Independent Scientific Review Panel

for the Northwest Power Planning Council

851 SW 6th Avenue, Suite 1100 

Portland, Oregon 97204 

isrp@nwppc.org

Preliminary Review 

of 

Fiscal Year 2003 

Mainstem and Systemwide 

Proposals

ISRP 2002-13 

August 2, 2002
Review Team

ISRP

Charles C. Coutant 

Susan Hanna 

William Liss 

Lyman McDonald 

Brian Riddell 

William Smoker 

Richard Whitney 

Richard N. Williams

Peer Review Group

Richard Alldgredge 

John Pizzimenti 

Staff

Erik Merrill 
ISRP Preliminary Review of Fiscal Year 2003 

Mainstem and Systemwide Proposals 

Table of Contents 

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

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

Response Instructions..................................................................................... 2 

Recommendation Categories: Who Needs to Respond? ................................ 3 

ISRP Preliminary Comments and Recommendations on Each Proposal....... 5 

Wildlife ................................................................................................................... 5 

White Sturgeon ....................................................................................................... 6 

Lamprey ................................................................................................................ 12 

Bull Trout.............................................................................................................. 16 

Avian and Fish Predation on Juvenile Salmonids................................................. 17 

Estuary/Plume and Lower Columbia .................................................................... 25 

Artificial Production Related Projects.................................................................. 35 

Mainstem Habitat.................................................................................................. 66 

Water Quality: Gas Bubble, Temperature, and Contaminants ............................. 73 

Juvenile and Adult Fish Passage........................................................................... 82 

Data Management ............................................................................................... 100 

Monitoring and Evaluation: Systemwide and Habitat Action Effectiveness...... 111 

Harvest................................................................................................................ 124 

Coded Wire Tag Monitoring Program................................................................ 132 

Conservation Enforcement.................................................................................. 138 

Fish and Wildlife Program Coordination, Analysis, and Communication ......... 145

i 
ISRP 2002-13 Mainstem and Systemwide Preliminary Review 

Index of Mainstem and Systemwide Proposals by Project ID 

ProjectID Title Sponsor FY03 Request 5YR Estimate Response

Needed

Page 

35001 Habitat Monitoring and Restoration 

Program for the Lower Columbia 

River and Columbia River Estuary 

LCREP $220,000 $1,720,000 No, Fundable 31

35002 Determine origin, movements and

relative abundance of bull trout in

Bonneville Reservoir. 

WDFW, YN $379,601 $1,525,101 No, Fundable 

(Qualified) 

16 

35003 Vitality based studies of Delayed

Mortality 

UW $207,180 $1,060,638 Yes 96

35004 Harvest Model Development UW $278,398 $794,416 No, Not

Fundable (but

response 

welcome) 

127 

35005 Independent Economic Analysis

Board

NPPC $170,000 $870,000 NA 149

35006 Use of Mainstem Habitats by Juvenile

Pacific Lamprey (Lampetra tridentata)

PNNL $100,985 $333,366 Yes 15

35007 Evaluate Restoration Potential of 

Snake River Fall Chinook Salmon

Spawning Habitat 

PNNL $315,000 $1,145,000 No, Fundable 67

35008 Systemwide Lamprey Program

Coordinator 

USGS, CRRL $111,370 $496,774 Yes 12

35009 Evaluate Status of Pacific Lamprey in 

the Willamette River Subbasin

ODFW $129,991 $977,991 Yes 16

35010 An Interactive Biodiversity

Information System for the Columbia 

River Basin

NW Habitat 

Institute 

$432,950 $3,079,050 Yes 105

35011 The Floating Net Pen Transportation 

System Pilot Project 

Columbia 

Basin Fishery 

Restoration 

L.L.C. 

$3,291,275 $10,196,875 No, Not

Fundable 

97 

35012 Spatial scales of homing and the 

efficacy of hatchery supplementation 

of wild populations 

NMFS $370,100 $1,545,100 Yes 47

35013 Species- and site-specific impacts of 

gas supersaturation on aquatic animals

CRRL $494,249 $2,731,036 Yes 74

35014 Measurement of Quantitative Genetic 

Variation Among Columbia River 

Basin Chinook Propagation Programs

CRITFC $313,855 $914,623 Yes 37

ii 
ISRP 2002-13 Mainstem and Systemwide Preliminary Review 

ProjectID Title Sponsor FY03 Request 5YR Estimate Response

Needed

Page 

35015 Replicated stream system for the 

evaluation of hatchery and wild

juvenile salmonid interaction and 

development of innovative culture 

technologies 

UI/CRITFC $300,114 $2,392,840 Yes 52

35016 A Pilot Study to Test Links Between

Land Use / Land Cover Tier 1 

Monitoring Data and Tier 2 and 3 

Monitoring Data 

NWFSC $436,000 $2,582,000 No, Not

Fundable 

113 

35017 Inventory and Synthesis of Physical

Process Models and Methods to

Supplement Habitat Conditions

Analysis and Subbasin Planning

KWA and

Golder 

$769,609 $1,730,082 No, Not

Fundable 

118 

35018 Evaluate recreational and commercial 

mark-selective fisheries. 

WDFW; UI $797,420 $2,292,260 Yes 126

35019 Develop and Implement a Pilot Status

and Trend Monitoring Program for 

Salmonids and their Habitat in the 

Wenatchee and Grande Ronde River 

Basins

NMFSNWFSC $270,000 $2,350,000 Yes 114

35020 Regional Project Effectiveness 

Monitoring Program for Columbia 

River Basin Listed Anadromous 

Salmonids. 

NMFSNWFSC $475,000 $2,010,000 Yes 116

35021 Purchase And Evaluation of

Automated Marking and Tagging 

Systems (MATS) 

ODFW $843,396 $2,564,454 No, Not

Fundable 

138 

35022 Habitat Mitigation Tracking System Steward & 

Assoc. 

$462,131 $1,372,107 Yes 120

35023 Establish Relationship between Fish

Passage Survival and Turbine

Operating Efficiency 

Norman-deau 

Assoc. 

$3,887,500 $11,932,468 No, Not

Fundable 

97 

35024 Evaluating the sublethal impacts of

current use pesticides on the 

environmental health of salmonids in

the Columbia River Basin. 

NMFS $364,105 $1,053,975 Yes 78

35025 Optimization of FCRPS Impacts on

Juvenile Salmonids: Restoration of

Lower-Estuary and Plume Habitats 

OHSU $435,192 $1,206,325 Yes 25

35026 On-line Subbasin Planning/Watershed

Newsletter 

Intermountain 

Comm. 

$115,200 $635,903 No, Fundable 145

35027 Evaluation of Two Captive Rearing 

Methods for Assisting with Recovery 

of Naturally Spawning Populations of

Steelhead and Coho Salmon 

USFWS $472,941 $2,046,091 Yes 54

iii 
ISRP 2002-13 Mainstem and Systemwide Preliminary Review 

ProjectID Title Sponsor FY03 Request 5YR Estimate Response

Needed

Page 

35028 Evaluate White Sturgeon Nutritional

Needs & Contaminant Effects 

Influenced by the Hydroelectric 

System

PSU $456,241 $1,064,326 Yes 10

35029 Transfer IHN virus genetic strain

typing technology to fish health

managers 

WFRC $116,479 $470,486 Yes 65

35030 Evaluate potential to enhance 

spawning of summer/fall chinook 

salmon in the tailrace of Chief Joseph 

Dam, Columbia River

PNNL and 

CCT 

$134,220 $539,984 Yes 68

35031 Tagging Study Technical Committee BPA $150,000 $850,000 No, Not 

Fundable 

88 

35032 Assess the Feasibility of Reducing

Predation on Juvenile Salmonids in

the Columbia River Through 

Operation of the Hydropower System

USGS,

CRRL; 

ODFW

$509,671 $2,394,540 Yes 23

35033 Collaborative, Systemwide 

Monitoring and Evaluation Program.

CBFWA $998,763 $2,996,293 Yes 111

35034 Fish Behavioral Guidance Through

Water Velocity Modification PHASE 

ONE 

Natural 

Solutions

$285,020 $1,104,596 Yes 99

35035 Incorporating Pit Tag Technology to

Evaluate and Monitor the 

Reintroduction Effort for Anadromous 

Salmonids in the Upper Cowlitz

Watershed 

WDFW $203,740 $619,182 Yes 33

35036 Identify the mechanisms of stranding

of juvenile fall chinook salmon in the 

Hanford Reach

USGSCRRL; 

USFWS 

$278,132 $786,000 Yes 69

35037 Measuring the potential for 

domestication selection of spawn

timing in chinook captive and 

supplementation programs;

implications for recovery. 

UW and

NMFS 

$129,498 $718,893 Yes 61

35038 Develop Computational Fluid

Dynamics Model to Predict Total 

Dissolved Gas Below Spillways 

ENSR $604,998 $604,998 Yes 76

35039 The influence of hatcheries and their

products on the health and physiology

of naturally rearing fish

USGS, CRRL $303,448 $2,375,918 Yes 60

35040 Determination of post-release survival 

of spring chinook salmon in a markselective sport fishery 

PNNL $268,745 $844,795 Yes 129

iv 
ISRP 2002-13 Mainstem and Systemwide Preliminary Review 

ProjectID Title Sponsor FY03 Request 5YR Estimate Response

Needed

Page 

35041 Monitoring the reproductive success 

of naturally spawning hatchery and

natural spring chinook salmon in the 

Wenatchee, Tucannon, and Kalama

Rivers 

WDFW, 

NMFS 

$1,079,140 $5,619,585 Yes 63

35042 Evaluate the Effects of Prey 

Availability on Recruitment of White 

Sturgeon in the Columbia River 

USGS, CRRL $248,445 $1,295,445 No, Fundable 7

35043 Monitoring and Models for Adaptive

Management of White Sturgeon 

USGS, CRRL $176,000 $626,000 No, Fundable 8

35044 Determine Effects of Contaminants on

White Sturgeon Reproduction and

Parental Transfer of Contaminants to 

Embryos in the Columbia River Basin

OSU $652,376 $1,755,005 Yes 8

35045 Modeling and Information 

Management System to Assess

Effectiveness of Alternative Actions

PNNL $500,000 $1,500,000 Yes 122

35046 Estimate juvenile salmon residence in

the Columbia River Plume using

micro-acoustic transmitters. 

NMFS $2,595,600 $17,172,100 Yes 27

35047 Evaluate Delayed (Extra) Mortality

Associated with Passage of Yearling 

Chinook Salmon Smolts through 

Snake River Dams

NMFS $1,083,900 $4,946,100 Yes 93

35048 NWFSC Salmon Data Management, 

Analysis, and Access for Research 

Monitoring and Evaluation Programs

NMFSNWFSC $763,150 $3,463,150 Yes 107

35049 A multiscale evaluation of steelhead

supplementation in the West Fork

Elochoman River 

NMFS $683,324 $3,278,533 Yes 49

35050 UW Offsite Habitat and Fish Survival 

Effectiveness Monitoring

UW $177,048 $1,074,065 No, Not

Fundable 

122 

35051 Evaluate Feasibility of a System-wide 

Multi-Agency Fish, Wildlife & 

Habitat Conservation Enforcement 

Web-Based Data Center 

Steven Vigg 

& Company 

$41,347 $41,347 Yes 143

35052 Conservation Enforcement to Enhance

and Restore Fish & Wildlife 

Resources of the Upper Columbia 

River under Jurisdiction of the 

Colville Tribes 

CCT $245,636 $1,357,294 Yes 142

v 
ISRP 2002-13 Mainstem and Systemwide Preliminary Review 

ProjectID Title Sponsor FY03 Request 5YR Estimate Response

Needed

Page 

35053 Biological Feasibility of

Reintroducing Fishwheels in the

Columbia River System [change

data] 

Steward & 

Assoc. 

$236,260 $292,770 Yes 131

35054 Engaging the Public in Watershed

Planning; A Tool Box for Cultural

Shift 

CBFWA $278,391 $941,612 No, Not

Fundable 

148 

35055 Role of Bacteria as Indicator 

Organisms for Watershed Assessment 

and in Determining Fish Pathogen

Relationships with Fauna of

Abernathy Creek

USFWS $76,000 $196,600 Yes 31

35056 Develop Human Resources Necessary

to Exercise Co-Management 

Responsibilities 

CRITFC $405,024 $2,217,111 No, Not

Fundable 

147 

35057 Habitat Condition and Restoration 

Potential of Columbia River Flood

Plains: A Critical, Missing Element 

of Fisheries Recovery Science and 

Policy 

UM $1,200,000 $4,692,124 Yes 71

35058 Evaluation of food availability and 

juvenile salmonid growth rates under 

differing thermal and sediment

regimes. 

CRITFC $218,885 $672,409 No, Not

Fundable 

80 

35059 Rapid Detection of White Sturgeon

Iridovirus in Spawning Fluids, Eggs

and Juvenile Tissues of White

Sturgeon 

USFWS $97,452 $191,306 No, Not

Fundable 

11 

35060 Instream evaluation of populations,

migration, individual adult return and 

wild-hatchery interactions of naturally 

produced salmonids 

USFWS $229,606 $964,645 No, Fundable 57

35061 Prophylactic Treatments for White 

Sturgeon Infected with the White 

Sturgeon Iridovirus (WSIV) 

USFWS $69,681 $127,661 No, Not

Fundable 

12 

35062 Impacts of Flow Regulation on

Riparian Cottonwood Ecosystems in

the Columbia River Basin

University of 

Idaho 

$382,024 $1,043,918 Yes 71

35063 Compare Bacterial Fish Pathogen 

Populations in Hatchery Water and in

Adjacent Creek Water and Evaluate

Possibile Disease Transfer Between 

Them. 

USFWS $71,678 $106,165 No, Not

Fundable 

58 

195505500 Umatilla Tribal Fish & Wildlife 

Enforcement 

CTUIR $178,073 $983,829 Yes 142

198201301 Coded-Wire Tag Recovery Program PSMFC $2,989,812 $16,132,108 Yes 132

vi 
ISRP 2002-13 Mainstem and Systemwide Preliminary Review 

ProjectID Title Sponsor FY03 Request 5YR Estimate Response

Needed

Page 

198201302 Annual Stock Assessment - Coded

Wire Tag Program (ODFW)

ODFW $218,132 $1,157,132 Yes 136

198201304 Annual Stock Assessment - Coded

Wire Tag Program (WDFW)

WDFW $334,412 $1,793,273 Yes 137

198331900 New Marking and Monitoring

Techniques for Fish 

NMFS $878,000 $2,886,900 Yes 89

198605000 White Sturgeon Mitigation and 

Restoration in the Columbia and 

Snake Rivers Upstream from

Bonneville Dam 

ODFW $2,041,140 $10,248,476 Yes 6

198712700 Smolt Monitoring by Federal and

Non-Federal Agencies 

PSMFC $2,481,100 $13,493,183 Yes 84

198740100 Assessment of Smolt Condition:

Biological and Environmental

Interactions 

USGS, CRRL $256,000 $1,781,050 Yes 59

198810804 StreamNet PSMFC $4,211,435 $24,027,308 Yes 100

198906201 Fish and Wildlife Program

Implementation 

CBFWA $2,217,415 $11,744,354 NA 148

198906500 Annual Stock Assessment - CWT 

(USFWS) 

USFWS $119,268 $672,288 Yes 137

198907201 Independent Scientific Advisory

Board Support

DOE/ ORNL $100,027 $300,027 NA 150

198909600 Monitor and evaluate genetic 

characteristics of supplemented

salmon and steelhead 

NMFS $593,900 $2,548,570 No, Fundable 39

198910700 Statistical Support for Salmonid

Survival Studies 

UW $265,850 $1,409,650 Yes 94

199007700 Northern Pikeminnow Management

Program

PSMFC $2,957,438 $16,520,975 Yes 17

199008000 Columbia Basin Pit Tag Information

System

PSMFC $2,532,711 $13,717,975 Yes 87

199009300 Genetic Analysis of Oncorhynchus

nerka (modified to include chinook 

salmon) 

U of I $126,436 $518,756 Yes 51

199105100 Monitoring and Evaluation Statistical

Support

UW $394,655 $2,137,255 Yes 95

199105500 Natural Rearing Enhancement 

Systems (NATURES) 

NMFS $1,158,969 $5,711,234 Yes 41

199302900 Estimate Survival for the Passage of

Juvenile Salmonids Through Dams

and Reservoirs of the Lower Snake 

and Columbia Rivers 

NMFS $1,884,200 $9,192,200 No, Fundable 90

199305600 Assessment of Captive Broodstock 

Technologies 

NMFS $1,498,981 $8,282,813 Yes 44

199403300 The Fish Passage Center PSMFC $1,316,323 $7,257,504 Yes 82

199600500 Independent Scientific Advisory

Board

CBFWF $681,876 $3,649,876 NA 149

199601900 Second-Tier Database Support UW $275,111 $1,379,983 Yes 104

vii 
ISRP 2002-13 Mainstem and Systemwide Preliminary Review 

ProjectID Title Sponsor FY03 Request 5YR Estimate Response

Needed

Page 

199602000 Comparative Survival Rate Study

(CSS) of Hatchery Pit Tagged

Chinook & Comparative Survival 

Study Oversight Committee 

PSMFC &

CBFWF

$1,742,776 $9,497,683 Yes 85

199602100 Gas bubble disease research and 

monitoring of juvenile salmonids 

USGS, CRRL $16,885 $94,079 Yes 73

199606700 Manchester Spring Chinook

Broodstock Project

NMFS $950,000 $4,828,825 No, Fundable 46

199702400 Avian Predation on Juvenile

Salmonids in the Lower Columbia 

River 

OSU/ USGS/ 

CRITFC/ 

RTR 

$713,000 $3,688,000 Yes 21

199705900 Securing Habitat Mitigation Sites - 

Oregon 

Oregon

Wildlife 

Caucus 

$4,043,000 $23,000,731 No, Fundable 

(Qualified) 

5 

199800401 Electronic Fish and Wildlife 

Newsletter 

Intermountain 

Comm. 

$179,800 $993,511 No, Fundable 145

199800800 Regional Forum Facilitation Services NMFS $153,300 $766,500 NA 146

199803100 Implement Wy-Kan-Ush-Mi WaKish-Wit Watershed Assessment and 

Restoration Plan Now 

CRITFC $314,093 $1,735,562 Yes 146

199900301 Evaluate Spawning of Fall Chinook 

and Chum Salmon Just Below the 

Four Lowermost Mainstem Dams

PSMFC, 

ODFW, 

USFWS,

PNNL 

$1,012,405 $5,594,177 Yes 66

200000700 Infrastructure to Complete FDA 

Registration of Erythromycin

UI-CNR $166,419 $514,419 No, Fundable 53

200001700 Kelt Reconditioning: A Research

Project to Enhance Iteroparity 

in Columbia Basin Steelhead

(Oncorhynchus mykiss) 

CRITFC $633,292 $1,957,441 Yes 35

200002900 Identification and thermal 

requirements of larval Pacific, river, 

and western brook lampreys 

USGS, CRRL $186,945 $261,945 Yes 13

200005200 Upstream migration of Pacific 

lampreys in the John Day River:

behavior, timing, and habitat use 

USGS, CRRL $250,000 $665,000 No, Fundable 14

200005500 Enhanced Conservation Enforcement 

for Fish & Wildlife, Watersheds of the 

Nez Perce 

NPT-CE $511,210 $2,824,759 Yes 141

200005600 Protect Anadromous Salmonids in the

Mainstem Corridor 

CRITFE $455,787 $2,518,411 Yes 139

200100300 ISO Adult Pit Interrogation System

Installations

PSMFC $1,972,106 $4,529,506 Yes 87

200100700 Evaluate live capture selective harvest 

methods for commercial fisheries on

the Columbia River 2001-007-00.

ODFW and 

WDFW

$579,039 $3,199,548 Yes 124

TOTAL REQUESTED $75,984,805 $354,720,247

viii 
ISRP 2002-13 Mainstem and Systemwide Preliminary Review 

ISRP Preliminary Review of Fiscal Year 2003 

Mainstem and Systemwide Proposals 

Introduction 

This report provides preliminary 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. 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. This preliminary report provides project 

sponsors and the public an opportunity to respond to ISRP concerns before the ISRP makes its 

final recommendation to the Council on October 23, 2002. This report also provides information 

to the Columbia Basin Fish and Wildlife Authority (CBFWA) for its use in project prioritization 

and the National Marine Fisheries Service (NMFS) and the Action Agencies’ (U.S. Army Corps 

of Engineers, U.S. Bureau of Reclamation, and the Bonneville Power Administration) Research, 

Monitoring and Evaluation Group in its project review and potential revision efforts. 

The review process to develop these preliminary recommendations and comments included 

several elements. Three or more ISRP reviewers were assigned to review each proposal. During 

the week of July 15th 2002, proponents of each proposal 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 

recommendations and comments on each proposal. These comments, with some general 

comments on sets of proposals, are provided below and are arranged by topic area. 

Importantly, the Bonneville Power Administration (BPA), in coordination with the National 

Marine Fisheries Service and the Council, added a new review element to the rolling review 

process for the Mainstem and Systemwide. This revised process includes a front-end projects 

review by the Research, Monitoring, and Evaluation (RME) group, comprised of scientists from

the Action Agencies and NMFS. For the solicitation, special emphasis was placed on requesting 

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 is 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 efforts. This process is intended to aid in the

development, selection, and funding of a suite of integrated projects that will meet the intent of 

these BiOp RPA actions in the most effective, economic way possible. 

For its review, 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 that describe how well the proposed project would 

meet the RME requirements of the BiOp. Some of the comments identify shortcomings in the 

proposal relative to BiOp requirements and/or how the proposals might be modified 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 are included in this report with 

1 
ISRP 2002-13 Mainstem and Systemwide Preliminary Review 

the relevant proposal following the ISRP comments. See the RME group comments at: 

www.cbfwa.org/files/province/systemwide/RME%20Proposal%20Comments%207-19-jrg.pdf) 

Among initial concerns with this approach was 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 this preliminary report, the ISRP remarks on the RME group 

comments are provided with the 43 projects the RME group commented on. For the most part, 

the ISRP and RME group comments are consistent or address different criteria and are not in 

disagreement. 

Unlike most ISRP rolling review reports, this preliminary report does not include a programmatic 

section with identification of general issues that have systemwide implications; however, the final 

report will likely include a programmatic section bringing mainstem and systemwide issues into 

the set of issues discussed in recent ISRP provincial reviews (see

www.nwcouncil.org/library/isrp/isrp2002-11.htm). The ISRP is especially interested in providing 

feedback on this first round of rolling reviews and the future review process. In addition, the 

ISRP intends to update its previous comments on efforts to establish regional research, 

monitoring, and evaluation programs and protocols. 

Response Instructions 

This preliminary report marks the completion of the first step in the project selection process. As 

stated above, project proponents and the public have the opportunity to respond to this report. 

Responses should focus on the technical comments, answer all review questions, and clarify

uncertain information. Responses should be formatted to address ISRP comments point by point, 

clearly identifying or repeating each concern/question and providing a response. In addition, 

project sponsors should provide their responses to the RME group comments and describe 

changes or planned changes to their project resulting from interactions with the RME group. 

The title and project number of the proposal should be displayed prominently on the front page of 

the response. Electronic documents should be named using the project ID number; e.g. “350--

response.doc” and email messages should contain the project ID number in the subject line. 

Important: If the response includes any change in the budget, the project sponsors must resubmit 

Part I of the proposal form with a revised budget section. 

Responses and comments must be received at the Northwest Power Planning Council no later 

than 5 p.m., August 23, 2002. Please email responses and comments to jhertz@nwppc.org. 

Attachments should be in Microsoft Word or Excel (for tables). 

If email is not available, please mail the response and diskette/CD to: 

Northwest Power Planning Council 

Attention: Judi Hertz 

Response to ISRP 

851 SW 6th Avenue, Suite 1100 

Portland, OR 97204 

The Council staff will verify that responses were received and successfully downloaded via 

email. If you have any questions regarding the response process or ISRP comments please contact 

Erik Merrill at the Northwest Power Planning Council at (503) 222-5161 or 1-800-452-5161, or 

2 
ISRP 2002-13 Mainstem and Systemwide Preliminary Review 

by email: emerrill@nwppc.org. For RME group comments, sponsors should contact Chris 

Jordan, NMFS, Chris.Jordan@NOAA.gov. If you need assistance incorporating graphs or maps 

in your response, please contact Eric Schrepel at the Council or by email: eschrepel@nwppc.org. 

Concurrently, CBFWA, with the ISRP and RME Group’s technical reviews in hand, will generate 

a list of projects recommended for funding and finalize the program summaries as part of its draft 

annual implementation work plan. The work plan is scheduled for release October 9, 2002. For 

more details on the CBFWA process and province reviews in general see www.cbfwa.org. 

The ISRP will then review the responses and CBFWA's recommended list of projects and provide 

a second and final report to the Northwest Power Planning Council by October 23, 2002. 

Thereafter, the Council will make its funding recommendations to Bonneville. It is anticipated 

that the Council’s funding recommendations will be made in December 2002. 

Recommendation Categories: Who Needs to Respond? 

Preliminary recommendations and comments are provided for each of the 104 proposals 

submitted. These recommendations are split into three basic categories: 1) fundable, further ISRP 

response review is not needed (14 proposals); 2) a response review is needed (71 proposals); and 

3) do not fund, a response is not warranted (14 proposals). Five proposals were considered not

amenable to the ISRP’s technical review. 

Proposals receiving “a response is needed” will be recommended as “fundable” by the ISRP only

if a response is provided that adequately addresses reviewer comments. Although the ISRP will 

not review responses to those proposals that received a “do not fund, a response is not 

warranted,” project sponsors are welcome to provide comments to the Council. 

ISRP recommendation categories are based on the 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 where its 

recommendations diverge from those of the ISRP. 

In its final report, 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 

3 
ISRP 2002-13 Mainstem and Systemwide Preliminary Review 

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 which objectives or tasks 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 

both background assessment work and concurrent major on-the-ground implementation that could 

not be supported before results of the assessment were known, and proposals that included use of 

unsound methods to meet a particular objective. 

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. The ISRP comments are intended to indicate areas where serious remedial 

effort, such as significant revision and review, is needed before funding continues. 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. 

4 
ISRP 2002-13 Mainstem and Systemwide Preliminary Review 

ISRP Preliminary Comments and Recommendations on 

Each Proposal 

Proposals are arranged by topic area, project sponsor, and project ID. Topics include and follow 

the order listed here: 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

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. 

Response Needed? No, Fundable (Qualified) 

ISRP Preliminary Comments: 

Fundable, but the monitoring and evaluation plan needs to be further developed. 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

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 

5 
ISRP 2002-13 Mainstem and Systemwide Preliminary Review 

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

for M&E. 

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

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. 

Response Needed? Yes 

ISRP Preliminary Comments: 

A response is needed. 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). 

In their 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 and a description of progress toward this goal or an explanation of why the synthesis has 

not occurred would be helpful. 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 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. 

The sponsors need to respond to the following ISRP questions: 

1. Both harvest restrictions and transplantation of juveniles from downriver stocks into 

mainstem reservoirs is occurring simultaneously. What were the harvest restrictions that 

were implemented? How do the sponsors plan to sort out the effects of each of these 

6 
ISRP 2002-13 Mainstem and Systemwide Preliminary Review 

mitigation activities sturgeon population dynamics? The sponsors indicate that since 

implementation of the more intensive harvest management growth of fish has slowed, 

perhaps indicating a density-dependent effect. How is this phenomenon being addressed? 

Will transplantation contribute further slowing of growth? 

2. Under Objective 1, Task 1b, Phase 2 of monitoring the sponsors propose to estimate 

survival and recruitment. Specifically, how will this be accomplished? 

3. Objective 2 purports to recommend actions that involve changes to the hydrosystem to 

optimize physical habitat. A much more comprehensive description of how the sponsors 

plan to accomplish this objective is needed. What information is available and how will it 

be utilized to produce the recommendations. Task 2a pertains only to completion of the 

USGS portion of the work, but this work alone is insufficient to provide 

recommendations for power system changes. 

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. 

Response Needed? No, Fundable 

ISRP Preliminary Comments: 

Fundable. 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. 

The 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 

7 
ISRP 2002-13 Mainstem and Systemwide Preliminary Review 

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). 

This proposal was not selected by the Action Agency/NMFS RME Work Group for further 

review. 

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. 

Response Needed? No, Fundable 

ISRP Preliminary Comments: 

Fundable. No response is needed. 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 PI. 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. 

Response Needed? Yes 

ISRP Preliminary Comments: 

A response is needed. 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., 

8 
ISRP 2002-13 Mainstem and Systemwide Preliminary Review 

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 noninvasive 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 

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 ISRP has, however, a question about the benefit to fish and wildlife, which should be 

addressed in a response. The proposal does not persuasively justify the extensive amount of 

proposed work based on the geographic distribution of contaminants and problems with white 

sturgeon recruitment. The ISRP understands that recruitment is good in the lower Columbia 

River, is moderate to annually variable in the middle river (e.g., John Day pool) and is poor to 

non-existent in the Priest Rapids pool. In addition, recruitment in the Kootenai River is also poor 

to non-existent. One might suspect that the contaminant loading of the Columbia River basin 

would be the reverse, that is, more contaminants in the lower river than in the upper reaches (with 

the exception of localized contaminant sources in headwaters affected by industries such as 

mining). The proposal usually does not indicate location when it cites literature as demonstration 

of contamination (with the exception of Bonneville pool). For this research to be funded as more 

than an exploratory sampling, the proposal needs to give more convincing evidence from existing 

literature that contamination and white sturgeon recruitment problems are geographically linked 

or that there is another persuasive rationale. 

The ISRP also questions whether extant contaminant levels cited are within the ranges believed to 

be biologically significant (for any species). That is, is there evidence that such levels in the lower 

river actually can lead to reduction of population output in biomass? Such evidence should be

provided in a response. Also, a response should discuss how we can know that the site the fish is 

captured and the toxin locations are the same (sturgeon move around a lot). 

A key issue for management is: 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. 

This project was not selected by the Action Agency/NMFS RME Work Group for further 

examination. 

9 
ISRP 2002-13 Mainstem and Systemwide Preliminary Review 

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. 

Response Needed? Yes 

ISRP Preliminary Comments: 

A response is needed. 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 is a thorough, basic research proposal that generally meets the ISRP review criteria, although 

there are several technical questions that need elaboration in a response (see below). 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. 

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 sponsors need a better justification of 

the ecological consequences of the research if it is to be useful to managers. The proposal also 

lacks clear, mechanistic hypotheses and methods for data analysis that are specific to testing these 

hypotheses. Several elements of the proposal need to be expanded. For example, objective 1, 

Task 1a purports to determine if food consumed by sturgeon are meeting their nutritional needs. 

Stomach contents and caloric value of the stomach contents will be assessed. Exactly how will 

the information gained from stomach contents and caloric value be used to determine if the 

nutritional needs are being met? How will nutritional status be assessed? How will the 

“relationship between stomach contents, caloric content, and nutritional status” (page 13) be 

assessed and what will it mean? 

Objective 2 purports to measure contaminant levels in sediments, stomach contents, and fish 

tissues and to use this information to assess the association between nutritional status and 

contaminant concentration, and to use sediment and water chemistry to evaluate locational 

differences and associations with tissue chemistry. How will this be done? What type of analysis 

10 
ISRP 2002-13 Mainstem and Systemwide Preliminary Review 

will be employed? Task 2b asserts that biological endpoints (e.g., CF, GSI) indicative of adverse 

effects will be measured. A better justification of the validity of these endpoints as indicators of 

adverse effects is needed. For example, what is an “adverse effect” and how much does an 

endpoint such as CF or GSI need to be reduced before an adverse effect occurs? How will the 

information gathered in this research be used to assess adverse effects on maturing sturgeon?

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. These difficulties need to be addressed in a response. 

This project was not selected by the Action Agency/NMFS RME Work Group for additional 

review. 

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. 

Response Needed? No, Not Fundable 

ISRP Preliminary Comments: 

Not Fundable. The proposal is technically inadequate. The proposal lacked clarity and adequate 

methodological detail. The proposal had poorly stated objectives (none at all really). There was 

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 PI’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 PI 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 PI could 

have shown slides that quickly and clearly showed the non-geneticists in the audience how PCR 

worked, how primer sets are generated for new applications, and how the presence / absence 

ELIZA-type tests are performed to determine. 

11 
ISRP 2002-13 Mainstem and Systemwide Preliminary Review 

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. 

Response Needed? No, Not Fundable 

ISRP Preliminary Comments: 

Not Fundable. The proposal was inadequate. This is a very short proposal to do routine screening 

of prophylactics for their efficacy in treating secondary bacterial and fungal 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 

Response Needed? Yes 

ISRP Preliminary Comments: 

A response is needed. 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. 

 

The proposal seems excessive and overly expensive. Most of the coordination given in the 

proposal is what we would expect of any PI having a lamprey project. Except for the hosting of 

an annual meeting, which can cost extra, all the things proposed could be done within one or

more existing lamprey projects. Is there support for one focal organization among the basin 

researchers and managers? A newsletter could also be rotated and done as a professional activity 

by one of the investigators. If some extra money is needed, then a registration or subscription fee 

could be charged that would tap the annual budgets of each lamprey project. 

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. 

12 
ISRP 2002-13 Mainstem and Systemwide Preliminary Review 

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 

5YR Estimate: $261,945 

Short Description: Determine morphological and molecular characteristics that differentiate 

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

Response Needed? Yes 

ISRP Preliminary Comments: 

A response is needed. This is a project, now (2002) in its third year, to 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 temperatureeffect 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. 

Because this is a 3-year solicitation, it was surprising that the proponents did not extend the 

proposal beyond the next two years. It is laudable to see a planned termination, but this may have 

been an oversight. The ISRP suspects there are more basic biological data needed in the early life 

stage development of the three species. There are likely limiting habitat factors other than 

temperature. Because the project’s monitoring and evaluation component (essentially none) is the 

weakest of the ISRP evaluation criteria, field sampling to use and test the identification 

techniques might have been proposed. The ISRP requests a response to address such follow-up 

13 
ISRP 2002-13 Mainstem and Systemwide Preliminary Review 

research for the third year of the solicitation cycle (or reaffirmation that only two years of funding 

was intended). 

This project was not selected for review by the Action Agency/NMFS RME Work Group.

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. 

Response Needed? No, Fundable 

ISRP Preliminary Comments: 

Fundable. 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

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. 

This project was not selected by the Action Agency/NMFS RME Work Group for further 

examination. 

14 
ISRP 2002-13 Mainstem and Systemwide Preliminary Review 

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. 

Response Needed? Yes 

ISRP Preliminary Comments: 

A response is needed. 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 ISRP 

believes this research is fundamental to lamprey recovery in the basin. 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 research is worthwhile, but more methodological detail is needed. What specific habitat 

criteria will be used to classify habitats as having high, medium, or low potential for lamprey

rearing and spawning (page 6)? How will spawning habitat and its use by adult lamprey be 

quantified? How large of an area will be sampled at each sampling site? To what water depth will 

sampling occur? How will abundance be quantified? Describe in more detail how ANOVA will 

be used to assess relationships between habitat and abundance. Is a multiple regression approach 

suitable for defining these relationships? Will stratified random sampling be incorporated into the 

study and, if so, what will be the sampling design? 

More detail is needed in characterizing how the landscape scale evaluation will be accomplished. 

For example, how will the site-specific information gathered in this work be scaled up or linked 

to the channel and reach level characteristics such as channel form, gradient, and discharge? What 

are the “geologic features” that will be used to in the landscape-scale extrapolation? How will 

historical habitats be identified? 

15 
ISRP 2002-13 Mainstem and Systemwide Preliminary Review 

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.

Response Needed? Yes 

ISRP Preliminary Comments: 

A worthwhile project that will improve understanding of lamprey abundance and distribution in 

the Willamette River, possibly the major production area for lamprey within the Columbia Basin. 

The sponsors need to address the following issues in the response loop: 

1. In sampling nearshore habitats in the lower Willamette, what is the justification for transects 

10m in length? Has a backpack electroshocker been tested for effectiveness in sampling lamprey

in these habitats? 

2. The sponsors propose to radio tag 40 adult lamprey below Willamette Falls in summer 2002 

and monitor movement during the subsequent year. Based on tag detections the previous year, the 

ISRP is concerned that 40 tagged fish will be an insufficient number to provide reliable 

information on movement and to meet the proposed objectives. The sponsors should decide how 

many tags are necessary to provide reliable information on movement and revise the proposal and 

budget appropriately. 

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

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

movements into Hood River and Klickitat River. 

Response Needed? No, Fundable (Qualified) 

ISRP Preliminary Comments: 

The ISRP suggests one year funding to explore feasibility of capturing bull trout in Bonneville 

Reservoir with subsequent funding contingent upon demonstration of the efficacy of capture 

techniques. 

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 

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. 

16 
ISRP 2002-13 Mainstem and Systemwide Preliminary Review 

The project hinges on the ability of the sponsors to effectively capture bull trout in the reservoir. 

There is considerable uncertainty associated 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. 

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

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. 

Response Needed? Yes 

ISRP Preliminary Comments: 

A response is needed. Based on this review and the previous ISRP comments, this 12-year old

program may be due for an in-depth cost-benefit or economic analysis with consideration of 

alternative methods of predator control or alternative strategies of deliveries. This year’s review 

was largely influenced by the previous independent review by Hankin and Richards, contracted 

by the Council to conduct a review after the ISRP review - see 

http://www.nwcouncil.org/library/2000/2000-16. This long-term program has met many goals, 

but cost-effectiveness appears to be on a downward trajectory. Possibly 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 numbers are likely declining and costs of the program

are going up in both direct dollars and value per unit dollar spent. 

Specific Comments on the Proposal: 

This is a well-written proposal to continue 12 years of northern pikeminnow harvest. The project 

has become more evaluative over time with the exception of economic considerations. Neither 

monitoring nor evaluation contains an economic component, but economics, including costeffectiveness monitoring, should be a core part of the project’s evaluation. This is an expensive 

project and there is an opportunity cost of funding this project at $3 million rather than other 

projects. 

“Success” of the benefits to salmon is measured strictly in numbers of pikeminnow caught. There 

is no analysis of the cost-effectiveness of the pikeminnow removal on salmon or any economic 

tradeoffs embedded in conducting this program in its current form. 

The Hankin and Richards report reviewing the program two years ago 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. A trained economist (not a 

biologist) should be subcontracted to conduct these analyses. Even more desirable would be an 

economic evaluation of the entire program. Additionally, we note that in the two years since that 

review, the catch per unit effort has dropped significantly, especially in site specific and dam

17 
ISRP 2002-13 Mainstem and Systemwide Preliminary Review 

fishing but also in the entire program. The total numbers, size and biomass of the program seems 

to have dropped by more than 50% since implementation in 1991, by the programs own numbers. 

The program does not seem to have presented a downward modified smolt consumption index 

related to the smaller 200 mm fish now considered a substantial part of the harvest. We recognize 

that removal of this smaller size fish was recommended in the Hankin and Richards review. The 

rationale that these fish contribute to future benefits is reasonable, but nonetheless, the reality is 

that actual smolts saved by removing non-predatory northern pikeminnow cannot be “counted 

twice”, once for what they might have eaten this year and what they might have consumed next 

year. 

Early feasibility analysis indicated the potential for commercial “rough fish” harvest and 

processing into minced product. However, implementation of a commercial fishery (other than 

the tribal long-line experiment) was precluded by policy decisions at ODFW and WDFW to use 

northern pikeminnow as a recreational fishing opportunity to compensate for diminished salmon 

fishing opportunities. 

Catch targets are cited for the sport-reward fishery, but none are cited for the dam angling fishery

or the site-specific fishery. The dam fishery caught 2751 fish in 2001. A total of $49,692 is 

budgeted for this fishery in 2003. If the numbers caught in the dam fishery continue at the 2001 

level this fishery will cost about $18 per fish removed. The site-specific fishery caught 518 fish in 

2001. $38,605 is budgeted for this fishery in 2003. If the numbers caught in the site-specific 

fishery continue at the 2001 level this fishery will cost about $74 per fish removed. The 

conversion of these costs to adult salmon returns will be several magnitudes larger. The reality is

there is a downward trend in Catch Per Unit Effort for all portions of the fishery. The proponents 

should provide an economic and efficiency evaluation of these fisheries with justification for their 

continuation. 

Past recommendations from ISRP indicated that future submissions of this program should 

endeavor to better describe the budget for the reward system and the $1 million personnel costs. 

A concern about current work is whether the investigators are continuing to do verification on the 

captured pikeminnows to confirm assumptions of predation rates on salmon. There are some 

questions that the “live” smolt index is accurate today given the new size removal index and the 

declining number caught per unit effort. Another previous concern not addressed was the request 

to address alternative approaches and their evaluation. None of these three recommendations has 

been followed. Some previous comments calling for new approaches include the following: 

Due to the high annual cost in this project, reviewers suggest that it may be time to creatively rethink how this program could be delivered. Given that northern pikeminnow are long-lived and 

slow growing, and that the number of northern pikeminnow that are being removed appears to be 

declining in recent years, a cost/benefit analyses should be conducted to assess alternative 

predator control strategies. Running the predator removal program every second or third year may

be equally effective; or less expensive designs could be developed for a variety of strategies, 

including running the program in alternate years but offering increased incentives for fishing (e.g. 

double or higher the current reward offered for each fish). The recruitment relationship for 

northern pikeminnow should also be determined and the size of fish for which rewards are 

offered should be tied directly to this recruitment (growth rate and size-at-age) relationship. The 

attractiveness and spin-off benefits (e.g. increased tourism) of other types of rewards, incentives 

and approaches (e.g. major international squawfish derby every year with large prizes for capture 

of tagged squawfish) could be investigated as a way to maintain effectiveness and control costs. 

Should we spend even numbered years capturing predators and alternate years salmon? 

18 
ISRP 2002-13 Mainstem and Systemwide Preliminary Review 

At the presentation workshop, the question was posed about how many adult salmon might be 

returning because of the predator management program. It may be possible to obtain some 

insights into this question. The following is a heuristic example but more detail could yield 

insights. Predators eat an estimated 16 million smolts out of 200 million. This is about 8% of the 

hatchery fish and possibly 5% or less of the total run. How do these losses compare to other 

sources of mortality? The northern pikeminnow program claims a 25% reduction in predation 

losses. This is a savings of 4 or 5 million smolts. Assuming a 1% SAR (adult return rate) 5 

million smolts provides a net value of returning adults is 50,000 adults. A program cost of $3 

million/year, or $60 per fish. This may be comparable to the costs incurred for other programs 

and can be compared once more actual numbers are obtained. 

Some other key questions:

1. Page 2 Para 2 and 4. Lab results show that northern pikeminnow prefer “dead” smolts to live 

ones. Yet evidence provided suggests that only 22% of the prey were “dead” experimental fish in 

stomachs sampled. How did the researchers know whether some of the unmarked stomach 

contents were not from dead but unmarked fish? 

2. Considering that turbine mortality is estimated at about 10%, cumulative numbers suggest that 

even if half of juveniles are transported, there are over 60 million stunned or killed smolts in the 

river below the dams. What percent of these are eaten by other fish? By Northern Pikeminnow?

Can we assume that the 1-2 million adult northern pikeminnows (calculated by dividing number 

harvested by % of population given on Table Page 9) are consuming all of these? If so, each fish 

must consume 30-60 smolts. How many more live fish would they consume? Do we have 

consumption rates? This would help characterize total losses in the system from northern 

pikeminnow and other predators and help determine how much more cropping of predators would 

be effective in the future. 

3. What are the current regulations on the take of smallmouth bass, channel catfish and walleye? 

If these have limits, and they are exotic predators of smolts, why don’t we lift all restrictions on 

their sport harvest? Are harvests on these species restricted?

4. Inflation is one factor, but the northern pikeminnow program is now paying about double the 

rate to capture fish in 2000-2001 compared to 1990? What is the CPUE in 1990 versus 2000? 

5. What is the cost to capture 500 NPM at dams and at site-specific locations? These represent 

less than 5% of the total population removed during the last 5 years? Compare cost per fish here 

versus cost per sport harvest fish? The use of a tiered bounty system might encourage collectives 

to artificially increase bounty and cost without increase in level of fishing effort. Is this a likely

significant cost factor? Or should other payment schemes be investigated? 

6. Does the northern pikeminnow program corroborate the actual location of fish harvested? 

What would be the consequence of inaccurate data?

7. Assuming that dead smolts will feed existing northern pikeminnow as well as live ones, has 

any attempt been made to artificially feed the northern pikeminnow with dead fish during the

juvenile salmon migration? The concept would be to bait an area, like a tailrace with an 

abundance of dead fish to sate the predators. Would this have the benefit of attracting larger 

numbers of northern pikeminnow to a site-specific location and make them more vulnerable to 

harvest. How are the captive northern pikeminnow used? Can they be cut up and fed to northern 

19 
ISRP 2002-13 Mainstem and Systemwide Preliminary Review 

pikeminnow? Will northern pikeminnow eat flesh of other northern pikeminnow? If so, these 

could be stockpiled to bait northern pikeminnow. 

Action Agency/NMFS RME Group Comments: 

HYDRO SUBGROUP -- This proposal addresses RPA Action 100, which is not explicitly linked 

to BO RME RPAs 179-199. However, the RME Planning Group suggested we offer commentary

on it. 

This proposal is for the continuation of the Northern Pikeminnow Management Program, which is 

the primary thrust of RPA 100. This is an implementation project to directly improve juvenile

salmonid survival within the FCRPS through the reduction of predation mortality; as such, it 

contributes directly to the hydrosystem juvenile reach survival performance standard. Integral to 

this project is a biological evaluation component to evaluate the effectiveness of removal 

fisheries. Results of biological evaluation indicate that annual predation losses have decreased 

approximately 25% when compared to pre-program levels and that there is no evidence of either 

inter- or intra-specific compensation. The management program and exploitation monitoring are 

implemented annually; the biological evaluation component is implemented in a 3-5 year cycle 

with the next evaluation in 2004. The RME group generally considers this project to be adequate 

for addressing northern pikeminnow predation. 

The RME group also notes that the other component of RPA 100, evaluation of methods to 

control predation by non-indigenous fishes, is not addressed by this project. While this project 

includes evaluation of the effect of northern pikeminnow removals on predation, growth, and 

reproduction of smallmouth bass, walleye, and channel catfish, it does not include potential 

methods to reduce predation mortality by these fishes. This component of the RPA is outside the 

scope of the Northern Pikeminnow Management Program. 

A new proposal is referenced, titled Assess the Feasibility of Reducing Predation on Juvenile 

Salmonids in the Columbia River through Operation of the Hydropower System” (Proposal No. 

35032) that attempts to address the second component of RPA 100. Specifically, the proposal 

entails review of existing data and evaluation of components of the riverine habitat that might be 

manipulated through operations to reduce the number of predators and associated predation 

losses. Sponsors propose to initially focus on areas downstream of Bonneville Dam, with some 

work in the lower Columbia and eventually in the lower Snake rivers. We note several areas of

concern that may reduce the immediate priority of this proposal. Based on the proposal, there is 

too limited information on the location and timing of spawning of smallmouth bass and walleye

for determining the feasibility of operational management alternatives; substantial resources may

need to be devoted to obtain this information before any direct evaluation of operations to reduce 

predation might be feasible. This may be true, but we question if general information on 

spawning of smallmouth bass and walleye (e.g., timing, conditions, etc.) may not provide 

sufficient basis for developing an operation scenario for evaluation. Also, the proposal is for the 

river reach below Bonneville Dam where water elevation is largely a result of river flow (and to a 

lesser extent tidal influence). Reservoirs in the lower Columbia or Snake rivers upstream of 

Bonneville Dam afford considerably greater flexibility for operations across a range of flow 

conditions that would be more conducive for evaluating the feasibility of operational control of 

these predators. Conditions below Bonneville, on the other hand, are largely subject to river flow 

and not easily manipulated for such control measures. We also want to note that control of nonnative species may be in direct conflict with regional fishery management objectives; this has 

important policy implications that must be addressed for this approach to be feasible. 

20 
ISRP 2002-13 Mainstem and Systemwide Preliminary Review 

ISRP Remarks on RME Group Comments: 

The ISRP elicited more concern about the cost:benefits and economic efficiencies of the northern 

pikeminnow program than those from the RME group. We share the RME group’s concern 

regarding management of exotic predators. 

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

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. 

Response Needed? Yes 

ISRP Preliminary Comments: 

A response is needed. This is a well-prepared proposal. The ISRP review criteria are met. The 

proponents have given a good summary of past results. A major shortcoming identified in 

previous years was the lack of peer-reviewed publications, a factor now taken care of with the 

latest crop of publications. Another previous shortcoming was the need for a more in-depth 

review of the program. This has been accomplished externally via the intensive court case led by

the Audubon Society, through which the study has been thoroughly reviewed (one might say

raked through the coals). Although this proposal does not dwell on the court case, there was 

impetus from it toward the directions this proposal now takes for looking at other bird predators 

of salmonids (to put terns into better context) and other potential nesting sites for research and 

management attention (upriver and coastal). The budget expanded along with the court-mandated 

tasks, as described in Part 1. Why BPA should have to pay for these studies is unclear. 

The experimental design is good. A key question however is the continued relevance and value of 

the program to the goals of saving salmon in the FCRPS. This five-year program is clearly in its 

mature if not senescent stages as far as benefits to the FCRPS system. Enormous amounts of 

information have been gathered about tern biology and feeding behavior to the credit of the avian 

research team. Key recommendations have been to move (if not eliminate breeding habitat). And 

this has been successful. Much of the future work however appears aimed more at preserving 

terns (see court comment above) than at preventing further degradation of salmonids due to 

predation. Additionally, it is less clear how details about bioenergetics of tern diet, stable isotope 

ratios studies, fatty acid signatures, and contaminant levels may be valuable to reducing tern 

impact on salmon. As elaborated in a previous ISRP Review two years ago in 2000, we agree 

with the previous review that: 

“ ...an in-depth independent peer-review be conducted to evaluate the results and conclusions 

generated from this project before proceeding with what would be potentially a very costly 

expansion of this work.” Like northern pikeminnow management, it would be good to know 

about more direct consequences and cost:benefits of the program on adult return rates. 

Several important questions that seem relevant to the FCRPS are 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 SAR’s (adult returns) from transported smolts exceeds SAR’s 

of juveniles that migrate through the FCRPS. One important strategy that could reduce tern 

21 
ISRP 2002-13 Mainstem and Systemwide Preliminary Review 

predation is the timing, location and release patterns 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 authors suggest there are differences between hatchery and wild fish losses. The NATURES 

artificial production program has a goal to produce fish with more wild like phenotypes, 

genotypes and behaviors. Experiments that test predator avoidance fitness values in different 

types of new NATURES program fish may also be worthwhile endeavors for future research of 

both the artificial hatchery improvement program and avian predator program. Research in the 

future should be more focused on experiments that would primarily assist salmonid recovery in

the FCRPS. 

Questions about cause and effect of the tern population also concern the ISRP. Could the recent 

upsurge in bird predators be a result of the overwhelming preponderance of hatchery-raised 

smolts (which seem to be more susceptible)? Could one response to supplementation in the basin 

and outright hatchery releases be the creation of behaviors conducive to being eaten by birds, 

even after the long in-river journey? Is it the result of barging and mass releases? Is there 

something we’re doing to enhance fish passage at dams that is making fish less fit farther 

downstream (delayed mortality)? Does less predation by northern pikeminnow because of the 

pikeminnow control program just mean more weak fish left for birds? Could the use of terns in 

hatcheries make hatchery fish more fit as far as predator avoidance is a learned response?

This project would be more valuable to the FCRPS with more focus on the salmon aspect of the 

problem. 

Some general questions. Why are tern populations expanding inland? Is new habitat being 

created? Will moving terns to new locations create a burden for other forage species? How much 

of the predation problem is a function of a fish hatchery system that artificially concentrates tens 

of thousands of smolts in the river? Should we rethink the artificial production and release 

strategy rather than predator removal strategy? Is there a correlation between the tern relocation 

effort and this year’s return rate of steelhead? 

Summary

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

about the impacts of terns to salmon. The obvious management actions are now in progress to the 

extent courts are allowing it (moving or reducing tern populations). Some further management 

options and experiments that relate to how transported fish are released from barges (where, 

when, etc) may be useful to the FCRPS. These have not been proposed but should be done. 

Much of the proposed new tern research is aimed at assisting the growth, development and 

monitoring of new tern colonies elsewhere, which seems counterproductive to 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. Their value to 

science is not questioned, but in a world of limited funding, projects with the greatest benefit to 

the recovery of salmon deserve the highest priorities. One program option would be to alter the 

project (and reduce funding) to refine how better to manage improvement of smolt production, 

transport and release programs as they relate to avian predation and other factors of smolt 

survival. 

22 
ISRP 2002-13 Mainstem and Systemwide Preliminary Review 

Action Agency/NMFS RME Group Comments: 

OCEAN AND ESTUARY SUBGROUP -- Action items addressed - 49; 101; 103; 104; 186; 195. 

This project is complete enough for funding. 

ISRP Remarks on RME Group Comments: 

The ISRP comments are focused on the relevance (benefits to salmon) more than the quality of 

the science in this proposal. The scientific design aspects are good and thus consistent with the 

RME group’s evaluation of the acceptability of the program.

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. 

Response Needed? Yes 

ISRP Preliminary Comments: 

Substantial questions exist and responses are needed.

Synopsis of the Proposal. The proposal intends to build upon current methods of harvest to 

control predators. The basic concept is that by changing depths and velocities of the river via 

hydro operations, spawning, rearing or other critical life history requirements of predators will be 

disrupted. In the 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 need to be addressed. 

First, the hydropower system management actions that are foreseen are not clearly presented. 

This leaves the question whether all this work might lead to some options that are infeasible or 

otherwise undesirable (such as artificially low springtime flows). 

Second, there is insufficient evidence concerning the exact mechanisms of life history disruption. 

The proposal seems to ask for funding to discover such possibilities. Such efforts could take a 

very long time. We know that hydropower operations such as reservoir pool fluctuation and 

peaking flows can disrupt fisheries and aquatic life. This is primarily by dewatering redds/eggs 

after spawning, changes in velocities or depths thus altering physical habitat or changing water 

quality such as temperature, DO, TDG etc. The emphasis on early life stages may ignore some 

other potential management actions other than hydropower changes such as shoreline habitat 

restoration. As an example, adult smallmouth bass do well in rip-rapped shorelines as habitat. 

Rip-rap is generally harmful to salmonids. Elimination of rip-rap may be more effective than

trying to change depth and velocity. The latter hydraulic changes may not get the desired outcome 

and even if it does, changes that have a negative affect on predators, may also negatively affect 

salmonids. More specifics such as this would be helpful. 

23 
ISRP 2002-13 Mainstem and Systemwide Preliminary Review 

Some other specific concerns are: 

A key target area of the proposal is downstream of Bonneville Dam. The ability of the 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 be helpful. Is it possible 

to define the desired effect? For example, northern pike minnow spawn as deep as 5 m (p. 17). 

Can the tailwaters of Bonneville Dam sustain 5 m fluctuations for periods needed to create a 

desired effect? Is there any specific evidence for depth, location and density of northern pike 

minnow habitat at the intended location? If so, the proposal could offer more specific approaches 

such as: draw tailwater down 2.5 m for 24 hours to dessicate 50% of known target eggs (or strand 

juveniles) in specific areas between June 15 and 30. Then, hydraulic models could be examined 

to see if this were feasible. Bonneville tailwaters are subject to tidal influence, further 

complicating the system. To dewater the tailwater area would require significant retention of 

storage and complicate water levels, flows and upstream operations that would likely have 

unidentified significant impacts on fish, wildlife and human uses upstream, not to mention 

constraining the power system normal operations. Discussion of the ramifications of such 

operations seem to be a vital component of the research to know that it could be feasible because 

of the possible negative consequences of changing system operations. 

In addition to depth changes, the authors suggest velocity changes might also disrupt target 

predators. What mechanism or hydraulic targets cold provide the desired outcome? Key

questions include: (1) what is the range of existing fluctuations of depth and velocity in the 

Bonneville tailwaters from both natural and man-made operations? (2) What evidence is there 

that it will be possible to superimpose a more drastic set of fluctuations? And (3) are these likely 

to have the desired effect on the target species but not cause impacts to salmon?

Years have been spent fine-tuning the operations of the spillways, turbines and ladders to 

maximize adult salmon passage and to direct juveniles to areas of highest passage survival. 

These and other possible conflicts should be addressed in the proposal. 

Likewise this holds for system operation impacts. What potential consequences to power 

generation might emerge? Changes in flows of the magnitudes needed might have repercussions 

for storage in Grand Coulee and even Canada. These concerns need to be addressed. 

In summary, the ideas in this proposal are intriguing but not sufficiently developed. As 

presented, the goals seem unattainable in any reasonable time frame. Direct impacts to salmonids 

and the hydropower system seem as likely if not more probable than the intended goal of predator 

elimination and thus diminish the potential of finding workable solutions to the idea. 

Action Agency/NMFS RME Group Comments: 

HYDRO SUBGROUP -- From comments on 199007700 -- A new proposal is referenced, titled 

Assess the Feasibility of Reducing Predation on Juvenile Salmonids in the Columbia River 

through Operation of the Hydropower System” (Proposal No. 35032) that attempts to address the 

second component of RPA 100. Specifically, the proposal entails review of existing data and 

evaluation of components of the riverine habitat that might be manipulated through operations to

reduce the number of predators and associated predation losses. Sponsors propose to initially 

focus on areas downstream of Bonneville Dam, with some work in the lower Columbia and 

eventually in the lower Snake rivers. We note several areas of concern that may reduce the 

immediate priority of this proposal. Based on the proposal, there is too limited information on the 

location and timing of spawning of smallmouth bass and walleye for determining the feasibility 

24 
ISRP 2002-13 Mainstem and Systemwide Preliminary Review 

of operational management alternatives; substantial resources may need to be devoted to obtain 

this information before any direct evaluation of operations to reduce predation might be feasible. 

This may be true, but we question if general information on spawning of smallmouth bass and 

walleye (e.g., timing, conditions, etc.) may not provide sufficient basis for developing an 

operation scenario for evaluation. Also, the proposal is for the river reach below Bonneville Dam

where water elevation is largely a result of river flow (and to a lesser extent tidal influence). 

Reservoirs in the lower Columbia or Snake rivers upstream of Bonneville Dam afford 

considerably greater flexibility for operations across a range of flow conditions that would be

more conducive for evaluating the feasibility of operational control of these predators. 

Conditions below Bonneville, on the other hand, are largely subject to river flow and not easily

manipulated for such control measures. We also want to note that control of non-native species 

may be in direct conflict with regional fishery management objectives; this has important policy

implications that must be addressed for this approach to be feasible. 

ISRP Remarks on RME Group Comments: 

The RME group comments above are in general agreement with those of the ISRP. 

Estuary/Plume and Lower Columbia 

With the exception of proposal 35046, these proposals were submitted for the Estuary and Lower 

Columbia River Province Reviews. The Council is still deliberating on those provincial 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 

Response Needed? Yes 

ISRP Preliminary Comments: 

A response is requested. This proposal makes a very strong 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 very 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 BPA RME comments below strengthen our support for this work 

and the 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 project emphasizes the need for understanding and dialogue but does not presume that the 

FCRPS would immediately be modified to meet only ‘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 

25 
ISRP 2002-13 Mainstem and Systemwide Preliminary Review 

developed 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 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. 

Consequently, and after further consideration of this proposal, the ISRP supports our 

recommendation presented June 7, 2002 (below). 

However, we 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 random opportunities (annual deviations 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. 

The proposal still could benefit from a more detailed description of the use of management 

science to articulate management scenarios. How will managers’ expectations and response to 

uncertainty be investigated? For example, the proposal includes some statements about different 

languages and time horizons among managers, researchers, and policymakers. This is a very

general statement that will apply to varying degrees within the FCRPS. It would be helpful to be 

more explicit about its particular application within the FCRPS, how large a problem it is, and 

potential remedies. The proposal describes the general problem as if it is a complete lack of 

understanding by one entity of all other entities. 

Since the proponents have comments on the ISRP recommendations very recently, they may not 

have further response to these comments. The ISRP is providing for a response to our comments 

and those of the Action Agency/NMFS RME group if they chose to. 

Past ISRP Review Comments: 

June 7, 2002 Province Review - Fundable in part (disagree with CBFWA ... to some 

extent), initially fund at a reduced amount and increase funding over 3 to 4 year period as 

information from the other projects increases and need for integration increases. The 

ISRP does agree that it is important to begin dialogue with the system managers on how 

to incorporate the lower river, estuary, and plume environments into their considerations. 

It is difficult to argue with the statement that the ultimate goal of the plume and estuary

studies are to link these to management of the water system (FCRPS) for the improved 

survival and production of salmonids in the Basin. Therefore, since we see nothing 

fundamentally wrong with this proposal’s presentation, we recommend funding. 

However, we also believe that this proposal is a couple of years ahead of its useful time 

and that it could be deferred if funding limitations required. To prompt development of 

the integration of the lower river and estuary programs with FCRPS and system

managers, we are recommending a revised approach to be developed by the contract 

managers and involving a phasing in of the proposal over the next few years. 

Further, the ISRP continues to be concerned with the reference to “habitat opportunity” 

metrics and the very limited definition of what this means, and that the area defined for 

26 
ISRP 2002-13 Mainstem and Systemwide Preliminary Review 

this proposal does not include the inner estuary or river up to Bonneville dam. The 

response continues to refer to the outer estuary but then other parts of the proposal refer 

more generally to the estuary proposal and FCRPS interest that clearly involves the river 

below Bonneville Dam and into the plume region. Finally, the response would have been 

strengthened with a clearer description of the use of management science to articulate 

management scenarios. 

CBFWA Review Comments: 

Project would provide information to managers regarding the effects of flow on % habitat 

available (i.e., what % of habitat would be lost/gained during different flows below 

Bonneville Dam). Project could lead to the development of management schemes. 

NMFS has identified this project as a BiOp project. 

Action Agency/NMFS RME Group Comments: 

HYDRO SUBGROUP -- This proposal establishes the need to link FCRPS river management to 

plume dynamics and productivity and ultimately salmon survival. Clearly there is a need to 

understand the contribution of early ocean conditions to salmon survival. The additional premise 

that the FCRPS might be managed to improve those conditions is less obvious. The river system

is already being managed for multiple purposes; flood control, hydropower, irrigation, recreation 

and optimization of inriver smolt survival. To suggest that the system can be substantively

altered further would require considerable reprioritization of existing river uses. This is not to 

diminish the importance of studying and understanding plume dynamics, but to be realistic with 

respect to expectations regarding the flexibility of the FCRPS. 

OCEAN AND ESTUARY SUBGROUP -- Action items addressed - 158, 194; 161, 187,196. 

Doesn't clearly address all the RPAs proposed by authors. Focus is on physical aspects of estuary

and plume. Compliments projects 199801400 and 30001 (estuary province numbers), so the 

project will be linked to understanding biological aspects of the estuary. This project is complete 

enough for current funding.

ISRP Remarks on RME Group Comments: 

See ISRP preliminary comments above. 

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

Short Description: Estimate juvenile chinook salmon residence time and areas of utilization 

within the Columbia River plume. 

Response Needed? Yes 

ISRP Preliminary Comments: 

A response is needed. This proposal is to complete development of micro-acoustic tag 

methodology, and to assess residence of salmonids in the Columbia River plume by deployment 

of fixed and mobile receiver arrays. 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), 

27 
ISRP 2002-13 Mainstem and Systemwide Preliminary Review 

size and age, to determine how they vary by season. It also proposes to assess the nature of 

juvenile distribution within the plume. The ultimate goal of this and companion project 

199801400 is to understand the importance of the Columbia River plume to survival of juvenile 

salmon. 

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. The number of 

uniquely identifiable tags was originally noted as a limiting factor, but the authors noted that the 

use of phase-shifts has effectively eliminated that concern. 

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. 

Also, the project is most closely related to a companion NMFS project (BPA 199801400) and to 

some USACE projects on estuarine physical dynamics. The tasks and methods are described in 

appropriate detail. A very strong development and research team has been organized for this 

proposal. 

The objectives 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 NMFS project to build a biophysical model relating Columbia River plume conditions 

to the growth, distribution and survival of juvenile salmonids. 

The ISRP wishes to complement these investigators for their substantial progress on the microtag to date. We have previously noted the essential need to study salmonid residency and use of 

the Columbia River estuary and plume, and this tag now offers the potential to achieve this. 

However, we have two major concerns with the receiver arrays. First, we note that 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 support 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? Are there valid 

technical reasons for not collaborating or is the intention of these investigators to develop totally 

different receivers and array systems? 

Concerning the arrays, we request 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 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 micro-habitat use by salmonids 

clearly addresses mechanisms effecting growth, survival, etc. but are finer scale questions that 

can be phased in over time.

Further, when the ISRP consider the development proposals by Dr. Welch, we proposed 

supporting a prototype or “proof of principle” scale program initially, followed by expansion if

28 
ISRP 2002-13 Mainstem and Systemwide Preliminary Review 

successful. In the development of this large-scale program that clearly has analogies, we request 

these researchers to consider a smaller scale demonstration project when the tag and detection 

systems are “developed”. The second year of the current proposal requests over $6 million, which 

we consider an unreasonable risk without adequate proof of performance. 

Action Agency/NMFS RME Group Comments: 

OCEAN AND ESTUARY SUBGROUP -- Action items addressed - 193; 195; 197. This project 

is complementary to the KinTama Proposal 30007, submitted under the Estuary Province. The 

tag being developed by NMFS is an important addition to the work completed under the 

KinTama innovative project. The smaller tags will fill a data need for NMFS' estuary/plume 

work, and as they are further developed, may be used for longer term studies on the shelf. The 

KinTama acoustic array feasibility study was funded as the ISRP’s top ranked Innovative Project 

in 2000 and is now complete. An appropriate scaled back deployment involving both contractors 

might include the estuary and plume and an array covering the shelf at the northern end of 

Vancouver Island. There is also a need to coordinate with studies funded by Portland District of 

the Corps. 

ISRP Remarks on RME Group Comments: 

The ISRP generally agrees with the BPA RME comments for this proposal. A collaboration 

between Dr. Welch (Kintama Research) and these authors may lead to useful developments in

receiver arrays and methods for retrieving data from these arrays. 

Kintama Proposal Submitted in the Estuary Province: 

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: 

Fundable but 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 

but 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 

29 
ISRP 2002-13 Mainstem and Systemwide Preliminary Review 

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 was now complete. He noted that there do remain issues with the deployment of the 

acoustic 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. 

30 
ISRP 2002-13 Mainstem and Systemwide Preliminary Review 

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. 

Response Needed? No, Fundable 

ISRP Preliminary Comments: 

Fundable, the likely benefits to fish and wildlife appear to be high. 

The technical background to this proposal is detailed and complete. The proposal is well 

connected to the regional program and to 3 BiOp RPAs. This is a new project, but a history of 

lower river and estuary habitat restoration is provided to establish some context for this proposal. 

The work in this project will build on work done with CREST under CWA Section 319. This 

group (LCREP/CREST) has a good track record with coordination, resulting in high quality

products: habitat maps of the lower river, multiparty habitat workshop that developed criteria for 

habitat projects, list of habitat projects and RFP for research on these. 

Action Agency/NMFS RME Group Comments: 

OCEAN AND ESTUARY SUBGROUP -- Action items addressed - RM&E - 161; 162. Also 

supports 158; 159; 160; 163. This project has been coordinated with BPA as part of the LCREP 

Science workgroup. The monitoring protocols proposed are supposed to integrate with the larger 

RM&E focus for the basin. Future direction on RM&E should be communicated to the project 

applicant to further refine this proposal in accordance with that direction. 

ISRP Remarks on RME Group Comments: 

The ISRP comments are consistent with the Action Agency/NMFS comments.

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.

Response Needed? Yes 

ISRP Preliminary Comments: 

The objective of this project is to identify bacterial fish pathogens as indicator species for fish and 

watershed health. This proposal will use polymerase chain reaction (PCR) and species-specific 

primers to show the presence of aquatic bacteria in water and tissues of living organisms to 

determine their relationships to aquatic life. The idea is to identify bacteria species that can serve 

as indicators of aquatic ecosystem health. The technical background to this problem is adequate, 

31 
ISRP 2002-13 Mainstem and Systemwide Preliminary Review 

as is the relationship to regional programs and other projects. It would help the project to place 

this work in the context of RPAs under the FCRPS BiOp: the presentation had these listed; they 

should be added to the proposal? 

Tasks and methods to meet these objectives are described in a fair amount of detail. However, 

detail about the sample design is absent. What is the reason for sampling in 10 locations? How 

did you derive this number of sites? The project proponents will consult with a biostatistician 

regarding data analysis: this consultation should be done in advance of sampling to ensure that 

the resulting data analysis has the appropriate statistical power. This comment also applies to the 

choice of the number of sample sites, which appears to already have been determined to be 10. 

How many samples will be taken from the ten sample sites, over which period of time? 

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. 

The ISRP completed a review of this proposal very recently under the Lower Columbia/Estuary

province (June 7, 2002 below). We note that the investigator did not provide further evidence of 

progress on development of the statistical design; consequently, we again request a response 

describing a statistically sound study design. This design needs to be in place before the project 

is started because the design will effect selection of sampling sites. 

June 7, 2002 Province Review - ProjectID: 30013 

Role of Bacteria as Indicator Organisms for Watershed Assessment and in Determining 

Fish Pathogen Relationships with Fauna of Abernathy Creek 

Sponsor: USFWS 

Province: Columbia Estuary

Subbasin: Elochoman 

FY03 Request: $71,100 

5YR Estimate: $189,690 

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 Recommendation: Fundable (Qualified - see comments)

CBFWA Category: Recommended Action 

ISRP Comparison with CBFWA: Agree - Fundable (Qualified) 

ISRP Final Review Comments: Fundable 

The research is interesting and the question is important in regard to non-point source 

pollution, but the proposal has a strong personal development aspect to its benefits. The 

ISRP had a number of comments that the author did try to address and did seek the 

statistical advice suggested. Our principal concern was that the PI did not have the 

statistical background required by this investigation but the PI has sought consultation on

this issue. A requirement of funding for this project should be that the PI is required to 

submit a completed experimental design developed with full collaboration of a 

statistician and agreed with by more senior USFWS staff. A design developed in advance 

of the sampling will assist in interpretation of results and will likely reveal sampling 

issues before the project begins. The ISRP acknowledges that the idea being examined in 

this proposal is both different and challenging but we are also recommending funding as 

a developmental step for a young researcher who impressed the review committee with 

his presentations and abilities to answer our questions. 

32 
ISRP 2002-13 Mainstem and Systemwide Preliminary Review 

CBFWA Review Comments: 

This project should be considered under the innovative category (or in the Mainstem and 

Systemwide Province). 

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. 

Response Needed? Yes 

ISRP Preliminary Comments: 

A response is needed to up-date the ISRP on progress towards a comprehensive study design in 

the upper Cowlitz River watershed. No further questions on this proposal. 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 committee 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 it the monitoring and evaluation capability that 

could be incorporated into this research. This proposal did not comment on develops of such a

research program but an organizational group was noted during the presentation. The ISRP has 

concluded that they must remain consistent with its recent recommendation: 

“Defer decision until an appropriate experimental design is developed. Funding of #31005 could 

proceed independent of #31017 but the value of that investment would be significantly reduced

without the full development of the potential studies in the upper Cowlitz River (project 

#31017).” (see below) 

We should note, however, that this proposal has 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. 

Past ISRP Review Comments: 

June 7, 2002 Province Review - 

Province: Lower Columbia 

Subbasin: Cowlitz 

FY03 Request: $257,130 

5YR Estimate: $971,730 

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 (Qualified - see comments) 

CBFWA Category: Recommended Action 

33 
ISRP 2002-13 Mainstem and Systemwide Preliminary Review 

ISRP Comparison with CBFWA: Disagree - Not fundable (Qualified) 

ISRP Final Review Comments: 

See comments on project #31017. 

CBFWA Review Comments: 

This project should be considered under the Mainstem and Systemwide Province. The 

data collected would contribute to a larger database for evaluating populations. NMFS 

has identified that this project is a BiOp project. 

ProjectID: 31017 

Monitor and evaluate the success of hatchery salmonid reproduction for reintroduction of 

anadromous salmonids to the upper Cowlitz Basin 

Sponsor: WDFW 

Province: Lower Columbia 

Subbasin: Cowlitz 

FY03 Request: $183,661 

5YR Estimate: $1,100,161

Short Description: Monitor the success of the reintroduction of anadromous salmonids to 

the upper Cowlitz Basin, including distribution, timing and success of reproduction of 

hatchery adults and success of upper basin seeding. 

ISRP Final Recommendation: Not fundable (Qualified - see comments) 

CBFWA Category: High Priority

ISRP Comparison with CBFWA: Disagree - Not fundable (Qualified) 

ISRP Final Review Comments: 

Defer decision until an appropriate experimental design is developed. Funding of #31005 

could proceed independent of #31017 but the value of that investment would be 

significantly reduced without the full development of the potential studies in the upper 

Cowlitz River (project #31017). 

The Basin has witnessed other unique opportunities to learn from new programs, that 

promised to develop appropriate experimental designs, but results have been less than 

expected. The upper Cowlitz offers one of the best environments and research 

opportunity but must be conducted under an appropriate design. At present the project is 

not conceived of as an experiment and appropriate hypotheses have not been developed. 

The response included three hypotheses (top page 5) but these only describe hypotheses 

that are implicit in the reintroduction program, rather than outlining an experimental 

design that would enable testing of hypotheses and methods for testing them. The study

design is not adequate and does not provide any confidence that valuable results will be 

gained from the project. Based on the responses for projects #31005 and #31017, the 

ISRP is inclined to recommend Do Not Fund. 

The ISRP has clearly indicated their support for the development of these two projects 

into a potentially important study for the Basin. 

“BPA has already invested heavily in the Cowlitz watershed by building the Fish Facility

($22 million) but this proposal has good cost sharing and local support. There is an 

opportunity for exciting and informative research programs concerning salmon 

restoration, role of nutrients in the ecosystem, and hatchery versus wild comparisons in 

the upper Cowlitz watershed.” 

34 
ISRP 2002-13 Mainstem and Systemwide Preliminary Review 

We continue to support the development of these projects and consequently recommend 

that a limited time (e.g. six months) be allowed for the development of an appropriate 

design before a final decision is made on these two projects. There are numerous

important questions in the Basin that could be studied in this environment, but the 

proponents do not seem to be aware of the opportunity presented. An advisory committee 

could be developed to assistant in the timely development of this design and execution of 

these projects.

Further, the responses to questions about recreational harvest focus on the regulation 

allowing targeting of marked hatchery fish and does not directly address the potential 

problem of incidental catch and release mortality. Discussion of the design should also 

consider the appropriateness of a recreational fishery in the upper Cowlitz. Can the 

fishery be relocated or limited to areas to minimize impacts?

CBFWA Review Comments: 

This project is considered part of the base for the Biological Opinion by NMFS.

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

Short Description: Continue to test and evaluate methods 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 

Response Needed? Yes 

ISRP Preliminary Comments: 

A response is needed. 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. 

Is there adequate scientific basis for the expansion of this project from a research-oriented activity

to a production prototype? The initial research does show interesting promise in development but 

does the degree of “unanticipated success in the early years” justify the extent and cost of 

expansion in 2003? The project would expand from a research-oriented program to a production 

35 
ISRP 2002-13 Mainstem and Systemwide Preliminary Review 

prototype activity, which may simply be ahead of the research at this time. Data presented 

suggest an increase in rematuration efficiency of kelts over the three years of study conducted 

(~15% 1st yr; ~30% 2nd yr; ~80% 3rd yr). These data probably do show increases in efficiency 

of rematuration due to learning during the three years of the study; however, the last value is 

skewed as all kelts were included in the first two year’s attempts at rematuration, while only those 

judged capable of rematuration (based on the 1st two years observation) were entered into the 

rematuration attempt on year 3. 

 

Another concern is coordination between this study and the large-scale kelt reconditioning 

program being operated by the USACE at Lower Granite Dam. In recent years, as many as 

15,000 kelts have been collected at Lower Granite Dam. This large number of kelts represents a 

potential resource for both experimental investigation and for population rebuilding of depressed 

upper basin steelhead stocks. The focus of this proposed project is on natural origin kelts only, 

whereas the large reconditioning and release effort by the USACE uses both natural and hatchery

origin steelhead. Reconditioning work and research objectives need to be coordinated between 

upper basin kelt reconditioning projects, so that larger-scale questions about recovery of upper 

basin steelhead stocks can be addressed in a coordinated manner. 

Additional questions concerning the methods are: 

1. The allocation of kelts captured is uncertain in the various objectives (Section 9f). Task 

1.3 refers to using the first 200 kelts for immediate transport and release, but then task 2.3 

establishes allocations of the kelts based on the number captured (i.e., > or < 200 kelts). 

If less than 200 kelts are captured then all are used for long term monitoring ... why this 

bias in the study?

2. Task 3.4 suggests that from 2003-2005 a minimum of 20 kelts and 20 virgin spawners 

would be radio-tagged and released and monitored upstream of the most adjacent

downstream hydroelectric facility. Why would these fish be transported downsteam with 

the inherent risk of mortality as opposed to being released into the river of origin

directly? Reviewers understand the value of tracking these reconditioned animals to the 

spawning grounds, but not the displacement downstream. 

3. Task 4 is a little difficult to understand. The ISRP’s understanding is that 40 virgin 

females will be collected and transported to the CRITFC/UI Collaborative Center for 

Applied Fish Science. This research will be performed as part of an MS degree research 

program under the supervision of salmon reproductive biologist Dr. Joseph Cloud at the 

University of Idaho. The females would be fertilized with cryopreserved sperm but the 

source of the sperm is not stated and why would cryopreserved sperm be required? If the 

intention is to avoid transporting males then sperm could be collected from males 

maintained at a local hatchery or from natural spawners. Further, in the spawning of the 

reconditioned female kelts, will the same males be used with each female? 

The proponents might also reconsider the issue of genetically effective population size with 

repeat spawners. These animals will increase the census population and could change the 

generation length (if they were a significant portion of the population), but they are likely to

decrease the Ne value due to the increased contribution from a small sample of the original 

parental stock. This issue may come down to a trade-off between demographic risk versus 

genetic but the actual effect/value of kelt reconditioning should at least recognize this potential.

Note: the ISRP has not reviewed the 3-Step submittal, but hopes to provide any additional review 

comments by mid-August. 

36 
ISRP 2002-13 Mainstem and Systemwide Preliminary Review 

Action Agency/NMFS RME Group Comments: 

HARVEST AND HATCHERY SUBGROUP -- Address critical element of RPA? It has no 

application to RPA 182, since hatchery/wild reproductive success is not evaluated as a part of the 

proposal. 

With respect to RPA 184, it has very limited application, since its goal is to simply use hatchery 

facilities as a means to “improve” the usefulness wild steelhead often found in juvenile collection 

facilities associated with hydro operations. This proposal fails to specifically address how 

conservation hatcheries can contribute to recovery. The proposal doesn’t develop an argument as 

to kelt reconditioning constitutes a hatchery reform. 

Opposing view. This could be a reform, if, for instance, a hatchery program live spawned fish 

and released them below Bonneville Dam or reconditioned them. Proposal may have relevance 

to RPA184, if it is characterized as a conservation hatchery strategy to replace current strategies. 

Scope? [ESU’s covered, Transferability, Species covered] Proposal targets steelhead, and may

have application to steelhead throughout Columbia River system. 

Study design adequate, as is, or as may be modified? Uncertain at this time. 

HYDRO SUBGROUP -- Elements of this proposal involve assessing the effectiveness of certain 

treatments relative to hydro passage experience by kelts. For example, some kelts will be 

transported to below Bonneville Dam in order to evaluate potential benefits of this passage 

option. This type of study would be classified as action effectiveness research in the RMEvernacular of the BO. It would be instructive if the authors provided additional detail regarding 

projected sample sizes and the ability to detect meaningful differences in adult returns, between 

hydro passage options (transport vs. not). 

ISRP Remarks on RME Group Comments: 

The RME group comments on 200001700 are consistent with the ISRP’s review comments. The 

RME group comments regarding the proposal’s failure to develop an argument about how kelt 

reconditioning could constitute a hatchery reform and the need for the authors to provide 

additional detail regarding projected sample sizes and the ability to detect meaningful differences 

in adult returns, between hydro passage options (transport vs. not) are worth addressing in the 

project sponsor’s response to the ISRP. 

ProjectID: 35014 

Measurement of Quantitative Genetic Variation 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. 

Response Needed? Yes 

ISRP Preliminary Comments: 

A response is needed. 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 

37 
ISRP 2002-13 Mainstem and Systemwide Preliminary Review 

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 would be predicted. However, if GxE 

interactions are insignificant, then one or a few genotypes may be best in all environments. 

The ISRP agrees with the importance of studies like this and strongly supports the integration of 

genetic methods in this study, however there are aspects of the design that should be 

reconsidered: 

1) The selection of 6 hatchery stocks and 3 treatments receives little justification. In the initial 

years of these studies the number of stocks could be limited (see comments in b) and pre-study 

tests of the treatments could be conducted before assuming that these treatments will result in the 

“stress” expected, or that the stress does not simply kill all the fish. What preliminary studies 

have been conducted? 

2) We are uncertain about a number of aspects of the proposed half-sib breeding design. 

a) Half-sib designs assume all males are independent; therefore, at least twice the number of 

males as females are needed. 

b) The design as described cannot directly estimate GxE interactions. For Task 2a, how do you 

expect to partition the GxE effect? 

c) There will likely be maternal effects that cannot be accounted for and there is no treatment 

replication within stock x family x treatment (i.e., no rearing container controls). Revising the 

design is likely to require more rearing containers and/or dropping some stocks to provide more 

containers. 

3) What is the value of maintaining the run-timing component within stocks? 

4) The budget implies three years of study but the text does not make any such reference (other 

than a reference to using rainbow trout later). What is the expected duration of these studies? 

5) Reliance on early development traits may not be appropriate. Phenotypic traits with strong 

relations to fitness (such as egg survival) may have very limited genetic variation. In which case, 

the outcome of this study may relate more to these specific traits than to a general feature of 

adaptive genetic variation. To minimize such a risk, it may be advisable to maintain the progeny

during early growth stages and examine additional traits less associated with immediate survival. 

6) There are issues in measuring GxE. First, the genotype being referred to is actually the family 

that will be composed of multiple genotypes. Here is where the real value of the molecular 

genetic studies could be used, but this aspect is not highlighted in the proposal. Second, if 

quantitative genetic methods are to be used to assess GxE interactions then there are specific 

breeding studies in multiple environments that can be used to estimate the interaction. Coupling 

these with the molecular genetic work could be a very original piece of research! 

7) Task 4 seems to imply that the results of these detailed studies will be compared with the 

production history of the source hatcheries. The inherent assumption that past production history

would relate to present genetic composition is weak and we question the utility of this part of the 

study. 

8) A final point for clarification is the authors’ use of ‘drift’. On page 9 Section 9, in the section 

on Genetic analysis of chinook salmon, the authors state “Differential success among family lines 

to environmental challenges will also be assessed by examining for changes in offspring genotype 

from that of the parents. Equalized familial representation across treatments will allow for the 

removal of variance associated with familial lines and variance due to drift.” It is not clear how 

these statements relate to the methods to be used and how genetic (presumably) drift relates to

38 
ISRP 2002-13 Mainstem and Systemwide Preliminary Review 

these analyses. Unless survival is very poor and/or highly variable between families, why does 

drift receive the profile it does in the proposal and why would equal family size control it?

The proposal should clarify who is actually conducting this research and the references cited in 

Section 2 should be completed. 

Action Agency/NMFS RME Group Comments: 

HARVEST AND HATCHERY SUBGROUP -- Address critical element of RPA? No. More 

relevant to RPA 179. The proposal does not attempt to address hatchery/wild reproductive 

success in RPA 182. With respect to RPA 184, it neither addresses the topic of hatchery

reform, nor address whether conservation hatcheries contribute to recovery. Too far removed 

from practical application and not adequately linked to specific reform under RPA 184. 

Opposing view. Relevant to RPA 184. Will examine genotype-environment interactions and 

will attempt to determine if incubation performance of a stock is related to life history 

performance and if incubation success could be used as a predictor of expected performance 

through the adult stage. Results of study may provide guidance in identifying and prioritizing 

populations for conservation activities. 

Scope? [ESU’s covered, Transferability, Species covered] Would address listed chinook. 

Results not transferable between species, ESUs, or populations, due to site- specific artificial 

selection regimes at experimental location. 

Study design adequate, as is, or as may be modified? 

No comment at this time. 

ISRP Remarks on RME Group Comments: 

The ISRP generally agrees with the RME group comments, siding more with the ‘opposing view’

but having concern about the study design. 

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. 

Response Needed? No, Fundable 

ISRP Preliminary Comments: 

Fundable, no response needed. This is an excellent, important, and well-written proposal. 

Summary statements of findings were provided showing 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 

39 
ISRP 2002-13 Mainstem and Systemwide Preliminary Review 

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). 

This proposal is well written and the researchers have maintained a very high level of scientific 

productivity. We would like the project sponsors to consider the following few comments: 

1. Our most basic concern is for the scope and size of this one project. The proposal 

provides very little in terms of numbers of samples taken, capability for timely processing 

of these samples, and technical basis of the sample sizes. The tier 2 sample sizes seem 

particularly small, but no basis for the determinations of these samples was provided. 

2. Section 9, page 16, Methods states that the captive brood chinook will not be sampled for 

DNA “because family-specific success data are already available through segregated 

rearing, marking, and enumeration.” It is not evident from this statement whether that 

family-success is based on breeding programs or a different DNA sampling task? If these 

fish have not been sampled for DNA and are released into Catherine and Lostine rivers 

they could not be included in the pedigree analyses. This point should be clarified to 

ensure there is no oversight. 

3. Section 9, page 12 Objective 1 Assumption. The authors suggest only partial sampling of 

potential parents can be compensated for by increasing samples sizes of offspring or the 

number of loci used. Increased sample size could improve precision, but we do not see 

how sample size alone can compensate for unknown parental genotypes? Increasing the 

number of loci sampled may assist if there are differences detected that are useful, but 

they also may not. The intention of this comment should be clarified. 

4. Two major cost items included were a new ABI 3100 capillary electrophoresis unit 

($150k, one-time cost, FY03 only) and the provision of an additional smolt weir in the 

Imnaha system ($115K). There is essentially no justification for these major expenses, 

what are the consequences of not funding? Is the smolt trapping coordinated (and 

agreed) with by others in the basin and why is it essential?

Action Agency/NMFS RME Group Comments: 

HARVEST AND HATCHERY SUBGROUP -- Address critical element of RPA? Relevant to 

both RPAs. The proposal applies to RPA 182, since it includes the study of reproductive success. 

Little Sheep steelhead portion addresses this RPA well. 

The proposal applies to RPA 184, as well. It relates to conservation hatcheries as a recovery tool 

(and the extent to which it might contribute). Some hatchery reforms are directed at reducing 

gene flow from hatchery fish to wild fish. 

Scope? [ESU’s covered, Transferability, Species covered] Target species are chinook salmon and 

steelhead. It covers most of an ESU and two listed species. Results should be broadly applicable. 

Study design adequate, as is, or as may be modified? Regarding Sheep Creek, the data presented 

at the captive brood workshop showed limited success at assigning parentage, an issue that 

40 
ISRP 2002-13 Mainstem and Systemwide Preliminary Review 

requires further discussion with investigators. This may be exacerbated for steelhead, where the 

genetic exchange with resident fish may be fluid, and where precocial and resident males are 

likely to contribute genetically. In general, good use of techniques available to determine 

contribution at this time. Incorporates latest genetic technology plus parentage analysis. This

may provide the most powerful insight to relative fitness of hatchery vs. wild spawners. 

It resembles some of the M&E programs addressing genetic effects from hatcheries – it describes 

basic genetic metrics (Ne, Fst, etc.), then tracks change over time. Continues long genetic data 

set, giving this special monitoring/evaluation value. For chinook, good monitoring for 

supplemented versus unsupplemented areas in the Grande Ronde (although straying into

unsupplemented areas has occurred, and will cloud results). 

ISRP Remarks on RME Group Comments: 

The RME group comments on 198909600 are consistent with the ISRP’s review comments. The 

BPA comments regarding Sheep Creek and the data presented at the captive brood workshop 

which showed limited success at assigning parentage, may be an issue that requires further 

consideration by the investigators. As noted in the RME group comments, the issue may be 

exacerbated for steelhead, where the genetic exchange with resident fish may be fluid, and where 

precocial and resident males are likely to contribute genetically. 

ProjectID: 199105500 

Natural Rearing Enhancement Systems (NATURES) 

Sponsor: NMFS 

FY03 Request: $1,158,969 

5YR Estimate: $5,711,234

Short Description: Evaluate NATURES effects on salmonid behavior, morphology, physiology, 

post-release survival, and ecological interactions. 

Response Needed? Yes 

ISRP Preliminary Comments: 

A response is needed. This proposal would continue evaluations of NATURES effects (seminatural 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 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. 

41 
ISRP 2002-13 Mainstem and Systemwide Preliminary Review 

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 

then 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. 

The ISRP is also concerned about the publication record of these studies. The authors note a good 

publication list but upon inspection of those publications there are really 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 should provide any available 

information about smolt to adult survival of NATURES-reared fish. 

Since the ISRP has extensively reviewed the designs to Objectives 1 and 2 in the past, we do not 

have significant questions on those portions. The proposers have responded to previous review by

incorporating study of the interaction between natures-reared and wild salmon. Concerning the 

sampling design for Objective 1 though, the proposed design includes monthly sampling of 100 

animals per replicate/treatment group. In large raceways with various levels of structure 

(NATURES treatments) we question that this is adequate to estimate the variance or size 

distribution in each treatment (likely is for mean size). The authors might re-consider their design 

by initially evaluating how variance decreases with increasing sample sizes. Further, in 

Objectives 1 and 2, all fish will be coded-wire tagged, but will they be mass-marked to indicate 

presence of the tag. Given that mass-mark selective fisheries for spring Chinook are commencing, 

the mark identification could influence the return of these tags. 

However, a major question related to Objectives 1 and 2 is not really technical in nature. It is

whether the Council’s FWP can support an additional 5-10 years of research into the NATURES 

components. Modified elements of NATURES are already being incorporated into facilities. 

Data collected so far on juvenile survival immediately post-release show small increments of 

greater survival by NATURES reared juveniles (above); but when translated into adult returns, 

the likely benefits could be small. 

In Objective 3 and 4, the authors refer to density in the treatment, but the reviewers’ reading is 

that this is the density at release into the artificial channels. How are the numbers of animals 

released determined and at what density are the animals reared? Reviewers suggest that the 

initial rearing density may be influential on the behavior of these fish even before they are 

released. 

The project requests a large budget: 

Objective 1 $624,300 Carson Hatchery NATURES study

Objective 2 $163,000 Carson Hatchery predator avoidance study

Objective 3 $173,284 Stream-channel rearing studies 

Objective 4 $169,285 Behavior studies in observation flume 

Objective 5 $ 29,100 Technology transfer 

Total $1,158,969 increases for 5+ years in proposal (9-10 years for total study)

Unfortunately there is essential no information in the budget description about how these values 

were estimated, what labor is involved and what charge-out rates were used. For example, 

Section 8 includes costs for Indirect but also includes costs for utilities, rents, communications, 

42 
ISRP 2002-13 Mainstem and Systemwide Preliminary Review 

printing under Other. What is the basis of these Other items that seem to be costs appropriate for 

Indirect cost accounting?

At present, the ISRP is inclined to recommend completion of the project after 3 brood years of the 

factorial study of NATURES components now underway at Carson NFH (the reduction from 5 

brood years would probably not entail an important loss of experimental power), and then a shift 

to evaluation studies at production facilities in the basin that are employing NATURES 

techniques. Oversight by the proposers could standardize experimental rearing approaches 

among the various facilities and coordinate data collection and analysis (as proposed in Objective 

5). Adaptive development of NATURES techniques could proceed at the various production

facilities. 

The ISRP is open to the proponent’s response to this suggestion in their reply.

Action Agency/NMFS RME Group Comments: 

HARVEST AND HATCHERY SUBGROUP -- Address critical element of RPA? Not relevant to 

RPA 182. Proposal has nothing to do with reproductive success of hatchery fish. Only juvenile

survival effects are examined. 

Relevant to RPA 184. By looking at effects of NATURES rearing on survival, and the ecological 

risk/benefits of NATURES fish released into wild, the project addresses both major issues 

associated with transforming (reforming) hatcheries to conservation tools, thus very pertinent to 

184. Conservation hatcheries may eventually employ NATURES rearing techniques to increase 

juvenile survival. 

It also has potential application to evaluating hatchery reforms under RPA 184. Hatchery

reform includes changes in rearing techniques, including the use of NATURES rearing, which 

deserve testing before universal application. 

Scope? [ESU’s covered, Transferability, Species covered] Target species include steelhead, 

chinook salmon, sockeye salmon and coho salmon. Results may be transferable to other 

hatcheries. 

Study design adequate, as is, or as may be modified? This is a continuation of the research on the 

effectiveness of NATURES hatchery rearing techniques. Adequate study design. No other 

comment at this time. 

ISRP Remarks on RME Group Comments: 

Our perception is somewhat different than the RME group; the proposal does have to do with 

reproductive success of hatchery fish in that it will study effects of NATURES components on 

smolt to adult survival. The ISRP agrees that the components of NATURES rearing should be 

tested before universal application, and in fact are concerned that the techniques are being applied 

universally without rigorous testing. The ISRP generally agrees that the design is good but we 

have some specific comments. The RME and ISRP apparently disagree in that the ISRP is 

concerned about the size of the budget and the justification for it. 

43 
ISRP 2002-13 Mainstem and Systemwide Preliminary Review 

ProjectID: 199305600 

Assessment of Captive Broodstock Technologies 

Sponsor: NMFS 

FY03 Request: $1,498,981 

5YR Estimate: $8,282,813

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. 

Response Needed? Yes 

ISRP Preliminary Comments: 

A response is needed. After the ISRP’s FY00 review, this project was funded for a one-year 

duration with subsequent funding contingent on inclusion of better details on organization, 

coordination, and subcontractors in the next proposal. The ISRP suggested that investigators 

structure this as an umbrella-type proposal with subsections related to: 1) growth and diet, 2)

health, 3) reintroduction strategies, and 4) genetic consequences. A detailed description of the 

overall organization and coordination structure should be included in the proposal. The present 

proposal is organized as the ISRP recommended, containing substantial detail on methods and 

organization. 

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 grey literature. The 

proposal also contains substantial methodological detail. This ongoing FWP project has an 

impressive list of accomplishments since 1994 and may be one of the better FWP projects in 

terms of publication of results in peer-reviewed scientific journals. 

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 Provincial review. 

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). 

44 
ISRP 2002-13 Mainstem and Systemwide Preliminary Review 

We are concerned about the idea that adults produced through the captive brood program can be 

released to reproduce with wild fish in natural streams (Idaho stocks only). Our concern is that as 

a means to re-introduce these stocks to the natural environment, the approach is far too high risk 

given the value of these fish and perhaps inappropriate. Given the extent of assessments 

conducted-to-date and reported in this proposal, we would recommend an immediate stop to this 

activity (except on a small research scale) until it can be proven that the strategy has any merit. 

The only merit we can see to this approach is allowing the animals to participate in mate selection 

and hopefully to interbreed with other conspecifics. However, a much more responsible approach 

may have been to develop controlled flow environments (artificial or natural sections of streams) 

where the animals could be protected. Re-introduction of captive brood fish is a major issue 

associated with this rearing strategy but there should be some minimum standard of care taken 

given the importance of these fish and the investment made by the Basin! 

The other issue is minor and concerns the wording involved in the inbreeding study. The authors 

refer to “progeny of mates chosen at random – the control”. However, our reading of the design 

would indicate that simply a random selection of returning adults (which would seem to ignore 

the use of the DNA pedigree data) would include some level of inbreeding accumulating in the 

control line. Is this correct or did the authors mean that their control would be composed of nonsibling relationships only? In these lines, these may be better described as an out-bred line, which 

would be an appropriate basis for comparison or control. 

Another area where the authors could further contribute to resolving critical uncertainties in the 

use of captive broodstock and supplementation technology is in the modeling of the timeframe 

and scale of incurring inbreeding effects via supplementation and captive broodstock programs 

(decrease in fitness) versus the potentially counterbalancing “cleansing” effect of natural 

selection on hatchery-produced fish as they become part of a naturally spawning population. 

Fitness impacts on populations can occur quickly in the hatchery environment (as documented in 

the literature), however, little information is available on how quickly the accumulated genetic 

load can be shed by salmon populations as they spawn naturally and local adaptation occurs. The 

balance between these two processes, including the magnitude of genetic (fitness) change and the 

timeframes over which they occur, may be the fulcrum upon which the long-term success or 

failure of these programs hinges. Thus, a major uncertainty is on what timescale can this 

“readaptation” occur? Is it compatible with our goals for recovery / rebuilding or does the 

readaptation process occur so slowly that it represents a constraint on how captive brood and 

supplementation programs can be used? 

The budget description is again quite limited and includes two points for clarification: what is the 

19% Leave surcharge and why are there costs under Other that again seem to be Indirect charges? 

The labor charges and cost sharing with NMFS needs clarification as this issue occurs in a few 

proposals. 

Action Agency/NMFS RME Group Comments: 

HARVEST AND HATCHERY SUBGROUP -- Address critical element of RPA? It has limited 

application to RPA 182, since it does not compare hatchery/wild reproductive success. Some of 

the proposed captive rearing evaluations compare the performance of hatchery fish to wild fish. 

Other evaluations in the proposal do not. 

Proposal is applicable to RPA 184. The use of captive broodstock as a conservation hatchery

technique is contemplated in the BiOp. Proposal may be useful to determining the potential of 

one type of conservation hatchery action to contribute to recovery.

45 
ISRP 2002-13 Mainstem and Systemwide Preliminary Review 

Scope? [ESU’s covered, Transferability, Species covered] Proposal will target chinook salmon 

and sockeye salmon. Results should be broadly applicable to most captive brood programs using 

these species/ESUs. 

Study design adequate, as is, or as may be modified? Yes. Generally, this proposal is for 

continued development/refinement of captive broodstock technology, focusing on a number of 

parameters that will ultimately affect success. However, some of the individual studies listed in 

the proposal do not fit under either RPA. 

ISRP Remarks on RME Group Comments: 

While there is no inconsistency between the ISRP’s comments on 199305600 and the RME group 

comments, there is also little relation. The ISRP’s comments focus on the technical soundness of 

the proposed integrated research program toward improving captive broodstock technologies and 

make several additional comments for further consideration and improvement of the project. The 

RME group comments note the degree to which the project relates to several RPAs and that the 

proposed research is likely to have broad application to most captive brood programs. The RME 

group comments will be useful in documenting the relationship of the project to the RPAs and 

BiOp. 

ProjectID: 199606700 

Manchester Spring Chinook Broodstock Project 

Sponsor: NMFS 

FY03 Request: $950,000 

5YR Estimate: $4,828,825

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. 

Response Needed? No, Fundable 

ISRP Preliminary Comments: 

Fundable. No response 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 Rhonde 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 including 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 how the program relates to other Basin programs were good, and the 

authors are preparing written protocols for all aspects of the captive rearing programs. 

46 
ISRP 2002-13 Mainstem and Systemwide Preliminary Review 

However, one omission would seem to be the M&E aspects ... 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 Rhonde 

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 back 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. 

Another uncertainty with the project that concerns reviewers is what are 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 that survive to be outplanted as 

adults constitute a representative sample of the initial broodstock population with respect to 

genetics and fitness attributes. 

Propagating captive brood stock 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. 

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. 

Response Needed? Yes 

ISRP Preliminary Comments: 

A response is needed. 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. 

47 
ISRP 2002-13 Mainstem and Systemwide Preliminary Review 

The specific objectives of this proposal are to: 

1) identify and compare the fine spatial and temporal patterns of homing and spawning of wild

and YKFP supplementation salmon relative to the Cle Elum hatchery, acclimation sites, and 

historical and current spawning reaches. 

2) describe and compare the prespawning migratory behaviors (e.g. exploring, proving, 

holding) and spawning site selection of homing wild and YKFP supplementation fish from

each of the acclimation sites using radiotelemetry; and 

3) characterize the site-specific physiological changes that occur in the olfactory system during 

imprinting to different acclimation sites to assess imprinting success. 

The Yakima 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. The EOG work is appropriately tied into the proposal and is relatively small scale 

compared to the work in-river. The lab is well equipped to conduct the research and the methods 

to be used are well established. The use of longer-term tags (6 months) will allow useful 

examination of holding areas and migration behaviors, and the coordination with the YFP 

samplings will provide for large samples of spawners and detailed sampling of redd locations. 

This research is really more consistent with Yakima M&E type work, but was not included in that 

proposal (there is no M&E in this proposal). 

Three issues need clarification in the response: 

1) At how fine a spatial scale can the redd mapping be conducted, and can it be related to 

the depth contours of the river? 

2) There seems to be a presumption that the distribution of spawners largely reflects homing 

or not (straying). How can homing be differentiated from simply selection of preferred 

spawning habitat and/or maintaining interaction with conspecifics? 

3) The proposal comments on the aggregation of hatchery fish. Will this aspect of behavior 

be routinely monitored? Some aspects of aggregations will be lost possibly by sampling 

carcasses only, will it be possible to sample groups of live fish (e.g., males are unlikely to

remain in a group following spawning)? 

Other points for comment: The budget includes sub-contracting with Dr. T. Quinn, U of 

Washington and support for one MS student and one Ph.D. student, plus hourly field assistants. 

The subcontracting is not noted in the proposal. Who would actually be conducting this research? 

Section 9g Facilities does not comment on the source of the fixed radio-tag receivers? 

Action Agency/NMFS RME Group Comments: 

HARVEST AND HATCHERY SUBGROUP -- Address critical element of RPA? 

It is relevant to RPA 184. Will provide information useful for planning/implementation of 

hatchery reform measures to increase homing fidelity and reduce straying of hatchery fish. 

With respect to RPA 182, a straying study may help determine the specific origin of hatchery fish 

spawning in the wild (some of whom are likely to be strays and should be so identified). 

48 
ISRP 2002-13 Mainstem and Systemwide Preliminary Review 

A portion of the proposal, the study of site-specific olfactory changes during imprinting, does not 

directly address either RPA 184 or 182. 

Scope? [ESU’s covered, Transferability, Species covered] The proposal does not address multiple 

listed species. The study offers no broader application than to the Yakima spring chinook

population. Could the scope of this proposal be broadened to include other species, e.g. 

steelhead?

Study design adequate, as is, or as may be modified? Yes. For RPA 184, the proposal will suffice 

to determine the spatial and temporal patterns of homing and spawning by wild and hatcheryreared salmon released from supplementation facilities (and to examine the physiological changes 

in the olfactory system during imprinting). 

ISRP Remarks on RME Group Comments: 

The ISRP’s comments are consistent with the RME group comments about the potential value of 

this study. The RME group comments will be useful in documenting the relationship of the 

project to the RPAs and BiOp. 

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. 

Response Needed? Yes 

ISRP Preliminary Comments: 

A response is needed. This proposal would evaluate the effects of the release of hatchery-reared 

steelhead (early summer release of yearlings) on the growth, survival, movement, and behavior of 

wild salmonids in the West Fork Elochoman River. Should this be an evaluation on wild 

steelhead or on salmonids generally? The text focuses on the former. 

While we believe this investigation under natural conditions would be useful, there are three 

critical issues to consider: 

1) The release of parr in early summer is not a typical strategy and draws into question the 

appropriateness of this design as a study of steelhead supplementation. Releases of large 

parr in the fall or as smolts would be more typical. This does not negate the value of this 

study but it should likely be considered a fishery research project more than a production 

or supplementation assessment. 

2) The use of the North Fork as a comparative base is not well justified. How do the streams 

compare in productivity, habitats, etc. Further, the likelihood of visual redd surveys, as an 

adequate assessment of adult returns and the value of supplementation is very risky and 

inadequate in the ISRP’s assessment. There will be a substantial amount of information 

and effort relying on the final assessment of adult returns and the proposed monitoring of 

adult returns seems inadequate. Without addressing this issue, reviewers believe the 

project is severely compromised. 

3) There is no information on the hatchery rearing of the fish to be outplanted. How large 

will hatchery parr be, at what density will they be reared, how many will be tagged, and 

49 
ISRP 2002-13 Mainstem and Systemwide Preliminary Review 

how will they be released? What is the basis of the 3000 parr to be outplanted? Is there a 

statistical basis for this value or is it based on some other criteria?

Other concerns related to the above are more specific points. 

a) Monitoring of growth and survival will be quarterly and based on “night 

seining”. The proposal suggests the performance of the parr will be related to 

“their location within the site will be recorded.” How is this possible with night 

seining? 

b) Will the movement of parr downstream be monitored year round? If large 

numbers of parr are displaced (hatchery or wild) it would be necessary to know 

their fate within the tributaries. Presumably, some could move downstream of the 

final site and out of the tributary.

c) Is it feasible to tag smolts or fall parr in the North Fork tributary to provide a 

marked population? This could provide a means or mark-recapture for smolt 

production and total adult census if a remote tag detection system was 

incorporated into this design. 

d) After this first out planting in 2004 there maybe “residual” fish holding into the 

next year when the outplanting occurs. Has this been considered and how will 

these fish be treated?

We support the development of individual-based models and think they could provide a useful 

tool in assessing supplementation and generally about the salmonid production in streams. 

However, there is no comment on how to validate the model. How will this be incorporated into 

the development steps?

It is very likely that a five-year study of steelhead in natural systems will have setbacks due to 

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.

Action Agency/NMFS RME Group Comments: 

HARVEST AND HATCHERY SUBGROUP -- Address critical element of RPA? 182- Poor fit. 

Mostly juvenile work. Since it does not study reproductive success or compare hatchery/wild 

spawning success, it does not address RPA 182 

Possibly relevant to RPA 184. It could be tied to reducing effects of juvenile hatchery fish, 

particularly competition after release in target stream. Some hatchery reforms target the 

ecological effects to listed fish from hatchery/wild interactions during the juvenile stage. But, it

is not clear whether this part of the study is related to any particular hatchery reform that has been 

effectuated or is being considered. 

Scope? [ESU’s covered, Transferability, Species covered] Target species include steelhead, coho 

salmon and cutthroat trout. Uncertain transferability, i.e., uncertain to what degree the 

conclusions would be transferable to Upper Columbia. 

Study design adequate, as is, or as may be modified? This proposal could be revised in order to

specifically relate it to a particular hatchery reform and tying the results to a metric for reducing 

extinction risk under RPA 184. 

50 
ISRP 2002-13 Mainstem and Systemwide Preliminary Review 

OCEAN AND ESTUARY SUBGROUP -- Does not address action items in BO related to the 

estuary. Focus is on hatchery fish interaction. There was a question whether this would be 

considered estuary or tributary during initial review. 

ISRP Remarks on RME Group Comments: 

The RME group comments are not inconsistent with the ISRP’s comments; however the RME 

group comments are clearly made through the lens of the RPA obligations and are useful in 

documenting the relationship of the project to the RPAs and BiOp. The narrow focus (and 

interpretation?) of the RPAs largely ignores the important contribution this study could make to 

better understanding interactions among wild and hatchery reared juvenile steelhead, which, in 

turn, could lead to more informed hatchery practices or release strategies that lessen the impacts 

of hatchery-reared juveniles on wild juveniles. 

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. 

Response Needed? Yes 

ISRP Preliminary Comments: 

A response is required. This is clearly high priority work that warrants continued funding and is 

overall a strong proposal. In general, the ISRP’s FY00 comments remain applicable. The 

proposal is well written and 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. 

The ISRP’s primary concern was why results of past monitoring were not presented? There are 

some obvious issues of concern such as what has been variation of family size in families of 

sockeye? Or, has mortality in the captive brood programs (sockeye or Chinook) been random

among families? How has data been used to structure mating schemes? In the absence of any

presentation of these data, the reviewers cannot comment on the timeliness of these analyses or 

adequacy of analyses. 

The proposal provides additional information on reports and publications that have resulted from

these studies to address some of the ISRP’s FY00 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 proposal has a long-term monitoring component that is needed to provide 

consistency and insights into the Redfish Lake sockeye captive broodstock effort. This effort, 

while necessary, is largely routine by this time. 

The most interesting aspect of the proposal, which could have been more fully described, is the 

more 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, West Fork of the Yankee 

Fork, and so on. This approach has very strong applied conservation biology implications and

51 
ISRP 2002-13 Mainstem and Systemwide Preliminary Review 

deserves to be better described in the proposal with respect to its methods, application, and 

management implications. 

This project also monitors the bi-catch of sockeye salmon in a sport fishery for kokanee in 

Redfish Lake and has demonstrated the bi-catch of anadromous or residual sockeye. While this 

concern is not the responsibility of this author, 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. What impact is allowed on sockeye in this fishery and how is it justified?

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. 

Response Needed? Yes 

ISRP Preliminary Comments: 

Response required. There is an important opportunity for a unique research facility, but we 

question the proposed initial use. While we agree that replication and use of controls could 

advance research on issues concerning hatchery-wild interactions in streams, the proposal does

not address whether 16 “streams” could truly be constructed as replicates and what the experience 

in other such studies have been. Have there been ecological studies that truly accomplished 

replication of environments? If so reference to them would have substantially aided in the 

presentation of this proposal. The author did comment on the issue of scale in ecological studies 

and that issue would be of consideration in this application, but if scale alone were the concern, 

then presumably the design could be modified to compensate. What is the origin of the proposed 

design of 16 replicate streams? Task 1 requests substantial funding for consultation but the 

design and choice of species is already proposed. Will these consultations lead to new research 

proposals? What is the basis of fall chinook use and why would these fish come from Hanford? 

What fish transfer and fish disease protocols would be implemented to protect investment in the 

facility and the local environment? 

We see little value in immediately undertaking such a demanding construction program. It would 

be reasonable to undertake the initial improvements as described and to distribute information on 

this facility; there may be substantial interest from other organizations with funds to support

independent research. Unless the technical capability of constructing several replicates can be

addressed more strongly (through support from the literature, etc.) and strong regional support for 

such an investment is provided, the ISRP does not support the immediate construction of these 16 

“stream sections”. We would favorably review a proposal to develop this research opportunity

but leaving the construction aspects to the needs of the chosen research program that eventually is 

provided access to this facility. Such programs may only want a few larger stream sections or, in 

an alternative use, may require construction of a few spawning reaches to experiment with the reintroduction of captive brood parents into a semi-natural (and protected) stream environment. 

The budget presentation should provide more information for review. For example, what does 5.7 

FTE but only $94,000 actually mean? 

52 
ISRP 2002-13 Mainstem and Systemwide Preliminary Review 

Action Agency/NMFS RME Group Comments: 

HARVEST AND HATCHERY SUBGROUP -- Address critical element of RPA? No. Proposal 

itself is not directly responsive to either RPA. Proposal is for design and construction of 16

experimental stream channels. There is a possibility that the experimental stream facility

proposed in this project could be used to investigate issues of relevance to RPA 184. 

Scope? ESU’s covered, Transferability, Species covered] Future research at the proposed facility 

would target fall chinook. No evidence in proposal of transferability to other populations, 

ESU’s, or species. 

Study design adequate, as is, or as may be modified? No comment at this time. 

ISRP Remarks on RME Group Comments: 

The ISRP generally agrees with the RME group comments, but the ISRP can see potentially

valuable uses for the facility other than those proposed that may have significant value for 

endangered ESU’s. 

ProjectID: 200000700 

Infrastructure to Complete FDA Registration of Erythromycin 

Sponsor: UI-CNR 

FY03 Request: $166,419 

5YR Estimate: $514,419 

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. 

Response Needed? No, Fundable 

ISRP Preliminary Comments: 

Fundable, high priority. The tasks included are required by FDA to allow continued use of 

erythromycin for salmon. This proposal seems to be a comprehensive response to FDA and 

proposes to maintain close interaction with the FDA in completion of this work. The PI 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. 

53 
ISRP 2002-13 Mainstem and Systemwide Preliminary Review 

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

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. 

Response Needed? Yes 

ISRP Preliminary Comments: 

Response Needed. After again reviewing this proposal as submitted to another provincial review, 

we continue to support the development of this proposal. However we are concerned that the 

design may not fully address the proposed objectives. 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). As proposed the project will measure

the reproductive value (juvenile production) of the cultured fish using DNA assessments, but the 

plan includes very little assessment of the animals during culture. Consequently, assessment of 

this research relies on the final assessment of the juveniles produced by the cultured and natural 

parents, but provides little information about mechanism/effects of culture. If, for example, the 

cultured parents do not demonstrate reproductive value similar to the natural parents there would 

be no information suggesting the cause of this result. A Ryman-Laikre effect could still occur 

through the proposed culture of 0+ parr for (essentially) 1.5 generations, but monitoring of the 

culture period would be required to observe this outcome. Minor changes in the design (see 

attached flow chart) would allow for the monitoring of the cultured population, but would depend 

on the availability of single-family tanks for initial rearing of juveniles and the capability of the 

personnel to sample the families. We request that the proponents review these suggestions and 

provide appropriate practical revision to the design. 

Our suggested enhancements to the study include: 

a) DNA sampling the original parr collected so that genetic variation in the source population is 

known 

b) Maintaining the families in individual rearing tanks until they are large enough to tag (CWT 

and/or PIT tags), sample families before pooling 

c) PIT tag at least 100 individuals per family before pooling in the raceways, this will facilitate 

studying family responses to culture (variation of growth--task 1.d.-- cannot be observed 

from observations of mean size of experimental groups.) 

d) Do not fin clip the fish as electronic sampling for blank wire will avoid the mortality

associated with these fin clips 

e) Incorporate culture regimens (diet, ration, schedules, etc.) that achieve natural growth 

trajectories of parr and pre-smolts rather than regimens that " Maximize...growth rate and 

minimize the variance in growth rate"--task 1.e. of the proposal. Physiological research on 

fitness of smolts (by Dickhoff and others) suggests that traditional growth-maximizing 

regimens may be inappropriate for supplementation programs. 

54 
ISRP 2002-13 Mainstem and Systemwide Preliminary Review 

f) Sample phenotypic traits of the PIT tagged fish as they are being released from the raceways 

as smolts including physiological assessments such as those proposed for coho smolts (task 

3.c.). 

g) Use the barrier fence to divert all adult steelhead through the facility and to electronically 

sample for CWT and PIT tagged fish. 

h) Incorporate truly randomized mate-assignment protocols (task 2.a.) (Quinn and others at 

Forks Cr Hatchery have shown that apparently random mate assignments in steelhead 

broodstocks are not random with respect to phenotypic characters) 

i) Consider how to sample and/or use kelts that will be produced and how to manage the barrier 

fence when the kelts are moving downstream.

The ISRP is taking this unusual step of providing detailed suggestions as this is the third time we 

have considered this proposal and each time have supported it. 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. The design as proposed would 

require a substantial investment in funds, facilities, and effort but, in our opinion, would not fully

investigate the objectives presented. 

We also note that 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. 

In our assessment, the recommended priority of these activities should be: 

i) Establishment of a Tier 3 Monitoring and Evaluation program complete with participation of 

WDFW, and replacement of the Abernathy fence through this submission. (High priority) 

ii) Conducting the steelhead broodstock study as expanded in the attached flow chart (with 

amended budget). (High-Medium priority), and 

iii) Conducting the coho over-wintering study (Low priority) What is the justification for the coho 

approach? Has overwinter instream survival of coho juveniles been identified as a limiting factor 

in the Abernathy Creek coho population?

Outline of Steelhead Research program for Project #35027 USFWS (figure - next page) 

55 
ISRP 2002-13 Mainstem and Systemwide Preliminary Review 

Outline of Steelhead Research program for Project #35027 USFWS 

X

Collect 400-500 0+ parr to be

reared to maturity in raceways at

Abernathy Hatchery.

Produce up to 100 full-sib families (1

male x 1 female) and incubate in

separate Heath trays

Sample every parent for DNA

screening and phenotypic traits ...

this is included in proposal

DNA sampling of parr not in

proposal, therefore, can not assess

effect of culture environmental

(potential impact on genetic

variation in brood stock).

At swim-up, families were to be pooled

for juvenile rearing. Family

differentiation is lost.

Suggestion: Transfer to single family

rearing tanks for grow-out until tagging. PIT

tag 100 fish per family and tag all with blank

wire. Increase budget by $6,500.

Proposal does not comment on

density of rearing in raceways

or methods used in culling?

What is density for rearing?

DO NOT finclip fish!

Pool all families in raceway for rearing to maturity. When sampled for size, PIT tags will allow tracking

of family performance. At release, all fish passed through PIT tag detector and PIT tagged fish sampled

for size and phenotypic traits.

On return, all fish diverted into Abernathy following installation of new barrier. All fish

electronically sampled for blank wire and PIT tags. All fish sampled for DNA and phenotypic

traits (sub-sampling maybe necessary depending on run size). May need to purchase

electronic sampling equipment (Tube detector $15-25,000). Fish released up-stream.

Sampling protocol for juveniles (parr

and/or smolts)? Estimated samples sizes

... basis of estimate? Objective 7

methods??

Is any information to be

collected from kelts? What

happens to kelts at the barrier?

56 
ISRP 2002-13 Mainstem and Systemwide Preliminary Review 

Action Agency/NMFS RME Group Comments: 

HARVEST AND HATCHERY SUBGROUP -- Address critical element of RPA? Relevant to 

RPA 182, 184. With respect to RPA 184, the steelhead aspect of the proposal may provide a 

viable alternative to "broodstock mining" and genetic bottlenecks for conservation hatchery

programs seeking to obtain and utilize local stocks (the thrust of many reforms). 

Scope? [ESU’s covered, Transferability, Species covered] Targeted species are as follows. 

Steelhead: Southwest Washington ESU, Coho salmon: Lower Columbia River, Southwest 

Washington coast ESU, Chinook salmon: Lower Columbia River ESU (naturalized population in 

Abernathy Creek). Proposal includes more than one listed species and ESU, and may have 

transferability to many others. As a side benefit, this technique, if successful, might have direct 

application to SNAPP (RPA 175) 

Study design adequate, as is, or as may be modified? Well designed and written. 

ISRP Remarks on RME Group Comments: 

The ISRP generally agrees, but has some questions and suggestions regarding the study design. 

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. 

Response Needed? No, Fundable 

ISRP Preliminary Comments: 

No response is needed. Fundable at a medium priority. The proposed project seems like a logical 

extension of the previously funded innovative project. 

As with proposal #35063, 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. 

Ms. Zydlewski has made a significant contribution through her work to develop stationary remote 

and portable detectors for PITs, and is now developing a proposal to utilize that technology. But 

in reviewing the objectives of this proposal, their Regional value 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. Her reference to life history

stages is really limited to pre-migratory, at migration and following in freshwater (residualism), 

and at adult return. For each of these stages, population size and survivals would be estimated 

but the methods for estimation are not fully described. 

57 
ISRP 2002-13 Mainstem and Systemwide Preliminary Review 

For example, in the three stages: 

i) in-river, pre-migration population size would be estimate by depletion methods (for 3 

sites), but how is this sample expanded to the total stream and species; 

ii) during migration, smolts population estimates would be estimated with the fixed

array and/or smolts traps, but it is not clear how the fixed array provides a population 

estimate; 

iii) at the adult stage (and assuming the new fish barrier is installed), all fish would be 

sampled but how would all the hatchery fish be identified (presumably associated

with #35063). 

In objective 2, they propose to assess frequency and magnitude of ecological interactions between 

hatchery-released and naturally produced salmonids. “Frequency and magnitude of individual 

interactions will be continually monitored at the stationary units and will be discontinuously

monitored, but on a regular basis, with the portable unit.” Page 13 of Section 9). However, these 

detections may monitor the movement and co-occurrence of these fish, but is this an adequate 

assessment of interactions? Objective 3 refers to novel tagging techniques but what is novel and 

important is not elaborated. 

Action Agency/NMFS RME Group Comments: 

STATUS MONITORING SUBGROUP -- This proposal seeks to evaluate stock status, 

distribution, and abundance of juvenile and adult salmonids using new PIT tag techniques. 

The proposal does not indicate applicability to either RPA 180 or RPA 181. None of the target 

species in the study area belong to ESUs covered by the NMFS 2000 FCRPS BiOp. The project 

proposes to study, among other things, the effects of PIT-tag size on juvenile fish survival and 

growth, which could be considered testing of tools (i.e., PIT tags) that are widely used in some

monitoring activities that do satisfy RPA 180. Therefore, while the proposal does not directly

meet RPA needs, the methodological aspects of the work, as well as its potential contribution to 

the development of Biological Opinion status monitoring performance standards merit 

consideration. 

ISRP Remarks on RME Group Comments: 

The ISRP and RME group comments are consistent. 

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. 

Response Needed? No, Not Fundable 

ISRP Preliminary Comments: 

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 Furunculosis, caused by Flavobacterium

psychrophilum and Aeromonas salmonicida. Coho and steelhead are most susceptible but other 

58 
ISRP 2002-13 Mainstem and Systemwide Preliminary Review 

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. 

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. This study won’t answer the question it proposes to 

answer. 

ProjectID: 198740100 

Assessment of Smolt Condition: Biological and Environmental Interactions 

Sponsor: USGS, CRRL 

FY03 Request: $256,000 

5YR Estimate: $1,781,050

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. 

Response Needed? Yes 

ISRP Preliminary Comments: 

Response required, this is a technically inadequate proposal. This proposal is difficult to really 

understand. 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. If 

the proponents wish to continue to provide smolt assessments on “an as needed basis” then that

should be clearly separated from a new research proposal. 

The new topic is to “determine if basic water chemistry and background levels of natural 

immunostimulants in rearing water sources affect early development of immune response, disease 

resistance, and long-term survival of eggs, fry, and smolts in relation to adult returns.” If during 

early development, biotic and abiotic characteristics of the aquatic rearing environment determine 

immune competence and disease resistance, then this innovative research could be very important 

to the basin. However, it is not possible to assess the research proposed from this proposal. The 

method isn’t well described here--a preliminary study design is given, but no data from that study

are presented. No design for statistical analysis is presented. The intention and value of the 

genetic screening are not clear. 

Annual ongoing tasks concerning smolt condition should be clearly identified in a separate 

proposal. It should be designed to directly assist facility managers throughout the program. 

59 
ISRP 2002-13 Mainstem and Systemwide Preliminary Review 

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 

Response Needed? Yes 

ISRP Preliminary Comments: 

This is a well designed program that will address three major issues: do hatcheries amplify the 

presence of Rs in the wild (water and fish), do hatchery juveniles with high Rs levels pose a risk 

to wild juveniles (tested in artificial stream tanks), and 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). 

It is not certain that the three proposed hatchery sites meet their stated (5) criteria. Added 

justification of the sites should be provided and the proponents should seek Regional input 

regarding these sites before implementing the study. 

What artificial streams would be used in objective 2? It seems that these are constructed 

fiberglass raceways but the point is not clearly presented in the proposal. 

What will be the statistical methods of analysis? 

Action Agency/NMFS RME Group Comments: 

HARVEST AND HATCHERY SUBGROUP -- Address critical element of RPA? Not relevant to 

RPA 182. 

This proposal would relate to RPA 184, since hatchery reforms include protocols to reduce 

disease transmission. Diseased wild fish would be less likely to survive to adult, which would 

affect the risk of extinction for listed fish. 

Relevant to RPA 184 and planning of hatchery reforms. Investigates influence of salmonid 

hatcheries and hatchery fish on transmission of disease to wild fish. Before the value of a reform

can be assessed, the occurrence of the problem needs to be assessed. 

Scope? [ESU’s covered, Transferability, Species covered] Spring Chinook, steelhead, and other 

hatchery-reared salmonids. Results generally transferable to other hatcheries and other ESUs, but 

may be pathogen specific. 

Study design adequate, as is, or as may be modified? Studies could also be combined with the 

heritability studies on disease resistance and immune function, this may also provide information 

on whether conservation hatchery breeding protocols may affect genetic traits for disease 

60 
ISRP 2002-13 Mainstem and Systemwide Preliminary Review 

resistance. This affects the degree to which conservation hatcheries may contribute to recovery,

at a genetic, in addition to a demographic, level (another topic under RPA 184). 

Could this proposal examine other pathogens at the same time? Proposal No. 35041 - Evaluate 

the relative fitness (mating success and progeny survival) of hatchery and wild spring chinook 

that spawn naturally in rivers 

Address critical element of RPA? Designed to directly address RPA 182. It is a direct 

examination of reproductive success hatchery fish relative to wild fish. This project has high 

likelihood of shedding light, based on empirical evidence using latest genetic analytical tools, on 

relative spawning effectiveness of hatchery fish vs. natural fish. 

The proposal may relate to a topic under RPA 184, i.e. conservation hatcheries. The issue of 

whether conservation hatcheries contribute to recovery depends, in part, on the reproductive 

success of hatchery F1s, and their progeny, spawning in the wild 

Scope? [ESU’s covered, Transferability, Species covered] Mainstem/system wide spring chinook. 

Transferability is good due to diverse experimental locations. 

Study design adequate, as is, or as may be modified? Good. Biological traits are suitable as 

surrogates for “fitness”. The inability to capture fish at Tucannon weir may weaken design for 

this captive stock. Significant precocious fish contribution would dilute ability to attribute 

progeny to hatchery or natural adult spawners. We may want to discuss with investigators ways

to improve the ability to carry comparison over into the success of progeny and other possible 

explanations for survival differences between hatchery and wild fish

ISRP Remarks on RME Group Comments: 

The ISRP generally agrees with the RME Group comments. 

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 

Response Needed? Yes 

ISRP Preliminary Comments: 

The development of a quantitative genetic program in Pacific salmon is a welcomed addition, and 

we encourage the proponents to continue to develop their experimental design. We are uncertain

about some aspects of the proposed research and are concerned about others: 

The experiment would be initiated in one spawning year and the second generation selected 

within lines and age-class. However, in the F2, generation selection at age-3 and then age-4 will 

generate two separate lines; this generates a risk of causing a bottleneck within the original 

selection lines (-ve, control, +ve lines). Further, unless there was good survival and maturity at 

ages 3 and 4, to produce sufficient numbers of progeny for the next generation only a very limited 

61 
ISRP 2002-13 Mainstem and Systemwide Preliminary Review 

selection pressure and differential may be possible. This is a diagram of our understanding of the 

proposed selection experiment: 

t0

Line 1, Gen 2, Age-4 maturity, captive brood

Cryopreserve?

smolts

Sea pens

Supplementation,

released to ocean

Age-2

maturity,

mostly males

Age-3

maturity,

both

Age-4

maturity,

mostly

females

Age-5

likely to

few fish

for use

Line 1, Generation 1, captive brood stock

Line 1, Gen 2, Age-3 maturity, captive brood

Each line (5 others) will have the same

problem but to differing degrees

depending on the survival and maturity

rates. In generation 2, the number of

lines and rearing space will double.

The proponents should clarify how they planned to deal with this scenario or demonstrate how 

their design would avoid this bottleneck. There seem to be three possible approaches: 

1) Initiate each line with adequate numbers of families/individuals to minimize this risk (this 

would be very dependent upon the freshwater facilities available) 

2) Select only one age-class for selection in the second generation, but this would have a 

significant effect on the desire to study correlated traits also, or 

3) Initiate the study during 2 or 3 years and determine how to conduct the selection during the 

second generation. How would a selection differential be determined with over-lapping brood 

years?

Objective 5 indicates that at least 2 generations will be followed and that further generations will 

be followed. There’s no analysis of how much response to selection may be observed in so few 

generations—there may be little evident response. 

The proposal also refers to using DNA analysis to monitor inbreeding in the lines. While it is not 

stated, we presume that the “pedigrees” refer to will not be used during the selection process and 

only used in tracking the change of inbreeding over time. If the potential effect of domestication 

is to be studied, then pedigrees should not be used to direct any of the matings. 

Domestication is a real concern in the use of artificial propagation and is deserving of 

experimental measurement and selection on return timing/spawn timing is known to be a source 

of domestication selection. While it’s understandable to want to observe correlated changes in 

maturation age in selected chinook, the difficulty of this experiment and the impractically long 

time commitment required by the experiment suggests that an experiment on a less complex, 

shorter lived, salmon, e.g. coho, would be more informative and could 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 maybe 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. 

62 
ISRP 2002-13 Mainstem and Systemwide Preliminary Review 

Action Agency/NMFS RME Group Comments: 

HARVEST AND HATCHERY SUBGROUP -- Address critical element of RPA? Although this 

proposal does not directly address either RPA 182 or 184, it may have some relevance to both. 

With respect to RPA 184, this proposal relates to hatchery reforms aimed at lessening 

domestication selection. The comparison of levels of domestication selection between 

supplementation programs and captive brood programs might provide insight on which types of

conservation hatcheries have the potential to contribute to recovery, compared to their respective 

domestication risks 

Opposing view. Of some relevance to RPA 184. Basic research, but not directly linked to what 

hatchery operators could apply in the real world to reform hatcheries. The problem already is 

"addressed," albeit imperfectly, by measures designed to minimize domestication selection. 

With respect to RPA 182, a study of domestication may provide information on a potential 

genetic risk of hatchery fish spawning in the wild, i.e. outbreeding depression. Likewise, the

inadvertent selection for altered run timing, and the transmission of those traits to wild fish via 

hatchery fish spawning in the wild, may be a valid biological concern. 

Scope? [ESU’s covered, Transferability, Species covered]Puget Sound Chinook ESU. Single 

species/ESU. Uncertain transferability. 

Study design adequate, as is, or as may be modified? Important basic research. The data from

this proposal concerning levels of inbreeding, however, might have limited , i.e. site specific, 

application, since the experimental populations at the UW have been under culture for several 

generations. 

ISRP Remarks on RME Group Comments: 

The ISRP generally agrees with the RME group comments but has stronger concerns about the 

design of the research. 

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

Short Description: Evaluate the relative fitness (mating success and progeny survival) of 

hatchery and wild spring chinook that spawn naturally in rivers 

Response Needed? Yes 

ISRP Preliminary Comments: 

Fundable, but could be funded in part if Provincial funds are limiting. 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 reviewers question whether 

there is any redundancy between this proposed work and the ongoing Moran and Waples work on 

steelhead? 

63 
ISRP 2002-13 Mainstem and Systemwide Preliminary Review 

The reviewers also note that the proposal is costly (10 years @ $1M per) due to conducting 

studies of juveniles and adults in three river systems. While we acknowledge the value of 

replicate studies and long-term monitoring to assess reproductive value, we question that each site 

is equally valuable and whether the researchers can complete the required work on all three. As 

the authors note, each of the sites has different attributes but the logistics of sampling is quite 

different in them. The Wenatchee system seems well suited to the sampling; the other two are less 

so. 

We also question the author’s comments on precocial male Chinook. “Age 1+ precocials may

migrate downstream, but generally do not reach the ocean. These fish are undesirable because 

of the potential for negative ecological and genetic impacts to natural fish, and because they are 

an undesirable fishery product.” (Page 17, Section 9). There is no doubt that hatchery rearing of 

spring chinook results in an abnormally high incidence of precocial development but precocity is 

likely associated with growth rates and an alternative male life history strategy. We strongly

agree with the author’s proposal to study this issue but would caution against concluding that the 

trait is “undesirable”. It may simply be a cost associated with intensive culture of spring chinook 

that are grown at unnatural rates. Reviewers are also unaware of any evidence that precocial 

males “do not reach the ocean”. This could be true, but what is the basis of this statement?

No comments were provided by the RME group on this proposal. Nevertheless, it is hard to 

believe that a project designed to evaluate the relative fitness (mating success and progeny 

survival) of hatchery and wild spring chinook that spawn naturally in rivers wouldn’t relate to 

several RPAs. Specifically, RPA 182 states: “to establish and provide . . . funding for studies to

determine the reproductive success of hatchery fish relative to wild fish ”. This mandate seems a 

near hand-in-glove fit to the title and objectives of Project 35041. 

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 seemingly at the core of RPA 182 also. Indeed, understanding differences in 

fitness between the two groups, and whether conservation-oriented hatcheries can produce fish 

that can integrate into natural populations and lead to long-term sustainability (i.e., the fitness 

question) is the $64 million question around which much of the present recovery plan hinges. 

64 
ISRP 2002-13 Mainstem and Systemwide Preliminary Review 

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. 

Response Needed? Yes 

ISRP Preliminary Comments: 

Response required. 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. 

There are three issues for response: 

1) the tasks associated with the technology transfer do not include “blind” tests of virus that the 

regional labs would process in order to confirm the accuracy of their work. Since several 

regional labs would be trained in these needed techniques, provided the necessary equipment, and 

then expected to contribute to the monitoring and control of the IHN M-clade, we suggest that 

regular testing for confirmation of methods should be incorporated.

2) The authors suggest that the overall goal of this work is to document the distribution of the Mclade and to control its spread in the Columbia basin. The proposal is not very explicit, however, 

in how prevention or control of the spread would result. This should be more clearly explained in 

the proposal. 

3) We ask the proponents to consider a more active investigation of the M-clade distribution and 

control of its spread. The authors make a good case for the importance of this research and 

monitoring, but if the spread of M-clade is a threat to recovery, why not take an immediate active 

role in sampling and examination of the current distribution and then management of the virus? 

The budget could be adjusted appropriately. 

We believe each of these points can be readily addressed by the authors and recommend a high 

priority for this proposal. The budget as presented seems very reasonable given the extent of risk 

presented by this virus. 

65 
ISRP 2002-13 Mainstem and Systemwide Preliminary Review 

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

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. 

Response Needed? Yes 

ISRP Preliminary Comments: 

A response is needed; this proposal is likely fundable in part. The proposal is aimed at obtaining 

information needed for management of chum salmon and chinook salmon spawning below 

Bonneville Dam. 

There is insufficient justification of the need for the effort to determine the “feasibility” of 

estimating the juvenile chum salmon production from the mainstem Columbia in the Ives/Pierce 

Island area, as proposed under Objective 2, Task 2.b. Furthermore, the proposed method, to 

employ a mark recapture estimation procedure, would need to be described in more detail before 

it could be considered to be likely to succeed. The investigators need to give 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 response should address the following points: 

• The background statement should be enlarged to establish an understanding of the

broader regional needs for flow and water management in the mainstem Columbia River. 

For example, it should be made clear that the investigators understand the tradeoffs that 

are involved in providing water to enhance spawning effectiveness in this area with use 

of water later to provide flow volumes to enhance outmigrations of upriver juvenile 

salmon. 

• An enlarged background statement would help identify 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. 

• It would seem to be appropriate to include in this proposal, either as background or as a 

specific task, exploration of the feasibility of opening up additional spawning area at the 

mouths of tributaries in the lower river. 

• Under Task 3.b Analysis, it is said that “Regression analysis will be used to determine in 

a statistically rigorous manner the extent to which each habitat metric plays in predicting 

habitat”. This statement needs to be enlarged upon for clarification and to establish 

credibility.

66 
ISRP 2002-13 Mainstem and Systemwide Preliminary Review 

Action Agency/NMFS RME Group Comments: 

HYDRO SUBGROUP -- This proposal appears to be in direct response to RPA 199, RA-2001. 

That RA (2001) calls for research to collect relevant information for lower Columbia fall chinook 

and chum salmon spawning populations. The tasks in this proposal appear to satisfy the 

information requested in that RA. The Willamette Lower Columbia TRT has been developing 

guidelines for delineating population structure of these species. Their finding would appear to 

have bearing on population sampling resolution that may be required to satisfy status monitoring 

requirements under the BO. Presumable that RME work group will treat that matter further. 

The proposal calls for the CWT implantation of Ives/Pierce Island fall chinook. It is not clear 

how these will be discriminate from other stocks that may move downstream and inhabit those 

locales. Clarifying this would be helpful. 

ISRP Remarks on RME Group Comments: 

The frequent use of the words “appear to” in the RME comments appear to hedge a bit. The RME 

technical comment on CWT implantation of fall chinook and the difficulty expected in 

discriminating from marked upstream stocks is a point that the proposers should address in their 

response. 

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. 

Response Needed? No, Fundable 

ISRP Preliminary Comments: 

Fundable. 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. Existing spawning areas to 

be used to clarify habitat criteria for 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 

67 
ISRP 2002-13 Mainstem and Systemwide Preliminary Review 

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 and that the proposal suggests consideration of changes in 

reservoir elevations and other power operations indicates that it may be taken seriously. The 

proponents give clear hypotheses followed by good objectives, tasks, and scientifically

appropriate methods to test the hypotheses. The proposal provides that there would be monitoring 

and evaluation of affected spawning habitats should any operational changes be implemented. 

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. 

The ISRP had several questions that do not require a response but which might usefully guide the 

research. There are legitimate questions 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. Is the Priest Rapids flow agreement for the mid-Columbia a potentially good 

model for the lower Snake River for fall chinook spawning? 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 embededness) 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)? 

In summary, this is a good proposal that warrants funding based on the ISRP review criteria. 

 

ProjectID: 35030 

Evaluate potential to enhance spawning of summer/fall chinook salmon in the tailrace of Chief

Joseph Dam, Columbia River 

Sponsor: PNNL and CCT 

FY03 Request: $134,220 

5YR Estimate: $539,984 

Short Description: Evaluate the potential to increase mainstem spawning habitat for summer/fall 

chinook salmon in the Upper Columbia 

Response Needed? Yes 

ISRP Preliminary Comments: 

A response is needed; generally fundable, but important background elements are missing from

the proposal. These elements would demonstrate that the proposers are aware of the complexities 

of the water management system that forms the context of the potential for increased spawning. A 

response is needed. 

 

The proposal is to explore the potential to enhance spawning of chinook in the tailrace at Chief 

Joseph Dam, but it needs to describe limitations to potential that are in place for other reasons. 

Operations at Chief Joseph Dam are already bound by the “Vernita Bar Agreement” for 

protection of fall chinook spawning, incubation, emergence, and now fry emigration in the 

Hanford Reach. The Agreement calls for stabilized flows out of Priest Rapids during those times. 

68 
ISRP 2002-13 Mainstem and Systemwide Preliminary Review 

Since Chief Joseph and the other mid-Columbia dams below Grand Coulee are “run-of-the-river” 

projects, operations of all are affected. (See for example ISG “Return to the River 2000”, 

NWPPC Doc 2000-12, p. 451-2 for a description of effects of the Vernita Bar Agreement). In 

what way does the Agreement affect chinook in the Chief Joseph tailrace? The proposal should 

also review the work of Chapman et al. 1983 that led up to the recommendations included in the 

Vernita Bar Agreement. That review would provide an appropriate context for the work proposed 

here. (Chapman, D.C., D.E. Wietkamp, T.L. Welch, and T.H. Schadt. 1983. Effects of minimum

flow regimes on fall chinook spawning at Vernita Bar 1978-82. Don Chapman Consultants, inc.

Report to Grant County P.U.D. No.2, Ephrata, WA. Boise ID, 123 p.) 

Description of these and other factors affecting operations and/or habitat conditions at Chief 

Joseph Dam should be provided in the proposal in order to establish boundaries within which 

potential enhancement of spawning of chinook in the tailrace at Chief Joseph Dam might be 

accomplished.

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 

Short Description: Predict stranding-related mortality using a GIS and statistical approach by

incorporating fish behavior and ramping rate information. 

Response Needed? Yes 

ISRP Preliminary Comments: 

Generally fundable, but a response is needed which would more adequately describe how this 

proposal might meet a management information need which is not available from previous 

studies. 

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. It appears that the proposal is in response to previous studies that have focused 

on features of the habitat that might lead to stranding. If this is so, then the proposal should 

provide more detail on shortcomings of previous studies, and more specifically identify the 

expected outcomes of this proposed project that might lead to improved management of flows or

other measures. It appears that the previous studies, which might be termed habitat studies, may

have provided a more direct approach to identifying what might be the same solution or set of

solutions to the stranding problem. One of the solutions that has already been identified and 

adopted is provision of stabilized flows during the time of emigration of fry from the Hanford 

Reach. While the proposal implies that this provision has not been adequate and the proposal 

provides some estimates of numbers of juveniles estimated to have been stranded in the previous 

three-year period in support of the claim, no information is provided on corresponding patterns of 

flow at the time of stranding other than to state that “This [previous study] has been used by

hydropower operators to liberalize fish protection programs since 1999.” 

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 

69 
ISRP 2002-13 Mainstem and Systemwide Preliminary Review 

to monitor fall chinook at Vernita Bar during spawning, incubation, fry emergence, and now fry

emigration. Before recommending this study for funding, the reviewers will need to be assured 

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. 

There is a need to more fully describe the measures that are in place to stabilize flows in the 

Hanford Reach as a result of the “Vernita Bar Agreement”, which calls for stabilized flows during 

spawning, incubation, fry emergence, and emigration in the Vernita Bar portion of the Hanford 

Reach. (See ISG 2000 “Return to the River 2000”, NWPPC Doc 2000-12, p. 451-2). 

The proposal does not present a convincing argument for the need to deliberately manipulate 

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). If on-the-ground studies are necessary, it 

should be possible to observe the effects on chinook fry of ramping rates and duration of flow 

reductions of various magnitudes during periods not encompassed by the Vernita Bar Agreement 

(as modified in 1999). The Agreement is not designed to protect down to the last fish. And the 

power operators are certain to undertake load following as soon as restrictions on operations are 

relaxed. 

Further to this point, the proposal raised questions about the potential for extraction of further 

important information from existing data. This should be discussed in the proposal. From the 

discussion on page 2 and the oral presentation it appears that estimates of entrapment area and 

estimates of stranded fry were pursued somewhat independently, with the result that knowledge 

of the effects of hydropower operations is not sufficient to be able to predict numbers of stranded 

fry to be expected under various operating scenarios. The possibility of using existing data to 

arrive at such a capability should be discussed in the proposal. It ought to be possible to relate 

estimates of stranded numbers and estimates of entrapment area, each that relates to the same 

operating conditions, i.e. develop a table that shows a set of conditions of ramping rate, duration, 

and relative volume of reduction (%), and corresponding estimates of numbers of fry stranded 

during each such episode, and estimated area of potential entrapment. Such a table could be used 

to develop a regression equation to estimate numbers of fry expected to be stranded under those 

scenarios. If this effort should prove to be successful, the pursuit of behavioral studies to identify 

mechanisms involved in stranding would not be necessary.

With information already available from previous studies, it ought to be possible to identify 

certain areas responsible for major strandings. Has thought been given to the possibility of 

opening these up with a dozer or other mechanical means, deepening a downstream outlet end of 

the pool to facilitate emigration of fry? 

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ISRP 2002-13 Mainstem and Systemwide Preliminary Review 

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. 

Response Needed? Yes 

ISRP Preliminary Comments: 

Generally fundable with high priority, but a response is needed on a few issues described below. 

This is a good long-term 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. 

A response should address how the economic, social, and regulatory factors related to existing 

floodplain development, or to the potential for changes in floodplain use, will be incorporated 

into the ranking system. These economic, property, and regulatory issues should be directly 

addressed during this investigation, ideally through bringing on another investigator trained in 

economics, or through a subcontract with an economist. The response should also include a 

monitoring and evaluation plan to allow determination of success of the project. A mechanism 

for an independent review of the resulting ranking of floodplains should be specified as part of 

the M&E plan. 

The ISRP recommends that Council carefully review the budget during the contracting period.

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. 

Response Needed? Yes 

ISRP Preliminary Comments: 

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 is worthwhile research project that should provide recommendations for 

normative changes in flow regimes in the Yakima that maximize recruitment of cottonwoods. The 

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ISRP 2002-13 Mainstem and Systemwide Preliminary Review 

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. The sponsors 

need to address the following: 

1. The sponsors need to provide better evidence of the linkage of changes in flow regimes, 

geomorphic processes, and cottonwood recruitment to changes in stream habitat and in the 

aquatic community, especially the fish community. What kinds of habitat changes are to be 

expected from improved cottonwood recruitment? Perhaps the research needs an empirical 

component that specifically addresses the relationship between changes in cottonwood 

communities and changes in the channel and aquatic community. At a minimum a much more

comprehensive discussion of the relevance and benefits of this research to fish communities is 

needed. 

2. How do differences in surface elevations (A and B in Figure 2 and Objective 2, Task a) relate

to cottonwood recruitment? What relative values of A and B are desirable and what ones are not? 

3. In discussing the results of the innovative project some empirical evidence needs to be 

presented supporting the contention that the current flow regime disrupts recruitment processes 

(page 26). A more thorough and concise discussion of the kinds of flow management options that 

could improve recruitment would be beneficial. 

4. Objective 4 related to model development needs to be expanded. What kinds of models are 

being considered? What are the critical parameters in the models? Exactly how will the data 

collected in the previous three objectives be used in model development? 

5. The sponsors propose additional studies to extend research to other important reaches (with 

distinct flow regimes) within the Yakima. Observation of variation among reaches of the Yakima 

Basin is claimed to be critical to the extension of research findings to other alluvial reaches of the 

Columbia Basin. The sponsors claim “Since cottonwoods are a keystone species in the 

biodiversity of riverine corridors, our findings will be critical to a number of large flow-regulated 

rivers in the western United States. Hence, our results will not only be significant for managing

regulated flows in the Naches and Yakima rivers, they will also be relevant where flows are 

regulated on alluvial reaches elsewhere in the Columbia River Basin.” If additional studies are 

necessary to extend the research to other important reaches within the Yakima Basin is it likely 

that the results will be relevant elsewhere? 

6. The project needs an M&E plan. 

Action Agency/NMFS RME Group Comments: 

HABITAT ACTION EFFECTIVENESS RESEARCH SUBGROUP -- Does the Proposal meet 

RPA Objectives?

They have one stated objective that suggests a potential experimental base upon which to ask the 

RPA 183 relevant question of action effectiveness: can regulated flows be modified to promote 

recovery of riparian cottonwood ecosystems? However, the sponsors do not propose to measure 

any listed salmonid survival rates or other variables directly relevant to 183, nor would this be

possible in their Flathead control area. As such, 35062’s direct relevant to 183 is very limited. 

Elements the proposal is lacking. 

Measurements of salmonid survival rates, variables directly relevant to 183, and site location to 

meet these objectives are lacking. 

Means and Opportunities to Strengthen Proposal. 

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ISRP 2002-13 Mainstem and Systemwide Preliminary Review 

This is a clear, focused and well-supported proposal. The focus is on the ecology of the trees 

with some superficial references to how that in turn affects habitat for anadromous fish. It is 

unclear if this project can be modified to address questions regarding the affects of riparian 

improvement projects on fish. 

ISRP Remarks on RME Group Comments: 

The ISRP’s comments, especially question 1, are consistent with RM&E comments. 

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 

Response Needed? Yes 

ISRP Preliminary Comments: 

Generally fundable, but a response is needed on administration and sampling. Could this 

proposal be combined with another larger program for efficiency and programmatic review? 

Comments from ISRP were mixed reflecting the historic value of the program but the declining 

needs due to mitigation being put in place and evidence that TDG levels up to 120% are not 

showing signs of GBD in salmonids. Also, there were and remain questions about the design of

the sampling. 

The FY00 ISRP recommendation was to fund for one year: “Subsequent funding would be 

contingent on programmatic review. Assuming the monitoring continues, this would be a 

candidate for a multi-year review cycle. This entire set of smolt monitoring projects needs to 

receive a programmatic review with one of the goals to develop and justify a program-wide 

design that really is capable of delivering enough data, of high enough precision, to answer 

specific management questions.” It appears that after ten years of GBD R&D the question of how 

much M&E is needed in the future needs complete examination. If the Council calls for an 

independent review, here are some of the topics and questions that it could address regarding 

GBD monitoring and associated TDG causes: 

1. A status report on the USACE on construction of TDG mitigation on all federal dams primarily

in the form of flip lips. How have those functioned and what is the TDG duration curve at each 

dam under various flow scenarios? 

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

and spill in recent years is largely voluntary. There are models that predict the amount of TDG 

expected for various flow/spill scenarios and flood conditions. If those analyses show that TDG is 

highly unlikely to be violated, then this might be evidence to eliminate or modify the GBD 

program. Do the models have good calibration so we can depend on them? 

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ISRP 2002-13 Mainstem and Systemwide Preliminary Review 

3. GBD risk to the population of juvenile migrants is primarily contingent upon the various 

passage strategies employed -- transportation, spill, bypass, etc. The GBD program should be 

keyed into regional plans of the use of transportation and in-river paths. 

4. TDG 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 

standard should be re-examined for Columbia and Snake river dams. 

5. During floods and emergency outages, TDG may rise unexpectedly and cause high levels of

GBD even with flip lips in place. It would be interesting to hear whether a GBD SWAT team

could be developed for limited but specific duty. For example in years when high flows are 

anticipated, uncontrolled spill and TDG’s 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 exposing higher numbers of migrants 

to high TDG. During emergencies, or future anticipated flood conditions, the agencies should 

maintain a capability to sample for GBD on short notice by having the expertise available that can 

mobilize to a specific site for a specific problem. 

ProjectID: 35013 

Species- and site-specific impacts of gas supersaturation on aquatic animals 

Sponsor: CRRL 

FY03 Request: $494,249 

5YR Estimate: $2,731,036

Short Description: Address critical uncertainties about effects of gas supersaturation on aquatic 

animals 

Response Needed? Yes 

ISRP Preliminary Comments: 

A response is needed. This is a well-prepared proposal to fill some key uncertainties in the gas 

bubble disease story. The initial impression is there is already extensive data on effects of TDG 

on many migrating fish but not these species. Thus except for documenting further fish response 

to assure that impacts are contained within a 120% TDG limit, is the research likely to lead to

alternative proposals that are already aimed at reducing gas in the river? 

Much work has been done showing the problem is not as great as once supposed for salmonids, 

but admittedly, persuasive data are not available for the species/groups proposed here. The 

proponents have built upon their own work and work of others (including regional planning 

documents) to identify the needed next steps. There are some good objectives and study plans for 

approaching them. The FWP is not mentioned but should be referenced in the response. The rest 

of the ISRP review criteria are met. The work is of an M&E nature. An organization question is

whether this project should be incorporated in the existing 199602100 (support to GBD 

monitoring by Smolt Monitoring Program) or vice versa (the existing project has dwindled to

very small funding). 

Two other factors also suggest the limited potential for new revelations about TDG as the studies 

are currently designed and located: (1) all three species tend to be bottom oriented and deep 

water species, and most TDG effects are in the upper two meters of the water surface due to 

hydrostatic compensation and (2) the levels of TDG are generally not excessive at either The 

Dalles or Bonneville. The exception might be for conditions requiring passage via ladders where 

shallow conditions exist in fishways. We share the concern regarding the limited numbers of bull 

trout at Hood River. 

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ISRP 2002-13 Mainstem and Systemwide Preliminary Review 

A location where bull trout are having problems with TDG is in Lake Pend Oreille. Annual spill 

from Cabinet Gorge dam in the Clarkfork River creates high TDG levels in a relatively shallow 

river, in the Lake and the dam blocks passage. Current efforts by AvistaCorp are aimed at 

improving TDG there and initiating passage. This area seems to have much greater value in 

archiving bull trout behavior and physiological data and would be a much more valuable 

laboratory as bull trout are abundant, but seriously reduced from historic levels. Unless the 

researchers can demonstrate a significant TDG flow duration curve at the proposed location, 

efforts there may be unlikely to yield the desired data due to inadequate test conditions. The low 

numbers of fish there also present a challenge to gathering sufficient data. 

Some of the objectives and tasks do not spell out samples sizes or sampling schedules that are 

intended to be used, e.g. for lamprey the proposal does not specify a sampling protocol that would 

be used to “Conduct field studies to determine if Pacific lamprey in the wild are impacted by high 

TDG.” Similarly, there is no information on how many adult salmon might be included under 

objective 4, nor at what TDG levels (page 11). 

As for white sturgeon data, the population appears to be in sufficient condition to allow 

significant harvest. If larvae are exposed to TDG, are the impacts likely to be significant to 

limiting the population below Bonneville? Recruitment is occurring. What mitigation would be 

possible over and above what is being done with flip lips, spill control etc? 

The lamprey studies seem to have more justification for study given the paucity of data and their 

differences from teleost fishes. However, TDG levels below BON dam may be insufficient for 

good data. Have the researchers examined other sites such as Willamette Falls for this study? 

Lamprey are abundant, easy to collect at the falls and the falls may present high TDG levels at 

times (this needs to be checked). The lab component of this study seems to have good merits. 

The data analysis of TDG exposure to migrating adult salmon and subsequent spawning seems 

like a good study to complete. Some data suggest adult migrants use the deeper sections of the 

thalweg of LGR reservoir to migrate. Thus, successful spawning of “exposed” adults may

demonstrate compensating mechanisms. The lab duplication has less value as the fish are not 

exposed to the other rigors of the river after a TDG exposure, but may shed some light on 

whether reproduction is physiologically hindered by TDG exposure. 

The response should include a review of Earl Dawley’s resident fish and benthic organism

studies. 

In summary, several elements of this study do not seem as potentially beneficial while others do. 

Less justified:

· Studies of bull trout at Hood River and near TDA dam

· Studies of lamprey at BON dam

More justified : 

· Studies of bull trout in Lake Pend Oreille and lower Clarkfork River 

· Studies of lamprey where TDG has higher/longer frequency, Willamette Falls? 

· Lab studies of lamprey exposure to TDG 

· Data analysis of spawning frequency of adults exposed to TDG during migration 

· Artificial propagation studies of salmon after TDG exposure. 

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ISRP 2002-13 Mainstem and Systemwide Preliminary Review 

Uncertain with Data Provided: 

· Studies of sturgeon larvae in populations below BON dam

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. 

Response Needed? Yes 

ISRP Preliminary Comments: 

A response is needed. 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. A wide variety of configurations and flows could be tested via these simulations (far 

more than 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. The proposal meets most of 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, but Bonneville Dam may

76 
ISRP 2002-13 Mainstem and Systemwide Preliminary Review 

not be the best place to test this model. The ISRP would prefer further consideration (calibration, 

validation) of the model at other dams so that the model is not constrained by any peculiarities of 

Bonneville. 

The ISRP has concerns, however, over the need for this model. 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 must cover a wide 

range of project operations. This data might be used as comparison among designs or operations

that would provide guidance in this regard. The ISRP reviewers remain skeptical that 3D 

computational fluid dynamics modeling can add much to the field data and analyses that have 

already been produced. The proposal could have provided a fuller discussion about the specific 

flaws or gaps in existing information that might be provided by a new mathematical model (that 

would need to have field data for input and validation). 

The presentation and discussion 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 others). The 

proponents need, however, to show how their near-field model will link with these existing farfield models. 

In summary, the ISRP has specific information requests: 

1. Describe how the CFD model could be linked to the existing far-field models so that the 

predictions could be compatible with existing monitoring station data. 

2. Better justify the model development in light of existing empirical spill/TDG data. Some points 

to respond to: What specific flaws or gaps in existing empirical information call for this model? If 

the CFD Model plans are for new designs, this makes sense. However, aren’t most spillways 

already fitted with TDG improvements (flip lips)? This would have been a valuable tool before 

the decision and commitment of funds to install flip-lips. Is this proposed because the Corps 

wants to rethink that decision? If this project is to model existing spillways and structures, it 

makes less sense. Is it to modify the existing spillways? Please explain what new structures are 

planned or contemplated and specifically how CFD modeling would benefit pre-design. 

3. Describe how other dam spillways besides Bonneville could be used in the 

calibration/validation process to make the model less specific to Bonneville Dam. 

4. Justify this expenditure as a BPA-funded project rather than as a Corps project, considering its 

close association with the hardware of a dam. 

 

77 
ISRP 2002-13 Mainstem and Systemwide Preliminary Review 

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

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.

Response Needed? Yes 

ISRP Preliminary Comments: 

A response is needed. The quality of this proposal is extremely high. This is an exceptionally

thorough proposal for research on a topic that needs attention. The investigators are highly

knowledgeable of the techniques and literature. The proposed research is scientifically sound; it 

is consistent with 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 staff seems 

exceptionally well qualified for the type of work proposed. Some very good science is likely to be 

done under this proposal. Thus, the expectations from the authors to implement the program and 

obtain results are not questioned. 

But a key question is whether the research is likely to lead to useful results and implementable 

mitigation? Do pesticides in question exist in sufficient quantities in the environment such that 

those concentrations are likely to have measurable effects and can be partitioned and separated

from other large and known sources of salmon mortality. Although a variety of pesticides are

used and detectible in the environment, what are the concentrations and identities that are 

expected at levels in which salmon would be affected. If there is evidence, it should be cited. 

Is the model realistic? The use of a copper based model and surrogate for organic pesticides 

seems convenient but not necessarily realistic. No evidence was provided to show copper 

concentrations exist in the Columbia River or most tributaries of the levels likely to be toxic or

have sub-lethal impacts. Copper does exist in the Clarkfork River in high concentrations. There 

the homing instincts of rainbow trout and bull trout, two potradromous species, seem extremely

well developed (Schmetterling, personal communication, MDFWP) in this extremely copper 

contaminated system. Milltown Dam is one of the most studied and evaluated cleanup sites on 

EPA’s superfund list. 

Is the work directly applicable to salmon? The proposed work is physiological research (driven 

by good ecological issues). The question arises is what is the actual relevance of the studies to the 

real world of salmon. For example, how applicable is the zebrafish model to salmon and what 

evidence is there that the rapid development rate of zebrafish embryos (a tropical species) 

represents much slower development of coldwater salmon embryos? 

Are natural concentrations and mortalities significantly detectable to warrant the research? The 

discovery of microscopic anatomical or physiological anomalies after exposure to high

concentrations of a toxin in a rapid developing model (zebrafish) in vitro may present unrealistic 

results and lead to unwarranted conclusions (Type 2 statistical error- i.e. find problems that don’t

actually exist for example, that pesticides from lab data extrapolated to the wild indicate a 

mortality component for wild salmon when there may be none). Response? 

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ISRP 2002-13 Mainstem and Systemwide Preliminary Review 

Are there potential affects on other species of fish and if so, what would be consequences to 

salmon? The authors hypothesize that predators may gain some advantage over smolts with 

impaired olfactory senses; however, should such a pesticide condition occur, why wouldn’t the 

predators species have similar impairment?

Does evidence exist in nature that shows any unusual patterns of straying that might be connected 

with pesticides? The authors hypothesize olfactory impairment from pesticides may be a source 

of straying. Is there even anecdotal evidence that specific basins, sub-basins or tributaries with 

higher levels of pesticides (even use, if not data) show higher rates of straying than other basins? 

Can we really get at the question of genetic consequences of pesticides? The authors hypothesize 

that genetic integrity of certain weak stock ESU’s may be compromised by straying. The 

introduction of artificial selection to 95% of the salmon migrants via various artificial 

propagation (hatchery) techniques and selective harvest of the past 50 years seems gargantuan

compared to the potential problem of incremental straying from a pesticide source. A simpler 

hypothesis is that if pesticides are entering the salmon’s life cycle, it is likely that those 

individuals and populations are carrying an additional genetic or environmental load. If this is

true, a more direct approach to warrant the physiological studies proposed herein would be to find 

at least one watershed that has physiological detectable concentrations of copper (or other toxins) 

and then emulate that condition in the lab. At the same time, the problem of toxicity can be 

addressed as a preventative measure while research confirms the extent of the mechanism and the 

extent of the problem in the lab. 

If any results suggested that pesticides were an additive component of lifecycle mortality, how 

would such a finding be extrapolated over all populations and with all other causes of mortality? 

This becomes statistically daunting when in even a healthy system, 95-98% of the smolts do not 

return, mostly for unknown causes. 

Alternative Research Designs. Is there any possibility of an alternative experiment that would use 

salmon, perhaps in populations known to be exposed to certain toxins; e.g. are there known 

exposed and control populations in nature that could be used as subjects of this study? The 

current approach asks us to extrapolate from zebrafish to salmon and do theoretical population 

modeling using a large suite of hypothetical variables about olfactory impairment and gene flow. 

The ISRP would be more enthusiastic if the model were with salmon and in a location where 

pesticide is actually found in known concentrations of concern in the environment? 

Summary. 

(1) Please address the basic evidence that pesticides in the environment are having a measurable 

and detectable impact on the return rates of salmon. Of the 100 pesticides identified, how many

exist at concentrations are physiologically affecting sub-populations of salmon. Please identify

evidence of specific impairment or straying or genetic or environmentally detectable load on any

population. Address the concern that the model of zebrafish in the lab has several limitations to

direct application to salmon in the wild. Address alternative approaches using salmon, potentially 

in nature. 

(2) If a potential connection between copper and salmon is found, how significant is this source 

of mortality versus dozens of other sources not only of other pesticides, but also of dams, harvest, 

predation, ocean losses etc. Normal mortality rates are already above 95%. This speaks to the 

previously defined experiment, as the treatment and control will be exposed to all these 

cumulative impacts. 

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ISRP 2002-13 Mainstem and Systemwide Preliminary Review 

(3) The research seems extremely interesting to basic science, but please elaborate more directly

on the likelihood that results will be directly applicable to the management of the FCRPS and 

salmon recovery. For example, hypothesize some expected and quantifiable impact, and what 

might be done about it. Wouldn’t it be simpler to keep concentrations of harmful chemicals at 

sub-physiological impairment levels? This is EPA’s mission and the toxicological research is

usually in the realm of EPA chemical use and approval domains. Shouldn’t this research wait for 

more details about natural concentrations of toxins? Some fascinating observations were cited by

the authors about physiological and behavioral responses to predator alarm pheromones. What 

types of research 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?

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. 

Response Needed? No, Not Fundable 

ISRP Preliminary Comments: 

Not Fundable. 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 

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 acronym RPA 

seems to have been used in several places when the general BiOp is meant. 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 

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ISRP 2002-13 Mainstem and Systemwide Preliminary Review 

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 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 (although known to the proponents 

from solicitation materials, they are not clearly identified in the proposal). 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. The ISRP’s concerns are unlikely to be 

resolved in a response. 

Action Agency/NMFS RME Group Comments: 

HABITAT ACTION EFFECTIVENESS RESARCH GROUP -- Does the Proposal address RPA 

Objectives?

This proposal is designed to examine the effect of temperature and food availability on juvenile 

salmon growth rates within the John Day Subbasin. While the experimental layout, with pristine 

treatment areas and anthropogenically altered control areas, is well designed for the study

objectives, its relevance to 183 is limited. 

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ISRP 2002-13 Mainstem and Systemwide Preliminary Review 

Elements the Proposal is Lacking. 

The proposal does not directly meet the requirements of RPA 183. The sample size and site 

selection do not adequately address monitoring needs. 

Means and Opportunities to Strengthen the Proposal.

It could be made more applicable by simultaneous measurement of salmonid survival rates in 

treatment and control areas, in addition to growth rates. This proposal will also benefit from

increased sample size and site selection that produces more representative sampling. The basic 

material is present to generate a high quality project. 

ISRP Remarks on RME Group Comments: 

The Action Agency/NMFS RME Work Group’s review concludes that the proposal, while 

directed at RPA 183, does not meet their needs. The ISRP concurs. 

Juvenile and Adult Fish Passage 

ProjectID: 199403300 

The Fish Passage Center 

Sponsor: PSMFC 

FY03 Request: $1,316,323 

5YR Estimate: $7,257,504

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. 

Response Needed? Yes 

ISRP Preliminary Comments: 

This is a useful and needed project; however the methods section is too brief to allow scientific 

review. Methods must be attached to each task and provided in sufficient detail (or adequate 

summaries and references given to written protocols or reports) to allow review and ensure 

documentation for future use of data. Results and plans for quantitative monitoring and 

evaluation of this project must be given. It is not appropriate for one of the most quantitative 

projects to not have a quantitative monitoring and evaluation plan for itself. 

The response should contain a careful self-review evaluating the advantages and disadvantages of 

combining this project with the CBFWA proposal #35033 to form a systemwide monitoring and 

evaluation project. 

Action Agency/NMFS RME Group Comments: 

STATUS MONITORING SUBGROUP -- These comments are aimed at how the 199403300 

Fish Passage Center proposal addresses RPA 180, which calls for the development of a program

to determine population and environmental status while allowing ground-truthing of regional 

databases. The proposal includes some important elements in the service of the Biological 

Opinion RPA 180, specifically, the measurement of annual juvenile population abundance, 

survival, and SARs. Useful guidelines for the proposal, taken from document 

Mainstem/Systemwide Province Stock Status Program Summary (February 22, 2002), are given 

below. We suggest that the sponsors address these guidelines in the proposal. Using these 

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ISRP 2002-13 Mainstem and Systemwide Preliminary Review 

guidelines, we have commented on how the proposal 199403300 can be strengthened or clarified 

to help meet the RME needs specified in RPA 180. 

Guidelines: Tier 2 Population Status-Juvenile Life Stage: 

1. Clearly identify the demographic unit (e.g., population, ESU, deme; wild/natural or hatchery 

origin) over which sampling will take place. 

Comments: It would be helpful if the proposal would clearly identify the demographic units 

targeted. According to reports on the FPC website, Comparative Survival Study work appears to 

be aimed at spring/summer chinook juveniles of hatchery-origin, while the Smolt Monitoring

Program is aimed at all salmon species. Presumably identifying demographic units can be done 

using PITTAGIS data system and FPC databases. As far as RPA 180 is concerned it is measures 

of population abundance, survival, and trend that are of interest. The proposal would be made 

more relevant to the RPA 180 if it had a thorough treatment of wild juveniles. The current FPC 

work is more relevant to hatchery-born juveniles, and, according to the CSS report, it cannot 

presently be demonstrated that hatchery-born juvenile survivals can be used to reliably estimate 

wild-born juvenile survivals. The method for constructing confidence intervals for wild fish 

juvenile numbers, adult numbers, and in-river survivals should be explicitly treated in the 

proposal. What progress has been made in this endeavor? Do the confidence intervals indicate 

that estimates are reliable?

2. Clearly identify the spatial scale represented by each samples (e.g., reach, watershed, basin). 

Comments: The location of the samples for the Smolt Monitoring Program (traps and dams) are 

clearly indicated in the proposal. For the Comparative Survival Study tagging sites, it was 

necessary to read reports on the FPC website. A link (or reference) should be supplied to this 

information, along with a table of the tagging sites. 

3. Identify the performance measure or indicator that will be monitored (e.g. summer/winter 

juveniles, outmigrating smolts). If different methods are used to enumerate the same population, 

specify. 

Comments: The performance measures are described in the proposal. They include smolt-to-adult 

ratios, juvenile passage survivals, and relative abundance measures. 

4. Describe the method used for enumerating the indices, e.g., snorkel surveys, electrofishing, 

smolt trap, and the error associated with the method. 

Comments: The method for estimating juvenile survival (the program MARK) is outlined in the 

proposal. The proposal should have greater detail in the methods for estimating relative 

abundance and smolt-to-adult ratios. It should reference papers and reports where detailed 

methods are given for estimating these measures. The proposal should describe which measures 

have standard errors and confidence intervals reported, and how they are developed. 

5. Specify any expansion factors (e.g. aerial expansions, trap efficiency) or other adjustments 

(e.g., daylight trapping only) that need to be applied to the raw counts. Provide the rationale 

supporting the use of those expansion factors, how the factors change over time, how they are 

estimated, and assess their reliability. 

6. Provide an assessment of the accuracy and precision associated with the proposed methods for 

estimating juvenile abundance or an index of juvenile abundance. 

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ISRP 2002-13 Mainstem and Systemwide Preliminary Review 

Comments: Estimates of bias and precision should be available for all estimates derived. When 

sample sizes are small biases can be large and precision poor. How will bias be assessed? 

HYDRO SUBGROUP -- As part of the FPC activities a variety of smolt survival estimates are 

generated using combinations of hatchery and wild fish. In the RME-context of the NMFS BO, 

these estimates could be useful in computations of D, EM and testing compliance with survival 

Performances Standards for the hydro system. It would be instructive if the investigators 

provided examples as to how these might be applied to such. Given there are a number of other 

NMFS (D, EM, inriver survival estimates) and CBFWA (CSS) studies producing hydro-related 

survival estimates, it would be useful to understand what the applications of the collective 

estimates are. It appears that there may be overlap for some stocks and river segments. However, 

this is difficult to decipher since the efforts are not treated as a whole. This is probably more of a 

regional process matter than one specific to FPC investigations. 

ISRP Remarks on RME Group Comments: 

In general the ISRP agrees with the comments provided. We would suggest that it may be 

adequate to reference and summarize written documents to provide some of the detail asked for in 

the comments.

ProjectID: 198712700 

Smolt Monitoring by Federal and Non-Federal Agencies 

Sponsor: PSMFC 

FY03 Request: $2,481,100 

5YR Estimate: $13,493,183

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. 

Response Needed? Yes 

ISRP Preliminary Comments: 

This is a useful and needed project; however, the methods section is too brief to allow scientific 

review. Methods must be attached to each task and provided in sufficient detail (or adequate 

summary and reference given to written protocols) to allow review and ensure that they are 

documented for future use. Results and plans for monitoring and evaluation of this project must 

be given. It is not appropriate for one of the most quantitative projects to not have a quantitative 

monitoring and evaluation plan for itself. 

This is one element of work by the Fish Passage Center. The response should clarify the tasks and 

budget for smolt monitoring that is contracted out to the states and tribes. To be consistent with 

ISRP’s statements on implementation of a systemwide M&E program (see proposal #35033) the 

proportion of the budget passed through for participation of other agencies and tribes that could 

potentially be reallocated under the overall CBFWA proposal #35033 should be identified. The 

response should contain a careful self-review evaluating the advantages and disadvantages of 

combining this with the CBFWA proposal #35033. 

Action Agency/NMFS RME Group Comments: 

HYDRO SUBGROUP -- The proposal identifies three BO research actions (1240,-41,-42) that 

can benefit from information obtained under this program. These research actions are linked to 

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ISRP 2002-13 Mainstem and Systemwide Preliminary Review 

RME RPA 199 in the FCRPS BO. We further note that some of the estimates generated in the 

SMP may also have utility in the context of juvenile performance standards (Hydro) specified in 

the BO. 

RA 1240. Specifies the evaluation of the spillway weir at LGR Dam using telemetry techniques. 

The contribution of the SMP would be to collect fish to use in the research. 

RA 1241. The action specifies that telemetry be used to assess smolt behavior and survival at 

dams in the Lower Columbia. The contribution of the SMP would be to collect fish to use in the 

research. 

RA 1242. The objective of this RA is to evaluate inriver migration survival and transportation 

survival from LGR to BON Dam. Fish PIT tagged under the SMP have the potential to 

contribute to this. However, it is not clear if the sample sizes described in the proposal will 

generate survival estimates with suitable precision. It would be instructive to detail these points 

in a revised version of the proposal, so the utility of the proposed survival estimates can be 

estimates can be evaluated a priori. 

Performance Standards. The survival estimates derived from the PIT tagged SMP fish can 

potentially have application in the evaluation of BO performance standards. However, concerns 

regarding the suitability of precision need to be addressed before this could be determined. Also, 

as we noted for the NMFS survival proposal, the reliance on hatchery stocks may restrict the 

utility of these fish, since ESA focuses on wild stock performance. If this proposal remains 

linked to ESA needs, then it should offer evidence or rationale to support the use of hatchery fish 

as surrogates for wild populations. 

ISRP Remarks on RME Group Comments: 

In general, the ISRP agrees with the comments on this proposal. Specifically, the response 

should address the precision associated with survival estimates of wild fish through the 

hydropower system and use of hatchery fish as surrogates for wild fish. 

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

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. 

Response Needed? Yes 

ISRP Preliminary Comments: 

The response must include an outside peer review of the estimation process by a qualified 

statistician(s) or there must be a programmatic review by the ISRP allowing adequate time for 

careful evaluation of the estimation process before a positive recommendation for funding can be 

given. Previous reviews by the ISAB and the ISRP resulted in the conclusion that the overall 

design of the data collection was adequate to meet the primary objectives of the project, but that 

the statistical properties of the proposed analysis procedures (mathematical formulas) should be 

further investigated before conclusions are based on data from this study. The previous ISRP and 

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ISRP 2002-13 Mainstem and Systemwide Preliminary Review 

ISAB reviews did not approve the specific mathematical formulas in the reports issued by this 

project. Adequate review of the proposed analysis procedures is not feasible in the time allocated 

for the review of all proposals in the Mainstem and Systemwide Province. 

When will the project end? The reason for the project stated on page 2 is to answer, “ can 

transportation of fish to below Bonneville Dam compensate for the effect of the hydrosystem on

juvenile survival rates of Snake River spring and summer chinook salmon during their 

downstream migration?” It appears that the direction of the project is changing to the point that 

the proposal should be considered a new proposal. The project began in 1996 yet the proposal 

notes a rather tentative goal on page 2, and repeated on page 3, " This study is intended to begin 

to provide the basis for the Mainstem Monitoring and Evaluation (M&E) Program’s analysis of 

long term alternatives for recovery of depressed listed and unlisted stocks of chinook and 

steelhead." The response should contain a careful self-review evaluating the advantages and 

disadvantages of combining this project with the CBFWA proposal #35033 to form a systemwide 

monitoring and evaluation project. 

The proponents should summarize progress toward publication of the results and methods in the 

peer reviewed literature, if any attempt has been made. 

It was mentioned that bootstrapping would be used to obtain confidence intervals on the point

estimates and we agree that this may be an appropriate procedure. However, the problem is 

deeper than estimation of variances. The formulas proposed are ratios of ratios and the 

magnitude of mathematical bias in the point estimates should also be evaluated. In addition, 

maximum likelihood estimators and perhaps others should be developed and contrasted to the 

proposed ad hoc estimators to determine the most accurate and precise estimates possible with the 

available data. 

Why is NMFS not on the interagency Comparative Survival Study (CSS) Oversight Committee? 

It seems that they are one of the primary users of the results and should be directly involved in

oversight of the project. 

Action Agency/NMFS RME Group Comments: 

HYDRO SUBGROUP -- The proposal identified several Hydro-related RME-RPAs that the 

research would support 185 (“D”), 187 (“D”), 188 (lower Columbia stocks), and 189 (EM). 

The RME Hydro work group recognizes that the proposed research has the potential to provide 

data and estimates useful in satisfying elements in those RPAs. Hydro-related RME RPAs 185, 

187, 188, and 189. The smolt survival estimates have further application in the context of testing 

compliance with the Hydro performance standards as noted for other proposals in this review. 

The proposal was thorough in specifying sample sizes comprising key index and treatment 

groups. However, it would be beneficial if that information was translated into precision 

estimates. Alternatively power analyses for key hypothesis tests could be presented to 

demonstrate the estimates will be satisfactory for evaluating key hypotheses remaining in the 

region. This would also aid in assessing the utility of the information in performance tests that 

would be performed at the checkins. 

ISRP Remarks on RME Group Comments: 

In general, the ISRP is in agreement with the comments. 

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ISRP 2002-13 Mainstem and Systemwide Preliminary Review 

ProjectID: 199008000 

Columbia Basin Pit Tag Information System

Sponsor: PSMFC 

FY03 Request: $2,532,711 

5YR Estimate: $13,717,975

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. 

Response Needed? Yes 

ISRP Preliminary Comments: 

The programmatic need for operations and maintenance support for collection of PIT tag 

information is clear. The relationship to many high priority programs is documented. The 

objectives and activities are clearly listed. Three aspects of the proposal should be clarified in the 

response. First, what is the process for obtaining metadata on data in PTAGIS and is the process 

adequate to ensure long-term usefulness of the data. Second, methods were attached to specific 

tasks, but are too brief to allow scientific review. The methods should include references to 

written protocols or details should be provided in the proposal to ensure consistent operations in 

the future. Third, quality assurance goals are specified but monitoring and evaluation of success 

should be given. A monitoring and evaluation plan must be given in this proposal. It is not 

appropriate for one of the most quantitative projects to not have a quantitative monitoring and 

evaluation plan for itself. 

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. 

Response Needed? Yes 

ISRP Preliminary Comments: 

Generally fundable -- the proposal deserves high priority -- but a response is needed. The 

proposal includes a Monitoring and Evaluation component. However, more detail should be 

given on study design and determination of sample size. The power to detect important “failures”, 

etc. should also be given. Are there quality control standards in place for performance of such 

devices?

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ISRP 2002-13 Mainstem and Systemwide Preliminary Review 

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; to 

Response Needed? No, Not Fundable 

ISRP Preliminary Comments: 

Do not fund. There is a need to integrate the entire smolt monitoring/PIT tagging and other 

tagging responsibilities into a systemwide monitoring and evaluation program. The 

responsibilities described in this proposal should be shifted to the Fish Passage Center. Review of 

proposals is a task included under this proposal, which overlaps the responsibility of the ISRP.

Action Agency/NMFS RME Group Comments: 

STATUS MONITORING SUBGROUP -- 

a. Does a proposal satisfy the objectives of RPA? 

This proposal is not explicitly linked to RPA’s 180/181 in the narrative, but it is implicit that 

some tagging studies can/do support RPA 180 (Population and Environmental Status Monitoring 

– Tiers 1 and 2) by having the potential to estimate life-stage specific survival rates such as SAR. 

The proposal does reference 15 unspecified RPA Actions that involve pit-tags. 

b. If not, explain what elements are lacking. 

An explicit linkage to RPA 180 and specific objective, tasks, and methods to ensure that pit-tag 

studies that can support RPA 180 are identified and reviewed by the proposed Tagging Study 

Technical Committee. The proposal in its current form is aimed at being a central clearinghouse 

for all proposed and on-going tagging studies. 

c. If the proposal partially satisfies the RPA objectives, suggest means or opportunities to 

strengthen the proposal. 

One approach the proposal should consider is using state and federal scientific take permits to 

track the who, what, and where in the application of tagging technologies. For example, in 

Oregon the 4d and State Take database can tell exactly who is pit-tagging how many of what

species where and for what reason. NMFS or States throughout the Columbia would require 

similar information. 

d. If a proposal is entirely satisfactory, indicate so and note the particular strong points. 

e. Assess the feasibility of the proposed work in general terms. 

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. 

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ISRP 2002-13 Mainstem and Systemwide Preliminary Review 

HYDRO SUBGROUP -- The Hydro work group sees a need for the coordination activities 

identified in this proposal. Many of the survival studies linked to RME RPAs appear redundant 

in coverage, while gaps can be evident. A forum to coordinate tag use and coverage, particularly

in terms of satisfying BO needs could be advantageous to the community. 

ISRP Remarks on RME Group Comments: 

The RME group comments on this proposal are rather lengthy compared to others, but none of

them is in conflict with ISRP comments. In fact, the most substantive comment is in full 

agreement with the ISRP recommendation to include the work under an existing project, such as 

the Fish Passage Center. It is quoted as follows: “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 on-going work statements with the same 

net result.” 

ProjectID: 198331900 

New Marking and Monitoring Techniques for Fish 

Sponsor: NMFS 

FY03 Request: $878,000 

5YR Estimate: $2,886,900

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 

Response Needed? Yes 

ISRP Preliminary Comments: 

Generally fundable, but a response is needed. Investigators should prioritize the subprojects and 

split out the budget into components. Each of the subprojects should include a plan for 

monitoring and evaluation of effectiveness of each task. 

Action Agency/NMFS RME Group Comments: 

HYDRO SUBGROUP -- The proposal sponsors indicate this project addresses RPA Actions 50, 

87, 192, and 193. The RME subgroup sees direct and critical association with 50, 87, and 192. 

However, we question the extent that this project contributes to 193 (RPA Action 193 includes 

discriminating hatchery and wild fish, tracking fish in oceanic environs, and determining growth 

and survival for specific wild stocks. 

This project provides PIT tag detection infrastructure support, specifically

development/refinement of transceivers, antenna, and associated hardware/software used at dams 

and in small streams. Its current focus is on the expansion of current PIT-tag interrogation 

technologies for adult PIT detection in fish ladders (RPA Actions 50 and 192) and juvenile PIT 

detection through high flow systems (e.g., Bonneville second powerhouse corner collector, fullflow surface bypass facilities, and small streams; RPA Action 87). These developments include 

transceiver upgrades for multiplexing and auto-tuning, and alternative antenna design (e.g., 

arrays, flat plate). 

Juvenile and adult PIT tag detection facilities at dams are critical to estimating reach survival, 

assessing progress toward hydrosystem performance standards, evaluation of transportation, and 

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ISRP 2002-13 Mainstem and Systemwide Preliminary Review 

addressing critical uncertainties such as delayed transportation mortality, extra mortality, passage 

through multiple bypasses, and adult return rates. 

For purposes of hydrosystem RME and performance standard tracking, objectives 1, 2, and 4 are 

very relevant. The RME subgroup wants to emphasize the continued importance of development 

of high flow juvenile PIT detection at the Bonneville second powerhouse corner collector - this is 

imperative for sustaining sufficient detection rates in the lower Columbia River. We also want to 

emphasize the continued support of developing adequate adult detection capability in fish ladders. 

Each is imperative to assessing progress toward hydrosystem performance standards. The Status 

Monitoring subgroup should assess the priority and adequacy of objective 3, development of instream PIT tag interrogation systems. Objective 5, adaptation of state-of-the-art technology to

tagging fish (e.g., video technology, spectral analysis) does not appear to be associated with any 

RPA Action. 

ISRP Remarks on RME Group Comments: 

The RME comments are primarily descriptive of the proposal. There is no conflict between ISRP 

and RME comments. We agree the proposal deserves high priority. 

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. 

Response Needed? No, Fundable 

ISRP Preliminary Comments: 

Fundable. 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 

record continues. The project cost has escalated as plans are made to partially absorb the trawl 

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ISRP 2002-13 Mainstem and Systemwide Preliminary Review 

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. 

Action Agency/NMFS RME Group Comments: 

HYDRO SUBGROUP -- The researchers indicate that the proposed research contributes 

information that supports RPAs 185, 189, 190 and 193. The RME group also notes the estimates 

can be important for evaluating compliance with certain Hydro-Performance Standards. But the

authors do not mention such. 

The thrust of the proposal is to continue generating inriver smolt survival estimates for Snake 

River stocks (steelhead, spring/summer chinook and fall chinook). The research contributes data 

useful in satisfying elements within each of the RPAs they identify. We generally agree. The 

Objective of RPA 185 is to produce useful estimates of “D”. The RPA states that extant 

estimates have wide confidence levels, implying their utility may be questionable. New estimates 

should exhibit improved precision. Part of that improvement may lay in the quality of inriver 

survival estimates that are a product of the proposed research. The proposal could be improved 

by describing precision associated with the inriver survival estimates and implications to the 

future utility of “D”. 

The objective of RPA 189 is to investigate causes of apparent discrepancies in adult return rates 

associated with different smolt passage routes. This proposed research may contribute 

information regarding the magnitude of survival exhibited by screen-bypassed fish, but not other 

routes individually. Furthermore, there is not expressed intent in this proposal to identify actual 

causes or mechanisms of mortality. Overall contribution to RPA seems limited. 

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ISRP 2002-13 Mainstem and Systemwide Preliminary Review 

The objective of RPA 190 is to improve our understanding of wild Snake River fall chinook early

life history, including juvenile survival. If the hatchery fish used in this research are suitable 

surrogates then this proposal has merit in contributing to RPA 190. However, the RME Hydro 

Work Group encourages the authors to incorporate information into the proposal that supports the 

use of hatchery fish as surrogates. 

The objective of RPA 193 emphasizes developing novel tools for discriminating hatchery and

wild fish, track fish in oceanic environs, and determine growth and survival for specific wild 

stocks. The linkage of the proposed research to this RPA is not readily apparent. 

In the opinion of the federal RME team the proposed research has important implications in 

evaluation compliance with performance standards at the BO-prescribed check in periods, 

although the authors did not explore this application. 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 be generating smolt survival estimates for Snake River 

stocks of interest, albeit using primarily hatchery fish. 

It would be instructive if the proposal specified sample sizes and precision associated with 

survival estimates. Lacking this information it is difficult to ascertain how useful the estimates 

will be in progress and compliance tests called for in the BO. Also, the performance standards in 

the BO are ESU-specific. The estimates from this research involve only Snake River ESUs. It 

seems there are opportunities to develop estimates for other stocks as well, such as Yakima and 

Leavenworth as Zabel et al. (2002) report. We encourage expanding stock coverage if tractable. 

Finally, the BO focuses on wild fish survival, where this research uses primarily hatchery fish. 

Justification for using these as surrogates should be discussed in the proposal. 

ISRP Remarks on RME Group Comments: 

The proposal was selected by the Action Agency/NMFS RME Work Group for review. The ISRP 

concurs with their observations 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 BOprescribed 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. 

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ISRP 2002-13 Mainstem and Systemwide Preliminary Review 

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. 

Response Needed? Yes 

ISRP Preliminary Comments: 

Fundable if a response can justify this design or if the design can be modified to provide valid 

estimates of extra mortality. 

The objective is to use empirical experiments to quantify delayed effects associated with 

hydrosystem passage. There is a logical need to address the problem of assessing dam passage 

mortality and the team possesses the experience and background to address the problem. 

The ISRP questions whether this experiment will settle the issue because concern was originally 

for extra mortality to Bonneville and it is not clear that results from this experiment will apply. In 

this proposal, although the objectives are clearly defined, the methods do not appear appropriate 

for determining a clear answer to the hypothesis being tested. Determination of significant 

differences in delayed mortality due to passage through 8 dams versus passage through 4 or fewer 

dams will not be possible with the current study. The proposal asserts that if the null hypothesis 

is rejected, it is highly likely that migration through Snake River dams does cause extra mortality 

in spring/summer chinook salmon smolts. An assumption (unstated) is that the effect due to 

transport is the same for fish experiencing dam passage plus transport stress as it is for fish 

experiencing only transport stress. Is this assumption justified? It is possible that some fish 

experiencing dam passage alone would survive but due to experiencing transportation stress prior 

to dam passage stress, they succumb. Therefore comparing extra mortality for transportation only

with extra mortality for transportation plus dam passage may not provide an unbiased estimate of 

the dam passage effect. 

Questions: Have the authors considered conducting a study on fall Chinook instead or in addition 

to spring/summer Chinook? Could something be done to estimate the effects of the different 

impacts of spill, turbines, and bypass system instead of merging everything in dam passage as one 

thing? Are there procedures in place to ensure that good estimates of expected mortality at the 

dams for fish migrating in-river are obtained so “extra mortality” is clearly defined? 

An excellent effort was made to do a power analysis in order to determine adequate sample sizes. 

One correction necessary is to note that a one-tailed procedure is required so alpha should be used 

rather than alpha/2 in the sample size formula. 

Action Agency/NMFS RME Group Comments: 

HYDRO SUBGROUP -- The authors indicate the proposed research provides information useful 

in satisfying RPAs 188 and 195. 

The objective of RPA 185 is to contrast productivity and hydrosystem effects (delayed) between 

wild stocks in upper Snake stocks and those in the Lower Columbia Basin. To accomplish this, 

the RPA calls for PIT-tagging both wild population complexes with PIT tags. This proposal relies 

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ISRP 2002-13 Mainstem and Systemwide Preliminary Review 

heavily on hatchery stocks from the Snake drainage as the population monitored. Thus its ability

to fully satisfy the intent of RPA 188 is not readily apparent. The primary objective of this 

research is to identify the existence and generally quantify the magnitude of extra mortality as 

associated with dam passage. The linkage to the RPA is not all that pronounced. 

The objective of RPA 195 is to establish how much post-Bonneville mortality is attributable to 

natural causes or other processes, such as hydrosystem passage or general fish fitness. This 

proposal is relevant to the fundamental intent of this RPA, i.e., identify delayed effects associated 

with hydrosystem passage. The proposed research clearly addresses the hydrosystem

contribution to any extra, unexplained mortality that may exist. The experimental approach 

appears sound. However, the sample sizes necessary to provide the precision targets are 

considerable (~ 236,000 PIT-tagged @ LGR) and may be a challenge to acquire in some brood 

years. 

Ancillary Benefits. These tagged yearling chinook will also yield inriver survival estimates. The 

large sample sizes all but ensure improved precision over most extant smolt survival estimates. 

This could be advantageous to the extent these estimates can be incorporated into survival 

Performance Standards tests prescribed in the BO. The proposal does not discuss the suitability 

of these estimates for such evaluations. The RME Hydro Work Group encourages the authors to 

explore this application and incorporate it as a section in the proposal. 

ISRP Remarks on RME Group Comments: 

The ISRP does not agree with the RME Workgroup comments that the experimental approach 

appears sound as noted above. Other RME Workgroup comments relate to RPA connections and 

ancillary benefits that are not noted in the ISRP review comments. 

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: 

The project develops analytical tools for tagging studies. This project 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. 

A response is needed to identify methodology for monitoring and evaluation. Information to aid 

in answering the following questions is needed: Have the products produced in the past benefited 

fish? How many client hours have been logged in the past? Is there evidence of client 

satisfaction? Who uses the products produced and how beneficial are they to users? 

Related questions are: How available is the service and to whom? What is the role of the author 

in review of project proposals? What is the means for providing statistical support to Council 

FWP funded projects. How are services advertised to the region? 

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ISRP 2002-13 Mainstem and Systemwide Preliminary Review 

The FY00 ISRP review noted that there was inadequate detail on what the principal investigator 

will do and that there should be a better description of indirect costs to the UW and direct costs 

for office space. These comments still apply.

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. 

Response Needed? Yes 

ISRP Preliminary Comments: 

Generally fundable, but a response is needed. 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. 

A response related to monitoring and evaluation is needed. Specifically, the following questions 

should be addressed or a protocol for answering these questions should be specified. How many

clients are supported by the statistical consulting service and is this service duplicated in other 

projects (e.g., 198910700)? What evidence is there of client satisfaction and cost effectiveness? 

What evidence is there that the extra-value information extracted has benefited fish? What is the 

basis for deciding which hypotheses to test, parameters to estimate, and interrelationships to 

investigate? What evidence exists that the in-season statistical support has been sufficiently

accurate to be useful?

The ISRP recommends that Task 3.2 “Statistical evaluation of performance standards.” be 

redirected to proposal #198910700, a proposal from the proponent that seems to more consistent 

with this task. In fact, the stated goal in the statement “The goal of this task is to design and 

analyze tagging studies using state-of-the-art statistical methods.” seems to be a direct overlap 

with proposal #198910700.

The FY00 ISRP review noted that plans for formal evaluation do not exist other than those 

provided by observing the continued use of the products from this on-going project and the 

success of the investigators in publishing results. The budget and personnel are not adequately

justified. These comments remain appropriate. 

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ISRP 2002-13 Mainstem and Systemwide Preliminary Review 

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. 

Response Needed? Yes 

ISRP Preliminary Comments: 

Generally fundable, but a response is needed. 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 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. 

A response is needed to clarify some issues. Is it possible to evaluate this theory with existing or 

anticipated data from the CSS? That is, can the model be validated based on existing data? 

Would it be possible to revise the proposal to incorporate data from project #35047 that includes 

fish released at Lower Granite? This collaboration would allow this project to compare the 

survival and SARs for the two groups: those released at Lower Granite and those released at 

McNary. 

Action Agency/NMFS RME Group Comments: 

OCEAN AND ESTUARY SUBGROUP -- The following ongoing projects are, or would, 

contribute to the delayed and extra mortality issues. Before funding this proposal a complete 

integration should be made with the COE's work, Carl Schreck, OSU, and with the ongoing 

NMFS and Dept. of Fisheries Oceans Canada project 1998-014 (now a separate proposal 30010), 

and the acoustic projects proposed in this RM&E section as 35046 and 35047, and the estuary as 

30007. 

ISRP Remarks on RME Group Comments: 

The ISRP and RME Workgroup concur that an exploration of connections with other projects 

would be beneficial. 

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ISRP 2002-13 Mainstem and Systemwide Preliminary Review 

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. 

Response Needed? No, Not Fundable 

ISRP Preliminary Comments: 

Not fundable. The experimental design is not technically sufficient. The proposal does not 

specify what benefits might be expected from use of net pens relative to existing methods of 

transportation of juvenile salmon, nor how any such benefits would be obtained or measured. 

Neither the need for transfer nor the method to be used for transfer of fish from hatchery

raceways or other sources to the net pens is discussed in the proposal. 

The reviewers are aware of an experiment on gas bubble trauma conducted by Earl Dawley that 

employed net pens in the Columbia River. Dawley couldn’t keep the net pens together. The 

proposers should review that experiment. 

Action Agency/NMFS RME Group Comments: 

OCEAN AND ESTUARY SUBGROUP -- Potential action items addressed - 187; 195. The 

artificial transportation aspect of this proposal is not in concert with the habitat restoration efforts 

and proposed research on ecosystem function of the lower river and estuary currently being 

conducted by LCREP, NMFS, and others. 

 

ISRP Remarks on RME Group Comments: 

The RME Group comments are descriptive. There is no conflict between the ISRP and RME 

Group comments. 

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 

Response Needed? No, Not Fundable 

ISRP Preliminary Comments: 

Not Fundable. 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 

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ISRP 2002-13 Mainstem and Systemwide Preliminary Review 

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). 

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.

The proposal lacks such estimates of the net benefit to the total population if turbine efficiency

were maximized. Turbine survival is currently about 85-95% at most mainstem dams. The 

installation of improved fish friendly turbines may enhance overall turbine survival rate by

maximally 5%, on average. Given that with screen efficiencies as high as 70% or more, spill

efficiencies as high as 30% and the use of transportation, it is possible that less than 10% of 

migrants will ever experience turbine passage in the mainstem FCRPS. Doubling this to 20%, 

with a turbine mortality improvement of 10% (twice its theoretical potential) provides a net 

FCRPS system survival increase of about 2%. In reality, we could probably achieve less than 1% 

with the equipment in place today for Snake River smolts and maybe the same for Columbia

River smolts. This would result if we changed out every turbine in the system to a fish friendly 

design and fine-tuned each operation. The cost of testing the current system at one dam is 

estimated at $12 million over next 5 years. It appears that as turbines require replacement, there 

are some energy benefits as well as fish benefits to using more fish friendly turbine designs. It

makes great sense to model, test and modify turbines based on previous studies of turbineinduced mortality as new designs are being developed, rather than concentrate on testing existing 

facilities such as McNary. 

The place of this proposal in overall FCRPS planning is not clear. Currently each fish-passage 

pathway is the focus of intense research that is costing enormous sums. The NMFS Pit Tag data 

is suggesting that transportation returns more adults from smolts transported high in the system

than in river or lower river transports. This database should enable construction of a Decision 

Support System to establish how many, when and where smolts should be transported, left in

river or both depending on river discharge conditions. Turbine passage survival is one component 

of such a Decision Support System. The question is do we have enough data on hand to build

such a model. An independent review panel might evaluate this question from the broader FCRPS 

perspective. 

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 study would be very expensive, and thus a more thorough scientific 

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ISRP 2002-13 Mainstem and Systemwide Preliminary Review 

justification is mandatory. 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. With very high costs, a favorable 

cost-to-biological-benefit ratio is not evident. 

The proposal was not selected by the Action Agency/NMFS RME Work Group for RME review. 

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 insitu the ability of induced turbulent flow and water velocity to 

simulate natural migratory ques for guiding fish to safe passage routes. 

Response Needed? Yes 

ISRP Preliminary Comments: 

A response is needed. This proposal has been improved from the innovative submission with 

additional input from biologists. It is still true that the proposal gives a tantalizing view of what 

might be accomplished, but it does not go far enough to allow evaluation of the chances for 

success. The proposal is too preliminary to be competitive. There are still issues that need to be 

addressed from the innovative review. 

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. For example, tests of surface collectors at Rocky Reach Dam

as well as Lower Granite and Bonneville dams probably have developed information on volume 

and velocity of water required (or that are inadequate) to attract juvenile salmon away from the 

turbine intakes and direct their movements elsewhere. A contact person would be Chuck Peven at 

Chelan County P.U. D. in Wenatchee, WA. 

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ISRP 2002-13 Mainstem and Systemwide Preliminary Review 

In this context, the lack of information on how eductor-based passage devices would fit into the 

forebay of a Columbia River low head dam may be indicative of a shortage of hydraulic physics 

and engineering content in the proposal. Figures are sorely needed to show the layout and 

positioning of project components (eductors, etc) for both a theoretical (or actual) fullscale 

forebay and for the prototype testing. The issue of scale needs to be addressed: what might be the 

size and cost of pumps and eductors needed to produce enough hydraulic change to be 

meaningful to fish. 

Specific questions and comments needing attention are given below. 

Is fish behavior going to be positive or negative to this attraction? In this connection, it must be 

said that the proposed use of cutthroat trout for tests of efficacy of the device or concept is not 

appropriate for a test of potential application to problems with juvenile fish passage in the 

mainstem Columbia and Snake rivers, which is where we perceive that its utility might lie. What 

is needed is a test with juvenile salmon that are ready to migrate downstream. Perhaps a test site 

could be found at a so-called acclimation pond somewhere in the Columbia Basin. 

There should be discussion of the plan for the intake end of the water line for the Venturi supply.

There would be a need to locate it outside of the area where fish might be affected by it. 

Engineering questions raised during the Innovative Review process need to be addressed. 

Data Management 

ProjectID: 198810804 

StreamNet 

Sponsor: PSMFC 

FY03 Request: $4,211,435 

5YR Estimate: $24,027,308

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. 

Response Needed? Yes 

ISRP Preliminary Comments: 

Streamnet is a necessary and useful project utilized by all agencies in the region. The ISRP 

recommends that the response more clearly separate the tasks and budget for long-term storage 

and distribution of data in StreamNet and the tasks and funding passed through to the states and 

tribes for preparation of data (so that the data are more comparable among the agencies and 

tribes). The response should identify and evaluate the increased scientific value of data in 

StreamNet and cost savings that would arise if agencies contributing data used common methods 

and data recording formats. The response should include objectives and timetable for 

development and use of standardized protocols for collection of primary field data by the states 

and tribes. The response should include a careful self-review including an evaluation of whether 

the structure of the current administrative oversight and advisory board is likely to result in 

standardization of field data protocols. 

The data are georeferenced (location coded) to the 1:100,000 hydrography GIS layer so that 

different kinds of information can be mapped together and spatially analyzed. The data are tied

to references in the StreamNet Library to document sources. An example of its usefulness is that, 

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ISRP 2002-13 Mainstem and Systemwide Preliminary Review 

data from StreamNet is used to populate the pilot database discussed in Proposal #35048 from the 

NMFS. 

Concerns in earlier reviews for overlap with other projects including other database operations 

were adequately addressed. 

The response should be more forceful on proposed additions to the project and segments of the 

project to keep. The proponent should give a prioritized list of data needs based on use of present 

segments of the database and on past requests for information including information requests for 

subbasin planning. Each task for collecting and maintaining high priority new data should 

include a detailed methods section. For example, the proponent states that “Some data are still

relegated to paper files or are retained by local biologists. If requested, StreamNet staff can 

effectively mine data from field offices.” One of the other areas that the proponents indicate a 

need for new effort is in collection of data on the fraction of hatchery fish on spawning grounds. 

The 40 data sources listed should be prioritized and methods (with proposed budget) given to

accomplish the individual tasks of acquiring and maintaining the data. To be consistent with 

ISRP’s statements on implementation of a systemwide M&E program (see proposal #35033) the 

proportion of StreamNet’s budget passed through for participation of other agencies and tribes 

could potentially be reallocated under the overall CBFWA proposal #35033 (approximately 3⁄4 of 

the StreamNet budget according to the oral presentation). 

Tasks and methods to meet the objectives (2 – 6) should be expanded and prioritized. For 

example, tasks and methods to accomplish Objective 6. Support and Services to Subbasin 

Planning are too brief to allow scientific review. 

The ISRP suggests that an alternative approach be used in the response. Namely, independent 

proposals should be prepared to provide suggested new data analyses for the region, in the spirit 

of DART and the FPC. The proposals should be to accomplish specific needed analyses, e.g., 

calculating and/or summarizing specific population estimates, or deriving results from other 

analyses, where not done by the originating agency. Data justifying demand for analyses should 

be given with detailed methods to provide the service. It is the opinion of ISRP that quality of the 

database service provided by StreamNet will be improved by funding an in-house, but 

independent project, to provide analyses and compete with other second tier database systems on 

an equal basis. 

The response must have a monitoring and evaluation section in the project history and a proposed 

monitoring and evaluation section for the proposed project. It is not acceptable for one of the 

most quantitative projects to not have a quantitative monitoring and evaluation plan for itself. 

Action Agency/NMFS RME Group Comments: 

DATA MANAGEMENT SUBGROUP -- The Stream net proposal claims specifically to address 

RPA’s 180 and 198 (at Section 1), and other RPA’s outside the Data Management Subgroup’s 

scope. 

Overall: 

The Action Agencies’ RME program calls for the systematic, rigorous and directed collection and 

maintenance of data for status and effectiveness monitoring as defined by the program. Like the 

NWFSC project (see comments on NWFSC proposal above), the StreamNet project only

manages data that is submitted to it by the participating agencies. The project is not designed in 

the base or new program to ensure that agencies that submit the data have a quality control and 

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ISRP 2002-13 Mainstem and Systemwide Preliminary Review 

quality assurance program that would meet the RME requirement. Hence data in the base 

program and data anticipated in the new program may be standardized but may be insufficient for 

the needs of the BO if the data collecting agencies have not used consistent, rigorous protocols as 

defined by the RME program. For example, because of the lack of protocols, the current 

StreamNet database does not adequately locate dams, barriers, points of diversion, amounts of 

each diversion, changes in points of diversion, etc. Any new data collection should proceed only

after common field collection protocols have been adopted. 

The StreamNet proposal has a considerably greater emphasis on Subbasin data than specific 

Opinion-generated RM&E data. 

RPA 180. 

It is not clear how the StreamNet proposal meets the requirements for the “development and 

implementation of a basinwide hierarchical monitoring program... the ground truthing of regional 

databases... and a draft program including protocols for specific data to be collected”. 

The text of the StreamNet proposal at page 8 refers to RPA 180 with the detail of the proposal 

offered by StreamNet stated as follows: “StreamNet’s experience and abilities with database 

management can be provided to support this effort on a more cost effective basis than through 

entities that are not already dealing with monitoring data in the basin”. This claim is not 

supported with any other information, and it does not address the concept of a basin wide 

monitoring program specified in RPA 180. It is not clear what the StreamNet deliverables for 

RPA 180 are. 

Note: StreamNet has two funding requests that it says do relate to RPA 180. 

The first is to deploy a prototype database to obtain and deliver water temperature data. This 

item, temperature recording for RPA 143, has a 2003 cost of $83,130. The second expenditure

is stream habitat data for 2003 expenditure of $89,799 to complete a needs assessment (scoping) 

with existing groups who collect habitat data, hold focus groups, define core data develop a 

database structure and manage the data. While this could be a part of a basin wide monitoring 

program it is by no means complete. 

RPA 198. 

There is a specific reference in the StreamNet proposal to work on the SAIC project as 

“Participation in Regional Data Initiatives”. The proposal is listed in a category of expenditure 

called “Services to Fish and Wildlife program”. The 03 budget for this category is $167,508 

however it is not possible to determine how much of thius funding is being proposed for RPA 198 

and, for that matter, what “Participation in Regional Data Initiatives means”. There is a reference 

at page 22 of the proposal as follows: “Work with state and local subbasin teams to identify 

priority information management and sharing needs. Share findings with SAIC project”. There 

is inadequate information here to determine what the deliverables are and who has responsibility. 

Pros: 

1. StreamNet’s willingness to address new information system development needs. 

 

1. 2. StreamNet’s experience in data management and knowledge of existing databasesThe 

project consolidates, standardizes and distributes fish information throughout the Columbia 

Basin; also some coastal streams. 

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ISRP 2002-13 Mainstem and Systemwide Preliminary Review 

2. It includes a library function. 

3. Through use of data exchange formats (DEFs), data are made comparable among the 4 states, 

CRITFC, PSMFC and USFWS. 

4. Relies on metadata, 1:100,000 hydrography; Uses LLIDs for accuracy. 

5. Program is distributed among F&W management agencies. The seven cooperating agencies 

represent the major F&W management agencies, except for NMFS. 

6. It uses restoration project database format developed by PSMFC and California; data from

states. 

7. Has ARC-IMS GIS application; on-line query system promotes distribution of standardized 

data. 

Cons: 

1. The proposed budget does not include budget items for Planning/Design or 

Construction/Implementation. This makes it difficult to determine how StreamNet will complete 

proposed tasks such at needs assessment which is a Planning/Design task. 

2. We cannot determine how and when StreamNet will meet RPA action item 180 and what the 

cost will be. The StreamNet proposal for RPA 180 does not address the requirements of RPA 

180 for a basin wide hierarchical monitoring program.

3. Data / information will be collected but not necessarily standardized. It will be a repository, no 

guarantee of data integrity.

4. For RPA 198, we cannot determine what the actual spending and deliverable is, apart from

generally described cooperation and coordination and completing a needs assessment for priority 

subbasin data. 

5. Current data categories are limited to those established as part of the StreamNet mission. 

Region needs other data but guidance previously lacking. 

6. Data are not distributed but partial distribution through State StreamNet servers has been 

evaluated. 

7. Lacks 1:24,000 level data of interest to IRICC agencies – difference in mission. 

8. Lack of NMFS in StreamNet may mean data are not standardized and cannot be exchanged 

with the StreamNet projects. 

9. NMFS proposing use of OWEB and PRISM restoration databases also. 

10. NMFS’ identified 30 tabular data layers might duplicate newly proposed StreamNet data 

layers and will need integration. Who serves the Region? 

 

ISRP Remarks on RME Group Comments: 

The ISRP agrees in general with the comments on this proposal. Specifically, “...the StreamNet 

project only manages data that is submitted to it by the participating agencies. The project is not 

designed in the base or new program to ensure that agencies that submit the data have a quality 

control and quality assurance program that would meet the RME requirement. Hence data in the 

base program and data anticipated in the new program may be standardized but may be 

insufficient for the needs of the BO if the data collecting agencies have not used consistent, 

rigorous protocols as defined by the RME program.” The ISRP agrees with this assessment, and 

recommends funding of Proposal #35033 from the CBFWA to coordinate the development of a 

basinwide research, monitoring and evaluation program, including potential reallocation of funds 

from StreamNet and other projects to accomplish the tasks and meet the needs of RPAs 180 and 

198. NMFS through participation in CBFWA would have more influence on data collected by 

the states and tribes and stored by StreamNet to help ensure that RPAs in the BiOp are satisfied. 

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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. 

Response Needed? Yes 

ISRP Preliminary Comments: 

A response is needed. This is a valuable project providing service to the scientific community in 

the region at relatively low cost. 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. The project history and technical background 

sections are informative, however the Section f. Proposal objectives, tasks and methods is too 

brief to allow scientific review. The response should provide specific tasks and detailed methods 

to accomplish each objective (some of the necessary material is in the other sections). Also, the 

project must have a monitoring and evaluation plan, including for example, lists of services 

provided. It is not acceptable for one of the most quantitative projects to not have a quantitative 

monitoring and evaluation plan in the proposal. 

Only 4 objectives are identified, but in the text, it is stated that an FTE is needed for objective 5. 

Please clarify.

Action Agency/NMFS RME Group Comments: 

DATA MANAGEMENT SUBGROUP -- Action 180: 

The DART proposal is not considered a core contribution to a basin wide hierarchical monitoring 

program and appears to be more closely directed to reporting and tracking the effect of 

temperature, flow and gas changes on populations and passage. 

Action 198 

Apart from indicating general support and suggesting actions that should take place DART does 

not propose any particular actions. 

Pros: 

1. Identified as a non-discretionary work element by BPA 

2. Project has created and maintains a number of mainstem FCRPS applications for TDG, flow 

operations and temperature. 

3. Applications integrate data from Fish Passage Center, Corps of Engineers, tagging programs, 

StreamNet, EPA and others. 

4. Will participate in Regional database integration using tools such as XML. 

5. Provides tracking of performance standards for the hydro system called for under the BiOp. 

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ISRP 2002-13 Mainstem and Systemwide Preliminary Review 

Cons: 

1. The DART proposals for RME are not specific enough to meet RME needs. 

ISRP Remarks on RME Group Comments: 

The ISRP is somewhat confused by comments on this and other proposals. In other cases, e.g., 

#35048, there is apparently strong support for analyses of primary data to be conducted in second 

tier databases, whereas there is weak support for similar analyses to be conducted under this 

project. The response should more clearly identify current and proposed tasks and services to

meet the needs of RPA 198. 

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

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 

tabular data. Interactive and decision support tools will also be developed. 

Response Needed? Yes 

ISRP Preliminary Comments: 

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 project is costly, leading to the question of whether it would produce information of 

sufficient value to the region to justify its expense. The proponents should address the question of 

demand for the improved databases. How extensively used is the present version and what are its 

primary uses? If this project is not funded what will happen to plans for improving this 

information system?

Additionally, more detail is needed on the products that would be delivered by this project. It is

unclear whether there will be sufficient detail in the output to satisfy many users. The sponsors

should provide explicit examples of the major types of outputs. For example, what do the terms in 

figure 3 mean and what will be the explicit information for the basis of Figure 3? The current 

descriptions are too general. 

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ISRP 2002-13 Mainstem and Systemwide Preliminary Review 

Maps alone would be of limited use in subbasin planning. Will the detailed 5th HUC-level data 

on which maps were based be accessible through the program? Will the results be available to 

users for free or will they have to buy a book and CD? 

Does the project duplicate USFS and BLM efforts? More detail should also be provided about 

the online peer review and processes for quality control. Is there an M&E plan for checking the 

accuracy and precision of the database? 

Action Agency/NMFS RME Group Comments: 

OCEAN AND ESTUARY SUBGROUP -- Action item addressed - 198. The proposal identifies 

data fields related to the entire basin, including estuarine resources (i.e., bays and estuaries; inland 

marine deeper waters; marine nearshore areas). The project applicant needs to identify which 

data fields are to be emphasized/actually used, and how this prioritization relates to the 

estuary/basin. This proposal identifies a specific data management structure. The structure needs 

to be reviewed to determine how the project fits with current conversations on data base 

management, including the ongoing StreamNet project, EDT, and with work that LCREP has 

been coordinating. 

DATA MANAGEMENT SUBGROUP -- Does the Proposal address RPA Objectives?

The proposal represents a substantial development of a stand-alone DBMS with addition of data 

and mapping and Internet capabilities. In other words it would represent a fully functional endto-end information system, with custom query tools, all for a subset of regional data. While each 

of the proposals have the potential to improve information system delivery, specifically by

overcoming technical constraints with the existing IBIS system, and by expansion to new data 

sets, the proposal does not document well the extent of these claims. The proposal does not 

adequately address RPA’s 180, 181, or 198. 

Elements the Proposal is Lacking. 

The strengths of the proposal are in it’s claims to overcome deficiencies in the current IBIS 

information system design, offer basin wide mapping utilities, and provide currently needed 

wildlife and related habitat data, and some resident fish data, not otherwise available in a regional 

as opposed to a state context. However there are many lacking elements within the proposal. 

Despite claims of developing materials to support monitoring; it is not clear how the proposal will 

actually meet goal 180 by developing or integrating with a monitoring program and groundtruthing data. This proposal appears to be to develop imagery technology rather than to provide

the imagery. The main problem with providing digital imagery is not the technology for delivery,

rather, it is the very high cost of acquiring the imagery. Since there is no budget request in this

proposal for actually acquiring spatial data layers, and it could take years to acquire “all the 

Columbia spatial data layers”, there is no guarantee of delivery of the spatial data from this 

proposal. It would make more sense to adopt the technology for spatial data provision when there 

is also a budget for acquisition of data layers. This claim the proposal will fulfill the needs for a 

regional information system is not supportable by information within the proposal since the needs 

are currently being identified by SAIC. Furthermore the report by Coutant et.al identified many

problems that concern information management per se rather than nominal collection and 

delivery of a subset of data. Since the claim of performance for this proposal is narrow it cannot 

reasonably claim to solve the problems identified by Coutant et.al. There appears to be potential 

for overlap with other data collection institutions: for example the plan to include marine fish 

habitat data into IBIS appears to overlap, at least in part, with the current recording of data by the 

PSMFC. The proposal requires a new DBMS design which results in a custom stand alone 

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ISRP 2002-13 Mainstem and Systemwide Preliminary Review 

solution for just a subset of regional data. The project currently lacks tabular database 

management; proposed project will develop interactive databases. 

Means and Opportunities to Strengthen Proposal. 

Clearly identifying how the proposed system is distinct and different from the proposal by

StreamNet to provide data collection for stream habitat data users would strengthen the proposal. 

Detailing the proposed advance query capabilities and decision support tools, and delineating cost 

effectiveness of off the shelf query tools versus custom query tools would also strengthen this 

proposal. Another adjustment possibility is to clearly demonstrate how the basin wide mapping 

utilities apply to other mapping initiatives and how they relate to RME needs. Finally the 

proposal needs t directly address RME information system design needs and in particular address 

RME needs with respect to anadromous fish and wildlife populations as opposed to only

addressing non-anadromous fish and wildlife populations. 

Feasibility of Work 

It is not clear whether the proposal is more or less efficient in terms of regional funding resources 

with a completely separate database organization and administration for collection of terrestrial 

wildlife and non-migratory fish species. It is also unclear that there is funding for obtaining actual 

data for digital imagery. 

ISRP Remarks on RME Group Comments: 

The ISRP agrees that the proposal should clarify how it will contribute to RPA 180 by developing 

or integrating with a monitoring program and ground-truthing data, Nevertheless, this is one of 

the few wildlife proposals in the systemwide solicitation and will provide needed wildlife and 

resident data for subbasin and basin planning. 

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. 

Response Needed? Yes 

ISRP Preliminary Comments: 

A response is needed. The proposed work is difficult to review because the objectives and tasks 

and methods are not organized in a clear and systematic way in this long rambling proposal. The 

proposal should be reviewed within the NMFS before resubmission. There is some description of 

the NMFS Salmon Data Management (SDM) program, but no specific list of objectives with 

associated tasks. A list of “general tasks” has no associated methods. Methods are embedded in 

longer narratives that do not clearly relate to specific tasks or objectives. The sponsors propose to 

add available useful information throughout the Region by meeting a number of objectives 

including: 1) access to data, tools and information to Internet and Intranet users via SDM Web; 2) 

access to NWFSC Salmonid database available to users inside and outside the NWFSC; 3) access 

to needed spatial data layers based on a just completed NWFSC spatial data needs assessment 

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ISRP 2002-13 Mainstem and Systemwide Preliminary Review 

including those needed by Technical Recovery Teams (TRT), Cumulative Risk Initiative (CRI), 

and Salmonid Watershed Analysis Modeling effort (SWAM); 4) Research Monitoring and 

Evaluation data management capability; 5) electronic access to currently inaccessible paper 

records for Columbia Estuarine Juvenile Data; 6) rewrite SWAM Avenue analysis tool to Visual 

Basic and add additional functionality for more general analysis purposes; 7) access to the 

NWFSC Genetic and Evolution database for users inside and outside the NWFSC. The 

proponents should rewrite the section f. Proposal objectives, tasks and methods, carefully listing 

specific tasks and detailed methods to accomplish each task. There must be 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 its own effectiveness. 

The proponent should clarify if the primary objective of this project is to: 1) be a part of a 

distributed database system providing NMFS primary data to the region, 2) develop a second tier 

database in the spirit of DART to analyze primary data for NMFS and the region, or 3) do both 1) 

and 2). 

This proposal is potentially for an important and needed project to provide assess to NMFS 

primary data and make available second tier analyses available via the internet on listed salmon 

(and steelhead, we assume) related data and metadata sources in the Columbia Basin. The ISRP 

believes that the objective to “consolidate” data is overstated and a better description of the 

intended activity is to analyze data from NMFS and other sources according to certain 

assumptions. Those assumptions and other metadata for the analysis must be made available with 

the “consolidated” data. The proponent should make it clear that responsibility for and long-term

storage of primary data from other agencies rests with other database programs elsewhere in the 

region, otherwise more than one version of primary data will exist. 

It would be helpful in evaluating the potential for overlap of efforts if letters of support are 

provided from other database projects in the region, including StreamNet, the Fish Passage 

Center, Data Access in Real Time (DART), the Columbia Basin PIT-Tag Information System

(PTAGIS), and from other agencies outside the NWFSC. 

This proposal is for partial support of a program that the NWFSC is already pursuing with limited 

funding. It embraces the NWFSC vision about the future of data sharing through multiple data 

portals, and of groups of individuals from different agencies sharing common project data. This 

appears to complement some projects (35016, 35019, 35020) but perhaps duplicates other efforts 

(35033). 

Action Agency/NMFS RME Group Comments: 

DATA MANAGEMENT SUBGROUP -- The NWFSC RM&E proposal is designed to make it 

possible for researchers to query the data, which will be collected from multiple regional 

databases, through a single portal. The NWFSC currently has a prototype that has been 

demonstrated using data from OWEB and PRISM databases. 

The project is not designed to ensure that agencies that submit the data have a quality control and 

quality assurance program that would meet the RME requirement. Hence data may be 

insufficient for the needs of the BO if the data collecting agencies have not used consistent, 

rigorous protocols as defined by the RME program. 

The proposal anticipates however that there will be concurrent improvements in data quality

through implementation of other elements in a regional RME program and the benefits of those 

improvements will roll up to the RME repository. 

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ISRP 2002-13 Mainstem and Systemwide Preliminary Review 

The Action Agencies’ RME program calls for the systematic, rigorous and directed collection and 

maintenance of data for status and effectiveness monitoring as defined by the framework. The 

framework implicitly distinguishes data and information. Information is developed from data 

through the use of analytical and decision tools. Preferably one develops the tools, and then one

seeks the data for the tools. Sometimes there is feedback in that the data suggest new tools. The 

NWFSC has developed tools such as SWAM which direct the collection of data. However it is 

unclear how the Council’s subbasin planning process and the Action Agencies’ RME program

would use SWAM and other NWFSC analytical tools. The appropriateness of the tools for the 

RME program needs resolution before the required data layers can be identified. 

RPA 180. 

The NWFSC proposed pilot proposal provides a solution to a part of the challenge of 

“development and implementation of a basinwide hierarchical monitoring program”, it does not 

propose the “ground truthing of regional databases” or a “draft program including protocols for 

specific data to be collected”. The proposal offers a way to bring together the RPA data from

many different RPA databases and provide access to it through a single web and GIS 

environment. It is a basinwide repository of all monitoring and evaluation data. 

RPA 198. 

The NWFSC proposal does propose to be repository for regional RME data. It also proposes to 

use a development called SDM web for an RPA tracking pilot at the Regional Office of NMFS. 

 

Pros: 

1. The proposed pilot RME database would be helpful to assess the potential problems in 

developing a larger database. The OWEB database for the coastal salmon restoration program

most likely represents the best example of data that was collected consistently with the RME 

guidelines. Since the NWFSC has previously collected this data, the NWFSC pilot project could 

assess the OWEB data and database, and propose changes to the OWEB project that would 

satisfy a BO data management program. 

2. The proposal extends badly needed, recently-developed corporate data / information 

management system. 

3. The proposal consolidates fish data collected from numerous sources and tied to metadata. 

4. It provides on-line access to NWFSC data and information; it will apply prototype systems 

technology to allow web access to databases used and needed inside and outside NWFSC. 

5. It is a distributed data system, with broad selection capabilities. 

6. The data are closer to some of the key regional researchers; 

7. The Salmonid Data Management (SDM) Web allows researchers to share all project 

information and includes a project tracking utility. 

8. The project may be consistent with SAIC recommendations if data access tools are the same; it 

promises to incorporate SAIC findings.

9. It will model similar capabilities without duplicating DART; 

10. It will use FPC smolt data. 

11. It obtained StreamNet backup files in March 2002. 

12. It will develop tools to enhance distribution of data and other info. 

13. It proposes linking and making available via the web the Center’s Genetic and Evolution

Database and the centers Salmonid database. 

14. It includes substantial in kind services (approximately 40%). 

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ISRP 2002-13 Mainstem and Systemwide Preliminary Review 

Cons: 

1. It has the potential to be inconsistent with approach of slow-moving SAIC project because of 

timing differences. 

2. Data / information will be collected but not necessarily standardized. It will be a repository, no 

guarantee of data integrity. 

3. Its deliverables may lack Data Exchange Formats to make data comparable from State-to-State 

and agency-to-agency?

4. It duplicates part of StreamNet responsibilities without being a part of it. For example, thirty

spatial data layers needed (including status information) might duplicate some new StreamNet 

data layers and will need integration. Will the States and Tribes cooperate? 

5. SDM prototype tool appears to duplicate StreamNet’s (and USFS?) restoration project 

databases from OWEB and PRISM. 

6. It lacks resident fish data that Action Agencies need for other BOs. Not part of agency 

mission. 

7. How will data be kept up to date? By periodic re-collection or update from sources? Two 

versions may be on the Web simultaneously. 

ISRP Remarks on RME Group Comments: 

In general the ISRP agrees with the RME comments and specifically, that the project is not 

designed to ensure that agencies that submit the data have a quality control and quality assurance 

program that would meet the RME requirement. Hence data may be insufficient for the needs of 

the BO if the data collecting agencies have not used consistent, rigorous protocols. However, 

some elements of the comments are very troubling to the ISRP. The comments imply that the

consistent, rigorous protocols are to be defined by the RME program and that concurrent 

improvements in data quality through implementation of other elements in a regional RME 

program and the benefits of those improvements will roll up to a “...RME repository of data.” 

The comment that “The proposed pilot RME database would be helpful to assess the potential 

problems in developing a larger database.” indicate to the ISRP that the RME Program

participants need to carefully consider and evaluate the roles of: 1) databases for storage of 

primary data, versus 2) databases for second tier analysis of primary data using various 

assumptions. In short, the ISRP strongly disagrees with the RME group implication under RPAs 

180 and 198 that this project might be “... a basinwide repository of all monitoring and 

evaluation data.” It is not clear to the ISRP that efforts within the Council’s FWP to develop 

consistent, rigorous protocols for monitoring and evaluation and long-term storage of data are 

well coordinated with the RME program. It seems that the RME program has significant 

potential for fragmentation and duplication of efforts within the region. 

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ISRP 2002-13 Mainstem and Systemwide Preliminary Review 

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

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. 

Response Needed? Yes 

ISRP Preliminary Comments: 

This proposal addresses one of the major management deficiencies in the basin, the lack of a topdown basin-wide monitoring protocol. Such a protocol is of critical importance for assessing 

changes in stock and environmental conditions and the effectiveness of restoration and mitigation 

actions. Thus, this proposal is potentially a high priority for funding. Several issues, however, 

need to be addressed by the sponsors. 

Implementation-related issues: 

1. Independent oversight of the project is needed to track progress and identify potential problems 

before they get out of hand. The ISRP should rigorously review the progress of this project 

annually if it is funded. All major work products such as the Design Plans and Data Analysis 

Reports should be subject to independent peer review by reviewers selected by the ISRP. The 

reports of the peer-review panels should be submitted to the ISRP and included in their annual

review of the project. The sponsors should comprehensively respond to each concern raised in the 

ISRP’s annual review. The ISRP’s recommendations for future funding will be based in part on 

these annual reviews. 

2. To what extent does the proposed work overlap, duplicate, or complement other ongoing or

planned monitoring and evaluation projects within the basin? If this project is funded will it 

replace the M&E component of other projects? If so, how will coordination be accomplished? 

How would this project affect the dedicated RME proposals submitted in this province? Action 

agencies may need to modify their current M&E protocols to conform to the recommendation of 

the basinwide program. Is there a firm commitment from state, federal, and tribal entities to adopt 

the monitoring protocols resulting from this project? The USFS and the BLM are not listed as 

cooperators in the proposal, yet they have management responsibility for the bulk of federal lands 

in the basin. How will coordination with these agencies be achieved? 

Project Organization Issues: 

1. The key questions developed for each Tier should be explicitly related to general recovery

goals and objectives for the basin and subbasins. For example, what are the basin-wide goals and 

objectives for salmonid recovery and how will addressing the key Tier 1 questions ensure 

progress toward meeting those goals? The same question could be asked for provinces, subbasins, 

and ESU’s. 

2. The proposal focuses principally on development of a basinwide monitoring program but the 

evaluation of the data collected through monitoring is barely discussed. Evaluation is a critical 

component in the M&E process without which the key questions cannot be answered. The 

proposal needs to explicitly address how the evaluation component (i.e., analysis of the 

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ISRP 2002-13 Mainstem and Systemwide Preliminary Review 

monitoring data) will be incorporated into the process. Specific methods for analysis are not 

required in the proposal but a general plan for the conduct of analyses is needed. Perhaps the 

proposal should be retitled “Collaborative, Systemwide Monitoring Program” with the 

monitoring data to be available to the region for evaluation? 

Methodological Issues: 

1. The key questions mostly appear to address system state, for example, biological and physical 

habitat “condition.” Physical (e.g., geomorphic and hydrologic) and biological (e.g., species 

interactions, habitat relationships) processes determine system state and are subject to 

modification by human actions. Critical ecological elements such as habitat stability and 

connectivity, metapopulation dynamics, and genetic and life history diversity are barely touched 

upon, if at all. The key questions and, in fact, the entire protocol development should be more 

process-based, explicitly emphasizing ecological processes and functions as much as states. 

2. Tier 3 is their “effectiveness monitoring of recovery projects” and is in direct competition with 

the BPA-RME program. The sponsors approach to effectiveness monitoring is an attempt to 

standardize research experiments from the top down, which may not be possible. Effectiveness 

monitoring (research) should be called for in RFPs to answer specific questions. For Tier 2 

monitoring, impacts of non-native species need to be explicitly considered. 

3. The proposal needs to more clearly define “classes” of management actions (page 6). 

4. A monitoring and evaluation plan for the project itself is needed. 

5. What is meant by the statement “...Tier 1 data layers are intended to be coarse-scale 

assessments that do not capture interannual variation and spatial variation in covariate 

magnitude.” Specifically what does “in covariate magnitude” mean?

In addition, the Coded Wire Tag Programs that are among the primary monitoring and evaluation 

programs for stock identification in the harvest, magnitude of harvest on various stocks, etc. 

should be brought under this integrated effort to catalogue, make available, critically assess, and 

improve systemwide monitoring and evaluation for fish and ecosystem status. Other projects that 

should be brought under this overarching project to provide system-wide monitoring and 

evaluation include parts of or all of projects #198810804 (StreamNet), #198712700 (Smolt 

Monitoring), #199008000 (PTAGIS), #199403300 (FPC), and #199602000 (CSS). 

Action Agency/NMFS RME Group Comments: 

PLANNING GROUP - This project is well written and has several valuable objectives and tasks 

that are needed by the region. However, most all of the objectives and tasks are currently

underway as part of other regional processes and associated contracts or proposals such as: 1) the 

NMFS Biological Opinion and the Federal Caucus’ Basinwide Salmon Strategy RME Program; 

2) NMFS and USFWS TRT Recovery Planning; 3) the NWPPC’s Provincial Review Process;4) 

Data Protocols and Data Needs Assessment Contracts; 4) Subbasin Planning; 5) the Regional 

Analytical Advisory Committee; 6) USFS , BLM, and EPA Monitoring Programs; 7) Oregon 

and Washington State Monitoring Programs; 8) the Lower Columbia River Estuary Program; and 

9) the Corps of Engineer’s AFEP Program. The NMFS and Federal Action Agencies have 

developed a draft RME framework that overlaps much of the needs of the Fish and Wildlife 

Program and other Federal and state RME programs. A regional workgroup session in 

September, 2002 with the formation of an RME Regional Coordination Group is already planned 

to provide a collaborative process for coordinating these overlapping programs. The state and 

tribal fishery agencies, CBFWA, USFWS, and the NWPPC will be included in this Regional 

Coordination Group as well as other key agencies for the RME Programs identified above. This 

coordination effort will include resident fish RME needs under the USFWS BiOp. The work 

proposed by 35033 would be redundant to these other processes and associated contracts. The 

proposal also appears to duplicate current CBFWA support contract objectives of coordinating 

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ISRP 2002-13 Mainstem and Systemwide Preliminary Review 

the state and tribal fisheries agencies and the region. In addition, funding is proposed for federal 

and state employees that are already requirements under current programs and activities. 

ISRP Remarks on RME Group Comments: 

The RME Committee comments raise similar issues as those identified in the ISRP’s question 2 

under Implementation-related issues above. 

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 

Response Needed? No, Not Fundable 

ISRP Preliminary Comments: 

Not Fundable. No response needed. The project is designed 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 but the proposal does not provide enough detail to effectively

evaluate its merit. 

Action Agency/NMFS RME Group Comments: 

STATUS MONITORING SUBGROUP -- This project is a pilot project to test the use of LU/LC 

spatial data in Willamette subbasin as Tier 1 monitoring data. The project will then link these 

data layers to Tier 2 fish data in Willamette River floodplain and potentially to Tier 3 data for 

floodplain restoration projects. Ultimately the approach will be applied to the John Day or 

Wenatchee River subbasins. 

a. Does a proposal satisfy the objectives of RPA? 

The proposed work directly addresses the landscape-scale monitoring component (Tier I) of RPA 

180. The proposed work indirectly addresses RPA 181 through the work’s dependence on remote 

sense (satellite imagery) data. 

b. If not, explain what elements are lacking. 

c. If the proposal partially satisfies the RPA objectives, suggest means or opportunities to 

strengthen the proposal. 

The concepts put forth in the proposal lack significant detail to effectively evaluate exactly what 

would be done and what the specific outcomes would be. A significant effort will need to be 

undertaken to explain exactly what goes into quantifying and assessing ecosystem status, how this 

relates to fish distribution (habitat associations), and how they will be linked to form a more 

synthetic analysis of the two. As the proposal is currently written it appears to focus on large 

floodplain systems in the Willamette basin, a tributary-based focus will need to be added to 

improve the export of this approach to systems throughout the Columbia. 

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ISRP 2002-13 Mainstem and Systemwide Preliminary Review 

d. If a proposal is entirely satisfactory, indicate so and note the particular strong points. 

e. Assess the feasibility of the proposed work in general terms. 

Given the track record of the researcher’s involved in this proposal and the general concepts they

describe, the proposal shows significant promise in principle to address key aspects of RPA 

180/181. Developing specific analyses linking population status and ecosystem status will be 

critical elements in the development of Tier 1-3 monitoring programs. This proposal potentially 

offers a significant opportunity to bridge some of these gaps to develop more quantitative and 

landscape-based analyses that inform managers about critical bottlenecks to population and 

watershed recovery. Development of a much more detailed proposal should answer just how the 

project would accomplish this. 

ISRP Remarks on RME Group Comments: 

The ISRP and RME Workgroup agree that the proposed project may have merit but a much more 

detailed proposal must be submitted before the project can be evaluated. 

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

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. 

Response Needed? Yes 

ISRP Preliminary Comments: 

A response is needed. This proposal may be premature and appears to duplicate some efforts in

ongoing projects in other provinces. The proposal should more clearly explain its relationship to

the ongoing projects and the overall RME planning activities in proposal #35033 of which the PI 

is a cooperating member. For example, do objectives 1 & 2 of this effort duplicate parts of 

#35033? This project proposal is also linked to others being submitted: 35016 (A Pilot Study to 

Test Links Between Land Use / Land Cover Tier 1 Monitoring Data and Tier 2 and 3 Monitoring, 

Feist); 35020 (Regional Project Effectiveness Monitoring Program for Columbia River Basin 

Listed Anadromous Salmonids); 35048 (NWFWC Salmon Data Management, Analysis and 

Access for Research, Monitoring and Evaluation Programs). The relationship to these proposals 

should be more clearly specified, e.g., are any of these projects necessary for the success of this 

proposal? The proponent might consider combining this proposal with #35033 to provide pilot 

data in association with a systemwide monitoring and evaluation project. 

The primary objective of this proposed status monitoring plan for Columbia River Basin is a 

statistically sound sampling design that when implemented will generate useful data with known 

analytical and predictive power. The primary complication arises from the enormous spatial scale 

and resulting heterogeneity of the sampling areas and indicators. The proponents propose to 

develop a modern and statistically rigorous sampling program informed by knowledge of 

demographic and habitat processes. In general the ISRP supports this effort to develop and test 

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status and trend monitoring approaches capable of the statistical rigor specifically required by the 

region’s natural resource management agencies and personnel. 

The ISRP recommends that the proponent consider modifying the proposal to include pilot 

projects in each of the four states (e.g., pilot projects for resident bull trout in Montana, 

anadromous species in a tributary of the Salmon River in Idaho in cooperation with the ongoing

Idaho production surveys, cooperation with the pilot M&E work in the John Day Basin of Oregon 

and perhaps the Wenatchee Basin in Washington). In particular it seems that the John Day Basin 

could be included to eliminate duplication of effort, where we understand that a pilot program is 

underway on many of the objectives of this proposal. 

The proponents should discuss the relationship of the habitat and riparian survey protocols 

selected for use and the protocols recommended in “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” (Johnson, et., al. 2001). 

Other points that need clarification are: 1) Is there a probabilistic sampling procedure for habitat 

surveys in Subtask 2.1.1. -- Test habitat assessment methods?, 2) Discuss the ongoing census 

based surveys that will act as the ‘truth’ in Subtask 2.1.2. -- Test adult population assessment 

methods. Are there no sources of error?, 3) How are data collected on juveniles in pools < 6 m2 

in surface area or < 40 cm deep or in other pools where snorkeling is not feasible? 4) In Subtask 

2.1.3 -- Test juvenile population/productivity assessment methods, it is unclear if abundance of 

juveniles is estimated or just presence/absence. How are abundance or presence/absence 

estimated if not all pools or other parts of the reach are not assessed? 5) What exactly is to be 

tested in Subtask 2.1.4 -- Test probabilistic sampling based approaches? 6) What do you mean by

“Since stream network geometry is a strong function of gradient, geology and precipitation, the 

weighting of streams in the sampling scheme should be tested for each major subbasin.”?, and 7) 

Develop a monitoring and evaluation plan. It is not appropriate for one of the most quantitative 

proposal to not have a quantitative monitoring and evaluation plan for itself. 

Action Agency/NMFS RME Group Comments: 

STATUS MONITORING SUBGROUP -- 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. 

This proposal most directly addresses RPA 180, and supports elements in up to 10 additional 

RME RPAs. 

RPA 180 – The objective is to develop and implement a basinwide hierarchical monitoring 

program, focusing on population and environmental status. This proposal is in direct response to 

that need. The approach is to initiate two pilot efforts in different subbasins to establish a 

foundation of suitable sampling protocols and estimation procedures. Our work group sees merit 

in this approach. Good thinking has gone into this product. However the proposal could be 

improved somewhat by providing more details on a few key issues. Those issues are specified as 

guidelines for implementing status monitoring, in a draft RME framework document that has had 

limited circulation (RME Framework for the 2000 Biological Opinion – NMFS and Action 

Agencies). Those guidelines are useful in proposal develop, as well as implementation. Clearly 

this proposal has adopted some of the guidelines. But we recommend the full complement of 

guidelines be considered. Separate guidelines were compiled for adult, juvenile life stages and 

environmental attributes. As an example we reproduce the population status adult life stage 

guidelines from that document here: 

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Proposed Guidelines -Adult Life Stage: 

1. Clearly identify the demographic scale (e.g. population, ESU, deme; wild/natural or hatchery 

origin) for which abundance estimates will be produced. 

2. Demonstrate that the target unit is readily distinguishable from other sympatric population 

units (e.g. spawning location, timing, etc.). 

3. Identify the performance measure or indicator that will be monitored/enumerated (e.g. redds, 

carcasses, weir counts, dam counts etc.) in order to estimate spawner escapement. If multiple 

methods (e.g., weir counts and redd counts) are used to enumerate the same population, specify. 

4. Describe the method used to enumerate the indices, e.g., aerial or ground surveys, peak or 

cumulative (repeated) counts, and the error associated with the method. 

5. Specify any expansion factors (e.g. spawners/redd, expansions beyond index areas) or other 

adjustments (e.g. harvest removals, passage mortality) that need to be applied to the raw counts. 

Provide the rationale supporting the use of those expansion factors, how the factors change over 

time, how they are estimated, and assess their reliability. 

6. Provide estimates of the annual age structure of the sampled population, and how this is 

estimated. 

7. Provide an assessment of the accuracy and precision associated with the proposed methods for 

estimating spawner escapement, or total numbers of returning adults. 

Data will be collected on an annual basis at the sub-basin scale: 

· Adults, Spawners, or Redds 

· Age structure of spawning population 

· Sex ratio of spawning population 

· Fraction of naturally spawning fish that are of hatchery origin, (CV should be specified.) 

ISRP Remarks on RME Group Comments: 

In general the ISRP agrees with the RME group comments. It is useful to have pilot efforts in 

different subbasins to establish a foundation of suitable sampling protocols and estimation 

procedures. The proposal could be improved by providing more details on key issues identified 

in the draft RME framework document (RME Framework for the 2000 Biological Opinion –

NMFS and Action Agencies). 

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. 

Response Needed? Yes 

ISRP Preliminary Comments: 

The proposal is too brief to allow complete scientific review. For example, the basic ideas are 

presented elsewhere, but there are no methods in the section f. “Proposal objectives, tasks and 

methods.” Methods should be included for each task, especially with respect to the proposed Task 

4: Implement 2-3 pilot studies of effectiveness monitoring. The proposal should be better 

coordinated with other M&E proposals from the same agency. The proposal does not provide 

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sufficient information to indicate that it can accomplish its objectives. The proposal must have a 

monitoring and evaluation section. It is not appropriate for one of the most quantitative proposals 

to monitor project effectiveness to not have a quantitative monitoring and evaluation plan for its 

own effectiveness. 

If funded, Proposal #34008 in the Innovative Solicitation “Use a Multi-Watershed Approach to 

Increase the Rate of Learning from Columbia Basin Watershed Restoration Projects” would seem 

to overlap the objectives of this proposal. This is an awkward situation because funding decisions

on proposals submitted under the Innovative Solicitation may not be complete. 

This proposal may be premature and appears to duplicate some efforts in ongoing projects in 

other provinces. The proposal should more clearly explain its relationship to the ongoing projects 

and the overall RME planning activities in proposal #35033 of which the PI’s agency is a 

cooperating member. This project proposal should also linked to others being submitted: e.g., 

35016 (A Pilot Study to Test Links Between Land Use / Land Cover Tier 1 Monitoring Data and 

Tier 2 and 3 Monitoring, Feist); 35019 (Develop and Implement a Pilot Status and Trend 

Monitoring Program for Salmonids and their Habitat in the Wenatchee and Grande Ronde River 

Basins); 35048 (NWFWC Salmon Data Management, Analysis and Access for Research, 

Monitoring and Evaluation Programs). The relationship to these proposals should be more clearly 

specified, e.g., are any of these projects necessary for the success of this proposal? A primary

contribution of this proposal would be to implement 2-3 pilot studies of effectiveness monitoring 

projects. This seems to overlap the objectives of proposal 35019 from the same agency. The 

proposals should be coordinated to avoid duplication of effort. 

Action Agency/NMFS RME Group Comments: 

HABITAT ACTION EFFECTIVENESS RESEARCH SUBGROUP -- Does the proposal satisfy

the objectives of RPA 183? 

The proposals intent to provide a mechanism to coordinate and prioritize implementation of 

projects, provide design guidelines for monitoring, and implement several pilot projects does not 

fully satisfy RPA requirements. 

Elements that are Lacking. 

Much of the work proposed here is already underway within the Action Agencies RME 

framework. What this proposal offers that the AER team is not currently doing is the 

implementation of several pilot projects. These pilot projects can be used to test the methods and 

guidelines established by the AER team. In addition, the pilot studies can test cause-effect 

linkages between management actions and the proposed indicators. Reviewers believe this is an 

important component of AER. 

Means and Opportunities to Strengthen Proposal. 

The study proposes to develop pilot projects aimed at grazing control, barrier removal, and 

installation of irrigation diversion screens. Providing information on how these studies will be 

developed or the methods that will be used would clearly strengthen the proposal. It is not clear 

if the pilot studies intend to test the protocols (and selected indicators) developed by the AER 

team, or if the pilot studies will “intensively” investigate the web of mechanistic relationships in 

the stream ecosystems (the latter is referred to as “intensive effectiveness research” by the AER 

team). 

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Feasibility of Proposed Work. 

More information on the development of the pilot studies is needed to ascertain the feasibility of 

the proposed work. It is not clear how the studies will be developed, nor is it clear if the sponsor 

intends to implement and test the protocols developed by the AER team. Reviewers sense that 

the sponsor intends to develop their own monitoring criteria and guidelines. 

OCEAN AND ESTUARY SUBGROUP -- Action item addressed - 183. Pilot projects have 

already been chosen that do not include the estuary. Unless that focus is going to be expanded, 

this proposal does not address the estuary. 

ISRP Remarks on RME Group Comments: 

The ISRP agrees with the RME group assessment that “More information on the development of 

the pilot studies is needed to ascertain the feasibility of the proposed work” and it is unclear if the 

proposal would meet the needs of RPA 183. 

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. 

Response Needed? No, Not Fundable 

ISRP Preliminary Comments: 

Not Fundable. The proposal is inadequate. 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 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: 

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Directory and Synthesis of Protocols for Management/Research and Volunteers in Washington, 

Oregon, Idaho, Montana and British Columbia” by Johnson, et al. 2001. 

Action Agency/NMFS RME Group Comments: 

STATUS MONITORING SUBGROUP -- This proposal would engage earth scientists, 

civil/systems engineers, geomorphologists, hydrogeologists and others familiar with the science 

of physical processes to conduct a synthesis inventory of tools and develop a Landform Library,

database, web based application, and model. 

a. Does a proposal satisfy the objectives of RPA? 

This proposal is vaguely linked to RPA 180 in the narrative but no specific linkages are 

established by the proposal. The proposal is really aimed more at supporting subbasin planning 

than monitoring, although data derived from monitoring will be necessary to model development 

and application. 

Proposal indicates applicability to RPA 180 as it would provide new overall subbasin analysis 

and planning capability similar/parallel to EDT, SSHIAP, and/or GIS-based analytical 

functionality. The primary purpose appears to be to provide tools that translate habitat treatments 

into specific changes in habitat attributes, which could then be used by EDT or other habitat 

analysis tools. Relevance to RPA 180 appears to be in which habitat attributes might be 

monitored. 

b. If not, explain what elements are lacking. 

Explicit linkage to RPA’s 180/181 is lacking. The proposed models/tools to be developed under 

this proposal would need environmental data developed under RPA’s 180/181, in addition to

providing some synthesis of the potential and/or realized benefits of restoration actions. The 

proposal is long on concepts but very sparse on the details, particularly in the objectives section. 

This project appears to relate more to RPA 183 (effectiveness monitoring) by identifying the 

physical attributes that might respond to specific habitat actions and predicting the potential 

magnitude of the responses. 

c. If the proposal partially satisfies the RPA objectives, suggest means or opportunities to 

strengthen the proposal. 

The authors need to integrate biological processes (riparian vegetation) into their conceptual 

framework of what processes control the environment. Ecosystem processes and structure are not 

simply based on physical processes controlling the environment. A more holistic conceptual 

framework would be useful. In addition, treatments need to be expanded to consider passive 

processes in addition to engineered solutions. Sometimes the best solution is just taking the 

human disturbance off the land, not just mitigating or engineering around it. 

d. If a proposal is entirely satisfactory, indicate so and note the particular strong points. 

e. Assess the feasibility of the proposed work in general terms. 

This proposal is highly ambitious as it attempts integrate significant known and unknown 

elements of putting together physically-based models and tools to quantify cause and effect in 

biophysical processes. The direction of their approach is based on physical processes and an 

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ISRP 2002-13 Mainstem and Systemwide Preliminary Review 

engineering-oriented perspective on how to address recovery of watersheds. There doesn’t seem

to be much emphasis on the biological processes (e.g. riparian vegetation) that also shape and 

form the habitat template. While the problem statements addresses by this proposal are laudable, 

it is unclear how the proposal will address many of these lofty goals. 

ISRP Remarks on RME Group Comments: 

The ISRP is in general agreement with the RME review comments on this project. 

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. 

Response Needed? Yes 

ISRP Preliminary Comments: 

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 the public. This project would introduce another level of M&E that 

may overlap with the responsibilities of the Council’s FWP. 

A response should include a description of provisions for monitoring and evaluation of the 

results. There should be a clear strategy for obtaining feedback from users of these products to 

determine if the project has been successful. More information on the relationship of this project 

with other ongoing activities is necessary. 

Action Agency/NMFS RME Group Comments: 

HABITAT ACTION EFFECTIVENESS RESEARCH SUBGROUP -- Does Proposal Satisfy 

RPA Objectives?

Principally, this proposal is not RPA 183 relevant because it doesn’t address monitoring or 

implementation of specific projects as identified under RPA 183 of the BIOP. Rather it requests 

funds to develop a programmatic structure. 

What Elements are Lacking. 

This proposal is weakened by a lack of specific information on what the developed products will 

look like. For example the proposal includes large scale quotes of the Paulsen et al (2002) 

document that describes what projects should look like, but does not identify current habitat 

projects that it would coordinate. 

This project received primary review by the Data Management Subgroup. Like 35001, 35020 

and 35050, it proposes to organize a project management team to track, prioritize, and coordinate 

projects within the Columbia River Basin. This project has three objectives: 1) develop a 

framework to track project implementation, 2) develop a system to confer credit on those doing 

the projects and 3) to develop habitat indicators as surrogates for fish responses. The criteria 

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ISRP 2002-13 Mainstem and Systemwide Preliminary Review 

above indicate that programmatic proposals that lack any supporting intention to do some

monitoring will receive low priority. In addition. 

Means and Opportunities to Strengthen Proposal. 

This proposal would be strengthened by more detailed information on what habitat improvement 

projects are currently out there to be monitored. If there were some assessment of current 

projects, then one might be able to provide some more details within the proposal to allow the 

reader to know that the proposal sponsors are constructing an appropriate team and that they 

know what they are getting into. 

DATA MANAGEMENT SUBGROUP -- Does the Proposal meet RPA needs?

The Action Agencies have an urgent need for tracking habitat related projects to meet its 

obligations under the Biological Opinion. This proposal addresses those obligations directly. 

The project seems to be designed particularly to address RPA 183 and the evaluation of the 

benefits of offsite mitigation habitat actions. The proposal does not seem to meet the Action 198 

goal to develop a Cooperative Information System. 

Elements the Proposal is Lacking 

The proposal does not state that it will provide a structured hierarchical program for status 

monitoring. There is some lack of clarity in the proposal. At one level it is described as a project 

compliance system. On the surface, this is a relatively simple data collection task: was the 

proposal completed as planned? At the next level the proposal plans to gather information about 

the success of these projects. This is a much more difficult task, especially since, as the 

proponents state, the indicators for success have not been developed or agreed upon. These 

issues need to be clearly resolved. 

Means and Opportunities to Strengthen Proposal 

The proposed information system, to be successful needs to be designed to at least reference other 

project data. While the proposed data collection system is focused on BPA funded projects there 

are potentially other projects that would need to be considered before the effectiveness of a 

particular BPA funded project could be evaluated. Stating the provisions for data retention and 

protection would greatly enhance this proposal. Private operation and maintenance of the 

database implies a long term and ongoing obligation for this service. On one hand the proposal is 

for private data management while the proposal also claims that the tracking system will reduce 

the BPA’s overall liability. On the surface these claims appear contradictory. More information 

on coordination with other ongoing projects would alleviate potential for duplication of other 

work currently in progress. For example, this proposal appears to duplicate the RME work 

group’s “Protocols for Monitoring Habitat-Based Environmental Indicators” study by Hillman 

and Giorgi. Broadening the project focus to a wider constituency beyond BPA Program

Managers, Scientists, and Administrators for needs gathering and evaluation would strengthen the 

proposal. 

Feasibility of Proposed Work 

There is no indication of adoption of metadata standards. 

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ISRP Remarks on RME Group Comments: 

There is agreement between the ISRP and the RME Workgroups that additional information is 

needed to explain the relationship between this project and other ongoing activities. The RME 

Workgroups indicated that more specific information was needed in order to strengthen the 

proposal and evaluate its benefits. This lack of detail may explain why one RME Workgroup

comments that this proposal is not RPA 183 relevant while another Workgroup states that the 

proposal is designed particularly to address RPA 183. 

ProjectID: 35045 

Modeling and Information Management System to Assess Effectiveness of Alternative Actions 

Sponsor: PNNL 

FY03 Request: $500,000 

5YR Estimate: $1,500,000

Short Description: 

Response Needed? Yes 

ISRP Preliminary Comments: 

A response is needed. This proposal is to develop a model and information system (MADIMS) to 

support the RME program by developing 3 functional capabilities: spatial and temporal scale 

changes in data, information and models; hypothesis testing; 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 proposal does not provide a clear picture of how the model building will be done. The 

response should provide more details such as exactly how neural networks and fuzzy logic will be 

used to obtain models. The response should describe how the project could contribute to the 

CBFWA (or other) systemwide design based M&E project by providing modeling aspects for 

making predictions based on data. 

This is an expensive project with a budget that is suspiciously rounded. 

ProjectID: 35050 

UW Offsite Habitat and Fish Survival Effectiveness Monitoring 

Sponsor: UW 

FY03 Request: $177,048 

5YR Estimate: $1,074,065

Short Description: 

Response Needed? No, Not Fundable 

ISRP Preliminary Comments: 

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. 

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Action Agency/NMFS RME Group Comments: 

HABITAT ACTION EFFECTIVENESS RESEARCH SUBGROUP -- Does the Proposal address 

RPA Objectives?

Overall, the proposal offers a useful approach to developing a central design that provides 

guidance and criteria for monitoring management actions within the Columbia Basin. However, 

much of what is proposed is already well established or is currently being developed by the 

Action Effectiveness Research (AER) The proposal also intends to develop and coordinate a 

WEB SITE that will centralize monitoring protocols, guidelines, data, and information. 

Reviewers believe this is necessary and beneficial, as it will help the Action Agencies coordinate 

current and future projects, provide quality control of data, and provide a central location for 

sharing information. This site would provide potential sponsors with all the information needed 

to develop a valid effectiveness monitoring study. 

What Elements are Lacking. 

This proposal lacks specific information on what the developed products will look like. There is 

not a clear indication of what investment the authors have made in determining which monitoring 

needs exist and what percent could be feasibly executed. 

Means and Opportunities to Strengthen Proposal. 

This proposal would be strengthened by some more detailed information on what habitat 

improvement projects are currently out there to be monitored. The development of a centralized 

WEB SITE is an excellent idea. The proposal should describe in more detail how it intends to

develop the site, how it will be managed, and how data quality will be controlled. A simplified 

outline or structure of the WEB SITE would be useful. 

Specific Comments: The proposal needs to provide more information on how it intends to 

evaluate past and current projects. The proposal needs to define the criteria by which it intends to 

evaluate the projects. For example, a checklist of questions that will be asked of each project is 

needed. Reviewers think the following list of questions could be asked of each project: 

1. What hypothesis is the project testing?

2. Where is the project located (province, subbasin, etc.)?

3. What type of project was implemented (e.g., road closure, addition of LWD, etc.)? 

4. How many sites were sampled? 

5. Where were the sites located?

6. What was the sampling design (sampling in test and control sites, sampling only in test sites, 

etc.)?

7. How were sites selected (e.g., random selection)? 

8. What fish species were targeted?

9. What factors were measured (include both physical/environmental and biological)? 

10. Where were these factors measured?

11. How were these factors measured?

12. How frequently were factors measured?

13. How were the data analyzed?

14. What are the key conclusions?

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A simple checklist of questions like these will not only help rank the validity of projects, but will 

also identifying gaps in our understanding of effects of management actions on fish populations 

within and across watersheds or provinces. 

ISRP Remarks on RME Group Comments: 

The RME comments are generally more positively disposed toward the proposal than the ISRP. It 

would seem that the RME comments on proposal 35033 also would be relevant to this proposal. 

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

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. 

Response Needed? Yes 

ISRP Preliminary Comments: 

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. 

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 2003 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? 

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ISRP 2002-13 Mainstem and Systemwide Preliminary Review 

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. 

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. 

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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. 

Response Needed? Yes 

ISRP Preliminary Comments: 

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). 

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In Objective 1 and 3, the committee 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 

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. 

ProjectID: 35004 

Harvest Model Development 

Sponsor: UW 

FY03 Request: $278,398 

5YR Estimate: $794,416 

Response Needed? No, Not Fundable (but response welcome) 

ISRP Preliminary Comments: 

Not Fundable but see comments and respond if appropriate. This proposal caused some

confusion among ISRP review team. The PI began his presentation by stating, “do not fund this 

proposal”, because apparently the managers (the Chinook Technical Committee - CTC) who 

would use the products of this proposal aren’t ready for the proposal; consequently, the proposal 

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won’t be effective. However, on paper, the proposal 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 need. 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 description of steps to model reconfiguration is 

adequate. 

The ISRP review raised several issues: 

1. The rationale for producing two basically similar (but not identical) models seems to be 

based on whether one organization has the technical ability to deal with the C++ model 

code. This calls into question whether harvest managers are either duplicating each 

others work, or running different models and computing different harvest scenarios that 

later create conflict over management decisions. How did the issue of two models 

develop and what model specifications have been used in developing this proposal? 

2. We have been informed that the task of re-coding the CTC model has already been 

assigned to two CTC committee members and advancements in the capabilities of the 

model are being addressed through a separate contract. Who requested the CTC work 

and have you the support of that committee to submit this request? 

3. The needs of the BiOp model were not described in the proposal but ISRP understanding 

is that they are very similar to the CTC model and that NMFS has proceeded with an RFP 

for this work. Is this proposal in response to a request from NMFS and if so, why has it 

been submitted to the Council? 

4. The point is made about accessibility of the code: why do managers need to understand 

the code? Please explain why option 2 is not selected: models developed in a simplified 

C++ format and harvest managers learn to use C++? Why shouldn’t harvest organizations 

be fluent in the tools of harvest management? The CTC is not a committee of managers 

but rather technical experts from each management agency associated with the Pacific 

Salmon Treaty. The issue of coding languages has been a trade-off in the committee since 

the committee frequently must modify code at meetings to complete an assessment and 

cannot have 3rd party software or advanced languages that CTC staff is not fully 

proficient in. Further, transparency of the model and the ability for others to use is an 

important consideration when agencies coastwide use one model for assessment of 

important harvest management decisions. 

5. Problems developing harvest model: The main question relates to the availability of data 

on by-catch and incidental mortalities resulting from that by-catch. What data exist on 

gear selectivity, incidental catch, and incidental catch mortality? 

Summary

The proposal is reasonably clear in its goals but it implies some conflict in the modeling/harvest 

management community on how to proceed. It appears that the level of effort and hence cost 

may be doubled due differences in preferences for coding languages. Further, the ISRP is 

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 has no 

intention of generating a potential problem of alternative models and should not consider this 

proposal unless the proponent can clearly demonstrate support of the user community for this

proposal and the ability to develop one model for useful in the Basin for assessment of harvest 

alternatives as an effective recovery tool. Further, the proposal does not comment adequately if

the data is available to support the developments suggested. 

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ISRP 2002-13 Mainstem and Systemwide Preliminary Review 

Finally, 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. Suggest funding 

one model if it is possible for involved organizations to work together with cohesive effort. 

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. 

Response Needed? Yes 

ISRP Preliminary Comments: 

A response is needed. This proposal presents a generally very good study design for the purposes 

intended with a good technical background and thorough knowledge of past literature and current 

issues. Highly relevant to NMFS RPA’s. The selection of the Yakima as study site is appropriate 

since the facilities exist to capture the fish, to track them throughout the system, and to assist in 

concerns about fishery impacts in this system (as noted in the proposal). Further, these tags 

would aid in the study of spring Chinook use of the upper river for holding. Although this study

may have several benefits, the proposed variations for future years do not seem as justified. Why

should the study be multiple-year? Funding this year should not be automatically committed to a 

multiple year study unless researchers have defined the rationale. Out-year rationale is 

inadequate in this proposal. 

1. Given the multiple studies that have been conducted on hooking mortality, discuss the potential 

for estimating losses in terms of existing mortality data rather than collecting more field data. For 

example, the proposal references a study on hooking mortality of recreationally caught fish on the 

Willamette. Why is this study not sufficient to answer the question about the effect of catch-andrelease on spawning success? Using existing data and literature, suggest you establish best and 

worst case scenarios (for example pre-spawn mortality is twice as high as worst hooking 

mortality and equivalent to best survival rates). Then estimate the acceptability of hooking losses 

on different run sizes. This would enable some a priori hypotheses about the impacts of hooking 

mortality. The proposal does not address the fact that in low run years, sport harvest of wild and 

even hatchery fish may have far greater impact than on high run years. Thus, harvest should be 

keyed to a worst-case scenario and limited such that sufficient escapements occur, especially in 

low run years. Comments?

2. The proposal does not address whether mortality might vary by timing of the run. It assumes 

that mortality will be constant over time. Is this reasonable? Will the timing of tags allocated to 

the control fish be matched to the tagging of the angled fish? How will the tags be allocated 

through the season? In Task 1a, Methods states that fish length would be estimated to the nearest 

10 cm. Is this correct and if so, what is the value of such a broad size range?

3. There will be concerns expressed about the use of selected anglers as opposed to the use of 

public anglers that may not handle the fish as carefully, etc. How will the anglers used be 

instructed to fish and what gear would be used? The length of time a fish is played and handled 

by experts and science techs may be less of an impact than inexperienced fisherman that take

longer to handle and may grab fish by gills and flop it on the bank. How can the study control for 

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ISRP 2002-13 Mainstem and Systemwide Preliminary Review 

differences between experiment and reality? How do you separate effect of tagging from angler 

handling when assessing post-release survival? It is not clear in the methods whether every sport 

caught fish would be tagged, or how the tagged fish would be chosen? Will this be a random

selection process or will certain wounds be eliminated from the study? 

4. The study has potential for coordination and cooperation from Law Enforcement perspectives 

and studies. For example, public outreach programs, publicity, tracking ultimate fate of fish. And 

catch and release of wild fish. Could you integrate efforts with Law Enforcement proposals? 

5. Existing PIT tags from smolts may provide additional information upon return as adults. 

Discuss the potential value of this information. 

6. Discuss the alternative value of live capture and spawning of some wild fish in the hatchery as 

opposed to release of wild fish. Are there some highly concentrated sport areas where wild 

caught fish could be taken live from anglers and transferred to hatchery? These anglers could be 

rewarded with money or receive two hatchery fish for one wild fish. This also could reap benefits 

in publicizing recovery and having the public actually have hands on support of such actions. It 

would also benefit some of the goals of the Law Enforcement programs of CRITFE. 

8. If passage is an issue at the dams, receivers upstream and downstream could provide valuable 

information on time to pass, fall back etc. and potentially provide data as to whether fish delay

passing ladders/dams after hooking. Cost for additional equipment and analysis might be very 

cost effective and could be coordinated via passage studies by U of Idaho. 

9. Why are agencies using a variety of hook types in their regulations? Rationale? No analysis of 

different hook types was suggested. Are there no potential differences? Has this been studied?

10. Harvest can be selective if more fish are caught early or late in the run. Additionally, since 

run size is not confirmed until mid to late in the season, it seems that harvest should be more 

restrictive early in the run to assure escapement goals will be met, then allow more fishing mid 

run. If the runs follow bell shaped curves, harvest in the middle of the run will create “stabilizing 

selection” rather than “directional selection” of run-timing. 

11. Water temperature is a key component of stress mortality. What temperature variations occur 

over the proposed time of the experiment? Should the experiment be restricted to conditions at or 

below 10 C or some comparable standard?

12. Run sizes are anticipated to be adequate for experiment, but no data are provided for 

comparison (top of page 7). What are the expected run sizes for 2000 outmigrants versus 1998-

99? 

13. Is the number of radio-tags sufficient? The sample sizes seemed small. The proposal refers to 

several classes of fish that would be considered in the analysis: marked vs. unmarked, size 

classes, sex and environmental conditions. There will be 100 sport tags allocated per year and 

only 50 controls. Given the number of categories potentially used in these analyses, how was a 

sample size of 100 tags determined? If there are widely distributed spawners, will there be no 

behavioral information for the time between catch and spawning. 

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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. 

Response Needed? Yes 

ISRP Preliminary Comments: 

This proposal is to test the efficacy of using the fish wheel as a selective terminal fishing gear in 

the Columbia River System. The intent is to use the fish wheel to catch hatchery salmon and 

American shad. The goal is to provide economic and cultural benefits to tribal fishermen while 

providing appropriate protections to protected species. 

As the ISRP indicated in its review of an earlier version of this proposal under the “Innovative” 

solicitation, the re-introduction of fish wheels as a selective fishing technique would be useful for 

the Columbia River Basin allowing harvestable numbers of healthy stocks of salmon or steelhead 

to be captured and kept, while allowing fish from other stocks to be released alive to continue to 

the spawning grounds or hatcheries. The ISRP supports a test of fish wheel feasibility. There are 

locations where the wheels are very effective and could be used as a selective fishing tool, but 

their success is site-specific. 

The feasibility questions surrounding this gear do not pertain to the gear’s technical or economic 

performance as much as to whether fish wheels are a feasible harvest method in the current 

regulatory context of ESA protected species, and whether acceptable allocation mechanisms for 

fish wheel harvests can be developed. 

Fish wheel gear makes fishing a collective, rather than individual operation. This is a fundamental 

change. It will require a cooperative, rather than competitive, approach to fishing and will also 

require that some sharing mechanism be worked out among fishers to allocate the catch. The 

proponents should address how this will be done: who will use the gear, how it will interact with 

other gear, and how harvest will be allocated. 

More detail should be provided about objectives, tasks and methods. For example, why is a 

literature review of fishwheel design necessary? How much is already known? What factors will 

be considered in identifying design characteristics of a Columbia River fishwheel? More detail 

should also be provided about how the experiment will be conducted and about the criteria to be 

used to evaluate performance. What gear types would it be compared against, and what metrics 

will be used to measure effectiveness? 

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Coded Wire Tag Monitoring Program

ProjectID: 198201301 

Coded-Wire Tag Recovery Program

Sponsor: PSMFC 

FY03 Request: $2,989,812 

5YR Estimate: $16,132,108

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. 

Response Needed? Yes 

ISRP Preliminary Comments: 

A response is required. First, let us acknowledge that this is a huge program that annual conducts 

a large number of activities that are essential to the Basin, and the data provided has been widely

utilized over many years. However, this proposal is a huge mixing pot of activities that needs to 

be more clearly delineated with corresponding budgets and BPA funding. The current proposal

requests $3 million from BPA and matches this with $2.5 million from 26 other sources! 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, but we should ensure that the CWT 

effort is linked/integrated with the CBFWA M&E proposal (35033). There are a lot of aspects of 

the CWT program that are of great interest for 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. 

Unfortunately, many of past ISRP comments seem to still be appropriate and the technical review 

issues do not seem to have been undertaken. 

For example, our Programmatic comments from the past review included: 

“The entire CWT program needs a programmatic review at regular intervals to confirm priorities 

and efficacy. We strongly recommend a technical/peer review to confirm the validity of the 

critical assumptions (e.g. current adequacy of the 20% sampling rate goal, and 30 tag recoveries 

per group, adequacy of using hatchery stocks as surrogates for monitoring wild stocks). Other 

key assumptions also need to be verified: 1) marked (CWT) fish suffer the same natural mortality

as unmarked fish, and 2) marked fish do not lose their marks.” 

This proposal does respond adequately to the key assumptions but the ISRP was particularly

surprised that the recommended statistical advisor position has not been staffed nor the technical 

review reported. Further, the ‘CWT program’ and management through the PSMFC is now much 

more than simply managing the CWT program and databases. This proposal covers analyses and 

data collection activities that are clearly the responsibility of state or Tribal agencies but for 

unstated reasons now seem to be managed through this program. The ISRP recognizes that there 

could be reasons of coordination and efficiency involved but technical review of the CWT 

program becomes substantially more difficult. 

The coded-wire tag (CWT) program has been fundamental to the management of chinook and 

coho salmon coast-wide. Before the development of the CWT, catches of specific stocks were 

unknown and sustainable exploitation rates of stocks could not be assessed (other than by the 

trend in their spawning escapements). Trends in spawning abundance may result, however, from

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over-exploitation or decreased survival, or the interaction of exploitation and declining stock

productivity (habitat impacts). The development of the CWT program and the establishment of a 

coast-wide recovery program allowed for the development of quantitative assessments of life 

history statistics for chinook, coho, and steelhead. As noted in the proposal, this tool allows 

estimation of catch and age distributions in fisheries, exploitation rates and patterns by fishery,

and estimation of annual survival rates (from point of release to adult return). By the early

1980’s, the CWT had become an essential tool for stock assessment and management and 

provided the technical basis for rationalizing ocean fishery exploitation under the PST and 

domestic agencies. This tool though is now under increased pressures due to the development of 

mass-mark selective fisheries and the need to implement electronic sampling for coded-wire tags. 

The rationale for this proposal is to provide comprehensive stock assessment and hatchery

production monitoring to regional management entities and all researchers. The program requires 

two components: tagging of representative groups of fish (by species, stock, brood year, etc.), and 

recovery of the tags in fisheries and spawning escapements. In the mid-1970’s, a coast-wide 

agreement requested all recovery agencies to sample 20% of commercial salmon catches for the 

recovery of CWT. While this percentage was not based on any statistical principle, it has been 

adopted as the “standard” rate of sampling in catches. As in any mark-recapture program, 

however, the rates of tagging and recovery should be dependent on the objective of the program. 

Consequently, the ISRP has previously recommended the CWT program review the “30 observed 

recoveries” guideline that is quoted in the proposal. That value was determined during a period

of good marine survival and well supported sampling programs. During periods of poor marine 

survival and/or reduced sampling (due to budget constraints), agencies would be well advised to 

increase the numbers of tags released, depending on the accuracy and precision desired in their 

programs. 

Further, we re-emphasize two points previously presented by the ISRP: 

1) It is still not possible to place tagging and recovery programs of this CWT program in a 

Regional context. For example, we are only notified of the requests of additional tagging or 

existing sampling programs. How can this be examined in a technical context without a 

comprehensive description of the supported tagging programs and related objectives? Do the

current tagging programs address all regional concerns, or are the best tagging programs being 

supported, are sampling programs meeting agency needs, etc.? 

2) The clarity of presentation would be dramatically enhanced by the use of a flow chart or other 

device to visually depict overall program structure and how subprograms fit into that structure, 

overall budget, etc. With so many agencies and tasks role into one program, it is not possible to 

advice the Council on the use of BPA funds or the technical rigor of programs funded by these 

resources. 

Rather than a list of specific points in this huge program, the ISRP requests responses to 

questions in the above text, and to five more general program issues: 

1) Are the current tag allocations appropriate to meet the needs of Regional managers and the 

recovery priorities of the ESA stocks? In your opinion, how should this be assessed and 

presented for technical review?

2) Are the current recovery programs and associated data appropriate to meet the needs of 

Regional managers and the recovery priorities of the ESA stocks? In your opinion, how should

this be assessed and presented for technical review?

3) Given the development of mass-mark selective fisheries, what are the additional costs imposed 

on this program, are the electronic sampling programs and equipment adequate and how is this

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ISRP 2002-13 Mainstem and Systemwide Preliminary Review 

being monitored (e.g., verification of wand performance, checks for missed marks, sampling 

coverage of fisheries)?

4) The complex of tasks outlined in this proposal must be clearly identified into sub-tasks by

activity, budget, funding source, and responsibility (i.e. which agency or group). Critical linkages 

should be identified and comment made on whether funding of these linkages is assured, at risk, 

etc. Are the data involved in these linkages adequate? For example, if PMSFC is responsible for 

run reconstruction (through this proposal), are escapement monitoring programs adequate for this 

assessment method, are inter-dam loss values included, etc.? 

5) During presentations and discussion, reference was made to a Regional review of tagging 

programs. What other Regional reviews of tagging are being conducted, by who, and how is this 

proposal’s staff integrated with any Regional reviews? 

6) Given the importance of this program to Regional assessments and coastwide obligations for 

sampling, it is probable that funding for this program will continue. How will program managers 

ensure that recommendations that develop from this review and from past reviews are addressed?

7) Various aspects of this proposal are dependent upon other labs or agencies to complete their 

sampling, decoding, etc. Are there critical bottlenecks or consistent problems in these other 

programs that limit the success of this program and utility of the data?

Further, there are some specific questions concerning budget items that have been noted by the 

committee: 

· the budget for statistical consulting (>$128k ) seems high, how was this determined? Are 

Indirect cost is still being charged on the CWT purchase and if so, why? 

· Task 1.b indicates that $20,000 is allocated to sampling SAFE fisheries, why does this program

pay for that program and are there plans to recover these costs?

· With the comments about handle-held data loggers and need for electronic sampling for CWT,

is zero the correct entry for Capital in Section 8? Do the agencies purchase that equipment?

Action Agency/NMFS RME Group Comments: 

STATUS MONITORING SUBGROUP -- 

198201301 - Coded-Wire Tag Recovery Program

198201302 - Annual Stock Assessment - Coded Wire Tag Program (WDFW) 

198201304 - Annual Stock Assessment – Coded Wire Tag Program (ODFW) 

198906500 - Annual Stock Assessment - Coded Wire Tag Program (USFWS) 

(These 4 proposals were considered as a block.) 

These proposals do not claim relevance to either RPA 180 or 181; they list only hatchery-release 

groups as being tagged, although Short Descriptions and Abstracts for some proposals indicate 

wild populations will also be assessed. Proposal narratives indicate that the tagged hatchery fish 

should be fairly representative of wild fish in migratory patterns, timing in the fisheries, etc., but 

the proposals do not suggest which ESUs or wild stocks might be represented by which hatchery

stocks being tagged. However, absent direct application to RPAs, CWTs may be very useful for 

estimating harvest of similar wild stocks in monitored fisheries, which would apply to status 

monitoring performance standards (e.g., stage-specific survival). 

For many stocks addressed by these proposals, release locations are Bonneville Pool or below 

Bonneville, so groups are exposed only to small reaches of the mainstem/estuary migration 

corridor and part of the inriver fisheries. PIT-tagging projects are probably better for monitoring 

smolt-adult-returns of listed stocks than are CWTs. 

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ISRP 2002-13 Mainstem and Systemwide Preliminary Review 

Sponsor may wish to clarify which ESA-listed stocks, if any, might be represented by the 

proposed release groups and the type of resulting data that might be applicable to those listed 

stocks. 

OCEAN AND ESTUARY SUBGROUP -- Potential action items addressed - 165; 166; 174; 179; 

184. Includes estuary and part of ocean in sample area. This proposal needs to be coordinated 

with proposal 35046 and 30007 which may be more effective means of tracking movement and 

habitat use, and the work that John Ferguson of the Northwest Fisheries Science Center is doing 

on acoustic tags to assess potential duplication of effort and do a better job of developing trend 

data on delayed mortality. It also needs to be coordinated (it has to some extent in the past) with 

the Dept. of Fisheries Oceans Canada, US/Canada Shelf sampling cruises, funded since 1998 

under project 1998-014 and now proposed as 30010. 

ISRP Remarks on RME Group Comments: 

RME comments concerning how representative tagged stocks are of an ESU should be addressed 

in a Regional review of tag allocations but some of the other RME comments are simply incorrect 

and/or poorly advised. 

1) “PIT-tagging projects are probably better for monitoring smolt-adult-returns of listed stocks 

than are CWTs.” These tags would only be better for data collected in-river but there is no 

sampling for PIT tags in ocean fisheries, there would be no historical perspective for perspective, 

and stock coverage comparable to CWT would be prohibitively costly. 

2) The development of acoustic tags “which may be more effective means of tracking movement 

and habitat use” maybe true but that has never been the application of CWT. Such a statement 

demonstrates a misunderstanding of the value of different types of tags. Acoustics tags likely will 

provide a better research application for their intended use but they will never provide the 

monitoring capability of CWT. 

The CWT program has been an integrated coastwide program since 1975 and is annually

coordinated through the Regional mark coordination meeting and two technical committees of the 

Pacific Salmon Treaty. The CWT is actually a commitment in the Memorandum of 

Understanding of the 1985 and 1999 Pacific Salmon Treaty.

The ISRP agrees that there is a need to ensure that the CWT provides the necessary stock 

coverage and assessments needed for salmon recovery, but there must be a clear understanding of 

the applications of different tags and their relative importance. 

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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

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. 

Response Needed? Yes 

ISRP Preliminary Comments: 

General ISRP comments on CWT Tagging #198906500, #198201302, and #198201304 

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 production monitoring 

program for Columbia Basin salmon hatcheries. The projects were initiated to address the 

problem of incomplete basin-wide 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. The description of tagging methods appears to be adequate. There is, however, 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 many 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 SFEC of the PST (Selective Fishery 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 be 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 are: 

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ISRP 2002-13 Mainstem and Systemwide Preliminary Review 

1) Are these tagging programs integrated with Regional tagging plans and how were these stocks 

selected for including 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.)? 

ProjectID: 198201304 

Annual Stock Assessment - Coded Wire Tag Program (WDFW) 

Sponsor: WDFW 

FY03 Request: $334,412 

5YR Estimate: $1,793,273

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. 

Response Needed? Yes 

ISRP Preliminary Comments: 

See general comments addressing #198906500, #198201302, and #198201304 under 198201302. 

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. 

Response Needed? Yes 

ISRP Preliminary Comments: 

See general comments addressing #198906500, #198201302, and #198201304 under 198201302. 

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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. 

Response Needed? No, Not Fundable 

ISRP Preliminary Comments: 

This proposal is technically inadequate. Do not fund, no response requested. The Oregon 

Department of Fish and Wildlife (ODFW) proposes to purchase and 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 

General Comments on Conservation Enforcement Proposals: 35051, 35052, 200005500, 

20005600, and 195505500 

A response is needed for this set of law enforcement proposals. The set of law enforcement 

proposals stresses the interdependency between public education and effective law enforcement. 

A basic question these proposals should address is how to determine the best mix of enforcement 

personnel and education to produce the greatest net enforcement benefits. 

The sponsors should also address concerns from the earlier BPA/Council review of the law 

enforcement program. Each proposal should justify the size of a core staff necessary for effective 

enforcement and place the current request in the context of core staffing needs. The Umatilla 

enforcement staffing level at .5 FTE appears to be the most deficient. The proposals should also 

describe the potential for matching effort; e.g. the Colvilles propose to train two officers from the 

existing force. Officers should be trained in fish and wildlife (as with the NPT). 

More thought should be given as to how the impact of public education – e.g . changes in public 

awareness or increases in enforcement effectiveness – will be measured. Metrics to measure 

success and evaluate program performance need to be identified. These metrics and the 

monitoring program they enable should be described in advance of program enhancement. 

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ISRP 2002-13 Mainstem and Systemwide Preliminary Review 

ProjectID: 200005600 

Protect Anadromous Salmonids in the Mainstem Corridor 

Sponsor: CRITFE 

FY03 Request: $455,787 

5YR Estimate: $2,518,411

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. 

Response Needed? Yes 

ISRP Preliminary Comments: 

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 outyear funding be contingent on the provision of more 

complete information on the magnitude of the illegal harvest problem and the expected benefits to 

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. 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. 

This proposal seems to demonstrate a potentially successful enforcement program. The incidence 

of violations appear very low with the current effort. Law enforcement is an effective tool and 

component part of the region’s effort toward recovery of endangered species. Compliance rate for 

harvest in Zone 6 appears high, which is laudable. 

In addition to the general comments provided above, the proponents should address the following 

comments specific to this proposal: 

• Development of the website (www.Eco-Law) is listed as a task in proposal 35052. How are 

the activities in the two proposals different? 

• More information on outcomes of interagency coordination should be provided.

• The funding request appears to be primarily for four FTE plus associated equipment (cars, 

radios, boats and air support). The budget needs review for particulars as this amounts to 

about $115,000 cost per FTE. The total increase in patrol hours for similar funding in 2000-

2001 resulted an increase in patrol hours from about 7700 hours to 9100 hours, or about 1400 

hours. This seems like a relatively low amount of leverage for an additional 8000 FTE hours 

added to the budget. The response should address why four FTEs increases patrol time by

less than 15% of the hours being paid for by BPA. 

• The results show total numbers of contacts and citations increased proportionally to the 

increase in patrol hours. Thus, it appears that the arrest rate is directly proportional to the 

effort rate. This suggests there is no increased deterrence at current levels of patrolling or 

fishing. In examining the crime rate (arrest/contacts), it is very low with compliance reported 

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ISRP 2002-13 Mainstem and Systemwide Preliminary Review 

from 95%-99% (Table 10). Thus an important question is whether the costs of the BPA 

program dollars are significantly leveraging results over and above “normal levels of 

funding”. For example, a very tangible benefit is number of illegal fish seized and live fish 

released. A total of 38 salmonids and 72 sturgeon were released alive. A total of 152 other 

dead fish were also seized. These are tangible benefits. But in proportion to the total run of 

fish or the total numbers of fish harvested, these represent an extremely small proportion of 

the population of fish. Assuming that without the additional funding, about 25% fewer fish 

would have been intercepted, the BPA dollars appear to be purchasing about 9 live salmon 

and 18 live sturgeon. This is based on the ratio of increased contacts and violations being 

about proportional to the increased hours of patrol. 

• There is clearly a “tipping point” in law enforcement when insufficient force will facilitate a 

significant increase in violation. This is well known for automobile speeding. Unpatrolled 

highways have much higher violation rates than where motorists see patrol cars and citations 

issued. The question is how much is enough. It appears that CRITFE has been doing a good 

job historically in enforcing harvest. Compliance rates have been high and remain high. 

They should better justify why an additional half million dollars would be well spent 

considering the above numbers. 

• The statistics that CRITFE uses to justify its operations are traditional and as such lack 

sufficient rigor to actually discern cause and effect questions and hence an effective 

“Adaptive Management” program. Quoting Peters et al., p.25, they use it to support the idea 

that law enforcement is a cost effective tool, which it is. However, the key phrase within the 

quote “while the outcomes are difficult to measure”, places the problem front and center. 

They are difficult to measure because proper data have yet to be collected to discern 

effectiveness. These questions were evaluated at length in over 200 pages of Peters et al., 

including using new techniques of data collection, public involvement and experiments. If 

the proposal were clearly aimed at these new ideas and changes, it would be far more

attractive. As it stands, much of the effort, data collection and M&E proposed is relatively

unchanged from the historic approaches of the 1990’s and critiqued in Peters et al. 

• The proposal is vague about how it will actually accomplish “adaptive management”. The 

author should explain in more detail what new data, and testable hypotheses can be used. 

Table 11 attempts to do this, however they are either untestable due to complex alternative 

hypotheses that could explain changes in metrics or the data already suggest that the program

has reached a zenith in compliance at least for harvest violations. For example: Salmon 

passage through the FCRPS corridor is already as high as 98% to LGR and missing fish have 

not been statistically adequately accounted for because radio tag experiments are not 

designed to assess anything except “dam effects”. Previous recommendations to track radiotag harvested fish and tributary migrations were rejected primarily for policy rather than 

scientific reasons. Such experiments might have both scientific as well as crime deterrent 

value. 

• Other metrics in Table 11 have not been historically recorded or analyzed but may be 

valuable such as compliance rates for pump operations, diversions and habitat destruction. 

However, no information is provided on enforcement in these arenas or the types of data that 

would be collected to demonstrate improvements over the status quo or baseline. 

• Resident fish are generally not endangered, thus unless CRITFE has plans for bull trout, this 

is not supportable by the NPPC program. Although benefits accrued toward sturgeon 

management are also laudable, these too are not the primary goal of the NPPC program. 

• Although interagency coordination/cooperation is an historic mode of operation, it is not clear 

how NPPC support enhances cooperation or leverages baseline efforts. Please indicate what 

metrics will be used to show the additional benefits of “more cooperation” over and above 

baseline cooperation. 

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ISRP 2002-13 Mainstem and Systemwide Preliminary Review 

• Peters et al.1997, recommended some new ideas for public involvement to enhance 

compliance. Few if any of those ideas appear within the proposed scope of activities. 

• Removal of ghost nets or unmarked gill nets was considered a major task in the 1990’s. Has 

this problem been solved? It represents a potential avenue of value for which a metric needs 

to be developed. 

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. 

Response Needed? Yes 

ISRP Preliminary Comments: 

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 T&E 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. 

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. 

In addition to the general comments provided above, the proponents should address the following 

comments specific to this proposal: 

· More detail should be provided on the metrics used to evaluate progress toward meeting 

objectives. 

· How would you determine whether voluntary compliance is optimized, or whether enforcement 

efficacy and accountability is maximized? Probably the best that can be done is to measure 

improvement to some specified standard. 

· Specify the type of coordination with other law enforcement units. 

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ProjectID: 195505500 

Umatilla Tribal Fish & Wildlife Enforcement 

Sponsor: CTUIR 

FY03 Request: $178,073 

5YR Estimate: $983,829 

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. 

Response Needed? Yes 

ISRP Preliminary Comments: 

This proposal is similar to those presented by the Colville and Nez Perce. All include increased 

enforcement, enforcement coordination among agencies, and public awareness. 

In addition to the general comments provided above, the proponents should address the following 

comments specific to this proposal: 

· More detail should be provided on the metrics used to evaluate progress toward meeting 

objectives. 

· How would you determine whether voluntary compliance is optimized, or whether enforcement 

efficacy and accountability is maximized? Probably the best that can be done is to measure 

improvement to some specified standard. 

· Specify the type of coordination with other law enforcement units. 

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

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. 

Response Needed? Yes 

ISRP Preliminary Comments: 

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 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 

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ISRP 2002-13 Mainstem and Systemwide Preliminary Review 

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. 

In addition to the general comments provided above, the proponents should address the following 

comments specific to this proposal: 

· Do enforcement plans currently exist? 

· An important component of this proposal is education of the public and “conservation” training 

of enforcement officers. Detail is given on the educational tools to be used, but more thought

should be given as to how the impact of that education – e.g . changes in public awareness or 

increases in enforcement effectiveness – will be measured. For example, will it be enough to have 

officers attend the ESA enforcement overview training, or will there be some evaluation of the 

effectiveness of that training? 

· Are educational programs already in place? What has been learned from their successes and 

failures? 

· Will coordination with other enforcement efforts be done primarily through the website or 

through other means? Is the website operational yet, to be developed during this project? 

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. 

Response Needed? Yes 

ISRP Preliminary Comments: 

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. 

However, it is not clear from the proposal what the web-based data center would provide over 

what is provided by the existing Eco-Law site. Could the Eco-Law website be expanded to meet 

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ISRP 2002-13 Mainstem and Systemwide Preliminary Review 

enforcement coordination needs? How does this proposal relate to the tribal enforcement 

proposals in terms of the www-based tasks? 

The PIs experience with enforcement monitoring and participation in several related tribal 

enforcement projects make it likely that this proposal will achieve its stated objectives. The 

enforcement data center offers potential benefits to fish and wildlife at low cost. 

The proposal lacks specifics about the data to be collected and its purpose. The effort seems

primarily to place existing data and databases in a web accessible format. Large sums of money

were expended during the 1990’s for a law enforcement database. Much of that effort is no longer 

funded. Two projects remain related to tribal efforts on mainstem and tributaries. Peters et al. 

(1997) analyzed the previous databases and were generally supportive that law enforcement was a 

valuable tool in ESA recovery efforts. However, that report suggested significant inadequacies of 

the database to determine whether the efforts of law enforcement were being efficient and 

effective. That was because there was no direct link between cause and effect variables being 

collected. For example, if large numbers of hours of law enforcement resulted in high numbers of 

enforcement actions (positive correlation) then justification for the effort was deduced in high 

citation rates. If the opposite occurred with high enforcement hours and low citation rate 

(negative correlation) then law enforcement could take credit for lower numbers of violations 

because there was the “deterrent” factor. Such data make it impossible to “objectively” evaluate 

and manage law enforcement effort via statistics. 

There is no doubt that law enforcement is needed and has both deterrence and a punitive effect. 

Logic tells us that without law enforcement (or the threat of it), poaching and illegal harvest 

commercial or sport, would likely get worse. “Community Policing” was offered as an 

alternative means to involve the public and fishers (Peters et al., op.cit.). The proposal suggests 

such data would be useful and valuable to educating the public. The proposal should clarify how 

the data would be used in public education. How will outreach be conducted to ensure that the 

existence of the web-based data center achieves greater public awareness? 

The proposal suggests coordination with radio-tag efforts of University of Idaho. Unfortunately, 

unless specific hypotheses about illegal harvest, and experiments are designed to test those 

hypotheses, determining the loss rate of salmon as they migrate mixes all of the causes of 

mortality because the fate of missing salmon are generally unaccounted. Until a specific set of 

hypotheses outlining exactly what data should be collected, how it will test or evaluate law 

enforcement effectiveness, this effort proposed herein will be simply an extension of a old 

database that tracked effort, tracked crime rate, number of fish lost to poaching in illegal nets, 

expenditures, and total violations rates. But it will not tell us whether we need more, less or 

different forms of law enforcement actions. 

Other concerns include the following: The level of future effort to populate, analyze and report 

on the database collection will be far greater than designing the pot in which to put the data. 

Thus, implied in this web database effort are large future investment costs. Those investments, to 

be worthwhile, must have a better handle on exactly why specific data will be collected, how it 

will be used. There is a high degree of value in law enforcement data if we design the proper 

framework for that data. Thus the key question for the researchers focuses on the findings of 

Peters et al. A future proposal should carefully weigh those recommendations and incorporate 

them into the “new” law enforcement database. 

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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. 

Response Needed? No, Fundable 

ISRP Preliminary Comments: 

Fundable. 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. 

Response Needed? No, Fundable 

ISRP Preliminary Comments: 

Fundable. 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. 

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. 

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ISRP 2002-13 Mainstem and Systemwide Preliminary Review 

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, grey 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 

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. 

Response Needed? NA 

ISRP Preliminary Comments: 

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. 

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. 

Response Needed? Yes 

ISRP Preliminary Comments: 

This proposal submitted for mid-term review is to continue the coordination of tribal watershed

activities, the previous review asked that more detail be provided on activities to be conducted by

subcontractors. 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. 

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? 

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ISRP 2002-13 Mainstem and Systemwide Preliminary Review 

More detail should be provided in the proposal on project results and accomplishments to date. 

Provide details and evaluation of the restoration handbook. Methods should be described with 

more specificity. Responsibility to other tribes if any should be clarified. 

The budget should be evaluated. Several budget components seem high. 

Action Agency/NMFS RME Group Comments: 

STATUS MONITORING SUBGROUP -- Proposal indicates applicability to RPA 180. 

Objectives and tasks that appear relevant (paraphrased): 

3.b. Promote incorporation of standards in Tribal Restoration Handbook... 

4.c Cooperate with StreamNet to gather digital data (GIS) on watersheds to identify and address 

data gaps. 

5.b. Train and use Salmon Corps members to collect necessary field data where gaps exist for 

assessments and project monitoring. 

7.b. Coordinate development of a comprehensive water quality monitoring program for the 

Columbia River, develop a protocol and coordinate installation of a comprehensive thermograph 

system in the lower tributaries and dam reservoirs throughout the Columbia and Snake rivers to 

monitor water temperature. 

Proposal lacks technical details, reports and documents (e.g., Handbook) describing project 

methods and results apparently are not available on either BPA or sponsor web pages, so cannot 

evaluate how any of these activities might satisfy RPA 180 or compare to RM&E guidelines 

being developed regionally. Need results and data. 

OCEAN AND ESTUARY SUBGROUP -- Potential action item addressed - 180. This proposal 

claims to support 23 different RPAs but is so broad and vague it is not possible to clearly

establish that support. It could possibly be focused on estuary and RM&E needs as the CRITFC 

Wy-Kan-Ush-Mi Wa-Kish-Wit report is one that the NMFS BO has supported. 

ISRP Remarks on RME Group Comments: 

The ISRP agrees with the RME comment that the proposal is so broad it is difficult to assess its 

support for particular RPAs. More information should be provided to support the claim of RPA 

support, specifically with regard to RPA 180 

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. 

Response Needed? No, Not Fundable 

ISRP Preliminary Comments: 

Not fundable. 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. 

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ISRP 2002-13 Mainstem and Systemwide Preliminary Review 

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. 

Response Needed? NA 

ISRP Preliminary Comments: 

Not applicable, not amenable to scientific review. 

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. 

Response Needed? No, Not Fundable 

ISRP Preliminary Comments: 

Not fundable. 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 that 

subbasin planning will require 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

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ISRP 2002-13 Mainstem and Systemwide Preliminary Review 

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 “bottom-up” 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? 

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 

Response Needed? NA 

ISRP Preliminary 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. 

ProjectID: 199600500 

Independent Scientific Advisory Board

Sponsor: CBFWF 

FY03 Request: $681,876 

5YR Estimate: $3,649,876

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 Preliminary Comments: 

Not applicable, conflict of interest. 

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ISRP 2002-13 Mainstem and Systemwide Preliminary Review 

150 

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 Preliminary Comments: 

Not applicable, conflict of interest. 

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