sponsor ISRP Final CBFWA 

Category1

ISRP 

Comparison 

with CBFWA

Page

30007 An Acoustic Tracking Array for 

Studying Ocean Survival and 

Movements of Columbia River Salmon

Kintama 

Research 

Corp.

Fundable in 

Part (Qualified)

TBD - Do Not 

Fund (Estuary)

Disagree -

Fundable in 

Part

28

30010 Canada-USA Shelf Salmon Survival 

Study

DFO Fundable in 

Part (Estuary)

TBD - Do Not 

Fund (Estuary)

Disagree -

Fundable in 

Part

29

35001 Habitat Monitoring and Restoration 

Program for the Lower Columb ia River 

and Columbia River Estuary

LCREP Withdrawn Withdrawn Withdrawn 31

35002 Determine origin, movements and 

relative abundance of bull trout in 

Bonneville Reservoir.

WDFW, 

YN

Fundable in 

Part

Urgent Disagree -

Lower Priority

19

35003 Vitality based studies of Delayed 

Mortality

UW Fundable Recommended 

Action

Agree 70

35004 Harvest Model Development UW Do Not Fund Do Not Fund Agree 89

35005 Independent Economic Analysis Board NPPC Not Applicable NWPPC 

responsibility

Not 

Applicable

103

35006 Use of Mainstem Habitats by Juvenile 

Pacific Lamprey (Lampetra tridentata)

PNNL Fundable Recommended 

Action

Disagree -

Higher 

Priority

18

35007 Evaluate Restoration Potential of Snake 

River Fall Chinook Salmon Spawning 

Habitat

PNNL Fundable Recommended 

Action

Disagree -

Higher 

Priority

50

35008 Systemwide Lamprey Program 

Coordinator

USGS, 

CRRL

Fundable in 

Part

High Priority Disagree 16

35009 Evaluate Status of Pacific Lamprey in 

the Willamette River Subbasin

ODFW Fundable High Priority Agree 19

 

1 CBFWA ranks the proposals in the following prioritization categories:

• Core Program - These projects are integral to the infrastructure and/or information needs of the F&W Program in 

the Columbia River Basin for planning and management. 

• High Priority - These projects or tasks within a project are high priority within the subbasin. The project 

addresses a specific need within the subbasin (program) summaries. 

• Recommended Actions - These are good projects that cannot demonstrate a significant loss by not being funded 

this year. These projects should be funded, but under a limited budget, they could be delayed temporarily without 

significant loss.

• Do Not Fund - These projects are either technically inadequate or do not address a need within the subbasin 

(program) summaries. These projects may be inappropriate for BPA funding.

For an explanation of ISRP recommendation categories go to page 2 of the report.
ISRP 2002-14 Final Mainstem and Systemwide

iii

ProjectID Title Sponsor ISRP Final CBFWA 

Category1

ISRP 

Comparison 

with CBFWA

Page

35010 An Interactive Biodiversity 

Information System for the Columbia 

River Basin

NW 

Habitat 

Institute

Fundable in 

Part

Core Program* Agree in Part 76

35011 The Floating Net Pen Transportation 

System Pilot Project

Columbia 

Basin 

Fishery 

Restoration 

L.L.C.

Do Not Fund Do Not Fund Agree 71

35012 Spatial scales of homing and the 

efficacy of hatchery supplementation of 

wild populations

NMFS Fundable High Priority Agree 41

35013 Species- and site-specific impacts of 

gas supersaturation on aquatic animals

CRRL Fundable in

Part

High Priority Agree in Part 55

35014 Measurement of Quantitative Genetic 

Variation Among Columbia River 

Basin Chinook Propagation Programs

CRITFC Fundable High Priority Agree 34

35015 Replicated stream system for the 

evaluation of hatchery and wild

juvenile salmonid interaction and 

development of innovative culture 

technologies

UI/ 

CRITFC

Do Not Fund High Priority Disagree 43

35016 A Pilot Study to Test Links Between 

Land Use / Land Cover Tier 1 

Monitoring Data and Tier 2 and 3 

Monitoring Data

NWFSC Do Not Fund High Priority Disagree 79

35017 Inventory and Synthesis of Physical 

Process Models and Methods to 

Supplement Habitat Conditions 

Analysis and Subbasin Planning

KWA and 

Golder

Do Not Fund Recommended 

Action

Disagree 82

35018 Evaluate recreational and commercial 

mark-selective fisheries.

WDFW; UI Withdrawn Withdrawn Withdrawn 84

35019 Develop and Implement a Pilot Status 

and Trend Monitoring Program for 

Salmonids and their Habitat in the 

Wenatchee and Grande Ronde River 

Basins

NMFS -

NWFSC

Fundable 

(Qualified)

Urgent* Agree 80

35020 Regional Project Effectiveness 

Monitoring Program for Columbia 

River Basin Listed Anadromous 

Salmonids.

NMFS -

NWFSC

Do Not Fund Urgent Disagree 81
ISRP 2002-14 Final Mainstem and Systemwide

iv

ProjectID Title Sponsor ISRP Final CBFWA 

Category1

ISRP 

Comparison 

with CBFWA

Page

35021 Purchase And Evaluation of Automated 

Marking and Tagging Systems 

(MATS)

ODFW Do Not Fund Recommended 

Action

Disagree 94

35022 Habitat Mitigation Tracking System Steward 

and Assoc.

Fundable 

(Qualified)

Do Not Fund Disagree 82

35023 Establish Relationship between Fish 

Passage Survival and Turbine 

Operating Efficiency

Normandeau 

Assoc.

Do Not Fund Do Not Fund Agree 71

35024 Evaluating the sublethal impacts of 

current use pesticides on the 

environmental health of salmonids in 

the Columbia River Basin.

NMFS -

NWFSC

Fundable Urgent Agree -

Priority 

Uncertain

59

35025 Optimization of FCRPS Impacts on 

Juvenile Salmonids: Restoration of 

Lower-Estuary and Plume Habitats

OHSU Fundable Recommended 

Action

Disagree -

Higher 

Priority

24

35026 On-line Subbasin Planning/Watershed 

Newsletter

Intermtn. 

Comm.

Fundable Recommended 

Action

Disagree -

Higher 

Priority

99

35027 Evaluation of Two Captive Rearing 

Methods for Assisting with Recovery 

of Naturally Spawning Populations of 

Steelhead and Coho Salmon

USFWS Fundable Urgent Agree 44

35028 Evaluate White Sturgeon Nutritional

Needs & Contaminant Effects 

Influenced by the Hydroelectric System

PSU Fundable Recommended 

Action

Agree 14

35029 Transfer IHN virus genetic strain 

typing technology to fish health 

managers

WFRC Fundable High Priority Disagree -

Urgent

49

35030 Evaluate potential to enhance spawning 

of summer/fall chinook salmon in the 

tailrace of Chief Joseph Dam, 

Columbia River

PNNL and 

CCT

Fundable Urgent Agree -

Fundable as 

Modified

51

35031 Tagging Study Technical Committee BPA Do Not Fund Recommended 

Action

Disagree 65

35032 Assess the Feasibility of Reducing 

Predation on Juvenile Salmonids in the 

Columbia River Through Operation of 

the Hydropower System

USGS, 

CRRL; 

ODFW

Do Not Fund High Priority Disagree 23

35033 Collaborative, Systemwide Monitoring 

and Evaluation Program.

CBFWA Fundable Core Program* Agree 78
ISRP 2002-14 Final Mainstem and Systemwide

v

ProjectID Title Sponsor ISRP Final CBFWA 

Category1

ISRP 

Comparison 

with CBFWA

Page

35034 Fish Behavioral Guidance Through 

Water Velocity Modification PHASE 

ONE

Natural 

Solutions

Fundable Recommended 

Action

Agree 72

35035 Incorporating Pit Tag Technology to 

Evaluate and Monitor the 

Reintroduction Effort for Anadromous 

Salmonids in the Upper Cowlitz 

Watershed

WDFW Do Not Fund Recommended 

Action

Disagree 32

35036 Identify the mechanisms of stranding 

of juvenile fall chinook salmon in the 

Hanford Reach

USGSCRRL; 

USFWS

Fundable Urgent* Agree 52

35037 Measuring the potential for 

domestication selection of spawn 

timing in chinook captive and 

supplementation programs; 

implications for recovery.

UW and 

NMFS

Fundable Recommended 

Action

Disagree -

Higher 

Priority

47

35038 Develop Computational Fluid 

Dynamics Model to Predict Total 

Dissolved Gas Below Spillways

ENSR Fundable Do Not Fund Disagree 57

35039 The influence of hatcheries and their 

products on the health and physiology 

of naturally rearing fish

USGS, 

CRRL

Fundable High Priority Agree 47

35040 Determination of post-release survival 

of spring chinook salmon in a markselective sport fishery

PNNL Do Not Fund Recommended 

Action

Disagree 90

35041 Monitoring the reproductive success of 

naturally spawning hatchery and 

natural spring chinook salmon in the 

Wenatchee, Tucannon, and Kalama 

Rivers

WDFW, 

NMFS

Fundable Urgent Agree 48

35042 Evaluate the Effects of Prey 

Availability on Recruitment of White 

Sturgeon in the Columbia River

USGS, 

CRRL

Fundable High Priority Agree 12

35043 Monitoring and Models for Adaptive 

Management of White Sturgeon

USGS, 

CRRL

Fundable Recommended 

Action

Disagree -

Higher 

Priority

13

35044 Determine Effects of Contaminants on 

White Sturgeon Reproduction and 

Parental Transfer of Contaminants to 

Embryos in the Columbia River Basin

OSU Fundable High Priority Agree 13

35045 Modeling and Information 

Management System to Assess 

Effectiveness of Alternative Actions

PNNL Do Not Fund Recommended 

Action

Disagree 83
ISRP 2002-14 Final Mainstem and Systemwide

vi

ProjectID Title Sponsor ISRP Final CBFWA 

Category1

ISRP 

Comparison 

with CBFWA

Page

35046 Estimate juvenile salmon residence in 

the Columbia River Plume using 

micro -acoustic transmitters.

NMFS Fundable 

(Qualified)

High Priority Disagree -

Higher 

Priority

26

35047 Evaluate Delayed (Extra) Mortality 

Associated with Passage of Yearling 

Chinook Salmon Smolts through Snake 

River Dams

NMFS Fundable High Priority Agree 68

35048 NWFSC Salmon Data Management, 

Analysis, and Access for Research 

Monitoring and Evaluation Programs

NMFS -

NWFSC

Do Not Fund 

(Qualified)

Recommended 

Action

Disagree 76

35049 A multiscale evaluation of steelhead 

supplementation in the West Fork 

Elochoman River

NMFS Fundable High Priority Disagree -

Lower Priority

42

35050 UW Offsite Habitat and Fish Survival 

Effectiveness Monitoring

UW Do Not Fund Do Not Fund Agree 83

35051 Evaluate Feasibility of a System-wide 

Multi-Agency Fish, Wildlife & Habitat 

Conservation Enforcement Web-Based 

Data Center

Steven 

Vigg & 

Company

Fundable Recommended 

Action

Agree 98

35052 Conservation Enforcement to Enhance 

and Restore Fish & Wildlife Resources 

of the Upper Columbia River under 

Jurisdiction of the Colville Tribes 

CCT Fundable Urgent Agree 97

35053 Biological Feasibility of Reintroducing 

Fishwheels in the Columbia River 

System 

Steward 

and Assoc.

Do Not Fund Recommended 

Action

Disagree 90

35054 Engaging the Public in Watershed 

Planning; A Tool Box for Cultural 

Shift

CBFWA Do Not Fund Recommended 

Action

Disagree 103

35055 Role of Bacteria as Indicator 

Organisms for Watershed Assessment 

and in Determining Fish Pathogen 

Relationships with Fauna of Abernathy 

Creek

USFWS Do Not Fund Recommended 

Action

Disagree 31

35056 Develop Human Resources Necessary 

to Exercise Co-Management 

Responsibilities 

CRITFC Do Not Fund Recommended 

Action

Disagree 102

35057 Habitat Condition and Restoration 

Potential of Columbia River Flood 

Plains: A Critical, Missing Element of 

Fisheries Recovery Science and Policy

UM Fundable 

(Qualified)

Recommended 

Action

Agree 53
ISRP 2002-14 Final Mainstem and Systemwide

vii

ProjectID Title Sponsor ISRP Final CBFWA 

Category1

ISRP 

Comparison 

with CBFWA

Page

35058 Evaluation of food availability and 

juvenile salmonid growth rates under 

differing thermal and sediment 

regimes.

CRITFC Do Not Fund Do Not Fund Agree 60

35059 Rapid Detection of White Sturgeon 

Iridovirus in Spawning Fluids, Eggs 

and Juvenile Tissues of White Sturgeon

USFWS Do Not Fund Do Not Fund Agree 15

35060 Instream evaluation of populations, 

migration, individual adult return and 

wild-hatchery interactions of naturally 

produced salmonids

USFWS Fundable High Priority Agree 45

35061 Prophylactic Treatments for White 

Sturgeon Infected with the White 

Sturgeon Iridovirus (WSIV)

USFWS Do Not Fund Do Not Fund Agree 15

35062 Impacts of Flow Regulation on 

Riparian Cottonwood Ecosystems in 

the Columbia River Basin

Univ. of 

Idaho

Fundable 

(Qualified)

High Priority Disagree -

Lower Priority

54

35063 Compare Bacterial Fish Pathogen 

Populations in Hatchery Water and in 

Adjacent Creek Water and Evaluate 

Possibile Disease Transfer Between 

Them.

USFWS Do Not Fund Recommended 

Action

Disagree 45

195505500 Umatilla Tribal Fish & Wildlife 

Enforcement

CTUIR Fundable Urgent Agree - but 2 

FTEs are 

justified

97

198201301 Coded-Wire Tag Recovery Program PSMFC Fundable Core Program Agree - but 

fund statistical 

position

91

198201302 Annual Stock Assessment - Coded 

Wire Tag Program (ODFW)

ODFW Fundable Core Program Agree 93

198201304 Annual Stock Assessment - Coded 

Wire Tag Program (WDFW)

WDFW Fundable Core Program Agree 93

198331900 New Marking and Monitoring 

Techniques for Fish

NMFS Fundable Urgent Agree 66

198605000 White Sturgeon Mitigation and 

Restoration in the Columbia and Snake 

Rivers Upstream from Bonneville Dam

ODFW Fundable Urgent Agree 11

198712700 Smolt Monitoring by Federal and NonFederal AgenciesPSMFC Fundable Core Program Agree 62

198740100 Assessment of Smolt Condition: 

Biological and Environmental 

Interactions

USGS, 

CRRL

Fundable in 

Part (Qualified)

High Priority Agree in Part 46
ISRP 2002-14 Final Mainstem and Systemwide

viii

ProjectID Title Sponsor ISRP Final CBFWA 

Category1

ISRP 

Comparison 

with CBFWA

Page

198810804 StreamNet PSMFC Fundable in 

Part (Qualified)

Core Program Agree in Part 73

198906201 Fish and Wildlife Program 

Implementation

CBFWA Not Applicable Core Program Not 

Applicable

102

198906500 Annual Stock Assessment - CWT 

(USFWS) 

USFWS Fundable Core Program Agree 93

198907201 Independent Scientific Advisory Board 

Support

DOE/ 

ORNL

Not Applicable NWPPC 

responsibility

Not 

Applicable

104

198909600 Monitor and evaluate genetic 

characteristics of supplemented salmon 

and steelhead

NMFS Fundable Urgent Agree 35

198910700 Statistical Support for Salmonid 

Survival Studies

UW Fundable Do Not Fund Disagree 70

199007700 Northern Pikeminnow Management 

Program

PSMFC Fundable in 

Part

Urgent Agree in Part 20

199008000 Columbia Basin Pit Tag Information 

System

PSMFC Fundable 

(Qualified)

Core Program Agree 64

199009300 Genetic Analysis of Oncorhynchus 

nerka (modified to include chinook 

salmon)

U of I Fundable Urgent Agree 42

199105100 Monitoring and Evaluation Statistical 

Support

UW Fundable Do Not Fund Disagree 70

199105500 Natural Rearing Enhancement Systems 

(NATURES)

NMFS Fundable Urgent Disagree -

Lower Priority

36

199302900 Estimate Survival for the Passage of 

Juvenile Salmonids Through Dams and 

Reservoirs of the Lower Snake and 

Columbia Rivers

NMFS -

NWFSC

Fundable Core Program Agree 66

199305600 Assessment of Captive Broodstock 

Technologies

NMFS Fundable Urgent Agree 38

199403300 The Fish Passage Center PSMFC Fundable Core Program Agree 62

199600500 Independent Scientific Advisory Board CBFWF Not Applicable NWPPC 

responsibility

Not 

Applicable

104

199601900 Second-Tier Database Support UW Fundable Do Not Fund Disagree 75

199602000 Comparative Survival Rate Study 

(CSS) of Hatchery Pit Tagged Chinook 

& Comparative Survival Study 

Oversight Committee

PSMFC & 

CBFWF

Fundable 

(Qualified)

Core Program Agree 63

199602100 Gas bubble disease research and 

monitoring of juvenile salmonids

USGS, 

CRRL

Fundable Core Program Agree 54

199606700 Manchester Spring Chinook 

Broodstock Project

NMFS Fundable Urgent Agree 40

199702400 Avian Predation on Juvenile Salmonids 

in the Lower Columbia River

OSU/ 

USGS/ 

CRITFC/ 

RTR

Fundable Urgent Agree 21
ISRP 2002-14 Final Mainstem and Systemwide

ix

ProjectID Title Sponsor ISRP Final CBFWA 

Category1

ISRP 

Comparison 

with CBFWA

Page

199705900 Securing Habitat Mitigation Sites -

Oregon

Oregon 

Wildlife 

Caucus

Fundable 

(Qualified)

Urgent Agree 10

199800401 Electronic Fish and Wildlife Newsletter Intermtn. 

Comm.

Fundable NWPPC 

responsibility

Not 

Applicable

99

199800800 Regional Forum Facilitation Services NMFS Fundable 

(Qualified)

Core Program Disagree 100

199803100 Implement Wy-Kan-Ush-Mi Wa-KishWit Watershed Assessment and 

Restoration Plan Now

CRITFC Fundable 

(Qualified)

Core Program Agree 101

199900301 Evaluate Spawning of Fall Chinook 

and Chum Salmon Just Below the Four 

Lowermost Mainstem Dams

PSMFC, 

ODFW, 

USFWS, 

PNNL

Fundable Urgent Agree 50

200000700 Infrastructure to Complete FDA 

Registration of Erythromycin

UI-CNR Fundable Urgent Agree 43

200001700 Kelt Reconditioning: A Research 

Project to Enhance Iteroparity

in Columbia Basin Steelhead 

(Oncorhynchus mykiss)

CRITFC Fundable Urgent Agree 33

200002900 Identification and thermal requirements 

of larval Pacific, river, and western 

brook lampreys

USGS, 

CRRL

Fundable Urgent Agree 16

200005200 Upstream migration of Pacific 

lampreys in the John Day River: 

behavior, timing, and habitat use

USGS, 

CRRL

Fundable High Priority Agree 17

200005500 Enhanced Conservation Enforcement 

for Fish & Wildlife, Watersheds of the 

Nez Perce

NPT-CE Fundable Urgent Agree 96

200005600 Protect Anadromous Salmonids in the 

Mainstem Corridor

CRITFE Fundable Urgent Agree 95

200100300 ISO Adult Pit Interrogation System 

Installations

PSMFC Fundable Core Program Agree 65

200100700 Evaluate live capture selective harvest 

methods for commercial fisheries on 

the Columbia River 2001-007-00.

ODFW and 

WDFW

Fundable in 

Part

Urgent Agree in Part 84
ISRP 2002-14 Final Mainstem and Systemwide

1

ISRP Final Review of Fiscal Year 2003 Mainstem and 

Systemwide Proposals

Introduction

This report contains the final comments and recommendations of the Independent Scientific 

Review Panel (ISRP) and Peer Review Groups on Mainstem and Systemwide projects submitted 

for Fiscal Year 2003 funding. A programmatic section identifying crosscutting issues is also 

provided. The programmatic section is intended to provide useful reference for proponents and 

the Council in the project selection process. The Mainstem and Systemwide review is the final 

segment of the rolling review process, which began in the spring of 2000 and covers all projects 

funded through the Columbia River Basin Fish and Wildlife Program. 

The process to review proposals and develop comments and recommendations included several 

elements. On August 2, 2002, the ISRP released a preliminary review of proposals (ISRP 2002-

13; www.nwcouncil.org/library/isrp/isrp2002-13.htm). The preliminary review report was 

developed in the following steps. Three or more ISRP reviewers were assigned to review each 

proposal. During the week of July 15th 2002, proponents of each project gave presentations to the 

ISRP. Each presentation was followed by a question and answer session. Once again, the 

Columbia Basin Fish and Wildlife Authority and project sponsors provided a well-organized 

workshop with informative presentations and discussions, which were invaluable in identifying 

potential issues and clarifying the nature of the proposed projects. On the last day of the 

presentation workshop, the ISRP met on its own to discuss the proposals and reach consensus 

preliminary comments and recommendations on each. 

With the release of the ISRP’s preliminary report, project sponsors were provided several weeks 

to respond to the ISRP’s comments by August 23, 2002. The ISRP received about 78 responses. 

The ISRP reviewers who had reviewed the original proposal reviewed the response related to that 

proposal, and the ISRP review teams collectively discussed the responses. The ISRP received 

Columbia Basin Fish and Wildlife Authority’s (CBFWA) Draft FY 2003-2005 Work Plans for 

the Mainstem and Systemwide on October 24, 2002 (see www.cbfwa.org), and compared the 

ISRP review team recommendations with CBFWA’s recommendations and comments. Each 

ISRP recommendation includes a comparison with CBFWA’s prioritization and takes into 

account project sponsor responses to the ISRP’s preliminary review. 

The CBFWA draft work plan included budget reductions for most proposals in CBFWA’s top 

category (Core Program and Urgent). These reductions were made in consultation with the 

project sponsors. The ISRP reviewed the project sponsors’ comments on the proposed reductions 

to assess whether the changes compromised the scientific integrity of the proposal. On most 

proposals, the budget savings involved cost or equipment sharing that did not affect the scientific 

content of the project. On a few projects, the reductions involved trimming tasks or positions 

(FTEs) that could affect the soundness of the proposal. The ISRP’s final comments on individual 

proposals include findings on these reductions.
ISRP 2002-14 Final Mainstem and Systemwide

2

Recommendation Categories

ISRP recommendations and comments are provided for each of the 104 proposals submitted. 

These recommendations are split into three basic categories: 1) fundable (57 proposals); 2) 

fundable in part or fundable (qualified) (23 proposals); and 3) do not fund (18 proposals). Four 

proposals were considered not amenable to the ISRP’s technical review, one was withdrawn, and 

one was combined with another proposal. In addition, ISRP recommendations are provided for 

two proposals from the estuary provincial review (An Acoustic Tracking Array for Studying 

Ocean Survival and Movements of Columbia River Salmon, 30007, and Canada-USA Shelf 

Salmon Survival Study, 30010), which were recommended for deferral to the Mainstem and 

Systemwide process. 

ISRP recommendation categories are based on criteria provided in the 1996 amendment to the 

Northwest Power Act. The amended Act directs the ISRP to review projects in the context of the 

Council’s program and in regard to whether they:

1. are based on sound science principles; 

2. benefit fish and wildlife; 

3. have clearly defined objectives and outcomes; and 

4. have provisions for monitoring and evaluation of results. 

Pursuant to the 1996 amendment, the Council fully considers the ISRP recommendations when 

making its recommendations regarding funding, and provides an explanation in writing when its 

recommendations diverge from those of the ISRP.

The ISRP uses “fundable,” “not fundable,” and variations to summarize the extent to which a 

proposal meets the ISRP review criteria and to capture the level of ISRP confidence in a proposal. 

After its Fiscal Year 1999 review, the ISRP began using “fundable” rather than “adequate 

proposal,” because funding recommendations are the common currency between the Council, 

CBFWA, and BPA. As such, the “fundable” categories enable a ready comparison with 

CBFWA’s recommendations, which is part of the ISRP review. 

Fundable is assigned to a proposal that substantially meets each of the ISRP criteria. Each 

proposal does not have to contain tasks that independently meet each of the criteria but can be an 

integral part of a program that provides the necessary elements. For example, a habitat 

restoration proposal may use data from a separate monitoring and evaluation proposal to measure 

results. The proposal must demonstrate this integration. Some “fundable” proposals may require 

minor clarifications and adjustments to methods and objectives by the sponsor in consultation 

with the Council and BPA in the final project selection process. “Fundable” is not an ISRP 

endorsement to fund the project or an opinion on the proposal’s priority.

Fundable in Part is assigned to a proposal that includes work that is scientifically supported, but 

also work that is not. In this case, the ISRP specifies the objectives or tasks that are not 

scientifically sound and recommends that these parts of the proposal not be funded. Examples are 

proposals that include objectives that are not scientifically supported, for instance a proposal for 

concurrent background assessment work and on-the-ground implementation that could not be 

supported before results of the assessment were known, and proposals that include use of 

unsound methods to meet a particular objective.
ISRP 2002-14 Final Mainstem and Systemwide

3

Not Fundable is assigned to a proposal that is significantly deficient in one or more of the ISRP 

review criteria. One example is a research proposal that is technically sound but does not offer 

benefits to fish and wildlife because it substantially duplicates past efforts and does not offer new 

insights. Another example is a proposal for an ongoing project that may offer benefits to fish but 

does not include provisions for monitoring and evaluation or report past results. Usually a 

deficiency in one area is a symptom of overall deficiency in the proposal. In most cases, 

proposals that receive “Not Fundable” recommendations lack detailed methods, provision for 

monitoring and evaluation, or have the potential for deleterious effects on native populations. 

The ISRP notes that numerous projects rated “not fundable” propose needed actions or are an 

integral part of a watershed effort, but the proposed methods, tasks or objectives are not 

scientifically sound. ISRP comments are intended to indicate areas where serious remedial effort, 

such as significant revision and review, is needed before funding. In some cases, an RFP is 

warranted to address the needed action.

Within these categories, some recommendations are “qualified,” meaning that the proposal needs 

to meet certain conditions or address outstanding concerns before the project is funded. Some of 

these conditions may call for additional ISRP review, but most require minor clarifications and 

adjustments to methods and objectives by the sponsor in consultation with the Council and BPA 

in the final project selection process. 

ISRP comments also include observations on budgetary, in lieu, and other issues that are not 

central to the scientific review. These observations do not dictate whether a project will receive a 

“fundable” or “not fundable” recommendation. Instead, these comments are intended to flag 

issues for the Council, BPA, CBFWA, and the public that require further inquiry.

Programmatic Issues

The programmatic issues identified below are those that are relevant to Council decisions on 

mainstem and systemwide proposals. The ISRP is drafting a Retrospective Report to be issued in 

early 2003 that will include an examination and synthesis of overarching programmatic issues 

identified in the past five years of ISRP review. The ISRP is especially interested in providing 

feedback on this first round of rolling reviews and making recommendations about the future 

review process.

Research, Monitoring, and Evaluation

The Bonneville Power Administration (BPA), in coordination with the National Marine Fisheries 

Service and the Council, added an important new element to the review process for the Mainstem 

and Systemwide. The revised process includes a front-end review of projects by the Research, 

Monitoring, and Evaluation (RME) group, comprising scientists from the Action Agencies and 

NMFS. The solicitation placed emphasis on projects that would meet the Action Agencies’ 

responsibilities under the National Marine Fisheries Services’ FCRPS 2000 Hydro Biological 

Opinion (BiOp), especially those responsibilities associated with Reasonable and Prudent 

Alternative (RPA) actions 179-199. The purpose of the RME group review was to provide some 

preliminary information to the ISRP and project sponsors on the ability of proposals to meet the 

RME needs identified in the Biological Opinion, or as further defined by the RME group. The 

process is intended to aid in the development, selection, and funding of a suite of integrated 

projects that will meet the intent of BiOp RPA actions in the most effective and economic way. 
ISRP 2002-14 Final Mainstem and Systemwide

4

The RME group identified a set of proposals (43 of the 104 submitted) that potentially addressed 

implementation of the RME BiOp RPA action items. For these proposals, the RME group 

provided written comments on the extent to which the proposed project would meet the RME 

requirements of the BiOp. Some of the comments identified shortcomings in the proposal relative 

to BiOp requirements and proposed modifications to more directly meet the intentions of the RPA 

actions. The RME group comments were first released to the ISRP and the project sponsors 

during the week of July 22 and were included in the ISRP’s preliminary report for the relevant 

proposals following the ISRP comments.

There was some initial concern that the RME group and the ISRP would provide inconsistent 

comments requesting divergent approaches from the project sponsors in the response loop. 

Consequently, the ISRP agreed to review the RME group comments for consistency with the 

ISRP review team comments. In the preliminary report, the ISRP remarked on the RME group 

comments on the 43 projects reviewed by the RME group. For the most part, the ISRP and RME 

group comments were consistent or addressed different criteria and were not in disagreement.

Summary of ISRP and RME review process and findings:

1. Adequacy. Most project sponsors adequately addressed the initial RME concerns; 

subsequent RME comments acknowledged this. See the RME group comments at: 

www.cbfwa.org/files/province/systemwide. 

2. Consistency. RME comments were generally helpful and consistent with ISRP 

comments, with the exception of the initial comment on the Coded Wire Tagging (CWT) 

program. However, some members of the RME group are also project sponsors, leading 

to a potential for conflicts of interest. Conduct of the RPA review by the ISRP would 

realize a lowered likelihood of conflicts of interest as well as cost savings. An RPA 

review by the ISRP would require some education of ISRP and PRG members on the 

specifics of RPA and BiOp needs, if more scrutiny of those are needed in ISRP 

comments than is implicitly given (e.g., most projects state they meet an RPA need).

3. Iterative Fix-it Loop. The ISRP found some proposals designed to meet RPA/RME 

needs technically inadequate. However, according to RME Group comments, some of 

these proposals, once reworked, were critical components of their plans to meet RPA 

needs. This raises a process issue of whether to revise proposals until they meet ISRP 

criteria and RME needs or to solicit another RFP. Does the Council make an exception to

established process for proposals because of the perceived BiOp priority and timeline? 

There is a fairness issue associated with such iterative “fix-it” reviews for these particular 

projects, given the single pass through of the fix-it loop for other FWP proposals under 

ISRP review. 

4. Conflict of Interest. Because NMFS authors the BiOp and RPAs, there is significant 

potential for conflict of interest when the RME group, whose membership includes 

NMFS, makes RPA and RME recommendations on NMFS’ and competing proposals. 

This internal review is analogous to the CBFWA review of its own members’ projects, 

which at times are specified as measures in the Fish and Wildlife Program. One of the 

reasons Congress created the ISRP through the 1996 amendment to the Power Act was to 

provide an independent check against this inherent conflict of interest. The potential for 

conflict of interest with NMFS is particularly acute given the threat of ESA noncompliance. There is no question that NMFS Northwest Fisheries Science Center has a 

capable scientific staff that is necessary to recovery implementation and monitoring. 

However, like other proposals funded under the Council’s Fish and Wildlife Program, 
ISRP 2002-14 Final Mainstem and Systemwide

5

proposals selected to meet RME/RPA needs should meet the scientific criteria of the 

ISRP’s independent review. 

5. Coordinated Research Monitoring Effectiveness. The larger issue of a coordinated RME 

looms as a result of a positive ISRP review of the CBFWA proposal and the apparent 

interest of ownership of the RME process by the Action Agencies. From the ISRP 

comments on proposal # 35033, it appears that this proposal is in direct competition with 

the planned activities of the Action Agency/NMFS RME Group. Competition between 

the RME Group, currently funded by BPA, and the Collaborative Systemwide 

Monitoring and Evaluation Program (CSMEP) project (#35033), proposed by CBFWA 

and recommended by the ISRP, is a problem to be resolved in the political arena. We 

emphasize that resolution of this competition and development of a coordinated 

Columbia Basin-wide monitoring program is critical for collection of the best quantity 

and quality of scientific data that will have the greatest utility to the region in the 

evaluation of efforts to recover fish and wildlife habitat and populations.

The CBFWA proposal #35033 addresses one of the major management deficiencies in 

the basin, namely the lack of a coordinated basin-wide monitoring program. This project 

provides an urgently needed umbrella framework to: 1) collaboratively develop 

systemwide M&E protocols; and 2) coordinate data collection activities, protocols, and 

standards. The basic objective of the CSMEP project is to provide a coordinating 

mechanism for individual M&E projects rather than assuming all M&E activities into 

itself. 

It was refreshing to see in the NMFS Proposal #35019 (Develop and Implement a Pilot 

Status and Trend Monitoring Program for Salmonids and their Habitat in the Wenatchee 

and Grande Ronde River Basins) that one of the Action Agencies agrees with the ISRP 

that the CBFWA proposal #35033 contains the necessary collaborative components to 

implement a comprehensive monitoring program basinwide. We note that NMFS is also 

an active member of CBFWA. Proposals #35033 and #35019 (and by extension, parts of 

the other NMFS proposals #35016, #35020 and #35048) could be combined with other 

ongoing projects to provide a systemwide monitoring and evaluation project. The ISRP 

strongly agrees with the statement in the NMFS proposal #35019 that:

“The absolutely essential elements of 35033 that the other projects lack is the basinwide 

perspective, both in the collaborative representation of nearly all fisheries management agencies, 

as well as the inclusion of fishes other than anadromous salmonids. Ultimately, the most efficient 

manner for the Columbia River basin to approach a comprehensive monitoring program would be 

in the form of integrated aquatic ecosystem health assessment. Components of the above 5 

projects, plus many ongoing monitoring programs, if coordinated within a single purpose, design, 

and data management and evaluation framework, could produce the ideal monitoring program for 

the basin’s aquatic natural resources.” 

Technical deficiencies or incomplete methods in NMFS proposals #35016, #35020 and 

#35048 and the ISRP prevent the ISRP from giving them unqualified support for funding.

The CBFWA proposal #35033 is broader, both in scope and participation, than other 

M&E projects proposed in the systemwide province and, therefore, has a higher 

probability of success and should receive priority for immediate funding. The CSMEP 

project provides an environment for developing and coordinating common data collection 

protocols and standards. Several logistical and institutional issues remain to be resolved, 
ISRP 2002-14 Final Mainstem and Systemwide

6

but the ISRP believes that this proposal has the best potential to significantly improve the 

quantity, quality, and utility of scientific data for evaluation of fish and wildlife recovery 

efforts in the Basin.

Finally, to emphasize the urgent need for a basinwide coordinated monitoring system, the ISRP 

added the following recommendation to about 75% of the proposal reviews: "If funded, this 

project should be coordinated with other monitoring projects to ensure compatibility of 

objectives, common methods and protocols. This coordination could be accomplished under the 

favorably reviewed CBFWA proposal #35033."

Measure Smolt Survival Directly

Various scientists in the region, in particular scientists from the Comparative Survival Study 

project and NMFS, have considered the problems in estimating the LGD to LGD smolt-to-adult 

survival rates (SARs) from currently available data and have apparently arrived at what they 

consider to be the “best” formulas. Unfortunately, the formulas are complicated, convoluted, and 

in general, very unsatisfactory from a statistical point of view. Accordingly, there is high 

probability that these methods will continue to spawn arguments and counter-arguments over 

trivial issues that will occupy the resources of the region, because the stakes are high; e.g., high 

costs of spill, high costs of transportation, unknown long term effects of the non-normative 

transportation, high costs of flow augmentation, etc. 

The long-term solutions to the mathematical and statistical problems in estimation of smolt-toadult return rates (Bonneville to Bonneville and Bonneville to Low Granite SARs) appear to be: 

1) detection of sufficient numbers of PIT tagged juveniles passing Bonneville No. 2 Dam at the 

planned corner collector; 2) estimates of mortality of fish passing via that route; 3) and/or 

sufficiently large sample sizes of PIT tagged fish downstream of Bonneville. The ISRP 

recommends that these sampling efforts for PIT tagged juveniles be given high priority by the 

Council and the Corps of Engineers. In particular, Task 2 of NMFS proposal #198331900 for 

development of PIT tag detection in the corner collector at Bonneville No. 2 Dam should be 

given high priority. 

Hanford Reach Stranding

The proposal “Identify the Mechanisms of Stranding of Juvenile Fall Chinook Salmon in the 

Hanford Reach,” #35036, raised the issue of the adequacy of the amended Vernita Bar Agreement 

of February 25th 2002, in protecting juvenile salmonids from stranding. The Council and NMFS’ 

Independent Scientific Advisory Board has a particular interest in this stranding issue (ISAB 99-

5) and in 1999 recommended to the Council that a revision of the Vernita Bar Agreement be 

adopted to extend protection to emigrating fry. We understand that Grant County P.U.D. led in 

the development of a revised agreement among all of the (numerous) affected parties in 1999. In 

addition to Fish and Wildlife Program funded studies, Grant County P.U.D. continues to monitor 

fall chinook at Vernita Bar during spawning, incubation, fry emergence, and now fry emigration. 

While the amended Vernita Bar Agreement is well intended and represents a step forward in 

protecting recently emerged fall chinook that have not yet moved out of the area, it contains 

loopholes that lead to less than desirable levels of protection. The loss of an estimated 2 million 

juvenile fall chinook in spring 2001 is an illustration of this point. At least two problems in the 

amended agreement are pointed out in the response to ISRP comments provided by the 
ISRP 2002-14 Final Mainstem and Systemwide

7

proponents of proposal #35036. First, the agreement specifies permissible fluctuations in flow 

under various river flow scenarios, but the frequency, duration, and rapidity of fluctuations are 

not adequately specified. Second, the provisions are not derived from field observations that 

indicate whether they would prevent mortality of fish. In practice the major changes in flow 

brought about by load following typically occur between 11 PM and 5 AM. By the time field 

crews arrive on the river in the morning, flows have increased and any dead fish have been 

washed down the river. The Vernita Bar Agreement should be modified to correct the problems 

with flow specifications, and field monitoring should be modified to include nighttime 

observations. 

Proposal #35036 focuses on “mechanisms” that might be involved in stranding of juvenile 

chinook in the Hanford Reach, and puts an emphasis on behavioral mechanisms of the fish that 

might affect rates of stranding. The study would provide useful information to the potential 

revision of the Vernita Bar Agreement. The ISRP agrees with CBFWA that implementation of 

proposal #35036 is urgent. 

Gas Bubble Disease 

It appears that after ten years of gas bubble disease research and development, the question of 

how much monitoring and evaluation is needed in the future needs complete examination. If the 

Council calls for an independent review, the review could address the following topics and 

questions regarding the causes of total dissolved gas and the monitoring of gas bubble disease:

1. A status report on the USACE construction of total dissolved gas mitigation on all federal 

dams, primarily in the form of “flip lip” spillways. Where have they been installed? How have 

those functioned and what is the total dissolved gas duration curve at each dam under various 

flow and spill scenarios?

2. FCRPS models indicate that spill can be controlled in most years through storage operations, 

and spill in recent years is largely voluntary (defined to include spill required by the Council 

and/or the BiOp of NMFS). Models exist that predict the amount of total dissolved gas expected 

for various flow/spill scenarios and flood conditions. If those analyses show that the total 

dissolved gas limit permitted by variances issued by state water quality authorities (120 % 

saturation) is highly unlikely to be violated, then this might be evidence to eliminate or modify 

the gas bubble disease monitoring program. Do the models have good enough calibration to be 

dependable?

3. The risk of gas bubble disease to the population of juvenile migrants is primarily contingent 

upon the various passage strategies employed -- transportation, spill, bypass, etc. The gas bubble 

disease program should be keyed into regional plans for the use of transportation and in-river 

migration paths.

4. Total dissolved gas levels of up to 120% appear to be an acceptable level of risk to salmonids 

given potential benefits of spillway passage across dams. Thus, the need to maintain 110%, the 

previous water quality standard, should be re-examined for Columbia and Snake River dams. A 

critical component of this re-examination would be to monitor the effects of gas bubble disease at 

120% on resident fish species and other biota. Proposal #35013 deals with the resident fish issue. 

5. During floods and emergency outages (load rejection), total dissolved gas may rise 

unexpectedly and cause high levels of gas bubble disease even with “flip lips” or other 
ISRP 2002-14 Final Mainstem and Systemwide

8

engineering devices in place. Is it feasible to develop a gas bubble disease SWAT team for 

limited specific duty? For example, in years when high flows are anticipated, uncontrolled spill 

and total dissolved gases are expected to rise above 130%. This can be modeled ahead of the 

event. Although the Corps could maximize transportation, current JBS capture efficiency will 

decline on the rising limb of the hydrograph due to the fact that juvenile salmonids will be 

diverted into spill, exposing higher numbers of migrants to high total dissolved gas. During 

emergencies, or future anticipated flood conditions, the agencies could maintain a capability to 

sample for gas bubble disease on short notice by mobilizing expertise to a specific site for a 

specific problem. 

Conservation Enforcement

Conservation enforcement programs are conducted by many different entitie s in the Columbia 

River Basin. These programs and their activities are similar enough in objectives and data needs 

that additional benefits could be generated through their explicit coordination. The ISRP 

recommends that a targeted RFP be developed to assess the efficacy of conservation enforcement 

in the Columbia Basin, to identify strengths, weaknesses, and opportunities for improvement. The 

assessment should develop performance measures that would apply across programs and would 

inform operational adaptive management. Opportunities for coordinated data collection and 

analyses should also be identified.

NATURES Rearing and Captive Broodstock Research

The region is investing significant resources into testing and implementing new and reformed 

protocols in the artificial production arena. One area of research involves the evaluation of 

NATURES effects (i.e., the semi-natural rearing of fish in hatcheries) on salmonid behavior, 

morphology, physiology, and post release survival of hatchery fish as well as their ecological 

interactions with wild fish. This technique is being employed in both supplementation (e.g., Cle 

Elum and the Nez Perce Tribal Hatchery) and captive broodstock approaches. 

NATURES-rearing Research

The primary research proposal for the NATURES rearing effort is NMFS’ proposal # 199105500 

(Natural Rearing Enhancement Systems (NATURES)). The ISRP has reviewed this proposal 

numerous times over the last two years, including an extended review and response loop. The 

proposal has two major foci, to test NATURES rearing-habitat components at production 

hatchery scale and determine interaction effects between rearing-habitat variables assessed based 

on smolt-to-adult survival, and to investigate benefits of predator conditioning to juvenile 

migratory and adult survival. This research program, which is designed to provide answers to 

uncertainties about NATURES effects but requires 8-10 years for results, is being superseded by 

the current implementation of NATURES rearing approaches to supplementation in the Yakima 

and Clearwater systems. This raises the larger question of whether supporting the NMFS’ 

NATURES proposed project is still warranted given issues of best use of funds, the expected 

modest gains from this investment, and the information that will be available near term from 

other application of the NATURES rearing approach within (e.g., Cle Elum) and outside (Puget 

Sound) the basin. The proposed value of this specific project was a production-scale test of the 

NATURES rearing approach conducted within a rigorous experimental design. Implementation 

of NATURES rearing approaches to supplementation in the Yakima and Clearwater systems are 

in fact now applying NATURES at production scales but don’t involve the rigorous statistical 

design developed by NMFS. 
ISRP 2002-14 Final Mainstem and Systemwide

9

In making a final determination on NATURES-rearing, Council should be advised that the 

NMFS’ NATURES proposal is a well-designed experimental assessment of NATURES 

treatments intended to inform subsequent application of the NATURES approach to 

supplementation and production programs. While implementation of NATURES rearing 

treatments in the Basin has preceded this experiment, this study could still improve the efficiency 

of those applications. However, there is general regional agreement that the relative benefits of 

NATURES rearing alone are likely to be relatively small. 

Captive Broodstock Research

The primary research proposal for the assessment of captive broodstock technology in the basin is 

NMFS’ proposal # 199305600 (Assessment of Captive Broodstock Technologies). The ISRP has 

reviewed this proposal previously and recommended a more integrated approach, which the 

current proposal provides. The proposal continues the development of technologies to improve 

genetic integrity, in-culture survival, maturation, and reintroduction success of ESA-listed salmon 

captive brood stocks. Research is conducted on physiology, behavior, genetics, ecology, 

microbiology, and nutrition and the captive brood fish and their re-introduction to the natural 

environments. Nevertheless, the ISRP has several concerns with this large complex project. 

While the proposal is a substantial improvement over its predecessor, it is very large and needs 

clarification or restructuring so that the individual studies can be thoroughly reviewed. The ISRP 

was unable, within the confines and time restraints of the provincial review process, to provide as 

in-depth a review of the set of related tasks or sub-projects, as they deserve. The scope of this 

program and importance of the work to the conservation of these stocks might justify a more indepth scientific review of this one project alone (not as one of 104 projects in this review) or in 

the context of basinwide captive broodstock efforts. 

The NMFS project is one in a set of about nine ongoing basin projects using captive broodstock 

technology, and the ISRP is aware of the Council’s Conditional Approval of Captive Propagation 

Projects as specified in an April 28, 2002 letter from Mark Fritsch to captive broodstock project 

sponsors. This letter captures the ISRP’s previous programmatic concerns and provides an 

approach to review the captive broodstock program as a whole. The information gained in the 

review will inform the Council’s Artificial Production/Review and Evaluation (APRE). The 

ISRP is open to participating in a more in-depth review of the regional captive broodstock 

program or providing input on review elements. This task could be undertaken by the ISRP in the 

immediate future during the interim between this provincial review process (now ending) and the 

next one, which is tentatively scheduled to begin no sooner than late 2003 and likely 2004. The 

ISRP notes that the Council letter misses two critical issues for captive brood as a recovery tool: 

how to get the progeny back into the natural environment and what is the fitness of the progeny in 

the wild? The ISRP had particularly significant concerns about current attempts at re-introduction 

and the policy of outplanting captive-bred adults as a reintroduction strategy.
ISRP 2002-14 Final Mainstem and Systemwide

10

ISRP Final Comments and Recommendations on Each 

Proposal

Proposals are arranged by topic area, project sponsor, and project ID. Topic areas are listed in the 

following order: Wildlife, Lamprey, Avian and Fish Predation of Juvenile Salmonids, 

Estuary/Plume and Lower Columbia, Artificial Production Related, Mainstem Habitat, Water 

Quality, Juvenile and Adult Fish Passage, Data Management, Monitoring and Evaluation: 

Systemwide and Habitat Action Effectiveness, Harvest, Coded Wire Tag Monitoring Program, 

Conservation Enforcement, and Fish and Wildlife Program Coordination, Analysis, and 

Communication. See the table of contents for page starts of topic areas and the index of proposals 

for the page that specific proposal comments are on.

Wildlife

ProjectID: 199705900

Securing Habitat Mitigation Sites - Oregon

Sponsor: Oregon Wildlife Caucus

FY03 Request: $4,043,000 5YR Estimate: $23,000,731

CBFWA Adjusted FY03: $2,153,000 3YR: $10,383,992

Short Description: Protect, restore, enhance, and maintain NWPPC target habitat types and 

associated species in all Oregon subbasins within the Columbia River Basin to mitigate for 

impacts caused by hydroelectric facilities.

ISRP Final Comments: 

Fundable (Qualified); the monitoring and evaluation plan needs to be further developed. Agree 

with CBFWA’s “urgent” recommendation. The proposed budget reductions seem reasonable, 

although the ISRP performed only a cursory review of the budget changes. 

This project continues to be a good example of an umbrella proposal for acquisition of land to 

satisfy mitigation requirements of BPA. This proposal describes Oregon mitigation activities 

related to coordination and planning between Oregon wildlife managers and the implementation 

of projects. It contains a general description of the approach to mitigate for Habitat Units (HUs) 

lost as a result of the construction and operation of the Columbia Basin hydropower system. 

Oregon acquires wildlife mitigation sites according to a prioritized list following well-formulated 

criteria. Criteria used to rank sites are listed. 

The proponents comment that they have already adopted portions of the Draft M&E Plan for the 

Albeni Falls Wildlife project to use in similar cover types found at the Burlington Bottoms and 

Ladd Marsh, WA Addition project sites. They propose to use the M&E Plan for the Albeni Falls 

Wildlife Mitigation project as a template for the Oregon M&E plan and state that ties will be 

made to national databases as well. However, the M&E program is not presented in the proposal. 

The proponents should have included and more completely developed the plans for monitoring 

and evaluation that were developed by the Albeni Falls Workgroup and reviewed by the ISRP in 

the addendum to report ISRP 2001-4 “Review of Draft Albeni Falls M&E Plan.” 

The ISRP notes that a similar effort to expand the Albeni Falls Wildlife monitoring plan, which is 

more appropriate for riparian habitat, to upland and more terrestrial wildlife habitat is underway 
ISRP 2002-14 Final Mainstem and Systemwide

11

in the Upper and Middle Snake Province. We suggest that the proponents of this project contact 

the IDFG, e.g., Project 199505701 in the Upper and Middle Snake Province, and continue to 

work to ensure that common and compatible methods are developed within the Columbia Basin 

for M&E (also see CBFWA proposal 35033).

The proposal is clearly connected to regional programs and to other habitat acquisition and 

restoration projects. However, given the current importance of the BiOp to FWP funding, it 

would help this proposal to include the specific RPAs that the proposed habitat projects might 

address.

White Sturgeon

ProjectID: 198605000

White Sturgeon Mitigation and Restoration in the Columbia and Snake Rivers Upstream from 

Bonneville Dam

Sponsor: ODFW

FY03 Request: $2,041,140 5YR Estimate: $10,248,476

CBFWA Adjusted FY03: $1,984,000 3YR: $6,191,029

Short Description: Restore and mitigate for hydrosystem-caused loss of white sturgeon 

productivity through intensive fisheries management, supplementation, and modified hydropower 

system operation. Assess success of mitigation and restoration efforts.

ISRP Final Comments: 

Fundable. We agree with CBFWA’s designation of the project as urgent. This proposal 

represents a culmination of nearly ten years of work on white sturgeon biology and management 

in the Columbia River reservoirs. The project has progressed logically from research on the 

population status, life history, and habitat requirements of sturgeon through development and 

implementation of mitigation, management, and monitoring actions based on the research. The 

accomplishments of the project to date are documented in the proposal (pages 9-11) and in the 

draft White Sturgeon Program Summary dated February 22, 2002. The researchers have also 

published numerous papers in well-respected, peer-reviewed fisheries journals (pages 17-19). The 

proposal lays out a clear description of accomplishments to date and provides a logical plan for 

completing the research objectives, evaluating mitigation actions, and monitoring population 

status through 2005. Long-term goals beyond 2005 are not presented.

In the 2000 review of this project, the ISRP recommended that the sponsors develop an umbrella 

proposal for all sturgeon research in the basin and a long-term strategy and plan indicating how 

the sponsors are moving toward their objectives. The draft Program Summary appears to fulfill 

this recommendation. However, the ISRP also called for a peer-reviewed synthesis of the state of 

the science on Columbia River white sturgeon. This is a highly desirable activity that still needs 

to be conducted. We do note, however, that the sponsors have published numerous peer-reviewed 

journal articles and are contributing two chapters to a book on North American sturgeon. 

The sponsors provided satisfactory and detailed answers to the ISRP’s questions. The sponsors 

have expanded cooperative efforts on sturgeon research and management to include a workshop 

for more than 50 sturgeon biologists and interested scientists from throughout the Basin and are 

working on establishing a web space and list-server that will allow sturgeon biologists from 

throughout the Basin to form working groups and contribute to the synthesis.
ISRP 2002-14 Final Mainstem and Systemwide

12

ProjectID: 35042

Evaluate the Effects of Prey Availability on Recruitment of White Sturgeon in the Columbia 

River

Sponsor: USGS, CRRL

FY03 Request: $248,445 5YR Estimate: $1,295,445

Short Description: Ascertain how forage influences recruitment by investigating the influence of 

food deprivation at the onset of exogenous feeding, compare prey availability among areas with 

differing recruitment, and determine growth rate potential among areas.

ISRP Final Comments: 

Fundable. We agree with CBFWA’s designation of the project as high priority. This is a research 

proposal to investigate the influence of early feeding and food availability on survival and growth 

of juvenile white sturgeon (under the premise that juvenile survival establishes recruitment). The 

research would include laboratory studies of feeding behavior at the time feeding begins and 

shortly thereafter and survival/growth studies under starvation and various feeding levels. Prey 

availability in the field would be compared among three Columbia River zones with contrasting 

white sturgeon recruitment to see if differing prey availability matches differing recruitment: 

Lower Columbia (good recruitment), John Day pool (moderate and variable recruitment), and the 

Priest Rapids Dam pool (poor to no recruitment). A white sturgeon bioenergetic growth model 

would be constructed that would include spatial differences in order to predict the growth 

potential for juvenile white sturgeon throughout the region (where food availability information is 

available). The proposal recognizes that BPA’s long-standing white sturgeon project (198605000) 

has moved away from research and into implementation, as was planned in the early 1980s. Thus, 

further research requires a new project. 

This well-written proposal meets ISRP review criteria. The background section provides a 

scientifically sound rationale for the work, with abundant citations of relevant papers. There is an 

excellent discussion of regional rationale and significance of the proposed research, with citations 

and discussion of the goals of the Action Agencies’ 5-year Implementation Plan for listed species, 

the Council’s Fish and Wildlife Program (with which the proposal is consistent), and the white 

sturgeon program summary for the Mainstem/Systemwide province. Other white sturgeon 

projects are discussed including those funded by BPA in the basin and Canada and by non-federal 

organizations in the basin. The need for a new research project is persuasively presented, based 

on the planned evolution of the main BPA project (198605000) to implementation of 

management strategies designed to compensate for poor natural recruitment in much of the basin. 

The objectives, tasks, and methods are presented clearly and completely. The staff is well 

qualified. The research is one of monitoring and evaluation, and thus no separate function is 

needed (although this might have been discussed). A minor criticism of the proposal is its 

emphasis on main channel ecology, whereas the ISG in Return to the River indicated that offchannel and riparian habitats may be especially important for food production and juvenile 

feeding (the development of riparian vegetation also follows a gradient paralleling white sturgeon 

recruitment, with high and nearly normative conditions in the lower Columbia and little, if any, 

riparian development in Priest Rapids pool). 
ISRP 2002-14 Final Mainstem and Systemwide

13

ProjectID: 35043

Monitoring and Models for Adaptive Management of White Sturgeon

Sponsor: USGS, CRRL

FY03 Request: $176,000 5YR Estimate: $626,000

Short Description: Develop a quantitative tool for adaptive management that allows feedback 

from monitoring data and adjust policies related to harvest translocation, and stocking.

ISRP Final Comments: 

Fundable. We place greater priority on funding this project than the funding priority inferred 

from CBFWA’s designation of the project as a recommended action. No response was requested. 

This is a worthwhile project with well-qualified investigators. The project provides a much 

needed modeling component to complement sturgeon research and management in the basin. The 

model would be a refinement and expansion of the Snake River model developed by the principal 

investigator. This project builds upon the Snake River study funded by EPRI and Idaho Power. 

The project plans to integrate basinwide sturgeon information, and then to develop a Columbia 

River basin model (including building in supplementation efforts). The model will then be used 

to identify adaptive policies. The plan is to use the model and simulations to identify critical 

uncertainties. Management decisions or actions that could come out of the model simulations 

might include migration (transplants, upstream passage of adults), supplementation (population 

augmentation via hatchery technology), harvest, etc. 

ProjectID: 35044

Determine Effects of Contaminants on White Sturgeon Reproduction and Parental Transfer of 

Contaminants to Embryos in the Columbia River Basin

Sponsor: OSU

FY03 Request: $652,376 5YR Estimate: $1,755,005

Short Description: Determine contaminant load in mature sturgeon and the effects of parental 

transfer of contaminants on non-specific immune factors and offspring fitness. Develop a 

nondestructive tool to monitor sturgeon contaminant load.

ISRP Final Comments: 

Fundable. We agree with CBFWA’s designation of the project as high priority. This is a 

research project to test the hypothesis that contaminant loading, particularly of reproductive 

tissue, is a major factor in poor recruitment of white sturgeon in the Columbia River basin. If it is, 

then mitigative measures could be taken to lessen contaminant loading of the environment, with 

benefits to recruitment of white sturgeon. The project would sample adult white sturgeon at 

several sites in the basin ranging from the tributaries (e.g., Kootenai River) to the lower mainstem 

(in collaboration with other studies) and assay them for a range of potential contaminants and 

contaminant-indicating physiological parameters. A non-invasive method of assay would be 

developed (most likely a blood analysis) although initial assays would be destructive. Eggs and 

sperm would also be assayed to quantify transfer of contaminants and parentally derived immune 

factors (that might be lower from contaminated adults) to young. The developmental survival 

and fitness of young would be determined and related to parental contaminant load. Exposures of 

fish in the laboratory to selected contaminants would establish dose-response relationships for 

uptake and certain other effects. 

The proposal is exhaustively thorough in both background and tasks/methods, with a long list of 

cited references. The proposal is clearly based on sound contaminant science. Consistency with 

the Council’s Fish and Wildlife Program is well demonstrated, as is relevance to regional 
ISRP 2002-14 Final Mainstem and Systemwide

14

programs such as the Action Agencies’ Implementation Plan and the Mainstem/Systemwide 

program summary for white sturgeon. There are clearly defined objectives with anticipated 

outcomes, and appropriate tasks and methods for each. The project is presented as a monitoring 

and evaluation project, so no explicit discussion of that ISRP criterion is given (although it would 

have been helpful). 

The response adequately and persuasively explained the distribution of contaminant sources in 

the basin and the resulting implications for white sturgeon and for the research that is proposed. 

The potential biological significance of contaminant levels was well presented. Contaminants 

remain high on the list of potential contributors to poor recruitment of white sturgeon and deserve 

to receive the attention proposed in this study. 

A key issue for management remains: What can we do about positive results? If we hold the line 

on further contamination, will nature heal this problem? Should we be concentrating on hot spot 

removal (Superfund)? Could contaminated sediments used by sturgeon be buried by clean 

sediment? These questions are not answerable at this time without results from the research, but 

should guide the perspective of the study.

ProjectID: 35028

Evaluate White Sturgeon Nutritional Needs & Contaminant Effects Influenced by the 

Hydroelectric System

Sponsor: PSU

FY03 Request: $456,241 5YR Estimate: $1,064,326

Short Description: Evaluate the effects of the hydroelectric system on white sturgeon nutritional 

needs and contaminant effects that would be used in white sturgeon management decisions for the 

mitigation and restoration of Columbia River white sturgeon populations.

ISRP Final Comments: 

Fundable at a low priority. We agree with the CBFWA review and “Recommended Action” 

ranking. This is a basic research study to try to unravel the mystery of why white sturgeon 

recruitment is low to non-existent in Columbia River reservoirs. Earlier studies have indicated 

potential impacts of certain contaminants on fish condition and certain physiological indicators 

that could suggest adverse effects on growth and reproduction of white sturgeon in Bonneville 

Pool. The proposal seeks to build upon this work by determining if food consumed by sturgeon is 

meeting their nutritional needs and if immature fish are being adversely affected by contaminants, 

particularly in their food.

This thorough proposal generally meets the ISRP review criteria, although there were several 

technical questions that needed elaboration. The response elaborated, but did little to clarify the 

ISRP’s questions. The ISRP requested a better justification of the ecological consequences of the 

research if it is to be useful to managers. 

The topic is of regional interest, and the proposal shows how it is included in the FWP, Action 

Agencies’ Implementation Plan, Mainstem Solicitation, and the Sturgeon Program Summary. The 

background section gives up-to-date details of prior work on the subject, including data. The 

objectives and tasks are fairly clear, and the planned methods (including sample sizes) are laid out 

in detail. There is a qualified staff, and they have demonstrated their capability to do the work 

with prior studies funded elsewhere. The study is highly contaminant oriented, and food and 

feeding are given attention mainly through analysis of stomach contents. There might have been a 

more ecological flavor.
ISRP 2002-14 Final Mainstem and Systemwide

15

There are two general difficulties with this sort of work. First, knowing with some certainty that 

changes in physiological and biochemical indicators will translate into biologically meaningful 

reductions in growth and reproduction and second, knowing with some certainty that the changes 

in physiological and biochemical indices that are observed are a direct consequence of exposure 

to contaminants and not a result of some other environmental factors (e.g., changes in flow 

regime, temperature) or a density-related phenomenon. The response did little to assuage our 

concerns on these points. 

Overall, most of the methods lack sufficient conceptual detail to convince a reviewer that the 

research will accomplish what it proposes. It is unclear how much new knowledge relevant to 

restoration and protection of sturgeon will be generated by this research beyond what is already 

known from past studies. 

ProjectID: 35059

Rapid Detection of White Sturgeon Iridovirus in Spawning Fluids, Eggs and Juvenile Tissues of 

White Sturgeon

Sponsor: USFWS

FY03 Request: $97,452

5YR Estimate: $191,306

Short Description: Develop a rapid nested PCR assay for the detection of White Sturgeon 

Iridovirus from reproductive fluids, eggs and tissues of infected fish. Utilize the assay to 

determine viral prevalence and geographic distribution within the Columbia River Basin.

ISRP Final Comments: 

Do Not Fund; agree with CBFWA. The proposal is technically inadequate. It lacks clarity and 

adequate methodological detail and has poorly stated objectives (just a list of tasks). The real 

objective of determining the prevalence of the virus in the basin was given in the narrative of 

background. The principal investigator’s brief CV and listed references suggest competence in 

the development and application of genetic -based disease assays, but neither the proposal nor the 

presentation provided adequate detail on laboratory or genetic assay methods to provide 

reviewers confidence that the project’s goals are likely to be realized. The principal investigator 

talked about PCR as a new technique. While PCR has clearly revolutionized many genetic -based 

analyses, it has been around for nearly a decade and is routine business in any genetic laboratory. 

The principal investigator could have shown slides that quickly and clearly showed the nongeneticists in the audience how PCR worked, how primer sets are generated for new applications, 

and how the presence / absence ELIZA-type tests are performed.

ProjectID: 35061

Prophylactic Treatments for White Sturgeon Infected with the White Sturgeon Iridovirus (WSIV)

Sponsor: USFWS

FY03 Request: $69,681 5YR Estimate: $127,661

Short Description: This project looks at a number of different prophylactic treatments targeting 

secondary pathogens found in outbreaks of the White Sturgeon Iridovirus in order to minimize 

total mortalities.

ISRP Final Comments: 

Do Not Fund; agree with CBFWA. The proposal is inadequate. This is a very short proposal to do 

routine screening of prophylactics for their efficacy in treating secondary bacterial and fungal 
ISRP 2002-14 Final Mainstem and Systemwide

16

infections of white sturgeon undergoing effects of a viral infection. Such checking of 

prophylactics doesn’t seem to be cutting edge research. The prophylactics are commonly used on 

other fish for similar infections. No literature documentation is provided for this common 

practice.

Lamprey

ProjectID: 35008

Systemwide Lamprey Program Coordinator

Sponsor: USGS, CRRL

FY03 Request: $111,370 5YR Estimate: $496,774

Short Description: Provide coordination for the Lamprey Technical Working Group

ISRP Final Comments: 

Fundable in part. We disagree with CBFWA’s high priority designation of the project. The 

response was not adequate. The ISRP does not recommend funding of the Lamprey Coordinator 

position, but does recommend funding support for an annual workshop that would allow 

biologists from throughout the basin to meet, review projects, and coordinate work. 

The ISRP favors coordination among lamprey projects, but the sponsors need to better justify 

why a formal, funded coordinator position is necessary and if the approach presented in the 

proposal is generally supported by lamprey researchers and managers throughout the basin. One 

coordination task that is not specified in the proposal is integrated, basinwide planning of lamprey 

research and restoration projects. This would seem an appropriate task for a Coordinator position. 

However, the sponsor’s response did not answer our questions; rather it merely commented on 

our comments. The absence of letters of support from the lamprey researchers demonstrating their 

support for the proposal, especially for the USGS as lead, may indicate a lack of support for a 

coordinator or for this agency as the lead. 

The draft Columbia River Lamprey Program Summary (February 22, 2002) appears to address 

many of the ISRP’s concerns about program level coordination. The Program Summary lists all 

ongoing lamprey research, describes how projects are interrelated and coordinated, and identifies 

critically needed research projects, major uncertainties, and future management actions. The 

Program Summary specifically addresses concerns raised by the ISRP during its review of 

lamprey projects in last year’s review of the Columbia Plateau Province. Pages 8-10 of the 

Program Summary lists proposed project needs and priorities for the lamprey program. It does not 

mention this proposal (35008) nor the need for a Systemwide Lamprey Program Coordinator to 

support the Lamprey Technical Working Group; thus, the ISRP is unclear of the level of support 

for this project from the LTWG, something that would be critical to program success if funded. 

ProjectID: 200002900

Identification and thermal requirements of larval Pacific, river, and western brook lampreys

Sponsor: USGS, CRRL

FY03 Request: $186,945 2YR Estimate: $261,945

Short Description: Determine morphological and molecular characteristics that differentiate 

sympatric larval lampreys and evaluate thermal tolerances of larval lampreys by species

ISRP Final Comments: 

Fundable to complete in two years as proposed. The response was adequate, but minimal. We

agree with the CBFWA review and “urgent” ranking. 
ISRP 2002-14 Final Mainstem and Systemwide

17

This project, now (2002) in its third year, will provide basic biological data on the species of 

lampreys occurring together in the Columbia River basin. With anadromous Pacific lamprey 

populations in decline, likely because of hydrosystem effects, and mitigation measures underway, 

there is a strong need to be able to identify that species from other lamprey species (western 

brook lamprey and river lamprey) that also reside in streams during early life stages. The project 

has focused initially on basic morphological tools of the taxonomist for differentiating eggs and 

early larvae raised in the laboratory, but there are plans to expand the effort to use biochemical 

genetic markers of species identity. Additionally, the rearing of larvae in the laboratory has been 

carried out at four temperatures in order to characterize the temperature requirements for survival 

of these stages, which might differ. An equipment failure caused delay in some aspects of the 

intended schedule, so the study team proposes another two years for completion. The final years 

will emphasize replicated work on morphological and temperature-effect studies, preparation of 

manuscripts on that work, and more emphasis on the genetic differentiation techniques. 

The proposal was well prepared and informative, and met the ISRP review requirements 

(monitoring and evaluation was not considered especially relevant). The project has yielded good 

results for the first years of the study that were well presented in the proposal. There is an 

adequately prepared rationale and justification based on the Council’s Fish and Wildlife Program 

and the uncertainties, goals, and objectives from the Columbia River Lamprey Program Summary 

and the Mainstem/Systemwide solicitation (which included the relevant Biological Opinion 

information). The proponents demonstrated knowledge of related projects in the basin, and 

coordinate with them informally. There are no monitoring and evaluation aspects to the planned 

studies. The staff seems well qualified to do the work. 

ProjectID: 200005200

Upstream migration of Pacific lampreys in the John Day River: behavior, timing, and habitat use

Sponsor: USGS, CRRL

FY03 Request: $250,000 5YR Estimate: $665,000

Short Description: Determine behavior (timing and movement patterns) of upstream migrating 

Pacific lampreys in the John Day River Basin using radiotelemtery. Characterize overwintering 

and spawning habitats of Pacific lampreys in the John Day River Basin.

ISRP Final Comments: 

Fundable. A response was not needed. We agree with the CBFWA review and “high priority” 

ranking. This is a proposal for continuation of a project begun in 2000 that was originally funded 

for a one-year duration. The ISRP noted in its favorable earlier review of the original 3-year 

proposal that some innovative aspects of the proposal could have application to lamprey research 

systemwide, and the project was funded for a first-year trial. The purpose of the initial project 

was, therefore, to demonstrate that Pacific lamprey could be radio-tagged and their movements, 

overwintering locations, and spawning habitats identified in the John Day River (the current 

proposal, however, chose to dwell unnecessarily on lost opportunities of the unfunded second and 

third years). The one-year demonstration project was successful for the summer through early 

spring migration and overwintering periods, as documented by data presented with this proposal 

and in a report to BPA. Timing of the funding cycle was not right to observe spawning. The 

current proposal would extend the one-year, initial effort to two more full tracking years 

(including the spawning component) and a data analysis/report preparation year. 

The proposal was generally well prepared and informative. The ISRP review criteria were met. 

The work was well justified on the basis of a need to understand the biology of Pacific lamprey in 
ISRP 2002-14 Final Mainstem and Systemwide

18

the face of population declines. The Council’s Fish and Wildlife Program, the regional planning 

documents for lamprey, subbasin plans for the John Day and Umatilla rivers, and other regional 

documents were cited, as well as previous ISRP reviews. Results from the one-year study were 

presented in detail, and persuasively demonstrated the feasibility and utility of this work. There

are clearly defined hypotheses, objectives, tasks (and even activities under tasks), which 

responded to earlier ISRP comments. The work as a whole is of a monitoring and evaluation 

nature. There will be clear benefits to lamprey from the greater understanding that this project has 

developed and will develop. 

The geographic bound of the proposal is limited, but there is purported systemwide relevance for 

the results. The John Day River is clearly the focus of the study, but the proposal claims that this 

work will aid lamprey studies in general and restoration work on the Umatilla River in particular. 

The ISRP suggests that a proposed study of lamprey in the Willamette River (35009) would also 

be benefited. The project would also participate actively in basinwide coordination of lamprey 

research.

If funded, this project should be coordinated with other monitoring projects to ensure 

compatibility of objectives, common methods, and protocols. This coordination could be 

accomplished under the favorably reviewed CBFWA proposal #35033.

ProjectID: 35006

Use of Mainstem Habitats by Juvenile Pacific Lamprey (Lampetra tridentata)

Sponsor: PNNL

FY03 Request: $100,985 5YR Estimate: $333,366

Short Description: Characterize the use of mainstem Columbia and lower Snake River habitats 

by juvenile Pacific lamprey and identify river reaches with high potential for restoration or 

expanded use.

ISRP Final Comments: 

Fundable. We disagree with CBFWA’s “recommended action” designation and believe the 

proposal should be higher priority. This research is fundamental to lamprey recovery in the 

basin, and this project is likely to contribute substantially to understanding mainstem rearing 

opportunities for juvenile lamprey. The sponsors propose to investigate utilization of shoreline 

habitats in riverine sections of the mainstem Columbia and Snake Rivers by juvenile lamprey and 

use this information to extrapolate habitat use and restoration potential to larger spatial scales. 

The proposal is well prepared and reflects the input of previous reviews by the working group on 

lamprey and the previous submission to the FWP. The sponsors are particularly well suited to 

conduct the research. The response adequately addressed the ISRP’s concerns about additional 

methodological detail. 

If funded, this project should be coordinated with other monitoring projects to ensure 

compatibility of objectives, common methods, and protocols. This coordination could be 

accomplished under the favorably reviewed CBFWA proposal #35033.
ISRP 2002-14 Final Mainstem and Systemwide

19

ProjectID: 35009

Evaluate Status of Pacific Lamprey in the Willamette River Subbasin

Sponsor: ODFW

FY03 Request: $129,991 5YR Estimate: $977,991

Short Description: Determine distribution and population status of Pacific lamprey in the 

Willamette River subbasin. Evaluate system-wide implications of trends in distribution and 

abundance of Willamette subbasin Pacific lamprey.

ISRP Final Comments: 

Fundable. Response adequate. We agree with the CBFWA review and “high priority” ranking. 

The Willamette may be a major, or the major, production area for lamprey in the Columbia Basin, 

but, currently, very little is known about specific utilization of the Lower Willamette. This project 

should provide useful information concerning lamprey distribution and abundance in the 

Willamette. The sponsors adequately addressed the ISRP’s concerns.

If funded, this project should be coordinated with other monitoring projects to ensure 

compatibility of objectives, common methods, and protocols. This coordination could be 

accomplished under the favorably reviewed CBFWA proposal #35033.

Bull Trout

ProjectID: 35002

Determine origin, movements and relative abundance of bull trout in Bonneville Reservoir.

Sponsor: WDFW, YN

FY03 Request: $379,601 5YR Estimate: $1,525,101

CBFWA Adjusted FY03: $293,351 3YR: $598,351

Short Description: Determine the abundance of bull trout in Bonneville Reservoir. Monitor 

movements into Hood River and Klickitat River.

ISRP Final Comments: 

Fundable in part. Agree with CBFWA and the sponsors’ revision of the proposal and the budget 

reduction. We disagree with the Urgent ranking assigned to the proposal by CBFWA and view 

the proposal as a lower priority action. 

If funded, this project should be coordinated with other monitoring projects to ensure 

compatibility of objectives, common methods, and protocols. This coordination could be 

accomplished under the favorably reviewed CBFWA proposal #35033.

Based upon the sponsor’s response, the ISRP suggests two years of funding to explore feasibility 

of capturing bull trout in Bonneville Reservoir with subsequent funding contingent upon 

demonstration of the efficacy of capture techniques. The project hinges on the ability of the 

sponsors to effectively capture bull trout in the reservoir. There is considerable uncertainty 

associa ted with this objective because bull trout apparently are rare and difficult to capture in the 

mainstem Columbia. Without an effective method of capture the essential parts of the proposed 

work could not be accomplished. 

Utilization of Bonneville Pool by migratory bull trout is poorly understood. This proposal seeks 

to improve understanding of the stream of origin and migratory patterns of bull trout found in 

Bonneville Pool. The work is consistent with the USFWS’s 2000 Biological Opinion. The 
ISRP 2002-14 Final Mainstem and Systemwide

20

proposed work would develop methods for effectively sampling bull trout in the reservoir, install 

a fish trap to monitor movement in the Klickitat, radio tag fish from the reservoir to monitor 

movements from the reservoir into tributary rivers, and conduct genetic analyses to determine 

river of origin. 

If funded, this project should be coordinated with proposal 35013; e.g. they should record 

observations of gas bubble disease symptoms in sampled bull trout.

Avian and Fish Predation on Juvenile Salmonids

ProjectID: 199007700

Northern Pikeminnow Management Program

Sponsor: PSMFC

FY03 Request: $2,957,438 5YR Estimate: $16,520,975

CBFWA Adjusted FY03: $2,870,000 3YR: $9,100,000

Short Description: Reduce predation on juvenile salmonids by implementing fisheries to harvest 

northern pikeminnow in the mainstem Columbia and Snake rivers. Monitor effects of fisheries 

on predation by northern pikeminnow and other resident fish.

ISRP Final Comments:

Fundable in part as agreed to by the sponsor and specified in CBFWA’s comments: “The O&M 

phase of the project has been reduced by $88,000 in order to remove the site specific and dam 

angling fisheries due to their reduction in cost effectiveness.” CBFWA’ continue to rank this 

project as “Urgent.” However, the ISRP urges more economic accountability and innovation. 

The ISRP disagrees with the budget reduction eliminating $40,000 to cover the expense of an 

economic analysis of promotion cost and sport reward costs. Additionally, the ISRP believes the 

economic analysis should include other elements discussed below.

This is a long-term project to continue 12 years of managed harvest of northern pikeminnow, the 

principal predator of salmonid smolts. The project has become more evaluative over time. Catch 

per effort of northern pikeminnow, appears to be on a downward trajectory. Probably, this is 

because of the success of the program in depressing northern pikeminnow populations. There is 

likely a net benefit to adult salmon returns, but those benefit numbers have likely stabilized. 

Neither monitoring nor evaluation contains an economic component, but economics, including 

independent cost-effectiveness monitoring, should be a part of the project’s evaluation. 

The Hankin and Richards report that reviewed the program two years ago (on recommendation of 

the ISRP) contained recommendations for improving the efficiency of the program. Two such 

recommendations not yet implemented are to conduct further study of the tiered reward system 

and to explore possibilities to increase rewards by decreasing promotion costs. To their credit, the 

sponsors have agreed to eliminate two major inefficiencies, the tribal fishery and the tailrace 

fishery, and to investigate various alternative reward systems. Calculations suggest a definite 

decline in biomass and average size of northern pikeminnow in recent years. As catch has been 

declining, so have costs of rewards, and this explains part of the continuing “improvement” in 

cost containment. 

Due to the high annual cost of this project, reviewers suggest that it may be time to creatively rethink how this program could be further improved. It would be worthwhile to consider new ideas 

for streamlining or economizing the approach. Considering that there is a trend of declining 
ISRP 2002-14 Final Mainstem and Systemwide

21

biomass (annual averages of 73 M grams in 1991-96 vs. 51 M grams in 1997-2001), analyses 

might be conducted to assess alternative predator control strategies. Alternative strategies, might 

be explored, that would increase the incentives for fishing. The attractiveness and spin-off 

benefits (e.g. increased tourism) of other types of rewards, incentives and approaches (e.g. a 

major international pikeminnow derby every year with large prizes for capture of tagged fish) 

might be investigated as a way to enhance public awareness, maintain effectiveness, and control 

costs. 

The ISRP raised related questions about control of other exotic predators that might be explored 

in the future. Smallmouth bass, channel catfish and walleye are exotic species whose harvest is 

regulated by the management agencies according to objectives that may be in conflict with 

objectives of the Council and NMFS with respect to enhancement and recovery of salmonids in 

the basin. Some or all restrictions on sport harvest of exotic species might be lifted in order to

reduce their populations and thus their predation on salmonid smolts. 

In summary, the project is recommended for continuation with the recommendation that thought 

be given to new, innovative, cost-saving approaches that might be used to reduce pikeminnow 

predation on salmonids. As mentioned above, the Council funded an economic review of the 

project by Hankin and Richards two years ago. Their report contained recommendations for 

improving the efficiency of the program. Considering the visibility of this program and its cost, 

we believe it would be in order for the Council to request a follow-up and more in-depth review 

of the program. Because the economic issues are intertwined with biological issues, further joint 

ISRP/IEAB review could be a constructive approach toward improving the effectiveness of the 

program.

ProjectID: 199702400

Avian Predation on Juvenile Salmonids in the Lower Columbia River

Sponsor: OSU/USGS/CRITFC/RTR

FY03 Request: $713,000 5YR Estimate: $3,688,000

CBFWA Adjusted FY03: $680,000 3YR: $2,080,000

Short Description: Determine predation rates by waterbirds on juvenile salmonids, evaluate the 

efficacy of management initiatives to reduce avian predation, and assist resource managers in the 

development of plans for long-term management of avian predation, as warranted.

ISRP Final Comments: 

Fundable, agree with CBFWA’s “Urgent” ranking. The sponsor offers to eliminate two tasks 3.2 

and 3.3 for budget savings. The ISRP has made some alternative suggestions to make the research 

more relevant directly to salmonid survival improvement and the researchers indicated 

willingness to consider such improvements. These were done without suggestions for budgetary 

reduction. 

This proposal is designed to determine predation rates by seabirds on juvenile salmonids, evaluate 

the efficacy of management initiatives to reduce avian predation, and assist resource managers in 

the development of plans for long-term management of avian predation. The current proposal is 

for continuation of work that has been underway for several years, but that is now being driven by 

a settlement agreement from an intensive court case that pitted the interests of bird 

conservationists against those restoring salmon. There is an expanded budget that reflects 

settlement-mandated tasks. 
ISRP 2002-14 Final Mainstem and Systemwide

22

The ISRP review criteria are met. The experimental design is good. This five-year program has 

gathered much new information about tern biology and feeding behavior. Key recommendations 

have been to move, if not eliminate, breeding habitat. These recommendations have been 

successful. The proponents have given a good summary of past results. They have measured the 

net effectiveness of tern removal on salmonid survival that is contributing positively albeit 

modestly to recovery according to population models. Bioenergetics of tern diet, stable isotope 

ratios studies, fatty acid signatures, and contaminant levels may be valuable in further assessing 

tern diets and impacts on salmon. 

A shortcoming identified in previous years was the lack of peer-reviewed publications, a factor 

now addressed by the latest group of publications. Another previous shortcoming was the need 

for a more in-depth review of the program. This review has been accomplished externally via the 

court case. Although this proposal does not dwell on the court case, there was impetus from it for 

looking at other bird predators of salmonids (to put terns into broader context) and other potential 

nesting sites to receive research and management attention (upriver and coastal). 

The authors were highly responsive to ISRP questions and (1) illustrate important facts that cast 

better light on the rationale for their studies and (2) suggest alternative approaches to gather data 

that may be more relevant to improving salmon survival. Much of the proposed new tern research 

is aimed at assisting the growth, development and monitoring of new tern colonies elsewhere, 

which must be balanced with colony reductions in the estuary for enhanced salmon recovery. 

Other parts of the monitoring and research proposal tasks seem to be on details and data not 

directly useful or have large payoffs for the FCRPS management objectives. The sponsors agreed 

to address several important questions that seem relevant to the FCRPS: the relationship of 

predation loss to juveniles that (1) migrated in river or (2) were transported near the estuary in a 

barge. Since PIT tags usually contain this information, a study of existing PIT tag data seems in 

order. Thus far, NMFS studies have shown that SARs (adult returns) from transported smolts 

exceeds SARs of juveniles that migrate through the FCRPS. One important strategy that could 

reduce tern predation might be adjustments in the timing, location and patterns of release of 

smolts from barges in the estuary. For example, if terns are daylight feeding birds, would release 

at night improve predator avoidance? Or, would release closer to the ocean reduce bird predation 

without other impacts to the SAR rate. The researchers indicated a willingness to include such 

analyses where possible with PIT tag data and to coordinate with the NMFS and USACE in such 

experiments.

The past five years of research has been good and has provided ample information about the 

impacts of terns to salmon. Logical management actions (moving or reducing tern populations) 

are now being implemented to the extent they are allowed by the courts. Some further 

management experiments that relate to how, where and when transported fish are released from 

barges may be useful to the FCRPS and the sponsors have agreed to address these options. The 

authors are willing to collaborate with transport release studies. Presumably, these would need to 

be included in research funded by the USACE. Another future research effort could examine the 

differences between hatchery and wild fish losses. 

If the proposal is funded, some restatement of tasks and goals would be in order to reflect the 

modifications and effort reorientation mentioned in the response. The sponsor identified the 

following tasks for elimination in the interest of cost savings: Task 3.2. Collect information on 

diet composition at selected gull colonies in the lower Columbia River between Bonneville Dam 

and the mouth of the Snake River; Task 3.3. Collect information on foraging aggregations of 

piscivorous seabirds along the lower Columbia River between Bonneville Dam and the head of 

McNary Dam pool.
ISRP 2002-14 Final Mainstem and Systemwide

23

The ISRP agrees that these tasks have lower priority. However, given the importance of other 

questions related to salmon survival posed in the review, the ISRP is not recommending reduction 

in the budget for this program. Instead, these tasks are given lower priority and should be 

addressed only if other more pressing tasks can be completed with the funds provided. If 

appropriate, the proposal could be recast to reflect these changes in priority.

ProjectID: 35032

Assess the Feasibility of Reducing Predation on Juvenile Salmonids in the Columbia River 

Through Operation of the Hydropower System

Sponsor: USGS, CRRL; ODFW

FY03 Request: $509,671 5YR Estimate: $2,394,540

Short Description: Evaluate components of riverine habitat that might be manipulated to limit 

predators and predation loss. Examine and collate existing information, evaluate methods to 

estimate effects on predator populations, and collect additional information needed.

ISRP Final Comments: 

Not Fundable. Disagree with CBFWA’s High Priority ranking. The ISRP had significant 

reservations and substantial questions about whether practical progress could be made with the 

proposal as presented. Responses to the ISRP questions were inadequate primarily regarding the 

research program design. 

In the oral presentation, the authors acknowledged that physical habitat modifications might also 

be possible. This concept presented is a generalized idea, but needs specific hypotheses. The 

study might take a decade or more and result in much data that can’t be well coordinated. 

Evidence needs to be given that specific actions have realistic management applications. The 

predators discussed all have different life histories. The study doesn’t show that it is in the realm 

of hydraulic possibility. There are two major concerns and a host of minor issues that needed to 

be addressed but were not in either the proposal or the response. 

First major concern: the hydropower system management actions that are foreseen were not 

clearly presented, which leaves the question whether all this work might lead to recommendations 

for physically impossible operations. Second, there was insufficient evidence concerning the 

exact mechanisms of life history disruption sought. The proposal seems to ask for funding to 

discover such possibilities. Such efforts could take indefinitely long periods. 

A key target area of the proposal is downstream of Bonneville Dam. The ability of the 

hydroelectric system to control depth and velocity in this area will be limited. Demonstration with 

hydraulic data that hydro operational changes could possibly have the desired effect would have 

been valuable in making the case for the research. Much is known about the habitat requirements 

of predatory fishes that might be targeted. A discussion of these in the context of what is known 

about present operations of the hydroelectric system would have been useful in justifying the 

proposal. For example to dewater or lower water levels in the tailwater area at Bonneville Dam 

would require significant retention of storage and complicate water levels, flows and upstream 

operations that might have undesired or unacceptable impacts on fish, wildlife, human uses 

upstream, in addition to constraining the normal power system operations. Furthermore, the 

proposal would need to consider possible negative effects on salmon or other desirable fishes of 

any proposed manipulation of operations. For example, many years have been spent fine-tuning 

the operations of the spillways, turbines, and fish ladders to maximize adult salmon passage and 
ISRP 2002-14 Final Mainstem and Systemwide

24

to direct juveniles to areas of highest passage survival. These would need to be taken into 

account. 

In summary, the ideas in this proposal are intriguing but were insufficiently developed and 

possibly targeted to the most difficult location in the FCRPS to implement, the tailwater of the 

Bonneville system.

Estuary/Plume and Lower Columbia

With the exception of proposal 35046, these proposals were also submitted for the Estuary and 

Lower Columbia River Province Reviews. 

ProjectID: 35025

Optimization of FCRPS Impacts on Juvenile Salmonids: Restoration of Lower-Estuary and 

Plume Habitats

Sponsor: OHSU

FY03 Request: $435,192 5YR Estimate: $1,206,325

Short Description: Restore Columbia River estuary and plume juvenile salmonid habitats and 

optimize FCRPS impacts on the plume through improved understanding of estuary and plume 

physical processes and definition of possible future management scenarios

ISRP Final Comments: 

Fundable. Disagree with CBFWA’s recommendation of “Recommended Action”. This is an 

important component of the estuary program, especially the monitoring objectives and warrants a 

higher priority. The response provided a clear articulation of the areas in which this project 

complements other projects and those in which it is unique. This project and #199801400 

(Plume) and #30001 (Estuary) are tightly integrated in the data they will produce and the analyses 

that will be conducted. The ISRP acknowledges that their past comments may have overemphasized the management science of this proposal.

Previous reviews by the ISRP in the Lower Columbia/Estuary province had primarily focused on 

the objectives related to interaction with policy makers on operation of the FCRPS, which is 

actually a relative minor component of the full project. In project 35025, 85% of the budget is for 

environmental monitoring (remote sensing) and development of their concept of “habitat 

opportunity” as a means to assess the suitability of the plume to salmon. The remote sensing 

component of project 35025 (allowing analyses of parameters not included in the Plume 

proposal) is an important component of the set of projects in Estuary and Plume. Two other 

considerations are notable: the development of remote sensing (in coordination with CORIE) and 

numerical models may reduce long-term costs of oceanographic surveys (i.e., in the Plume 

proposal), and these investigators may provide large returns through other funding agencies. 

The remaining 15% of the costs associated with this proposal is directed to the Project 

Management Board and interactions with the FCRPS. Proceeding with the above data aspects 

and beginning dialogue with the FCRPS should proceed so that when analyses of flow and plume 

issues are complete, the FCRPS is familiar with the issue and have an informed basis for 

response. A strength of this project is its emphasis on the eventual application and 

implementation of project results in management actions. The management science approach to 

laying out alternative scenarios for FCRPS managers will probably be quite useful in helping to 
ISRP 2002-14 Final Mainstem and Systemwide

25

articulate opportunity costs of particular river management strategies and to distinguish low-cost 

from high-cost management actions. It should enable a systematic assessment of tradeoffs. 

This proposal makes a persuasive case for the integration of flow management with the needs of 

salmonids in the lower Columbia River, estuary, and plume environments. Dr. Jay has assembled 

a strong research group and has obviously tried to more clearly enunciate the value of this project 

to Columbia River salmonids and impacts of future climate scenarios. The RME comments 

strengthen our support and the obvious need for mutual consideration of flow and fish. 

The purpose of this program (section 9, page 24, Tasks and Methods) is “to optimize the 

interactions of the FCRPS with juvenile salmonids in the lower-estuary and plume.” The 

technical background in this proposal is thorough and reasonable but we must still acknowledge 

that the importance of the plume environment to salmon survival remains unquantified or tested. 

With the current developments in the micro-tags and extensive studies in the lower river, estuary, 

and plume, we may have answers to these questions in the near future. Therefore, in considering 

this proposal, it is important to note that the proposal emphasizes the need for understanding and 

dialogue with hydro-system managers, but does not presume that the FCRPS would immediately 

be modified to meet the ‘habitat opportunity’ needs of the fish. The intent of the program is 

clearly to examine if fish needs can be incorporated into the water management planning cycle, 

and to explore how modifications of flow could benefit salmon while remaining within the limits 

imposed by other requirements. Further, if agreements could not be reached on how to respond to 

specific scenarios, then the models and sampling programs developed in this project provide an 

ideal opportunity to design a truly adaptive management approach to understanding the 

“integration of flow management with the needs of salmonids in the lower Columbia River, 

estuary, and plume environments.”

The ISRP believe there is an obvious need to initiate dialogue with the FCRPS managers so that 

an understanding of the proposed research and process is begun. If FCRPS managers are not 

prepared to consider possible alterations in flow plans or how to respond to different climate 

conditions or annual devia tions in weather, then there are a number of extensive programs that 

may not need to be funded at all. The costs and benefits of all recovery opportunities need to be 

considered, none should be excluded particularly given the investment made in science within the 

Columbia River Basin.

Two points for clarification remain after the response. The ISRP is not certain that the definition 

and analysis of “habitat opportunity” will be addressed in areas upstream of the estuary to 

Bonneville Dam. If this was not the intention, then it must be integrated into project 35025. 

Further, the final definition of “habitat opportunity” continues to need clarification and we 

request that these investigators maintain communication with Basin agencies on this issue.
ISRP 2002-14 Final Mainstem and Systemwide

26

ProjectID: 35046

Estimate juvenile salmon residence in the Columbia River Plume using micro-acoustic 

transmitters.

Sponsor: NMFS

FY03 Request: $2,595,600 5YR Estimate: $17,172,100

CBFWA Adjusted FY03: $878,300 3YR: $5,908,600

Short Description: Estimate juvenile chinook salmon residence time and areas of utilization 

within the Columbia River plume.

ISRP Final Comments: 

Fundable (Qualified). Specifics of the collaboration with Dr. Welch, including budgets, need 

further discussion. Disagree with CBFWA recommendation of High Priority; development of 

the smaller 400 kHz tag is essential to investigating the residence of salmon within the Columbia 

River plume and is urgent. The development of the new tag also requires the development of new 

detection equipment, including work to define the acoustic environment for the tag in the estuary 

and the plume. The majority of the tag development and the estuary detection are currently 

funded under a USACE program. Development of the open-water detection equipment for the 

plume environment and the anchoring systems is included in this project and through a proposed 

collaboration with Dr. Welch (Estuary proposal #30007). 

The overall objectives of this proposal are to determine plume residence times of ocean and 

stream type salmon, characterize fine-scale spatial use of the plume by these two types, and 

integrate results with the companion project (the NMFS Plume study, project #199801400) to 

build a biophysical model relating Columbia River plume conditions to the growth, distribution 

and survival of juvenile salmonids. 

This proposal would complete development of micro-acoustic tag methodology and assess 

residence of salmonids in the Columbia River plume by deployment of fixed and mobile receiver 

arrays. The approach taken by the project will be to characterize the acoustic environment of the 

plume, model signal propagation (to adjust for noise in the plume environment), design the 

detection system, set tag criteria and design, conduct prototype tests, then proceed to full-scale 

monitoring. Risks identified by the proponents are the difficulties of obtaining adequate sample 

sizes, the fixed array design, cost, and limited detection range due to phase shift encoding. 

Ultimately, the goal of the project is to answer the critical uncertainty about temporal and spatial 

use of the plume habitat by juvenile salmon (see past ISRP comments on NMFS project 

199801400). The project will compare the residence times of different life history types (stream 

and ocean) of chinook salmon, timing of outmigration (early versus late), size and age, to 

determine how they vary by season. It also proposes to assess the nature of juvenile distribution 

within the plume.

The technical background is well written and complete. The rationale for the importance of 

understanding juvenile use and survival in the plume is clearly significant to regional programs 

(as evidence by the comments to proposal 35025 above). The tasks and methods are described in 

appropriate detail and a very strong development and research team has been organized. The 

ISRP wishes to compliment these investigators for their substantial progress on the micro-tag to 

date. This tag may now offer a real opportunity to study salmonid residency and use of the 

Columbia River estuary and plume. 
ISRP 2002-14 Final Mainstem and Systemwide

27

However, in the preliminary ISRP report, we requested a response to two major concerns with the 

receiver arrays. First, the development of the fixed and mobile arrays apparently doubles the costs 

for this portion of the work. Secondly, we are familiar with the work of Dr. David Welch (CDFO, 

Pacific Biological Station, project proposal #30007, Estuary province), and BPA has previously 

supported his research. Dr. Welch has put a substantial investment of time into designing fixed 

arrays, their deployment, and how to retrieve the data received. Since this must be a very small 

group of researchers in this field, we were concerned by the evident lack of collaboration. The 

response received addressed these questions by proposing a collaboration with Dr. Welch and by 

phased development of the detection systems.

When the ISRP considered the development proposals by Dr. Welch (in the Estuary provincial 

review), we proposed supporting a prototype or “proof of principle” scale program initially, 

followed by expansion if successful. In this response, a 4-line array to address the “proof of 

principle” concern is proposed by Dr. Welch and the NMFS proponents. Four anchored arrays 

would be established in 2003 and include one array south of the Columbia River, two off the 

Washington coast, and one at the north end of Vancouver Island, BC. This is similar to Dr. 

Welch’s proposal to the Estuary province. The collaboration between proposals would be the 

possible use of the anchored arrays to also hold the 400 kHz detection systems (requires 

completion of detection system first, not expected before 2004). While the ISRP recognizes the 

efforts to collaborate, we are not convinced the array locations are adequate to test the detection 

systems. The arrays are very widely separated and would initially only go out to the 100m 

contour. We fully understand the interest in testing the existing acoustic tags and their detection 

in the open ocean, but the primary responsibility of the ISRP is whether the proposed design will 

provide an adequate test of the arrays. We clearly disagree with comments like “”the fixed array 

locations selected are sufficient and adequate “exit” stations that can be used to document plume 

usage and initial shelf oriented behaviors” (point 2, 1st para. John Ferguson letter). The task that 

NMFS was to address was residence and survival in the plume ... how could 4 lines of fixed 

arrays over several hundred miles of the coast be “sufficient” to address this? The ISRP does not 

support funding this collaboration until an acceptable design for a “proof of principle” scale 

program is presented. This should include what criteria would be recommended for the “proof” 

and the number of arrays needed to truly test this important issue (expand numbers if necessary 

but justify).

Concerning the 400 mHz detection arrays, we requested the proponent to consider a phased 

development plan for the two systems (if both are needed) and provide justification for the choice 

of array. From the perspective of the ISRP, development of the fixed arrays would seem to best 

address Regional priorities at this time. The issue of residence time and habitat use for 

downstream migrating smolts actually begins below Bonneville Dam. Questions about their rate 

of migration and estuary residence are equally as important to the estuary studies and could also 

be assessed with this technology. Concerning research in the ocean plume environment, our first 

priority is to determine the duration of use and overall survival. The detailed mic ro-habitat use by 

salmonids clearly addresses mechanisms effecting growth, survival, etc. but are finer scale 

questions that can be phased in over time. The proponents’ response was that they should 

continue to develop the technology for both systems but that they would only use the fixed anchor 

arrays initially, and that their development would be phased in over the next three years.

During this development, the ISRP again recommends a smaller scale demonstration project 

when the tag and detection systems are completed. The full implementation of this proposal could 

eventually cost millions of dollars a year, which we consider unreasonable risk without adequate 

proof of performance. The ISRP also notes that a phased project would require annual 

evaluations.
ISRP 2002-14 Final Mainstem and Systemwide

28

ProjectID: 30007

An Acoustic Tracking Array for Studying Ocean Survival and Movements of Columbia River 

Salmon

Sponsor: Kintama Research Corporation

Province and Subbasin: Columbia Estuary

FY03 Request: $2,930,535

5YR Estimate: $7,345,735

Short Description: Development of a skeleton acoustic array to demonstrate an approach to 

tracking movements of individual fish through the river and along the West Coast of North 

America. The project will initially be focused on salmon, but has much wider application.

ISRP Final Recommendation: Fundable in Part

CBFWA Category: Do Not Fund

ISRP Comparison with CBFWA: Disagree - Fundable in Part

ISRP Final Review Comments from Estuary Province: 

See comments on 35046. Specifics of the collaboration with 35046, as proposed in the Mainstem 

and Systemwide response loop, need further discussion. Fundable in Part (Qualified) at a reduced 

level of support, disagree with CBFWA. Development of the final design for the acoustic arrays 

is high priority. This is an innovative but expensive research project that could provide new and 

important insights into the early sea-life of salmonids and their use of the ocean environment. 

However, as we have noted in previous reviews, the funding for proposals in this province will be 

very competitive. The ISRP suggests though that it would be a reasonable process to discuss the 

final array design with the proponents and to develop an incremental budget over the next few 

years.

This proposal continues to be technically innovative and the investigators have essentially 

completed the Innovative Project (#200008000) tasks. These results are presented and relevance 

to the FWP is well described. The purpose of this proposal is “to expand research on the acoustic 

tag and develop a prototype array which will allow demonstrating the capabilities of the 

technology to establish both river and ocean movements of chinook salmon (page 5).” The author 

states that the basic technology is now commercially available and the efficiency of its 

components has been tested. However, he does also note that, 

 “the logistics of deploying the equipment and gathering the data from fish tagged at 

various locations will require extensive effort over a wide geographic area. Deployment 

of equipment in the ocean will require significant R&D design effort (in particular, we 

intend to place the entire array sub-surface so that surface floats vulnerable to vessel 

traffic, fishing activities, and “curious” individuals are eliminated). Designs have been 

developed and partially field-tested for deploying the equipment on a semi-permanent 

basis to withstand the severe conditions that may be encountered at various sampling 

sites.” 

The importance of this technology is that it provides a means to actually measure migration rates 

(not necessarily migration paths, they will be inferred between two points), residency time in an 

area (e.g., within the Columbia River plume), and mortality rates. 

In general, fairly comprehensive responses were provided for most of the ISRP concerns. The 

author noted that he will comply with the requirements of the Innovative proposal and that the 

work is now complete. He noted that there do remain issues with the deployment of the acoustic 
ISRP 2002-14 Final Mainstem and Systemwide

29

detection arrays but also noted the recent success of deployments in the Atlantic Ocean. There 

was an additional discussion concerning an interaction with the NMFS Plume project to assist in 

the assessment of residence times and mortality rates. However, this would be an additional task 

that was not included in the Plume response and is not relevant for our consideration. The major 

issue of concern is how to scale the development of these acoustic arrays. The authors have 

proposed a deployment plan and argued that a critical mass of receivers are required and that the 

preferred strategy is multiple array lines (compared to fewer lines with more receivers per line). 

The authors provide adequate justification for this strategy but a minimum number of line arrays 

were not specified (although a proposed number was suggested). 

The ISRP concerns regarding dedicated time of the investigators were addressed and the PI 

suggested that if the project was supported that he would likely request a three-year leave from 

his current position. The other budget issue noted was that an allowance for 20% loss of the 

receivers per year was added to the annual budgets. The budget was re-profiled over time but, in 

total, it increased. 

A remaining limitation of these studies is the size of the acoustic tag. The tag may be suitable for 

juvenile spring chinook and steelhead (and likely coho), but not for smaller juvenile salmonids. 

While this may be a limitation for some in-river studies or plume studies for fall Chinook, it is not 

likely a reason to delay testing of the receiver arrays that can be tested with the larger tag.

CBFWA Estuary Review Comments:

Reviewers believe this proposal may be better suited for the Systemwide Province since this issue 

is not exclusive to the estuary. If the tracking could be scaled down to include only the plume, 

then the project could be considered for review in the Estuary. The project sponsor should 

resubmit this proposal for the Mainstem and Systemwide solicitation.

NOTE: The ISRP reviews from the Estuary Provincial review for proposals 30007 (above) 

and 30010 (below) should be considered in any Council decision on funding of these 

proposals through the Mainstem and Systemwide project selection process.

ProjectID: 30010

Canada-USA Shelf Salmon Survival Study

Sponsor: DFO

Province and Subbasin: Columbia Estuary

FY03 Request: $418,800

5YR Estimate: $2,094,000

Short Description: This project surveys the size, condition, and biological condition of juvenile 

salmon occupying the British Columbia & SE Alaskan continental shelf regions in the autumn 

(October). The survey also includes extensive collection of oceanographic data.

ISRP Final Recommendation: Fundable in Part

CBFWA Category: Do Not Fund

ISRP Comparison with CBFWA: Disagree - Fundable in Part

ISRP Final Comments from the Estuary Province Review: 

Fundable in part. Clarification of personnel and management issues are essential before 

supporting this project. This proposal requests funding from BPA for an October coastwide 

survey of juvenile salmonids and oceanographic conditions along the continental shelf to 

complement summer surveys conducted by the Science Branch, Canadian Department of 

Fisheries and Oceans (CDFO). The proposal includes an extensive and informative summary of 

recent findings based on similar surveys conducted since 1998 by CDFO (some previous funding 
ISRP 2002-14 Final Mainstem and Systemwide

30

apparently provided by BPA but not reviewed by ISRP). Based on these surveys, the proponents 

indicated that salmon from the Columbia River tend to migrate northward along the continental 

shelf, that growth of salmon (in particular chinook and coho salmon) and marine environmental 

conditions are not equal along the shelf, and that certain stocks of salmon have a propensity to 

rear in specific areas of the coast. These investigators’ hypothesize that the productivity of some 

Columbia River salmon stocks is more dependent upon where they rear in the ocean than due to 

their freshwater or estuary conditions. 

The proposal requests ongoing (5 years) support for 28 days of ship-time for an October survey 

and sample processing. The survey is intended to map ocean conditions determining the growth 

and survival of Pacific salmon along the West Coast of North America from the British 

Columbia-Washington border to South East Alaska, and to identify which stocks of Columbia 

River salmon forage in these areas. The stated objectives were (Section 9f, page 29): 

(1) identify the extent of the region of poor growth and survival, 

(2) measure the growth and feeding conditions of the salmon within these areas, 

(3) identify the physical and biological changes in the ocean that lead to reduced ocean survival 

through changes in growth, and 

(4) identify the identity of the fish occurring in this region of poor growth using DNA.

While the response was adequate, it generates significant concerns about what portion of the 

researchers’ time the Council would be supporting. The proposal is for an October cruise along 

the Pacific west coast but that cruise is only one of four such cruises each year. The basis of the 

labor costs continues to be unclear ... how many months are associated with the October cruise, 

at least two of the positions noted are not staffed, and who else is contributing funding for these 

PDFs and graduate students? While the ISRP is supportive of this research we must also be 

aware that funding in this province will be extremely competitive and involves several large 

projects. Consequently, we are inclined to recommend provision of operating expenses for the 

October cruise and not personnel costs unless these can be more accurately described and the 

costs are fairly accounted for and distributed over other sponsors also (i.e., who supports 3 of the 

4 annual cruises?). Further, there is now an additional concern regarding the PI. Given his 

statement in project #30007, if that project was supported the PI expected to take a 3-year leave to 

focus on that project. What would be the consequence of that action and would this project 

(#30010) continue? In the response to project #30007, the PI indicates that his other programs 

should be able to proceed without him but this leaves a level of uncertainty that would not be 

treated lightly in any other proposal reviews. 

CBFWA Estuary Review Comments:

Reviewers suggest that it may be more appropriate to review this proposal through the 

Systemwide Province review since it has systemwide implications (i.e., looking at fish from 

throughout the system). The issues to be reviewed are not necessarily affected by the 

plume/estuary. The project sponsor should resubmit this proposal through the Mainstem and 

Systemwide Province. NMFS has identified this project as a BiOp project.
ISRP 2002-14 Final Mainstem and Systemwide

31

ProjectID: 35001

Habitat Monitoring and Restoration Program for the Lower Columbia River and Columbia River 

Estuary

Sponsor: LCREP

FY03 Request: $220,000 5YR Estimate: $1,720,000

Short Description: Establish ecosystem-based program to identify, prioritize and implement 

habitat restoration projects and implement pilot project to develop habitat monitoring protocols 

for monitoring and evaluation of habitat protection and restoration projects.

ISRP Final Comments: 

Withdrawn, this project was funded through the Lower Columbia and Columbia Estuary 

Provinces. Our recommendation was: Fundable, the likely benefits to fish and wildlife appear to 

be high. 

ProjectID: 35055

Role of Bacteria as Indicator Organisms for Watershed Assessment and in Determining Fish 

Pathogen Relationships with Fauna of Abernathy Creek

Sponsor: USFWS

FY03 Request: $76,000 5YR Estimate: $196,600

Short Description: The purpose of this project is to develop techniques to assess watershed 

health and fish health using bacteria as system indicator organisms.

ISRP Final Comments: 

Not Fundable. Disagree with CBFWA’s Recommended Action ranking. The ISRP’s earlier 

recommendation of Fundable (qualified) in the Lower Columbia/Estuary Province was contingent 

upon submission of a completed experimental design developed with full collaboration of a 

statistician. The Mainstem and Systemwide solicitation and response provided an opportunity to 

complete an experimental design, but the proposal and response does not provide this. 

The objective of this project was to identify bacterial fish pathogens as indicator species for fish 

and watershed health. This proposal would use polymerase chain reaction (PCR) and speciesspecific primers to show the presence of aquatic bacteria in water and tissues of living organisms 

to determine their relationships to aquatic life. The idea was to identify bacteria species that can 

serve as indicators of aquatic ecosystem health. The technical background to this problem is 

adequate, as is the relationship to regional programs and other projects. The response placed this 

work in the context of RPAs under the FCRPS BiOp.

Tasks and methods to meet these objectives are described in a fair amount of detail. However, 

detail about the sample design is absent. The response to the question about sampling design 

takes the approach of sampling within the constraints of time and personnel, and seems to miss 

the point that a sampling scheme is determined by the requirements of the statistical analysis 

necessary to answer the research questions. We are not sure the principal investigator is aware 

that some analysis may not be better than none if the data are inadequate, and were confused at 

the process he describes for determining the power of the test etc. after he has sampled. These are 

the things that determine sample size.

The proposal could be clearer on how presence of bacteria types will be linked to the level of 

ecosystem health. Without a control, this work will be limited to establishing a description of the 

presence of ecosystem conditions in association with certain groups of bacteria, but the study will 

not generate understanding of processes by which these bacteria/conditions associations work. 
ISRP 2002-14 Final Mainstem and Systemwide

32

The ISRP does note that the use of bacteria as an indicator of watershed health is a topic worthy 

of consideration. This proposal though is technically inadequate. 

ProjectID: 35035

Incorporating Pit Tag Technology to Evaluate and Monitor the Reintroduction Effort for 

Anadromous Salmonids in the Upper Cowlitz Watershed

Sponsor: WDFW

FY03 Request: $203,740 5YR Estimate: $619,182

Short Description: We propose to update pit tag system to basin ISO standards at the Cowlitz 

Falls Dam and Fish Facility and use pit tags to monitor and measure collection, collection 

efficiency, smolt production, and a prototype surface collector entrance. 

ISRP Final recommendation: 

Not Fundable; disagree with CBFWA (Recommended Action). The response briefly describes a 

process for developing a study plan for the upper Cowlitz watershed, but does not provide an 

adequate response to the ISRP. The response was clearly influenced by the comments from 

CBFWA and NWPPC staff which indicated that even with an adequate and timely response, the 

Cowlitz proposals would not be funded given basin priorities and available funds (as part of the 

Lower Columbia project selection process). Consequently, the response did not supply the needed 

information. The ISRP reiterates that the upper Cowlitz offers one of the best environments and 

research opportunity to study supplementation. 

The ISRP recently reviewed this proposal and project # 31005 (Incorporating Pit Tag Technology 

to Evaluate and Monitor the Reintroduction Effort for Anadromous Salmonids in the Upper 

Cowlitz Watershed, WDFW) under the Lower Columbia/Estuary province. The ISRP was 

supportive of the upgrading of the PIT detectors to be consistent with downstream detectors, but 

we strongly noted the unique opportunities for important research in the upper Cowlitz River 

tributaries. We noted that the real value to the Basin in this upgrade is the monitoring and 

evaluation capability that could be incorporated into this research. The current proposal did not 

provide a study design but commented on a group organized to develop the research design. 

The ISRP also noted that the proposal had very strong BPA cost sharing already in-place and that 

costs in this proposal are distributed over a couple of years. Proceeding with the upgrade would 

be advisable in order to be prepared for future studies. If a research program did not subsequently 

develop, then the benefit of this investment would be much more localized. There would still be 

value in the assessment of Cowlitz salmon production.

The provision of an inadequate response clearly limits any recommendations of the ISRP but we 

must emphasize that lack of progress in developing this study site and provision of the necessary 

detectors is potentially a major loss of information for the Columbia River Basin! As a regional 

study site, the upper Cowlitz has enormous research potential that is unavailable in most other 

basins. Consequently, the lack of response and the associated events are disturbing to the ISRP.

If funded, this project should be coordinated with other monitoring projects to ensure 

compatibility of objectives, common methods, and protocols. This coordination could be 

accomplished under the favorably reviewed CBFWA proposal #35033.
ISRP 2002-14 Final Mainstem and Systemwide

33

Artificial Production Related Projects 

ProjectID: 200001700

Kelt Reconditioning: A Research Project to Enhance Iteroparity in Columbia Basin Steelhead 

(Oncorhynchus mykiss)

Sponsor: CRITFC

FY03 Request: $633,292 5YR Estimate: $1,957,441

CBFWA Adjusted FY03: $555,121 3YR: $1,662,928

Short Description: Continue to test and evaluate to recondition steelhead kelts and/or transport 

them around the hydrosystem, generate science-based management recommendations, and assist 

in their implementation to rebuild wild steelhead populations throughout the Basin

ISRP Final Comments: 

Fundable. We agree with CBFWA’s review, study design and budget reduction, and “urgent” 

priority ranking. The sponsor’s response also addresses most of the ISRP’s concerns from the 

simultaneous Three-Step Review. 

The proposal is well written and presents a logical and justified approach to examining 

uncertainties associated with kelt reconditioning. The proposal builds on work in this area over 

the last 2-3 years by the Yakama Nation and the US Army Corps. The proposal also addresses 

concerns expressed by the ISRP in its FY00 review of this ongoing project. 

Strengths of the proposal include a systematic investigation of various reconditioning and 

transportation strategies, collaboration with other projects to expand the PIT tag and radio-tag 

information that can be collected, and a series of replicated treatments. This is a strong proposal 

that merits funding support due to its solid design and to the important information it may provide 

on enhancing steelhead populations. Another advantage of this study, as compared to the 

supplementation projects, is the 1-3 year timeframe for data collection, rather than the 5-6 years 

required in supplementation studies due to generation time. There is good cost sharing associated 

with this proposal, so apparently there is strong user support for the work.

Overall the project sponsors provided an acceptable response to the ISRP preliminary comments, 

but some remaining concerns should be addressed prior to implementation contracting. 

First, there is an issue associated with the proposed tagging and release of reconditioned kelts 

below dams, and the percentage of fish that would be expected to return to the natal stream. 

What percentage of release is it reasonable to expect to return? A fundamental issue is that not all 

kelts should be expected to recondition in the first year and repeat spawn. In BC, steelhead kelts 

frequently stay at sea for more than one year before returning. In this study then, if a radiotagged kelt does not return, what does this tell the researchers about its fate and the efficacy of the 

program? A return of less than 100% represents a loss in production and a reduced efficiency of 

the kelt reconditioning program. To address questions related to maximizing the efficiency of the 

program, sponsors need to determine the relationship between the degree of reconditioning, 

triggers for maturation, and natal fidelity (homing). From these relationships, managers can then 

plan how the kelt reconditioning program could be managed to maximize the number of 

reconditioned adults that return to the spawning grounds. 

We initially identified a concern about genetically effective population size to which the project 

sponsors responded. In the fourth paragraph of their response to ISRP comment 6, sponsors state 

that “reduction of Ne should only result from...” reduction of the population size or increased 
ISRP 2002-14 Final Mainstem and Systemwide

34

relatedness of the parents (or both). They then state that neither of these should occur. We 

disagree. The effect of iteroparity on the census population size (N) will vary between 

generations but should generally increase N. However, the inbreeding coefficient or relatedness 

will increase with iteroparity. The effect of these two factors though will depend on N and the 

degree of relatedness. Monitoring the effect will be very informative. Iteroparity is a natural trait 

that has been suppressed, but the size of the spawning populations has also been reduced (relative 

to pre-dam times). The effect of iteroparity could be very different now than in the past; we only 

asked the proponents to consider this when assessing the value of reconditioning and the scale at 

which they may want to conduct it.

The stated objectives in the proposal and descriptions of actions (in response) related to Objective 

4 (University of Idaho, Hagerman reconditioning experiment) are not consistent. These need to be 

clarified prior to funding. 

We also have concerns about the potential for domestication selection in the kelt reconditioning 

program that were not adequately addressed in the proposal, the response, or the 3-Step Scoping 

Document. The discussion of domestication in the Scoping Document (pp 18-19) assumes that 

domestication selection will operate at a very low level, if at all on kelts. This may or may not be 

true, but at this point, is an untested assumption. It is entirely possible that failure to recondition 

and subsequent mortality on the part of some kelts is a response to the artificial hatchery 

environment, meaning that within the remaining cohort of kelts, some level of artificial selection 

has indeed occurred. 

Finally, also in the 3-step review material, but pertinent to the final project proposal review, 

sponsors defined carrying capacity by the size of the returning run. However, carrying capacity is 

defined by the habitat and not by the run size. More thought needs to be applied to this question 

including after the present 3-year study, incorporating natural production via reconditioned kelts 

back into system carrying capacity estimates, and scaling more traditional hatchery-produced 

steelhead juvenile releases to levels consistent with the expected increase in natural production. 

ProjectID: 35014

Measurement of Quantitative Genetic Varia tion Among Columbia River Basin Chinook 

Propagation Programs

Sponsor: CRITFC

FY03 Request: $313,855 5YR Estimate: $914,623

Short Description: To investigate the existence of genotype-environment interactions in salmon, 

the building block of local adaptation, and thus refine the concept of conservation units.

ISRP Final Comments: 

Fundable at a medium priority. We agree with the CBFWA review and middle ranking of “High 

Priority.” This proposal involves the application of quantitative genetic and molecular genetic 

methods in the “search for significant genotype x environment interaction and stock effects. The 

presence of such effects would presumably denote different distributions of quantitative variation 

among life history types and geographic regions spanning the range of chinook salmon within the 

Columbia River Basin.” The proposal is well presented and would provide one of the very few 

studies assessing the quantitative genetic basis to phenotypic variation in life history traits in the 

basin. In particular, the research proposes a study (involving a half-sib breeding design) to assess 

Genotype x Environment (GxE) interactions in traits associated with early development, coupled 

with DNA analyses to assess genotypic changes between the family parentages and the surviving 

progeny. If GxE interactions were strong, then selection for genotypes in different environments 
ISRP 2002-14 Final Mainstem and Systemwide

35

would be predicted. However, if GxE interactions are insignificant, then one or a few genotypes 

may be best in all environments. 

The authors considered each of the ISRP’s preliminary review comments and have strengthened 

their proposal. Project sponsors propose to change the breeding design to a factorial design 

capable of estimating interactive effects, and discuss the changes this will entail within the 

available facilities. The duration of the project has been shortened. The basic notion here that 

variation of survival during embryogenesis among families would be related to variation of other 

fitness traits in later development is still a concern, but we understand the notion that variation of 

development time may be an important component of adaptation to local environments by 

chinook in the basin and that this study of high altitude and low altitude spawning populations 

might elucidate an important mechanism of adaptation. 

No doubt the region will learn from this investigation, but we continue to wonder if more could 

be learned with the inclusion of molecular data. If the genotype of each individual can be 

assessed (presumably across families and stock), a more direct test of genotype x environment 

interactions would seem to be to relate “type” to performance -- more of a regression analysis 

(common in quantitative genetic studies for GxE).

ProjectID: 198909600

Monitor and evaluate genetic characteristics of supplemented salmon and steelhead

Sponsor: NMFS

FY03 Request: $593,900 5YR Estimate: $2,548,570

Short Description: Direct and indirect estimates for reproductive success. Estimate selection 

gradients in hatchery and wild. Monitor changes in hatchery, natural (supplemented), and wild 

(unsupplemented) populations. Evaluate effectiveness of hatchery supplementation.

ISRP Final Comments: 

Fundable. We agree with the CBFWA review and the Urgent priority ranking. This is an 

excellent, important, and well-written proposal. The researchers have maintained a very high 

level of scientific productivity. A response was not needed; however, the project sponsors 

subsequently responded thoughtfully to the preliminary ISRP review comments. 

The proposal provided summary statements of findings that showed significant progress over the 

history of the project. Several papers based on the results have been published in peer-reviewed 

journals, which indicate acceptance of the work by the scientific community. The study 

continues to make an important contribution to the understanding of the genetic structure of 

Columbia River anadromous salmonids.

Expansion of the budget is explained and justified. It includes both an actual expansion of the 

data collection and lab analysis to the Lostine River, Catherine Creek, and Little Sheep Creek 

steelhead, as well as expanding the project to include the development of pedigree analysis and a 

strategy shift to increasing reliance on microsatellite DNA analysis rather than allozyme analysis. 

In particular, the latter change is justified and warranted. Shifting to the pedigree/paternity 

analysis is needed in order to investigate the more subtle effects of hatchery/wild fish interactions 

through supplementation to which the allozyme results were relatively insensitive. Microsatellite 

DNA pedigree analysis should be insightful for this purpose. At the same time, continuing the 

allozyme data collection at a base level is warranted in order to retain continuity of data over time 

(nearing two decades). 
ISRP 2002-14 Final Mainstem and Systemwide

36

If funded, this project should be coordinated with other monitoring projects to ensure 

compatibility of objectives, common methods, and protocols. This coordination could be 

accomplished under the favorably reviewed CBFWA proposal #35033.

ProjectID: 199105500

Natural Rearing Enhancement Systems (NATURES)

Sponsor: NMFS

FY03 Request: $1,158,969 5YR Estimate: $5,711,234

CBFWA Adjusted FY03: $559,800 3YR: $1,737,200

Short Description: Evaluate NATURES effects on salmonid behavior, morphology, physiology, 

post-release survival, and ecological interactions.

ISRP Final Comments: 

Fundable at a low/moderate priority. We disagree with CBFWA’s Urgent ranking; this should be 

lower priority. In regard to potential elimination of Objective 1, this is the component that raised 

the most ISRP concern and debate (this debate resulted in a strong experimental design); 

however, Objectives 2-4 as reflected in CBFWA’s comments are of higher regional priority than 

Objective 1. Objective 5, regional consultation, is not discussed in enough detail in the proposal 

to assure its benefits, although the NMFS group was instrumental in developing the NATURES 

concept.

This proposal would continue evaluations of NATURES effects (semi-natural rearing of fish in 

hatcheries) on salmonid behavior, morphology, physiology, post release survival, of these 

hatchery fish and their ecological interactions with wild fish. 

The current proposal has two major foci. Objectives 1 and 2 test NATURES rearing habitat 

components (cover, structure, and substrate) at production hatchery scale and to determine 

interaction effects between rearing habitat variables assessed based on smolt-to-adult survival 

(design to detect a 20% difference between treatments with 80% power), and secondly to 

investigate benefits of predator conditioning to juvenile migratory and adult survival (same 

power). Research under Objectives 3 and 4 is intended to help determine ecological risks and 

benefits of release of NATURES reared under yearling steelhead to cohabit stream environments 

with wild cohorts (steelhead and spring Chinook). The latter studies are to be conducted in 

experimental channels and observation flumes already available at NMFS facilities.

The proposal presents results of past studies and suggests that in-stream post-release survival of 

fish reared in these special habitats is significantly greater than that of their counterparts reared 

conventionally. These statements, however, are based on relative survival of NATURES rearedfish compared to conventionally reared hatchery fish and have not yet compared survival to adult 

returns. The studies in 1997-2000 included components to evaluate survival to adult returns.

While we acknowledge the efforts in these past studies, the ISRP believes it is important to keep 

these past results in proper perspective. In the summarized studies, the average improvement in 

survival (NATURES vs. conventional) is +18% (range +1% to 50%, n = 7 years). Given that 

smolt-to-adult survival for hatchery fish has frequently been <1%, these improvements (based on 

short-term smolt survival only to-date) are inadequate to provide the substantial improvement in 

survival needed for recovery or improved economical value of these hatchery fish. It is essential 

that these 1997-2000 studies be reported as the data is available in order that any improved 

benefits to the adult stage may be accounted for.
ISRP 2002-14 Final Mainstem and Systemwide

37

The project sponsor’s response did not adequately address several of the ISRP’s preliminary 

criticisms. The experiment at Carson should be restricted to three brood years; the loss of power 

will be marginal, and the results of other studies within (Cle Elum) and outside (Puget Sound) the 

Basin will be available to compensate for the loss of power. This shift to evaluation studies at 

production facilities in the basin that are employing NATURES techniques could be assisted 

through oversight by the proposers to standardize experimental rearing approaches among the 

various facilities and coordinate data collection and analysis (as proposed in Objective 5). 

The response does not provide any current data on smolt to adult survival rates associated with 

NATURES within the Basin and now concur that the expected benefits of NATURES may be 

small as currently estimated based on juvenile survival differences. The proposers note that 

incomplete returns to a study in Puget Sound at Forks Cr (lacking 5 yr old return) show an 

advantage in marine survival of NATURES-reared smolts (0.0595% vs 0.0514%). These are 

obviously small differences in marine survival rates and may be statistically indistinguishable 

from one another.

The ISRP commented that the project had thus far generated few peer-reviewed publications (in 

contrast, for example, to the NMFS Captive Brood Research program). In the proposal the 

authors credit themselves with a good publication list, but upon inspection of those publications 

there are really only 4 papers in recognized primary journals (4 of 32 listed). There does not 

seem to be any primary paper actually on the NATURES rearing studies? In their response the 

proposers say they’re working on it; this is not responsive. This criticism has been leveled in 

earlier reviews and there continue to be no peer-reviewed publications of analyses of the 

elemental features of Natures.

The ISRP was concerned that sample sizes of 100 may not be adequate to describe variances of 

body size, etc. and that larger sample sizes may be necessary. The proposers did not respond to 

the question. The review suggested an investigation of how the precision of estimates of variance 

would improve with increased sample size, but the response seemed to infer that the criticism was 

about the ability to collect unbiased samples from raceways with structure in them. 

The ISRP commented that mass-marking and selective fisheries on marked fish may bias results. 

The proposers responded that there will be intensive sampling to discover wire tagged fish among 

harvested fish and at the rack and that the bias will effect all treatment groups and controls 

similarly and that the effect on expected recoveries has been accounted for in the experiment 

design.

ISRP concerns about how the numbers of animals released were determined and at what density 

the animals were reared were answered adequately. The ISRP also had concerns that the budget 

was unjustified and apparently over estimated. The proposers explained the differences in the 

budget adequately. 

An important outstanding issue remains: the ISRP’s suggestion that the project could be reduced 

from 5 to 3 years of releases without a significant loss of power. In the proponents’ response, 

they calculate that statistical power to detect a difference between treatments would be reduced 

from 0.87 to 0.65 by reducing the releases to 3 years. They argue this is unacceptable as it is 

below the design standard of 0.8 (based on detecting at least a 20% difference between rearing 

treatments at a 95% confidence level). While the ISRP agrees with the technical basis for this 

argument, the basis of our concern was the relative benefit (modest at best) achieved for the 

substantial expense of an additional two years of rearing releases. The reason a 5-year treatment 

plan is supported by the NMFS sponsors is that they are trying to measure a small difference 
ISRP 2002-14 Final Mainstem and Systemwide

38

among treatments with very high confidence. Such precision may be not warranted, given the 

small potential biological benefits observed to date between treatments. 

A larger concern is whether supporting the proposed project at all is warranted given issues of 

best use of funds, given the expected modest gains from this investment, and the information that 

will be available near term from other application of the NATURES rearing approach within 

(e.g., Cle Elum) and outside (Puget Sound) the basin. The proposed value of this specific project 

was a production-scale test of the NATURES rearing approach conducted within a rigorous 

experimental design. Implementation of NATURES rearing approaches to supplementation in 

the Yakima and Clearwater systems are in fact now applying NATURES at production scales. 

Because of this mismatch in timing between the Carson facility research project and the 

implementation of NATURES rearing at other sites, the main benefit that would arise from this 

proposal would be measurements of the relative contributions and interactions among elements of 

the NATURES treatments (cover, rearing substrates, rearing densities, exposure to predators). 

In making a final determination, Council should be advised that this NATURES proposal is a 

well-designed experimental assessment of NATURES treatments intended to inform subsequent 

application of the NATURES approach to supplementation and production programs. However, 

implementation of NATURES rearing treatments in the Basin has preceded this experiment 

already, but this study could still improve the efficiency of these applications. We should note, 

however, that there is general agreement that the relative benefits of NATURES rearing alone, are 

likely to be relatively small. As the sponsors state in their response to the ISRP comments 

(August 21, 2002 letter):

“In regards to concerns that NATURES alone may be “inadequate to provide the substantial 

improvement in survival needed”, we too believe that we must be realistic about our expectations. 

There is no one “silver bullet” that will by itself restore the Region’s anadromous salmonid 

resources. The most likely scenario is that recovery will be accomplished by threading together 

many “modest increases” in survival, such as those potentially offered by NATURES.”

If funded, this project should be coordinated with other monitoring projects to ensure 

compatibility of objectives, common methods, and protocols. This coordination could be 

accomplished under the favorably reviewed CBFWA proposal #35033.

ProjectID: 199305600

Assessment of Captive Broodstock Technologies

Sponsor: NMFS

FY03 Request: $1,498,981 5YR Estimate: $8,282,813

CBFWA Adjusted FY03: $1,468,100 3YR: $4,631,300

Short Description: Develops technologies to improve genetic integrity, inculture survival, 

maturation, and reintroduction success of ESA-listed salmon captive broodstocks. Applies 

research on physiology, behavior, genetics, ecology, microbiology, and nutrition.

ISRP Final Comments: 

Fundable. We agree with the CBFWA review and Urgent ranking. This complex multi-faceted 

proposal represents a disciplined aggressive attack on many of the key uncertainties associated 

with captive broodstock use. The proposers responded carefully to previous ISRP concerns and 

review comments. The proposal contains extensive documentation from the general fisheries 

literature, as well as relevant Columbia River basin gray literature. The proposal also contains 

substantial methodological detail. This ongoing FWP project has an impressive list of 
ISRP 2002-14 Final Mainstem and Systemwide

39

accomplishments since 1994 and may be one of the better FWP projects in terms of publication of 

results in peer-reviewed scientific journals.

This proposal continues the development of technologies to improve genetic integrity, in-culture 

survival, maturation, and reintroduction success of ESA-listed salmon captive brood stocks. 

Research is conducted on physiology, behavior, genetics, ecology, microbiology, and nutrition 

and the captive brood fish and their re-introduction to the natural environments (from authors’ 

short description).

The five objectives of the project are as follows

1. Improve reintroduction success

2. Improve olfactory imprinting and homing

3. Improve physiological development and maturation

4. Improve in-culture survival through prevention and treatment of disease

5. Evaluate effects of inbreeding and inbreeding depression

Each of these is a relevant and necessary aspect of the captive brood technology, and the authors 

have an excellent scientific record of publication on these works (28 primary publications based 

on past work). 

Nevertheless, the ISRP has several concerns with this large complex project. While the proposal 

is a substantial improvement over its predecessor, it is very large and needs clarification or 

restructuring so that the individual studies can be thoroughly reviewed. The scope of this program 

and importance of the work to the conservation of these stocks might justify a more in-depth 

scientific review of this one project alone, not as one of 104 projects in this review.

The sponsor’s response was adequate to address the ISRP’s concerns raised in the preliminary 

review. However, the response on the release of captive reared fish to breed with wild fish (in 

Idaho) was in essence that this was a policy decision by the state and tribal managers rather than a 

decided part of the research project and an action currently being implemented, albeit on a small 

scale. Thus attention to it as a research component by this project was appropriate. While all of 

this is logical, it sidesteps the issue of whether this is an appropriate release strategy for these 

endangered and valuable stocks without significantly more research conducted under controlled 

conditions first. 

If funded, this project should be coordinated with other monitoring projects to ensure 

compatibility of objectives, common methods, and protocols. This coordination could be 

accomplished under the favorably reviewed CBFWA proposal #35033.
ISRP 2002-14 Final Mainstem and Systemwide

40

ProjectID: 199606700

Manchester Spring Chinook Broodstock Project

Sponsor: NMFS

FY03 Request: $950,000 5YR Estimate: $4,828,825

CBFWA Adjusted FY03: $877,600 3YR: $2,436,800

Short Description: Smolt to adult seawater rearing of spring and summer chinook salmon 

broodstocks from Idaho’s Salmon River and Oregon’s Grande Ronde River sub-basins. Provides 

adult fish for spawning or direct release in recovery programs for ESA-listed stocks.

ISRP Final Comments: 

Fundable. We agree with the CBFWA review and Urgent ranking. A response was not needed. 

This project is designed to develop and maintain captive broodstocks of chinook salmon in 

saltwater at Manchester, WA. It is needed to support many other projects and to meet ESA 

requirements on several upper basin listed stocks. The proposal is thorough with respect to 

hatchery procedures and describes the scientific and technical background of the problem, 

including a discussion of the potential risks and benefits of captive broodstock techniques. It 

clearly relates to a regional need and has strong connection to other projects.

This proposal continues the smolt-to-adult seawater rearing of spring and summer chinook 

salmon brood stocks from Idaho’s Salmon River and Oregon’s Grande Ronde River subbasins. 

Adult Chinook are provided for spawning or direct release in recovery programs for ESA-listed 

stocks. The proposal includes a request for $200,000 capital for improvements to the Manchester 

saltwater delivery system (cost shared with NMFS). The proposal provides explanation for the 

increased costs relative to previous projections inc luding the need to improve the saltwater 

system, but it does not provide any explanation concerning the substantial increasing costs in the 

operating fund through to 2007.

The proposal is generally well written and includes some data on past performance of the rearing 

program. The rationale and relationship of the program to other Basin programs were good, and 

the authors are preparing written protocols for all aspects of the captive rearing programs.

However, one omission would seem to be the M&E ... of which there is none. Obviously there 

is monitoring since growth and survival of the animals in culture is being assessed; however, in a 

program with such intensive culture of such small numbers of original animals, reviewers would 

also be concerned about genotype x environment interactions and the survival of these fish after 

release into the wild. It does seem surprising that no monitoring of this aspect is being 

undertaken given that NMFS seems to be measuring DNA in every other salmonid in the Basin. 

The survival in the culture systems is quite high so people may argue there is no need to conduct 

such monitoring but there could be significant differences in how certain genotypes respond to 

the culture system and how they respond to the reintroduction to the wild. Is this being assessed 

by other programs or should it be implemented?

Secondly, given the difficulties being encountered in reintroducing adults into the Idaho streams 

(in proposal #199305600) and the known depressed state of production in the Grande Ronde 

populations, is there a need to complete the “safety net” by maintaining true captive brood stocks 

(multiple generations) in these remote rearing sites (i.e., should live-gene bank programs be 

established)? Why has this rather obvious step not been undertaken? Its absence suggests that a 

decision has been made not to do this.
ISRP 2002-14 Final Mainstem and Systemwide

41

Another uncertainty with the project that concerns reviewers relates to the outcomes of the project 

with respect to the reproductive performance of the adult fish after they are released back into 

natal streams for spawning. Another is whether the fish surviving to be outplanted as adults 

constitute a representative sample of the initial broodstock population with respect to genetics and 

fitness attributes. 

Propagating captive broodstock as a protection measure under ESA cannot be viewed as a longterm strategy. Many problems are inherent in such propagation -- a program that is not ultimately 

consistent with the needs of endangered species. The authors of this proposal seem to be aware 

of these problems and have included a discussion of several in their proposal.

If funded, this project should be coordinated with other monitoring projects to ensure 

compatibility of objectives, common methods, and protocols. This coordination could be 

accomplished under the favorably reviewed CBFWA proposal #35033.

ProjectID: 35012

Spatial scales of homing and the efficacy of hatchery supplementation of wild populations

Sponsor: NMFS

FY03 Request: $370,100 5YR Estimate: $1,545,100

Short Description: Determine the spatial and temporal patterns of homing and spawning by wild 

and hatchery-reared salmon released from supplementation facilities and examine the 

physiological changes in the olfactory system during imprinting.

ISRP Final Comments: 

The project is fundable at a moderate priority. We agree with the CBFWA review and middle 

ranking of High Priority. The project supports (and is dependent on) the Yakima Spring Chinook 

salmon supplementation program (Cle Elum Hatchery), and the proposed research is suggested to 

be useful for the biologists operating the YKFP supplementation program. In particular, this study 

will examine the effectiveness of supplementation and releases from satellite facilities for 

facilitating successful imprinting, minimizing straying, and contributing to wild salmon recovery.

The courteous response adequately addressed all of the ISRP’s preliminary concerns, but the 

results of this fieldwork will be very weather dependent (modest-high risk). It was unclear 

whether the Yakamas support the proposed work. The Yakama investment in supplementation 

and acclimation sites has been extensive and this project could be useful in “tuning” their 

program to be more successful in seeding spawning habitat.

If funded, this project should be coordinated with other monitoring projects to ensure 

compatibility of objectives, common methods, and protocols. This coordination could be 

accomplished under the favorably reviewed CBFWA proposal #35033.
ISRP 2002-14 Final Mainstem and Systemwide

42

ProjectID: 35049 

A multiscale evaluation of steelhead supplementation in the West Fork Elochoman River

Sponsor: NMFS

FY03 Request: $683,324 5YR Estimate: $3,278,533

Short Description: Evaluate the effects of the release of hatchery-reared steelhead on the growth, 

survival, movement, and behavior of wild salmonids in the West Fork Elochoman River.

ISRP Final Comments: 

Fundable at moderate priority; we disagree with the CBFWA High Priority ranking and 

recommend a lower priority. This proposal would evaluate the effects of the release of hatcheryreared steelhead (early summer release of yearlings) on the growth, survival, movement, and 

behavior of wild salmonids in the West Fork Elochoman River. This may be a good approach to 

assessing the “conservation” hatchery concept, but does it have the priority to merit this level of 

funding? This would be a very in-depth assessment with modest risk of failure due to working in 

the natural environment, but it would provide a critical and biologically based assessment of 

supplementation.

It is very likely that a five-year study of steelhead in natural systems will have setbacks due to 

annual variation in weather, etc. However, this is the type of study that is needed to fully assess 

the utility of supplementation. There is clearly a modest risk that natural variability will limit 

what is learned from such an investigation, but these are the risks we need to take. 

The sponsors systematically addressed all ISRP preliminary concerns; however, answers were 

concise if not superficial, and did not provide adequate detail to instill confidence that the 

experimental aspects of the project are well thought out and likely to succeed. If funded, this 

project should be coordinated with other monitoring projects to ensure compatibility of 

objectives, common methods, and protocols. This coordination could be accomplished under the 

favorably reviewed CBFWA proposal #35033.

ProjectID: 199009300

Genetic Analysis of Oncorhynchus nerka (modified to include chinook salmon)

Sponsor: U of I

FY03 Request: $126,436 5YR Estimate: $518,756

Short Description: This ongoing project provides genetic information to assess immediate and 

long-term genetic risks to federally endangered Snake River sockeye and threatened Salmon 

River chinook salmon currently in artificial production programs.

ISRP Final Comments: 

Fundable. We agree with the CBFWA review and Urgent ranking. This is clearly high priority 

work that warrants continued funding. The proposal is well written. The project addresses the 

genetic variation in Columbia River sockeye salmon, particularly in the listed stock (Redfish 

Lake) and its captive breeding program, plus the impact of captive rearing on three listed chinook 

salmon populations. These populations are severely depressed and require careful genetic 

monitoring to maintain the remaining genetic variation. This project also monitors the bycatch of 

sockeye salmon in a sport fishery for kokanee in Redfish Lake and has demonstrated the bycatch 

of anadromous or residual sockeye. While this concern is not the responsibility of this project, it 

is a concern that in a lake with a listed sockeye salmon stock, at an extremely depressed 

population size, that a kokanee fishery would be allowed at all. The ISRP remains concerned 

about what impact is allowed on sockeye in this fishery and how is it justified? 
ISRP 2002-14 Final Mainstem and Systemwide

43

The proposal has a long term monitoring component that is needed to provide consistency and 

insights into the Redfish Lake sockeye captive broodstock effort. The proposal also provides 

additional information on reports and publications that have resulted from this study (and related 

ones) to address some of the ISRP’s FY00 review comments. One hopes that with the long-term 

dataset that is being generated by this study that additional peer-reviewed publications will arise 

from the work. The project sponsors provided a thorough response that adequately addressed the 

ISRP’s preliminary review questions, including additional description and details on the recent 

use of microsatellite loci analyses to develop pedigrees, identify parentage, and to set up MAI 

(Maximal Avoidance of Inbreeding) matrices to guide captive breeding options for severely 

depressed chinook populations in the East Fork of the Salmon and West Fork of the Yankee Fork. 

ProjectID: 35015

Replicated stream system for the evaluation of hatchery and wild juvenile salmonid interaction 

and development of innovative culture technologies

Sponsor: UI/CRITFC

FY03 Request: $300,114 5YR Estimate: $2,392,840

Short Description: Develop sixteen independent streams using spring water at the University of 

Idaho Hagerman Research Station with the goal of providing a research facility for investigating 

interaction between wild and hatchery salmonids and rearing technique development.

ISRP Final Comments: 

Do Not Fund. We disagree with the CBFWA ranking of high priority. The proposal focuses on 

an important opportunity for a unique aquaculture research facility in southern Idaho at the 

University of Idaho’s Hagerman Experimental station and a new acquisition on the nearby 

Billingsley Creek. However, we do not support the proposed initial use: construction of a series 

of replicated streams on the Billingsley Creek site. While the project sponsor provided a detailed 

response to the ISRP preliminary review comments, we continue to have a fundamental problem 

with building a research facility without identifying the research to be conducted. The ISRP 

recognizes the potential value of this site, understands that the facility is under the care and 

ownership of the University of Idaho, and believes the site offers potential as a regional 

aquaculture research facility. It seems logical therefore, to regionally solicit input and identify 

aquaculture and conservation research needs and interest on the part of potential participants and 

funding agencies before proposing construction of a specific aquaculture facility design. 

The requested evidence of regional support for the facility (three letters attached to the response) 

acknowledged the potential value of such a facility, but the letters were certainly not extensive 

responses, nor convincing in arguments. Further, despite the ISRP’s suggestion, the response did 

not present a more basic research proposal.

ProjectID: 200000700

Infrastructure to Complete FDA Registration of Erythromycin

Sponsor: UI-CNR

FY03 Request: $166,419 5YR Estimate: $514,419

CBFWA Adjusted FY03: $160,919 3YR: $450,919

Short Description: Continue to provide agencies and tribes access to erythromoycin feed 

additive while working to complete FDA approval of erythromycin feed additive, a therapeutant 

needed for sustained hatchery production and maintenance of captive broodstocks of salmon.

ISRP Final Comments: 

Fundable, high priority. We agree with the CBFWA review and Urgent ranking. The tasks 

included are required by the FDA to allow continued use of erythromycin for salmon. This 
ISRP 2002-14 Final Mainstem and Systemwide

44

proposal seems to be a comprehensive response to FDA and proposes to maintain close 

interaction with the FDA in completion of this work. The principal investigator has a long 

productive history in this issue and has the necessary facilities and credentials to proceed. In the 

absence of different treatments for BKD, there is no other option but to proceed and meet the 

FDA requirements.

ProjectID: 35027

Evaluation of Two Captive Rearing Methods for Assisting with Recovery of Naturally Spawning 

Populations of Steelhead and Coho Salmon

Sponsor: USFWS

FY03 Request: $472,941 5YR Estimate: $2,046,091

CBFWA Adjusted FY03: $396,116 3YR: $932,966

Short Description: Test and evaluate two hatchery reform methodologies; Assess natural 

reproductive success of returning hatchery-origin adults; Establish Abernathy, Germany, and Mill 

creeks as a Tier 3 "monitoring and evaluation" site for anadromous salmonids.

ISRP Final Comments: 

Fundable. We agree with the CBFWA review, budget reductions, and Urgent ranking. This is a 

strong proposal that the ISRP has reviewed twice prior to the Mainstem / Systemwide provincial 

review. Each time we have supported it, as we do now. The proposal has four components: the 

steelhead brood stock study, rearing of coho salmon in the hatchery to reduce over-winter 

mortality, replacement of the electronic fence in Abernathy Creek, and the development of a Tier 

3 Monitoring and Evaluation Site (NMFS RPA No. 183) for Lower Columbia and Southwest 

Washington ESUs of steelhead, coho salmon, chinook salmon, and coastal cutthroat trout. 

The authors’ propose to assess the use of juveniles, rather than adults, to initiate local brood 

stocks for supplementation programs. Removing juveniles would impose less of a demographic 

loss on a depressed population and may reduce the risk of a Ryman-Laikre effect on the genetic 

composition of the population (i.e. the expansion of a small sample of the population into a much 

larger portion of the supplemented population with associated changes in genetic variation). 

In our preliminary comments, the ISRP took the unusual step of providing detailed suggestions 

on study design modifications to the project sponsor, as this is the third time we have considered 

this proposal. The project sponsor’s response to the ISRP preliminary concerns was adequate and 

demonstrated full consideration of the ISRP comments. The sponsors modified the proposed 

design to address ISRP concerns so that the proposed monitoring now includes both natural and 

cultured populations. 

We also note that there is a strong cost sharing aspect to the program as WDFW will provide 

three rotary screw traps, and USFWS is proposing to recruit additional staff and has the facilities 

to conduct the proposed work. If funded, this project should be coordinated with other 

monitoring projects to ensure compatibility of objectives, common methods, and protocols. This 

coordination could be accomplished under the favorably reviewed CBFWA proposal #35033.
ISRP 2002-14 Final Mainstem and Systemwide

45

ProjectID: 35060

Instream evaluation of populations, migration, individual adult return and wild-hatchery 

interactions of naturally produced salmonids

Sponsor: USFWS

FY03 Request: $229,606 5YR Estimate: $964,645

Short Description: Evaluate stock status, distribution, and abundance of juvenile and adult 

salmonids using new PIT tag techniques.

ISRP Final Comments: 

Fundable at a medium priority. We agree with CBFWA’s review and middle ranking of High 

Priority. A response was not needed. The proposed project seems like a logical extension of the 

previously funded innovative project. This is the second time we have reviewed this proposal 

recently. The value we see in this work is in Objective 1: to assess “abundance and natural 

production of juvenile, smolt and adult salmonids while developing and providing standard 

protocols for stock monitoring programs.” If standard methods, tools, and protocols can be 

established for small stream assessments in the Basin, this could have significant general value 

outside of the immediate stream. We encourage the proponents to prioritize their work with 

emphasis on population assessment methods and sampling protocols.

The project sponsor has made a significant contribution through her work to develop stationary 

remote and portable detectors for PIT tags, and is now developing a proposal to utilize that 

technology. However, in reviewing the objectives of this proposal, their value to the region seems 

limited to the development of sampling protocols for small stream assessments (useful), 

examination of tagging impacts on growth (assessed within a hatchery environment and with 

hatchery fish ... limited value), or otherwise mostly of local value in Abernathy Creek. 

If funded, this project should be coordinated with other monitoring projects to ensure 

compatibility of objectives, common methods, and protocols. This coordination could be 

accomplished under the favorably reviewed CBFWA proposal #35033.

ProjectID: 35063

Compare Bacterial Fish Pathogen Populations in Hatchery Water and in Adjacent Creek Water 

and Evaluate Possible Disease Transfer Between Them.

Sponsor: USFWS

FY03 Request: $71,678 5YR Estimate: $106,165

Short Description: Determine the presence of bacterial fish pathogens within a hatchery water 

system and in the waters of an adjacent creek used as part of the hatchery water supply. 

Determine the potential for pathogen transfer between the two water systems.

ISRP Final Comments: 

Do Not Fund. We disagree with the CBFWA Recommended Action ranking. The same proposal 

was reviewed by the ISRP recently and given a Do Not Fund recommendation. Other than the 

addition of a summary of the investigator’s qualifications and a paragraph suggesting which 

textbook the statistical test may be drawn from and that an unnamed statistical consultant would 

be sought (but giving no sampling designs, etc.), we see very little basis for changing the past 

assessment. With the information provided, the ISRP is not confident that the proposal will 

answer the question it proposes to answer. This proposal would investigate the possible 

exchange, between hatcheries and the environment, of two of the most serious bacterial diseases 

found in salmonid hatcheries of the Pacific Northwest, Bacterial Cold Water disease and 
ISRP 2002-14 Final Mainstem and Systemwide

46

Furunculosis, caused by Flavobacterium psychrophilum and Aeromonas salmonicida. Coho and 

steelhead are most susceptible but other salmonid species can be infected or act as carriers. These 

diseases are not limited to hatchery fish but also occur among wild populations. The proposed 

work could complement a similar proposal (#35039, USGS-CRRL) but the content of this 

proposal is very limited. 

ProjectID: 198740100 

Assessment of Smolt Condition: Biological and Environmental Interactions

Sponsor: USGS, CRRL

FY03 Request: $256,000 5YR Estimate: $1,781,050

CBFWA Adjusted FY03: $187,000 3YR: $849,000

Short Description: Provide research support to regional hatchery and fishery managers to 

determine interactions between juvenile salmonid physiological development and the 

environment that affect smoltification, disease resistance and smolt-to-adult returns.

ISRP Final Comments: 

Fund in part (qualified). Agree in part with CBFWA’s High Priority ranking. The annual ongoing 

tasks concerning smolt condition or quality, clearly identified in a project designed to directly 

assist facility managers, appear fundable. However, regional support needs to be demonstrated 

that this is a needed ongoing required task. The sponsor’s proposal to begin a major new project 

on environmental determinants of early development of the immune system may be valuable; but 

the Council should understand what it is supporting. A well-designed experiment on this issue 

could have significant scientific value, but an adequate design is not provided in the proposal or 

response.

The research topic is interesting and the researchers have a long history of working with smolt 

monitoring in the basin. They are well qualified to conduct this research but the descriptions of 

methods and tasks are inadequate. This proposal is putatively developed from a continuing task in 

the basin, but appears largely to be about developing a new research topic.

It is worth noting that the CBFWA reviewers raised many of the same concerns as the ISRP about 

whether this represented evolving ongoing work, or a new proposal. 

CBFWA: There appears to be a significant change in scope for this ongoing project. 

There was some question whether this project should be viewed as a new proposal, 

rather than an ongoing, planned study as originally proposed. The proposal is taking on 

a new path in developing its own study design and research plan. The ISRP has raised 

significant concerns regarding the study design. Some of the CBFWA reviewers agree 

with their concerns and will provide additional comment. 

The ISRP’s preliminary comments noted that the new portion of the proposal needed to be 

separated from the ongoing portion of the proposal, the new portion needed to be justified as to 

why it was appropriate as an extension of “smolt condition”, and it needed to be supported by an 

appropriate experimental design (including clarification of the genetic issues). The response 

failed to provide adequate detail on the ISRP preliminary concerns about study methods, 

statistical design, and additional information on the intention and value of the genetic screening. 

Also in their response, project sponsors strongly disagreed with the ISRP and CBFWA 

assessment that the proposed research is new, and should be separated from their continuing 

provision of smolt assessments. 
ISRP 2002-14 Final Mainstem and Systemwide

47

ProjectID: 35039

The influence of hatcheries and their products on the health and physiology of naturally rearing 

fish

Sponsor: USGS, CRRL

FY03 Request: $303,448 5YR Estimate: $2,375,918

Short Description: This research will determine whether standard hatchery or supplementation 

operations influence the concentration of Renibacterium salmoninarum in streams and 

subsequently affects the health of naturally rearing salmonids

ISRP Final Comments: 

Fundable. We agree with the CBFWA review and High Priority ranking. This is a well-designed 

program that will address three major issues: 1) do hatcheries amplify the presence of 

Renibacterium salmoninarum (Rs) in the wild (water and fish); 2) do hatchery juveniles with high 

Rs levels pose a risk to wild juveniles (tested in artificial stream tanks); and 3) do carcasses 

outplanted for nutrient supplementation pose a Rs risk to the natural environment. There are two 

issues to note: the methodology for detection of Rs in large water samples is uncertain (but 

expected to be functional within a year), and several aspects of objective 3 depend on the freezing 

treatment of carcasses. For the latter, if freezing does kill the Rs bacteria then the remainder of 

objective 3 tasks (3b-3h) will not be conducted (requiring a budget adjustment). 

The response was adequate for both the ISRP and RME concerns. Project sponsors explained the 

status of developing an Rs detection method and what it will likely be. They provided 

justification for the tentative choice of hatchery sites and demonstrated how regional input will be 

used in the choice. They explained the nature of the raceways to be used and indicated their 

intended methods of statistical analysis.

ProjectID: 35037

Measuring the potential for domestication selection of spawn timing in chinook captive and 

supplementation programs; implications for recovery.

Sponsor: UW and NMFS

FY03 Request: $129,498 5YR Estimate: $718,893

Short Description: Analyze the genetic response to (and recovery from) inadvertent 

domestication selection for spawn timing in supplementation and captive programs, using 

quantitative genetic approaches to trend analysis

ISRP Final Comments: 

Fundable at high priority. We disagree with CBFWA’s “Recommended Action.” The 

development of a quantitative genetic program in Pacific salmon is a welcomed and needed 

addition to the Fish and Wildlife Program. Domestication is a real concern in the use of artificial 

propagation and merits direct study. Changes in return timing/spawn timing are known to result 

from artificial propagation and domestication selection. Studies such as these will be essential to 

truly understand the degree of risk imposed by hatchery programs and practices.

The proposal involves a 3-generation directional selection experiment to study the response to 

selection for run timing and correlated traits in chinook salmon. Three independent lines of 

Chinook would be initiated from a single starting population (early timing, late timing, and 

control lines) and each line would be subjected to captive rearing (sea pen rearing to maturity) 

and released to the wild (i.e., similar to a hatchery supplementation program). The ISRP initially 

identified three concerns about the design; these included the choice of the specie s used, a 

potential bottleneck in the expected returns of age-3 chinook, and the ability to identify families 
ISRP 2002-14 Final Mainstem and Systemwide

48

within lines. The authors’ responded to each, but the ISRP continues to have concerns for the 

first two items. The third involving family identification was adequately clarified (through the 

use of DNA sampling and coded-wire tags).

The response to using chinook salmon involved their objective to study correlated changes in 

maturation rates at age in lines selected based on run timing. The ISRP accepts this response, but 

notes that using chinook presents difficulties in the experimental design (authors’ provided a 

detailed diagram of the experiment) and a long time period for completion of the study. Less 

complex designs with shorter-lived salmon (coho or pink salmon) could be as informative and 

provide useful results within ten years. Studies of correlated responses could still be conducted 

on other traits (e.g. size at maturity, growth rate, fecundity). Further, the space required for these 

species may be more consistent with that available, and if coho salmon were used their survival 

rate would likely be sufficient to maintain a reasonable selection differential in the selected lines. 

An associated concern about using chinook salmon may simply be unavoidable. The issue 

involves the development of the selected lines in the second-generation returns. Given the 

expected survival rate and maturation rate of the chinook stock used, there will likely be a limited 

number of Age-3 mature chinook returning from the line released to the wild. The authors also 

acknowledged this concern. However, if a substantial bottleneck did occur, then the DNA 

sampling would provide a good sampling tool to monitor the impact and additional insight could 

result. Further, even if this problem resulted in a loss of an age-selection line, there would be 

substantial returns of Age-4 chinook to maintain the selection line without compromising the 

main objective of the study. The ISRP also discussed the relative risk of this happening versus 

the value of undertaking such experiments. We strongly support undertaking these studies and 

accepting the risk of the Age-3 bottleneck issue. 

The ISRP also considered further the comments of the NMFS RME groups, and would suggest 

that they significantly underestimate the potential value of such quantitative genetics research. 

Many of the issues that people have speculated about concerning hatchery domestication and 

impacts on fitness continue due to the lack of direct investigation. Only through the use of 

quantitative genetic studies and/or DNA analyses (or both) can these issues be truly investigated. 

The addition of this research facility and the development of the University of Idaho/CRITFC 

facility are essential and much needed additions to the Fish and Wildlife Program! 

ProjectID: 35041

Monitoring the reproductive success of naturally spawning hatchery and natural spring chinook 

salmon in the Wenatchee, Tucannon, and Kalama Rivers

Sponsor: WDFW, NMFS

FY03 Request: $1,079,140 5YR Estimate: $5,619,585

CBFWA Adjusted FY03: $830,474 3YR: $2,946,438

Short Description: Evaluate the relative fitness (mating success and progeny survival) of 

hatchery and wild spring chinook that spawn naturally in rivers

ISRP Final Comments: 

Fundable. We agree with the CBFWA review and Urgent ranking. The proposal will evaluate 

the relative fitness (mating success and progeny survival) of hatchery and wild spring chinook 

that spawn naturally in rivers using DNA analyses proposed in several other projects as well. The 

proposal is well written and appropriate background is presented. The critical uncertainty about 

differences in fitness between wild and hatchery-produced fish lies at the heart of most of the 

ongoing and proposed research into captive brood and supplementation technology, and 
ISRP 2002-14 Final Mainstem and Systemwide

49

seemingly at the core of RPA 182 also. Indeed, understanding differences in fitness between the 

two groups, and whether conservation-oriented hatcheries and hatchery practices can produce fish 

that can integrate into natural populations and lead to long-term sustainability (i.e., the fitness 

question) is the primary question around which much of the present recovery plan hinges. 

Project sponsors provided thoughtful and adequate responses to the ISRP preliminary questions, 

including discussion of the expected research contributions from each of the three proposed study 

sites, the Wenatchee, Tucannon, and Kalama Rivers. The Wenatchee system seems well suited to 

the sampling; the other two are less so, as the sponsors acknowledge. 

If funded, this project should be coordinated with other monitoring projects to ensure 

compatibility of objectives, common methods, and protocols. This coordination could be 

accomplished under the favorably reviewed CBFWA proposal #35033.

ProjectID: 35029

Transfer IHN virus genetic strain typing technology to fish health managers

Sponsor: WFRC

FY03 Request: $116,479

5YR Estimate: $470,486

Short Description: Application of new genetic strain typing technology to epidemiology of IHN 

virus throughout the Columbia River basin, and transfer of technology to agency fish health 

laboratories.

ISRP Final Comments: 

Fundable. We disagree with the CBFWA priority; this should be urgent. This is a well-written 

proposal from scientists who demonstrate high productivity and application of current 

methodologies. Their proposal for technology transfer is strengthened by their past success. The 

model transfer of IHNV strain typing technology to fish health labs serving the basin may serve 

for other significant pathogens. 

The project sponsors provided an adequate response to the ISRP’s preliminary review concerns. 

The proposers will incorporate repeated blind testing of virus isolates into the protocol without an 

increased budget. Prevention of virus spread and control of outbreaks will result from educated 

management decisions enabled by the project. Active control was an intended part of the proposal 

as submitted and the response convincingly explains that increased effort beyond that budgeted in

the proposal will not be needed.

Two remaining issues merit additional consideration: (1) if M-clade IHNV is not in the upper 

Columbia, why not stop all transportation of fish to that area until all labs are trained and a 

response plan is developed; and (2) if IHN is transferable through seawater and in any 

environment with high fish densities, this could certainly be an issue for barged salmon or in 

holding areas of the river system. This virus likely merits high priority attention until it is better 

understood.
ISRP 2002-14 Final Mainstem and Systemwide

50

Mainstem Habitat

ProjectID: 199900301

Evaluate Spawning of Fall Chinook and Chum Salmon Just Below the Four Lowermost 

Mainstem Dams

Sponsor: PSMFC, ODFW, USFWS, PNNL

FY03 Request: $1,012,405 5YR Estimate: $5,594,177

CBFWA Adjusted FY03: $994,000 3YR: $3,134,000

Short Description: Monitor, protect, and enhance the spawning populations of fall chinook and 

chum below Bonneville Dam. Search for evidence of fall chinook spawning below The Dalles, 

John Day, and McNary dams.

ISRP Final Comments:

Fundable. Agree with CBFWA’s Urgent ranking. This is an ongoing proposal with some new 

tasks. The thorough and excellent response adequately addressed the ISRP questions. It appears 

that differences in timing of appearance of upstream chinook will make it possible to discriminate 

between them and the local stock. The proposed method, to employ a mark recapture estimation 

procedure, was described in adequate detail. The investigators gave more thought to the problem 

of meeting the necessary assumptions in employing such methods, i.e. that emigration and 

immigration are negligible under the circumstances to be expected with chum salmon juveniles. 

The background statement was enlarged and shows an understanding of the broader regional 

needs for flow and water management in the mainstem Columbia River. They identified the key 

questions that need to be answered and the tradeoffs that must be addressed as more and more 

salmon are observed to be adapting to the FCRPS. They also addressed the ISRP comments 

concerning exploration of the feasibility of opening up additional spawning area at the mouths of 

tributaries in the lower river. The regression analysis was clarified.

If funded, this project should be coordinated with other monitoring projects to ensure 

compatibility of objectives, common methods, and protocols. This coordination could be 

accomplished under the favorably reviewed CBFWA proposal #35033.

ProjectID: 35007

Evaluate Restoration Potential of Snake River Fall Chinook Salmon Spawning Habitat

Sponsor: PNNL

FY03 Request: $315,000 5YR Estimate: $1,145,000

Short Description: The research to be conducted under this proposal will evaluate the restoration 

potential of mainstem habitats for fall chinook salmon, especially spawning habitat in the lower 

Snake River.

Final ISRP Comments: 

Fundable. Disagree with CBFWA, the priority of this project should be higher than a 

recommended action. This is a proposal to identify operational alternatives for the hydrosystem 

that would allow enhanced spawning of endangered Snake River fall chinook salmon in tailwater 

and reservoir-headwater zones. This goal would be accomplished by more thoroughly 

characterizing the physical attributes of such zones now used successfully for spawning and 

contrasting these same characteristics in other such zones that are suspected of having spawning 

potential. Operational changes for making the potential spawning areas more suitable (by 

inducing more appropriate riverine processes in the zones) would be recommended. The proposal 

provides for monitoring and evaluation of affected spawning habitats should any operational 

changes be implemented. Existing spawning areas to be used to clarify habitat criteria for 
ISRP 2002-14 Final Mainstem and Systemwide

51

spawning include the Wanapum Dam tailrace and the Hanford Reach above the influence of 

McNary pool; the potentially enhanced spawning areas are the lower Hanford Reach at the 

McNary reservoir interface, the Ice Harbor Dam tailrace, and the Lower Granite Dam tailrace. 

The proposal was well written and meets the ISRP review criteria. The background is concise and 

germane to the proposal, and demonstrates sound science principles. The rationale is well stated 

and significance to regional programs is described by explicit reference to the BiOp’s RPA, the 

Council’s FWP, the Mainstem/Systemwide solicitation and program summary, and relevant ISG 

and ISRP publications. The progression of the previous PNNL studies of spawning habitats in 

both the Snake and Columbia rivers to the point of developing this proposal is well presented. 

Previous ISRP concerns that the project would not identify management applications for restoring 

habitat have been alleviated by objectives specifically oriented to identifying potential operational 

changes. The work has general application but the focus would be on restoring spawning for fall 

chinook salmon in the Snake River. The proposal seems likely to produce useable results. There 

is a potential for increased production of fall chinook that could be substantial. The fact that the 

COE is a party to the proposal is encouraging. There is an excellent reference list and resumes for 

a well-qualified staff. Facilities and equipment are available based on past work by the 

investigators. 

If funded, this project should be coordinated with other monitoring projects to ensure 

compatibility of objectives, common methods, and protocols. This coordination could be 

accomplished under the favorably reviewed CBFWA proposal #35033.

Additional Suggestions:

The ISRP had several suggestions that did not require a response but which might be of 

assistance. Questions arose about coordination with other PNNL proposals for related work, such 

as the hyporheic flow project and other proposals for habitat suitability studies (such as for below 

Chief Joseph Dam). Although there are differences in location and in the primary emphasis of 

each of the proposals/projects, the proponents should be aware of the need for coordination. The 

reviewers wondered if there are habitat improvement alternatives other than flow rate and water 

elevation that might be considered. Can the recent knowledge about complex physical 

characteristics beyond the usual depth, velocity, substrate, slope, etc. (such as hyporheic flow and 

embeddedness) be integrated into effective physical habitat modifications? Can the prior attempts 

to build artificial spawning channels be used as a guide (or alternatively, can proponents of 

spawning channels learn from this study)? 

ProjectID: 35030

Evaluate potential to enhance spawning of summer/fall chinook salmon in the tailrace of Chie f 

Joseph Dam, Columbia River

Sponsor: PNNL and CCT

FY03 Request: $134,220 5YR Estimate: $539,984

CBFWA Adjusted FY03: $25,000 3YR: $280,000

Short Description: Evaluate the potential to increase mainstem spawning habitat for summer/fall 

chinook salmon in the Upper Columbia

Final ISRP Comments:

Fundable as revised for redd counts only. We agree with CBFWA that the project is fundable, but 

the ISRP questioned CBFWA’s urgent ranking of this project especially given that proposal 

#35007 received a lower ranking although it targeted an endangered stock. The response to ISRP 

comments marginally addressed the concerns. These concerns had to do with limitations to the 
ISRP 2002-14 Final Mainstem and Systemwide

52

potential enhancement of spawning that are created by existing requirements on the hydropower 

system for flood control, hydropower production (especially with respect to the mid-Columbia 

Coordination Agreement), and the existing Vernita Bar Agreement to protect fall chinook in the 

Hanford Reach, all of which may produce benefits or disadvantages that are currently 

experienced by salmon in the Chief Joseph tailrace. While the proponents discussed some of the 

existing limitations on flow manipulations, they dismissed the implications of these rather lightly, 

as though that is not their problem. While we could agree that status quo ought not to be a 

restriction on what is undertaken in a scientific investigation, nevertheless, one needs to be aware 

of the status to understand how it will affect one’s observations, (in this case observations on 

potential habitat) and one’s ability to include deliberate manipulations in one’s study plan. If any 

potential habitat lies outside of what is likely to be under water in foreseeable flow conditions 

then identification of these will not be helpful or relevant. Also, the proponents did not answer the 

question why this project will require 3 years rather than 1.

If funded, this project should be coordinated with other monitoring projects to ensure 

compatibility of objectives, common methods, and protocols. This coordination could be 

accomplished under the favorably reviewed CBFWA proposal #35033.

ProjectID: 35036

Identify the mechanisms of stranding of juvenile fall chinook salmon in the Hanford Reach

Sponsor: USGS-CRRL; USFWS

FY03 Request: $278,132 5YR Estimate: $786,000

CBFWA Adjusted FY03: $250,332 3YR: $683,200

Short Description: Predict stranding-related mortality using a GIS and statistical approach by 

incorporating fish behavior and ramping rate information.

ISRP Final Comments:

Fundable and agree with CBFWA that this project is urgent. The proposal focuses on 

“mechanisms” that might be involved in stranding of juvenile chinook in the Hanford Reach, and 

puts an emphasis on behavioral mechanisms of the fish that might affect rates of stranding. The 

response provided more detail on shortcomings of previous studies, how this project fit into those 

studies, and more specifically identified the expected outcomes of this proposed project that 

might lead to improved management of flows or other measures.

The ISRP raised questions primarily whether sufficient information already exists on the 

stranding and entrapment of juvenile fall chinook in the Hanford Reach. The response identified 

important shortcomings in existing information. This proposal is planned to fill the gaps.

The Council and NMFS’s ISAB has a particular interest in this stranding issue (ISAB 99-5) and 

made a recommendation to the Council that a revision of the Vernita Bar Agreement be adopted 

to extend protection to emigrating fry. We understand that Grant County P.U.D. led in the 

development of a revised agreement among all of the (numerous) affected parties in 1999. In 

addition to studies under the Council’s program, funded by BPA, Grant County P.U.D. continues 

to monitor fall chinook at Vernita Bar during spawning, incubation, fry emergence, and now fry 

emigration. The response assured the ISRP that the principal investigators are familiar with 

provisions of the Vernita Bar Agreement and its revision, including the monitoring and evaluation 

provisions that are ongoing. Specifically, we had questions whether the amended Vernita Bar 

Agreement might adequately address the problem. The sponsor provided a copy of the amended 

Vernita Bar Agreement and discussed the problems it fails to address. 
ISRP 2002-14 Final Mainstem and Systemwide

53

The amended Vernita Bar Agreement of February 25th 2002, while it is well intended and 

represents a step forward to protect recently emerged fall chinook that have not yet moved out of 

the area, contains loopholes that lead to less than desirable protection. The loss of an estimated 2 

million juvenile fall chinook during the spring of 2001 is an illustration of this point.

There are at least two problems that can be seen in the new agreement that are pointed out in the 

response. The agreement specifies permissible fluctuations in flow under various river flow 

scenarios, but the frequency, duration, and rapidity of fluctuations are not specified. The 

provisions do not spring directly from field observations that indicate whether they would prevent 

mortality of fish or not. In practice the major changes in flow brought about by load following 

occur at night between 11 PM and 5 AM. By the time field crews arrive on the river in the 

morning, flows have increased and any dead fish have been washed down the river. The Vernita 

Bar Agreement should be modified to correct the problems with flow specifications, and the field 

monitoring should be modified to include nighttime observations.

The response agreed with the ISRP comment that there is a need to exercise caution when 

deliberately manipulating flows in order to study their effects on stranding, particularly since they 

are planned for times when fry are expected to be present (Task 1.a, p. 7). 

The response adequately addressed questions about the potential for extraction of further 

important information from existing data. The ISRP suggested that information already available 

from previous studies might be used to identify certain areas responsible for major strandings. 

The sponsors agreed it might be useful to open these up with a dozer or other mechanical means, 

deepening a downstream outlet end of the pool to facilitate emigration of fry, but the current 

status of the Reach as a National Monument could make it infeasible. 

ProjectID: 35057

Habitat Condition and Restoration Potential of Columbia River Flood Plains: A Critical, Missing 

Element of Fisheries Recovery Science and Policy

Sponsor: UM

FY03 Request: $1,200,000 5YR Estimate: $4,692,124

Short Description: Restoration of alluvial floodplains is critical if fisheries are expected to 

flourish. We will identify all floodplains in the Columbia River Basin and assess ecological 

integrity relative to human disturbance.

ISRP Final Comments:

Fundable (qualified). Agree with CBFWA’s Recommended Action ranking. This is a good longterm research project that should result in significant management actions over the next two or 

three decades to improve fish and wildlife habitat. The project is designed to catalog alluvial 

flood plains in the Columbia River Basin, assess ecological intactness of these flood plains, 

identify major changes in ecosystem structure of flood plains, and identify actions needed to 

restore, protect and sustain damaged flood plains to normative conditions. The scientific 

framework is consistent with river recovery theory so the results should help provide a basis for 

coordination of restoration activities.

The value of this approach is the demonstration of this technique in the prioritization of 

floodplain restoration projects. The prioritization should be based on biophysical properties. The 

social and economic segment of the project as proposed in the sponsor’s response to ISRP 

preliminary review comments is inadequate and should not be funded. The review panel proposed 

in the sponsor’s response to ISRP preliminary review comments is inadequate as a monitoring 
ISRP 2002-14 Final Mainstem and Systemwide

54

and evaluation program. Funding should be contingent on the development of a monitoring and 

evaluation plan. The budget should be reviewed carefully. 

ProjectID: 35062

Impacts of Flow Regulation on Riparian Cottonwood Ecosystems in the Columbia River Basin

Sponsor: University of Idaho

FY03 Request: $382,024

5YR Estimate: $1,043,918

Short Description: Research riparian cottonwoods and geomorphic responses to regulated flows 

in the Yakima Basin, compare responses to an unregulated reach of the Flathead River with the 

objective of enhancing flows to restore riparian habitats in the Columbia Basin.

ISRP Final Comments: 

Fundable (qualified). Disagree with CBFWA’s High Priority ranking; this is of lower priority. 

The project represents good science conducted by well-qualified investigators. The scientific 

background is extensive and well written. The project is related to other projects and regional 

programs. Objectives, tasks and methods are well written and complete. This proposal builds on 

work begun under one-year innovative funding to examine the impact of regulation flows on 

riparian cottonwoods in the Yakima and Kootenai River Basins. The use of remote-sensing tools 

and field sampling methods for further studies of riparian cottonwoods in other alluvial reaches of 

the Columbia River Basin was the “proof of concept” aspect of the innovative project. This 

project should provide recommendations for normative changes in flow regimes in the Yakima 

that maximize recruitment of cottonwoods, and the sponsors make a convincing case based on 

published literature that normative changes in flow regime will improve fish habitat. However, 

the project does not provide direct measurement of habitat and fish community changes 

associated with flow regime change. This unmeasured applicability to stream habitat and aquatic 

communities is a distinct shortcoming of the proposal.

The response repeats many of the assertions from the original proposal. Some members of the 

sponsors’ proposed “review team” appear to have close connections to project personnel, raising 

a question of objectivity.

Water Quality: Gas Bubble, Temperature, and 

Contaminants

ProjectID: 199602100

Gas bubble disease research and monitoring of juvenile salmonids

Sponsor: USGS, CRRL

FY03 Request: $16,885 5YR Estimate: $94,079

Short Description: Provide support for the Smolt Monitoring Program (SMP) monitoring 

juvenile salmonids for signs of gas bubble disease. Activities include (1) care and maintenance of 

equipment, (2) training, and (3) QA/QC

ISRP Final Comments: 

Fundable agree with CBFWA’s Core Program Ranking, a response was provided on 

administration and sampling. This project provides necessary operation and maintenance services 

and training for the Fish Passage Center’s gas bubble disease monitoring. Could this proposal be 

combined with another larger program for efficiency and programmatic review, such as the Fish 
ISRP 2002-14 Final Mainstem and Systemwide

55

Passage Center? The proponent may be correct in their response that such an arrangement would 

actually increase cost of administration, but this administrative issue deserves further 

consideration from Council or BPA. If funded, this project should be coordinated with other 

monitoring projects to ensure compatibility of objectives, common methods, and protocols. This 

coordination could be accomplished under the favorably reviewed CBFWA proposal #35033.

ProjectID: 35013

Species- and site-specific impacts of gas supersaturation on aquatic animals

Sponsor: CRRL

FY03 Request: $494,249 5YR Estimate: $2,731,036

CBFWA Adjusted FY03: $263,783 3YR: $694,902

Short Description: Address critical uncertainties about effects of gas supersaturation on aquatic 

animals.

ISRP Final Comments:

Fundable in Part. Agree in part with CBFWA’s High Priority ranking. Parts of the proposed 

research are fundable. However, serious doubt exists as to whether adequate data will be 

gathered to test some of the hypotheses due to sample design or location. The ISRP agrees with 

CBFWA’s “High Priority”, i.e. that this study is not urgent although parts of it can be acceptably 

accomplished per the experimental designs provided. 

The first part of this proposal intends to provide information on some key uncertainties about 

effects of gas supersaturation on three species of resident fish for which there is not much data: 

sturgeon, lamprey, and bull trout. If the states’ water quality agencies are to continue to approve 

an upper limit of 120% total dissolved gas saturation (TDG) in river water (in contrast to the

national water quality criterion of 110%), then they need a higher level of proof that 120% gas 

will not harm resident fishes (all life stages). The proposed study may not adequately answer the 

question. The ISRP has the following concerns over sample sizes and experimental designs.

All three species tend to be bottom oriented and deep water species, whereas most TDG effects 

are induced in the upper two meters of the water surface due to hydrostatic compensation. Thus, 

the frequency and geographic preponderance of gas bubble trauma (GBT) may be rare and 

difficult to find in these species. This problem calls for (1) especially well thought out 

experimental design and sampling of large numbers of fish, and (2) excellent control of TDG at 

the proposed sites for the exposure experiments. The study proposal does not clearly meet these 

criteria. In general, high TDG conditions are not excessive and chronic at either The Dalles or 

Bonneville, except in rare flood flow discharges. Thus, looking at only these two locations may 

not be the best “laboratory” because the desired test conditions near 120% may not occur. For 

valid tests of the effects of circa 120% TDG, a site where these conditions occur would be 

scientifically preferable. The ISRP also shares the proponents concern regarding the limited 

numbers of bull trout at Hood River for adequate sample sizes. 

Regarding sturgeon components of the research, the ISRP agrees with the proponents’ response 

that juvenile sturgeon in the Columbia may temporally circulate near the surface and hence be 

exposed to high TDG. Sturgeon larvae enter the surface waters when they are in their swim-up 

mode for dispersal. However, the lower Columbia population of sturgeon is healthy in terms of 

spawning, recruitment, and age structure. Thus, unlike other white sturgeon populations upstream 

where there are significant age class gaps in the populations, it is unclear that factors such as 

TDG are adversely affecting larvae below Bonneville. Documentation of larvae without GBT 
ISRP 2002-14 Final Mainstem and Systemwide

56

signs at the surface in circa 120% TDG water below Bonneville Dam would be valuable 

information. 

For the bull trout and lamprey components of the study, the researchers were open to the ISRP’s 

suggestion, described further below, to improve sampling and experimental field conditions by 

selecting study sites that are more likely to have high TDG levels. If the study’s objective is to 

determine if 120% is benign, then the experiment must include that value. Apparently, BPA 

expressed concern over conducting the study outside the FCRPS. Nonetheless, good experiments 

require good design and better test and control conditions than may be found in the lower 

Columbia River. If acceptable test conditions and sample sizes are more likely to be found at 

locations other than BON and TDA dams, then it may be fiscally and scientifically more prudent 

to do experiments where relevant results are more likely to be obtained, with the results 

generalized to the sites of actual concern. The TDG curves submitted in the response suggest it 

will be difficult to maintain control of TDG at or near 120% in normal or low flow conditions for 

periods of time needed to assure a good “treatment” condition is administered in the river at BON 

and TDA. Flows in 1997 were atypically high and cannot be expected again with sufficient 

likelihood to plan an in situ experiment. Although artificially high spill could be implemented to 

create high TDG if low flow conditions prevail in 2003, the FCRPS operators may be reluctant to 

implement such large spills to achieve 120%. If experiments are performed in appropriate TDG 

levels at locations outside the FCRPS and prove “positive” (show GBT signs in fish), then the 

studies could be followed up at FCRPS installations in subsequent years, especially when it is

likely that high flow conditions might prevail. A location where bull trout may be regularly 

exposed to high levels of TDG is in Lake Pend Oreille and the lower Clark Fork River. This area 

seems to have much greater potential for collecting adequate samples of bull trout and for 

exposing bull trout to the high TDG levels of concern. The management and operations of these 

dams on the Clark Fork are under study and it is much more likely that study of impacts, 

treatments and monitoring will increase our knowledge of bull trout, dams and TDG there than at 

the locations proposed in this proposal. 

Given the general concern over adequacy of statistical design to determine whether fish are 

responding to habitat changes, a recent report to Washington State Independent Science Panel, 

May 7, 2002 may be of use. Dr. Peter Bayley, Oregon State University, suggested that much of 

the existing design of field observational research is inadequate to elucidate cause and effect 

habitat-population response mechanisms.

The exploratory lamprey studies were better justified given the paucity of data and the differences 

between lamprey and teleost fishes. Again, location for the experimental data collection raise 

doubts about adequacy of control and test conditions and the potential to collect adequate samples 

to test hypotheses. The lab component of this study seems to be better designed.

The study of TDG exposure to migrating adult salmon and subsequent effects on spawning is 

more likely to yield useful results with the design presented. The hypothesis that TDG exposure 

may not kill, but could impair reproduction of adults is reasonable. The technology exists in PIT 

and archive tags to test this hypothesis. Again, the ability to collect data with an adequate sample 

size will be a question. Depth of exposure will also be an issue, for some data suggest adult 

migrants use the deeper sections of the thalweg of LGR reservoir to migrate. Thus, successful 

spawning of “exposed” adults may be the result of depth compensation mechanisms. The lab 

duplication may have less value than the field experiment, because the fish are not exposed to the 

other rigors of river migration during and after a TDG exposure. However, lab studies carried out 

together with field experiments may shed some light on whether reproduction is physiologically 
ISRP 2002-14 Final Mainstem and Systemwide

57

hindered by TDG exposure. This experiment should be considered a screening test for more 

rigorous sampling if any indications of impairment is observed.

In summary, although the proposed work is important, several elements of this study are not 

adequately designed to assure statistically useful results while others show more promise and 

justification for at least exploratory investigation.

The less justified elements include:

• Studies of bull trout at Hood River and near The Dalles Dam due to low population levels 

and concerns about adequate sample size and the availability of needed exposure 

conditions. TDG studies of bull trout in Lake Pend Oreille and lower Clarkfork River 

may yield larger populations for study and more desired exposure conditions, which 

could be generalize to other locations.

• Studies of lamprey at Bonneville Dam due to the inability to regulate TDG exposures for 

experimental purposes. Studies of lamprey where TDG has higher/longer frequency, 

possibly at Willamette Falls, or a location where adequate fish samples can be obtained 

and where exposure conditions can be better controlled would provide more assurance of 

a successful study.

More justified elements would include:

• Lab studies of lamprey exposure to TDG

• PIT and archive tag data analysis of spawning frequency of adults exposed to TDG 

during migration

• Artificial propagation studies of salmon after TDG exposure.

If funded, this project should be coordinated with other monitoring projects to ensure 

compatibility of objectives, common methods, and protocols. This coordination could be 

accomplished under the favorably reviewed CBFWA proposal #35033.

ProjectID: 35038

Develop Computational Fluid Dynamics Model to Predict Total Dissolved Gas Below Spillways

Sponsor: ENSR

FY03 Request: $604,998 5YR Estimate: $604,998

Short Description: Develop a computational fluid dynamics model to predict total dissolved gas 

levels below spillways that can be used to manage operation of a particular project and/or to 

predict benefit of proposed structural changes prior to their implementation.

ISRP Final Comments:

Fundable. Disagree with CBFWA’s Do Not Fund recommendation. The response addressed the 

ISRP concerns. This is a project to develop a computational fluid dynamics (CFD) computer 

model of processes that cause dissolution of air into water during spill. These processes cause 

high total dissolved gas levels in dam tailwaters and supersaturated conditions with respect to 

atmospheric pressure, which can injure and kill fish. Such a model would predict gas levels in a 

tailwater based on the physical geometry of the spillway and water flows. The proponents justify 

the model development by the anticipated ability to compare predicted total dissolved gas levels 

under different simulated physical configurations at a spillway (e.g., testing whether different 

designs of flip lips will work as expected) or under different simulated spill flow regimes. The 

predictions would be used to design or modify spillways so that they cause less dissolved gas. A 

wide variety of configurations and flows could be tested via these simulations (far more than 
ISRP 2002-14 Final Mainstem and Systemwide

58

could be empirically tested at an actual dam). Currently, such predictive power is believed not to 

exist, and only empirical observations under a limited number of different conditions are 

available. As clarified in the presentation, the CFD model is a near-field model and does not 

compete with far-field models that are designed to calculate gas flux (mostly loss) in a river or 

reservoir downstream of a dam.

The proposal is technically excellent and meets the ISRP review criteria. It is based on sound 

scientific principles, it is consistent with the Council’s Fish and Wildlife Program, it has clearly 

defined objectives (with appropriate tasks and methods), and it provides for monitoring and 

evaluation of its results through model verification. The proposal is claimed to meet a regional 

need in adapting and applying well-known methods and software to help the region better 

understand the benefits and consequences of spill events and to forecast the effects of changes in 

spillway configurations designed to reduce gas supersaturation (but see below). 

The ISRP recognizes that Computational Fluid Dynamics (CFD) models are being used for many 

hydraulic applications, and it seems logical to try this technique here. The adaptation combines 

deterministic equations with limited use of statistical models to understand the magnitude and 

distribution of dissolved gases below spillways. The logic for the model seems good. The 

proponents are well qualified to do the work, and the collaboration (including a large cost share) 

between ENSR and the Corps is an excellent mix of interests, capabilities, and eventual users. 

The problem of modeling air entrainment in the plunge pool may be a particularly difficult one to 

solve. The basic concept that mass exchange of gas between bubbles and water is an equilibrium 

process where the history of bubbles entrained below the spillway in time controls the TDG 

below the spillway has a firm basis in physical science. The success of the modeling effort will be 

tested against the relatively abundant data at Bonneville Dam spillway. The proponents agreed to 

further consider calibration and validation of the model at other dams so that the model is not 

constrained by any peculiarities of Bonneville. 

The ISRP concerns over the need for this model were adequately alleviated by the response. The 

proposal states on page 1 that “To date, prediction of spill-induced TDG is based on empirical 

relationships developed from project-specific field data. These predictive relationships are only 

applicable for the range of project operations for which the field data were collected and are only 

valid for the existing spillway geometry.” The proposal goes on to assert that there are no tools 

available for accurately predicting expected improvements prior to implementing changes in the 

field. However, existing models that use empirical data over a range of spillway operating ranges 

with prescient forebay conditions have already been developed and they use real data, real 

conditions and are calibrated sufficiently to predict the TDG behavior of spill scenarios expected 

over most operations. Field data have been collected in a designed program for more than 20 

years, and cover a wide range of project operations. 

The ISRP reviewers were skeptical that 3D computational fluid dynamics modeling could add 

much to the field data and analyses that have already been produced. The response was helpful in 

explaining how the model might be useful as an adjunct to existing models, and in fact if properly 

developed and subsequently employed, might result in cost savings by reducing or even 

eliminating the need for continuing extensive monitoring of TDG. The "Benefits of the Proposed 

CFD Model" section of the response was particularly to the point. One could imagine a situation 

where periodic random sampling of TDG would suffice - once the model was verified.

The presentation, discussion, and response clarified the distinction between the CFD spillway 

model and the existing water quality models that predict far-field TDG effects. These water 

quality models were completed by Battelle over the past 5 years (see Richmond et al. 1999 and 
ISRP 2002-14 Final Mainstem and Systemwide

59

others). The proponents showed in their response how their near-field model will link with these 

existing far-field models. 

In summary, the proponents do a good job of showing that this “first principles” CFD model can 

provide more information for design of low gas spillways than can the accumulation of 

monitoring data from user-specific and limited cases. They also are persuasive that not all 

structural modifications have been made on spillways that cause DGS and that the model will 

have uses. They clearly show that the Bonneville Dam case to be modeled was selected because 

of the wide array of empirical data for model validation/calibration, and not because of the 

greatest need to use it at Bonneville. The Bonneville case will be used to develop and test the 

model, and then it can be applied elsewhere where the needs are likely greater. The proponents 

adequately show how their model would be interfaced with the far-field models used for the 

basinwide modeling by providing tables of input values rather than direct linking.

ProjectID: 35024

Evaluating the sublethal impacts of current use pesticides on the environmental health of 

salmonids in the Columbia River Basin.

Sponsor: NMFS/NWFSC

FY03 Request: $364,105 5YR Estimate: $1,053,975

CBFWA Adjusted FY03: $304,905 3YR: $875,775

Short Description: Screen for the effects of a broad range of current use pesticides on a model 

species (zebrafish). Evaluate the effects of specific pesticides on the physiology and fitness of atrisk chinook. Incorporate data into a model of chinook population viability.

ISRP Final Comments:

Fundable, we agree with CBFWA that this is fundable; however, it is not apparent that this 

project should be among the highest priority for BPA funding. This exceptionally high quality 

proposal contains well-designed scientific experiments on toxicological effects of pesticides on 

zebrafish physiology. The premise for the research is that pesticides exist in the environment at 

concentrations that are physiologically affecting sub-populations of salmon and have a 

measurable and detectable impact on the return rates of salmon. The investigators are highly 

knowledgeable of the physiological laboratory techniques and literature and well qualified for the 

type of work proposed. The proposed research is scientifically sound; it is consistent, albeit not 

directly or likely immediately useful to the FWP. It has clearly defined objectives and related 

tasks; and it has a monitoring component. It is well connected to other pesticide studies in the 

basin. 

The response was thorough and provided convincing evidence that embryonic development is a 

highly canalized physiological phenomenon in all vertebrates and thus the zebrafish model is 

relevant; i.e. zebrafish are an accepted standard for such screening tests, and as such are logical to 

use. The proponents make a persuasive case for the rapidity of the zebrafish assay compared to 

salmon. They also clarified that copper is a primary ingredient of many pesticides and therefore 

relevant. 

The ISRP’s concern with the proposal is with the next step, that is, making the link to salmonids 

and other Columbia River basin fish, but this is not what they propose. The authors hypothesize 

olfactory impairment from pesticides may be a source of straying, but do straying, physiological, 

or behavioral anomalies exist differentially in the basin and could those be related to pesticide 

concentration? No data exist according to the authors; thus, the hypothesis that straying is 

affected by pesticide would need to be corroborated. Whether pesticides exist in quantities 
ISRP 2002-14 Final Mainstem and Systemwide

60

sufficient to affect salmon and especially salmon embryos in the wild remains hypothetical. The 

authors present evidence that some of the pesticides are detectable in agricultural basins at ppb 

levels of concentrations. Are these sufficient levels to raise concerns to warrant in vitro tests on 

zebrafish? The authors indicate that if, after three years of research on zebrafish, there is 

significant justification they will then proceed to transfer hypotheses directly to salmon. The 

ISRP would be more enthusiastic about the priorities of this research if there were field evidence 

for the hypothesized issue, i.e. observed data that the problem exists to which the proposed 

research might explain or mitigate the problem in salmonid populations

The research seems extremely interesting to basic science, but potentially a long shot, based on 

the likelihood that results will be directly applicable to the management of the FCRPS and 

salmon recovery. Near-term benefits to salmon are unlikely because of the long-term nature of 

the studies including the need for connections in the field. 

Some fascinating observations were cited by the authors about physiological and behavioral 

responses by salmon to predator alarm pheromones. Although not the intended subject of this 

research, the ISRP would be interested in research that can be done to develop more wild-like 

traits in hatchery-reared smolts. Does this area of physiological research hold potential large 

benefits to salmon? 

We agree with CBFWA’s suggestion that this research should be funded through other sources 

like EPA. 

ProjectID: 35058

Evaluation of food availability and juvenile salmonid growth rates under differing thermal and 

sediment regimes.

Sponsor: CRITFC

FY03 Request: $218,885 5YR Estimate: $672,409

Short Description: Evaluate food availability as an index to potential salmonid growth and 

survival on stream continua representing varied combined land management effects, such as 

water temperature regime, substrate composition, and riparian condition.

ISRP Final Comments: 

Do Not Fund; agree with CBFWA. This proposed study would contrast food availability and 

growth rates of bull trout, steelhead and spring chinook salmon in different qualities of stream 

habitat in the John Day watershed, with emphasis on water temperature. Stream reaches 

encompassing orders 2-4 are viewed as river continua (gradients) in which temperature is 

expected to range from cold in the headwaters to warm in lower reaches. Continua that have 

undergone landscape disturbance (e.g., agriculture, forestry) are expected to be warmer, have less 

total optimal thermal habitat over the fish growing season, and have additional changes in 

physical structure such as substrate composition, bank stability, and riparian vegetation. The 

study would quantify physical stream features, macroinvertebrate abundance (largely as drift of 

aquatic and terrestrial forms), and fish growth. This study would be tied closely with ones 

conducted by the ODEQ and ODFW, which will conduct the initial site screening and allow the 

proposed study to select the most suitable study reaches. The expected result is that certain land 

management actions will be shown to result in reduced productivity of food and lowered growth 

of fish (due, in part, to less optimal temperature habitat). 

Although the topic of salmonid production is important and temperature effects issues are timely, 

the proposal lacks clarity. The background section is long and not well organized. It lacks focus 

on the salient features leading up to a hypothesis for the proposed study. Although temperature is 
ISRP 2002-14 Final Mainstem and Systemwide

61

a key element, few thermal references are given for the many generalizations. Some topics are 

introduced that do not seem germane to the proposal. Information on ESA listings seems to have 

been tacked on at the end of the section with little thought. The Council’s Fish and Wildlife 

Program is not mentioned although the rationale lists RPAs from the Biological Opinion, but does 

not say what they are or discuss the Action Agencies’ need to address them. The rationale uses 

stated needs for food and feeding studies in the mainstem, estuary and ocean as justification for 

the work in the John Day watershed, without clarifying that this seems to be a general need over

salmonid life histories. In the section on relationship to other projects, the proposal discusses the 

linkage with the ODEQ and ODFW studies, but does not make clear just which organization will 

do what (there does not appear to be any cost sharing). 

It is not apparent that the study would have the ability to separate effects of abundance, growth, 

and the influence of competition The proposed study focuses on growth as the response variable 

to water temperature and food availability. It will depend upon other studies (by ODEQ and 

ODFW) for measurement of fish abundance (page 10). Those studies are said to provide 

information on presence/absence of juvenile salmonids and indices of abundance. Experience 

suggests that adjustments in abundance will be the primary response by populations of juvenile 

salmonids. Dominance hierarchies are established, leading to emigration of less competitive 

individuals or species. In this way, growth rates will not necessarily reflect the influence of 

environmental factors on the population. It is proposed (page 12, item 3) to temporarily confine 

salmonids in stream reaches for the purpose of measuring their growth rates. This is an unrealistic 

procedure that is unlikely to satisfy the requirements of an appropriate sample of conditions in a 

natural stream. For example, the method of confinement may, in itself, modify the production of 

invertebrate stream drift. A further problem is that other than specifying that the study is proposed 

to be conducted in the John Day Basin, no sites have been chosen for the study. It is at this stage 

uncertain that appropriate sites, that will represent “...key stream continua representing 

substantially different thermal regimes (and land management effects) ...” can be found. (page 

12).

It is not clear that the proposal meets the ISRP review criteria. There is sound science described 

in the background, but its application to the study is not clear. The study seems to lack rigor of 

purpose (perhaps more a matter of quality of explanation than of intent). There appears to be 

benefit to fish and wildlife in larger fish at outmigration when growth is high, but the benefit of 

the project in guiding land management is not broached. The objectives and expected outcome 

are not clearly stated. The proposal’s objectives are actually tasks, and the listed tasks are detailed 

elaboration on them. The real objectives remain to be clearly stated. Reference is made to 

meeting the objectives stated in subbasin documents, but these are not given or addressed. The 

methods are very detailed and instructive (perhaps leading to quibbles over details). The figure 

was not labeled so that reviewers could tell what the notations mean. The whole project is 

considered monitoring and evaluation, with no further discussion. 

In summary, the proposal is poorly presented and not well organized. Hypotheses are not clear 

and the implicit ones are rather simplistic given our current understanding of temperature 

impacts, feeding ecology, competition, etc. Study sites (and therefore the land use practices to be 

compared) have not been selected. The proposal is not fundable in its present form and the 

deficiencies were not clarified in the presentation. 
ISRP 2002-14 Final Mainstem and Systemwide

62

Juvenile and Adult Fish Passage

ProjectID: 199403300

The Fish Passage Center

Sponsor: PSMFC

FY03 Request: $1,316,323 5YR Estimate: $7,257,504

CBFWA Adjusted FY03: $1,302,904 3YR: $4,109,391

Short Description: Provide the fishery agencies and tribes with technical expertise regarding 

hydrosystem operations, analysis of smolt monitoring data for daily, weekly and monthly fish 

passage management decisions, and regional fish passage data base management.

ISRP Final Comments: 

Fundable. Agree with CBFWA’s Core Program ranking. The ISRP appreciates the careful and 

complete responses that provided adequate details on methods, monitoring, and evaluation. The 

explanation of relationships to other projects was useful. For example, the relationship to the 

proposed CBFWA project #35033 was particularly helpful. As we understand the proposals, the 

FPC project, and others, e.g. the smolt monitoring program (SMP), are all CBFWA sponsored 

and jointly developed proposals in terms of joint sponsorship by the state, federal and tribal 

fishery managers. If #35033 is funded then the functional melding of #35033 with the FPC and 

the SMP is likely assured.

ProjectID: 198712700

Smolt Monitoring by Federal and Non-Federal Agencies

Sponsor: PSMFC

FY03 Request: $2,481,100 5YR Estimate: $13,493,183

CBFWA Adjusted FY03: $2,435,941 3YR: $7,604,034

Short Description: Daily passage data through the mainstem, Snake, Columbia and midColumbia Rivers to facilitate fish passage management decisions, including Biological Opinion 

implementation, is collected daily. Sampling and marking occur at 8 sites of the larger region.

ISRP Final Comments: 

Fundable. Agree with CBFWA’s recommendation of Core Program. The ISRP appreciates the 

careful and complete responses given to our comments and to the RME Group comments. While 

there may be some differences of opinion concerning particular methods, the response is 

adequate. Specifically, the response provided adequate details on methods, monitoring and 

evaluation activities, and connections with other projects such as 35033. If #35033 is funded then 

the functional melding of #35033 with the FPC and the SMP is likely assured.

The responses to the RME Group comments illustrate the need for a coordinated, cooperative 

systemwide monitoring and evaluation program. The RME Group expressed the need for certain

abundance estimates of juveniles migrating from the Snake and Salmon Rivers. The Smolt 

Monitoring Program sponsors responded, “Historically, SMP estimated trap efficiencies at the 

Snake and Salmon River Traps. The Nez Perce tribe as part of their SMP monitoring at the 

Imnaha trap have also estimated trap efficiency at the Imnaha Trap. .... Given that the NMFS 

RME group has identified abundance as a critical component of their performance measures in 

the BiOp, the SMP program could add those objectives and modify trap operations to begin to 

estimate trap efficiencies and population abundance passing the trap. The SMP proposal for 2003 

can be modified to include these tasks if the region desires.” This is an example of the need for 

better communication of the Action Agency/NMFS RME and CBFWA. This lack of 
ISRP 2002-14 Final Mainstem and Systemwide

63

communication is particularly puzzling to the ISRP, because some of the Action Agencies/NMFS 

members are also members of the CBFWA.

ProjectID: 199602000

Comparative Survival Rate Study (CSS) of Hatchery Pit Tagged Chinook & Comparative 

Survival Study Oversight Committee

Sponsor: PSMFC & CBFWF

FY03 Request: $1,742,776 5YR Estimate: $9,497,683

CBFWA Adjusted FY03: $1,736,542 3YR: $5,420,981

Short Description: Adult and juvenile PIT tag recovery data are analyzed to compare survival 

estimates for transported fish of known origin, downriver stocks, wild and hatchery transported 

fish and fish handled and not handled at dams.

ISRP Final Comments: 

Fundable (Qualified), agree with CBFWA’s Core Program ranking, but some reallocation of 

effort for mathematical and statistical research, as indicated in the following, should be worked 

out by the Council during the project selection process and implemented by BPA in the 

contracting process. The response provided adequate details on monitoring activities, and 

connections with other projects such as 35033. If 35033 is funded then the functional melding of 

35033 with the CSS is likely assured.

A subcommittee of the ISRP met with representatives of the Comparative Survival Study (CSS) 

in Seattle on September 24, 2002. We appreciate the sponsor’s willingness to meet and discuss 

the technical issues of the design and analysis of the study. The long-term solutions to the 

mathematical and statistical problems in estimation of smolt-to-adult return rates (Bonneville to 

Bonneville and Bonneville to Low Granite SARs) appear to be: 1) detection of sufficient numbers 

of PIT tagged juveniles passing Bonneville No. 2 Dam at the planned corner collector, estimates 

of mortality of fish passing via that route, and/or 2) sufficiently large sample sizes of PIT tagged 

fish downstream of Bonneville. The ISRP recommends that these sampling efforts for PIT tagged 

juveniles be given high priority by the Council and the Corps of Engineers. In particular, task 2 of 

proposal 198331900 from NMFS for development of PIT tag detection in the corner collector at 

Bonneville No. 2 Dam should be given high priority. 

Various scientists in the region, in particular scientists from the CSS project and NMFS, have 

considered the problems in estimation of the LGD to LGD SARs from currently available data 

and have apparently arrived at what they consider to be the “best” formulas. Unfortunately, the 

formulas are complicated, convoluted, and in general, very unsatisfactory from a statistical point 

of view. There is high probability that the complicated, convoluted methods will continue to 

spawn arguments and counter arguments over trivial issues that will occupy the resources of the 

region, because the stakes are high (e.g., high costs of spill, high costs of transportation, unknown 

long term effects of the non-normative transportation, high costs of augmented flow, etc). 

We do not provide unqualified endorsement of the particular estimation formulas that are 

proposed, and we recommend that continuing statistical methods research be directed at 

investigating the performance of various proposed estimators and possible alternatives, including 

but not limited to the proposed methods and planned bootstrapping. Such research on 

mathematical and statistical methods could be pursued by the sponsors of this project, and by 

others. As an aid to clarity in comparison among possible alternative analyses, we recommend 

that the FPC make available a single reference data set which includes all the necessary 

interpretation of route of passage of PIT tagged fish and culls any suspect or ambiguous data that 
ISRP 2002-14 Final Mainstem and Systemwide

64

might be subject to further interpretation. The budget for the recommended mathematical and 

statistical analyses is relatively minor compared to the total cost of the project so investigation of 

our unresolved questions about statistical methods should not require substantial reallocation of 

the budget in this project.

ProjectID: 199008000 

Columbia Basin Pit Tag Information System

Sponsor: PSMFC

FY03 Request: $2,532,711 5YR Estimate: $13,717,975

CBFWA Adjusted FY03: $2,431,442 3YR: $7,441,185

Short Description: Provides basic infrastructure for all PIT tag related projects in Columbia 

River Basin. Operates and maintains long-term data repository for PIT tag information. Operates 

and maintains permanent PIT tag interrogation sites. Supports other PIT research.

ISRP Final Comments:

Fundable (qualified). Agree with CBFWA that this is a Corp Program. However, the project 

should not be funded until the sponsor and the Columbia Basin PIT Tag Steering Committee 

develop and implement required procedures for storage and retrieval of full metadata on PIT 

tagged fish before records are stored in PTAGIS. Given the urgent need for the project to include 

metadata, the budget should not be reduced and may need to be increased. 

The ISRP acknowledges that some metadata are available in the record stored in PTAGIS for a 

given PIT tagged fish. However, the metadata are insufficient due to the fact that much of it is

optional and the fields are too small to include full information concerning how a given fish has 

been treated prior to release (e.g., the treatment history of fish reared under a NATURES program 

or genetic background in a captive breeding program). There should be a requirement to:

Tie the record (tagging and detections) for each PIT tagged fish to the verified migration path 

of the fish and to a published or electronic permanent document that describes the capture or 

rearing history and treatment of the fish.

At the present time, it is our understanding that the initials of the principal investigator 

responsible for tagging a fish are stored in the record and one must contact that person to obtain 

required metadata on a tagged fish. This procedure may have been adequate given the short time 

that PIT tags have been in use, but in the not too distant future the principal investigators are 

going to retire or die and the required metadata will be lost.

The ISRP recognizes that this lack of adequate metadata is not the full responsibility of the 

sponsor and that ownership of data is a concern. However, the verified migration path of a PIT 

tagged fish and the published documents (or hatchery reports, progress reports, etc.) are 

absolutely required to ensure maximum long-term scientific value of the information in the 

database. Perhaps the required documents could be stored in the StreamNet library and then be 

made available to the public within a limited amount of time. This problem has been pointed out 

in previous ISRP and ISAB reviews and it appears that little if any progress has been made in 

resolving the issues.

If funded, this project should be coordinated with other monitoring projects to ensure 

compatibility of objectives, common methods and protocols. This coordination could be 

accomplished under the favorably reviewed CBFWA proposal #35033.
ISRP 2002-14 Final Mainstem and Systemwide

65

ProjectID: 200100300

ISO Adult Pit Interrogation System Installations

Sponsor: PSMFC

FY03 Request: $1,972,106

5YR Estimate: $4,529,506

Short Description: Provides for procurement of PIT tag interrogation system electronic 

components and labor for assembly and installation in adult fish ladders at Ice Harbor, Lower 

Granite and the Dalles in FY02/03 and at John Day, Lower Monumental and Little Goose in 

FY03.

ISRP Final Comments: 

Fundable. Agree with CBFWA’s Core Program ranking. The ISRP preliminary comments asked 

for more detail on quality control, study design and determination of the sample size and power. 

The response addressed these issues satisfactorily. If funded, this project should be coordinated 

with other monitoring projects to ensure compatibility of objectives, common methods and 

protocols. This coordination could be accomplished under the favorably reviewed CBFWA 

proposal #35033.

ProjectID: 35031

Tagging Study Technical Committee

Sponsor: BPA

FY03 Request: $150,000 5YR Estimate: $850,000

Short Description: This project will establish a forum – the Tagging Study Technical Committee 

– to assist the region in mapping and tracking PIT-tag studies to help identify gaps and overlaps; 

to coordinate funding and implementation among the Corps, BPA, and the PUDs.

ISRP Final Comments: 

Do not fund. Disagree with CBFWA’s Recommended Action ranking. There is a need to 

integrate the entire smolt monitoring/PIT tagging and other tagging responsibilities into a 

systemwide monitoring and evaluation program. The RME group agrees with the ISRP 

comments on this proposal. The ISRP recommendation is that the work should be conducted 

under an existing project, such as the Fish Passage Center. The RME group stated, “Although the 

appeal of this type of effort is apparent, it seems that instead of creating another entity to 

oversee/advise another aspect of activities in the CRB, the essential elements of this proposal 

could be incorporated into another project already addressing PIT-tags. These might include the 

PTAGIS or Fish Passage Center. The tasks and responsibilities could be incorporated into ongoing work statements with the same net result.” If funded, this project should be coordinated 

with other monitoring projects to ensure compatibility of objectives, common methods and 

protocols. This coordination could be accomplished under the favorably reviewed CBFWA 

proposal #35033.
ISRP 2002-14 Final Mainstem and Systemwide

66

ProjectID: 198331900

New Marking and Monitoring Techniques for Fish

Sponsor: NMFS

FY03 Request: $878,000 5YR Estimate: $2,886,900

CBFWA Adjusted FY03: $816,500 3YR: $2,123,400

Short Description: Develop, install, and evaluate PIT-tag interrogation systems and ancillary 

equipment to expand the capabilities of the Columbia River Basin (CRB) PIT-tag technology to 

meet fishery resource stakeholders’ needs

ISRP Final Comments: 

Fundable, agree with CBFWA that this is of Urgent priority. An adequate response was provided 

prioritizing subprojects and providing budget information by components. The ISRP emphasizes, 

as does the RME Group, the importance of task 2 to develop and evaluate a high-flow 

interrogation system for the corner collector at Bonneville Dam. This information would help the 

region answer longstanding questions concerning SARs for in-river and transported fish. If 

funded, this project should be coordinated with other monitoring projects to ensure compatibility 

of objectives, common methods and protocols. This coordination could be accomplished under 

the favorably reviewed CBFWA proposal #35033.

ProjectID: 199302900

Estimate Survival for the Passage of Juvenile Salmonids Through Dams and Reservoirs of the 

Lower Snake and Columbia Rivers

Sponsor: NMFS/NWFSC

FY03 Request: $1,884,200 5YR Estimate: $9,192,200

Short Description: Provide precise measurements of survival of juvenile salmon as they pass 

through dams and reservoirs in the Snake and

Columbia Rivers and relate to adult returns.

ISRP Final Comments: 

Fundable. Agree with CBFWA Core Program ranking. This is an ongoing research project to 

provide precise estimates annually of survival of juvenile salmonids migrating through reservoirs, 

dams, and free-flowing reaches of the Snake and Columbia Rivers. Survival information is 

important for evaluating the success of strategies to recover depressed stocks and to evaluate 

success in meeting the passage survival performance standards in the NMFS 2000 Biological 

Opinion. The project plans to continue to PIT tag yearling chinook salmon and steelhead at 

Lower Granite Dam as needed to estimate their survival through the hydropower system. When 

possible, the project will also follow fish PIT-tagged in other studies. The project will also 

continue to PIT tag hatchery subyearling fall chinook salmon for release above Lower Granite 

Dam to estimate their survival through the Snake River and PIT tag and release river-run 

subyearling fall chinook salmon (mostly wild Hanford stock) at McNary Dam to estimate their 

survival through the lower Columbia River. The research will determine where losses occur for 

subyearling chinook salmon between the free-flowing Snake River and Lower Granite Reservoir 

using a streambed flat-plate PIT tag detector. Results will be used to explore the relationships 

among survival, travel time, environmental variables, and dam operations using the expanding 

database generated by this study. As PIT-tagged adult fish return, the research will continue to 

explore survival to adult for fish with different passage histories.

This is a very well prepared proposal that meets the ISRP review criteria. The ISRP’s comments 

on the FY 2000 proposal (selectively quoted below) remain germane. The excellent publication 
ISRP 2002-14 Final Mainstem and Systemwide

67

record continues. The project cost has escalated as plans are made to partially absorb the trawl 

netting conducted below Bonneville Dam in order to obtain lower river survival estimates. The 

size and complexity of the project warrant periodic special review. The region is again advised to 

think about the future of this research and monitoring effort, which is a cornerstone of salmon 

evaluations in the mainstem. 

In FY 2000, the ISRP commented: 

“This proposal is very well presented, reports progressive development of methods and 

techniques over time, and demonstrates a timely and strong publication record of 

research. The proposal is well integrated with other related projects and presents a 

logical sequence of objectives and methods. The project is a core PIT tag application 

program that has been expanding its area of study as new detectors are installed and 

developed. This kind of information is vital if agencies wish to develop priorities for 

research and/or to develop a relative ranking of mortality sources in the Columbia.

The scope of the project is again so huge that it is extremely difficult to provide any 

cogent or constructive comments. Given this scope, the annual cost, and projected 

duration of this request, it seems advisable to conduct periodic programmatic reviews 

using expert panels. Such panels should provide a broader scientific basis for review and 

the necessary regional perspective to better evaluate the merits of the on-going research. 

This would assist in determining the appropriate scope and direction for future work.”

In 2000, the ISRP asked whether the results obtained to date were sufficient, or whether the 

project should continue as a key component of basinwide monitoring. The question was again 

raised (and answered) in review. It is clear that the project has been a cornerstone for monitoring 

juvenile survival in the Columbia River system, and that it should continue for the foreseeable 

future. In summary, the proposal meets ISRP criteria, represents a particularly valuable project 

for the basin, and warrants continuation.

The proposal was selected by the Action Agency/NMFS RME Work Group for review. The ISRP 

concurs with the RME group observations on this proposal including opportunities exist for better 

aligning the work to RME objectives. Their primary conclusion was that this excellent proposal 

could better state the important implications in evaluation of compliance with performance 

standards at the BO-prescribed check in periods. They noted that ESU-specific life stage survival 

for juveniles and adults while migrating through the FCRPS are key performance measures 

detailed in the BO. The proposed research will generate smolt survival estimates for Snake River 

stocks of interest, albeit using primarily hatchery fish. The RME group also sought specification 

of sample sizes and precision associated with survival estimates, for without this information it is 

difficult to ascertain how useful the estimates will be in progress and compliance tests called for 

in the BO. They also noted that the performance standards in the BO are ESU-specific, whereas 

the estimates from this research involve only Snake River ESUs. They wondered whether there 

are opportunities to develop estimates for other stocks as well, such as Yakima and Leavenworth 

as Zabel et al. (2002) report, and encouraged expanding stock coverage, if tractable. Finally, the 

RME group mentioned that the BO focuses on wild fish survival, where this research uses 

primarily hatchery fish. Justification for using hatchery fish as surrogates should be discussed in 

the proposal.

If funded, this project should be coordinated with other monitoring projects to ensure 

compatibility of objectives, common methods and protocols. This coordination could be 

accomplished under the favorably reviewed CBFWA proposal #35033.
ISRP 2002-14 Final Mainstem and Systemwide

68

ProjectID: 35047

Evaluate Delayed (Extra) Mortality Associated with Passage of Yearling Chinook Salmon Smolts 

through Snake River Dams

Sponsor: NMFS

FY03 Request: $1,083,900 5YR Estimate: $4,946,100

Short Description: Determine if downstream migration through Snake River dams results in

extra or delayed mortality.

ISRP Final Comments: 

Fundable; agree with CBFWA’s high priority ranking. The ISRP commends the proponent for 

efforts to address estimation of “extra mortality”, which has been a contentious issue for many 

years. Of necessity, any study to address what the proposal refers to as a “hypothetical value” 

will be complex and require careful thought, analysis and planning. The proposal exhibits these 

features. 

It has been argued by process of elimination that "extra mortality" is attributable to conditions 

experienced by smolts of Snake River stocks of chinook in their outmigrations through the 

hydrosystem. Arguments purporting to demonstrate the existence of "extra mortality" are 

primarily based on unconvincing comparisons with SARs of Lower Columbia River Basin stocks 

that are outside the Snake River. Since the differences observed favor the lower river stocks to a 

larger degree than expected based upon the “measured” in-river losses of upriver stocks, it was 

postulated that there might be an element of “delayed or extra mortality” that occurred in the 

ocean after the fish passed Bonneville Dam, the point of the last “measurement”. In fact, the 

“measurements” consist of projections of average losses measured in the Snake River that are 

assumed to apply from McNary Dam to below Bonneville Dam. In our view, the assumptions and 

the methods used to develop the projections are of highly questionable validity.

The present proposal is adopting a definition of "extra mortality" as a component of mortality in a 

MCN-BON SAR attributed to conditions experienced previously in the in-river smolt passage 

LGR-MCN. This has a narrower focus than the PATH definitions, since it does not include the 

MCN-BON reach for smolt passage.

This is a design with two treatments and no control. The design measures MCN-to-BON SAR for 

two treatment groups: fish that were truck-transported as smolts LGR-ICE, and fish that spent 

equivalent truck transportation time going nowhere followed by in-river passage LGR-ICE. The 

truck-only treatment group is subject to "delayed mortality," and the truck-followed-by-in-river 

treatment group is subject to "delayed mortality" plus "extra mortality." This experiment 

provides information about delayed effects of transport plus passage through a differing number 

of dams for the two groups. It does not provide information about the effect of differing number 

of dam passages alone. There is an implicit assumption of additivity for these effects. With the 

additivity assumption, and the assumption that "delayed mortality" does not begin to be expressed 

until the fish are below MCN, one could calculate "extra mortality" as the difference between the 

mortality rates measured in the MCN-BON SAR for the two treatment groups. Regardless of the 

assumptions, there would be no opportunity just with this design to estimate "delayed mortality." 

Delayed mortality and extra mortality might be isolated by providing an additional experimental 

group not transported, as recommended in item 2 below. 

A power to detect a 20% difference, with 95% confidence, 80% of the time, for the data from one 

year may be inadequate. This scenario is probably a best-case calculation, since variation between 

the within-year replicates may turn out to be large. If possible, the sample size should be 

increased.
ISRP 2002-14 Final Mainstem and Systemwide

69

The ISRP strongly recommends:

1) reaching an agreement so that the PIT tagged fish from the truck-followed-by-in-river 

treatment group from this project will always be returned to migrate in-river, rather than taken 

into transport, whenever they hit a bypass detector. This can be done automatically with the "sort 

by code" hardware at the collector dams (LGO and LMO). This will preserve sample size for this 

treatment group, and it will also present opportunities for stratifying on the number of bypass 

detections between LGR and MCN.

2) developing a method to estimate “delayed mortality” by using PIT tagged fish from outside 

this study but with coordinated release dates from the hatcheries to match batches of treatment 

groups from this study. An alternative would be to include an additional real control group of 

PIT tagged fish that are allowed to migrate in river from LGR to MCN, without the truck detour. 

This would permit estimation of "delayed mortality," which is not possible with the present 

design.

3) creating a CD of the "consensus interpreted data" as part of its annual reporting process. This 

would allow statistical researchers to try various statistical methods for analyzing these data, 

without the confounding issue of how the different researchers made their decisions about which 

data to cull.

Further recommendations are:

1) increasing the budget to create another treatment group that is collected at LGR and barged to 

the tail race of ICE. This would allow investigation of the question concerning whether the 

"delayed mortality" from truck transportation is the same as from barges. 

2) estimating mortality from recoveries of fish released below Lower Granite Dam and recovered 

downstream. Similarly, estimating mortality for fish released below Ice Harbor Dam and 

detected at McNary Dam. This would allow directly estimating the mortality in transportation 

itself rather than assuming the usual 5% mortality rate used in modeling transportation. 

Finally, it should be noted that the ISRP recommends that NMFS, CBFWA, and the Corps of 

Engineers concentrate on development of better estimates of SARs that will directly answer 

critical questions for recovery of endangered stocks in the Columbia Basin. For example, direct 

answers are needed to questions concerning return rates of transported versus in-river migrating 

fish, adequacy of return rates needed to recover stocks, indirect mortality, extra mortality, “D”, 

etc. The ISRP has recommended elsewhere in this report, and again emphasizes the importance 

of installation of a PIT tag reader in the corner collector at Bonneville 2 (project 199302900). 

Data collected there will provide information that would more directly estimate SARs for groups 

of in-river migrants than the efforts in this project.

If funded, this project should be coordinated with other monitoring projects to ensure 

compatibility of objectives, common methods and protocols. This coordination could be 

accomplished under the favorably reviewed CBFWA proposal #35033.
ISRP 2002-14 Final Mainstem and Systemwide

70

ProjectID: 198910700

Statistical Support for Salmonid Survival Studies

Sponsor: UW

FY03 Request: $265,850 5YR Estimate: $1,409,650

Short Description: Improve monitoring and evaluation capabilities by developing better 

measurement tools and study designs to estimate juvenile and adult salmonid survival and 

survival relationships. Provide statistical guidance to investigators in the Columbia Basin.

Response Needed? Yes

ISRP Preliminary Comments: 

Fundable (high priority). Disagree with CBFWA’s Do Not Fund recommendation. This project 

develops analytical tools for tagging studies and provides support for the design and analysis of 

tagging studies to groups requesting assistance. This project offers a valuable system of checks 

and balances for evaluation of statistical analysis of complex tagging studies (PIT tags, radios, 

etc.) and other studies. The response provided details on past and present users of the products 

and services related to this project. The ISRP suggests that logs of time spent in client support be 

kept, client satisfaction surveys be collected, and these items be summarized and presented in 

support of future proposals.

ProjectID: 199105100

Monitoring and Evaluation Statistical Support

Sponsor: UW

FY03 Request: $394,655 5YR Estimate: $2,137,255

Short Description: Develop statistical methods for monitoring and evaluating salmonid recovery 

plans. Provide added-value analyses and statistical support on regional fisheries issues. Provide 

smolt migration timing predictions on the internet.

ISRP Final Comments: 

Fundable (high priority). Disagree with CBFWA’s Do Not Fund recommendation. The main 

elements of the project are to provide real-time analyses of PIT-tag data and smolt passage 

indices to predict outmigration timing and to provide value-added analyses of historical tagging 

data by testing hypotheses, estimating parameters, and investigating interrelationships. An 

additional element is to provide statistical assistance to the BPA and the NW fisheries community 

on an as-needed basis. The response provides information on clients and contributions. The 

project provides a valuable service. The ISRP suggests that in the future a summary of the 

following be provided in support of proposals: 1) data on the amount and nature of use of 

electronic data and analyses posted on the web, 2) responses to satisfaction surveys by internet 

users, 3) number of requests for analyses and the time taken to respond to those requests.

ProjectID: 35003

Vitality Based Studies of Delayed Mortality

Sponsor: UW

FY03 Request: $207,180 5YR Estimate: $1,060,638

Short Description: Based on the vitality survival model we will develop and deploy a field 

procedure to evaluate the contributions of freshwater events on delayed and extra mortality.

ISRP Final Comments: 

Fundable, but at low priority. Agree with CBFWA “Recommended Action”. The project is 

designed to characterize the factors contributing to delayed and extra mortality. The technical 

background is addressed well with references and links to other work. The problem of identifying 

and solving delayed and extra mortality problems is complex due a variety of mechanisms 
ISRP 2002-14 Final Mainstem and Systemwide

71

through which mortality may operate. The proposed research is designed to study these 

mechanisms through theory, laboratory studies, and field studies. The study could be valuable in 

helping to resolve these complex issues. However, as noted elsewhere in this report (project 

35047) the estimation of extra mortality would be better addressed with direct data on survival 

collected in the river.

The sponsor made a substantial and successful effort to address the ISRP comments. The 

response demonstrates that the project sponsor has explored connections with other projects and 

made definite plans to integrate this work with other projects. The sponsor has been instrumental 

in encouraging the several people working on delayed mortality questions to meet in a workshop. 

The workshop proceedings are enlightening. We encourage continued exploration of 

opportunities for integration with other projects.

ProjectID: 35011

The Floating Net Pen Transportation System Pilot Project

Sponsor: Columbia Basin Fishery Restoration L.L.C.

FY03 Request: $3,291,275 5YR Estimate: $10,196,875

Short Description: The transportation of Chinook salmon smolts in floating net pens from 

various fish hatcheries and collector systems to be released at the mouth of the Columbia River or 

in the Pacific Ocean.

ISRP Final Comments: 

Do Not Fund; agree with CBFWA. The proposal is incomplete. While the response attempts to 

deal with many of the comments by the ISRP, it still falls short of being adequate to accomplish 

its stated objective, "Net pens are proposed as a low cost alternative to the present system of 

transporting molts in the Columbia River.", page 1 of the response. No method is described for 

comparing the performance (survival or return rates) of fish transported in net pens with those 

transported "in the present system". 

ProjectID: 35023

Establish Relationship between Fish Passage Survival and Turbine Operating Efficiency

Sponsor: Normandeau Associates

FY03 Request: $3,887,500 5YR Estimate: $11,932,468

Short Description: Provide guidance to turbine operators for maximizing passage survival; 

provide quantitative information for turbine rehabilitation/replacement at dams; and assess 

whether survival targets are met

ISRP Final Comments: 

Do Not Fund; agree with CBFWA. This is a proposal to determine if fish passage through 

turbines is least damaging at peak electrical generating efficiencies of the turbines, which is a 

commonly held belief that currently guides operations. A sub-objective is to establish whether 

consistent results are obtained from several turbines at the same dam, under the premise that 

turbines’ effects may differ even when the turbines are nominally similar. The study would 

determine immediate mortalities and damages at McNary Dam using the proponent’s balloon tag, 

longer-term effects after holding of test fish in tanks, and even longer-term survival of in-river 

fish tagged with sonic tags (all with appropriate controls released at the base of the dam). The 

ultimate objective is to establish more scientifically grounded rules for operating turbines for 

benefit of fish (or for balancing fish survival and power production). 
ISRP 2002-14 Final Mainstem and Systemwide

72

This is a generally well-written proposal from a group with outstanding credentials. There is little 

doubt that they can achieve what they propose to do. The basic question is whether it is worth 

investing $12 million to arrive at recommendations that might lead to improvements of 1 to 2% in 

survival of juvenile salmonids (based on the text and tables at the end of the proposal) that pass 

through turbines, particularly given the emphasis in the region on measures to divert the juveniles 

away from the turbine intakes. The question might boil down to an economic one, of how 

valuable it is to the power operators to be able to diverge from the criterion of operating within 

1% of the peak efficiency of turbines? If it is quite valuable, in the millions of dollars, then it 

ought to be desirable for them to fund this study.

Aside from economics and FCRPS planning, the proposal does not meet the ISRP review criteria. 

It is strong on methodology (good science) but short on justification. The technique of balloon 

tagging has become a staple in hydropower survival studies nationally following patenting of the 

technique by the proponent. The approach, including the detailed statistical design, is well tested 

in the Columbia River basin and has been shown to be scientifically sound and fruitful (a useful 

table of results from many studies in the basin is included at the end). The novelty of this study is 

the inclusion of more than one turbine (to evaluate consistency of results) and longer-term, inriver survival (a topic for which the balloon tag work is often criticized). The study objectives, 

tasks and methods are described in adequate detail. However, the justification for this study is 

brief and incomplete. The previous studies are not well summarized to demonstrate that this 

proposal is the next logical step in obtaining more successful fish-passage. How much change in 

fish survival and electricity generation are we talking about in shifting from the peak efficiency 

level (large amounts, small amounts)? That is, what level of biological benefit (an ISRP review 

criterion) is at stake? What evidence is there now that adjacent turbines differ in their 

performance? What literature suggests that in-river mortality may be higher than indicated by the 

immediate or short-term effects shown by the balloon tag (and by how much)? The relationships 

of the proposed work to previous or on-going studies are given briefly and very generally (what 

are the project numbers listed in Part I?). The RPA’s from the NMFS BiOp are listed, but neither 

named nor discussed as justification for this work. No priorities from the mainstem/systemwide 

province solicitation or program summary are mentioned. There is no mention of the Council’s 

Fish and Wildlife Program, for which the ISRP must determine if the proposal is consistent. The 

whole project is considered one of “monitoring and evaluation” but the proposal would have 

benefited from a short discussion of how any operational changes implemented as a result of this 

study would be monitored and evaluated short of redoing this whole study. 

In summary, the proposal falls short of meeting the ISRP review criteria. This is particularly true 

for the criterion of demonstrating likely biological benefit, which is slight. It might be better 

justified as a hydropower proposal. 

ProjectID: 35034 

Fish Behavioral Guidance Through Water Velocity Modification PHASE ONE

Sponsor: Natural Solutions

FY03 Request: $285,020 5YR Estimate: $1,104,596

Short Description: Field evaluation of a prototype mechanism for guiding juvenile and adult fish 

through a hydro facility. Test in situ the ability of induced turbulent flow and water velocity to 

simulate natural migratory cues for guiding fish to safe passage routes.

ISRP Final Comments: 

Fundable. Agree with CBFWA’s “Recommended Action,” but this project could have application 

beyond the dams that would be relevant to the Fish and Wildlife Program such as at acclimation 
ISRP 2002-14 Final Mainstem and Systemwide

73

ponds to stimulate migration. The response is thorough and shows a serious effort on the part of 

the sponsor to take advantage of comments received. The effort should be encouraged. This 

proposal has been improved from the innovative submission with additional input from 

biologists. The proposal gives a tantalizing view of what might be accomplished. 

The potential value of this concept might be in the creation or enhancement of attraction flows at 

surface collectors or other bypass systems currently under development at dams in the Columbia 

Basin. Biological information already available ought to make it possible to develop criteria for 

deciding whether development and application of a large bore eductor would have the desired 

effects on guiding juvenile salmon. Mortality from effects of shear is a concern that can be tested 

with non-anadromous fish as proposed.

What is needed is a test with juvenile salmon that are ready to migrate downstream. Perhaps a test 

site could be found at Cowlitz Falls or at an acclimation pond somewhere in the Columbia Basin. 

As for demonstrating a full-scale application, reviewers agree with the proponent that this would 

be premature until the data the sponsor proposes to get are obtained and evaluated.

Data Management

ProjectID: 198810804

StreamNet

Sponsor: PSMFC

FY03 Request: $4,211,435 5YR Estimate: $24,027,308

CBFWA Adjusted FY03: $2,261,033 3YR: $7,148,077

Short Description: Provides regionally consistent, georeferenced data pertaining to fish and their 

habitats obtained from the basin's state, tribal and federal fish management agencies via the 

Internet at www.streamnet.org, and custom data services to FWP participants.

ISRP Final Comments:

Fundable in Part (Qualified). Agree with CBFWA’s Core Program ranking, base funding 

recommendation, and comment to start a regional planning effort to provide guidance (see ISRP 

comments below). The base program is fundable and serves an important role in the Basin. In 

addition to the base program, the ISRP finds many of the additional tasks identified by Streamnet 

to be high priority for the region. We strongly support expanding the tasks and objectives of 

StreamNet to provide the most utility to the basin. Unfortunately, adequate information is not 

presented in the proposal to provide scientific review and fully evaluate the methods, budget, 

personnel, and infrastructure necessary to accomplish the listed tasks. 

The Council could consider amending the base budget of StreamNet and partial funding of 

#35048 (NWFSC Salmon Data Management, Analysis, and Access for Research Monitoring and 

Evaluation Programs) to allow for prioritization and funding of some of the additional tasks 

proposed (see below). Obviously, StreamNet and the sponsors of #35048 would have to provide 

more complete study plans on each high priority task. The plans for capturing additional data 

could be reviewed by CBFWA staff and the ISRP. If the Council agrees to extend the period for 

consideration of funding of this and perhaps other monitoring proposals (e.g., new data to be 

captured by StreamNet and the NMFS Proposal #35048, Tier I monitoring proposed by #35016, 

and Tier III monitoring proposed by #35020) then the ISRP could review the set at a later time.
ISRP 2002-14 Final Mainstem and Systemwide

74

Council members should carefully review the roles that their respective States play in providing 

data to StreamNet. It would be helpful for the Council members to exert what influence they may 

have on their respective state government agencies to cooperate with and actively provide 

information to StreamNet using common methods and protocols. Also, much of the Tribal data 

from the various States are not currently included in the base program of StreamNet. 

Much of the data collected by Fish and Wildlife Program projects are not readily available to the 

public in a timely manner from any source, and in particular, not from StreamNet (e.g., data from 

the various artificial production studies). We note that this is not a problem with StreamNet but 

rather with the failure of project sponsors to provide their data and metadata to StreamNet in a 

timely manner or to provide links from the StreamNet web site to locations of the data and 

metadata. Requirements should be implemented that all project sponsors provide their data in a 

timely manner after being provided adequate time to write final reports and manuscripts for the 

open scientific literature. Coordination of these efforts could be accomplished under the 

recommended CBFWA proposal #35033.

Of the new tasks (in parentheses) proposed by StreamNet, the ISRP would list 12 as urgent for 

evaluation of habitat and fish recovery efforts: 

1. (#39) Start capture of data on straying and spawning of hatchery fishes and 

monitoring of spawning by wild populations where hatchery influences exist in 

Idaho, from the Tribes, and expand efforts in Oregon. The ISRP is curious as to why 

the State of Washington is not included.

2. (#6) Expand capture of natural spawner abundance data, e.g., anadromous data 

collected by USFS, BLM, Yakama Nation, and Nez Perce Nation.

3. (#8) Expand capture of hatchery release data, e.g., to Tribal hatcheries.

4. (#10) Expand capture of hatchery return data, e.g., to Tribal hatcheries.

5. (#26) Capture additional data for calculating return rates of hatchery and natural 

fishes by brood year for all priority basins in Oregon and start the process with the 

Tribes.

6. (#18) Capture new habitat restoration and improvement information from Idaho and 

Oregon. The ISRP is curious as to why the State of Washington and the tribes are 

not included. 

7. (#20) Expand capture of information on barriers, e.g., culverts in Oregon and 

expanded information from Idaho.

8. (#22) Expand capture of information on diversions and screen status in Idaho and 

Oregon. The ISRP is curious as to why the State of Washington is not included. 

9. (#3) under “Support subbasin planning.” Capture subbasin planning data being 

collected and compiled.

10. (#40) Develop a water temperature database.

11. (#5) under “Data related services.” Start an analysis function as a specific part of 

StreamNet.

12. (#30) Capture stream habitat data (currently very low priority in the base program).

Finally, we are concerned that the full function and potential value of StreamNet to the basin’s 

scientific community are being encumbered by its steering committee. The ISRP believes that the 

scientific value of StreamNet to the region could be enhanced by a reorganization of its 

administration to provide greater autonomy.
ISRP 2002-14 Final Mainstem and Systemwide

75

If funded, this project should be coordinated with other monitoring projects to ensure 

compatibility of objectives, common methods and protocols. This coordination could be 

accomplished under the favorably reviewed CBFWA proposal #35033.

ProjectID: 199601900

Second-Tier Database Support

Sponsor: UW

FY03 Request: $275,111 5YR Estimate: $1,379,983

Short Description: Provide single-point, internet-based access to a subset of information to 

guide and support BPA's independent decisions pertaining to its responsibilities under the Power 

Act and Endangered Species Act.

ISRP Final Comments: 

Fundable. Disagree with CBFWA’s recommendation of Do Not Fund. This valuable project 

provides service to the scientific community in the region at relatively low cost. Specifically, it 

provides access to and analysis of data from multiple databases. Previous concerns of the ISRP 

with overlap of responsibilities between database projects have been addressed. In fact, some 

degree of overlap of services provided by second tier database projects (modeling, projections, 

analysis, use of multiple first tier (primary) databases) is healthy for the region, because it 

promotes careful evaluation of assumptions made in analyses of primary data. This project is also 

on the frontier in providing a prototype reporting and analysis application for access to distributed 

databases, a need that has previously been identified by the ISRP.

The project history and technical background sections are informative, and the sponsor provided 

careful and complete responses to the ISRP concerns with objectives, tasks, methods, and 

monitoring and evaluation. The sponsor understood and responded to the concern that 

quantitative projects that monitor and analyze data from other projects have an internal 

component for monitoring and evaluation of themselves. For example, a number of DART’s 

tools report predictions of adult or juvenile passage, water quality and transport. These tools can 

be evaluated on the correspondence of predictions to observed data. Each year, DART provides 

an on-line, post-season analysis of the accuracy of these predictions.

Again, the ISRP would like to comment that we were somewhat confused by the Action 

Agency/NMFS RME Group Comments on this and other proposals. In other cases, e.g., proposal 

#35048, there is apparently strong support by the RME group for analyses of primary data to be 

conducted in second tier databases, whereas there is very weak support for similar analyses to be 

conducted by DART. The ISRP believes there is an inconsistency here. 

The next proposal should include an evaluative summary of usage to date that indicates the 

distribution of use across different types of users, as well as the distribution of use across 

different products. It should include the details of a plan for how DART assesses demand for 

current and new products, the type of outreach that is done to assess demand, and methods used 

to inform and expand the user base.
ISRP 2002-14 Final Mainstem and Systemwide

76

ProjectID: 35010

An Interactive Biodiversity Information System for the Columbia River Basin

Sponsor: NW Habitat Institute

FY03 Request: $432,950 5YR Estimate: $3,079,050

CBFWA Adjusted FY03: $460,926 3YR: $1,656,380

Short Description: To complete development of a resident fish and wildlife information system 

on the Internet to allow users/resource managers to access, query, and retrieve spatial, text, and 

ISRP Final Comments:

Fundable in part for the update and maintenance of the wildlife habitat database. Agree (in part) 

with CBFWA’s Core Program ranking. This is a well-written and detailed proposal to provide 

needed wildlife data for subbasin planning. The approach is to enhance an existing internet site 

(IBIS) to provide biodiversity databases through an improved database management system. The 

IBIS site currently exists and is maintained by the Northwest Habitat Institute, but is inadequate 

and in need of improvement. 

The goal is to have a more accessible common data management system of peer-reviewed data on 

fish and wildlife and their habitats that would provide consistent data throughout the basin. The 

project would provide information and services relevant to regional planning efforts. The data 

described would be useful in establishing resident fish and wildlife distributions and the linkages 

among them for subbasin planning. Objectives are to restructure the existing database on IBIS to 

allow concurrent use and more complicated data queries. Decision support tools and a manual 

will be developed. Proposers also intend to monitor the use and effectiveness of IBIS through 

user feedback.

The thorough response addressed the ISRP concerns. It indicates extensive regional agency 

involvement in the development of IBIS to date, with reasonable expectation of that involvement 

continuing. With regard to the resident and anadromous fish habitat data they recommend 

collecting, the ISRP believes that these data should be available to the region, but are unsure as to 

the utility of adding another database; e.g. with EDT and other concentrations on anadromous 

freshwater habitat. 

Detail on the amount and type of usage is provided. IBIS data will be provided free of charge. A 

registration gateway to the site will generate data for monitoring use. Quality control mechanisms 

sound sufficient, and the on-line peer review process is described in more detail.

ProjectID: 35048

NWFSC Salmon Data Management, Analysis, and Access for Research Monitoring and 

Evaluation Programs

Sponsor: NMFS-NWFSC

FY03 Request: $763,150 5YR Estimate: $3,463,150

Short Description: Assess and consolidate all listed salmon related data and metadata sources in 

the Columbia Basin, develop and deploy Internet-based information repository and related 

analysis/reporting tools in support of science based research. 

ISRP Final Comments:

Not fundable (qualified). Disagree with CBFWA’s Recommended Action ranking. The ISRP is 

very supportive of the basic objectives of this project to capture primary data. However, the 

proposal is inadequate. It is too vague and general to be recommended for funding as written. 
ISRP 2002-14 Final Mainstem and Systemwide

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The sponsor proposes to: 1) make available unspecified NMFS data, 2) to capture and make 

available unspecified data necessary for NMFS to meet its obligations under the ESA, and 3) 

conduct unspecified analyses necessary for NMFS to meet its obligations under the ESA. The 

ISRP has no doubt that NMFS has primary data of interest to the region (some examples were 

given), that certain data are not readily available (some examples were mentioned), and that 

certain analyses are necessary for NMFS to meet its obligations under the ESA (some were 

mentioned). The ISRP believes that there is a strong need in the region to not only capture and 

provide additional primary data to the region, but also to allow the sponsors to analyze and 

provide “derived data” (with associated metadata and assumptions of the analyses). The ISRP 

believes that the scientific value of a database is enhanced when the people who administer the 

database are required to analyze some of it!

The Council could consider partial funding of #35048 and increased base funding of StreamNet 

(#198810804) to allow for prioritization and capture of necessary monitoring data (see the review 

of StreamNet and #35033). Obviously, StreamNet and the sponsors of #35048 would have to 

provide more complete study plans on each high priority task. The plans for capturing additional 

data could be reviewed by CBFWA staff and the ISRP. If the Council agrees to extend the period 

for consideration of funding of this and perhaps other monitoring proposals (e.g., new data to be 

captured by StreamNet and the NMFS Proposal #35048, Tier I monitoring proposed by #35016, 

and Tier III monitoring proposed by #35020) then the ISRP could review the set at a later time.

If funded, this project should be coordinated with other monitoring projects to ensure 

compatibility of objectives, common methods and protocols. This coordination could be 

accomplished under the favorably reviewed CBFWA proposal #35033.

This proposal lacks sufficient technical detail for scientific review. Most objectives in the 

proposal have a Stage II step to identify the team, tasks, costs, etc. For example, the sponsor 

provided the following generic statement on most tasks “Detailed Project Plan: To be completed 

within four weeks of acceptance of funding. The plan will identify: the project team; all tasks; the 

estimated costs of each task including the cost of any necessary software and hardware and a 

detailed budget; any dependencies between tasks such as which task must finish before another 

can begin; who will complete each task; identification of a probable user group for the project; 

other needed consultation and participants; the actual deliverables such as code and 

documentation; the dates the deliverables are due; project team meeting schedule; project team 

reporting requirements; the project manager; and, the program manager to whom the project 

manager reports.”

The section of this proposal to monitor and evaluate the success or failure of itself, the proposed 

work, is inadequate. The response to the comment about potential overlap with other efforts 

illustrates an absence of collaboration with other agencies. Activities under this project provide an 

opportunity to strengthen StreamNet and other regional databases. We encourage NMFS to work 

more closely with the other State, Tribal, and Federal agencies through CBFWA to establish 

priorities for capture of additional needed data and to establish a comprehensive collaborative, 

systemwide monitoring and evaluation program. 
ISRP 2002-14 Final Mainstem and Systemwide

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Monitoring and Evaluation: Systemwide and Habitat 

Action Effectiveness

ProjectID: 35033

Collaborative, Systemwide Monitoring and Evaluation Program.

Sponsor: CBFWA

FY03 Request: $998,763 5YR Estimate: $2,996,293

CBFWA Adjusted FY03: $968,800 3YR: $2,906,404

Short Description: This project proposes an integrated effort of state, tribal and federal fisheries 

managers to catalogue, make available, critically assess, and improve system-wide monitoring 

and evaluation for fish and ecosystem status.

ISRP Final Comments: 

Fundable. High priority. Agree with CBFWA’s Core Program ranking. This proposal addresses 

one of the major management deficiencies in the basin, namely the lack of a coordinated 

basinwide monitoring program. Such a program is of critical importance for assessing changes in 

stock and environmental conditions and the effectiveness of restoration and mitigation actions. 

Thus, this proposal is of urgent priority for immediate funding. 

The sponsors answered all questions and addressed all concerns expressed by the ISRP in our 

preliminary review including the need for independent oversight and outside peer review. 

This project provides an urgently needed umbrella framework to 1) collaboratively develop 

systemwide M&E protocols and 2) coordinate data collection activities, protocols, and standards. 

The basic objective of the Collaborative System wide Monitoring and Evaluation Program

(CSMEP) project is a coordinating mechanism for individual M&E projects rather than assuming 

all M&E activities into itself. 

It appears to the ISRP that this proposal is in direct competition with the planned activities of the 

Action Agency/NMFS RME Group. Competition between the RME Group, currently funded by 

BPA, and this project CSMEP (#35033), proposed by CBFWA and recommended by the ISRP, is 

a problem to be resolved in the political arena. We emphasize that resolution of this competition 

and development of a coordinated Columbia Basin wide monitoring program is critical for 

collection of the best quantity, quality, and utility of scientific data to evaluate the efforts of the 

region to recover fish and wildlife habitat and populations.

Several ongoing monitoring and database projects are already under the general direction of the 

CBFWA or advisor committees made up of mostly CBFWA members, including parts of or all of 

projects #198810804 (StreamNet), #198712700 (Smolt Monitoring), #199008000 (PTAGIS), 

#199403300 (FPC), and #199602000 (CSS). If #35033 is funded then the functional melding of 

#35033 with these projects is likely assured. CBFWA as the project sponsors do not propose to 

formally bring other existing M&E projects under this project in the foreseeable future, but rather 

to coordinate activities with these other projects, and collaboratively improve the systemwide 

information to aid decision-making. As proposed by CBFWA, project #35033 does not propose 

to incorporate administration and implementation of these projects, or to dictate individual project 

M&E actions and protocols for existing M&E projects. However, project #35033 does propose to 

integrate relevant Tier 1, 2 and 3 data from component programs into a systemwide M&E 

program, and make recommendations for filling critical information gaps related to key 

management questions facing the region.
ISRP 2002-14 Final Mainstem and Systemwide

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It was refreshing to see in the NMFS Proposal #35019 (Develop and Implement a Pilot Status and 

Trend Monitoring Program for Salmonids and their Habitat in the Wenatchee and Grande Ronde 

River Basins) that one of the Action Agencies agrees with the ISRP that the CBFWA proposal 

#35033 contains the necessary collaborative components to implement a comprehensive 

monitoring program basinwide. We note that NMFS is also an active member of the CBFWA. 

Proposals #35033 and #35019 (and by extension, parts of the other NMFS proposals #35016, 

#35020 and #35048) could be combined with other ongoing projects to provide a systemwide 

monitoring and evaluation project. The ISRP could not agree more with the statement in the 

NMFS proposal #35019 that “The absolutely essential elements of 35033 that the other projects 

lack is the basinwide perspective, both in the collaborative representation of nearly all fisheries 

management agencies, as well as the inclusion of fishes other than anadromous salmonids. 

Ultimately, the most efficient manner for the Columbia River basin to approach a comprehensive 

monitoring program would be in the form of integrated aquatic ecosystem health assessment. 

Components of the above 5 projects, plus many ongoing monitoring programs, if coordinated 

within a single purpose, design, and data management and evaluation framework, could produce 

the ideal monitoring program for the basin’s aquatic natural resources.” Unfortunately, there are 

some technical deficiencies or incomplete methods in the NMFS proposals #35016, #35020 and 

#35048 and the ISRP cannot give unqualified support to these proposals at this time.

The proposed Project #35033 is broader, both in scope and participation, than other M&E 

projects proposed in the systemwide province and, therefore, has a higher probability of success 

and should receive priority for immediate funding. The CSMEP project provides an environment 

for developing and coordinating common data collection protocols and standards. Several 

logistical and institutional issues remain to be resolved, but the ISRP believes that this proposal 

has the best potential to significantly improve the quantity, quality, and utility of scientific data 

for evaluation of fish and wildlife recovery efforts in the Basin.

ProjectID: 35016

A Pilot Study to Test Links Between Land Use / Land Cover Tier 1 Monitoring Data and Tier 2 

and 3 Monitoring Data

Sponsor: NWFSC

FY03 Request: $436,000 5YR Estimate: $2,582,000

Short Description: Pilot test use of LU/LC spatial data in Willamette subbasin as Tier 1 

monitoring data base, link to Tier 2 fish data in Willamette River floodplain and Tier 3 data for 

floodplain restoration projects; transfer lessons of same to John Day/Wenatchee

ISRP Final Comments: 

Not Fundable. Disagree with CBFWA’s High Priority ranking. The proposal was to apply 

findings from the use of spatial data in the Willamette River subbasin to other subbasins. The 

main objective is to link LU/LC data to field data to improve understanding of changes in riparian 

and aquatic resources. This appears to be a good idea. However, the proposal was inadequate and 

did not provide enough detail to effectively evaluate its merit or to warrant further response 

review. 

The respondents submitted a completely new proposal that the ISRP hasn’t had an opportunity to 

evaluate and discuss as a group. If this proposal were to be reviewed at this time it would be 

without oral presentation, the opportunity to ask questions of the presenter, and a response loop. 

The ISRP feels that to allow submission of an entirely new proposal after receiving a rating of 
ISRP 2002-14 Final Mainstem and Systemwide

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“not fundable, no response necessary” as part of the mainstem and systemwide process would be 

unfair to other sponsors and would set a harmful precedent to the review process. 

However, this proposal may provide a critical level of monitoring that should be considered 

urgent for funding in the Columbia Basin. If the Council agrees to extend the period for 

consideration of funding of this and perhaps other monitoring proposals (e.g., new data to be 

captured by StreamNet and the NMFS Proposal #35048, Tier I monitoring proposed by #35016, 

and Tier III monitoring proposed by #35020) then the ISRP could review the set at a later time.

If funded, this project should be coordinated with other monitoring projects to ensure 

compatibility of objectives, common methods and protocols. This coordination could be 

accomplished under the CBFWA proposal #35033.

ProjectID: 35019

Develop and Implement a Pilot Status and Trend Monitoring Program for Salmonids and their 

Habitat in the Wenatchee and Grande Ronde River Basins

Sponsor: NMFS-NWFSC

FY03 Request: $270,000 5YR Estimate: $2,350,000

CBFWA Adjusted FY03: $250,000 3YR: $1,250,000

Short Description: This proposal seeks to develop, as subbasin scale pilot programs, status and 

trend monitoring efforts for anadromous salmonids and their habitat in the upper Wenatchee and 

Grande Ronde River basins.

ISRP Final Comments: 

Fundable (qualified). Agree with CBFWA’s Urgent ranking. The sponsors adequately and 

carefully addressed the ISRP’s concerns relative to potential overlap with other proposed 

monitoring and evaluation programs. In addition, the responses to the ISRP’s concerns on 

individual technical issues were thoughtful, complete, and persuasive.

The response to our concerns indicated a refreshing willingness to cooperate in the difficult task 

of development of a comprehensive monitoring and evaluation program for the Columbia Basin 

and Subbasins. The ISRP recommends that this project be funded if the sponsors follow through 

with their commitment to cooperate under CBFWA’s umbrella proposal #35033. The sponsor 

agreed with the ISRP preliminary review comment that the CBFWA proposal #35033 contains 

the necessary collaborative components to implement a comprehensive monitoring program in 

the subbasins and the entire Columbia basin.

The ISRP agrees that proposals #35033 and #35019 (and by extension, parts of the other NMFS 

proposals #35016, #35020 and #35048) be somehow combined to provide a systemwide 

monitoring and evaluation project together with the many ongoing M&E efforts (e.g., StreamNet, 

coded wire tagging program, smolt monitoring by the FPC, the Idaho Production Studies, DART, 

ongoing M&E in the John Day Subbasin, etc., etc. etc.). The ISRP could not agree more with the 

statement that “The absolutely essential elements of 35033 that the other projects lack is the 

basinwide perspective, both in the collaborative representation of nearly all fisheries management 

agencies, as well as the inclusion of fishes other than anadromous salmonids. Ultimately, the 

most efficient manner for the Columbia River basin to approach a comprehensive monitoring 

program would be in the form of integrated aquatic ecosystem health assessment. Components of 

the above 5 projects, plus many ongoing monitoring programs, if coordinated within a single 

purpose, design, and data management and evaluation framework, could produce the ideal 

monitoring program for the basin’s aquatic natural resources.” We see no advantage to 
ISRP 2002-14 Final Mainstem and Systemwide

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fragmentation of the regions efforts to monitor and evaluate recovery efforts for anadromous and 

resident fishes.

ProjectID: 35020 

Regional Project Effectiveness Monitoring Program for Columbia River Basin Listed 

Anadromous Salmonids.

Sponsor: NMFS-NWFSC

FY03 Request: $475,000 5YR Estimate: $2,010,000

Short Description: This proposal seeks to coordinate the design and implementation of 

experimental monitoring projects aimed at determining the impact of specific habitat actions. As 

part of this effort, it will coordinate and implement 2-3 pilot projects.

ISRP Final Comments: 

Not fundable. Disagree with CBFWA’s Urgent ranking. The proposal lacks sufficient technical 

detail to allow scientific review and evaluation. This is a proposal to develop a proposal, rather 

than a proposal describing specific projects. The objectives of this project are worthwhile, but 

the proposal and the response lack sufficient technical detail to permit scientific evaluation. The 

need for the project, alone, does not justify funding. The proposal should contain specific 

objectives for each pilot project, detailed experimental designs, methods of data analysis and 

specific empirical methodologies for obtaining the data.

We note the overlap of the overall objectives of this proposal with those submitted by ESSA in 

their “innovative project proposal.” The approach proposed by ESSA is that of an observational 

study leading to comparison of watersheds or stream reaches by standard statistical methods, e.g., 

regression modeling techniques and other empirical methods. The ESSA approach le ads to 

standard, acceptable scientific inferences, however we grant that the approach does not lead to the 

same level of “cause and effect” relationships as true treatment-control experiments.

Even though it is important to include controls and create a true experimental design, we caution 

the sponsor on the difficulty of designing adequate paired or BACI (treatment-control) 

experiments on the scale indicated. It is difficult to find and maintain the number of replicates of 

treatment and control stream reaches necessary to carry out the design and analysis. Also, the 

presence of confounding factors introduces extreme variation in measured variables (e.g., in 

evaluation of the effects of additional large wood in streams, some of the streams may have 

livestock fenced out and others may not). The ISRP’s experience with projects like the Idaho 

Supplementation Study (ISS) lead us to believe that the fundamental elements of the design of the 

proposed pilot projects may not be feasible. In the ISS, study sponsors had extreme difficulty 

obtaining and maintaining treatment and control streams that can be captured in a rigorous 

experimental design. Similar logistical problems in the proposed pilot projects will likely limit 

conclusions that can be drawn.

The sponsors propose to work with other ongoing project managers to implement their pilot 

monitoring projects. This will require extensive regional buy-in and therefore to be successful, 

this project should be coordinated with other monitoring projects to ensure compatibility of 

objectives, common methods and protocols. This coordination could be accomplished under the 

CBFWA proposal #35033.

There are severe deficiencies with the present proposal to develop a proposal. However, the 

ISRP grants that if the objectives could be met, such a project would provide critical monitoring 

of habitat recovery efforts in the Columbia Basin. If the Council agrees to extend the period for 
ISRP 2002-14 Final Mainstem and Systemwide

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consideration of funding of this and perhaps other monitoring proposals (e.g., new data to be 

captured by StreamNet and the NMFS Proposal #35048, Tier I monitoring proposed by #35016, 

and Tier III monitoring proposed by #35020) then the ISRP could review the set at a later time.

ProjectID: 35017

Inventory and Synthesis of Physical Process Models and Methods to Supplement Habitat 

Conditions Analysis and Subbasin Planning

Sponsor: KWA and Golder

FY03 Request: $769,609 5YR Estimate: $1,730,082

Short Description: Engage earth scientists, civil/systems engineers, geomorphologists, 

hydrogeologists and others familiar with the science of physical processes. Conduct a synthesis 

inventory of tools and develop a Landform Library, database, web based app. and model. 

ISRP Final Comments: 

Not Fundable. Disagree with CBFWA’s Recommended Action. The proposal is inadequate and a 

response was not requested. This long rambling proposal did not provide adequate detail in the 

critical Section f. Proposal objectives, tasks and methods to allow review of methods (methods 

are too brief). In future proposals the proponents might consider reducing the level of effort and 

propose to produce a directory of and synthesis report containing protocols and recommendations 

for how and when physical process methods should be used. Proposals must include a 

monitoring and evaluation section. It is not appropriate for one of the most quantitative proposals 

to not have a quantitative monitoring and evaluation plan for success of the project.

The proponents propose to link the biological and physical worlds through cause and effect

processes and to develop an overarching “model” called the Physical Process Method (PPM) 

process. The project would provide input to the EDT process of evaluating aquatic habitat and 

predicting effects of habitat changes on anadromous fish populations. The ISRP is not convinced 

that a highly sophisticated mathematical approach in combination with EDT is appropriate at this 

time. The sub-models are available (and some were listed in the proposal) for many of the 

processes they want to link. Users may be better off to leave them unlinked and use them as 

needed, based on the combined expertise of several disciplines working together. An overarching 

Physical Processes Model may gain little not available from individual models for discrete 

processes. However, part of Phase 1, a directory of and synthesis report containing protocols and 

recommendations for use of individual physical process models in subbasin planning, may be 

useful. The ISRP agrees that a useful form for this inventory would be the style of presentation 

of protocols in the report “Inventory and Monitoring of Salmon Habitat in the Northwest: 

Directory and Synthesis of Protocols for Management/Research and Volunteers in Washington, 

Oregon, Idaho, Montana and British Columbia” by Johnson, et al. 2001. 

ProjectID: 35022

Habitat Mitigation Tracking System 

Sponsor: STEWARD AND ASSOCIATES

FY03 Request: $462,131 5YR Estimate: $1,372,107

Short Description: Assist BPA in meeting its habitat mitigation obligation and, if appropriate, 

receiving credit, as specified under RPAs 180 and 183 in the FCRPS Biological Opinion.

ISRP Final Comments: 

Fundable (qualified). Disagree with CBFWA’s Do Not Fund ranking. This proposal outlines 

work designed to ensure that mitigation projects make a positive, measurable contribution 

towards salmon recovery, that BPA receives credit for its efforts, and that additional mitigation 

opportunities and constraints are identified and communicated to fish and wildlife managers and 
ISRP 2002-14 Final Mainstem and Systemwide

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the public. The response is complete, adequately addressing ISRP review comments. However, 

we raise the same concern with this project that we have indicated for the RME program in terms 

of duplication and fragmentation of effort. An entirely new database system for habitat projects is 

being proposed. The ISRP agrees with CBFWA that there is extensive overlap with #35033 and 

that to be successful this project would have to have regional buy-in. The project contains good 

ideas that would enhance the scientific credibility of the monitoring data. If funded, this project 

should be coordinated with other monitoring projects to ensure compatibility of objectives, 

common methods and protocols. This coordination could be accomplished under the favorably 

reviewed CBFWA project #35033.

ProjectID: 35045

Modeling and Information Management System to Assess Effectiveness of Alternative Actions

Sponsor: PNNL

FY03 Request: $500,000 5YR Estimate: $1,500,000

ISRP Final Comments: 

Do not fund. Disagree with CBFWA’s Recommended Action ranking. This proposal is to 

develop a model and information system (MADIMS) to support the RME program by developing 

3 functional capabilities: 1) spatial and temporal scale changes in data, information and models; 

2) hypothesis testing; 3) information exploitation. The goal of building a complex model to allow 

alternative actions to be evaluated without experiments is laudable. The difficulty is in the details 

of building a model that is realistic enough to be useful, yet tractable for solution. Models may 

predict cause-effect relationships but to establish such relationships requires links to empirical 

data.

The ambitious goals of using a system to manage models and data to capture cause-effect 

relationships in the region seem to be unattainable. The proponents exhibit an expectation that 

models can establish cause and effect relationships. Furthermore, the proposed framework 

supports identifying and prioritizing future model developments raising a concern about how 

models will be selected for inclusion and how competing models be compared?

The response overall, while interesting in its description of the application of neural networks and 

fuzzy logic in information-poor environments, does not allay earlier concerns that the modeling 

framework to be developed would have “legs” in the region; i.e. be adopted and used in a way 

that will enhance understanding and knowledge. The response to questions about the budget fails 

to provide information as to its components and magnitude. Finally, every research project 

funded by the Council’s Fish and Wildlife Program must have an adequate monitoring and 

evaluation plan. 

ProjectID: 35050

UW Offsite Habitat and Fish Survival Effectiveness Monitoring

Sponsor: UW

FY03 Request: $177,048 5YR Estimate: $1,074,065

ISRP Final Comments: 

Do Not Fund; agree with CBFWA. The proposal is inadequate. The proposal is not clearly 

written, is not well-coordinated with action agencies and other proposed and ongoing monitoring 

programs within the basin, and it does not have enough methodological detail to provide a clear 

understanding of how the work will be done and what the products will be like. It isn’t clear from 

the regional perspective why this project should be the one to do the activities described or that 

the activities described are even appropriate or possible.
ISRP 2002-14 Final Mainstem and Systemwide

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Harvest

ProjectID: 200100700

Evaluate live capture selective harvest methods for commercial fisheries on the Columbia River 

2001-007-00.

Sponsor: ODFW and WDFW

FY03 Request: $579,039 5YR Estimate: $3,199,548

Combined Budget/CBFWA Adjusted FY03: $923,551 3YR: $2,680,653

Short Description: Evaluate the use of live capture commercial fishing gears and methods to 

capture hatchery-produced spring chinook and minimize catch of, and impact to, bycatch 

including ESA listed species.

Combined with: 

ProjectID: 35018

Evaluate recreational and commercial mark-selective fisheries.

Sponsor: WDFW; UI

FY03 Request: $797,420 5YR Estimate: $2,292,260

Short Description: Estimate post-release survival of steelhead bycatch in tangle net fishery. 

Evaluate post-release spawning success of spring chinook and steelhead. Measure hooking 

mortality in recreational salmon fisheries.

ISRP Final Comments:

Given the extensive comments initially provided on these proposals, and the anticipated concern 

with the ISRP final recommendations, the detailed preliminary ISRP comments on both proposals 

have been left in this final ISRP discussion.

ISRP Preliminary Comments 200100700: 

The development of selective fishing methods for commercial fishermen was supported by the 

ISRP in the FY2001 Innovative proposals and again by BPA in 2002. This proposal is a 

continuation of work begun under those proposals. The statement objectives of this proposal were 

(target species is spring Chinook and bi-catch issue is winter steelhead):

“Objective 1. - Determine effects of varying net mesh size on species-specific catch rates, 

condition at capture profiles, immediate-, short-, and moderate-term survival rates.

Objective 2. - Investigate the feasibility of using live capture fishing methods and gear in a full 

fleet commercial fishery.”

However, while this proposal is now substantially more expensive than previous version, it is not 

clear what, if anything, new would be gained by this research. One reviewer summarized the 

proposal as more socially motivated than scientifically driven. There are significant issues with 

the current proposal:

a) While the general background and broad results are summarized from past work, there are no 

actual data or analyses presented, nor are there any experimental designs presented for the 

proposed research. The way that past research results are presented is confusing and limits the 

understanding about what is known, what is unknown, and the quantitative results. There is also 

no sense of an integrating experimental design to this project.
ISRP 2002-14 Final Mainstem and Systemwide

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b) The results of the 2002 study of a commercial fishery are initially used as the basis for 

suggesting more research in 2003 since the bi-catch of winter steelhead was so large and 

inadequate data on mesh size were collected. However, in task 2, these same 2002 data are to be 

used in establishing the 2003 regulations but in the absence of any results from the 2002 research. 

How then does the 2003 commercial fishery “experiment” build on new information and how 

would the steelhead bi-catch issue be addressed? For example, what mesh size is proposed for the 

2003 fishery?

c) Given (b), what is new that would allow improved protection of steelhead in the commercial 

fishery? What allowable mortality of steelhead and unmarked spring Chinook is provided for the 

experimental commercial fishery and how will it be incorporated in the regulations and 

monitored? If the fishery is limited to 1-2% of the winter steelhead return, how would you known 

when such a limit was met?

d) A commercial fishery introduces an additional mortality that small test sampling does not 

involve, i.e., the potential for multiple encounters and cumulative mortality of the released fish. 

This issue was asked at the presentation but there did not seem to be a plan to addresses this in the 

proposed monitoring.

e) While the committee could infer the definitions of immediate, short-term, and moderate-term 

mortality; clearly, such fundamental terms should be defined in the proposal. Further, the ISRP 

has previously asked how delayed mortalities would be measured.

This proposal is driven by a need to find ways to increase gear selectivity in order to be able to 

continue in-river commercial fishing on hatchery fish while continuing to protect co-distributed 

weak stocks. The strategy is to find more selective harvest methods and effective live-release 

techniques. Although the proposal says it is to evaluate aspects of live capture commercial fishing 

gears and methods, the project is limited primarily to a single gear (tangle nets) methods of using 

and configuring that gear (drift length, mesh size, the use of recovery boxes for fish to be 

released) and the degree it can be used successfully by gillnet fishermen.

Reference is made to data from previous experiments not being adequate to address certain 

questions, but it is not clear whether the proposers have a plan to ensure that the proposed work 

does deliver data adequate to answer the questions. The structure of the experimental design does 

not seem to have been clearly thought about. What statistical analysis is proposed to determine 

significance of differences? What are the data requirements of this analysis? What sample design 

follows from the data requirements? How does the beach seine function as a control? It is not 

clear from the proposal the extent to which the proposed work is new versus a repetition of 

previously conducted experiments. Objective 2: Continue to investigate feasibility...creates the 

impression of an ongoing project that will never end.

Reference is made to enforcement and compliance – how does this fit with the full observer 

coverage on vessels? Is enforcement a post-project issue? Further, enforcement and compliance 

are fishermen behavior issues that the fishery should pay, or at least, contribute to. The 

development of these fishing techniques clearly are to the benefit of those fishers, have they been 

approached to monitor their fishery.

Why does this need to be a five-year project? A strong justification would be needed for 5 years! 

The ISRP clearly sees the merit in developing new fishing techniques given the number of factors 

limiting fisheries in the Columbia River. However, the provision for these fisheries must stand-up 

to technical review and compliance with ESA limits on protected stocks. Based on the material 

presented in this proposal we cannot make that assessment and cannot, at this time, conclude that 

this new proposal would provide a sound scientific basis for such an assessment.
ISRP 2002-14 Final Mainstem and Systemwide

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NOTE: Objective 1 of this study is very similar to the study proposed by WDFW (#35018), both 

use radio tagging of fish captured and released from experimental fishing but differ in the 

methods proposed to capture fish for control treatments. Objective 2 is specific to this proposal. 

It should not be necessary for the Council to consider two essentially identical research projects 

on this issue. The proponents should reconcile these two proposals before any further funding is 

provided, including their respective definitions of soak times.

ISRP Preliminary Comments 35018: 

This proposal is similar to proposal #200100700 (ODFW) and addresses incidental mortalities 

associated with mass-mark selective fisheries in the Columbia River. Fishery managers have 

implemented mark-selective fisheries in both the commercial and recreational sectors to preserve 

declining and listed salmonid populations while providing harvest on healthier stocks. In these 

fisheries, the marked fish (hatchery-origin) may be retained while the unmarked portion (which 

would include listed wild stocks) must be released. The assumption is that the survival of the 

released fish is high enough that they will contribute to rebuilding weak populations. The ODFW 

proposal considered mesh-size to use in tangle nets and evaluation of a “full fleet” commercial 

fishery on spring Chinook. 

The objectives of this WDFW proposal are: 

1) to estimate the survival of steelhead captured and released from a tangle net that would be 

suitable for harvesting spring chinook salmon;

2) to estimate the effect of capture and release from a tangle net on the condition and spawning 

success of spring chinook salmon and steelhead in the Kalama and Cowlitz river systems; and

3) to estimate the survival of spring chinook, coho and fall chinook captured and released in a 

mark selective recreational fishery conducted below Bonneville Dam.

The proposal would estimate these survival rates using a series of mark-recapture experiments 

over the next three years. 

Objective 1 is very similar to the study proposed by ODFW (radio tagging of fish captured and 

released from experimental fishing) except for differences in the methods proposed to capture 

fish for control treatments. Objective 2 and 3 are specific to this proposal. It should not be 

necessary for the Council to consider two essentially identical research projects on this issue. The 

proponents should reconcile these two proposals before any further funding is provided, including 

the respective definitions of soak times.

This proposal provides more background on past studies and presents some analyses. The 

reviewers particularly noted the difference between comparisons of short term survival estimates 

by gear type and the results of the long-term survival studies. Short term survival rates of 

released spring Chinook were quite comparable between three treatments but long-term survival 

of fish released from the conventional gillnet were only 50% of the control compared to 91% for 

the tangle nets (section 9b). Consequently, Objective 2 seems a logical extension of these longerterm studies and merits support. We also agree with the author’s comments concerning the 

variability in catch-and-release mortalities in recreational fisheries and would support the 

Objective 3, following consideration of our comments on the use of controls (below).

In Objective 1 and 3, the ISRP had concerns about the source of the control fish and whether they 

are comparable to the treatment fish. Objective 1 involves radio-tagging released fish caught in 

tangle nets fished downstream from Bonneville Dam. The proposed controls would be captured in 

the Bonneville fishway, radio-tagged, and released back to the fishway. While the authors 
ISRP 2002-14 Final Mainstem and Systemwide

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acknowledge concern about this comparison they do not offer a solution. We recommend this be 

considered further and offer the following suggestion: 

To improve the control, consider taking half the experimental fish up to the Bonneville Ladder 

and release half at the net site or half of the control fish downstream to be released. The Null 

hypothesis is no difference in survival of the two groups. If there is significant loss between the 

two groups, the assumption would be violated and the control procedure compromised.

Similarly, Objective 3 involves capture of control fish in the fishway but the tags proposed in this 

study are colored jaw tags, not radio-tags. This situation is more difficult to assess since any loss 

of tags released downstream from the fishery could be due to emigration from the study area, tag 

loss, or mortality. A response is required on both control issues.

There are two other specific points for consideration:

a) Task 1a states that for each steelhead captured, they will note the net type (mesh size) it was 

captured in and estimate the depth from the top of the net at which it was captured. Unless this 

depth definition is very general, quantification of this is variable and slow when handling a 

gillnet. A more direct means to investigate the depth of steelhead encounters would be to use 

variable depth “weed” lines, as conducted by CDFO, or to apply depth monitoring tags (the 

former is much cheaper). Weed lines allow the gillnet to be set at varying depths below the 

surface to investigate changes in the encounter rates with steelhead. Were these other methods 

considered and/or how will depth of capture in the gillnets be measured?

b) Hypothesis 1, Objective 2 appears to establish an acceptable difference in egg-to-fry survival 

of winter steelhead and spring chinook salmon released from tangle nets. What is the basis for 

“will not be greater than 10% different than that of fish not captured”. Is 10% based on other 

studies, measures of variation, etc.?

 

Two budget concerns are notable. First, Task 2c. Compare spawning success of tagged and 

untagged spring chinook salmon in Kalama River is contingent upon funding of proposal #35041. 

Secondly, the budget presented in section 8 should include more justification/explanation for the 

14 FTE and fringe rate applied, the very large travel budget ($163k per year), and the equipment 

to be purchased with the capital is very generally mentioned in section 9g but should be more 

explicitly stated.

ISRP Final Recommendations on the combined proposal:

Fundable in part, Objectives 1-3 moderate to high priority. During the response cycle, Project 

#200100700 and #35018 were combined under #200100700. The objectives combined from the 

WDFW 35018 are fundable (objectives 1 to 3 in the current). However, for the two objectives 

originally under 200100700, the research components of objective 4 are fundable, but objective 5 

is not fundable. Disagree with CBFWA’s Urgent recommendation and disagree with the funding 

reduction proposed by the sponsor.

The combination of the two proposals recognized the ISRP comments, and the WDFW 

researchers reconsidered a number of their proposals in light of those comments (e.g., the 

controls). Reviewers are not, however, as positive about the responses from ODFW. The two 

ODFW studies to be included were the studies of mesh size and net structure on immediate and 

short-term mortality (objective 4); and then the feasibility test of a mass-mark selective 

commercial fishery (objective 5). The latter was the focus of an extensive response received from 

Washington Trout, Oregon Trout, and the Native Fish Society (Gayeski response) that was 

considered by the ISRP during their review. While the ISRP still had a number of small 

comments on the WDFW proposals, the sponsors adequately replied to our questions. 
ISRP 2002-14 Final Mainstem and Systemwide

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The ISRP was not so certain for the ODFW responses, particularly about our concern for multiple 

encounters in the commercial fishery, or who should fund the enforcement of that fishery. 

Further, given the extensive comments in the Gayeski response (and presented to the Columbia 

River Compact meeting, July 25, 2002), the ISRP is strongly inclined to recommend proceeding 

with the research components of objective 4 only but defer any support for a commercial fishery 

trials (objective 5) until the requirements under the ESA are established, appropriate mesh sizes 

and associated mortality rates are determined, and all users agree on the fishery. It is clearly not 

the position of the ISRP to make recommendations about fisheries, but we can advise when the 

technical assumptions and analyses do not seem to support such an expansion of this research 

program. 

Numerous analytical questions remained concerning the 35018 response. That response did 

provide some preliminary analysis of the 2002, but not the data from 2000 and 2001 that were 

used in decisions to continue and expand the commercial trials. For 2002 data, marked and 

unmarked Chinook and steelhead are aggregated. Were there differences between marked and 

unmarked fish in condition at capture or in levels of delayed mortality? How was the sample size 

-- number and proportion to examine -- determined? (.7% Chinook total catch sampled for 

condition at capture; 3.7% steelhead). What were the proportions of marked and unmarked fish in 

the samples? How informative are the pooled data collected under different protocols? The focus 

in 2003 would be on 3.5” and 4.5” mesh. If mesh size and gear configuration are changed from 

the past fishery, how useful are the regressions estimated only on mesh size? How will the 

multivariate data for mesh size, hanging ration, etc be analyzed? What sample design does the 

project have to support the analysis? Mention is made of ANOVA techniques, but the question 

about sample design to support the ANOVA is not answered. Sample size for the monitoring 

program is also not addressed. 

The response describes the process for choosing mesh size for the 2003 fishery: this will not be 

based entirely on data from the project but will be decided by the two state fish and wildlife 

commissions. Decisions about ESA protected steelhead will be made to keep “impacts” within 

2%. Impacts to wild steelhead would be estimated using data from the project, but are wild and 

hatchery steelhead analyzed separately? Is the sampling rate of wild steelhead sufficient to 

calculate impacts? “Impact” isn’t defined, but presumably assumptions about post-release 

survival will influence their determination. Immediate and short-term mortality are defined; 

moderate term mortality is not. 

Overall, the response concerning #35018 does not provide confidence that the work will be 

conducted according to scientific standards. This ISRP was particularly surprised that comments 

were not submitted from the proponents of 35018 concerning the analyses presented in the 

Gayeski response and to the Columbia River Compact prior to the ISRP’s preliminary report.
ISRP 2002-14 Final Mainstem and Systemwide

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ProjectID: 35004

Harvest Model Development

Sponsor: UW

FY03 Request: $278,398 5YR Estimate: $794,416

ISRP Final Comments: 

Do Not Fund; agree with CBFWA. There is not clear Regional support or need for developing 

these new management models. In the absence of strong user-group agreement on a management 

model, investment in this work is very likely to be ineffective and potentially controversial. The 

ISRP does not necessarily disagree with duplication of models as new ideas/methods and 

verification of results could be important results. However, without clear regional support, the 

potential development of competing models is not a wise investment.

This proposal initially caused some confusion. The PI began his presentation by suggesting that 

the proposal should not be funded. His statement related to differences of opinion between the PI 

and the model users, i.e., the salmon management agencies and the Chinook Technical 

Committee (CTC) of the Pacific Salmon Commission. The proposal would not be effective if not 

supported by these key users. The proposal, however, looks generally acceptable and the 

development of new models to reflect new management needs for selective fisheries as expressed 

in the BiOp RPAs appears to be a reasonable suggestion. The proposal makes an effective 

argument for the benefit of models that will provide managers with information they need to 

minimize catch of protected stocks. The proposal explains how existing data will be used to 

model the new questions about harvest management.

The ISRP review questioned the rationale for producing two basically similar models, whom 

requested these new models when existing models are being used, clarification of the PI’s 

comments about the need for managers to be conversant in model codes, and whether the data 

existed to develop these new models (e.g., data on gear selectivity, incidental catch, and 

incidental catch mortality)?

The ISRP also stated that they were uncertain of the necessity for this proposal since the CTC is 

proceeding with modifications of their model and the basis of the request for a BiOp model is not 

presented. The ISRP noted a potential problem of alternative models and would not be 

supportive of this proposal unless the proponent can clearly demonstrate support of the user 

community for this proposal and whether a model for assessment of harvest alternatives would be 

useful in the Basin as an effective recovery tool.

The ISRP also provided a programmatic note: some connection to enforcement goals of the 

region should be coordinated with harvest management tools. Previous M&E (Peters et al., 1997) 

have shown enforcement is most effective when harvest rules are simple and easy to enforce.

The response was thorough to the questions raised by the reviewers, but we conclude that it 

confirms the PI’s comment that the proposal is not fundable due to lack of support from the user 

groups. If there is not clear support or need for developing new management models, then 

fundamentally the ISRP cannot support this proposal. The ISRP has again clarified that the CTC 

has already proceeded to further develop their model, that their work is supported by all 

management agencies involved, and that NMFS has begun work on a BiOp-oriented model. 

As a program note, however, the ISRP was not particularly concerned about a duplication of 

models if the work had regional support. The idea that two models are undesirable has two sides: 
ISRP 2002-14 Final Mainstem and Systemwide

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one is the cost efficiency and potential for conflicting answers, but the other is the role of 

independent development and verification. Ironically, the CTC model noted in this proposal has 

already been through the latter process during the development of the Coast model. As for the 

BiOp model, the author makes a valid point that one coast-wide model may not have the terminal 

fishery detail desired. There is a valid concern in this comment but the specification of the model 

and regional support must be clarified. Any terminal run model will, however, have to be 

associated with the CTC model since terminal returns are contingent on what occurs in the ocean 

fisheries addressed through the Pacific Salmon Commission and the CTC.

ProjectID: 35040

Determination of post-release survival of spring chinook salmon in a mark-selective sport fishery

Sponsor: PNNL

FY03 Request: $268,745 5YR Estimate: $844,795

Short Description: Determine the effects of capture and release by angling on the post-release 

survival of spring chinook salmon and steelhead. Different groups (one control, one treatment) 

will be radio-tagged and tracked through spawning.

ISRP Final Comments: 

Not fundable. Disagree with CBFWA’s Recommended Action ranking. Although interesting and 

relevant, the study is not fundable due primarily to inadequate statistical design considerations to 

answer the questions or test the hypotheses as presented. No statistical treatment to demonstrate 

that even the primary hypothesis was likely to have sufficient sample size was delivered after this 

question was raised. Sub-hypotheses about the population structure appear even less likely to be 

adequately sampled. The proposed methods also did not address the potential that “real-world” 

catch and release impacts from average sportfishers could be very different from those impacts 

imposed by experimental “sportfishers”.

Other concerns were: 

• The proposal did not address whether mortality might vary by timing of the run. It 

assumes that mortality will be constant over time. 

• Agencies impose unique gear requirements at different locations throughout the basin 

making it difficult if not impossible to extrapolate local results more broadly.

• Water temperature is a key component of stress mortality and will be different from the 

beginning to the end of the experiment and may vary from year to year. No experimental 

control for temperature and stress from angling were included in the design. 

ProjectID: 35053

Biological Feasibility of Reintroducing Fishwheels in the Columbia River 

Sponsor: STEWARD AND ASSOCIATES

FY03 Request: $236,260 5YR Estimate: $292,770

Short Description: This project will determine whether a fishwheel can be successfully 

constructed and operated as selective harvest and sampling gear.

ISRP Final Comments:

Not Fundable. Disagree with CBFWA’s Recommended Action ranking. As indicated in the 

preliminary comments and innovative review, the ISRP supports a test of fish wheel feasibility as 

a selective fishing tool. However, the response was technically inadequate and too many issues 

remain unresolved for this project to be funded. The literature review would add little to this 

project’s outputs and should instead be part of proposal preparation. The methods response is 
ISRP 2002-14 Final Mainstem and Systemwide

91

inadequate. The limited research design compares sites and day/night fishing, but does not 

compare fishwheels to other gears. There is no comment on estimating long-term survival of fish 

intercepted by the wheels. The catchability of the wheels could be estimated by using paired 

wheels, as conducted by LGL Ltd, but the response contains no comment on this option. The 

sponsors now recognize but will not address the issues of cooperative gear use and whether 

acceptable allocation mechanisms for fish wheel harvests can be developed. 

Coded Wire Tag Monitoring Program

ProjectID: 198201301

Coded-Wire Tag Recovery Program

Sponsor: PSMFC

FY03 Request: $2,989,812 5YR Estimate: $16,132,108

CBFWA Adjusted FY03: $2,672,053 3YR: $8,327,359

Short Description: Recovery of CWTs and PIT Tags from salmonids sampled in the 

commercial/sport fisheries (Col. R and Oregon ocean), spawning grounds and hatcheries. 

Provides critical stock identification information required to evaluate the status of Columbia 

Basin stocks.

ISRP Final Comments: 

Fundable. Agree with CBFWA’s Core Program recommendation, but strongly disagree with 

reducing the budget by eliminating funding for a statistical position. This position would not be 

redundant with what is provided by the oversight committees. This position could provide the 

appropriate focus for a statistical program of this magnitude and could result in cost savings.

The Coded-wire Tag Program is a huge program that annually conducts a large number of 

activities that are essential to the Basin, and the data provided has been widely utilized over many 

years. The current proposal requests $2.99 million from BPA (48.8% of total budget) based on 

inclusion of the new proposed activities. Matching funds for specific activities in the total 

program are received from 11 other sources (involving 26 activities)! Given the use and value of 

the CWT data to regional assessment and monitoring, it is appropriate that BPA funds make a 

significant contribution to the program. There are a lot of aspects of the CWT program that are of 

great interest to coastwide harvest management agencies including commitments in the Pacific 

Salmon Treaty (PST); researchers in fisheries, oceanography, and climate; and for monitoring of 

hatchery production, stock status and salmon recovery. 

In their response to the ISRP, the proponents made a very significant effort to address each of the 

ISRP’s comments. The response clarified the various sources of funding and corrected some 

values in their presentation. The response recognized the need for integration with project 

#35033 and stated a commitment to cooperate. Concerning the lack of progress on past 

recommendations, the program managers explained that they had not proceeded with staffing the 

statistical position or its technical review due to budget constraints (recent funding guidelines 

stated “no new tasks and funding increases limited to 3.4% cost of living”). Funding for a 

statistical position is included in the current proposal. Further, a flow chart to depict the program 

and costs was included in the response and a detailed table was provided that identified each task 

and funding source.

Concerning the array of tasks included in the proposal, a regional mark committee determined the 

rationale for existing tagging and recovery rates, and the tasks currently included in this proposal 
ISRP 2002-14 Final Mainstem and Systemwide

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were assigned following a NWPPC review (Sept. 1998). Concerning the technical review of the 

program previously requested by the ISRP, a regional response to RPA 174 has led to a 

“Comprehensive Marking Strategy Group” and a contract for technical evaluation of the CWT 

system (funded by BPA according to the response). This work is ongoing but should address 

many of the previous comments for the ISRP. Associated with any technical work were 

questions concerning the implementation of mass-marking of hatchery fish and the use of 

electronic detection of coded-wire tags in these fish. This issue is likely to become an 

increasingly important aspect of the CWT program and merits more careful evaluation.

Probably the least informative response concerned whether there were “critical bottlenecks or 

consistent problems in these other programs that limit the success of this program and utility of 

the data?” The ISRP suggests that the technical review that is currently being undertaken 

consider the need to establish a timetable of sampling and data needs to ensure that agencies meet 

these and/or a budget process is established that has flexibility to deal with variations in annual 

sampling or work needs. Issue of timely catch data is a common concern along the coast.

The remaining questions addressed smaller budget issues. These were adequately explained with 

the exception of the $20,000 for sampling SAFE fisheries in the lower Columbia River. The 

response noted that the predecessor fisheries were sampled at MRP expense and that there is 

some cooperative nature to the current sampling (note that WDFW and ODFW do pay for this 

differently). However, the ISRP question concerning whether these fisheries should pay for this 

sampling did not seem to stimulate a response.

The ISRP wishes to acknowledge the detailed response received. The committee will be 

interested in the results of the technical review and recommends that following completion a 

briefing be provided to the ISRP. The latter would ensure that the ISRP is aware of 

recommended actions or issues to be addressed, etc. If funded, this project should be coordinated 

with other monitoring projects to ensure compatibility of objectives, common methods and 

protocols. This coordination could be accomplished under the favorably reviewed CBFWA 

project #35033.
ISRP 2002-14 Final Mainstem and Systemwide

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ProjectID: 198201302

Annual Stock Assessment - Coded Wire Tag Program (ODFW)

Sponsor: ODFW

FY03 Request: $218,132 5YR Estimate: $1,157,132

CBFWA Adjusted FY03: $217,881 3YR: $673,881

Short Description: Apply coded-wire tags to production releases of coho and chinook salmon at 

ODFW Columbia Basin hatcheries for stock assessment of hatchery and wild salmon populations. 

Evaluate survival, contribution and stray rates of hatchery-reared salmon.

ProjectID: 198201304

Annual Stock Assessment - Coded Wire Tag Program (WDFW)

Sponsor: WDFW

FY03 Request: $334,412 5YR Estimate: $1,793,273

CBFWA Adjusted FY03: $319,137 3YR: $991,312

Short Description: Apply coded-wire tags to production of coho and chinook salmon at WDFW 

Columbia Basin hatcheries for stock assessment of hatchery and wild populations. Evaluate 

survival, contribution and stray rates of hatchery reared fish and compare to wild fish.

ProjectID: 198906500

Annual Stock Assessment - CWT (USFWS)

Sponsor: USFWS

FY03 Request: $119,268 5YR Estimate: $672,288

Short Description: Apply coded-wire tags to production groups of salmon at federal hatcheries 

not tagged by other programs. Prepare report on survival trends and distribution of anadromous 

stocks from 11 federal hatcheries for basin-wide stock assessment. 

ISRP Final Comments on CWT Tagging projects 198906500, 198201302, and 198201304: 

Fundable for the three proposals (198201302, 198201304, 198906500). Agree with CBFWA 

(Core Program). 

These proposals are tagging components of the Columbia Basin coded-wire tag program 

(proposal #198201301) submitted by USFWS, WDFW, and ODFW respectively. The program 

goal for these three proposals is to tag enough coho and chinook salmon from each hatchery to 

estimate survival and distribution in the ocean, in freshwater fisheries and escapement areas.

The proposals would provide continuation of a consistent time series of survival and distribution 

data to estimate abundance trends of selected hatchery stocks. In addition, the tagged hatchery 

stocks will be used to provide data relevant to the management of natural stocks, including many 

that are listed as threatened and endangered under the ESA.

The proposals are intended to create a comprehensive post-release monitoring program for 

Columbia Basin salmon hatcheries. The projects were initiated to address the problem of 

incomplete basinwide stock assessment that lacked representative tagging of hatchery production 

groups. The projects were also established to monitor and evaluate hatchery production in terms 

of adult returns. Each proposal provides an extensive description of the tagging program and how 

they related to regional programs and individual projects. The brief history of project 

performance focuses primarily on funding levels and numbers of fish tagged by each of these 

agency projects. Objectives and tasks are limited to tagging fish and the recovery of those tags. 
ISRP 2002-14 Final Mainstem and Systemwide

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The description of tagging methods appears to be adequate, but there is very little to be reviewed 

from a scientific basis.

Any assessment of the stocks to be tagged should be considered within an overall Basin context 

and priorities set based on ESU information needs or other specified agency objectives. These 

tagging programs should be considered with the CBFWA M&E proposal (35033) and overall use 

of CWT within the Columbia Basin. There may not, however, be any need to change the tagging 

of the stocks included in these proposals since the overall costs are relatively minor. These costs 

though could increase substantially if mass-mark selective fisheries impact these stocks. If the 

stocks that are currently being tagged under these proposals are subject to any mass-mark 

selective fishery, then there is a need to implement double -index tagging (doubles tagged 

allocated) as recommended by the Selective Fishery Evaluation Committee of the Pacific Salmon 

Treaty (See: Selective Fisheries Evaluation Committee. 2002. Investigation of methods to 

estimate mortalities of unmarked salmon in mark-selective fisheries through the use of double 

index tag groups. TCSFEC(02)-1. Pacific Salmon Commission, Vancouver, BC., available at 

www.psc.org/Pubs/sfec02-1.pgf). If these stocks are not included in the double -index tagging, 

then they must be associated with another DIT stock so that the difference between marked and 

unmarked mortality can be accounted for.

There are also small issues of differences in budgets that contract managers should review, but 

the only points for response to the ISRP were:

1) Are these tagging programs integrated with Regional tagging plans and how were these stocks 

selected for inclusion in these proposals?

2) Since double-index tagging is not included in these proposals, how is the additional mortality 

in mass-mark selective fisheries being accounted for?

3) An issue not addressed in any proposal is how tagging quality is assessed, and how 

consistently application standards are being met? For example, how long are tagged groups held 

to evaluate tag loss before release? Is any effort made to inspect tagging quality (placement of the 

CWT, quality of fin clip, etc.)?

The two responses reviewed were adequate and specifically addressed each of these three points.

The content in the responses was very similar between proposals but each indicated that double -

index tagging was included for each indicator stock, and that quality control measures were 

implemented in each tagging program. The responses could have been strengthened if the 

frequency of compliance with the quality control measures were reported. The issue of allocation 

of tags between stocks is addressed by a regional committee and will be re-considered by the 

Comprehensive Marking Strategy Group.

ProjectID: 35021

Purchase And Evaluation of Automated Marking and Tagging Systems (MATS)

Sponsor: ODFW

FY03 Request: $843,396 5YR Estimate: $2,564,454

Short Description: ODFW proposes to purchase and further evaluate equipment designed to 

mass mark hatchery reared juvenile fish. The technology for automated fin marking and/or 

Coded Wire Tagging has recently been advanced and new equipment is available.

ISRP Final Comments: 

Not Fundable, disagree with CBFWA’s “Recommended Action” This proposal is technically 

inadequate. The Oregon Department of Fish and Wildlife (ODFW) proposes to purchase and 
ISRP 2002-14 Final Mainstem and Systemwide

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further evaluate automated systems for mass marking hatchery reared juvenile salmon and 

steelhead. The proposal would purchase 3 systems over the next 3 years at an annual cost of 

nearly $900,000. 

However, the proposal provides no technical background to the mass-marking proposals or past 

evaluations of mass-marking, not even a description of what it is! There were essentially no 

methods presented only a short list of tasks. The presentation of this proposal contained much of 

the material that could have been incorporated into the proposal. For example, the oral 

presentation made clear that evaluation of the equipment has been adequate to justify 

incorporating the automated systems into current operations. Fundamentally, this proposal 

requests BPA to purchase 3 trailer marking systems that would save the State substantial funds 

each year. Unless there is an error in this simplistic logic, the State should purchase these 

systems and recover their costs over time. 

Conservation Enforcement

ISRP Final Comments on Conservation Enforcement Proposals: 35051, 35052, 

200005500, 20005600, and 195505500:

This group of responses addresses the review comments adequately. Responses include 

justifications of core staff and acknowledgement of how the size of a “core” changes as legal 

restrictions influence the demand for enforcement and funding changes affect the supply of 

enforcement. The responses provide thoughtful discussions of the interaction of enforcement and 

education as well as issues surrounding measuring the effectiveness of each. The enforcement 

proposals as a group and the responses provided to address ISRP review comments give a good 

impression of an evaluative approach to the performance of both enforcement and education. 

There is overlap in the responses of the individual proposals that derives from their coordination. 

The coordination among these proposals and responses is a positive factor that is likely to lead to 

collection of integrated data that will be useful for systemwide analysis of enforcement 

effectiveness.

ProjectID: 200005600

Protect Anadromous Salmonids in the Mainstem Corridor

Sponsor: CRITFE

FY03 Request: $455,787 5YR Estimate: $2,518,411

CBFWA Adjusted FY03: $435,787 3YR: $1,416,816

Short Description: Protect anadromous salmonids from illegal take throughout the Columbia 

Basin -- with emphasis on conservation of depleted stocks. CRITFE will concentrate protection 

in the Zone 6 migration corridor (Bonneville to McNary dams) and focus on adult spawners.

ISRP Final Comments:

Fundable, agree with CBFWA that its fundable - CBFWA “urgent”. This is a well-written 

proposal to increase the level and effectiveness of enforcement in Zone 6 tribal fishery and 

tributaries. Its relation to the Fish and Wildlife Program is clear. Objectives, tasks and methods 

are clearly defined. The proposal takes an evaluative approach to the components of enforcement. 

Last year the ISRP recommended that out-year funding be contingent on the provision of more 

complete information on the magnitude of the illegal harvest problem and the expected benefits to 
ISRP 2002-14 Final Mainstem and Systemwide

96

fish and wildlife from enhanced enforcement. The ISRP also asked for more detail on how 

efficiency and compliance will be improved and cross-zone enforcement coordinated through this 

project.

Statistics are provided on the increase in patrol effort enabled by the funding of last year’s 

project. The number of contacts and violations reported both increased. Seizures of illegal gear 

and fish increased. More detail is also provided on the effectiveness of the enforcement activities 

in terms of inputs, outputs, and outcomes. Patrol hours, enforcement contacts and arrests all 

increased between 1999 and 2000. The inclusion of specific monitoring criteria in tasks is very 

positive.

Law enforcement is an effective tool and component part of the region’s effort toward recovery 

of endangered species, and this proposal seems to demonstrate a potentially successful 

enforcement program. The incidence of violations appears very low with the current effort. 

Compliance rate for harvest in Zone 6 appears high, which is laudable. 

The response to ISRP concerns was thorough. A good discussion of the various possible 

definitions of “core” and “effective” is given, although despite the cited difficulty in deriving a 

single definition the response does in fact present one in the course of the discussion: to maximize 

the cost-effectiveness of BPA funded projects. A complete staffing analysis is provided. The 

responses provided more detail on the justification of budgets, indicating that BPA funding is not 

so much augmenting historic levels as replacing loss.

The ISRP agrees that the conservation enforcement data center has the potential to enhance the 

system-wide effectiveness and coordination of enforcement as well as to be a public education 

tool. 

The graphs of trends in performance measures are useful. However, some questions about 

determining optimal levels of enforcement remain: (1) how can we determine how much 

additional funding is needed, if any, when compliance is already near 100%; (2) what metrics can 

be used to show cause and effect results; (3) Loss of fall chinook via unaccounted losses over 

dams has not been resolved because experiments had not been designed to account for all 

potential sources of mortality (dam loss, harvest, tributary turn off, other sources of mortality). 

ProjectID: 200005500

Enhanced Conservation Enforcement for Fish & Wildlife, Watersheds of the Nez Perce

Sponsor: NPT-CE

FY03 Request: $511,210 5YR Estimate: $2,824,759

Short Description: Increase conservation law enforcement (CE) protection of fish, wildlife, 

critical habitats and other natural resources within watersheds managed by the Nez Perce Tribe. 

The CE program will be coordinated with all of the NPT resource enhancement projects.

ISRP Final Comments: 

Fundable, agree with CBFWA that its fundable - CBFWA “urgent”. This well written proposal 

is similar to those submitted by the Colville and Umatilla Tribes for increased and enhanced 

enforcement presence and education to protect threatened and endangered stocks and their 

habitat. It also takes an evaluative approach to the enforcement problem and builds in continual 

monitoring, evaluation, and adjustment. Project activities are evaluated in terms of inputs, 

outputs, and outcomes. 
ISRP 2002-14 Final Mainstem and Systemwide

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Last year the ISRP asked for a more complete background on the magnitude of the illegal harvest 

problem. This is provided in the form of identification of species of concern, trends in calls to 

enforcement and numbers of trespass. Pre and post funding of enhanced enforcement activities 

are compared in term of numbers of contacts and reports of violations, but with specific note that 

linking the changes in enforcement effort to biological outcomes will require more evaluation, to 

be done in subsequent years of the project.

Some of the responses overlap with those of 2000-056-00. For those specific to the Nez Perce 

proposal: the justification of core staff is adequate. The response acknowledges that public 

education and outreach plans have fallen victim to budget cuts and subsequent decisions to 

concentrate resources in enforcement presence, but it does provide an adequate plan for 

conducting public outreach and monitoring its effectiveness. The response does a good job 

outlining performance criteria and their associated metrics.

ProjectID: 195505500

Umatilla Tribal Fish & Wildlife Enforcement

Sponsor: CTUIR

FY03 Request: $178,073 (108,320) 5YR Estimate: $983,829

CBFWA Adjusted FY03: $108,320 3YR: $324,960

Short Description: Increase law enforcement (LE) protection to fish, wildlife, their critical 

habitats and other essential natural resources within watersheds managed by CTUIR. The 

program will be coordinated with all other resource enhancement projects of the tribe.

ISRP Final Comments:

Fundable, agree with CBFWA that its fundable - CBFWA “urgent”, but recommend funding 2 

FTEs. This response has overlap with other responses. The need for new enforcement officers 

seems especially acute for the CTUIR, where only .5 FTE is now dedicated for conservation 

enforcement. In its response, the project sponsor offered to reduce the FTE request from 2 to 1 

FTE. However, the ISRP concludes that because a Umatilla conservation enforcement presence is 

clearly needed the minimum request should be for 2 FTEs. The ISRP recommends against 

reducing the budget to fund only 1 FTE. Umatilla enforcement will use same performance 

criteria and metrics as the Nez Perce.

ProjectID: 35052

Conservation Enforcement to Enhance and Restore Fish & Wildlife Resources of the Upper 

Columbia River under Jurisdiction of the Colville Tribes 

Sponsor: CCT

FY03 Request: $245,636 5YR Estimate: $1,357,294

CBFWA Adjusted FY03: $241,221 3YR: $728,961

Short Description: Protect anadromous salmonids from illegal take throughout the Columbia 

Basin - with emphasis on conservation of depleted stocks. We will focus fish & critical habitat 

protection - Chief Joe tailrace, Wells Pool and Okanogan R. fisheries/water diversions.

ISRP Final Comments: 

Fundable, agree with CBFWA that its fundable - CBFWA “urgent”. This is a well-written 

proposal to add enforcement personnel to the Natural Resources Law Enforcement Division of 

the Colville Tribes. The additional enforcement presence would be directed toward protection of 

ESA listed stocks and their habitat through training, fishing compliance monitoring, water 

regulation enforcement, inter-agency coordination and public education. The proposal states that 
ISRP 2002-14 Final Mainstem and Systemwide

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the project aims not only to increase the level of enforcement in the 3 million acre jurisdiction but 

also to increase the efficiency of the enforcement through interagency coordination and to 

increase compliance through greater public awareness of threats to listed stocks. 

The potential benefits to fish and wildlife seem high, and the cost reasonable. A strength of the 

proposal is that it emphasizes expected outcomes throughout all tasks. 

An extensive technical background is provided, including a complete description of present and 

historical Colville Tribal fisheries that includes detail on the nature of the issues facing each 

fishery and a history of the development of the Tribes’ legal authority. Protection needs of critical 

habitat and water withdrawals are also detailed. The nature of the present enforcement effort is 

also described in detail. 

The description of monitoring as a component of the existing enforcement program is thoughtful 

and evaluative enough to inspire confidence that an appropriate M&E plan will be developed for 

the enhanced enforcement program in its first year, as the proposal indicates. The quarterly 

schedule for producing monitoring and evaluation reports will ensure continual assessment of 

effectiveness and allow scope for in-season changes. 

The rationale and significance to regional programs is clear. Objectives, tasks, and methods are 

adequately described. The proposed project had strong relationships with other enforcement and 

recovery projects that are implicit throughout but could be made more explicit in the 

“relationships to other projects” section.

 The response is adequate. The response provides a good justification of enforcement needs, 

accompanied by maps of the very large enforcement jurisdiction of the Colville Tribes. There is a 

lot of overlap with the other conservation responses. An enforcement plan is provided. 

ProjectID: 35051

Evaluate Feasibility of a System-wide Multi-Agency Fish, Wildlife & Habitat Conservation 

Enforcement Web-Based Data Center

Sponsor: Steven Vigg & Company

FY03 Request: $41,347 5YR Estimate: $41,347

Short Description: Develop a Columbia Basin web-based data center - within a GIS framework -

to facilitate conservation law enforcement data compilation & analysis and information sharing 

for enforcement programs, resource managers, and public information & education.

ISRP Final Comments: 

Fundable, agree with CBFWA that it is fundable - CBFWA “recommended action.” The 

existence of the web-based data center would probably increase the efficiency of interagency 

enforcement coordination and would most certainly improve the monitoring and evaluation 

within and across enforcement programs. The communication link could be valuable and could 

include an email alerting system. The response does a good job outlining the additional services 

that would be provided by the Conservation Enforcement Data Center. The description of the data 

to be collected is adequate. Typical law enforcement data will be enhanced by GPS coordinates, 

which should greatly increase their utility to monitoring and evaluation. The database could be 

layered with “at risk” habitat sites.

Hypotheses are presented to test the effectiveness of enforcement activities in reducing illegal 

take. The project will include in its feasibility assessment an evaluation of alternative approaches 
ISRP 2002-14 Final Mainstem and Systemwide

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to populate the database once established. The feasibility assessment done by this project has the

potential to lead to value-added to systemwide enforcement. 

The ISRP suggests that the data center explicitly consider in its feasibility assessment the 

limitations of the data to be collected, the use of the University of Idaho data to better partition

mortality, and mechanisms to provide continuing motivation for enforcement interests to 

participate in the data center.

Fish and Wildlife Program Coordination, Analysis, and 

Communication

ProjectID: 199800401

Electronic Fish and Wildlife Newsletter

Sponsor: Intermountain Communications

FY03 Request: $179,800 5YR Estimate: $993,511

Short Description: Delivers by e-mail (and posted on the web) to policymakers, Basin 

stakeholders, and general public a weekly electronic newsletter containing objective, timely, 

summary information about Columbia Basin fish and wildlife issues.

ISRP Final Comments: 

Fundable. A comparison with CBFWA is not applicable. CBFWA recommends funding through 

the Council’s budget rather than the FWP. Last year the ISRP noted that although the Columbia 

Basin Bulletin is widely distributed and respected as a quality product, the proposal to fund the 

effort was inadequate. This year the proposal corrects those weaknesses by establishing the 

programmatic need for information to enhance public involvement, coordination of recovery 

programs, and adaptive management. The proposal presents some summary statistics representing 

various components of CBB use, as an indicator of demand. Mechanisms of data collection are 

described, but details about quality control are lacking, as is M&E methodology to assess the 

impact of CBB. The oral presentation was very informative about quality control, and some of 

this information should be included in the proposal.

ProjectID: 35026

On-line Subbasin Planning/Watershed Newsletter

Sponsor: Intermountain Communications

FY03 Request: $115,200 5YR Estimate: $635,903

Short Description: Delivers on-line news, information about Columbia Basin subbasin planning 

and other locally based fish and wildlife restoration efforts to public and private stakeholders and 

interested parties.

ISRP Final Comments: 

Fundable. Disagree with CBFWA’s Recommended Action ranking, should be higher priority. 

The services to be provided by this newsletter go beyond public outreach activities. This proposal 

is to extend the approach used in the Columbia Basin Bulletin to subbasin watershed planning. 

The project will provide an on-line subbasin planning newsletter for the use of agencies, 

watershed councils, and the public in the 52 subbasins. It will build on the experience of the 

Columbia Basin Bulletin and share staff and equipment with the Bulletin.
ISRP 2002-14 Final Mainstem and Systemwide

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The proposed newsletter, as an information clearinghouse, is clearly relevant to regional 

programs, and, based on the performance of the Bulletin, is likely to provide a timely, useful 

communication product that will enhance information transfer and education within and among 

subbasins. The budget is extremely modest for an effort of this magnitude. By sharing facilities 

and personnel with the CBB the newsletter would be able to be a cost-effective way to add value 

to the subbasin planning process.

The oral presentation was informative about methods to be used to monitor and evaluate 

performance of the newsletter. The proposal would be strengthened by adding a description of 

these methods. 

Suggestions for the newsletter:

· include a calendar of upcoming events or be linked to the NPPC or other regional coordinating 

calendar 

· develop an appendix to the newsletter listing new publications (popular, gray literature and 

professional publications) on topics that are of interest to subbasin planning.

ProjectID: 199800800

Regional Forum Facilitation Services

Sponsor: NMFS

FY03 Request: $153,300 5YR Estimate: $766,500

CBFWA Adjusted FY03: $101,000 3YR: $303,000

Short Description: Provide professional facilitation services to enhance communication, assist in 

conflict resolution, and improve decision-making capabilities among participants in the NMFS 

Regional Forum Process, which addresses hydropower operations for salmon.

ISRP Final Comments: 

Fundable (qualified). Disagree with CBFWA’s Core Program ranking. The proposal is to 

continue to provide facilitation to the Regional Forum and all its teams. As with last year’s 

proposal, the proposal does not establish why such extensive facilitation services are needed, nor 

does it provide any evaluation of success from past facilitations. The ISRP has made similar 

review comments for the past three years. 

The ISRP did not ask for a response in its preliminary report and, because of the primarily 

administrative nature of the project, stated an ISRP recommendation was not applicable despite 

the concerns expressed in the paragraph above. After further discussion the ISRP emphasizes that 

this proposal continues to be presented without justification or evaluation. The Council should 

carefully evaluate the performance of this program and investigate the budget to determine 

whether this activity should not belong under the CBFWA budget. If funded, the sponsor should 

develop a monitoring and evaluation program during the project selection process. The proposal 

purports to be building human capital in negotiation skills and meeting skills: how well are they 

doing?
ISRP 2002-14 Final Mainstem and Systemwide

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ProjectID: 199803100

Implement Wy-Kan-Ush-Mi Wa-Kish-Wit Watershed Assessment and Restoration Plan Now

Sponsor: CRITFC

FY03 Request: $314,093 5YR Estimate: $1,735,562

Short Description: Provide effective and efficient watershed restoration through coordination 

and support of tribal restoration planning and project implementation consistent with the WyKan-Ush-Mi Wa-Kish-Wit and the NPPC Fish & Wildlife Program.

ISRP Final Comments: 

Fundable (qualified); an evaluation plan is needed. Agree with CBFWA’s Core Program ranking 

administratively. This proposal submitted for mid-term review is to continue the coordination of 

tribal watershed activities. A brief technical background is presented. The project is relevant to 

several regional programs and tied to other projects. A summary of project achievements to date 

is presented. Detail is presented on the types of activities conducted by the CRITFC Watershed 

Department. However, many of the earlier review comments made by the ISRP still apply. 

The previous review asked that more detail be provided on activities to be conducted by 

subcontractors. The response provides more detail on activities and outputs under this project, 

but is still missing the substantive point of ISRP comments. There are clearly many coordination 

activities being conducted under this project, but the project still lacks evaluative content. How do 

the project sponsors decide where activities should be focused, what is most important to do, 

what outcomes have resulted from the various activities, and which activities are making the 

greatest difference? 

Even with the BPA and NWPPC indirectly establishing required activities through frameworks 

such as the subbasin process – within which this project operates – limits on time and resources 

mean that priorities for activities must be set within the project. The project would be improved 

by taking a more targeted evaluative approach to coordination. New activities should be 

prioritized to reflect what has been learned about watershed restoration. A plan to monitor and 

evaluate project effectiveness is needed. How does the project determine whether coordination 

processes are effective? 

One of the project objectives should be to evaluate the effectiveness of the overall program 

portfolio. The project should set up formal evaluation processes to establish how it is making a 

difference and if it is achieving its objectives of enhancing the quality of CRITFC input and 

participation in regional processes. For example, instead of saying “informal feedback indicates 

readers have found the handbook a valuable resource ...” do a formal follow-up evaluation.

More detail is provided on the budget, but it is hard to determine the appropriateness of line 

amounts. If funded, a COTR should take a look at it.

The Council should consider whether adequate technical support service for subbasin planning is 

provided to all 13 tribes in the Basin. In addition to the tribes represented in CRITFC, there are 

nine other tribes that would benefit from such technical services. 
ISRP 2002-14 Final Mainstem and Systemwide

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ProjectID: 35056

Develop Human Resources Necessary to Exercise Co-Management Responsibilities 

Sponsor: CRITFC

FY03 Request: $405,024

5YR Estimate: $2,217,111

Short Description: This proposal will assist the tribes to develop human resources necessary to 

exercise their co-management responsibilities, effectively manage production facilities and 

implement ecologically sound artificial production programs.

ISRP Final Comments: 

Not fundable, disagree with CBFWA’s Recommended Action ranking. This proposal is to 

coordinate and implement artificial production training programs for members of the Warm 

Springs, Umatilla, and Nez Perce tribes. The Yakama Nation is submitting a separate proposal for 

training programs. Training includes community college courses, university courses, short 

courses and workshops.

The basic tasks of this project are to establish goals and objectives for a training program and to 

see that students are recruited and the program is implemented. The proposal is brief and does not 

provide detail as to how these tasks will be accomplished. While the ISRP supports the idea of 

providing educational opportunities in artificial production to tribal members, we question 

whether it is necessary to develop custom programs rather than using existing educational 

programs followed by internships at tribal hatcheries.

The budget is large and does not include explanation of its various components. The project is 

very heavy with administration costs. For example, the training coordinator is budgeted at more 

than $100k. What is the reason for this large a budget? The responsibilities of this person are to 

be a liaison between tribal education programs, colleges and universities, and CRITFC.

ProjectID: 198906201

Fish and Wildlife Program Implementation

Sponsor: CBFWA

FY03 Request: $2,217,415

5YR Estimate: $11,744,354

Short Description: Coordinate fish and wildlife participation in regional mitigation activities in 

implementation of the FWP, annual project and funding recommendations, rolling provincial 

review, subbasin planning, program amendment recommendations, etc.

ISRP Final Comments: 

Not applicable, not amenable to scientific review.
ISRP 2002-14 Final Mainstem and Systemwide

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ProjectID: 35054

Engaging the Public in Watershed Planning; A Tool Box for Cultural Shift

Sponsor: CBFWA

FY03 Request: $278,391 5YR Estimate: $941,612

Short Description: WATERSHED LEGACY will demonstrate the principles of participatory 

planning in partnership with Walla Walla and Tualatin communities in developing a set of faceto-face and web-based tools and processes for citizen engagement in watershed planning.

ISRP Final Comments: 

Not fundable, disagree with CBFWA’s Recommended Action ranking. This proposal seeks funds 

to develop strategies to increase public participation in watershed planning. It proposes to test the 

Watershed Legacy approach that it asserts has proven effective in Walla Walla. We agree with 

the proponent that the subbasin planning process, as it currently stands, is fragile. 

While the watershed legacy approach might be successful in facilitating grassroots support 

required by subbasin planning and to help gain local acceptance of solutions to the decline in fish 

and wildlife resources, the likelihood of success cannot be determined from the information 

presented in the proposal. The proposal is inadequate for scientific review. It takes the approach 

of selling the success of Watershed Legacy rather than evaluating its effectiveness. No 

explanation is provided about the measures of effectiveness or why further tests are necessary in a 

different subbasin. Methods to be used to accomplish the tasks are absent. E.g. how is a “needs 

analysis” done? What does it contain? How are the elements measured? 

The claim is made that lack of efficient tools and processes embedded in local organizational and 

communications infrastructure is the primary problem in watershed planning. However, the tasks 

and method to develop the tools and databases and to monitor and evaluate the project are 

underdeveloped. It is not clear that this group has a high probability of success in designing and 

implementing web-enhanced analytic and communication tools. Success probably depends on 

the enthusiasm and direct work of the proponent more than the tools they describe. The “bottomup” collection of disparate datasets is problematic in terms of generating data useful for analysis.

No analysis of present problems or past success is provided. Observation of “control groups” is 

supposed to provide a test of the strategy’s effectiveness, but no details on observational variables 

or metrics is provided. How is the participatory planning modeled? What are the ecological, 

economic, and social indicators?

The response did not instill any additional confidence that this project would be beneficial.

ProjectID: 35005

Independent Economic Analysis Board

Sponsor: NPPC

FY03 Request: $170,000 5YR Estimate: $870,000

Short Description: Analyze the cost effectiveness of fish and wildlife projects as requested by 

the Northwest Power Planning Council. Help fulfill NW Power Act requirements for cost 

effectiveness determination of Fish and Wildlife Program and projects

ISRP Final Comments: 

The proposal is a reasonable description of the background and context of he IEAB. The IEABs 

reviews have been of high quality and provide information useful to NPPC decisionmaking. 
ISRP 2002-14 Final Mainstem and Systemwide

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ProjectID: 199600500

Independent Scientific Advisory Board

Sponsor: CBFWF

FY03 Request: $681,876 5YR Estimate: $3,649,876

Sponsor Adjusted FY03: $550,277

Short Description: Provide independent scientific advice and recommendations on issues related 

to regional fish and wildlife recovery programs under the Northwest Power Act, the Endangered 

Species Act, and tribal treaties.

ISRP Final Comments:

Not applicable, conflict of interest.

ProjectID: 198907201

Independent Scientific Advisory Board Support

Sponsor: DOE/ORNL

FY03 Request: $100,027 5YR Estimate: $300,027

Short Description: Provide support through contract with DOE for Dr. Charles Coutant for the 

Independent Scientific Advisory Board (ISAB), for scientific advice to the NWPPC’s FWP, 

NMFS's ESA program, and the Columbia River Basin Indian Tribes fish and wildlife programs.

ISRP Final Comments:

Not applicable, conflict of interest.
ISRP 2002-14 Final Mainstem and Systemwide

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Index of Proposals by Project ID

ProjectID Page ProjectID Page ProjectID Page

30007 28 35037 47 198907201 104

30010 29 35038 57 198909600 35

35001 31 35039 47 198910700 70

35002 19 35040 90 199007700 20

35003 70 35041 48 199008000 64

35004 89 35042 12 199009300 42

35005 103 35043 13 199105100 70

35006 18 35044 13 199105500 36

35007 50 35045 83 199302900 66

35008 16 35046 26 199305600 38

35009 19 35047 68 199403300 62

35010 76 35048 76 199600500 104

35011 71 35049 42 199601900 75

35012 41 35050 83 199602000 63

35013 55 35051 98 199602100 54

35014 34 35052 97 199606700 40

35015 43 35053 90 199702400 21

35016 79 35054 103 199705900 10

35017 82 35055 31 199800401 99

35018 84 35056 102 199800800 100

35019 80 35057 53 199803100 101

35020 81 35058 60 199900301 50

35021 94 35059 15 200000700 43

35022 82 35060 45 200001700 33

35023 71 35061 15 200002900 16

35024 59 35062 54 200005200 17

35025 24 35063 45 200005500 96

35026 99 195505500 97 200005600 95

35027 44 198201301 91 200100300 65

35028 14 198201302 93 200100700 84

35029 49 198201304 93

35030 51 198331900 66

35031 65 198605000 11

35032 23 198712700 62

35033 78 198740100 46

35034 72 198810804 73

35035 32 198906201 102

35036 52 198906500 93

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