Lower Snake River 

Compensation Plan

Spring/Summer Chinook 

Program Review

November 30-December 2, 2010

Boise, Idaho
 

Table of Contents 

PREFACE ..................................................................................................................................... 4 

MEETING AGENDA ..................................................................................................................... 5 

A BRIEF HISTORY OF THE LOWER SNAKE RIVER COMPENSATION PLAN 

HATCHERY PROGRAM FOR SPRING & SUMMER CHINOOK SALMON ........................... 7 

YANKEE FORK CHINOOK SALMON SUPPLEMENTATION PROGRAM – UPDATE .............. 13 

SOUTH FORK SALMON RIVER SUMMER CHINOOK SALMON ............................................. 29 

IDFG RESPONSE TO THE ISRP COMMENTS-South Fork Salmon River ............................ 38 

UPPER SALMON RIVER SPRING CHINOOK SALMON ........................................................... 44 

IDFG RESPONSE TO THE ISRP COMMENTS-Upper Salmon River .................................... 54 

CLEARWATER RIVER SPRING CHINOOK SALMON .............................................................. 60 

IDFG RESPONSE TO THE ISRP COMMENTS-Clearwater River .......................................... 69 

SPRING CHINOOK SALMON, DWORSHAK NATIONAL FISH HATCHERY, Clearwater 

River Idaho ............................................................................................................................ 73 

USFWS RESPONSE TO THE ISRP COMMENTS-Dworshak ................................................ 84 

TUCANNON RIVER SPRING CHINOOK SALMON HATCHERY SUPPLEMENTATION 

PROGRAM ............................................................................................................................ 86

GRANDE RONDE BASIN SPRING CHINOOK SALMON HATCHERY REVIEW: 

INTRODUCTION AND THE EARLY YEARS ........................................................................ 97 

ODFW RESPONSE TO ISRP COMMENTS - Grande Ronde Basin ..................................... 109 

UPPER GRANDE RONDE RIVER SPRING CHINOOK SALMON HATCHERY 

PROGRAM REVIEW .......................................................................................................... 111 

ODFW RESPONSE TO ISRP COMMENTS – Upper Grande Ronde River .......................... 129 

CATHERINE CREEK SPRING CHINOOK SALMON HATCHERY PROGRAM REVIEW ....... 130 

ODFW RESPONSE TO ISRP COMMENTS – Catherine Creek ........................................... 149 

LOSTINE RIVER SUPPLEMENTATION PROGRAM (1997 – 2009) ....................................... 152 

REINTRODUCTION OF SPRING CHINOOK SALMON IN LOOKINGGLASS CREEK: 

ANALYSIS OF THREE STOCKS OVER TIME ................................................................... 164 

IMNAHA RIVER SPRING/SUMMER CHINOOK SALMON HATCHERY PROGRAM 

REVIEW .............................................................................................................................. 185 

ODFW RESPONSE TO ISRP COMMENTS – Imnaha River ................................................ 208 

SIZE-AT-RELEASE OF IMNAHA RIVER CHINOOK SALMON HATCHERY SMOLTS: 

DOES SIZE MATTER? ....................................................................................................... 210 

ODFW RESPONSE TO ISPR COMMENTS – Size at Release: Imnaha River Smolts ......... 223 

GRANDE RONDE BASIN SPRING CHINOOK SALMON CAPTIVE BROODSTOCK 

PROGRAM: F1 GENERATION PERFORMANCE ............................................................. 225 

ODFW RESPONSE TO ISRP COMMENTS – Grande Ronde Captive Broodstock .............. 245 
MANAGEMENT OF BACTERIAL KIDNEY DISEASE IN CHINOOK SALMON 

HATCHERIES BASED ON BROODSTOCK TESTING BY ENZYME-LINKED 

IMMUNOSORBENT ASSAY (ELISA): A MULTI-YEAR STUDY ......................................... 249 

GENETIC ANALYSIS OF NATURAL-ORIGIN SPRING CHINOOK AND COMPARISON 

TO SPRING CHINOOK FROM AN INTEGRATED SUPPLEMENTATION PROGRAM 

AND CAPTIVE BROODSTOCK PROGRAM IN THE TUCANNON RIVER ........................ 250 

PREVALENCE OF BACTERIAL KIDNEY DISEASE IN NATURAL VS. HATCHERYREARED ADULT CHINOOK SALMON SPAWNED IN A HATCHERY AND IN 

NATURE ............................................................................................................................. 251 

ODFW RESPONSE TO ISRP COMMENTS – Bacterial Kidney Disease .............................. 252 

THE USE OF PASSIVE INTEGRATED TRANSPONDER (PIT) TAGS AS A TOOL TO 

MONITOR AND MANAGE ADULT CHINOOK SALMON RETURNS TO IDAHO .............. 253 

IDFG RESPONSE TO ISRP COMMENTS – PIT tags ........................................................... 257 

2010 LSRCP SPRING/SUMMER CHINOOK PROGRAM REVIEW ROLLUP ......................... 260 

APPENDIX 1. AN INDEPENDENT SCIENTIFIC REVIEW PANEL RETROSPECTIVE 

REPORT ............................................................................................................................. 297 

APPENDIX 2. LSRCP RESPONSE TO ISRP REPORT 2011-14 ........................................... 355 

 
PREFACE 

The 2010 Lower Snake River Compensation Plan (LSRCP) Spring/Summer Chinook Program 

Review (Review) was conducted to: 1) report on production, survival, and rearing metrics of 

Spring/Summer Chinook produced in LSRCP hatcheries that have not been reported since the 

last Review was conducted in 1998; and 2) fulfill a Northwest Power and Conservation Council 

(NPCC) requirement to independently review projects receiving funding from the Bonneville 

Power Administration (BPA). This document is a collection of the written reports of presentations 

made during the 2010 Review. Reports were provided on presentations made on projects 

supported with LSRCP funding. In some cases links to previously written reports, instead of the 

written report, are provided. Some presentations made during the Review are not included in this 

collection of reports. Projects not included in this collection of reports were not supported by 

LSRCP funding. 

The Independent Science Review Panel’s (ISRP) Report on this Review is included in this 

document as Appendix 1. LSRCP’s responses to general comments in the ISRP report are 

included as Appendix 2. Individual project responses to ISRP specific comments on individual 

projects are included at the end of each project report. 

 
5 

MEETING AGENDA 

Lower Snake River Compensation 

Plan 

2010 Spring Chinook Hatchery Program Review Symposium

AGENDA 

Tuesday 11/30/2010 

Title Presenter

11:00 - 1:00 Registration/Check In 

Introduction 

1:00 - 1:10 Welcome Scott Marshall 

1:10 - 1:30 A Brief History of the LSRCP Hatchery Program for 

Spring & Summer Chinook Salmon 

Scott Marshall 

1:30 - 2:00 Life cycle limiting factors Robin Waples 

2:00 - 2:45 Population Status of Snake River Spring/Summer 

Chinook Salmon 

Tom Cooney 

2:45 - 3:05 Break 

Salmon River 

3:05 - 3:20 Yankee Fork Chinook Salmon Supplementation 

Program – Update 

Lytle Denny 

3:20 - 3:55 South Fork Salmon River Hatchery Program - McCall 

Fish Hatchery 

Brian Leth 

3:55 - 4:20 Upper Salmon River Hatchery Program - Sawtooth Fish 

Hatchery 

John Cassinelli 

4:20 - 4:30 Break 

4:30 - 6:00 ISRP-Salmon River Program Questions ISRP, Brian Leth, Lytle 

Denny 

 

Wednesday 12/01/2010 

8:00 - 8:10 Announcements Steve Yundt 

Clearwater River 

8:10 - 8:40 Clearwater River Hatchery Programs - Clearwater Fish 

Hatchery 

Brian Leth 

8:40 - 9:10 Dworshak National Fish Hatchery Spring Chinook 

Program 

Howard Burge 

Tucannon River 

9:10 - 9:55 Tucannon River Spring Chinook Salmon 

Supplementation Program 

Michael Gallinat 

9:55 - 10:15 Break 

Grande Ronde River 

10:15 - 10:30 Grande Ronde Basin Spring Chinook Hatchery program: 

Introduction and the Early Years 

Rich Carmichael 

10:30 - 10:55 Upper Grande Ronde River Spring Chinook Salmon 

Hatchery Supplementation Program Review 

Rich Carmichael 

10:55 - 11:20 Catherine Creek Spring Chinook Salmon Hatchery 

Supplementation Program Review 

Rich Carmichael 

11:20 - 11:45 Lostine River Supplementation Program Peter Cleary 

11:45 - 12:10 Reintroduction of Spring Chinook Salmon in 

Lookingglass Creek: Analysis of Three Stocks Over 

Time 

Steve Boe 

12:10 - 1:10 Lunch 

Imnaha River 

1:10 - 2:10 Imnaha River Spring/Summer Chinook Salmon 

Hatchery Supplementation Program Review 

Rich Carmichael 
6 

2:10 - 2:30 Size at Release Imnaha River Smolts: Does Size 

Matter? 

Joseph Feldaus 

2:30 - 3:00 Grande Ronde Basin Spring Chinook Salmon Captive 

Broodstock Program: F1 Generation 

Tim Hoffnagle 

3:00 - 3:20 Break 

3:20 - 6:00 ISRP-Clearwater, Tucannon, Grande Ronde, and 

Imnaha Questions 

Brian Leth, Howard 

Burge, Rich Carmichael, 

Steve Boe, Gene 

Shippentower, Mark 

Schuck, Michael 

Gallinat, ISRP 

Thursday 12/02/2010

8:00 - 8:10 Announcements Steve Yundt 

8:10 - 8:35 Benefits of Hatchery Management of BKD Using ELISAbased Culling Doug Munson 

8:35 - 8:55 Genetics Analysis of Natural-origin Spring Chinook and 

Comparison to Spring Chinook from an Integrated 

Supplementation Program and Captive Broodstock 

Program in the Tucannon River 

Todd Kassler 

8:55 - 9:20 Prevalence of Bacterial Kidney Disease in Natural vs. 

Hatchery-Reared Adult Chinook Salmon Spawned in a 

Hatchery and in Nature 

Sally Gee 

9:20 - 9:40 Use of Passive Integrated Transponder (PIT) Tags as a 

Tool to Monitor and Manage Adult Chinook Salmon 

Returns to Idaho 

John Cassinelli 

9:40 - 10:00 Reproductive Success of Hatchery-reared Spring 

Chinook in Catherine Creek 

Ewann Berntson 

10:00 - 10:20 Break 

10:20 - 11:20 Program Roll up Mark Schuck 

11:20 - 12:20 How is LSRCP Meeting Cooperator's needs? LSRCP Cooperator 

Policy Representatives 

12:20 - 12:35 Wrap-up Scott Marshall 

12:35 - 1:35 Lunch 

1:35 - 4:00 ISRP-Clearwater, Tucannon, Grande Ronde, and 

Imnaha Questions (Continued) 

Brian Leth, Howard 

Burge, Rich Carmichael, 

Steve Boe, Gene 

Shippentower, Mark 

Schuck, Michael 

Gallinat, ISRP 

ISRP Program Review Report 

LSRCP Response to ISRP Program Review Comments
7 

A BRIEF HISTORY OF THE LOWER SNAKE RIVER COMPENSATION PLAN HATCHERY 

PROGRAM FOR SPRING & SUMMER CHINOOK SALMON 

Scott L. Marshall 

USFWS 

Lower Snake River Compensation Plan 

ABSTRACT 

The Lower Snake River Compensation Plan (LSRCP) hatchery program for anadromous fish was 

designed to replace lost adult salmon & steelhead caused as a consequence of construction and 

operation of four hydroelectric dams on the Lower Snake River in Washington. For spring/summer 

Chinook salmon, an adult return goal back to the project area, post harvest below the project area 

of 58,700 was established. It was anticipated that after the hatcheries were built and achieved full 

production that some 176,100 adults would be caught in commercial fisheries and 58,700 in 

recreational fisheries below the project area. Other than assuming that enough broodstock would 

return to the hatcheries to perpetuate further generations, no other beneficial use for retuning 

adults was identified in the plan. Congress authorized the U.S. Army Corps of Engineers to build 

six hatcheries in 1976 capable of producing 6.75 million smolts. The hatcheries were distributed 

in the Snake River Basin to reflect a desire to mitigate for the estimated losses “in kind and in 

place”. Construction of the first facility was completed in 1980 and the last facility was completed 

in 1991. Since the program was authorized three factors have impacted the LSRCP program. 

First, the smolt to adult survival rate has been less than expected. Second, Snake River 

spring/summer Chinook were listed as threatened under the Endangered Species Act. The need 

to reduce harvest rates in mainstem fisheries to protect natural-origin fish resulted in a much 

higher proportion of the annual runs to escape mainstem fisheries and return to the project area 

than expected at the time the program was authorized. Third, states and tribes through the U.S. 

v. Oregon court stipulated Fishery Management Plan have established specific hatchery 

production agreements between the states, tribes and federal government. This agreement has 

substantially diversified the spring Chinook hatchery program by adding new off station releases 

sites and stocks designed to meet short term conservation objectives. The presentations by the 

LSRCP cooperators over the next three days will review the successes and challenges we have 

faced over the last 20-30 years implementing the LSRCP spring/summer Chinook program. 

INTRODUCTION1

The Lower Snake River Compensation Plan (LSRCP) for anadromous fish was designed to 

replace lost adult salmon & steelhead caused as a consequence of construction and operation of 

four hydroelectric dams on the Lower Snake River in Washington. Specifically the plan is to 

“..... provide the number of salmon and steelhead trout needed in the Snake River system 

to help maintain commercial and sport fisheries for anadromous species on a sustaining 

basis in the Columbia River system and Pacific Ocean” (NMFS & BSF&W 1972 pg 14) 

The LSRCP was authorized by the Water Resources Development Act of 1976, Public Law 94-

587. The Act implementing the LSRCP simply states; 

 

1 This paper draws liberally from a history written on the LSRCP program by Herrig in 1990. 
8 

“...Fish and Wildlife Compensation Plan for the Lower Snake River, Washington and 

Idaho, substantially in accordance with a report on file with the Chief of Engineers, at an 

estimated cost of $58,400,000.” 

The “report on file with the Chief of Engineers” referred to in the Act is the Special Report, Lower 

Snake River Fish and Wildlife Compensation Plan, Lower Snake River, Washington and Idaho, 

June 1975 (US Army Corps of Engineers 1975 (COE)). 

The four lower Snake River projects (dams, power plants, and locks) were authorized by P.L. 74, 

79th Congress, in March 1945, but no funds for construction were authorized. Congressional 

authorization absent funding set up a major political battle in the Northwest between those 

advocating for construction and those opposed. A history of this political battle can be found in 

(Petersen and Reed 1994 and Petersen 1995). Highlights of the struggle included: 

 In 1950 the COE requested $2 million for funding construction of Ice Harbor Dam. The 

request was denied because of concerns over fish, runaway government spending, the 

cost in relation to other options for generating power, and the proposition that such new 

projects should be undertaken by a consortium of government and private capital. 

 In 1953 President Truman requested $5 million for construction in his final year as 

president, but after newly elected President Eisenhower was inaugurated he cut the 

funding stating that there would be “no new starts on dams”. He cited a need to curb 

federal spending and cost share with states and private enterprise for his decision to 

eliminating funding in the project. 

 The deadlock over construction was broken in 1955 when Senator Warren Magnuson of 

Washington “slipped” $1.0 million into an omnibus spending bill for construction, and once 

construction had started, there was no stopping future appropriations. 

The four dam & locks projects took almost 20 years to complete. The lower-most dam, Ice Harbor, 

was completed in 1961; moving upstream, Lower Monumental was completed in 1969, Little 

Goose was completed in 1970 and Lower Granite was completed in 1975. Each dam is 

approximately 100 feet high. These dams create a total of approximately 140 miles of reservoir 

from about 10 miles above the mouth of the Snake River to its confluence with the Clearwater 

River. The series of locks allow for barge traffic to travel inland to Lewiston, Idaho. 

In 1959, four years after the initial appropriation for construction of Ice Harbor Dam & Locks, the 

U.S. Fish and Wildlife Service (Service) started to evaluate the impact of these hydroelectric 

projects on fish and wildlife resources. The limited engineering and biological data available at 

the time resulted in the Service making only general recommendations regarding fish passage 

and artificial propagation. In 1966, some seven years into developing recommendations on a byproject basis the COE District Engineer in Walla Walla requested that the Service produce a single 

report, rather than four separate reports, that would cover all the Lower Snake River projects, 

including the yet to be constructed Lower Granite Dam and Locks. 

Over the next 6 years, the Service, National Marine Fisheries Service (NMFS) and the state 

wildlife agencies of Oregon, Washington, and Idaho collaborated to evaluate the effects of the 

four projects. A final Fish and Wildlife Coordination Act Report was produced by the NMFS and 

the Service in September 1972 and submitted to the COE. 

The COE questioned several of 1972 report’s findings and it was not until 1975 that these issues 

were resolved and the COE submitted its final report to Congress. By September 1976 the COE 

had finalized an Environmental Impact Assessment of the LSRCP and in that year Congress 
9 

authorized the COE to design and construct the LSRCP “substantially in accordance” with their 

June 1975 Special Report. 

LSRCP GOAL 

Specific mitigation goals for the LSRCP were established in a three step process. First the adult 

escapement that occurred prior to construction of the four dams was estimated. Second an 

estimate was made of the reduction in adult escapement (loss) caused by construction and 

operation of the dams (e.g. direct mortality of smolt). Last, a catch to escapement ratio was used 

to estimate the future production that was forgone in commercial and recreational fisheries as 

result of the reduced spawning escapement and habitat loss. Assuming that the fisheries below 

the project area would continue to be prosecuted into the future as they had in the past, LSRCP 

adult return goals were expressed in terms of the adult escapement back to, or above the project 

area. Other than recognizing that the escapements back to the project area would be used for 

hatchery broodstock, no other specific priorities or goals were established in the enabling 

legislation or supporting documents regarding how these fish might used. 

For spring Chinook salmon the escapement above Lower Granite Dam prior to construction of 

these dams was estimated at 122,200 adults. Based on a 15% mortality rate for smolts transiting 

each of the four dams (48% total mortality), the expected reduction in adults subsequently 

returning to the area above Lower Granite Dam was 58,700. This number established the LSRCP 

escapement mitigation goal back to the project area. This reduction in natural spawning 

escapement was estimated to result in a reduction in the coast wide commercial/tribal harvest of 

176,100 adults, and a reduction in the recreational fishery harvest of 58,700 adults below the 

project area. In summary the total number of adults that was expected to be produced was 

293,500. 

Component Number of 

Adults 

Escapement above Lower Granite Dam 58,700 

Commercial Harvest (below project area) 176,100 

Recreational Harvest (below project area) 58,700 

 Total 293,500 

 

HATCHERY DEVELOPMENT PLAN 

Historical distribution and abundance data were used by a hatchery subcommittee of the 

Columbia Basin Fisheries Technical Committee to recommend release sites for the future 

hatcheries (Tollefson 1974). Table 1 outlines the recommended distribution of returning LSRCP 

produced adult spring Chinook salmon by state and river basin. 

Once the adult return goals were established the subcommittee calculated the number of smolts 

that would have to be released to achieve the desired adult run size. The model made 

assumptions about each life history stage of the fish, including eggs per female, survival of eggs 

to smolt, and survival of smolt to returning adult (after passing thru fisheries below the project 

area). The most important and difficult part was the smolt-to-returning adult rate, because this 

part is highly variable and subject to many uncontrollable natural factors. 
10 

Cowley et al. (1987) did a literature search of the methods used by the CBFTC to estimate the 

smolt-to-adult rates and determined that the rate was based on historical returns to the Idaho 

Power facility operated by the Idaho Department of Fish and Game at Rapid River. 

Table 1. Recommended distribution of returning LSRCP produced adult spring/summer 

Chinook salmon. 

Drainage Washington Oregon Idaho 

Tucannon 1,152 

Snake River at/above Hells Canyon Dam 1,200 

Clearwater River 288 

Grande Ronde River 5,856 

Imnaha River 3,216 

Salmon River 46,656 

Small tributaries 288 

Total by State 1,152 9,072 48,432 

Program Total 58, 656 

Percent of Program 2.0% 15.5% 82.6% 

Table 2. The estimated hatchery production necessary to return the required number of 

adult spring Chinook salmon to meet LSRCP escapement goals, post harvest 

below project area (COE 1975). 

Adult loss level for basing hatchery size (rounded) 58,700 

Estimated smolt to adult survival rate back to Lower Granite 

Dam after harvest below project area 

 0.87% 

Estimated number of smolts that would have to be produced 6,750,000 

Target size of smolts in fish per pound 15 

Target number of pounds of smolts to be produced 450,000 

Estimated percent survival from eggs to smolt 70% 

Estimated number of eggs needed 9,650,000 

 
11 

Table 3. Smolt production goals (in pounds) for the six LSRCP hatcheries that rear spring 

Chinook salmon, and dates of completion. 

Hatchery 

(Operator) 

Pounds of 

smolt 

Satellite Facilities Date of Completion

Lookingglass 

(ODFW) 

69,600 Lookingglass Hatchery November 1982 

Imnaha River July 1989 

Lyons Ferry 

(WDFW) 

8,800 Lyons Ferry Hatchery November 1983 

Tucannon Hatchery November 1984 

Curl Lake February 1985 

Sawtooth (IDFG) 149,000 Sawtooth Hatchery January 1985 

E.Fk. Salmon R. November 1983 

Dworshak (FWS) 70,000 Dworshak Remodel November 1982 

Clearwater (IDFG) 91,300 Clearwater Hatchery December 1991 

Red River November 1986 

Crooked River May 1990 

Powell August 1989 

McCall (IDFG) 61,300 McCall Hatchery September 1981 

South Fork Salmon River July 1980 

ODFW = Oregon Department of Fish and Wildlife; WDFW = Washington Department of Fish and 

Wildlife; IDFG = Idaho Department of Fish and Wildlife; FWS = U.S. Fish and Wildlife Service 

FUNDING THE LSRCP 

The Special Report states that “...Operations and maintenance would be funded through future 

appropriations to the U.S. Fish and Wildlife Service or National Marine Fisheries Service.” In 1977 

an agreement was signed by the COE, NMFS, and the Service stating that the Service would 

budget for and administer the operation and maintenance of the LSRCP Program. 

When funding mitigation programs the COE must decide how to partition the flow of benefits of 

these dam & lock projects as a way to distribute cost. Electric power benefits were generally 

considered the largest benefit from COE dam projects in the Columbia Basin and the benefactors, 

the electric rate payers are required to pay that portion of the cost. Bonneville Power 

Administration (BPA) is the marketer of the generated power by these projects and was required 

to pay the share of costs commensurate with the benefits ascribed to power generation. Whatever 

benefits are ascribed to flood control, irrigation, transportation etc. are borne by the Congress 

through annual appropriations to the COE. The Lower Snake River program is unique among 

mitigation programs in the Columbia basin because the COE determined that 100% of the benefits 

of these projects were for power generation. As such BPA pays all the costs. 

From the LSRCP’s beginning through FY 2001, the Service requested funding from Congress 

each year through the President’s Budget Request to Congress. Congressional appropriations 

were reimbursed to the treasury at the end of each fiscal year by BPA as well as capitalized 

construction costs of the LSRCP facilities. When the Service and BPA signed a direct funding 

agreement in July 2001 a new business oriented atmosphere developed that allows the Service 

and BPA to work in a business oriented manner to meet short and long term mitigation 

responsibilities. 
12 

IMPORTANT CHANGES SINCE THE LSRCP WAS AUTHORIZED 

Since 1976 when the LSRCP was authorized, many of the parameters and assumptions used to 

size the hatchery program and estimate the magnitude and flow of benefits have changed. These 

changes will become evident as during the presentations by our cooperators. 

 The smolt to adult survival rate has been less than expected and this has resulted in fewer 

adults retuning than planned. 

 The listing of spring Chinook under the Endangered Species Act has resulted in significant 

curtailment of commercial, recreational and tribal fisheries throughout the mainstem 

Columbia River. This has resulted in a higher percentage of the annual run returning to 

the project area than was expected. 

 States and tribes through the U.S. v. Oregon court stipulated Fishery Management Plan 

have established specific hatchery production agreements. This agreement has 

substantially diversified the spring Chinook hatchery program by adding new off station 

releases sites and stocks designed to meet short term conservation objectives, in 

partnership with the Northwest Power and Conservation Council’ Fish and Wildlife 

program. 

LITERATURE CITED 

Corps of Engineers. 1975. Special Report, Lower Snake River Fish and Wildlife Compensation 

Plan. Lower Snake river Washington and Idaho. U.S. Army Engineer District, Walla Walla 

Washington. 96 pgs plus appendices. 

Corps of Engineers. Final Environmental Impact Statement, Lower Snake Rover Compensation 

Plan. Chief of Engineers, Dept. of the Army, Washington, D.C. 

Herrig, D.M. 1990. A Review of the Lower Snake River Compensation Plan Hatchery Program. 

U.S. FWS, LSRCP Boise Id. 47 pgs. 

NMFS & B. Sport Fish & Wild. 1972. A Special Report on the Lower Snake River Dams, Ice 

Harbor, Lower Monumental, Little Goose, Lower Granite, Washington and Idaho. US. 

Dept. Commerce, National Marine Fishers Service and U.S. Dept. Interior, Bureau Sport 

Fisheries & Wildlife. Portland Oregon 41 pgs. (may be found as Appendix A of COE 1975 

Special Report) 

Petersen, K and M. Reed. 1994. Conflict and Compromise: A History of the Lower Snake River 

Development. Walla Walla District U.S. Army Corps of Eng. Walla Walla WA. 248 pgs. 

Petersen, K. 1995. River of Life, Channel of Death: Fish and Dams on the Lower Snake River. 

Confluence Press, Lewiston ID. 328 pgs. 

Tollefson, T.C. 1974. Letter from Washington Dept. of Fisheries to Col. N.P. Conover, Walla Walla 

District office U.S. Army Corps of Eng. Washington Department of Fisheries. Olympia, 28 

pgs. 

 
13 

YANKEE FORK CHINOOK SALMON SUPPLEMENTATION PROGRAM – UPDATE 

Lytle Denny and Kurt Tardy 

Shoshone-Bannock Tribes 

Fish and Wildlife Department 

 
14 

INTRODUCTION 

The Yankee Fork Chinook Salmon Supplementation (Yankee Fork) Program was initiated in 

2006. The Yankee Fork program was developed with input from key individuals sitting in this room 

that have significant experience in the LSRCP Hatchery Program as well as BPA’s Fish and 

Wildlife Program. With input from these individuals, the Yankee Fork Program was developed to 

incorporate the best available science and learn from adaptive management. Given that 

supplementation is a highly debated management strategy, the Yankee Fork program initiated 

monitoring and evaluation to document the successes or failures of supplementation. This is a 

summary of what has been accomplished thus far. 

OVERVIEW 

The goal of this presentation is to provide the necessary information to allow the audience to leave 

here today with a greater understanding of the Yankee Fork program, its relationship to the 

LSRCP, and how we intend to move forward. The presentation will orient you to the study area, 

provide information on the drainage statistics, and highlight important history which led to program 

implementation. The presentation also contains information on the programs goals and 

objectives, methods, results, and moving forward. Lastly we acknowledge the key cooperators in 

the program, as well as potential cooperators. 

STUDY AREA 

Yankee Fork Salmon River is a major tributary to the Salmon River (Figure 1). Yankee Fork is 

located near the headwaters of the Salmon River about 15 miles downstream of the town of 

Stanley. The watershed is located in central-Idaho within lands administered by the U.S. Forest 

Service, Salmon-Challis National Forest. 

Figure 1. Location map of the Yankee Fork Salmon River and key hatchery facilities. 
15 

Yankee Fork is one of the nine populations of Snake River spring/summer Chinook salmon within 

the Upper Salmon Major Population Group (Figure 2). Yankee Fork is currently rated by the 

Interior Columbia-basin Technical Recovery Team (ICTRT) for high risk of extinction. The 

population is not replacing itself and the geometric mean abundance is 13 spawners; which is far 

from the recommended 500 spawners. 

Figure 2. Map of the Snake River spring/summer Chinook salmon Upper Salmon River 

Major Population Group and Yankee Fork Salmon River population. 
16 

Mainstem Yankee Fork flows 42 km through narrow canyons and moderately wide valleys of 

lodgepole pine. The headwaters originate at an elevation of 2,500 meters. The drainage is 

composed of 313 square kilometers and includes 10 major tributaries. Average precipitation is 

68.6 centimeters and is mostly from snow, base flows are 1.13 m3/s and mean flows are 6.99 

m3/s. 

HISTORY 

So why are the Tribes supplementing the Yankee Fork Chinook salmon population? In 1977, 

when Chinook salmon runs across Idaho began to dwindle, the Tribes established sanctuary 

areas in the Salmon River to allow rebuilding to occur. At the time, the belief was if we stopped 

fishing, the runs could rebuild. This was a noble philosophy, but our harvest was miniscule, when 

compared to downriver harvest and mortality associated with fish migrating through the lower 

Snake and Columbia River hydropower systems. In any event, the Tribes believed this was the 

right thing to do. About that same time frame, Yankee Fork, along with several other tributaries 

were designated as permanent areas for Tribal fishing. Fish were released to support Tribal 

fishing. Over time, as many as three different stocks of fish were released into Yankee Fork as 

fry, parr, pre-smolt, smolt, and adult with nearly 2.8 million fish released (Table 1). Fish were 

released from 1977 – 1991, but once the ESA listing was passed in 1992, hatchery fish were not 

released into Yankee Fork to support Tribal fishing opportunity. 

Table 1. Yankee Fork Salmon River Chinook salmon production history, 1977 – 1991. 

BY RY Number Location Stock Size fish/lb Hatchery

1977 56,700 WFYK fry-fingerling Mackay 

1978 75,036 Yankee Fork fry-fingerling Mackay 

1985 61 Yankee Fork Sawtooth adult Sawtooth 

1985 659 Yankee Fork adult Pahsimeroi 

1986 61 Yankee Fork Sawtooth adult Sawtooth 

1986 1,505 Yankee Fork adult Pahsimeroi 

1986 386,348 Yankee Fork fry-fingerling Pahsimeroi 

1987 157,877 Yankee Fork fry-fingerling Sawtooth 

1987 600 Yankee Fork adult Pahsimeroi 

1986 1987 158,000 Yankee Fork Ponds Salmon R. pre-smolt 250 Sawtooth 

1986 1988 725,500 Yankee Fork Ponds Pahsimeroi smolt 20 Sawtooth 

1987 1988 50,100 Yankee Fork Ponds fry-fingerling 120 Sawtooth 

1987 1989 198,200 Yankee Fork Ponds Salmon R. smolt 24 Sawtooth 

1988 1989 125,000 Yankee Fork Ponds Salmon R. fry-fingerling 100 Sawtooth 

1988 1990 200,800 Yankee Fork Ponds Salmon R. smolt 21 Sawtooth 

1989 1990 50,000 Yankee Fork Ponds fry-fingerling 100 

1989 1990 491,300 Yankee Fork Salmon R. smolt 45 Sawtooth 

1989 1990 50,000 Yankee Fork Ponds Salmon R. fry-fingerling 111 Sawtooth 

1990 1991 50,000 Yankee Fork Ponds fry-fingerling 120 Sawtooth 

Fast forward to today, and like all co-managers, the Tribes are interested in providing a fishery in 

Yankee Fork. There are a few other places where Tribal members can go and actually see a fish 

and currently, Yankee Fork is not one of those areas. In order to provide a meaningful fishery, the 

Tribes view hatchery supplementation as a short-term option for increasing abundance to meet 
17 

the Tribes’ harvest and conservation objectives. The Tribes plan is to ensure natural fish in 

Yankee Fork are restored. Therefore, our supplementation efforts focus on providing natural 

spawning escapement. Our long-term management strategies also include restoring habitat, 

managing harvest, and monitoring and evaluating our activities to learn from our results. 

Annual redd counts are presented below, prior to Yankee Fork program supplementation, from 

1952 – 2007 (Figure 3) to demonstrate the continued decline of the population. Shortly after the 

last dams were installed in the lower Snake River, Yankee Fork Chinook salmon abundance 

severely declined and never rebounded. This figure shows a peak count of 615 redds in 1968 to 

zero redds in 1984 and 1995. These estimates do not account for harvest, which was substantial 

prior to 1970 and truly insignificant since then. 

1960 1970 1980 1990 2000

Total Redds

0

100

200

300

400

500

600

700

Figure 3. Annual redd counts conducted in the Yankee Fork Salmon River from 1952-2007. 

Looking closer at the redd count data from the previous figure. We plotted a redd frequency 

distribution to highlight the skewed distribution of redds observed from 1952 – 2007, which is 56 

years of information (Figure 4). Since counting was initiated, 35 out of the 56 years, or 63% of the 

time, less than one hundred redds have been observed. A healthy population should have a 

normal distribution curve, which is not the case in Yankee Fork. Further analysis, reveals the 0 -

10 redds is the most common distribution frequency for Yankee Fork, with ten years of data 

(Figure 5). This information supports the conclusions by the ICTRT; Yankee Fork Chinook salmon 

are at high risk of extirpation and highlights the need for an aggressive restoration approach, such 

as supplementation. 
18 

Redds

0 - 100

101 - 200

201 - 300

301 - 400

>401

Frequency

0

10

20

30

40

Frequency 

Figure 4. Yankee Fork Chinook salmon redd frequency histogram, 1952 – 2007. 

Redds

0 - 10

11 - 20

21 - 30

31 - 40

41 - 50

51 - 60

61 - 70

71 - 80

81 - 90

91 - 100

Frequency

0

2

4

6

8

10

12

Frequency

Figure 5. Yankee Fork Chinook salmon redd frequency (1 – 100) histogram, 1952 – 2007. 
19 

GOALS AND OBJECTIVES 

The Tribes are working to achieve the long-term goal of returning 2,000 adult Chinook salmon to 

the Yankee Fork. We believe adult returns to the Yankee Fork will help the LSRCP meet its adult 

return mitigation goals. In order to attain broodstock to meet the adult return goal, the Tribes first 

phase is to develop a locally-adapted Chinook salmon run. Since there are very few natural-origin 

adults returning to Yankee Fork, we plan to jump start the population with the release of up to 

1,500 pre-spawn adults and 200,000 – 400,000 smolts, obtained from Sawtooth Fish Hatchery. 

Sawtooth hatchery fish will crossbred with the naturally returning Yankee Fork adults. Once the 

locally adapted run is developed, broodstock will be collected entirely from the crossbred naturalorigin returning adults to Yankee Fork. 

The Tribes long-term adult goal is divided into four objectives. The conservation objective will 

provide 750 adults for natural spawning and contribute to recovery of the Snake River 

spring/summer Chinook salmon ESU by restoring Yankee Fork to a “maintained” population of 

local Chinook salmon. All aspects of the program will be consistent with the ESA and HSRG/HRT 

review criteria. The harvest objective will provide up to 1,000 adults for harvest in Columbia, 

Snake, Salmon, and Yankee Fork fisheries. The Tribes also want to ensure that Tribal harvest in 

the Yankee Fork can be achieved by traditional hunting methods. Traditional hunting methods 

include spear fishing, netting, and snagging. To ensure the adult return goal is attained, the Tribes 

are seeking to utilize adult fish for broodstock to produce 200,000 – 400,000 smolts for release 

until Crystal Springs Fish Hatchery is constructed. Once Crystal Springs Fish Hatchery is 

constructed, smolt production will increase to meet the necessary release target of ~600,000 

smolts to meet all adult return objectives. The Crystal Springs Fish Hatchery is currently in the 

Northwest Power and Conservation Council’s 3-step planning process. 

STUDY DESIGN 

The Tribes plan to utilize a treatment and control study design to monitor and evaluate the 

program. Select treatment tributaries will be utilized to evaluate supplementation and may include 

the following supplementation projects: 1) South Fork Salmon River, Upper Salmon River, 

Pahsimeroi River, and Johnson Creek. Our control streams will be selected from streams already 

being evaluated for supplementation under the Idaho Supplementation Studies, since data is 

already being collected. We plan to investigate and evaluate the interactions between natural and 

hatchery-origin fish in the Yankee Fork. Our study design will allow us to track performance of 

multiple groups of fish within Yankee Fork and compare this performance to natural only control 

streams. 

METHODS 

The primary methods employed by the Program in order of season implementation, include 

operating a rotary screw trap, releasing smolts, operating two portable picket weirs, conducting 

adult trapping, conducting harvest monitoring, outplanting adults and conducting spawning 

ground surveys. 
20 

Rotary Screw Trap 

A rotary screw trap is installed in lower Yankee Fork and operated from April through November, 

pending conditions (Figure 6). At the screw trap, species are enumerated and biological data 

collected. A proportion of juvenile Chinook salmon are PIT tagged or stained for mark-recapture 

and survival through the FCRPS. We also collect tissue samples from all PIT tagged fish to 

compare performance between unknown hatchery and natural-origin fish. 

Figure 6. Yankee Fork rotary screw trap. 

Smolt Release 

In mid-April, juvenile fish reared at Sawtooth are transported to Yankee Fork for release (Figure 

7). Currently, there are 400,000 juvenile Chinook salmon being reared at Sawtooth, but the longterm production number is still being discussed. Approximately 50% of the juveniles are adipose 

fin-clipped, with the other 50% having intact adipose fins. Both groups, clipped and non-clipped 

received approximately 2,200 PIT tags. All fish with intact adipose fins are coded wire tagged for 

identification. Smolt releases are paired to compare performance from direct stream releases to 

semi-acclimated releases. Juvenile survival through the FCRPS and adult returns will be 

evaluated. 

Figure 7. Yankee Fork Chinook salmon smolt release. 
21 

Weirs 

In late June the Tribes erect two portable picket weirs to collect broodstock and segregate the 

spawning aggregate. The Pole Flat Weir is located approximately 5.2 rkm upstream from the 

confluence with the Salmon River and Five Mile Weir is 21.5 rkm upstream. Both weirs are vshaped structures with an attached trap box to hold captured adults (Figure 8). 

Figure 8. Map of Yankee Fork Salmon River and location of two portable picket weirs. 

Adult Trapping 

Normal trapping protocols are followed at both weirs. We enumerate species, collect broodstock, 

collect tissue samples, and standard biological information including length, gender, and origin 

(Figure 9). All fish are scanned for internal tags. Five Mile Weir is used to segregate hatchery fish 

from spawning in West Fork Yankee Fork and confounding the ISS study. 
22 

Figure 9. Adult Chinook and sockeye salmon trapped at Pole Flat weir. 

Harvest Monitoring 

Harvest monitoring is conducted on a daily basis. Since very few fish are currently returning to 

Yankee Fork, this is a relatively easy task. Tribal staff monitor the fishery from June 25 through 

August 11. All Tribal members encountered are surveyed (Figure 10). 

Figure 10. Harvest monitors and Tribal fisherman. 

Adult Outplanting 

Adults are outplanted in upper Yankee Fork above Five Mile Creek Weir (Figure 11). The annual 

objective is to obtain 1,500 adults from Sawtooth Fish Hatchery. We strive to achieve a sex ratio 

of 60% males, of which 5% can be jacks, and 40% females. Prior to outplanting, all hatchery adult 

outplants are tissue sampled and biological data collected for parentage analysis studies. 
23 

Figure 11. Outplanting hatchery Chinook salmon in upper Yankee Fork. 

Spawning Ground Surveys 

Spawning ground surveys are completed annually. Surveyors walk the entire spawning habitat 

identifying redds and collecting spawned out carcasses. Four total passes are completed each 

year and efforts are coordinated with IDFG personnel working in West Fork Yankee Fork, as part 

of IDFG Captive Chinook Program. Each redd is recorded and gps taken to document spawn 

timing, redd enumeration, and distribution (Figure 12; Figure 8). Carcasses are collected for key 

biological information, and are useful to determine percent spawned, age structure, and for markrecapture estimates. 

Figure 12. Female Chinook salmon on redd in Yankee Fork Salmon River. 
24 

RESULTS 

Rotary Screw Trap 

Since initiating the program, approximately 534,024 (SE 17,348) BY 2008 and 129,661 (SE 5,619) 

BY 2009 juvenile Chinook salmon were estimated (Figure 13). Our estimates are considered 

minimum since we were unable to quantify BY 08 fry and smolt and our BY 09 estimates for fry 

and parr only represent 12% of the normal trapping season. In BY 08, approximately 305,722 (SE 

8,546) parr and 228,252 (SE 20,670) pre-smolt were estimated. In BY 09, approximately 46 (SE 

10) fry, 15,114 (SE 3,369) parr, and 114,501 (SE 7,627) pre-smolt were estimated. Again, there 

was insufficient information to estimate BY 08 fry and smolt and the estimates for BY 09 fry and 

parr is extremely limited. We were unable to estimate BY 08 fry because we did not have a screw 

trap. The screw trap was compromised as a result of high water in 2009 and we were unable to 

sample this spring period to develop precise and accurate estimates for BY 08 smolt, BY 09 fry, 

and BY 09 parr. 

Figure 13. Juvenile Chinook salmon (pre-smolt) collected in the Yankee Fork Salmon River. 

Smolt Release 

The Yankee Fork program has released smolts in 2006 and 2010, respectively. The first release 

occurred in 2006 with 135,934 BY 04 Chinook salmon (Table 2; Figure 14). The second release 

occurred this spring with 398,444 smolts from BY 08 Chinook salmon. Adult returns from the 2006 

release are complete and a total of 381 hatchery adults returned to Yankee Fork for an SAR of 

0.28%. This estimate does not include the number of jacks that returned in 2007. Adults from the 

BY08 release are expected to return in 2011 – 2013. 

 
25 

Table 2. Smolt release numbers and returning adults. 

Return Age From BY

Brood 

Year 

Number 

Released 

Year 

Released 

1-ocean 2-ocean 3-ocean Total SAR 

(%) 

2004 135,934 2006 NA 357 24 > 381 > 0.280 

2008 398,444 2010 

Figure 14. Smolt loading at Sawtooth Fish Hatchery and unloading at Yankee Fork. 

Adult Trapping, Outplants, and Redds 

Since initiating the Yankee Fork program in 2008, an average of 1,213 fish have spawned yearly. 

The spawning escapement is made up from naturally returning natural fish, returning hatchery 

fish, strays, and outplanted hatchery fish. Approximately, 2,955 hatchery adults obtained from 

Sawtooth Fish Hatchery were outplanted in upper Yankee Fork in 2008 – 2009 (Table 3). In 2010, 

returns to Sawtooth were insufficient and no hatchery adults were outplanted. Since 2008, we 

trapped a total of 205 hatchery fish and 89 natural fish, for an average of 30 natural-origin fish per 

year. Adult migration typically begins prior to installation of the weirs, since flows are not typically 

safe for installation. A total of 163 fish passed the structures without being detected and 228 

spawned below the Pole Flat Weir. 

Table 3. Number of adult Chinook salmon contributing to spawning escapement and redd 

production. 

Year Adult 

Outplants

Trapped at Lower 

Weir

Passed Weir 

Undetected

Spawned 

Below Lower 

Weir

Spawning 

Escapement

Redds

Hatchery 

Origin 

Natural 

Origin 

2008 1,438 185 43 125 144 1,935 660 

2009 1,517 20 29 2 72 1,640 414 

2010 0 0 17 36 12 65 28 
26 

Run-Timing 

Run-timing for natural and hatchery fish appear to be different, but both groups exhibit bi-modal 

run-timing distribution (Figure 15). There are more natural fish returning early in the year as 

compared to hatchery fish and more hatchery fish returning later in the year than natural fish. 

Jun-30

Jul-15

Jul-30

Aug-14

Aug-29

Sep-13

# of fish trapped

0

5

10

15

20

25

HOR 

NOR 

Figure 15. Run-timing of Yankee Fork hatchery and natural Chinook salmon. 

Harvest Monitoring 

We have recorded only a handful of Tribal fisherman efforts each year in Yankee Fork since 2008. 

The majority of Tribal members are currently fishing below Sawtooth Fish Hatchery, in the South 

Fork Salmon River, or Bear Valley Creek. This highlights the importance of two LSRCP facilities 

and one natural production area at producing Tribal harvest opportunities. We anticipate harvest 

will increase substantially in Yankee Fork once returns begin to increase as a result of 

supplementation. Since 2008 a total of four natural-origin Chinook salmon have been harvested. 

One adult was caught in 2008 and 2010 and two were caught in 2009. The Tribal fisheries were 

curtailed in the areas where adult hatchery Chinook salmon were outplanted. 

Spawning Ground Surveys 

In 2008, 2009, and 2010, a total of 660, 414, and 28 redds were recorded for an average of 367 

redds per year (Figure 16). The proportion of hatchery-origin spawners (pHOS) from 2008 – 2010 

was 95%, 98%, and 0%, respectively. 
27 

1960 1970 1980 1990 2000 2010

Total Redds

0

100

200

300

400

500

600

700

Figure 16. Yankee Fork Salmon River historical redd number. 

MOVING FORWARD 

The Tribes are moving forward with the Yankee Fork program and are thankful the LSRCP has 

provided key funds for O&M and M&E. We are hopeful that the adult returns to Yankee Fork will 

help the LSRCP come closer to meeting their mitigation goals. We are also hopeful that we will 

be able to utilize Bonneville Power Administration (BPA) funds, acquired through our fish accord 

for supplementation activities such as Yankee Fork. 

We are currently in the Northwest Power and Conservation Councils’ Categorical Review process 

with the Independent Scientific Review Panel for expanded monitoring and evaluation funds for 

this program. The expanded funds will allow us to complete parentage analysis studies to reveal 

the relative reproductive success of naturally spawning hatchery and natural-origin Chinook 

salmon in Yankee Fork. Funds will also be used to provide an on-site residence for program staff. 

In addition, funding may be utilized to collect additional data in control streams. 

The Tribes are also working on the development of the Crystal Springs Fish Hatchery. We have 

met with IDFG, LSRCP, and NOAA-Fisheries staff to refine plans for Yankee Fork, its relationship 

to Sawtooth and the overall goals of the Crystal Springs Fish Hatchery. The Crystal Springs Fish 

Hatchery proposal includes plans for constructing adult trapping and holding facility in Yankee 

Fork, as well as an improved weir. 

We plan to continue to work with NOAA-Fisheries to process our HGMPs and TRMPs. We are 

also planning to publish our results in scientific journals. And lastly, we recognize the Program 

limitations and hope we can continue to move forward in a positive manner. 
28 

ACKNOWLEDGMENTS 

We would like to acknowledge the support we received from the Shoshone-Bannock Tribes Fort 

Hall Business Council and key program staff including Carlos Lopez, Alex Graves, Scott Brandt, 

Brock Moss & the numerous staff that assisted with the program over the years. We are especially 

thankful to Scott Marshall, Steve Yundt, Chris Starr, Joe Krakker, Margaret Anderson and Tammy 

Froscher at the Lower Snake River Compensation Plan – Office for their support of the program, 

both financially and fundamentally. We would like to thank Idaho Department of Fish & Game 

including Pete Hassemer, Sam Sharr, and Tom Rodgers at headquarters; Brent Snider, Mel 

Hughes, and Danielle Dorsch at Sawtooth Fish Hatchery. We would like to thank NOAA-Fisheries 

and the US Forest Service for supporting this Tribal supplementation program. 

And lastly, we are hopeful that BPA will become a program sponsor. Funding from BPA for the 

project was negotiated in our Fish Accord and the Tribes’ Supplementation Program is currently 

being reviewed by the ISRP through the Council’s Categorical Review. 

 
29 

SOUTH FORK SALMON RIVER SUMMER CHINOOK SALMON 

Brian Leth, John Cassinelli, Shane Knipper 

Idaho Department of Fish and Game 

1414 East Locust Lane, Nampa, Idaho 

BACKGROUND 

The South Fork Salmon River (SFSR) summer Chinook salmon mitigation program was 

established to provide in-kind mitigation for summer run Chinook salmon losses associated with 

construction and operation of the four lower Snake River hydroelectric dams. The McCall Fish 

Hatchery, which is responsible for all the incubation and rearing for this program, is located on 

banks of the Payette River approximately one half mile below the outlet of Payette Lake in McCall, 

Idaho. Construction of this hatchery and the associated satellite facility was completed in 1980. 

The satellite facility is located on the mainstem SFSR approximately 113km upstream from the 

confluence with the Salmon River. All adult trapping and spawning for this program occurs at this 

facility. In 2007 a permanent concrete sill and catwalk were constructed at this site that allows for 

trapping the entire adult return. Prior to 2007, a removable picket weir was used to divert fish into 

the trap but lacked the structural integrity to efficiently trap throughout the entire adult migration. 

The relative locations of both the hatchery and satellite facility are shown in Figure 1. The Lower 

Snake River Compensation Plan (LSRCP) adult mitigation goal for the McCall Fish Hatchery is 

8,000 adult Chinook salmon above Lower Granite Dam (LGD) and 32,000 adults available for 

downriver (Columbia and lower Snake rivers) commercial and sport harvest. The release goal is 

1 million smolts and is based on a 0.80% smolt-to-adult survival rate applied to the LGD mitigation 

objective of 8,000 adults. All smolts are transported from the McCall Fish Hatchery and released 

directly into the upper SFSR at Knox Bridge (RKm 115). 

 

MANAGEMENT AND MONITORING/EVALUATION OBJECTIVES 

Statewide management objectives for SFSR Chinook salmon are to restore and maintain the 

natural populations. Objectives for the hatchery program are to meet the LSRCP adult mitigation 
30 

objectives in the SFSR, to restore and maintain recreation and tribal Chinook salmon fisheries, 

and to minimize the impacts of the hatchery program on the natural Chinook salmon populations 

in the SFSR. In addition to meeting harvest mitigation objectives, IDFG has committed some of 

the hatchery resources to maintaining a conservation component for the SFSR though an 

integrated broodstock that is consistent with recommendations from the (Hatchery Scientific 

Review Group) HSRG. Managers feel that returns from the integrated broodstock are more 

suitable to supplement natural spawners than returns from the segregated brood. Additionally, 

the integrated broodstock will maintain genetic continuity of the hatchery and natural populations 

which is expected to be advantageous during time of extreme lows in natural-origin escapement. 

Monitoring and evaluation (M&E) objectives for the SFSR include monitoring production, 

productivity, and life history characteristics of hatchery and natural populations and to evaluate 

broodstock and rearing strategies to increase and maximize adult returns. M&E activity on the 

SFSR is a cooperative effort between the Idaho Department of Fish and Game (IDFG) and the 

Nez Perce Tribe (NPT). 

PROGRAM AND BROODSTOCK HISTORY 

Initial broodstock for the SFSR hatchery program was collected at Little Goose and Lower Granite 

dams from 1974 to 1979 during the time period when summer run adults were migrating through 

the Snake River. In 1980, broodstock was collected at both Lower Granite Dam and the upper 

SFSR. Since 1981, broodstock collection has been exclusively from adults collected in the SFSR. 

Because mass marking was not initiated until brood year 1991, the origin of adult returns (hatchery 

or natural) could not be distinguished until 1995. Prior to 1995, both the hatchery broodstock and 

the adults spawning naturally above the weir were mixtures of hatchery- and natural-origin returns 

and the program was essentially operated as a de facto integration/supplementation program 

even though the emphasis was on harvest mitigation. 

The original intent of the program was to mitigate for lost harvest opportunity that resulted from 

the construction and operation of the four lower Snake River hydroelectric dams and thus 

management efforts have focused on mitigating for the lost harvest opportunity. During the period 

1991-2002, part of the production capacity at McCall Fish hatchery was devoted to developing an 

integrated broodstock that was part of a statewide Idaho Salmon Supplementation (ISS) 

experimental research study (See Bowles and Leitzinger 1991) designed to evaluate the utility of 

using a supplementation strategy to increase the number of natural-origin spawners. This 

integrated supplementation broodstock was developed using approximately equal numbers of 

hatchery- and natural-origin adults and accounted for approximately 15-20% of the production 

capacity at the McCall Fish Hatchery. Progeny from the supplementation broodstocks were 

marked differentially from the segregated mitigation program. 

From 1995-2009 all hatchery production, with the exception of the ISS experimental broodstock, 

has been produced from segregated hatchery-origin returns. In 2010, managers initiated the 

development of a conservation broodstock component in the hatchery that would be used to 

supplement spawners above the adult weir on the upper SFSR consistent with recommendations 

from the Hatchery Scientific Review Group (HSRG) review. Numbers of integrated hatchery fish 

released above the weir are based on a sliding scale that is driven by the number of natural-origin 

returns. A complete description for this program is provided in the draft Hatchery Genetic 

Management Plan (HGMP) submitted to NOAA in November 2010. Copies of the draft HGMPs 

are available at the LSRCP Website: 

http://www.fws.gov/lsnakecomplan/Reports/HGMPreports.htm. 
31 

STATUS OF NATURAL POPULATION 

The natural populations of Chinook salmon in the SFSR were listed as threatened in 1992 and 

the hatchery population was added to the listing in 2005. The natural population of Chinook 

salmon in the SFSR mainstem is part of the SFSR Major Population Group (MPG) which is 

composed of four independent populations. From 1982 to 2009, the estimated natural adult 

abundance in the SFSR mainstem has ranged from 100 to 2,380 fish (Figure 5). The Interior 

Columbia Technical Recovery Team (ICTRT) 2005 status assessment of the SFSR natural 

population indicates the population is not viable, is at a high risk for abundance and productivity 

and is at moderate risk for spatial structure and diversity. 

IN-HATCHERY AND POST RELEASE SURVIVAL 

Broodstock performance over the life of the hatchery program has been good with levels of 

prespawn mortality for both males and females consistently below 20%. Exceptions to this were 

in 2003 when approximately 46% of the female broodstock was lost and in 2008 when 34% of the 

females and 30% of the males died prespawn. These outliers are associated with elevated water 

temperature or high turbidity events during late summer. In-hatchery survival has been high 

across the history of the program. For all years, eyed egg-to-release survival has exceeded 70% 

and in several years has been greater than 90% (Figure 2). 

The number of juveniles released from McCall Fish Hatchery has fluctuated over the history of 

the program (0.12 - 1.2M) but since 1983, the production target of 1 million juveniles has been 

achieved in all but six years, and in every year since 1997 (Figure 3). 
32 

Passive Integrated Transponder (PIT) tags have been used to estimate survival from release to 

LGD for this program since the early 1990s. Estimated survival for hatchery-origin juveniles 

released in the upper SFSR has fluctuated from 40 – 68% while natural-origin smolts have 

fluctuated from 35 – 61% (Figure 4). Survival of hatchery-origin parr has ranged from 4 – 14% 

(Figure 4). This is higher than normally observed for parr releases from other hatchery programs 

and is likely associated with a three month acclimation period for the parr releases in the upper 

SFSR. Regardless, due to the low return rates from subyearling releases, IDFG has generally 

moved away from this release strategy. 

The number of adults produced annually for this hatchery program has been highly variable 

across the history of the program. Estimates of the total number of adults back to the Columbia 
33 

River mouth, by return year, has fluctuated from a low of 80 (80 adults, 0 jacks) fish in return year 

1981 to a high of 19,378 (18,134 adults, 1,244 jacks) fish in 2001. The record return in 2001 

represents approximately 50% of the total mitigation goal. Harvest rates of summer Chinook 

salmon from this hatchery program in the Columbia and lower Snake rivers have generally been 

very low most likely due to the adult migration timing through the Columbia and Snake rivers. For 

this reason, the adult returns to LGD are very similar to the total adults produced for any year. 

Adult returns to LGD ranged from a low of 80 (80 adults, 0 jacks) fish in return year 1981 to a high 

of 18,039 (16,819 adults, 1,220 jacks) fish in 2001 (Figure 5). Also shown in Figure 5 are the 

natural returns to the upper SFSR which reflects synchrony in survival between the hatchery and 

natural populations for most years. Across the life of the McCall Fish Hatchery program, the total 

LSRCP mitigation goal has never been achieved while the project area goal of 8,000 adults to 

LGD has been met seven times, all of which occurred in the last ten years (Figure 5). 

Similar to annual adult return numbers, highly variable smolt-to-adult survival (SAS) and smoltto-adult return (SAR) rates have been observed over the history of the program. SARs to LGD 

are shown in Figure 6 and have ranged from 0.004 -2.0%. Similarly, smolt-to-adult survival rates 

to the Columbia River mouth have ranged from 0.004 – 2.2%. Fluctuations in survival for the 

aggregate natural-origin returns to LGD are similar to the SFSR hatchery population but are 

consistently higher than the hatchery population (Figure 6). The modeled 0.8% SAR necessary 

to meet to LGD escapement objective has been achieved in eight years. While this gives the 

appearance that the mitigation goal has been reached in these years, the modeled 0.8% SAR is 

a post harvest estimated and is based on the assumption there would be a 4:1 catch to 

escapement ratio to LGD. The SAS necessary to achieve the total mitigation goal is 4.0% and the 

highest observed SAS was 2.2% for brood year 1997. 
34 

LIFE HISTORY CHARACTERISTICS OF THE HATCHERY AND NATURAL POPULATIONS 

The average (1997-2009) cumulative adult run timing for hatchery- and natural-origin fish to the 

SFSR adult trap is similar (Figure 7). The median arrival date to the trap varies between years 

but within years remains similar between the hatchery and natural fish. Figure 8 shows the 

estimated age composition of hatchery- and natural-origin adult returns, by brood year, over the 

life of the program. Prior to brood year 1991, age composition data for the natural population is 

limited. Likewise, prior to brood year 1991, the number of hatchery-origin returns was very low in 

some years which may have influenced some of the large fluctuations in the estimated age 

composition of the hatchery population (i.e. small sample sizes). Over the entire time series for 

the hatchery population there appears to be a decrease in the proportion returning as jacks, an 

increase in the proportion returning as 2-ocean adults, and a slight decrease in the proportions 

returning as 3-ocean adults. Since brood year 1991, there is no significant trend in the hatchery 

or natural age composition. No significant trends in the age composition of the aggregate return 

of natural fish to LGD were observed for brood years 1995-2003. It is important to note that for 

most brood years, the hatchery population returned younger than either the SFSR natural 

population or the aggregate natural population at LGD. 

Length-at-age, by brood year, for both the hatchery- and natural-origin male and female returns 

to the SFSR is displayed in Figure 9. For brood years 1979-2004, no significant trends in lengthat-age for the hatchery population were observed with the exception of the age-4 males which 

showed a positive slope of 0.14cm/yr. For brood years 1991-2004, regression slopes were 

negative for all age/gender combinations for the natural population in the SFSR but the only 

significant trend was for the age-4 males which showed a negative slope of 0.30 cm/yr. For the 

aggregate natural-origin population at LGD, regression slopes for length-at-age were negative for 

all age/gender combinations and were significant for age-4 males and age-5 females. Annual 

variations in length-at-age for the hatchery and natural populations are similar over time and are 

presumably driven, in large part, by environmental conditions. 

In addition to the above life history characteristics, we also looked at spawn timing and fecundity 

of hatchery-origin SFSR Chinook salmon over time and found no significant trends in either metric 

over the life of the program. The median spawn date across all years is August 27 (range: Aug 

20- Sep 2) with no significant trend. Fecundity has ranged from 3,684 to 5,401. The observed 
35 

fluctuations were likely a result of the varying proportions of two and three ocean females in the 

adult returns. 

CONTRIBUTION OF HATCHERY FISH TO FISHERIES 

As mentioned earlier, due to the later run timing of McCall Fish Hatchery origin Chinook salmon 

through the Columbia and lower Snake rivers, little downriver harvest has occurred on this stock 

in recent years. Harvest estimates from fisheries below LGD have fluctuated from zero fish in 

some years to a high of 1,383 fish in 2004 (Figure 10). The first sport fishery in the SFSR targeting 

fish produced by this program occurred in 1997. There were no sport fisheries in 1998 or 1999 

but there have been sport fisheries every year since 2000. Sport fishery harvest has ranged from 

a low of 364 fish in 2006 to a high of 6,847 fish in 2002 and angler effort exceeded 80,000 hours 

in 2003 (Figure 10). Some level of tribal harvest has occurred on the SFSR in most years since 

1987. Tribal harvest estimates have ranged from zero to 1,630 Chinook salmon (Figure 10). 
36 

Observed straying has been minimal for the SFSR hatchery stock. In many years, no strays have 

been recovered above or below LGD and the highest percentage of strays for any year was 2.7% 

in 1983. The next closest year is 1988 with a stray rate of 1.3%. One important note is that 

estimates of straying are minimum estimates as stray recoveries downriver are typically 

opportunistic at hatchery traps and on spawning grounds. There are many areas where strays 

might not be recovered throughout the basin, but overall straying is still expected to be very low. 

Determining the beneficial use of McCall Fish Hatchery origin Chinook salmon that escape 

fisheries and return to the SFSR trap is a collaborative effort between IDFG and the tribes. The 

first priority of returning fish is to meet broodstock needs with a representative take across the 

run. In addition, we make an effort to maximize harvest opportunity for both sport and tribal 

fisheries by recycling fish through the fisheries when deemed appropriate. Also, fish from the traps 

can be transferred to the tribes for ceremonial and subsistence (C&S) use, given to local food 

banks, or outplanted for natural spawning within the SFSR basin. 

Overall, disease has not been an issue at the McCall Fish Hatchery and there have been no 

significant losses due to disease. 

SUMMARY AND OUTLOOK FOR THE FUTURE 

The SFSR program will continue to be managed to meet the management objectives outlined in 

this report. In an effort to assist in the restoration and maintenance of the natural population, an 

integrated supplementation approach was initiated in 2010 that is consistent with 

recommendations from the HSRG. Because the natural population in the SFSR is not large 

enough to fully integrate a one million smolt program, managers have implemented a steppingstone approach that includes maintaining two broodstocks (integrated and segregated). Returns 

from the integrated brood will be used to supplement the natural-origin population above the 

hatchery weir and produce the next generation of integrated broodstock. Weir and broodstock 

management will be based on a sliding scale approach. During times of low natural-origin 

abundance, guidelines will be relaxed to allow for more hatchery influence in both the hatchery 
37 

and natural environments. As natural-origin adult returns increase, the proportionate influence 

from natural fish in the hatchery and on the spawning grounds will also increase. Efforts to restore 

and maintain sport and tribal fisheries will continue. While there has been significant rebuilding of 

these fisheries since 2000, future fisheries will be highly dependent on post release survival. 

This hatchery program has made significant progress over the years with culture practices and 

consistently achieves high egg-to-smolt survival rates and since 1991 has achieved juvenile 

production targets in all but three years. Post release survival rates have been highly variable and 

in general far less than was originally modeled during the program development. For most of the 

early years of this program, minimal contribution to the harvest mitigation goal was made. During 

the mid-80s and early 90s, relatively low levels of tribal harvest occurred. In 1997 and every year 

since 2000, adult returns have supported both tribal and recreational fisheries in the SFSR. Since 

1997 the average annual recreational angler participation (in angler hours) has averaged 36,000 

hours and has ranged from 9,400 to 81,000. While this program has made contributions to 

mainstem Columbia River fisheries, it is far less than the modeled 4:1 catch to escapement ratios. 

Realizing that many of the factors that influence post release survival are not a result of the 

hatchery culture process and that the total mitigation goal has never been reached, managers do 

feel that the hatchery program has provided significant benefits with regards to mitigating for lost 

harvest opportunities and has made significant progress towards restoring and maintaining 

recreational and tribal fisheries. 

The outlook for M&E includes continued monitoring of hatchery production and productivity and 

contribution to sport, tribal, and commercial fisheries. This will be accomplished using a variety of 

tools including the continued use of Coded Wire Tags (CWT) and PIT tags and the implementation 

of Parental Based Tagging (PBT). PIT tags have been, and will continue to be used to estimate 

adult survivals back to LGD, monitor returns for in-season fisheries management, and to look at 

migration timing and inter-dam conversion rates. PBT, along with CWTs, will be used to monitor 

catch contribution and stock identification. The continued effort to monitor the status and trends 

of the natural populations in the SFSR is a collaborative effort between the IDFG and the NPT 

The SFSR Chinook salmon program will continue to support both harvest and conservation 

objectives, mitigation for lost sport and tribal fishing opportunity, and expanded coordination 

between state, tribal, and federal managers. Through the development of a Hatchery Genetic 

Management Plan (HGMP), managers are incorporating both current and emerging science and 

have incorporated suggestions generated through the Hatchery Scientific Review Group (HSRG) 

and Hatchery Review Team (HRT) review processes. 

ACKNOWLEDGEMENTS 

We would like to thank Gene McPherson and the dedicated staff at the McCall Fish Hatchery for 

their continued efforts in maintaining a high quality fish culture operation and ultimately a high 

quality fishery in South Fork Salmon River. We would also like to thank the many cooperators in 

the basin that help to make this a successful program including staff at the IDFG regional office 

in McCall, the Pacific States Marine Fisheries Commission, IDFG harvest monitoring crews and 

the monitoring and evaluation staff from the Nez Perce Tribe. Lastly, we would like to thank the 

staff at the LSRCP office in Boise, ID for providing funding and support to maintain this valuable 

program. 
38 

REFERENCES 

Bowles, E., and E. Leitzinger. 1991. Idaho Department of Fish and Game, Salmon 

Supplementation in Idaho River (Idaho Supplementation Studies) Experimental Design, 

Report to Bonneville Power Administration, Contact No. 1989BP01466, Project No. 

198909800, 200 electronic pages (BPA Report DOE/BP-01466-1). 

IDFG RESPONSE TO THE ISRP COMMENTS-South Fork Salmon River 

We would like to thank the members of the ISRP for their review of the program summary and 

oral presentation and suggestions for improving the quality of the reports. In several sections of 

the report, we have added detail to address some of the questions and comments that were made 

by the ISRP. Below are direct responses to the individual comments made by the ISRP. 

The primary intent of this report was to describe the history and performance of the hatchery 

program relative to meeting the mitigation objectives for the program. Many of the comments 

provided by the ISRP were related to providing additional detail about the management objectives 

and status of the natural population. Addressing the recovery of listed natural Chinook salmon 

populations goes well beyond the LSRCP mitigation program and the IDFG is fully engaged in 

this process through the development of HGMPs, TRT viability assessments, consultations with 

NOAA Fisheries, and incorporating adaptive management actions to the hatchery programs. 

One thing that is apparent from the ISRP comments is the misunderstanding that the 

management objective for the hatchery program is to restore the natural population. While the 

IDFG statewide management objectives include maintaining and restoring natural populations, 

this hatchery program has been managed primarily to meet harvest mitigation objectives. As a 

result of declining hatchery and natural populations of spring Chinook salmon populations and 

the impending listing of the Snake River spring Chinook salmon in 1992, IDFG developed a 

multigenerational experiment to evaluate the use of a supplementation strategy to increase the 

number of naturally produced adults. The initiation of this study was based on the uncertainty of 

supplementation effectiveness and its impacts to natural populations. At the beginning of this 

evaluation (BY1991), IDFG implemented mass-marking of hatchery produced Chinook that 

allowed the differentiation of hatchery and natural fish. At the same time, IDFG also implemented 

the use of segregated broodstocks to reduce potential impacts to the natural populations. 

More recently, IDFG has implemented changes in the hatchery program that resulted from two 

regional hatchery review processes. These reviews reflect the current state of knowledge 

regarding best management practices of anadromous hatchery programs. As part of the 

recommendations, IDFG has implemented the development of an integrated broodstock through 

a stepping-stone approach and a weir management that is based on a sliding scale of natural 

origin adult abundance. 

ISRP comment #1 from the Introduction section-The broodstock history for the SFSR has 

been continually changing since the program’s inception. This has made it impossible to estimate 

the contributions of the several founding stocks and difficult to evaluate the program. In recent 

years, the program has swung from focusing on segregated hatchery origin broodstock (1995-

2009) to an integrated stepping-stone broodstock protocol, which was initiated in 2010. 
39 

IDFG Response to Comment #1-Detail has been added to this section in the body of the report 

to better describe the broodstock history and direction. To be clear, the “broodstock history” has 

not changed and this program has not used several founding stocks. Initial broodstock was 

collected at Little Goose and Lower granite dams from 1974-1979 during the periods when 

summer run fish were passing through the Snake River projects. Since 1981, all broodstock has 

come from adult returns to the SFSR. The proportion of hatchery- and natural-origin adults 

contributing to broodstocks has varied over the years, for reasons explained in the narrative, but 

has consistently been of SFSR stock. The original program strategy was more similar to what 

today managers refer to as an integrated program. Actual SARs experienced by both hatchery 

and natural fish were far less than those modeled to establish the original program strategy. 

Declines in all stocks as a result of poor SARs and ESA listing in 1992 resulted in the adaptive 

management shift to a segregated hatchery program for the harvest mitigation program. 

ISRP comment #2 from the Management and Monitoring/Evaluation Objectives section-It 

is not clear how the actions in this program contribute to the objective “restore and maintain 

natural populations of Chinook salmon in the SFSR,” or how the program is being implemented 

to “minimize the impact of the hatchery program on the natural Chinook populations in the SFSR.” 

IDFG Response to Comment #2-Additional detail was added to the report to clarify 

“management objectives” for the hatchery and natural populations. The statewide management 

objective is to maintain and restore natural Chinook salmon populations in Idaho. The 

management objective of the McCall Fish Hatchery is to meet established mitigation goals and to 

maintain both recreational and tribal fisheries in the SFSR while minimizing impacts to the natural 

population. IDFG is confident that best management practices have been and will continue to be 

implemented in this program. In response to declines in natural-origin abundance the 

supplementation evaluation was implemented in 1991 to evaluate the use of hatchery strategies 

to rebuild natural populations. Other management decisions are made to reduce or minimize the 

potential impacts of hatchery fish on the natural populations, i.e. to maintain the natural 

population. 

ISRP comment #3 from the Management and Monitoring/Evaluation Objectives section-The 

sentences on monitoring and evaluation do not identify the individual metrics that are being used 

to evaluate the various program objectives. Some are self-evident, e.g., adult abundance, harvest, 

etc, but other objectives are not, e.g., restore and maintain natural populations and minimize 

impacts. It would be helpful to identify how the information is being gathered. For example, are 

estimates of adult abundance determined from CWT data collected at LGD or the hatchery rack? 

Is there representative PIT-tagging and CWT-tagging? 

IDFG Response to Comment #3-As mentioned earlier, the intent of this report was to describe 

the history and performance of the hatchery program funded through the LSRCP program. While 

the statewide management objectives include maintaining and restoring the natural populations, 

the hatchery program has been managed primarily to achieve harvest mitigation objectives. An 

ongoing supplementation evaluation study that is funded through the BPA Fish and Wildlife 

program is evaluating the use of a supplementation strategy to increase the number of naturally 

produced adults (Bowles and Leitzinger, 1991). While we did not provide results from the ISS 

evaluation, we did provide some data (adult abundance, and life history characteristics) for the 

natural population in the SFSR to show the synchrony in the variability observed for the hatchery 

and natural populations with respect to survival and life history characteristics. 

With regards to how information is being gathered, a key metric provided in this review that allows 

the monitoring of production and productivity is the estimate of annual adults abundance by age 
40 

(prior to human exploitation). For the hatchery population, estimates are derived by summing up 

returns to the hatchery trap, escapement estimates (above and below the weir), and terminal and 

mixed stock harvest estimates. Determination of age is based on the recovery of CWTs in the 

escapement and in fisheries. For the natural population, annual adult abundance estimates by 

age are derived from summing up escapement estimates from spawning ground surveys and the 

collection of biological data from carcasses. 

ISRP comment #4 from the Status of Natural Population section-Additional specific details 

would enhance this section. The section states that the SFSR mainstem is part of a SFSR major 

population group that has four independent populations. Identify the ESU, the names and number 

of MPGs in the ESU, and then name the SFSR MPG independent populations and perhaps 

provide a map with their geographic distribution. There should be a description of where this 

hatchery program interacts with other spring Chinook populations, and the nature of the 

interaction. For example, genetic interactions may occur in tributaries where hatchery fish stray. 

It would be helpful to include a figure showing the trends in abundance of natural stocks and the 

viability assessment/recovery plan thresholds for viability.

IDFG Response to Comment #4-We agree that such detail is informative. This document 

describes the history and performance of the hatchery program. The natural population status 

information and potential impacts of the hatchery program on natural populations are described in 

NOAA-Fisheries Draft Recovery Plan (.http://www.idahosalmonrecovery.net), NOAA Status 

Reviews (http://www.nwr.noaa.gov/ESA-Salmon-Listings/5-yr-review.cfm) and the SFSR Hatchery 

and Genetic Management Plan (http://www.fws.gov/lsnakecomplan/Reports/HGMPreports.htm).

ISRP comment #5 from the Adult Return section-A description of how adults at LGD partitioned 

into the different Snake/Salmon river MPGs and independent populations would be useful. Are 

there hypotheses on how/why juvenile survival from release to LGD is greater for hatchery than 

wild smolts, yet SARs are lower for hatchery fish from smolt to adult? 

IDFG Response to Comment #5-The estimated returns to Lower Granite dam that we provided 

were developed by summing the hatchery returns, escapement data and the harvest information. 

Information to directly estimate escapement by stock at Lower Granite dam was not available for 

the time series presented in this report. With regards to potential reasons why survival from 

release to Lower Granite dam is typically higher for the hatchery population, see our response to 

ISRCP Comment #9 

ISRP comment #6 from the Life history characteristics and age composition section-It is 

not clear from the text and figures whether the age composition data is estimated for a “run” year 

or a “brood” year. Given the variation in survival from brood year to brood year, it seems that 

should be how age classes are reported, not on run years. 

IDFG Response to Comment #6-All of the analyses were done based on brood years. The text 

in the body of the report has been updated to make this clear. 

ISRP comment #7 from the Key Findings section-Like many of the LSRCP hatcheries, the 

SFSR hatchery has made admirable progress over its roughly 30-year history toward solving inhatchery production problems and achieving within-hatchery survival, and occasionally, 

production goals, depending upon broodstock availability. However, the mixed pedigree of the 

broodstock, the ever-changing broodstock management strategy, and the shifting nature of the 

supplementation strategy (from segregated to integrated stepping-stone over the last few years) 

creates uncertainty about what we can expect to learn from the SFSR supplementation 
41 

experiment, as well as uncertainty about its future performance. A constantly shifting program 

becomes difficult to track and assess due to shifting goals and shifting data baselines. 

IDFG Response to Comment #7-We believe that there was some confusion about the history of 

the broodstock and the broodstock management of this program that was likely due to an 

insufficient amount of information we provided in the Broodstock History section of the initial 

report. We have since added detail to this section that better describes the broodstock and 

management strategy. This is also addressed in our response to the ISRP Comment #1 above. 

To reiterate, the management strategy from the onset of this program has been focused on 

mitigating for lost harvest opportunity. During the brood years 1991-2002, a statewide 

supplementation experimental design was conducted to evaluate the utility of using a 

supplementation strategy to increase the number of naturally produced adults. A portion of the 

production capacity for the SFSR hatchery program was dedicated for this effort. During this 

period, approximately 15-20% of the total production was from an integrated broodstock that was 

differentially marked from the segregated mitigation production. This marking strategy allowed for 

the evaluation of both broodstock components. We do not feel that the ability to evaluate the 

supplementation experiment has been compromised and in fact, managers have been resisting 

proposed changes that would likely impact the supplementation evaluation. 

ISRP comment #8 from the Key Findings section-While methods were not described, key 

metrics were presented in the report and presentation. It would be helpful if the data reporting 

were summarized as explicit statements reflecting the managers’ self-evaluation of how well the 

program is achieving the objectives established. 

IDFG Response to Comment #8-Narrative was added to the Summary section to address this 

comment. 

ISRP comment #9 from the Key Findings section-Please comment on why survival of hatchery 

smolts to LGD is consistently higher than that of natural smolts given that survival to adult stage 

of hatchery smolts is consistently lower. Does high early survival of hatchery smolts reflect 

distance or size? This finding is opposite that of Upper Salmon River spring Chinook.

IDFG Response to Comment #9-We have observed higher rates of survival from release to 

Lower Granite Dam for releases from other hatcheries relative to natural-origin smolts in the same 

area even though SARs for hatchery releases are consistently lower than those for natural-origin 

smolts. There appears to be some advantage gained in the hatchery environment that favors 

early survival subsequent to release and is likely associated with hatchery fish over wintering in 

a relatively benign environment and the additional energy reserves gained from artificial feeding 

prior to release. Because SARs of natural fish are consistently higher, this advantage at some 

point is lost. Why we see increased early survival (release to Lower Granite) relative to natural 

smolts in one hatchery group and not another could be the focus of future evaluations and 

investigations. At this point in time, one hypothesis might be that there is a time/distance 

component to post-release survival of hatchery smolts. The upper Salmon River smolts, because 

of their longer migration distance, may have experienced this effect before arriving at LGD 

whereas the SFSR fish may not be subject to the effects until after passing LGD. 

ISRP comment #10 from the Key Findings section-The presentation of life history data of 

hatchery and natural Chinook was helpful. Older age of maturation by natural Chinook is important 

because older fish produce more numerous and larger eggs and therefore contribute to higher 
42 

adult returns per spawner. Are there any differences in mean length-at-age of hatchery versus 

natural Chinook (ANOVA test)? It is difficult to tell from graphs given the Y-axis scale. 

IDFG Response to Comment #10-Average length-at-age for hatchery- and natural-origin returns 

in the SFSR was not significantly different for any age/gender combination (see table below). 

. 

ISRP comment #11 from the Key Findings Section-Stray Rate-Indicate if the reported values 

estimated the percentage of the hatchery return that stray to streams. Provide any information on 

the fraction of natural spawners that are hatchery strays. If there is natural spawning near the weir 

site, provide what fraction are hatchery fish.

IDFG Response to Comment #11-The stray rates we report represent the fraction of the entire 

return that strayed from the SFSR. As noted in the report, this is considered a minimum estimate 

because there are places that fish could stray where they would not be recovered. However, for 

the SFSR hatchery program, representative tagging with CWTs has been used from the inception 

of the program and intensive spawning ground surveys are conducted in the SFSR drainage, 

throughout Idaho, and the Snake River basin. If straying of SFSR hatchery fish was significant, 

CWT recoveries would likely reveal this. Through the implementation of a PBT marking program 

currently underway, any stray recovered from this program would be identifiable (i.e. PBT would 

result in a 100% tagging rate). 

The fraction of naturally spawning fish that are of hatchery origin in the area immediately below 

the SFSR weir is consistently high (>50%). The hatchery fraction in the Poverty Flat production 

area (approximately 15 miles downstream of the weir) is much lower and has averaged 15% over 

the last 14 years. 

 

ISRP comment #12 from the Outlook and Recommendations section-The “Summary and 

Outlook for the Future” section of the written report describes in broad brush the future direction 

of the program including the implementation of Parental Based Tagging (PBT), which along with 

CWTs, will be used to monitor catch contribution and stock identification. This section should also 

include a brief summary of the findings from the USFWS hatchery review and the HSRG review, 

and how the program is addressing those findings.

IDFG Response to Comment #12-The major programmatic recommendation from the HSRG 

was the implementation of the integrated stepping –stone broodstock which is also consistent 

with the approach recommended by the USFWS Hatchery Review Team (HRT). Responses to 

all of the HSRG and HRT comments and suggestions are in the draft HGMP. The draft is available 

on the LSRCP website: http://www.fws.gov/lsnakecomplan/Reports/HGMPreports.htm. 

ISRP comment #13 from the Outlook and Recommendations section-The detailed methods 

of this approach and consideration of the uncertainties associated with it are not addressed in the 

Age-3 Age-4 Age-5

Average Length of Hatchery Males 55.7 78.7 95.3

Average Length of Natural Males 57.0 77.6 95.1

p-value 0.29 0.18 0.88

Age-4 Age-5

79.3 91.9

78.3 90.8

0.20 0.71

Comparrison of Average Length at Age for for Hatchery- and Naturalorigin Male Chinook salmon in the SFSR

Comparrison of Average Length at Age for for Hatchery- and Naturalorigin Female Chinook salmon in the SFSR

Average Length of Hatchery Males

Average Length of Natural Males

p-value
43 

written document and deserve greater discussion and scrutiny. It is our recommendation that the 

SFSR plans that design the dual programs be reviewed by the ISRP or an equivalent body when 

it is available. 

IDFG Response to Comment #13-The programs strategies will be reviewed by NOAA-Fisheries 

as part of the ESA Section 10 permitting process. Opportunities to comment will be provided 

through Federal Register notices. 

 
44 

UPPER SALMON RIVER SPRING CHINOOK SALMON 

John Cassinelli, Brian Leth, Shane Knipper 

Idaho Department of Fish and Game 

1414 East Locust Lane, Nampa, Idaho 

BACKGROUND 

The upper Salmon River (USR) spring Chinook salmon program was established to provide inkind mitigation for losses of spring run Chinook salmon associated with the construction and 

operation of the four lower Snake River hydroelectric dams. The Sawtooth Fish Hatchery is 

located on the Salmon River approximately seven miles upstream from the town of Stanley, Idaho. 

All adult trapping, spawning, incubation and rearing occurs at this facility. Construction of the 

hatchery was completed in 1985. A satellite facility associated with the Sawtooth Fish Hatchery 

is located on the East Fork Salmon River and was completed in 1984. Currently, this facility is 

used to monitor adult abundance of the natural population and no broodstock is collected at this 

site. The relative locations of both the hatchery and satellite facility are shown in Figure 1. The 

Lower Snake River Compensation Plan (LSRCP) adult mitigation goal for the USR spring Chinook 

salmon hatchery program is 19,400 adult Chinook salmon above Lower Granite Dam (LGD) and 

77,000 adults available for downriver (Columbia and lower Snake rivers) sport and commercial 

harvest. The original release target of 2.3 million yearling smolts was based on an assumed 0.87% 

smolt-to-adult survival rate applied to the LGD mitigation objective. The original release strategy 

included 700,000 smolts released at the East Fork Satellite Facility, 300,000 smolts released into 

Valley Creek, and 1.3 million smolts to be released at the Sawtooth Fish Hatchery. However, due 

to limitations with well water availability and ice thickness in outdoor rearing containers during the 

winter months, the actual facility capacity was adjusted down to 1.7 million yearling smolts. 

Currently, the release strategy is for 1.5 million smolts released directly into the Salmon River at 

Sawtooth Fish Hatchery and 200,000 smolts released into the Yankee Fork as part of the 

Shoshone Bannock Tribe supplementation program. 
45 

MANAGEMENT AND MONITORING/EVALUATION OBJECTIVES 

Statewide management objectives for USR Chinook salmon are to restore and maintain the 

natural populations. Objectives for the hatchery program are to meet the LSRCP adult mitigation 

objectives in the USR, to restore and maintain recreation and tribal Chinook salmon fisheries, and 

to minimize the impacts of the hatchery program on the natural Chinook salmon populations in 

the USR. In addition to meeting harvest mitigation objectives, IDFG has committed some of the 

hatchery resources to maintaining a conservation component for the USR though an integrated 

broodstock that is consistent with recommendations from the Hatchery Scientific Review Group 

(HSRG). Managers feel that returns from the integrated broodstock are more suitable to 

supplement natural spawners than returns from the segregated brood. Additionally, the integrated 

broodstock will maintain genetic continuity of the hatchery and natural populations which is 

expected to be advantageous during time of extreme lows in natural-origin escapement. 

Monitoring and evaluation (M&E) objectives for the USR include monitoring production, 

productivity, and life history characteristics of hatchery and natural populations and to evaluate 

broodstock and rearing strategies to increase and maximize adult returns. 

BROODSTOCK HISTORY 

In 1966, an earthen pond (Decker Pond) was developed near the current site of the Sawtooth 

Fish Hatchery as an experiment to evaluate the ability to rear Chinook salmon in earthen ponds 

as opposed to building a conventional rearing hatchery. From 1968-1976 hatchery-origin Chinook 

salmon (combination of USR, Lemhi and Rapid River stocks) were released from the pond 

(Reingold, 1977). For brood year 1966-1968 fish were released as yearling smolts but pre-release 

survival was very poor for those broods and only a total of 33,000 yearling smolts were release 

for the three years combined. For brood years 1969-1975 all fish were subyearlings released in 

late September. Contribution of the Decker Pond releases to adult returns for brood years 1966-

1972 was estimated from the recovery of marked adults in fisheries and from spawning ground 

surveys. For the return years 1970-1976 the percent of the adult returns estimated to have 

resulted from the Decker Pond release was less than 2% for all years except 1974. In 1974, 

21.5% of the return was estimated to be from the Decker Pond releases. Evaluation of Decker 

Pond ended in 1976. Additional Rapid River hatchery-origin juvenile Chinook salmon were 

released in the upper Salmon River in 1977, 1978, and 1979. In 1978 and 1979, 700,000 and 

914,000 yearling smolts, respectively, were released in the USR near the current site of Sawtooth 

Fish Hatchery. 

Initial broodstock for the USR program was collected at a temporary weir in the USR from 1981 

to 1984 just prior to the construction of Sawtooth Fish Hatchery (construction completed in 1985). 

It was estimated that approximately 50% of the adult return to the weir in 1981 was from the 

release of 914,000 Rapid River yearling hatchery smolts in 1979. In 1982 it was estimated that 

approximately 26% of the return was from the same release in 1979. No hatchery-origin juveniles 

were released during the period 1980-1982. Since 1983, all hatchery releases in the upper 

Salmon River have been USR stock. While hatchery releases of Rapid River stock did occur 

throughout the 1970s, contribution to the adult returns was very low for most years and for a single 

year in 1981 made a significant contribution to the founding hatchery broodstock. 

Because mass marking was not initiated until brood year 1991, the origin of all adult returns 

(hatchery or natural) could not be distinguished until 1995. Prior to 1995 the program operated 

essentially as a de facto integration/supplementation program with both hatchery- and naturalorigin adults being incorporated into the broodstock and also released above the weir to spawn 
46 

naturally even though the emphasis was on harvest mitigation. The original intent of the hatchery 

program was to mitigate for lost harvest opportunity that resulted from the construction and 

operation of the four lower Snake River hydroelectric dams and thus management efforts have 

focused on mitigating for the lost harvest opportunity. During the period 1991-2002, part of the 

production capacity at Sawtooth Fish Hatchery was devoted to developing an integrated 

broodstock that was part of a statewide Idaho Salmon Supplementation (ISS) experimental 

research study (See Bowles and Leitzinger 1991) designed to evaluate the utility of using a 

supplementation strategy to increase the number of natural-origin spawners. This integrated 

supplementation broodstock was developed using approximately equal numbers of hatchery- and 

natural-origin adults. Progeny from the supplementation broodstocks were marked differentially 

from the segregated mitigation program. 

From 1995-2009 all hatchery production, with the exception of the ISS experimental broodstock, 

has been produced from segregated hatchery-origin returns. In 2010, managers initiated the 

development of a conservation broodstock component in the hatchery that would be used to 

supplement spawners above the adult weir on the upper Salmon River consistent with 

recommendations from the Hatchery Scientific Review Group (HSRG) review. Numbers of 

integrated hatchery fish released above the weir are based on a sliding scale that is driven by the 

number of natural-origin returns. A complete description for this program is provided in the draft 

Hatchery Genetic Management Plan (HGMP) submitted to NOAA in November 2010. Copies of 

the draft HGMPs are available at the LSRCP Website: 

http://www.fws.gov/lsnakecomplan/Reports/HGMPreports.htm. 

STATUS OF NATURAL POPULATION 

The natural populations of Chinook salmon in the USR were listed as threatened in 1992 and the 

hatchery population was added to the listing in 2005. From 1991 to 2009, the estimated naturalorigin adult abundance in the USR mainstem population has ranged from 18 to 1,431 fish. The 

upper Salmon River mainstem population is one of nine independent populations within the upper 

Salmon River Major Population Group (MPG) and is classified as a “large” population based on 

historic habitat potential. The Interior Columbia Technical Recovery Team (ICTRT) concluded 

that the USR natural population is not currently viable, is at a high risk for abundance and 

productivity measures and is at moderate risk for spatial structure and diversity. 

IN-HATCHERY AND POST RELEASE SURVIVAL 

Broodstock performance over the life of the hatchery program has been good with levels of 

prespawn mortality for both males and females consistently below 20%. Exceptions to this were 

in 2006 when approximately 60% of the broodstock was lost due to an Ichthyophthirius multifilis

(Ich) outbreak. With one exception, juvenile in-hatchery survival has been high across all years 

of the program. In 1992, a bacterial outbreak caused high mortality. For all remaining years, eyed 

egg-to-release survival was greater than 70% and for most years was near 90% (Figure 2). 
47 

The number of juveniles released from Sawtooth Fish Hatchery has fluctuated dramatically over 

the history of the program from a low of 5,000 smolts released in 1997 (BY 1995) to 2,430,000 

smolts and subyearling parr released in 1986 (Figure 3). While parr releases occurred for this 

program through the early 1990s, low observed post-release survival rates prompted the 

discontinuation of this release strategy. 

Passive Integrated Transponder (PIT) tags have been used to estimate survival from release to 

LGD for this program since the early 1990s. Estimated survival for hatchery-origin yearling smolts 

released in the USR has fluctuated from 20-65% while the survival of natural-origin smolts has 

ranged from 30–75% (Figure 4). 
48 

The estimated number of adults surviving to the Columbia River mouth annually from this program 

is less than 2,000 for most years and has fluctuated from 15 (7 adults, 8 jacks) fish in return year 

1995 to 7,141 (4,869 adults, 2,272 jacks) fish in 2008. Run timing of Sawtooth Fish Hatchery 

adults through the lower Columbia and Snake rivers is later than most of the spring run Chinook 

salmon stocks, which has contributed to low observed harvest rates. Estimated adult returns to 

LGD have ranged from 15 (7 adults, 8 jacks) fish in return year 1995 to 6,558 (4,570 adults, 1,988 

jacks) fish in 2008 (Figure 5). This hatchery program has never achieved either the LGD or total 

mitigation objectives. Also shown in Figure 5 are the natural returns to the upper USR which 

reflects synchrony between the hatchery and natural populations for most years. 

Smolt-to-adult survival (SAS) and smolt-to-adult return (SAR) rates were very low for brood years 

through the early-1990s and have ranged from (0.001-1.1%) over the entire history of the program 

(Figure 6). The modeled 0.87% SAR to LGD has only been achieved in two years. It is important 

to note that the modeled 0.87% SAR is post downstream (below LGD) harvest and is based on 

the assumption there would be a 4:1 catch to escapement ratio to LGD. The SAS necessary to 

achieve the total mitigation goal is 4.35%. To date, the highest observed SAS for this program is 

1.1% for brood year 1997. Figure 7 shows SARs of the hatchery population overlaid with the 
49 

SARs of the aggregate return of natural-origin Chinook salmon at LGD and reveals synchrony 

between the two. 

LIFE HISTORY CHARACTERISTICS OF THE HATCHERY AND NATURAL POPULATIONS 

The average (1997-2009) cumulative adult run timing for hatchery- and natural-origin fish to the 

Sawtooth Fish Hatchery adult trap is similar. The median arrival date to the trap varies between 

years but within years is similar for the hatchery and natural fish (Figure 8). 

The estimated age composition of the hatchery and natural populations in the USR and the 

aggregate natural population at LGD are displayed in Figure 9. Prior to brood year 1991, age 

composition data for the natural population in the USR is limited. Prior to brood year 1995, the 

number of hatchery-origin returns in the USR was very low in most years which likely influenced 

some of the large fluctuations in the estimated age composition of the hatchery population (i.e. 

small sample sizes). For the natural population in the upper Salmon River, data for brood years 

1991-2004 is presented and for the aggregate natural-origin returns at LGD, data for brood years 

1995-2003 is presented. Overall, there appears to be a high degree of synchrony between the 
50 

USR and LGD natural populations. As observed in other hatchery stocks, the hatchery population 

returns at a younger age than the natural population for most years. Over the period 1984-2004 

there was a significant increase in the age-3 component of the hatchery return but no significant 

change for the age-4 or age-5 components. For brood years 1996-2004, there were no significant 

trends for any of the age classes in the hatchery population. For the period 1991-2004 there were 

no significant trends for any of the age classes in the USR natural population. Likewise, there 

were no significant trends for the aggregate natural population at LGD for brood years 1995-2003. 

Average length-at-age (age-3, age-4, and age-5) for the hatchery- and natural-origin populations 

in the USR and the aggregate natural population at LGD is displayed in Figure 10. Similar to the 

age composition data, prior to brood year 1995 the number of hatchery-origin returns in the USR 

was very low in most years which likely influenced some of the large fluctuations in the length-atage estimates of the hatchery population (i.e. small sample sizes). Overall, length-at-age was 

similar for hatchery- and natural-origin fish. For brood years 1996-2004, there were no significant 

trends for the hatchery and natural populations in the USR with the exception of the age-5 
51 

hatchery males that showed a significant increase in length. For the aggregate natural-origin 

population at LGD, regression slopes for length-at-age were negative for all age/gender 

combinations and were significant for age-4 males and age-5 females. Annual variations in lengthat-age for the hatchery and natural populations are similar over time and are presumably driven, 

in large part, by environmental conditions. 

The median spawn date of the hatchery population for the period 1981-2007 is August 24th

(min=Aug 18, max=Sep 2) with no significant trend. Mean fecundity of hatchery-origin females for 

the period 1981-2009 is 5,012 (min=3,688, max=6,388) with no significant trend. Annual 

fluctuations in fecundity are generally associated with age composition, particularly for years when 

few hatchery females returned to Sawtooth Fish Hatchery. 

CONTRIBUTION OF HATCHERY FISH TO FISHERIES 

Estimated harvest of hatchery-origin Chinook salmon downstream of LGD from this program has 

ranged from zero in some years to 279 in 2008. In more recent years, the later migration timing 

of Sawtooth Chinook salmon through the Columbian and Snake rivers has contributed to lower 

harvest rates than observed for other earlier migrating spring run Chinook salmon hatchery fish 

from Idaho In 2007, 158 hatchery-origin Chinook salmon from Sawtooth Fish Hatchery were 

harvested downstream of LGD. Prior to 2007, the highest harvest estimate downstream of LGD 

was 142 fish in 1986. Within Idaho, numerous tribal fisheries have occurred on the USR since the 

mid 1980’s and tribal harvest estimates have ranged from zero to 941 Chinook salmon (Figure 

10). Only two sport fisheries have occurred on the USR since the inceptions of the program, one 

in 2008 and one in 2009 
52 

In 2008, Idaho sport anglers fished for 13,745 hours and harvested 388 fish. In 2009, Idaho sport 

anglers fished for 36,370 hours to harvest 779 fish (Figure 10). 

Straying has been minimal for the USR hatchery stock. In most years, no strays have been 

recovered above or below LGD and the highest percentage of strays for any year was 0.59% in 

1999. Estimates of strays are considered minimum as stray recoveries downriver are typically 

opportunistic at hatchery traps and on spawning grounds. There are areas where strays might 

not be recovered throughout the basin, but overall straying is still expected to be very low based 

on a long history of CWT recovery information. 

Determining the beneficial use of hatchery-origin Chinook salmon from Sawtooth Fish Hatchery 

that return to the hatchery trap is a collaborative effort between IDFG and the tribes. The first 

priority for returning fish is to meet broodstock needs that include fish trapped across the entire 

run. In addition, considerable effort is made to maximize harvest opportunity for both sport and 

tribal fisheries by recycling fish through the fisheries when deemed appropriate. Fish from the trap 

can also be transferred to the tribes for ceremonial and subsistence (C&S) use, donated to food 

banks, or outplanted for natural spawning within the USR basin. 

Overall, disease has not been a major issue at Sawtooth Fish Hatchery. As mentioned earlier, Ich 

resulted in a 60% loss of the broodstock in 2006. Ich is a more recent issue at Sawtooth Fish 

Hatchery and currently, adults being held for broodstock are treated with formalin three to seven 

times per week based on the water temperature. Whirling disease has been a concern at 

Sawtooth since a positive testing in the mid 1980’s. As a precaution, fry are moved outside on 

river water later in the rearing cycle so that they are larger. Sawtooth Fish Hatchery uses EnzymeLinked Immunosorbent Assay (ELISA) testing to cull females from the broodstock to reduce the 

incidence of Bacterial Kidney Disease (BKD). This culling method has proven to be very effective 

at limiting BKD at the Sawtooth Fish Hatchery. 

SUMMARY AND OUTLOOK FOR THE FUTURE 

The USR program will continue to be managed to meet the management objectives outlined in 

this report. In an effort to assist in the restoration and maintenance of the natural population, an 

integrated supplementation approach was initiated in 2010. Because the natural population in the 

USR is not large enough to fully integrate a 1.7 million smolt program, managers will maintain two 
53 

broodstocks (integrated and segregated). Returns form the integrated brood will be used to 

supplement the natural-origin population above the hatchery weir and produce the next 

generation of integrated broodstock. Weir and broodstock management will be based on a sliding 

scale approach. During times of low natural-origin abundance, guidelines will be relaxed to allow 

for more hatchery influence in both the hatchery and natural environments. As natural-origin adult 

returns increase, the proportionate influence from natural fish in the hatchery and on the spawning 

grounds will also increase. Efforts to restore and maintain sport and tribal fisheries will continue. 

In recent years there has been some progress in rebuilding fisheries but future fisheries will be 

highly dependent on post release survival. 

This hatchery program has made significant progress over the years with culture practices and 

consistently achieves high egg-to-smolt survival rates. Production targets have been achieved 

less frequently and is due primarily to low hatchery-origin adult returns and low post release 

survival. Post release survival rates have been highly variable and in general far less than was 

originally modeled during the program development. Over all years, smolt to adult survival for this 

program has been about half of that observed for the SFSR program and approximately 66% of 

that observed for the Powell stock from Clearwater Fish Hatchery and similar to the survival of 

the South Fork Clearwater stock from Clearwater Fish Hatchery. It is important to note that the 

Sawtooth hatchery program is located at the extreme end of the range (distance and elevation) 

for Snake River spring Chinook salmon. This program has made some contribution to tribal 

harvest throughout the program history. The first recreational fishery since the program’s 

inception occurred in 2008 and has occurred every year since. The fisheries in 2010 and 2011 

targeted only jack returns. While this program has made contributions to mainstem Columbia 

River fisheries, it is far less than the modeled 4:1 catch to escapement ratios. 

Realizing that many of the factors that influence post release survival are not a result of the 

hatchery culture process and that the total mitigation goal has never been reached, managers do 

feel that the hatchery program has the potential to provide significant benefits with regards to 

mitigating for lost harvest opportunities. 

The outlook for M&E includes continued monitoring of hatchery production and productivity and 

contribution to sport, tribal, and commercial fisheries. This will be accomplished using a variety of 

tools including the continued use of Coded Wire Tags (CWT) and PIT tags and the implementation 

of Parental Based Tagging (PBT). PIT tags have been, and will continue to be used to estimate 

adult survivals back to LGD, monitor returns for in-season fisheries management, and to look at 

migration timing and inter-dam conversion rates. PBT, along with CWTs, will be used to monitor 

catch contribution and stock identification. Efforts to monitor the status and trends of the natural 

population in the USR will also continue. 

The USR Chinook salmon program will continue to support both harvest and conservation 

objectives, continue to mitigate for lost sport and tribal fishing opportunity, and expand 

coordination between state, tribal, and federal managers. Through the development of a Hatchery 

Genetic Management Plan (HGMP), managers are incorporating both current and emerging 

science and are incorporating suggestions generated through the Hatchery Scientific Review 

Group (HSRG) and Hatchery Review Team (HRT) review processes. 

 

ACKNOWLEDGEMENTS 
54 

We would like to extend our sincere appreciation to Brent Snider and the staff at the Sawtooth 

Fish Hatchery for their dedication and commitment to the upper Salmon River program. We would 

also like to thank the cooperators in the basin that help to make this a successful program 

including staff at the IDFG regional office in Salmon, the Pacific States Marine Fisheries 

Commission, IDFG harvest monitoring crews and the monitoring and evaluation staff from the 

Shoshone-Bannock Tribe. Lastly, we would like to thank the staff at the LSRCP office in Boise, 

ID for providing funding and support to maintain this valuable program. 

REFERENCES 

Bowles, E., and E. Leitzinger. 1991. Idaho Department of Fish and Game, Salmon 

Supplementation in Idaho River (Idaho Supplementation Studies) Experimental Design, 

Report to Bonneville Power Administration, Contact No. 1989BP01466, Project No. 

198909800, 200 electronic pages (BPA Report DOE/BP-01466-1). 

Reingold, M. 1977. Idaho Department of Fish and Game, Salmon and Steelhead Investigations, 

Evaluation of Pond Rearing Fish Culture Methods and Survival of Pond Reared Chinook 

Salmon, Federal Aid in Fish and Wildlife Restoration, Job Completion Report, Project F49-R-15, 14 electronic pages. 

IDFG RESPONSE TO THE ISRP COMMENTS-Upper Salmon River 

We would like to thank the members of the ISRP for their review of the program summary and 

oral presentation and their suggestions to improve the quality of the report. In several sections of 

the report, we have added detail to address some of the questions and comments that were made 

by the ISRP. Below are direct responses to the individual comments made by the ISRP. 

The primary intent of this report was to describe the history and performance of the hatchery 

program relative to meeting the mitigation objectives for the program. Many of the comments 

provided by the ISRP were related to providing additional detail about the management objectives 

and status of the natural population. Addressing the recovery of listed natural Chinook salmon 

populations goes well beyond the LSRCP mitigation program and the IDFG is fully engaged in 

this process through the development of HGMPs, TRT viability assessments, consultations with 

NOAA Fisheries, and incorporating adaptive management actions to the hatchery programs. 

One thing that is apparent from the ISRP comments is the misunderstanding that the 

management objective for the hatchery program is to restore the natural population. While the 

IDFG statewide management objectives include maintaining and restoring natural populations, 

this hatchery program has been managed primarily to meet harvest mitigation objectives. As a 

result of declining hatchery and natural populations of spring Chinook salmon populations and 

the impending listing of the Snake River spring Chinook salmon in the early 1990s, IDFG 

developed a multigenerational experiment to evaluate the use of a supplementation strategy to 

increase the number of naturally produced adults. The initiation of this study was based on the 

uncertainty of supplementation effectiveness and its impacts to natural populations. At the 

beginning of this evaluation (BY1991), IDFG implemented mass-marking of hatchery produced 

Chinook that allowed the differentiation of hatchery and natural fish. At the same time, IDFG also 
55 

implemented the use of segregated broodstocks to reduce potential impacts to the natural 

populations. 

More recently, IDFG has implemented changes in the hatchery program that resulted from two 

regional hatchery review processes. These reviews reflect the current state of knowledge 

regarding best management practices for anadromous hatchery programs. As part of the 

recommendations, IDFG has implemented the development of an integrated broodstock and a 

weir management that is based on a sliding scale of natural origin adult abundance. 

ISRP comment #1 from the Introduction-The broodstock history and AP strategy for the USR 

has changed several times since the program’s inception. This has made it impossible to estimate 

the contributions of the USR and Rapid River founding stocks and difficult to evaluate the 

program. Prior to 1995 the program was a de facto integration/supplementation program with both 

hatchery- and natural-origin adults incorporated into the broodstock and also released above the 

weir to spawn naturally. In recent years, the program has swung from focusing on segregated 

hatchery origin broodstock (1995-2009) to an integrated stepping-stone broodstock protocol, 

which was initiated in 2010 

IDFG Response to Comment #1-Detail has been added to this section in the body of the report 

to better describe this broodstock history and direction. To be clear, the “broodstock history” has 

not changed since the program’s inception. The LSRCP mitigation program in the USR began in 

1981 with adult collections from a temporary weir at the current site of Sawtooth Fish Hatchery. 

Since 1981, broodstock for the USR hatchery program has been exclusively from USR returns. 

The proportion of hatchery- and natural-origin adults contributing to broodstocks has varied over 

the years, for reasons explained in the narrative, but has consistently been of USR stock. The 

original program strategy was more similar to what today managers refer to as an integrated 

program. Actual SARs experienced by both hatchery and natural fish were far less than those 

modeled to establish the original program strategy. Declines in all stocks as a result of poor SARs 

and ESA listing in 1992 resulted in the adaptive management shift to a segregated hatchery 

program for the harvest mitigation program. 

ISRP comment #2 from the Management and Monitoring/Evaluation Objectives section-It 

is not clear how the actions in this program contribute to the objective “restore and maintain 

natural populations of Chinook salmon in the USR,” or how the program is being implemented to 

“minimize the impact of the hatchery program on the natural Chinook populations in the USR.” 

IDFG Response to Comment #2-Additional detail was added to the report to clarify 

“management objectives” for the hatchery and natural populations. The statewide management 

objective is to maintain and restore natural Chinook salmon populations in Idaho. The 

management objective of the Sawtooth Fish Hatchery is to meet established mitigation goals and 

to maintain both recreational and tribal fisheries in the USR while minimizing impacts to the natural 

population. IDFG is confident that best management practices have been and will continue to be 

implemented in this program. In response to declines in natural-origin abundance the 

supplementation evaluation was implemented in 1991 to evaluate the use of hatchery strategies 

to rebuild natural populations. Other management decisions are made to reduce or minimize the 

potential impacts of hatchery fish on the natural populations, i.e. to maintain the natural 

population. 

ISRP comment #3 from the Management and Monitoring/Evaluation Objectives section in 

the introduction-The sentences on monitoring and evaluation do not identify the individual 

metrics that are being used to evaluate the various program objectives. Some are self-evident 
56 

(e.g., adult abundance, harvest) but other objectives are not (e.g., restore and maintain natural 

populations and minimize impacts). It would be helpful to identify how the information is being 

gathered. For example, are estimates of adult abundance determined from CWT data collected 

at LGD or the hatchery rack? Is there representative PIT tagging and CWT tagging? 

IDFG Response to Comment #3-As mentioned earlier, the intent of this report was to describe 

the history and performance of the hatchery program funded through the LSRCP program. While 

the statewide management objectives include maintaining and restoring the natural populations, 

the hatchery program has been managed primarily to achieve harvest mitigation objectives. An 

ongoing supplementation evaluation study that is funded through the BPA Fish and Wildlife 

program is evaluating the use of a supplementation strategy to increase the number of naturally 

produced adults (Bowles and Leitzinger, 1991). While we did not provide results from the ISS 

evaluation, we did provide some data (adult abundance, and life history characteristics) for the 

natural population in the USR to show the synchrony in the variability observed for the hatchery 

and natural populations with respect to survival and life history characteristics. 

With regards to how information is being gathered, a key metric provided in this review that allows 

the monitoring of production and productivity is the estimate of annual adults abundance by age 

(prior to human exploitation). For the hatchery population, estimates are derived by summing up 

returns to the hatchery trap, escapement estimates (above and below the weir), and terminal and 

mixed stock harvest estimates. Determination of age is based on the recovery of CWTs in the 

escapement and in fisheries. For the natural population, annual adult abundance estimates by 

age are derived from summing up escapement estimates from spawning ground surveys and 

redd counts and the collection of biological data from carcasses. 

ISRP comment #4 from the Broodstock History section in the introduction-This section 

notes that broodstock collected in 1981 (and 1982) likely included adults from Rapid River smolts 

released into the upper Salmon River in 1979. It appears to be appropriate and necessary to 

provide an expanded explanation of Chinook salmon smolt releases in the upper Salmon River in 

the years preceding the development of this program. 

IDFG Response to Comment #4-Additional detail was added to the Broodstock History section 

to address this comment. 

ISRP comment #5 from the Status of the Natural Population section in the introductionAdditional specific details would enhance this section. The section states that the USR mainstem 

is part of a USR major population group that has nine independent populations. The sponsors 

should identify the ESU, the names and number of MPGs in the ESU, and then name USR MPG 

independent populations, and provide a map with their geographic distributions. There should be 

a description of where the USR hatchery program interacts with other spring Chinook populations, 

and the nature of the interaction. For example, genetic interactions may occur in tributaries where 

hatchery fish stray. It would be helpful to include a figure showing the trends in abundance of 

natural stocks and the viability assessment/recovery plan thresholds for viability. 

IDFG Response to Comment #5-We agree that such detail is informative. This document 

describes the history and performance of the hatchery program. The natural program status 

information and potential impacts of the hatchery program on natural populations are described in 

NOAA-Fisheries Draft Recovery Plan (), http://www.idahosalmonrecovery.net), NOAA Status 

Reviews (http://www.nwr.noaa.gov/ESA-Salmon-Listings/5-yr-review.cfm) and the SFSR Hatchery 

and Genetic Management Plan (http://www.fws.gov/lsnakecomplan/Reports/HGMPreports.htm). 
57 

ISRP comment #6 from the Data section-Methods were not described, but key metrics were 

presented. Greater detail, or references to key documents where the methods are adequately 

described, would be of benefit to the report. 

IDFG Response to Comment #6-Detailed descriptions of the methods used to estimate the 

metrics presented are described in the IDFG annual Monitoring and Evaluation Reports and are 

available from IDFG. 

ISRP comment #7 from the Data section-An explanation of how adults at LGD are partitioned 

into the different Snake/Salmon river MPGs and independent populations; whether they are these 

based on CWT or PIT tag data, and the precision of the estimates would improve the report. How 

robust are the estimates? 

IDFG Response to Comment #7-The estimated returns to Lower Granite dam that we provided 

were developed by summing the hatchery returns, escapement data and the harvest information. 

Information to directly estimate escapement by stock at Lower Granite dam was not available for 

the time series presented in this report. 

ISRP comment #8 from the Key Findings section-Like many of the LSRCP hatcheries, the 

USR hatchery has made admirable progress over its 26-year history toward solving in-hatchery 

production problems and achieving within-hatchery survival, and occasionally, production goals, 

depending upon broodstock availability. The mixed pedigree of the broodstock and the shifting 

nature of the supplementation strategy (from segregated to integrated stepping-stone over the 

last few years) create uncertainty about what we can expect to learn from the USR hatchery 

program, as well as uncertainty about its future performance. A constantly shifting program 

becomes difficult to track and assess due to shifting goals and shifting data baselines. 

IDFG Response to Comment #8-We believe that there was some confusion about the history of 

the broodstock and the broodstock management of this program that was likely due to an 

insufficient amount of information we provided in the Broodstock History section of the initial 

report. We have since added detail to this section that better describes the broodstock and 

management strategy. This is also addressed in our response to the ISRP Comment #1 above. 

To reiterate, the management strategy from the onset of this program has been focused on 

mitigating for lost harvest opportunity. During the brood years 1991-2002, a statewide 

supplementation experimental design was conducted to evaluate the utility of using a 

supplementation strategy to increase the number of naturally produced adults. A portion of the 

production capacity for the Sawtooth Fish hatchery program was dedicated for this effort. During 

this period, integrated broodstock was differentially marked from the segregated mitigation 

production. This marking strategy allowed for the evaluation of both broodstock components. 

ISRP comment #9 from the Key Findings section-It would be helpful if the data reporting were 

summarized as explicit statements reflecting the managers’ self-evaluation of how well the 

program is achieving the objectives established in the background. 

IDFG Response to Comment #9-Narrative was added to the Summary section to address this 

comment. 

ISRP comment #10 from the Key Findings section- 
58 

Smolt Survivals. Why is release to LGD survival higher here for natural versus hatchery smolts, 

a pattern that is opposite that for the South Fork? 

Adult timing. The high degree of synchrony of hatchery and natural Chinook return timing 

suggests that time cannot be used to reduce bycatch of natural Chinook. Harvests of hatchery 

Chinook were presented (Note: two Figure 10s were shown). How many natural Chinook were 

harvested? 

Straying. Are the presented values the percentage of hatchery fish on the spawning grounds or 

fraction of hatchery return that were found in streams? If the former, it would be good to present 

information on the locations sampled and level of effort. If the former, it is surprising that only 

0.59% of the spawners were hatchery origin given that hatchery fish tend to stray, harvest rates 

are low, and natural fish abundance is very low. 

IDFG Response to Comment #10- 

Smolt Survival-We have observed higher rates of survival from release to Lower Granite Dam 

for releases from other hatcheries relative to natural-origin smolts in the same area even though 

SARs for hatchery releases are consistently lower than those for natural-origin smolts. There 

appears to be some advantage gained in the hatchery environment that favors early survival 

subsequent to release and is likely associated with hatchery fish over wintering in a relatively 

benign environment and the additional energy reserves gained from artificial feeding prior to 

release. Because SARs of natural fish are consistently higher, this advantage at some point is 

lost. Why we see increased early survival (release to Lower Granite) relative to natural smolts in 

one hatchery group and not another could be the focus of future evaluations and investigations. 

At this point in time, one hypothesis might be that there is a time/distance component to postrelease survival of hatchery smolts. The upper Salmon River smolts, because of their longer 

migration distance, may have experienced this effect before arriving at LGD whereas the SFSR 

fish may not be subject to the effects until after passing LGD. 

Adult Timing-this issue is not isolated to the USR. Run timing of all our hatchery stocks show a 

high degree on synchrony with natural returns. All recreational fisheries in Idaho are mark 

selective so there is no bycatch with the exception of catch and release mortality. All Chinook 

salmon fisheries are managed not to exceed take limitations established through consultation with 

NOAA Fisheries. 

Straying-The stray rates we report represent the fraction of the entire return that strayed from the 

USR. As noted in the report, this is considered a minimum estimate because there are places that 

fish could stray where they would not be recovered. However, for the USR hatchery program, 

representative tagging with CWTs has been used from the inception of the program and intensive 

spawning ground surveys are conducted in the USR drainage, throughout Idaho, and the Snake 

River basin. If straying of USR hatchery fish was significant, CWT recoveries would likely reveal 

this. Through the implementation of a PBT marking program currently underway, any stray 

recovered from this program would be identifiable (i.e. PBT would result in a 100% tagging rate). 

ISRP comment #11 from the Outlook and Recommendations section-The TRT concluded 

that the natural population was not viable. The “Summary and Outlook for the Future” section of 

the written report describes in broad brush the future direction of the program including the 

implementation of Parental Based Tagging (PBT), which, along with CWTs, will be used to 

monitor catch contribution and stock identification. This section should also include a brief 

summary of the findings from the USFWS hatchery review and the HSRG review, and how the 
59 

program is addressing those findings. The project sponsors also indicate that development of an 

HGMP is underway. It is our recommendation that the USR HGMP be reviewed by the ISRP or 

an equivalent body when it is available. 

IDFG Response to Comment #11-The major programmatic recommendation from the HSRG 

was the implementation of the integrated broodstock which is also consistent with the approach 

recommended by the USFWS Hatchery Review Team (HRT). Responses to all of the HSRG and 

HRT comments and suggestions are in the draft HGMP. The draft is available on the LSRCP 

website: http://www.fws.gov/lsnakecomplan/Reports/HGMPreports.htm. 

ISRP comment #12 from the Outlook and Recommendations section-The Summary section 

also describes the integrated stepping-stone approach to supplementation that includes 

maintaining two broodstocks (integrated and segregated). Returns from the integrated brood will 

be used to supplement the natural-origin population above the hatchery weir and produce the 

next generation of integrated broodstock. Weir and broodstock management will be based on a 

sliding scale approach. There is text indicating that this program will initiate supplementation 

above the existing weir. The management and monitoring of that program should be summarized. 

IDFG Response to Comment #12-The management and monitoring for this program is 

described in the draft HGMP mentioned above. 
60 

CLEARWATER RIVER SPRING CHINOOK SALMON 

Brian Leth, John Cassinelli, Shane Knipper 

Idaho Department of Fish and Game 

1414 East Locust Lane, Nampa, Idaho 

BACKGROUND 

The Clearwater River spring Chinook salmon program was established to provide mitigation for 

losses of spring Chinook salmon associate with the construction and operation of the four lower 

Snake River hydroelectric dams. Infrastructure for this program includes a rearing hatchery and 

three satellite facilities used for adult trapping and broodstock collection. The Clearwater Fish 

Hatchery is located on the North Fork Clearwater River in Ahsahka, Idaho and was completed in 

1992. The Powell satellite facility is located on the upper Lochsa River and was completed in 

1989. The Red River satellite is located on the upper Sour Fork Clearwater River and was 

completed in 1976 as part of the Columbia River Fisheries Development Program and was 

updated in 1986 as part of the LSRCP mitigation program. The Crooked River satellite facility is 

located on Crooked River in the South Fork Clearwater River and was completed in 1989. The 

relative locations of the hatchery and three satellite facilities are shown in Figure 1. The Lower 

Snake River Compensation Plan (LSRCP) adult mitigation goal for the Clearwater Fish Hatchery 

is 11,900 adult Chinook salmon above Lower Granite Dam (LGD) and 47,600 adults available for 

downriver (Columbia and lower Snake rivers) harvest. The original smolt release goal of 1.4 

million yearling smolts was based on a 0.87% smolt-to-adult survival rate applied to the LGD adult 

mitigation objective. The distribution of the release goal is 700,000 smolts at Red River, 335,000 

smolts at Crooked River, and 335,000 smolts at Powell. However, the current juvenile release 

from Clearwater Fish Hatchery is 2.335 million smolts and 300,000 parr. The distribution of the 

actual release is 235,000 smolts at Clear Creek, 400,000 smolts to the lower Selway River, 

400,000 smolts to Powell, 1.1 million smolts to Red River, 200,000 smolt transferred to the Nez 

Perce Tribal Hatchery, and 300,000 parr to the upper Selway River. 
61 

MANAGEMENT AND MONITORING/EVALUATION OBJECTIVES 

Statewide management objectives include restoring and maintaining natural populations of 

Chinook salmon in the Clearwater River. Management Objectives for the Clearwater Chinook 

salmon hatchery program are to meet the LSRCP adult mitigation objectives, to restore and 

maintain recreation and tribal Chinook salmon fisheries, and to minimize the impact of the 

hatchery program on the natural Chinook salmon production in the Clearwater River. Monitoring 

and evaluation (M&E) objectives for the Clearwater River program include monitoring production, 

productivity, and life history characteristics of hatchery and natural populations and to evaluate 

broodstock and rearing strategies to increase and maximize adult returns. M&E activities in the 

Clearwater and South Fork Clearwater rivers are a cooperative effort between the Idaho 

Department of Fish and Game (IDFG), the Nez Perce Tribe (NPT), and the U.S. Fish and Wildlife 

Service. 

BROODSTOCK HISTORY 

The construction of Lewiston Dam in 1927 on the Clearwater River four miles upstream of the 

mouth virtually eliminated natural populations of Chinook salmon. Adult passage improvements 

were made in the 1940’s and the dam was removed in 1973. In addition, Harpster Dam was 

constructed on the South Fork Clearwater River (SFCR) in 1910 and blocked all passage of fish 

into the upper reaches of the South Fork Clearwater River. That dam was removed in 1963. 

Reintroduction efforts began in the 1950’s and ramped up in the 1970’s. These reintroductions 

consisted primarily of Rapid River stock but also included some Dworshak, Kooskia, Carson, and 

Cowlitz stocks. Since the mid 1990’s, localized SFCR and Powell stocks have been collected at 

the satellite facilities. In years were there are not enough returns to meet production, backfilling 

occurs between the two stocks or from Rapid River Fish Hatchery. Because not all hatchery 

releases were differentially marked or tagged until brood year 1991, de facto 

integration/supplementation occurred in the Clearwater River until 1995. From 1995 to present, 

hatchery releases have been differentially marked and production broodstock have been 

segregated. From brood year 1991-2002, the Idaho Supplementation Study (ISS) research study 

was conducted in the Clearwater River basin to assess the utility of using supplementation as a 

tool to increase the number of returning adults. Broodstock for this supplementation research 

included both hatchery and natural adults and accounted for approximately 15-20% of the 

hatchery production capacity. Since 2002, all hatchery production has utilized only segregated 

hatchery-origin broodstock. The natural populations of Chinook salmon in the Clearwater River 

are not part of the Snake River spring/summer ESU and are not included in the ESA listing. 

 

IN-HATCHERY AND POST RELEASE SURVIVAL 

Broodstock performance for the life of the hatchery has been good with mean prespawn mortality 

rates ranging from 5-12% for both males and females across both stocks. In-hatchery survival 

has been high across the history of the program with a mean survival of 85% (min- 64%, max98%) (Figure 2). 
62 

Juvenile releases from Clearwater Fish Hatchery have fluctuated greatly over the history of the 

program from a low of 14,300 smolt/parr released from brood year 1991 to a high of over 

3,680,000 smolt/parr released from brood year 2001 (Figure 3). Over the last ten years, managers 

have prioritized increasing the Chinook salmon smolt release numbers at Clearwater Hatchery in 

an effort to increase the number of adult returns. Some of the rearing space that was initially 

programmed for steelhead rearing has been prioritized for Chinook salmon. Prior to brood year 

2002, a significant proportion of the total production at Clearwater Hatchery was composed of 

subyearling parr and presmolt releases. Low observed post-release survival rates from these 

releases prompted the discontinuation of this release strategy in favor of yearling smolts. One 

exception is a 300,000 parr release in the upper Selway River that is not accessible by ground 

transport in the spring to allow a smolt release. 

 

Passive Integrated Transponder (PIT) tags have been used to estimate survival from release to 

LGD for this program since the early 1990s. Estimated survival for hatchery-origin juveniles from 

release to LGD has ranged from 36-86% for the Powell stock and 37–74% for the SFCR stock at 

Red River and Crooked River. Survival of subyearling parr is considerably lower and has ranged 

from 0.06 – 12%. 
63 

Estimated survival of natural-origin smolts has ranged from 23 – 84% across the basin (Figures 

4 and 5). 

 

The number of adults surviving annually to the Columbia River mouth for this hatchery program 

has been highly variable across the history of the program. Estimates of the total number of adults 

back to the Columbia River mouth, by return year, have ranged from 15 (1 adult, 14 jacks) fish in 

return year 1995 to 11,092 (9,864 adults, 1,228 jacks) in 2008 (Figure 6). The record return in 

2008 for this program represents 18.6% of the total mitigation objective. 

Adult returns to LGD ranged from 14 (1 adult, 13 jacks) fish in return year 1995 to 6,902 (5,680 

adults, 1,222 jacks) in 200 (Figure 7). Across the life of the Clearwater Fish Hatchery program, 

the LSRCP mitigation goal at LGD has ever been reached. 
64 

Smolt-to-adult survival (SAS) and smolt-to-adult returns (SAR) rates were very low for brood years 

through the early-1990s and has ranged from (0.06-1.2%) over the entire history of the program 

(Figures 8 and 9). The modeled 0.87% SAR to LGD was only achieved in two years (Figure 9). It 

is important to note that the modeled 0.87% SAR is post downstream harvest and is based on 

the assumption there would be a 4:1 catch to escapement ratio to LGD. The SAS necessary to 

achieve the total mitigation goal is 4.35%. To date, the highest observed SAS for this program is 

1.2% for brood year 1997. 

 

LIFE HISTORY CHARACTERISTICS OF THE HATCHERY AND NATURAL POPULATIONS 

The average (1997-2009) cumulative adult run timing of hatchery- and natural-origin fish to the 

SFCR trap is similar (Figure 10). Run timing of hatchery-origin Chinook to the Powell Satellite 

facility is similar to that at the SFCR. The Powell Satellite trap is on Walton Creek, a small tributary 

to the Lochsa River. There is no natural population in Walton Creek so no comparison of naturalorigin Chinook salmon run timing is provided for the Powell stock. 

. 
65 

Figures 11 and 12 show the estimated age composition of the adult returns to the SFCR and 

Powell traps for brood years 1993-2004. Over this period, there were no significant trends in age 

composition for either the hatchery or natural populations in the SFCR. For the Powell stock, a 

significant increase in the proportion of age-3 hatchery fish was observed and was driven primarily 

by the brood year 2004 return. The aggregate natural-origin population at LGD is also shown in 

both Figure 11 and Figure 12 and shows synchrony with regards to annual fluctuations of the age 

compositions indicating that environmental conditions are likely a key driver for this life history 

metric. Similar to other hatchery programs, hatchery-origin adults from the SFCR and Powell 

return younger than the natural populations for most years. 

 

Length-at-age of male and female hatchery-origin fish returning to Powell and both hatchery- and 

natural-origin male and female returns to the SFCR are displayed in Figures 13 and 14. No 

significant trends in length-at-age were detected for any of the age classes from either the SFCR 

or Powell hatchery stocks. However, regression slopes of all age/gender combinations for the 

SFSR hatchery stock were negative. For the aggregate natural-origin population at LGD, 

regression slopes for length-at-age were negative for all age/gender combinations and were 

significant for age-4 males and age-5 females. 
66 

 

In addition to the above life history characteristics, we also looked at spawn timing and fecundity 

of hatchery-origin Clearwater River Chinook salmon over time. For brood years 1990-2006 no 

significant trend in mean spawn time was observed for either stock. Mean fecundity for Powell 

and SFCR stocks is 4,279 (range: 3,456-5,259) and 4,194 (range: 3,459-5,249) respectively. A 

significant negative trend in fecundity for the Powell stock was observed. Annual fluctuations in 

fecundity are generally associated with varying proportions of two and three ocean females in the 

adult return. 

CONTRIBUTION OF HATCHERY FISH TO FISHERIES 

The estimated number of Chinook salmon harvested in the Columbia River and in the Snake 

River below LGD has ranged from zero in some years to 4,173 in 2008. The estimated harvest in 

2008 represents an exploitation rate of 42%. Within Idaho, tribal fisheries have occurred on the 

Clearwater River sporadically throughout the history of the program though data available at the 

time of this report was very limited. Tribal harvest estimates have ranged from zero to 467 Chinook 

salmon (Figure 15). The first sport fishery since the inception of the hatchery program occurred 

in 1997 and with the exception of 1999, sport fisheries have occurred every year since then. The 

estimated number of fish harvested annually has ranged from zero (for fisheries in the Lochsa 

and SFCR) in 1997 to 7,033 fish in 2001 (Figure 15). For the period 1997-2010 average angler 

effort for recreational Chinook salmon fisheries in the Clearwater River drainage has averaged 

90,343 angler hours per year (range: 7,227 - 307,681) not including effort for the fishery in the 

North Fork Clearwater River which is associated with production from Dworshak National Fish 

Hatchery. It should be noted that effort estimates provided above include effort associated with 

fish released from Kooskia and Nez Perce Tribal fish hatcheries due to the mixed stock nature of 

the fishery. 
67 

Stray rates observed for the Clearwater Fish Hatchery stocks have been higher than observed in 

other Chinook salmon hatchery programs in Idaho but are still less than 6% for most years. The 

above average stray rates observed in areas upstream of LGD are most likely associated with 

the release strategy used for most years in the program that included a significant proportion (up 

to 100% is some years) of the total production devoted to subyearling parr and presmolt releases. 

Since brood year 2004, 90% of the releases have been full term yearling smolts. Stray rates in 

the areas below LGD have ranged from 0.0-5.8% but were below 2% for most years. It should be 

noted that estimated stray rates are minimum estimates as recoveries of strays downriver are 

typically opportunistic at hatchery traps and on spawning grounds. There are other areas where 

strays might not be recovered throughout the basin, but overall straying is still expected to be very 

low. 
68 

Determining the beneficial use of Clearwater Fish Hatchery Chinook salmon that escape fisheries 

and return to the satellite traps is a collaborative effort between IDFG and the tribes. The first 

priority for fish returning to hatchery traps is to meet broodstock needs with a representative take 

across the run. In addition, an effort is made to maximize harvest opportunity for both sport and 

tribal fisheries by recycling fish through the fisheries when deemed appropriate. Fish from the 

traps may also be transferred to the tribes for ceremonial and subsistence (C&S) use, given to 

food banks, or outplanted for natural spawning within the Clearwater basin. 

Overall, disease has not been a major issue at the Clearwater Fish Hatchery and there have been 

few significant losses due to disease. Early on, Ichthyophthirius multifiliis (Ich) was more 

prevalent, but it has not been an issue since 2000. Similarly to other anadromous hatchery 

programs in Idaho, Clearwater Hatchery employs a culling program to reduce the incidence of 

Bacterial Kidney Disease (BKD). This culling method has proven to be so effective at limiting BKD 

at the Clearwater Fish Hatchery that medicated erythromycin feedings are no longer used. 

SUMMARY AND OUTLOOK FOR THE FUTURE 

The Clearwater River program will continue to be managed to meet the management objectives 

outlined in this report. Efforts will continue to be made to restore and maintain sport and tribal 

fisheries. There has been significant rebuilding of these fisheries since 1997 but future fisheries 

will be highly dependent on post release survival. In general, we have observed consistently high 

survival during hatchery culture, highly variable post-release survival, poor survival of subyearling 

releases, and an upswing is post-release survival since the mid 1990s. To facilitate achieving the 

mitigation objective, the development of a summer run of Chinook salmon has been initiated in 

the SFCR with plans to expand this program to the Selway River. There is anecdotal evidence to 

suggest that wild populations in the Clearwater River contained a summer run life history. The 

hope of this program is to expand harvest opportunity and potentially increase survival rates for 

this hatchery program. 

The outlook for M&E includes continued monitoring of hatchery production and productivity. This 

will be accomplished using a variety of tools including the continued use of Coded Wire Tags 

(CWT) and PIT tags and the implementation of Parental Based Tagging (PBT). PIT tags have 

been, and will continue to be used to estimate adult survivals back to LGD, monitor returns for inseason fisheries management, and to look at migration timing and inter-dam conversion rates. 

PBT, along with CWTs, will be used to monitor catch contribution and stock identification. Future 

M&E plans also include continued monitoring of natural populations throughout the basin both 

above and below weirs where appropriate. 

The Clearwater River Chinook salmon program will continue to support both harvest and 

conservation objectives, mitigate for lost sport and tribal fishing opportunity, and expand 

coordination efforts between state, tribal, and federal managers. Through the development of a 

Hatchery Genetic Management Plan (HGMP), managers are incorporating both current and 

emerging science and have incorporated suggestions generated through the Hatchery Scientific 

Review Group (HSRG) and Hatchery Review Team (HRT) processes. 

ACKNOWLEDGEMENTS 
69 

We would like to thank to Jerry McGhee and the dedicated staff at the Clearwater Fish Hatchery 

for their continued efforts in maintaining a successful hatchery program in the Clearwater River. 

We would also like to thank the many cooperators in the basin that help to make this a successful 

program including staff at the IDFG regional office in Lewiston, the Pacific States Marine Fisheries 

Commission, IDFG harvest monitoring crews, the monitoring and evaluation staff from the Nez 

Perce Tribe and the US Fish and Wildlife Service. Lastly, we would like to thank the staff at the 

LSRCP office in Boise, ID for providing funding and support to maintain this valuable program. 

IDFG RESPONSE TO THE ISRP COMMENTS-Clearwater River 

We would like to thank the members of the ISRP for their review of the program summary and 

oral presentation and suggestions for improving the quality of the report. In several sections of 

the report, we have added detail to address some of the questions and comments that were made 

by the ISRP. Below are direct responses to the individual comments made by the ISRP. 

ISRP comment #1 from Key Findings section-The shift to native broodstock and to releases of 

full term smolts, rather than parr, has been justified based on post-release survival performance; 

however, the management change appears to have also resulted in increased production of jacks. 

IDFG Response to Comment #1-We do not believe that the data supports a conclusion that the 

transition to full term smolt releases has increased the proportion of returns for a brood that are 

jacks (i.e. that it has increased the jacking rate). There does appear to be synchrony in “jacking” 

rates across hatchery programs and with natural populations that would indicate variation in 

environmental conditions as being a key contributor. There is no doubt that hatchery fish are 

returning younger-at-age than natural populations and may be related to size at release. However, 

we feel that the transition to a full term smolt release strategy was justified. The program would 

not be sustainable if we relied on a subyearling release strategy. 

ISRP comment #2 from Key Findings section-Although performance of fish in the hatchery is 

measured based on survival, and in-hatchery survival rates appear to be adequate to the smolt 

stage (generally 70% and above except for the South Fork in 2008), survival as measured by 

SASs and SARs is not. With low SAR and SAS results, the hatchery is not producing adult returns 

that meet its mitigation goals. The program is averaging 5% of mitigation goals to the mouth of 

the Columbia and a maximum success of only 18.5% of its mitigation goals. 

IDFG Response to Comment #2-We agree that post release survival rates have prevented the 

program from reaching the numeric mitigation goals; this is true for all the LSRCP Chinook 

programs. Since 1999, escapement to Lower Granite dam of Clearwater Hatchery origin Chinook 

salmon has averaged 43% of the mitigation goal to Lower Granite Dam. Even though mitigation 

goals have not been reached, since 1997 this program has made a significant contribution 

towards restoring recreational and tribal fisheries in Idaho. 

ISRP comment #3 from Key Findings section-The ecological and genetic impacts of the 

programs on wild fish are shown primarily through comparisons of life history characteristics 

between hatchery and wild fish. Although in the presentation it was concluded that impacts to wild 

fish were not significant, we note that the percentage of jacks among hatchery fish returns has 

increased in BY 2002 and 2003, and that returns of jacks were higher in 2007, 2008, and 2009, 

and returns of 3 SW fish were lower. 
70 

IDFG Response to Comment #3-With regards to impacts on wild populations, we don’t think we 

concluded that there were no significant impacts of hatchery fish on natural fish. As we compared 

life history characteristics of hatchery and natural populations, we indicated for some metrics there 

were not significant trends and that there was synchrony in the variability for hatchery and natural 

fish. This synchrony indicates that environmental variation likely influences expression of those 

characteristics. It is also important to keep in mind that wild populations in the Clearwater River 

basin were extirpated by the construction and operation of the Lewiston Dam and that current 

natural populations are a direct result of supplementation from the hatchery program. 

ISRP comment #4 from Key Findings section-Survival rates of smolts have declined from the 

mid-1990s as numbers of smolts released has increased. The causes of this undesirable pattern 

are not identified. 

IDFG Response to Comment #4-For the releases associated with the Powell broodstock in the 

Lochsa River, survival of both hatchery and natural smolts are similar or above the rates observed 

in the mid-1990s. For the South Fork Clearwater River, survival rates of hatchery smolts are 

similar to rates observed in the mid 1990s. Since 2004 the survival gap between hatchery and 

natural smolts to Lower Granite Dam is larger than observes in previous years. We have not 

identified a cause for this change and are unsure if it will result in a long term trend. 

ISRP comment #5 from Key Findings section-Evaluation of supplementation could be 

improved. In particular, it was not clarified why survival rates of wild smolts exceeded hatchery 

smolts in 1994-1996, but not in any recent years except 2007 (by a narrow margin). Has the 

quality (or size) of hatchery smolts risen sufficiently or is there some unknown interaction of 

released fish and wild fish? 

IDFG Response to Comment #5-Over the history of the program, there have been a few years 

when the survival of natural smolts have exceeded that of hatchery smolts for the South Fork 

Clearwater releases and several years where they were similar. Across all Chinook salmon 

hatchery programs, we generally observe higher survival rates (from release to Lower Granite 

Dam) of hatchery fish relative to adjacent natural populations. We also observe that SARs for 

natural fish are almost always higher than those observed for the hatchery populations. The 

advantage that hatchery fish demonstrate immediately after release is lost at some point. 

ISRP comment #6 from Key Findings section-It is unclear why survival to Lower Granite Dam 

is only 60-70%, whereas it is higher for releases from Powell. What are the primary factors 

affecting survival of both the hatchery and wild smolts, and how well is that understood? 

IDFG Response to Comment #6-The Powell stock has generally demonstrated one of the 

highest juvenile survival rates across all our hatchery programs in both the Salmon and 

Clearwater Rivers. Survival from release to Lower Granite dam in the 60-70% range is good based 

on all historic data. Regarding explanations of why survival is variable form one release site to 

the next, one thing that is apparent is the relationship between distances (from release site to 

Lower Granite Dam) and survival. While distance does explain some of the variation, other factors 

likely include several environmental factors (temperature, flow, water quality etc.), as well as fish 

size and condition but we have not described these relationships or interactions. 

ISRP comment #7 from Key Findings section-No information was provided on the possibility 

of residualization of precocious males (mini-jacks) from these increasingly large smolt releases 

and potential effects on wild fish. This issue may deserve study and discussion among LSRCP 

entities. 
71 

IDFG Response to Comment #7-The ability to monitor the abundance of mini-jacks historically 

has been limited to observed fish the adults traps during the adult migration. More recently PIT 

tags have been used to estimate the number of fish returning as mini-jacks. As with other stocks 

of hatchery fish released, we do observe a small fraction (approximately 0.2%) of the smolt 

release that return as mini-jacks. 

ISRP comment #8 from Outlook and Recommendations section-The low SARs indicate that 

existing approaches for rearing and releasing smolts do not result in fish capable of returning as 

adults to the Columbia River and Lower Granite Dam in numbers sufficient for meeting existing 

LSRCP mitigation goals. Under existing conditions, the long-term outlook for successfully meeting 

project area mitigation objectives is not favorable and appears unlikely. The overall mitigation 

goals of returning 59,500 fish to Columbia River mouth and 11,900 adults above Lower Granite 

do not appear achievable within the foreseeable future. No actions proposed seem to provide 

much likelihood of an improved outlook. The main benefit of the program as of 2010 has been to 

provide modest state recreational and tribal harvest fisheries, which, from any perspective beyond 

satisfying immediate harvest demands, do not seem justifiable unless it is shown that those fish, 

if not harvested and allowed to spawn, would result in reproductive success leading to a density 

dependent suppression of the natural production potential of the basin. The genetic and long-term 

fitness implications of the harvest are not evaluated. A science-based plan for deciding the most 

goal-oriented disposition of returning adults (harvest, allow to spawn naturally, broodstock, etc.) 

was not provided. A key question is how many fish should be used to meet longer-term mitigation 

goals before immediate harvest is pursued. At present, the only realistic prognosis for this 

program is to provide the modest fishery well below its mitigation goals. 

IDFG Response to Comment #8-We agree that given the current observed post release survival 

rates we are not likely to meet the LSRCP mitigation goal. However this program has contributed 

significantly to the goal of restoring and maintaining recreation and tribal fisheries in Idaho since 

1997. Management of the disposition of adult returns is prioritized to meet broodstock objectives. 

Hatchery-origin returns in excess of broodstock needs are prioritized to meet harvest mitigation 

objectives. A component of the total Clearwater Fish Hatcher rearing capacity has been utilized 

for evaluation of supplementation effectiveness as part of the ISS experimental design since 

Brood Year 1991. Results from that evaluation will be used to help guide future supplementation 

activities in the Clearwater River. 

ISRP comment #9 from Outlook and Recommendations section-In addition, it would be useful 

to have the information presented in terms of the Interior Columbia River Technical Recovery 

Team (ICTRT) goals and findings on VSPs, as well as HRSG review and recommendations, and 

a description of how the program releases are justified when the these recommendations are 

considered. 

IDFG Response to Comment #9-Natural populations of spring Chinook salmon in the Clearwater 

River are not part of the Snake River ESU and are not included in the ESA listing. The ICTRT did 

not complete VSP status assessments for the populations in the Clearwater River drainage. Other 

than using the Clearwater, Dworshak, Kooskia and Nez Perce hatchery facilities in a more 

coordinated manner, the HSRG had no specific programmatic recommendations for the Lochsa 

River or the South Fork Clearwater River programs. Responses to all of the USFWS Hatchery 

Review Team (HRT) comments are in the draft HGMP. The draft is available on the LSRCP 

website: http://www.fws.gov/lsnakecomplan/Reports/HGMPreports.htm. 
72 

 
73 

SPRING CHINOOK SALMON, DWORSHAK NATIONAL FISH HATCHERY 

CLEARWATER RIVER, IDAHO 

Howard Burge and Ray Jones 

U.S. Fish & Wildlife Service 

INTRODUCTION 

Dworshak National Fish Hatchery (NFH) is located at the confluence of the main stem and North 

Fork Clearwater rivers in North-central Idaho (see map above). The Clearwater is a tributary to 

the Snake River and enters the Snake at Lewiston, Idaho approximately 40 miles downstream of 

the hatchery. Lower Granite Dam is the first lower Snake River dam that fish released from 

Dworshak NFH encounter and is located approximately 70 miles downstream of the hatchery. 

FACILITY DESCRIPTION 

Dworshak NFH was originally built in 1969 to mitigate for steelhead lost from the construction and 

operation of Dworshak Dam and Reservoir on the North Fork Clearwater River. In 1982 the 

hatchery was expanded to include spring Chinook salmon as part of the LSRCP to mitigate for 

fish loss associated with development of the lower Snake River hydrosystem. Thirty raceways 

were built to rear approximately 1.4 million spring Chinook smolts, which is what was estimated 

to meet the adult return goal. 
74 

PROGRAM GOALS 

The adult return goal for the Dworshak program is 9,135 spring Chinook to the project area above 

Lower Granite Dam. This was after an expected harvest of 36,500 in the ocean, Columbia River 

and Lower Snake River sport, tribal and commercial fisheries. The original production goal of 1.4 

million smolts was changed in 1996 to 1.05 million smolts due to a change in rearing density. 

MANAGEMENT OBJECTIVES 

Given the location on the main stem of the Clearwater River the primary objective for the 

Dworshak spring Chinook program is to provide for lost sport and tribal fishing opportunities in 

the Lower Clearwater River. Other objectives are to return adequate broodstock to meet 

production needs, to minimize impacts to natural populations in the Clearwater and downstream 

migration corridor, and to assist other production programs in the Clearwater basin. 

MONITORING AND EVALUATION OBJECTIVES 

There are several M&E objectives for the spring Chinook program including: Evaluating the 

effectiveness of the program so it can be managed adaptively; Determining the total adult return 

to assess if the program is meeting its mitigation goals; To document and communicate the 

program’s success at meeting its program and management goals; and coordination of hatchery 

production and research, monitoring, and evaluation activities. 

BROODSTOCK GENETICS 

Lewiston Dam, which was located on the Clearwater River above Lewiston from 1929 to 1972 

extirpated the historic spring Chinook run in the Clearwater River. Therefore when the spring 

Chinook program was started at Dworshak fish were obtained from a number of sources including: 

Little White Salmon (1983 & 85), Leavenworth (1983 & 86), and Rapid River (1987 - 88) 

hatcheries. Since 1989 we have primarily utilized fish returning to Dworshak as the brood source, 

with the exception of 1995 when a third of the production was from Kooskia NFH returns. It was 

the extirpation and subsequent reintroduction of non-endemic stock that prompted not listing 

Clearwater spring Chinook salmon as threatened or endangered under ESA. 

BROODSTOCK CHARACTERISTICS 

On average the adults that return to Dworshak NFH have the following characteristics: a 50:50 

ratio of adult males to females, approximately 65% of returning Chinook are 2-ocean, and the 

average size of a 2-ocean adult is 29 inches (740 mm). Spring Chinook arrive in the Clearwater 

in May and will continue to come into the hatchery until August, they are held until spawning, 

which takes place in late August to early September. The average pre-spawn mortality from 1995-

2010 was 3.1% (range 1.6 – 6.0%). 
75 

JUVENILE PERFORMANCE 

Incubation and rearing lasts approximately 20 months, followed by direct release from the 

hatchery into the North Fork Clearwater River in late March. Eyed egg-to-smolt survival from 

1998-2009 averaged 83.2% (range 66.6 – 97.8%) and smolt-to-Lower Granite Dam survival from 

1998-2009 averaged 79.6% (range 69.1 - 85.3%) based on SURPH model estimates. 

RESULTS 

For the remainder of the paper results will be provided only for the last 12 to 16 years, depending 

on whether it’s Brood Year or Return Year data. Earlier data were reported on in the last LSRCP 

review (Burge and Jones 1998), also in the 1980’s the returns were low when the program was 

building and then during the mid-1990’s Chinook returns throughout the basin were depressed. 

SMOLT RELEASES 

Dworshak generally meets, or is close to, its release goal of 1.05 million smolts, Figure 1. The 

exception was 2001, when too few adults returned in 1999 to meet brood needs and there were 

no extra eggs in the basin to backfill the program. 

Figure 1. Dworshak NFH spring Chinook salmon releases, 1998 – 2009, the release goal of 

1.05 million is indicated by the horizontal line. 

ADULT RETURNS 

Figure 2 shows the adult returns to the Dworshak NFH rack (top graph), the project area above 

Lower Granite Dam (middle graph), and to the mouth of the Columbia River (bottom graph). These 
76 

data include fish collected and estimated harvest in all fisheries, but do not include the unharvested and un-collected fish that remained in the river, so they are a conservative estimate of 

total return. As displayed we typically return enough to meet brood needs (except for 1999 as 

mentioned above). However, we rarely meet the LSRCP project area goal of 9,135 and have 

never come close to meeting total return goal of 45,635. 
77 

Figure 2. Adult returns to the Dworshak NFH rack (top), the project area above Lower 

Granite Dam (middle), and to the mouth of the Columbia River (upper), 1996-2009. 

ADULT SURVIVAL AND REPLACEMENT 

Figure 3 indicates the total smolt-to-adult survival (SAS) to the mouth of the Columbia River and 

the smolt-to-adult return (SAR) to the project area for Dworshak Chinook. It was estimated that 

0.87% was needed to meet the LSRCP goal to the project area, but 4.3% return would be needed 

to meet the total return goal. Figure 4 displays the effectiveness of the Dworshak program relative 

to replacement (1.0). Progeny-to-parent ratio has been well above 1.0, averaging 8.2 to the 

project area and 10.1 overall from 1994 to 2003. 
78 

Figure 3. Smolt-to-adult survival to the Columbia River and smolt-to-adult return to above 

Lower Granite Dam for Dworshak NFH spring Chinook salmon, 1994-2003. 

Figure 4. Progeny-to-parent ratio, total return and above Lower Granite Dam for Dworshak 

NFH spring Chinook salmon, 1994-2003. 

 
79 

STRAYING 

Figure 5 presents the overall stray rates for Dworshak Chinook from 1996 to 2006. Straying is 

defined here as anything that is captured outside the normal migration route and includes jacks 

and adults. The data is further broken down into four categories, above and below McNary in the 

Columbia River, and above and below Lower Granite in the Snake River. Strays above Lower 

Granite Dam are typically fish captured above Dworshak NFH. Stray rates for 1996 – 1999 

averaged 13.8%, whereas from 2000 – 2006 they averaged 2.3%, this significant drop is attributed 

to two changes in the production program for fish released in 1998. First was a change in size of 

release from 12-14 fish/pound to ~20 fish/pound and the second change was time of release, we 

began releasing fish 2 weeks earlier, from April 11 to March 28, based on results from a time of 

release study (Jones and Burge 2002). 

Figure 5. Stray rates for Dworshak NFH spring Chinook salmon in the Columbia and Snake 

rivers, 1996 - 2006. 

FISH HEALTH 

Dworshak began segregation and culling of high Bacterial Kidney Disease (BKD) Chinook in the 

late 1980s and this has proven very successful at reducing losses to BKD. Currently to help 

control BKD all females spawned are tested for BKD using ELISA. Also eggs from each female 

are tested and those with an ELISA Optical Density greater than 0.25 are culled. Females are 

injected with erythromycin prior to spawning and juveniles are monitored by ELISA. Due to this 

aggressive BKD program we have not seen any high ELISA values in juveniles for the last 8 years 

and only 1 low value in the last 5 years. Occasional outbreaks of other diseases do occur and are 

treated appropriately. 
80 

HARVEST 

Harvest was examined by area, above and below Bonneville Dam in the Columbia River (Figures 

6) and in the Snake River (Figure 7) and in the Clearwater River (Figure 8). All graphs show the 

same pattern of peak harvest in 2001. 

Figure 6. Harvest of Dworshak NFH spring Chinook salmon in the ocean and below 

Bonneville Dam (upper graph) and above Bonneville Dam (lower graph), 1996-

2006. 
81 

Figure 7 demonstrates the low harvest of Dworshak Chinook in the mainstem Snake River. Also 

the reader should note that Figure 8 has a different y axis scale to show the successful harvest 

of Dworshak Chinook in the main project area of the Clearwater River. For each year beginning 

in 1997 (excluding 1999) there has been a sport fishing season for Dworshak spring Chinook 

salmon in the Clearwater River. 

Figure 7. Harvest of Dworshak spring Chinook salmon in the mainstem Snake River, 1996-

2006. 

Figure 8. Harvest of Dworshak spring Chinook salmon in the Clearwater River, 1996-2006. 
82 

Angler effort is displayed in Figure 9 and it mirrors the Chinook harvested graph in Figure 8. It 

should be noted that this also includes spring Chinook returning to other Clearwater facilities. 

Figure 9. Spring Chinook salmon sport angling effort from Lewiston, Idaho into the North 

Fork Clearwater River, 2000-2006. 

Dworshak spring Chinook salmon provide a major boost to the economy as shown in the table 

below. These data are from a USFWS study completed in 2010 and were compiled from a number 

sources including: Economic Effects From Columbia River Basin Anadromous Salmonid Fish 

Production, NWPCC Independent Economic Analysis Board 2005; Status Report: Columbia River 

Fish Runs and Fisheries 2005; 2006 National Survey of Fishing, Hunting, and Wildlife - 

Associated Recreation, USFWS, 2007; and Sportfishing in America, American Sportfishing 

Association, 2008. 

Dworshak NFH Spring Chinook 

Release Year 2006 Economic Impact

Commercial 

 Dock Sales $72,817 

 Job Income $207,051 

Recreational 

 Angling Retail $2,399,946 

 Angling Days 31,842 

 Industrial $3,817,704 

 Job Income $1,210,315 

 Federal Tax $170,472 

 State and Local Tax $152,734 

Total $8,031,039 
83 

SUMMARY 

The Dworshak spring Chinook salmon program has essentially eliminated losses to BKD as a 

result of the BKD culling program. Changing size and time of release significantly reduced 

straying. While the Dworshak Chinook program rarely meets its project area adult return goal and 

has never come close to achieving the downriver harvest goal, it has provided a sport fishery in 

13 out of the last 14 years and a tribal fishery in 21 out of the last 24 years. 

HSRG AND HRT RECOMMENDATIONS 

The Hatchery Scientific Review Group (HSRG) recommended that all salmon production 

programs in the Clearwater basin be coordinated. This is something all the co-managers have 

been working on, and since 2004 we have developed a Clearwater Basin Annual Operating Plan 

that includes all fish production in the basin. Starting in 2009 there have been weekly conference 

calls during the spring Chinook run to update managers and coordinate fish collection, harvest 

allocations, and improve communication. A fully coordinated program will take time, but the comanagers are moving in that direction. They also recommended continuing our successful BKD 

culling program; this is something we do not plan to stop. Lastly they recommended that Dworshak 

improve the water supply to address disease and temperature issues at the hatchery. This is 

something all the co-managers endorse and the funding agencies, the U.S. Corps of Engineers 

and LSRCP, are investigating options. 

The Hatchery Review Team (HRT) also advocated improving the water supply issue mentioned 

above. Additionally the HRT suggested maintaining a locally adapted stock and while Dworshak 

strives to maintain this the co-managers all agree that since this is not a conservation program 

maintaining a full program is also a priority and may occasionally require backfilling from other inbasin facilities. The HRT recommended continuing efforts to improve the facility, as well as the 

assessment, tagging, and documentation of the program, this is something we concur with and 

we will always strive for improvement of the program. 

ACKNOWLEDGEMENTS 

The authors would like to acknowledge and thank others who helped collect and analyze the data 

presented, Carrie Bretz, Idaho FRO and the Dworshak NFH crew, especially Thomas Trock. We 

also thank the Nez Perce Tribe and Idaho Dept. of Fish and Game for harvest monitoring and 

analysis and of course the LSRCP staff for support and funding for the Dworshak spring Chinook 

program. 

REFERENCES 

Burge, H. L., and R. N. Jones. 1998. Spring Chinook program, Dworshak National Fish Hatchery, 

Clearwater River Basin, Idaho. Pages 154-158 in Lower Snake River Compensation Plan 

Status Review Symposium. Unpublished proceedings by the U.S. Fish and Wildlife 

Service, LSRCP, Boise, ID. 

Jones, R. N., and H. L. Burge. 2002. The effects of release time on smolt development, migration 

time, survival, and adult returns for spring Chinook salmon. Unpublished report by the U.S. 

Fish and Wildlife Service, Idaho Fishery Resource Office, Ahsahka, ID. 
84 

USFWS RESPONSE TO THE ISRP COMMENTS-Dworshak 

Key Findings 

There were a few Key Findings we’d like to clarify: 

2. The shift to native broodstock and to release full term smolts rather than parr has been justified. 

One result, however, has been an increase in the production of jacks. 

For the Dworshak NFH spring Chinook salmon program there was no shift to native broodstock, 

as there is no native broodstock in the Clearwater River. In 1989 there was a prioritization to utilize 

returning Dworshak Chinook for broodstock, so we would hopefully benefit from any local 

adaptation. Also Dworshak has always released full term smolts, it never was a parr program. 

3. Although performance of fish in the hatchery is measured based on survival, and in-hatchery 

survival rates appear to be adequate to the smolt stage (mean 83.2%), there was little information 

presented to indicate that other aspects of smolt quality are being significantly improved upon at 

the hatchery at this time. 

We would need to know specifically what ‘other aspects of smolt quality’ the ISRP is referring to 

before we can adequately address this comment. We did present information on the BKD culling 

program and how that has significantly reduced the incidence of BKD in the spring Chinook 

production program. Also why you can always make improvements in production, significant 

improvements are hard to achieve. The recent 5 year survival to smolt stage is 87.1%, however, 

if you look at the data below you can see that it would be tough to identify where we might make 

additional improvements, especially when you factor in enumeration errors. 

Life Stage Survival 5 Yr Ave 

Green eggs to eye up 96.8% 

Eyed eggs to marking 92.3% 

Marking to smolt release 97.5% 

Overall green to smolt 87.1% 

6. The ecological and genetic impacts of the programs on wild fish are not evaluated in the 

material provided. As in the Clearwater hatchery, we note that the percentage of jacks among 

hatchery fish returns has increased in 2007, 2008, and 2009 returns years. 

Again we would need more specifics to adequately address this comment, since there are no wild 

spring Chinook salmon populations remaining in the Clearwater River. Is the concern to other 

species within the basin or wild fish outside the basin? We do evaluate the programs effects on 

ESA-listed salmonid populations in the HGMP. However, even with considerable sampling efforts 

and data collection, it would be quite difficult to demonstrate quantitatively that the hatchery 

program was really impacting wild fish populations. For example, we would have to know that 

Dworshak spring Chinook are actually spawning with wild fish to even know there is a potential 

for genetic impacts. 

Also the increase in the percentage of jacks occurred throughout the Columbia basin in 2007, 

2008, and 2009 return years not just at Dworshak or in Clearwater basin, as suggested. 
85 

Outlook and Recommendations Response 

The main benefit of the program as of 2010 (and the prognosis) is to provide continued State 

recreational and Tribal harvest fisheries well below mitigation goals. 

The LSRCP hatchery program was originally established to offset losses caused by the four 

Lower Snake River dam and navigation projects and that includes loss of State recreational and 

Tribal harvest fisheries. Dworshak NFH was included in the LSRCP program to help replace those 

loss fisheries. Since Dworshak is located in a nonproduction area and in a basin that does not 

have listed spring Chinook, it can provide fisheries. This also helps to compensate for other 

programs that cannot provide fisheries because of ESA concerns or low adult returns. 

A science-based plan for deciding the most goal-oriented disposition of returning adults (harvest, 

allow to spawn naturally, broodstock, etc.) was not provided. 

As mentioned in your Introduction paragraph ‘The hatchery is not located in a natural spawning 

area.’ Therefore the only uses for returning adults are for broodstock and harvest; any natural 

spawning above the hatchery would be considered straying. 

To an outside evaluator, the close proximity of Clearwater and Dworshak LSRCP programs 

suggests that the programs should be combined and administered jointly with overall goal-setting 

process. 

The two programs, while not jointly administered, do coordinate closely and together the two 

programs mesh very well. Coordination occurs formally through a joint Clearwater Basin Annual 

Operating Plan (AOP) and also in-season with weekly conference calls. The programs also 

coordinate closely on water issues since they both utilize water from a Dworshak reservoir 

pipeline. Dworshak NFH is not located in a production area and has a ladder at the facility, 

whereas Clearwater Hatchery does not have a ladder, but operates satellite facilities located in 

natural production areas and employs supplementation of natural spawning as a component of 

the program. Dworshak’s primary goal is to replace loss sport and tribal fisheries, while 

Clearwater’s primary goal is to restore and maintain natural populations of Chinook in the 

Clearwater River, while contributing to sport and tribal fisheries. 

How many fish should be used to meet longer-term mitigation goals before immediate harvest is 

pursued. 

Since there is no natural spawning component for the Dworshak Chinook program its uses are 

broodstock and harvest. Broodstock need is integral in determining yearly harvest goals, so 

broodstock collection is prioritized especially in low return years. Furthermore, we believe that 

providing harvest, at even a low level, is very important and essential to fostering public support 

for spring Chinook salmon recovery efforts throughout the Snake River basin and especially in 

areas where harvest cannot yet occur because of low returns and ESA concerns. 

 
86 

TUCANNON RIVER SPRING CHINOOK SALMON HATCHERY 

SUPPLEMENTATION PROGRAM 

Michael P. Gallinat 

Washington Department of Fish and Wildlife 

Fish Program, Science Division: Snake River Lab 

Dayton, WA 

INTRODUCTION 

Mitigation Goal 

The Water Resources Act of 1976 authorized the establishment of the Lower Snake River 

Compensation Plan (LSRCP) to replace adult salmon and steelhead lost by construction and 

operation of the hydroelectric dams on the Lower Snake River. During the mitigation negotiations 

it was determined that 2,400 spring Chinook salmon annually escaped into the Tucannon River. 

The Tucannon River spring Chinook hatchery mitigation program was designed to escape 1,152 

adults to the Tucannon River (replacement of the 48% loss attributed to the construction and 

operation of the dams), with the expectation that the remaining 1,248 adults would come from 

natural production. It was also assumed that 4,608 (4x escapement goal) Tucannon spring 

Chinook would be harvested below the project area (Here the “project area” is defined as above 

Ice Harbor Dam). Hatchery mitigation was to be accomplished by the annual release of 132,000 

yearling smolts with an assumed SAR of 0.87%. 

Management Objectives 

The management objectives for the Tucannon River Spring Chinook population are: 1) Meet the 

LSRCP mitigation goal, 2) Restore and maintain fisheries (long-term goal – 2,400-3,400 hatchery 

and natural fish), 3) Restore and maintain the natural population (population viable threshold – at 

least 750 natural origin fish over a 10 year geometric mean), and 4) Minimize impacts of the 

hatchery fish on the natural population. 

Monitoring and Evaluation Objectives 

The monitoring and evaluation objectives are to: 1) Determine if the program is meeting its 

mitigation goals, 2) Monitor production, productivity, and life history characteristics of both the 

hatchery and natural components of the population, and 3) Evaluate hatchery rearing strategies 

so that we can maximize adult returns. 

Location and Hatchery Facilities 

The Tucannon River is located in southeastern Washington and flows into the Snake River 

between Lower Monumental and Little Goose Dams (Figure 1). Lyons Ferry Hatchery is located 

on the Snake River and is used for broodstock holding, spawning, egg incubation, and early 

juvenile rearing. The Tucannon Hatchery is used for broodstock collection at the adult trap, and 

juvenile rearing before release. Pre-smolts are transported to Curl Lake Acclimation Pond (AP) in 

February for acclimation and are volitionally released in April. 
87 

Figure 1. Location of the Tucannon River, and Lyons Ferry and Tucannon Fish Hatcheries 

within the Snake River basin in Washington State. 

HATCHERY OPERATIONS AND RESULTS 

Hatchery Spawning 

The Tucannon River stock was derived from fish captured at the Tucannon Hatchery adult trap, 

thereby representing individuals that were endemic to the Tucannon River. The broodstock goal 

was to collect 100 adults for the production of 132,000 smolts annually from 1986-2005. This 

broodstock collection goal was achieved 50% of the time during that period. It was revised by the 

co-managers beginning with the 2006 brood year to adjust for lower than expected smolt to adult 

return survivals. The new goal is 170 adults (target - 50% natural origin) which are to be collected 

from throughout the run to meet the new smolt production/release goal of 225,000. The new 

broodstock collection goal has been met 40% of the time through 2010. Returning Tucannon 

hatchery salmon are identified by a coded-wire tag in the snout or presence of a visible implant 

elastomer tag. A 2x2 factorial spawning matrix approach is utilized to increase effective population 

size and ensure the highest likelihood of fertilization. 

Captive Brood Program Implementation 

The Washington Department of Fish and Wildlife initiated a captive brood program in 1997 due 

to extremely low escapement in the mid 1990’s (the total run in 1995 was estimated at 54 fish). 

The program began by collecting sac fry from the hatchery supplementation program from five 

(1997-2001) brood years (one generation) with additional sac fry collected from the 2002 BY in 

order to have extra males on hand to spawn. The project goal was to rear the captive salmon to 

adults, spawn them, rear their progeny, and release approximately 150,000 smolts annually into 

the Tucannon River between 2003-2007. This was expected to provide a return of about 300 adult 

fish to the Tucannon River of captive origin per year between 2005-2010. These smolts, in 
88 

combination with the conventional hatchery supplementation program and natural production, 

were expected to produce 600-700 returning adult spring Chinook to the Tucannon River each 

year from 2005-2010. 

Fish Health 

Broodstock are given injections of erythromycin and oxytetracycline at trapping. Injections of 

erythromycin are given on monthly intervals before spawning. Spawned females are examined 

for Bacterial Kidney Disease (BKD) using the Enzyme Linked Immunosorbent Assay (ELISA) 

technique. However, unlike most other programs there is no culling or segregation of eggs based 

on ELISA results. This strategy has resulted in only two minor losses due to BKD in the last ten 

brood years (2000 and 2002 BY’s). Broodstock mortality was high during the beginning of the 

program when fish were held at Tucannon Fish Hatchery (Figure 2). Beginning with the 1992 

brood year, broodstock were held at Lyons Ferry Hatchery (LFH) and pre-spawn mortalities fell 

sharply due to lower water temperatures and pathogen free well water at LFH. 

Figure 2. Pre-spawn mortalities (%) of wild/natural and hatchery origin Tucannon River 

spring Chinook salmon broodstock for the 1985 to 2009 brood years. 

Rearing, Production, and Adult Returns 

Only in three brood years out of the last 24 have we been below the 70% goal for eyed-egg to 

smolt survival (Figure 3). 

0

10

20

30

40

50

60

70

80

90

100

85 87 89 91 93 95 97 99 '01 '03 '05 '07 '09

Pre-Spawn Mortality (%)

Brood Year

Wild/Natural

Hatchery
89 

Figure 3. Eyed-egg to smolt survival for Tucannon River spring Chinook for the 1985 to 2008 

brood years. 

For various reasons we have not always met our smolt production goal (Figure 4). When the 

Tucannon River spring Chinook captive brood program was in place, it at least allowed us to meet 

our goal which otherwise would not have been met with just the conventional supplementation 

program alone. Beginning with the 2006 brood year, the tribal co-managers and WDFW agreed 

to increase the smolt production goal to 225,000 due to low hatchery origin smolt to adult returns. 

Figure 4. Number of smolts produced by brood year for both the conventional hatchery 

supplementation and captive brood programs. 

Both the numbers and distribution of redds has varied over the years (Figure 5). During low runs 

in the mid 1990’s the majority of fish were collected at the adult trap in an effort to save the 

population from extinction due to early life history survival advantages in the hatchery. This action, 

combined with all smolts being released from the hatchery, led to a majority of natural spawning 

occurring below the hatchery weir. We have also documented trap avoidance based on radio 

0

10

20

30

40

50

60

70

80

90

100

85 87 89 91 93 95 97 99 '01 '03 '05 '07

Eyed Egg to Smolt Survival (%)

Brood Year

0

50

100

150

200

250

300

85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 '00 '01 '02 '03 '04 '05 '06 '07 '08

No. of Smolts (1,000s)

Brood Year

Conv. Suppl. C.B.

70% Goal

225,000 Goal 

132,000 Goal 
90 

telemetry studies and visual observation. Beginning with the 1997 brood year (released as smolts 

in 1999) we began using Curl Lake AP which is located above the adult trap. This appears to 

have improved the distribution of redds above the weir. 

Figure 5. Number of spring Chinook redds above and below the adult trap on the Tucannon 

River for the 1985-2010 run years. 

While we have come close in recent years we have not met the hatchery mitigation goal of 1,152 

(Figure 6). We have had at least 750 natural origin fish [minimal viable population (MVP) 

abundance level] return to the Tucannon River in the last two years. 

Figure 6. Escapement to the Tucannon River by origin for the 1985-2010 return years. 

 

0

50

100

150

200

250

300

350

85 87 89 91 93 95 97 99 '01 '03 '05 '07 '09

Number of Redds

Run Year

Below Weir

Above Weir

0

200

400

600

800

1000

1200

1400

1600

85 87 89 91 93 95 97 99 '01 '03 '05 '07 '09

Number of Salmon

Return Year

Natural

Hatchery Hatchery Mitigation Goal = 1,152 
91 

The majority of both the hatchery and natural components of the Tucannon River spring Chinook 

population return at age-4 (Figure 7). Hatchery rearing causes earlier maturation with more age3 and fewer age-5 fish than the natural component of the population. 

Natural origin precocial parr (age-0 and age-1) have been observed on the spawning grounds but 

are missed at the adult trap and during carcass recoveries so they are excluded from the spawner 

age composition graph. In the hatchery environment, males that mature at these ages are 

included in the monthly mortality counts since hatchery origin fish are not released until April (age1+). 

Figure 7. Age composition of hatchery and natural origin Tucannon River spring Chinook for 

the 1985-2009 run years. 

Fecundity 

Natural origin Tucannon River spring Chinook females were significantly (P <0.05) more fecund 

than hatchery origin females for both age-4 and age-5 (Table 1). 

Table 1. Mean number of eggs per female by age for natural and hatchery origin Tucannon 

River spring Chinook broodstock, 1990-2009 return years. 

 Age 4 Age 5 

 Natural Hatchery Natural Hatchery 

Mean Fecundity 3,485 3,092 4,405 3,671 

(S.D.) (640.3) (658.1) (883.4) (767.6) 

Strays 

Hatchery strays from other systems are found in the Tucannon River which we have been able to 

remove at the adult trap when they are fin clipped. Umatilla River spring Chinook have historically 

comprised the majority of the strays. However, the numbers of strays are typically below the 5% 

stray proportion deemed acceptable by NOAA Fisheries. We cannot remove strays that may 

0

10

20

30

40

50

60

70

80

Age 3 Age 4 Age 5

Percent

Hatchery

Natural
92 

spawn below the adult trap/weir, only document their abundance based on carcass recoveries 

during spawning ground surveys. 

Coded-Wire Tag Recoveries 

The majority of Tucannon River spring Chinook coded-wire tags are recovered in the Tucannon 

River (Figure 8). With the exception of a couple of brood years, few fish have been captured in 

fisheries. It is important to point out however, that due to historic low runs we stopped adipose fin 

clipping beginning with the 2000 brood year in order to maximize escapement back to the 

Tucannon River. If only adipose clipped fish are scanned for wire in these fisheries, than this 

would under-represent the contribution of Tucannon River spring Chinook in the catch. 

Figure 8. Coded-wire tag recoveries of Tucannon River spring Chinook salmon from the 

1985 to 2006 brood year hatchery releases. 

Run Timing 

The cumulative percentage of arrival timing of natural and hatchery origin fish shows nearly 

identical run timing to approximately the 60% mark (Figure 9). After that point it appears that the 

natural origin fish arrive at a slower rate than the hatchery origin fish. Similar trends have been 

observed in other basins. 

0

10

20

30

40

50

60

70

80

90

Percent

Ocean

Zones 1-5

Zone 6

Above McNary

Terminal (Tribal)

Strays

Tucannon
93 

Figure 9. Mean percent of total run captured by date at the Tucannon Fish Hatchery adult 

trap on the Tucannon River for both natural and hatchery origin Tucannon River 

spring Chinook salmon, 1993-2009. 

The program has never met the LSRCP hatchery origin smolt-to-adult return (SAR) goal of 0.87% 

(Figure 10). We are short of the goal even when all known recoveries are included in the smoltto-adult survival (SAS). 

Figure 10. Comparison of hatchery origin smolt-to-adult return (SAR) and smolt-to-adult 

survival (SAS) for the 1985 to 2005 brood years (jacks excluded). 

Natural origin smolt-to-adult returns have consistently been higher than hatchery origin returns 

(Figure 11). Based on the current mean hatchery origin SAR of 0.21% it would take a hatchery 

program of over 500,000 smolts to meet the mitigation goal of 1,152 hatchery fish. After 

discussions with the tribal co-managers it was decided to increase the smolt goal from 132,000 

to 225,000 beginning with the 2006 brood year. It was felt that while for some years the increased 

0

10

20

30

40

50

60

70

80

90

100

4/28 5/13 5/28 6/12 6/27 7/12 7/27 8/11 8/26 9/10 9/25

Percent

Date

Natural

Hatchery

0.00

0.20

0.40

0.60

0.80

1.00

85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 '00 '01 '02 '03 '04 '05

Percent

Brood Year

Hatchery SAR

Hatchery SAS
94 

goal wouldn’t be met – we would hope to make the original 132,000 goal at a minimum. The 

program is currently examining size at release as a possible means to improve SAR survival 

rates. 

Figure 11. Comparison of smolt-to-adult returns of hatchery and natural origin Tucannon 

River spring Chinook for the 1985 to 2005 brood years (jacks excluded). 

Captive Brood Program Results 

The captive brood program had problems with low fecundity, high egg losses, and progeny to 

parent ratios that were less than natural origin fish. Therefore, the program was discontinued as 

originally planned after one generation. 

Genetics 

Microsatellite DNA analysis was conducted to determine if there have been any changes to the 

genetic diversity of spring Chinook in the Tucannon River from before the hatchery program 

began (1986) to 1997-1998 and 2000-2008 samples of natural, conventional hatchery, and 

captive brood origin fish. The results showed that the genetic diversity of spring Chinook in the 

Tucannon River has not significantly changed as a result of the supplementation or captive brood 

programs. This study is more adequately described in Todd Kassler’s report which is included in 

these proceedings 

Adult PIT Tag Returns 

Fifty-five adults originally PIT tagged as juveniles (1995-2008 tag years) have been detected 

returning to the Columbia River System. Of those, about 24% swam past the Tucannon River and 

were detected at Lower Granite Dam. This behavior does not appear to be a hatchery effect since 

both hatchery and natural origin fish bypassed the Tucannon River at nearly the same rate (23.5% 

for hatchery origin and 23.8% for natural origin). This information is based on a small sample size 

but we have seen the same bypassing issue with the Tucannon River steelhead which have had 

much larger numbers of PIT tagged fish. WDFW is increasing PIT tag numbers (up to 25,000 for 

the 2009 BY) to further study this issue. 

0

1

2

3

4

5

6

7

8

9

85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 '00 '01 '02 '03 '04 '05

Percent

Brood Year

Hatchery SAR

Natural SAR
95 

Progeny to Parent Ratio 

Examining progeny to parent ratios shows that natural origin fish have been above replacement 

in only six of the last 21 brood years (Figure 12). This is in comparison to the hatchery origin fish 

which are typically above replacement. That the natural origin fish are typically not replacing 

themselves is the most pressing question for this population since extinction is inevitable for a 

population should this situation continue. Preliminary WDFW evidence suggests that densitydependent factors (larger runs = smaller smolts = lower survival) below carrying capacity (based 

on Ricker and Beverton-Holt stock-recruit functions) may play an important role. 

Figure 12. Progeny to parent ratios (with replacement line) for natural and hatchery origin 

Tucannon River spring Chinook for the 1985-2005 brood years. 

Hatchery Reviews 

The Tucannon River spring Chinook hatchery supplementation program underwent a hatchery 

scientific review process during 2009 and 2010. The Hatchery Scientific Review Group (HSRG) 

and Hatchery Review Team (HRT) made recommendations to improve the Tucannon spring 

Chinook hatchery program. 

The HSRG recommended that the population be managed as a Primary Population because it is 

the only extant population within the Lower Snake River MPG, and therefore it is required to meet 

highly viable status under ESA recovery plans. The HSRG suggested that WDFW and the tribal 

co-managers develop a sliding scale management approach so that in low abundance years, 

more of the appropriate stock is allowed to reach the spawning grounds. The HSRG also 

recommended that the straying of Tucannon spring Chinook above Lower Granite Dam be further 

investigated. 

The HRT provided numerous suggestions including changing the size and nature of the program, 

rethinking the prophylactic use of medicated feed for bacterial kidney disease, and possible 

changes to hatchery facilities used in the program. 

0

1

2

3

4

5

6

7

8

9

85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 '00 '01 '02 '03 '04 '05

Progeny:Parent Ratio

Brood Year

Natural

Hatchery

Replacement Line 
96 

Full responses to the HSRG and HRT comments are found in the Tucannon River Endemic Stock 

Spring Chinook Hatchery and Genetic Management Plan (HGMP) and are available at the LSRCP 

website (http://www.fws.gov/lsnakecomplan/Reports/HGMPreports.htm). These 

recommendations are being discussed between WDFW and the tribal co-managers. A series of 

alternatives have been devised under the HGMP for consideration by the co-managers, however 

the existing program was agreed upon under the 2008-2017 U.S. v. Oregon agreement and any 

changes will need to be addressed in that forum. 

SUMMARY 

The assumptions made at the beginning of the mitigation program have not been realized and 

the program has failed to meet expected returns to the Lower Snake area. In addition the mean 

progeny to parent ratio of in-river spawners is below replacement. However, the failure of the 

hatchery program to restore the population may be beyond the control of the program due to 

potential density-dependent factors. 

We continue to look for hatchery production methods to maximize hatchery fish survival (SAR’s) 

in order to reach the mitigation goal. However, more research is needed to identify the underlying 

reasons for the failure of the natural population to replace itself and correct them if possible. The 

reasons for the population decline, which was the incentive for the LSRCP hatchery program, 

have apparently not been alleviated. A self-sustaining reference population of spring Chinook 

would be beneficial in identifying possible causes and directing necessary corrections. 

ACKNOWLEDGMENTS 

I would like to thank the staff of the Snake River Lab and others from the Washington Department 

of Fish and Wildlife, who over the years collected the data presented here. In particular I would 

like to thank Lance Ross, Mark Schuck, and Glen Mendel. I also thank the Confederated Tribes 

of the Umatilla Indian Reservation and the Nez Perce Tribe. Special thanks to Scott Marshall and 

the LSRCP staff for support and funding of the Tucannon spring Chinook program. The captive 

broodstock program was funded primarily through the Bonneville Power Administration’s Fish and 

Wildlife Program. 

 
97 

GRANDE RONDE BASIN SPRING CHINOOK SALMON HATCHERY REVIEW: 

INTRODUCTION AND THE EARLY YEARS 

Richard W. Carmichael 

Tim Hoffnagle 

Joseph Feldhaus 

Debra Eddy 

Nick Albrecht 

Oregon Department of Fish and Wildlife 

203 Badgley Hall, EOU 

One University Blvd 

La Grande OR 97850 

 

This program is a cooperative effort of the Oregon Department of Fish and Wildlife, the Nez Perce 

Tribe and the Confederated Tribes of the Umatilla Indian Reservation. The program is funded by 

the Bonneville Power Administration and administered by the United States Fish and Wildlife 

Service under the Lower Snake River Compensation Plan. 

INTRODUCTION AND BACKGROUND 

This paper provides background information, program development history, and assessment of 

early program performance of the Grande Ronde basin spring Chinook salmon Lower Snake 

River Compensation Plan (LSRCP) hatchery program. We cover the period from initiation of the 

program in the late 1970s through the late 1990s, when significant hatchery reform measures 

were implemented in response to ESA listing and other policy influences. Separate papers are 

presented that review the recent performance of the Upper Grande Ronde River, Catherine Creek 

and the Lostine River Spring Chinook hatchery programs. 

The Grande Ronde basin historically supported diverse and robust populations of Chinook salmon 

Oncorhynchus tshawytscha. Abundant runs supported tribal and recreational fisheries throughout 

the basin. The recreational fisheries closed in the mid-1970s due to the depressed status of the 

populations and limited tribal fishing occurred from the mid-1970s - 1990s. 

The Grande Ronde basin is located in Northeast Oregon, originating in the Wallowa and Blue 

mountains. The river flows 340 km from the headwaters to the confluence with the Snake River 
98 

at rkm 271. Historically the primary production areas included the Wenaha, Minam, Lostine, 

Wallowa and the Upper Grande Ronde rivers and Lookingglass and Catherine creeks (Figure 1). 

Figure 16. Map of the Grande Ronde River basin including major spring Chinook salmon 

production areas and hatchery facilities. 

Table 1. Lower Snake River Compensation Plan mitigation goals for Oregon’s spring 

Chinook salmon in the Grande Ronde River basin. Adult and survival goals are 

expressed for returns to the compensation area and total catch plus escapement. 

Category Goal 

Annual smolt goal

Annual pounds of production

Annual adult goal

Brood year smolt–to-adult return rate (SAR)

Annual adult goal

Brood year smolt-to-adult survival rate (SAS)

Compensation Area

Total Catch and Escapement

900,000 Smolts

45,000 lbs.

5,820 Adults

0.65%

29,100

3.25%

The Grande Ronde Basin LSRCP spring Chinook salmon program was established in the late 

1970s in response to the severe declines that occurred in the mid-1970s and the depressed status 

of all populations in the basin. Annual adult mitigation, broodyear specific smolt-to-adult return 

and total survival rates, and annual smolt production goals were established to compensate for 

the estimated annual loss of 48% of the basin adult production. 

0 8 1 6 24 32 4 Miles

!

!

!

!

!

!

!

!

!

Gran de Ro nd e W eir

G ran de R on de W eir 

(old location) Grande Rond e 

A cclim ation

Catherin e W eir

Ca therine 

Acclim ation

Lostine 

Acclim ation

Lo okin gglass 

Fish H atch ery

Lostine W eir

Im nah a W eir

ImnahaRiver

Wallo wa River

Grande R on de R iver

Wenaha R iver

Cather ine Creek

Snake River

Snake River
99 

The adult and smolt-to-adult return goals for the compensation area represent the required 

performance to the area above Lower Granite Dam. The total annual adult and smolt-to-adult 

survival rate goals were determined based on an assumed four-to-one catch to escapement ratio 

that existed prior to construction of the four Lower Snake River Dams. 

Prior to the development of the program, the Oregon Department of Fish and Wildlife developed 

six management objectives to guide implementation of the program including; 1) establish 

adequate broodstock to meet annual production needs; 2) restore and maintain natural spawning 

populations of spring Chinook salmon in the Grande Ronde Basin; 3) reestablish historic tribal 

and recreational fisheries; 4) establish an annual return of 5,820 hatchery fish; 5) maintain 

endemic wild populations of spring Chinook salmon in the Minam and Wenaha rivers; and 6) 

minimize impacts of the hatchery program on resident stocks of game fish. These objectives 

guided implementation of the program for about the first 15 years. Lookingglass Fish Hatchery 

(LFH) was constructed in 1982 and serves as the central production facility for the program. The 

hatchery is located on Lookingglass Creek at rkm 3.7 (Figure 1). The program operations were 

initially simple with adult broodstock collected and spawned at LFH, incubation and rearing to 

smolt at LFH and smolt releases into Lookingglass Creek or at sites in tributaries elsewhere in 

the basin (Figure 2). 

Figure 2. Diagram of initial hatchery program operations for spring Chinook salmon in the 

Grande Ronde basin.

A comprehensive research, monitoring, and evaluation (RM&E) program was initiated in 1984. 

The primary objectives for the RM&E included; 1) document and assess fish culture and hatchery 

operation practices; 2) determine optimum rearing and release strategies that will produce 
100 

maximum survival to adult; 3) determine total catch and escapement and assess if adult 

production meets mitigation goals; and 4) determine the success of maintaining genetic integrity 

of endemic wild spring Chinook salmon in the Minam and Wenaha rivers. 

PROGRAM ASSESSMENT 

When considering options for broodstock sources in the late 1970s, managers believed, there 

were too few natural-origin fish available in the basin to meet broodstock needs. To initiate 

broodstock development, 1978 brood year Rapid River stock smolts were released into 

Lookingglass Creek. The use of Rapid River stock was discontinued from the 1980-84 brood 

years due to disease and availability. Carson stock, imported from the Willamette River Hatchery 

Program, was used in the interim until the 1985 brood year when Rapid River stock was brought 

into use again. Rapid River stock was used through the 1999 brood year when it was phased out. 

Table 2. History of spring Chinook salmon broodstock sources used in the Grande Ronde 

basin spring Chinook hatchery program, 1978-1997 brood years. 

Brood year Stock Source 

1978 

1980-84 

Rapid River 

Carson / Willamette Hatchery 

1985-87 Carson/ Lookingglass Hatchery Rapid River Idaho 

1988 Rapid River / Idaho 

1989 Carson/ Lookingglass Hatchery Rapid River Idaho 

1990-99 Rapid River/ Lookingglass Hatchery 

Lookingglass Fish Hatchery produced and released presmolts and smolts in the early production 

years. Total production from LFH met the production goal of 900,000 for most brood years from 

1983-1992 (Figure 3). 
101 

Figure 3. Releases of Carson and Rapid River stock hatchery spring Chinook salmon in the 

Grande Ronde River basin, 1980-1999 brood years.

Figure 4. Annual spring Chinook salmon adult returns to the LSPCP area resulting from 

releases in the Grande Ronde basin, 1987-2001. The goal is 5,820 adults.

Brood year

1980 1985 1990 1995

Number released

0

500000

1000000

1500000

2000000

2500000

3000000

Smolts 

Pre-smolts 

Carson stock

Rapid River stock

0

250

500

750

1000

1250

1500

1750

2000

2250

2500

Number of adults

Return year
102 

Most releases occurred at LFH, however supplementation releases of pre-smolts and smolts 

occurred in Catherine Creek and Upper Grande Ronde River for the 1980-1988 brood years and 

surplus Carson stock adults were outplanted into Catherine Creek, Upper Grande Ronde River 

and the Wallowa River from 1987-1989. Annual adult returns to the compensation area were 

generally well below the mitigation goal of 5,820 from 1987-2001 with the highest return reaching 

42% of the goal (Figure 4). Smolt-to-adult survival and return rates were generally poor and the 

return rate goal of 0.65% was reached in only two of thirteen years for the 1985-1997 brood years 

(Figure 5). 

We monitored the proportion of natural spawners that were hatchery strays in the Minam and 

Wenaha rivers to assess the success in meeting the management objective of maintaining these 

populations as endemic-wild. Stray hatchery adults from LFH releases comprised a majority of 

the spawners in these populations for many years from 1986-1994 (Figure 6). The estimated stray 

rates into these unsupplemented areas were high, exceeding 25% in some years (Figure 7). 

The early years of hatchery operation and the results of monitoring the performance of the 

program in achieving priority management objectives provided critical conclusions about the 

success. Importing Carson and Rapid River Hatchery stocks to quickly build brookstock allowed 

smolt production goals to be met quickly and consistently. Smolt-to-adult return rates were poor, 

resulting in adult returns to the compensation area that were consitently below the goal. Sufficient 

numbers of adults were not consistently available to reestablish recreational fishing. Tribal fishing 

opportunties were provided in only a few years and in restricted locations. Stray rates for hatchery 

fish were high and hatchery strays represented a high proportion of natural spawning fish in the 

Lostine, Minam and Wenaha rivers. Natural population status in supplemented populations was 

severly depressed and supplementation efforts had failed as indicated by poor recruits-perspawner and very low abundance of natural-origin spawners. 

Two policy-based rulings in the early 1990s influenced the direction of the hatchery program. 

ODFW adopted a Wild Fish Management Policy in 1990, which established criteria for the 

maximum acceptable level of non-local origin hatchery spawners in natural populations. In 1992, 

natural spring Chinook populations were listed initially as endangered and later as threatened by 

the National Marine Fisheries Services (NMFS) under the ESA. Given the high proportion of stray 

hatchery spawners throughout the basin, the hatchery program was operating well outside the 

ODFW Wild Fish Policy criteria and was generating outcomes that were inconsistent with ESA 

recovery and sound conservation principles. 
103 

Figure 5. Smolt-to-adult survival and return rates for spring Chinook salmon smolts released 

in the Grande Ronde basin, 1985-1997 brood years. 

Figure 6. Percentage of naturally spawning fish in the Lostine, Minam, and Imnaha rivers 

that were Lookingglass Fish Hatchery-origin strays, 1986-1997.

0

0.2

0.4

0.6

0.8

1

1.2

1.4

Survival Rate (%)

Brood year

Smolt-to-adult Survival

Smolt-to-adult Return

0%

10%

20%

30%

40%

50%

60%

70%

80%

90%

100% Percent of total fish in river

Year

Lostine

Minam

Wenaha
104 

Figure 7. Stray rates of Lookingglass Fish Hatchery spring Chinook salmon into the Lostine, 

Minam and Wenaha rivers, 1986-1992.

Managers decided that significant hatchery reform measures were needed. However, information 

addressing critical uncertainties was required prior to developing hatchery reform approaches. 

The key information needs included: 1) What is the demographic status and the near term risk of 

extinction of Chinook salmon populations in the basin?; 2) What genetic effects had resulted from 

natural spawning non-local origin hatchery spawners?; and 3) How much genetic differentiation 

remained between natural populations and between hatchery and natural populations? 

Natural-origin spawner abundance reached critically low levels throughout the 1990s. There were 

fewer than 50 spawners for numerous years in the Upper Grande Ronde River, Catherine Creek 

and Lostine River populations and spawner numbers fell below 10 in some populations (Figure 

8). Recruits-per-spawner for Catherine Creek, Upper Grande Ronde River and Lostine River 

populations were below 1.0 for spawning years 1986-1993. Recruits-per-spawner for all three 

populations were above 0.5 in only two of the eight years (Figure 9). 

Based on the status and trends in natural-origin abundance and productivity, we concluded that 

extinction risk was high. In addition, comprehensive genetic analyses indicated there was still 

significant genetic differentiation between hatchery and natural populations and between the 

Minam River, Wenaha River, Upper Grande Ronde River, Lostine River and Catherine Creek 

natural populations. 

0%

2%

4%

6%

8%

10%

12%

14%

16%

18%

20%

1986 1987 1988 1989 1990 1991 1992

Percent

Year

Lostine

Minam

Wenaha
105 

Figure 8. Natural-origin spawner abundance in Catherine Creek, Upper Grande Ronde 

River and Lostine River spring Chinook salmon populations. Pre-1990s data are 

presented for reference benchmarks.

Figure 9. Recruits-per-spawner (spawner to spawner) for natural spawners in Catherine 

Creek, Upper Grande Ronde River, and Lostine River. Spawners include natural 

spawning hatchery and natural-origin fish and recruits are natural-origin only, 

1986-1993 brood years. 

0

500

1,000

1,500

2,000

2,500

3,000

3,500

Number of spawners

Year

Catherine Creek

Upper Grande Ronde

Lostine River

0.00

0.10

0.20

0.30

0.40

0.50

0.60

0.70

0.80

0.90

1986 1987 1988 1989 1990 1991 1992 1993

Recruits per spawner

Year

Catherine Creek

Upper Grande Ronde

Lostine River
106 

There was consensus reached by co-managers that hatchery programs using endemic local 

broodstock should be initiated immediately in Catherine Creek, Upper Grande Ronde River and 

Wallowa-Lostine River populations. In addition, given the uncertainties associated with 

supplementation, a diversified risk management approach (low to high risk) should be employed 

and wild fish management sanctuaries should be maintained in the Minam and Wenaha river 

populations. Specific hatchery reform management actions that were taken, beginning in 1995, 

included the following: 1) eliminated releases of Rapid River stock Chinook salmon in the Grande 

Ronde Basin after the 1999 brood year and uniquely marked and conducted trap and removal of 

adults at Lower Granite Dam; 2) initiated captive broodstock program with collection of parr from 

Catherine Creek, the Upper Grande Ronde and Lostine rivers in 1995; 3) we began conventional 

supplementation programs (natural adult broodstock) in Catherine Creek (2001), the Upper 

Grande Ronde (2001) and Lostine (1997) rivers using sliding scale management strategies; 4) 

constructed acclimation and adult capture facilities on Catherine Creek and Upper Grande Ronde 

and Lostine rivers and made significant modifications to LFH; and 5) completed a comprehensive 

hatchery management and monitoring plan to guide programs into the future (NEOH). 

The Interior Columbia Basin Technical Recovery Team (ICTRT) was formed in the mid-2000s, in 

part to identify independent populations, develop population viability criteria, and complete 

viability assessments. The ICTRT identified the Grande Ronde and Imnaha basin spring/summer 

Chinook salmon populations as a unique Major Population Group (MPG). A total of six 

independent populations were identified in the Grande Ronde basin, including the Wenaha River, 

Lookingglass Creek, Lostine-Wallowa Rivers, Minam River, Catherine Creek and the Upper 

Grande Ronde River. In addition, two populations were identified in the Imnaha Basin: Imnaha 

River and Big Sheep Creek. Both Lookingglass Creek and Big Sheep Creek populations were 

characterized as functionally extirpated and the status of the remaining six populations was 

assessed as high risk of extinction (Figure 10). 
107 

Figure 10. Viability status of spring/summer Chinook salmon populations in the Grande 

Ronde/ Imnaha Major Population Group (from ICTRT). 

The ICTRT population designations paralleled the designations made by co-managers previously 

in the hatchery planning efforts completed in the mid-1990s. The initiation of local broodstock 

development and population specific hatchery programs resulted in the need to partition smolt 

and adult mitigation goals for each specific Grande Ronde basin Chinook hatchery program 

(Table 3). The implementation of population specific programs and captive broodstock added 

substantial complexity to the Grande Ronde basin Chinook hatchery programs. 

Table 3. Population specific mitigation goals for Grande Ronde River basin spring Chinook 

salmon hatchery program. 

Population Goal 

Upper Grande Ronde River 250,000 Smolts 1617 Adults 

Lookingglass Creek 250,000 Smolts 1617 Adults 

Lostine River 250,000 Smolts 1617 Adults 

Catherine Creek 150,000 Smolts 970 Adults 

All programs 0.65% Smolt-to-Adult Return 

Implementation required the use of additional hatchery facilities and transport of adults and smolts 

to and from various locations. The complexity of the conventional and captive broodstock 

programs at the peak of implementation is illustrated by (Figure 11). 
108 

Figure 11. Northeast Oregon Chinook salmon hatchery program operational schematic 

illustrating the complexity of implementing conventional and captive broodstock 

programs for five population specific hatchery programs. CC = Catherine Creek, 

UGR = Upper Grande Ronde River. LOS = Lostine River, Imnaha = Imnaha River. 

Numerous agencies and projects contribute to implementation of hatchery programs and RM&E 

for Grande Ronde basin Chinook salmon. The LSRCP program serves as the central hub for a 

network of projects that enable successful implementation (Figure 12). The diverse funding 

sources, projects, agencies, and individuals that contribute to this collaborative joint venture have 

provided the energy and creativity required to implement the large-scale hatchery reform that has 

been accomplished in the Grande Ronde River basin. 

Captive parr

collection

Irrigon FH

Oxbow

Bonneville FH

Manchester

Captive parr

collection

UGR trap and

acclimation

UGR

LOS

Lookingglass FH

LOS Trap and

acclimation

Imnaha

E

S

P

A

A

E

S

P

E

S

S

A

P

P

P

A

S

S A

CC trap and

acclimation

Lookingglass CK

S

Manchester Captive parr

collection CC

LOS Trap and

acclimation

Today
109 

Captive Broodstock/Safety Net 

O&M and M&E

•ODFW, NPT, CTUIR, NOAA

•BPA

LSRCP – O&M and 

M&E

•ODFW, NPT, CTUIR

•USFWS/BPA

Adult - Juvenile 

Telemetry

•NPT, ODFW

•OWEB, BOR, Freshwater 

Trust

Grande Ronde Supplementation –

Acclimation, Adult Trapping and 

M&E

•CTUIR, NPT, ODFW

•BPA

Chinook Salmon Life 

History and Survival

•ODFW

•BPA

Comparative Survival 

Study

• ODFW

•PSMFC/BPA

Relative 

Reproductive 

Success

•NOAA

•BPA

Smolt Monitoring 

Program

•ODFW, NPT

•BPA

Figure 12. Grande Ronde River basin Chinook salmon hatchery program organization. 

Preliminary results of the new hatchery programs are presented in separate papers. The true 

measure of success of these programs will be determined by the response of the natural 

populations, smolt survival, adult returns, and the ability to restore and sustain tribal and sport 

fisheries in the future. 

ODFW Response to ISRP Comments - GRANDE RONDE BASIN 

Key Findings 

ISRP comment page 44: “Fig. 7. Please define how stray rates were calculated or provide a 

reference to these methods.” 

Response: Stray rates were calculated as the proportion of hatchery origin fish that returned to 

the Grande Ronde Basin and that were destined for Lookingglass Fish Hatchery that were 

estimated to have returned to the Minam, Wenaha and Lostine rivers. Hatchery fish were 

identified based on fin marks and coded-wire tags. We also used scale pattern analysis for years 

when unmarked hatchery fish returned. 
110 

ISRP comment page 44: “Can hatchery practices be improved to improve homing and to reduce 

straying?” 

Response: We have implemented many hatchery reform measures that are thoroughly discussed 

in the Catherine Creek and Upper Grande Ronde River supplementation papers. These actions 

include development and use of local broodstocks, release location changes to upper tributary 

locations, and acclimation in tributary release areas. These changes have resulted in substantial 

and significant reductions in stray rates and the proportion of hatchery stray spawners in the 

Minam River and Wenaha River populations. Data for recent years that illustrate the reductions 

are presented in Figures 21 and 22 in the paper “Catherine Creek Spring Chinook Salmon 

Hatchery Program Review,” Carmichael et al. 2011. 

 
111 

UPPER GRANDE RONDE RIVER SPRING CHINOOK SALMON HATCHERY 

PROGRAM REVIEW 

Richard W. Carmichael 

Tim Hoffnagle 

Joseph Feldhaus 

Debra Eddy 

Nick Albrecht 

Oregon Department of Fish and Wildlife 

203 Badgley Hall, EOU 

One University Blvd 

La Grande OR 97850 

 

This program is a cooperative effort of the Oregon Department of Fish and Wildlife, the 

Confederated Tribes of the Umatilla Indian Reservation and the Nez Perce Tribe. The program is 

funded by the Bonneville Power Administration and administered by the United States Fish and 

Wildlife Service under the Lower Snake River Compensation Plan. 

INTRODUCTION AND BACKGROUND 

This paper provides background information, program development history, and an assessment 

of program performance for the Upper Grande Ronde River spring Chinook salmon 

Oncorhynchus tshawytscha hatchery program. We cover the time period from the initiation of the 

program in the mid-1990s to present. General background information and discussion of the now 

endemic hatchery programs were previously presented in Grande Ronde Basin Spring Chinook 

Salmon Hatchery Review: Introduction and the Early Years. 

The Upper Grande Ronde River Spring Chinook hatchery program was initiated with the collection 

of wild parr for the captive broodstock program in 1995 due to the depressed status of this 

population (Figure 1). Adult trapping and smolt acclimation facilities were constructed to 

implement the program (Figure 2). The Upper Grande Ronde adult trapping and smolt acclimation 

facilities are operated by the Confederated Tribes of the Umatilla Indian Reservation (CTUIR) and 

function as satellite facilities of Lookingglass Fish Hatchery (LFH). The LFH serves as the adult 

holding, spawning, incubation, and rearing facility for the program. Smolts are transported from 

LFH to the Upper Grande Ronde River acclimation ponds for a short period of acclimation prior 

to release. Annual adult mitigation, smolt production, and brood year specific smolt-to-adult return 
112 

goals were developed for the Upper Grande Ronde program to represent 27.8% of the Grande 

Ronde basin goals (Table 1). 

The implementation has been guided by nine priority management objectives: 1) Prevent 

extinction of Upper Grande Ronde River Chinook salmon population; 2) Establish adequate 

broodstock to meet annual production needs; 3) Establish an annual return of 1,617 hatchery fish 

to the compensation area; 4) Provide a demographic foundation to rebuild from after the key 

limiting factors and threats are addressed; 5) Maintain and enhance natural production while 

maintaining long term fitness; 6) Maintain genetic and life history characteristics of the natural 

population; 7) Operate the hatchery program so that the genetic and life history characteristics of 

hatchery fish mimic wild fish; 8) Re-establish historical tribal and recreational fisheries; 9) Maintain 

endemic wild populations of spring Chinook salmon in the Minam and Wenaha rivers – minimize 

straying. 

Figure 1. Natural-origin adult spawner abundance in the Upper Grande Ronde River spring 

Chinook salmon population. 

Run year

1953 1957 1961 1965 1969 1973 1977 1981 1985 1989 1993 1997 2001 2005 2009

Natural adults

0

200

400

600

800

1000
113 

Figure 2. Map showing the location of the Upper Grande Ronde River Chinook salmon 

hatchery facilities. 

Table 1. Lower Snake River Compensation Plan mitigation goals for Oregon’s Upper 

Grande Ronde River spring Chinook salmon hatchery program. Adult and survival 

goals are expressed for returns to the compensation area. 

Category Goal

Annual smolt goal 250,000 smolts 

Annual adult goal 1617 adults 

Brood year specific smolt-to-adult return rate 0.65% 

A comprehensive research, monitoring and evaluation program has been underway with the 

primary objectives to: 1) Document and assess fish culture and hatchery operation practices and 

performance; 2) Determine optimum rearing and release strategies; 3) Determine total catch and 

escapement, smolt survival, smolt-to-adult survival, and assess if adult production meets 

mitigation goals; 4) Compare recruits-per-spawner for hatchery and natural origin fish; 5) Assess 

response in natural population abundance and productivity (adult recruits-per-spawner, smoltsper-spawner) to supplementation; 6) Assess and compare life history characteristics (age 

structure, run timing, sex ratio, smolt migration, fecundity) of hatchery and natural fish; 7) 

Determine the success of maintaining genetic integrity of endemic wild spring Chinook salmon in 

the Minam and Wenaha rivers; 8) Assess success in restoring fisheries. 
114 

PROGRAM ASSESSMENT 

When co-managers developed supplementation program strategies for the Grande Ronde River 

basin spring Chinook salmon populations they adopted a “spread the risk” strategy. The Upper 

Grande Ronde River population was the most severely depressed and the most aggressive 

hatchery intervention program was developed for this population. The sliding scale management 

framework for the Upper Grande Ronde River population is simple and places few constraints on 

proportions of hatchery fish in broodstock or spawning in nature. There are no limits on the 

proportion of broodstock that must be natural-origin or the proportion of natural spawners that are 

hatchery-origin. There are only two constraints in the sliding scale. 1) not to exceed collection of 

the 50% of the natural-origin adults for hatchery broodstock, and 2) no retention of returning 

captive broodstock progeny for hatchery broodstock. 

The Captive Broodstock Program served as the only source of broodstock for the 1998-2000 

spawn years. From 2001-2004, captive broodstock adults and a small number of natural-origin 

adults were used for broodstock (spawned as separate groups). Conventional hatchery produced 

adults, captive broodstock, and natural-origin adults all contributed to production from 2005-2009, 

although natural-origin adult broodstock numbers were low (Table 2). Conventional hatchery 

adults and natural-origin adults have been spawned together and the captive broodstock have 

always been spawned separately. Offspring of the two groups are reared separately and uniquely 

marked for management purposes. 

Table 2. Hatchery broodstock history for the Upper Grande Ronde River spring Chinook 

salmon hatchery program. 

Spawn year 

Number of females in broodstock Percent natural 

origin adults in 

broodstock 

Number of Captive 

Natural Hatchery Broodstock females

1998 0 0 0 4 

1999 0 0 0 5 

2000 0 0 0 188 

2001 8 0 100 199 

2002 17 0 100 56 

2003 20 0 100 1 

2004 7 0 93.3 1 

2005 3 38 7.7 58 

2006 12 71 17.7 5 

2007 8 25 23.3 77 

2008 5 8 36.0 109 

2009 6 52 12.9 64 

Few Upper Grande Ronde River stock hatchery fish spawned naturally from 1998-2003. Hatchery 

fish represented a high proportion of natural spawners (51.6-95.8%) from 2005-2009. 

Subsequently, the Proportionate Natural Influence (PNI) has been low for the past five years 

(Table 3). 
115 

Table 3. Vital statistics for natural spawning spring Chinook salmon in the Upper Grande 

Ronde River. 

Spawn year 

Total Number 

spawning in 

nature 

Percent hatchery 

spawning in 

nature 

Percent natural 

retained for 

broodstock PNI 

1998 88 0 4.3 

1999 4 0 0 

2000 51 0 3.8 

2001 56 0 27.3 

2002 60 5.0 47.2 0.913 

2003 196 18.9 31.8 0.917 

2004 638 94.8 32.7 0.512 

2005 354 95.8 31.8 0.076 

2006 62 51.6 48.3 0.253 

2007 34 52.9 47.2 0.423 

2008 465 84.9 11.4 0.090 

2009 309 85.4 19.6 0.137 

During the early years of broodstock collection a significant proportion of adults escaped the weir 

un-trapped. However, since 2001 a majority of adults were captured in most years (Figure 3). 

Prespawning mortality at LFH has been highly variable ranging from 2-45%. Green egg-to-smolt 

survival has been consistently high, near 80% in all years (Figure 4). Smolt production has varied 

widely due to variable performance of the Captive Broodstock Program, as well as availability of 

natural origin and conventional hatchery adult returns. The smolt production goal of 250,000 has 

been met in only one year and many production years have been below 50% of the goal (Figure 

5). Hatchery smolt survival to Lower Granite Dam is similar to the survival of Upper Grande Ronde 

River natural-origin smolts, however it is lower than survival of most of the other NE Oregon 

hatchery programs (Figure 6). The smolt migration pattern of hatchery fish is different than 

natural-origin smolts. Hatchery fish have a compressed distribution with a much earlier time of 

migration completion (Figure 7). 
116 

Figure 3. Estimated proportion of the Chinook salmon run trapped at Upper Grande Ronde 

River Weir., 1997-2009. 

Figure 4. Prespawn mortality of broodstock collected at the Upper Grande Ronde River Weir 

and held at Lookingglass Fish Hatchery and green egg-to-smolt survival of their 

offspring, 2001-2009 brood years.

Return year

1997199819992000200120022003200420052006200720082009

Proportion of run trapped

0.0

0.1

0.2

0.3

0.4

0.5

0.6

0.7

0.8

0.9

1.0

Brood Year

2001 2003 2005 2007 2009

Prespawn mortality

0.0

0.2

0.4

0.6

0.8

1.0

Green egg-to-smolt survival

0.0

0.2

0.4

0.6

0.8

1.0

Prespawn mortality

Egg-to-smolt survival

No data
117 

Figure 5. Chinook salmon smolt releases in the Upper Grande Ronde River, 1998-2008 

brood years.

Figure 6. Upper Grande Ronde River spring Chinook salmon conventional hatchery and 

natural-origin smolt survival to Lower Granite Dam, 1997-2007 brood years. 

Brood Year

1998 2000 2002 2004 2006 2008

Number of smolts (thousands)

0

5 0

100

150

200

250

300 C aptive 

C onventional 

R elease G oal

Brood Year

1997

1998

1999

2000

2001

2002

2003

2004

2005

2006

2007

% Survival to Lower Granite Dam 

(+ 95% CI)

0

20

40

60

80

100 Hatchery

Natural No data
118 

Figure 7. Migration timing at Lower Granite Dam of natural-origin and conventional hatcheryorigin Upper Grande Ronde River smolts, mean at 2003-2009 migration years.

Adult returns to the compensation area have been well below the goal of 1617 (Figure 8). Two 

factors that have contributed to poor adult returns are: smolt production has been below the goal 

and smolt-to-adult return rates that have consistently been below the goal of 0.65% (Figure 9). 

We have not observed a consistent relationship between hatchery and natural SARs. Natural 

SARs are better in some years and poorer in others (Figure 10). 

Upper Grande Ronde River Chinook salmon are exploited at low rates in ocean, Columbia River 

and tributary fisheries. On average, 87.1% of adults produced escape to the Upper Grande Ronde 

River (Table 4). Very low exploitation in mainstem Columbia River sport fisheries in recent years 

is a result of not fin marking the hatchery smolts and mark-selective sport fishery regulations that 

allow only marked hatchery fish to be retained. Most of the hatchery adults that return to the Upper 

Grande Ronde are used for broodstock or passed upstream to spawn naturally (Figure 11). 

Date

4/1 5/1 6/1 7/1

Proportion

0.0

0.2

0.4

0.6

0.8

1.0

Hatchery

Natural
119 

Figure 8. Adult returns to the LSRCP compensation area for Upper Grande Ronde River 

hatchery Chinook salmon, includes conventional and captive broodstock F1 

returns. 

Figure 9. Smolt-to-adult survival (SAS) and return (SAR) rates for Upper Grande Ronde 

River conventional hatchery Chinook salmon, 2001-2006 brood years. Note: the 

2005 and 2006 brood years include only ages 3 and 4 and age 3 returns, 

respectively. 

Run year

2002 2004 2006 2008

Escapement to LGD

0

200

400

600

800

1000

1200

1400

1600

1800

Mitigation goal

Brood year

2001 2002 2003 2004 2005 2006

SAR/ SAS

0.0

0.2

0.4

0.6

0.8

1.0

SAR

SAR SAS

Mitigation

goal
120 

Figure 17. Conventional hatchery and natural-origin smolt-to-adult return (SAR) for Upper 

Grande Ronde River spring Chinook salmon, 1996-2006 brood years. Note: the 

2005 and 2006 brood years include only ages 3 and 4 and age 3 returns, 

respectively.

Total adult spawners in nature have varied widely since hatchery adults have returned. In 2004 

there were over 500 natural spawners, however, in 2007 there were less than 20 spawners. 

Hatchery fish have comprised a majority of the spawners in recent years (Figure 12). The hatchery 

program is providing a significant full life cycle survival advantage over naturally spawned fish. 

The R/S for hatchery fish has exceeded 1.0 for all recent brood years while natural R/S has been 

a small fraction of 1.0 in all years (Figure 13). Natural smolt production has varied considerably 

and has not increased significantly since we started supplementation (Figure 14). Smolts 

produced per adult spawner appears depressed for years when significant numbers of hatchery 

fish spawned naturally (Figure 15). 

We found a significant negative relationship between adult spawner abundance and smolts-perspawner. Smolts-per-spawner decreased at substantially lower spawner abundance levels than 

what we had assumed based on prior Ecosystem Diagnosis Treatment analyses and recent 

historical escapements (Figure 16). We did not find any relationship between percent hatcheryorigin adults in nature and smolts-per-spawner. However, we have only three years in the data 

series where hatchery fish were a significant component of the adult spawners (Figure 17). 

Brood year

1992 1994 1996 1998 2000 2002 2004 2006

SAR

0.0

0.2

0.4

0.6

0.8

1.0

1.2

1.4

Hatchery

Natural

no datano datano data
121 

Table 4. Catch and escapement distribution (%) of Upper Grande Ronde River spring 

Chinook salmon. Data are for captive and conventional broodstock fish combined. 

 Brood Year 

 2001a 2002b 2003c 2004d Mean 

Ocean 0.7 2.2 0.0 0.0 0.7 

Columbia River Harvest 

Tribal 0.0 0.0 0.0 3.2 0.8 

Sport 11.9 0.0 0.0 0.0 3.0 

Commercial Net 3.3 0.0 0.0 0.0 0.8 

Snake River 

Stray below LGD 0.0 0.5 0.0 0.0 0.1 

Stray above LGD 4.1 6.5 12.0 7.1 7.4 

Sport above LGD 0.0 0.0 0.0 0.0 0.0 

Tribal above LGD 0.0 0.0 0.0 0.0 0.0 

Escapement to River 80.0 90.8 88.0 89.7 87.1 a > 99% released with AD CWT 

b > 99% CWT only, no fin clips 

c

 50% CWT only, no fin clips 

d 95% CWT only, no fin clips 

We have not observed a difference in age-at-return for hatchery-origin and natural-origin fish, 

however the sample size for natural-origin age is small (Figure 18). This is the only spring Chinook 

hatchery program in NE Oregon where we have not seen earlier age-at-return for hatchery fish. 

Adult migration timing at the Upper Grande Ronde River weir is similar for hatchery and naturalorigin fish (Figure 19). We assess and compare spawning distribution of natural and hatcheryorigin adults based on location of female carcass recoveries. We have observed a difference in 

spawning distribution between hatchery and natural-origin females. The range in spawning is 

similar, however hatchery female distribution is concentrated further upstream than natural 

females, near the acclamation/release location (Figure 20). 
122 

Figure 11. Escapement disposition of Upper Grande Ronde River hatchery spring Chinook 

salmon from the 2001-2004 brood years. Data include captive and conventional 

fish.

Figure 12. Adult spawner abundance in the Upper Grande Ronde River and Minam River 

populations. Spawners include natural-origin and all hatchery-origin fish.

Tribal 

distribution

2%

Fish in river

42% Kept for 

Hatchery

56%

ReturnYear

1995

1996

1997

1998

1999

2000

2001

2002

2003

2004

2005

2006

2007

2008

2009

Adult spawners in nature

0

200

400

600

800 Natural

Hatchery

Minam River

ICTRT Viability Threshold
123 

Figure 13. Upper Grande Ronde River Chinook salmon recruits-per-spawner (jacks omitted) 

for hatchery spawned adults and natural spawning hatchery and natural-origin 

adults, 2001-2004 brood years. 

 

Figure 14. Upper Grande Ronde River Chinook salmon natural-origin smolt abundance, 

1992-2006 brood years, no estimates for 1994, 1995, and 1999.

Brood year

2001 2002 2003 2004

Recruits-per-spawner

(adults only)

0

1

2

3

4

5

6

Hatchery

Natural

ICTRT

Viability

Criterion

Brood year

1992 1994 1996 1998 2000 2002 2004 2006

Number of smolts

0

10000

20000

30000

40000

Pre-supplementation Post-supplementation
124 

Figure 15. Upper Grande Ronde River Chinook salmon naturally produced smolts-perspawner, 1997-2006 brood years. 

Figure 16. Relationship between adult spawner abundance and smolts-per spawner for the 

Upper Grande Ronde River spring Chinook salmon, 1996-2006 brood years (no 

data for 1999). 

Brood year

1997

1998

1999

2000

2001

2002

2003

2004

2005

2006

Smolts / spawner

0

50

100

150

200

250

Pre-supplementation Post-supplementation

First hatchery

spawners in

nature (3 females)

Adult spaw ners

0 100 200 300 400 500 600 700

Smolts / spawner

0

2 0

4 0

6 0

8 0

100

120

140

160

180

200

220

P = 0.0488

r 2

 = 0.3277
125 

Figure 17. Relationship between percent hatchery-origin adults in nature and smolts-perspawner for Upper Grande Ronde River spring Chinook salmon, 1996-2006 brood 

years (no data for 1999). 

Figure 18. Mean age-at-return distribution for conventional hatchery- and natural-origin Upper 

Grande Ronde River spring Chinook salmon, 2001-2004 brood years.

% H atchery origin adults in nature

0.0 0.2 0.4 0.6 0.8 1.0

Smolts / spawner

2 0

4 0

6 0

8 0

100

120

140

160

180

200

220

Age class

Age 3 Age 4 Age 5

Proportion

0.0

0.2

0.4

0.6

0.8

1.0

Natural

Hatchery

P=0.863

P=0.576

P=0.403
126 

Figure 19. Adult migration timing (date of annual at weir) of conventional hatchery- and 

natural-origin fish at Upper Grande Ronde River weir, mean 2005-2009.

Figure 20. Spawning distribution of all hatchery- and natural-origin females in the Upper 

Grande Ronde River, natural is 2002-2008 and hatchery is 2004-2008 spawn 

years. 

Date

Apr May Jun Jul 

Proportion

0.0

0.2

0.4

0.6

0.8

1.0

Hatchery

Natural

Survey section (upstream )

1234

Proportion of female carcasses

0.0

0.1

0.2

0.3

0.4

0.5

0.6

0.7

0.8

Hatchery

Natural

Acclimation
127 

SUMMARY AND CONCLUSIONS 

Broodstock Development and Management 

The transition from non-local origin broodstock to local endemic broodstock has been relatively 

successful. However, a number of significant challenges have limited the success. The very small 

number of natural-origin adults that return to the Upper Grande Ronde River has limited 

broodstock availability and smolt production in all years. The low abundance of natural-origin 

adults produces high proportions of hatchery fish in the broodstock and in the natural spawners, 

resulting in very low PNIs. Significant numbers of adults have remained below the adult weir in 

some years. These fish were subject to extremely high temperatures (over 22 C) and suffered 

extensive prespawning mortality. The weir was relocated in 2005 to address these issues. 

However, delay and mortality remained a problem at the new weir site. A new weir management 

strategy was adopted in 2010 to minimize weir effects on adult migration. The weir is removed 

and adult handling/collection is discontinued when river temperature exceeds 20 C. Although 

this strategy may prove effective for eliminating delay and exposure to warm river temperatures, 

it will result in selective broodstock collection of fish from the early component of the run. 

In-Hatchery Performance 

Prespawning mortality of adults collected and held for broodstock is typically low. However, 

mortality has exceeded 30%, in two of nine years of program operations. This limited egg and 

smolt production for some brood years. Egg-to-smolt survival for the conventional program has 

been high and has not limited the program. 

Production, Survival, and Adult Return Performance 

We have only reached the smolt production goal in one year due to availability of adult returns 

and poor performance of the captive broodstock program in some years. Smolt survival to Lower 

Granite Dam is among the lowest observed for Oregon’s hatchery spring Chinook salmon smolts. 

Adult returns to the compensation area have improved in recent years but remain below the goal 

of 1,617. The low returns are a result of low smolt release numbers and SARs that are below the 

goals for most years. The SARs have improved through time and have been near or at our goal 

for about 50% of the recent brood years. 

Upper Grande Ronde River Chinook salmon are exploited at low rates with a majority of the adults 

produced escaping to the Grande Ronde River basin. There are few Upper Grande Ronde River 

hatchery fish straying into the Minam and Wenaha rivers, however a substantial number stray into 

Lookingglass Hatchery. Although tribal fisheries have occurred in some years, we have been 

unable to open tributary sport fisheries that target Upper Grande Ronde River hatchery fish for 

many reasons. The low abundance of natural origin adults, which is well below the critical 

abundance threshold, prevents any impact on the natural-origin returns. In addition, in some years 

hatchery fish are not visibly marked, prohibiting the ability to execute a mark-selective fishery. 

Supplementation: Life history and Spawning Characteristics 

We have not observed significant differences in life history characteristics (including age-at-return 

or adult migration timing) between hatchery and natural-origin adults. This is in contrast to Imnaha 

River hatchery Chinook that show differences in both age-at-return and migration timing. We have 
128 

few completed brood years to assess life history differences so our conclusions should be 

considered preliminary. 

Supplementation: Abundance and Productivity 

We are early in program implementation so our observations and supplementation conclusions 

should be considered preliminary. It appears that we have increased the total number of adults 

spawning in nature with the addition of large numbers of F1 captive and conventional hatchery 

adults to the spawning grounds. We have not seen a consistent increase in smolt abundance in 

response to increased adult spawners. We observed a strong signal of density dependence with 

a significant reduction in smolts-per-spawner at higher spawner densities associated with high 

proportions of hatchery fish. We have not observed an increase in natural-origin adult spawner 

abundance since supplementation was initiated. Natural spawner productivity has remained 

below 0.5 for the four recent completed brood years, 2001-2004. 

FUTURE PROGRAM CHALLENGES AND NEEDS 

The consistently poor productivity of natural spawners and the low abundance of natural-origin 

and hatchery-origin adult returns continue to limit the success of the program. Low and variable 

numbers of returns make it difficult to meet annual smolt production goals and to improve PNI. In 

addition, limited harvest can be provided with the current level of returns. Improved smolt survival 

to Lower Granite Dam and improved SARs are needed to increase hatchery adult returns. 

Improving natural spawner production and natural-origin abundance is a difficult challenge 

because it requires significant improvement in survival across the entire life cycle. Improvements 

in tributary and mainstem migratory habitat will take many years. The Upper Grande Ronde River 

spring Chinook salmon population is at the highest risk of extinction of any population in the 

Grande Ronde/Imnaha Chinook Major Population Group. 

Our lack of understanding of the mechanisms driving the poor natural spawner productivity and 

low adult abundance, limits our ability to focus management actions and make adaptive changes 

to the program. Research has been initiated to begin developing a better understanding of the 

primary habitat factors that are influencing productivity. This new research, along with ongoing 

supplementation studies will provide new knowledge needed to inform future management 

decisions. 

The hatchery supplementation program appears to be an essential conservation action required 

to maintain this genetic resource. Given the low current natural spawner productivity, this 

population is at very high risk of extinction and would not persist long if the spawner abundance 

is not continually supplemented with hatchery fish. The hatchery program should only be 

considered an interim measure to conserve the population in the near term. The hatchery program 

can do nothing to enhance natural productivity and cannot serve as a cornerstone for recovery of 

this population. Recovery to healthy sustainable levels can only be achieved by addressing the 

primary limiting factors via restoration of high quality habitat conditions and natural processes 

throughout the entire life cycle. Mainstem migration and hydrosystem survival and tributary habitat 

conditions must be improved or this population will linger on the edge of extinction indefinitely, 

even with continued aggressive hatchery intervention. 

 
129 

ODFW Response to ISRP Comments – Upper Grande Ronde River 

Key Findings 

ISRP comment page 46: “Return per spawner of natural Chinook is exceptionally low. What 

fraction of this low ratio is related to smolts per spawner versus adults per smolts?” 

Response: The low return per spawner for this population is a result of poor performance in both 

smolts per spawner and spawners per smolt. The most recent five year mean of smolts per 

spawner was 70, which is well below the mean for the Minam River population, which was 100 

for the same time period. Smolt to adult return rates have averaged less than 0.4% for the most 

recently completed brood years. In contrast, the SARs for the Minam River averaged 1.4% for the 

same time period. Our modeling results indicate that an SAR of 1.5% is needed to achieve a 

spawner to spawner replacement rate of 1.0 given an average of 70 smolts per spawner. With 

the recently observed SARs, an increase of over 300% is needed to reach replacement 

productivity for the Upper Grande Ronde River Spring Chinook population. 

ISRP comment page 46: “If low smolt productivity is indicated by low smolts per spawner, what 

measures might be taken to improve habitat?” 

Response: We have conducted numerous limiting factors assessments as part of subbasin and 

ESA recovery planning processes. In all cases stream flow, temperature, and sediment have been 

identified as key limiting factors in the spawning and rearing areas. There have been many habitat 

improvement measures implemented during the past 20 years (riparian recovery, road 

decommissioning, flow augmentation, upslope improvements, plantings, channel and flood plain 

reconnections and instream structures) to decrease temperature, increase flow and improve 

riparian conditions. However, even with aggressive and intense protection and restoration efforts 

it will take many salmon generations to produce biologically significant improvements in the 

degraded conditions in the Upper Grande Ronde Chinook salmon populations. 

ISRP comment page 46: “What is the size of the smolts (and earlier fingerling migrants)?” 

Response: Fish that leave the upper Grande Ronde summer rearing areas in the fall and over 

winter in the Grande Ronde Valley have a mean size range of 69-96 mm, with significant withinyear and between-year variability. Fish that remain in the upper Grande Ronde River through the 

winter and begin seaward migration in the spring as yearling smolts have a mean size range of 

80-109 mm, with significant within-year and between-year variability. 

ISRP comment page 46: “What is the timing of juveniles leaving the watershed? Is it associated 

with return per spawner?” 

Response: There are two primary juvenile life history patterns exhibited in the Upper Grande 

Ronde River population. Spawning and summer rearing for all production occurs in the upper 

reaches of the Grande Ronde River watershed. Some juveniles migrate to the mid reaches of the 

Grande Ronde River in the Grande Ronde Valley in the fall, overwinter, and then begin seaward 

migration in the spring. Typically, less than 20% of the parr migrate downstream to the valley in 

the fall. Juveniles that do not move downstream in the fall overwinter in the upper reaches and 

begin seaward migration in the spring. We have observed similar survival to the smolt stage for 

the two different life history patterns. We have an insufficient number of PIT tagged juveniles to 

compare full life cycle survival of the two patterns. 
130 

CATHERINE CREEK SPRING CHINOOK SALMON HATCHERY 

PROGRAM REVIEW

Richard W. Carmichael 

Tim Hoffnagle 

Joseph Feldhaus 

Debra Eddy 

Nick Albrecht 

Oregon Department of Fish and Wildlife 

203 Badgley Hall, EOU 

One University Blvd 

La Grande OR 97850 

 

This program is a cooperative effort of the Oregon Department of Fish and Wildlife, the 

Confederated Tribes of the Umatilla Indian Reservation and the Nez Perce Tribe. The program is 

funded by the Bonneville Power Administration and administered by the United States Fish and 

Wildlife Service under the Lower Snake River Compensation Plan. 

INTRODUCTION AND BACKGROUND 

This paper provides background information, program development history, and an assessment 

of program performance for the Catherine Creek spring Chinook salmon hatchery program. We 

cover the time period from initiation of the program in the mid-1990s to present. General 

background information and pre mid-1990s hatchery program performance were previously 

presented in Grande Ronde Basin Spring Chinook Salmon Hatchery Review: Introduction and 

the Early Years. 

The Catherine Creek spring Chinook hatchery program was initiated with collection of wild parr 

for the Captive Broodstock Program in 1995 due to the depressed status of this population (Figure 

1). Adult trapping and smolt acclimation facilities were constructed to implement the program and 

are operated by the Confederated Tribes of the Umatilla Indian Reservation (CTUIR). These 

facilities function as satellite facilities of Lookingglass Fish Hatchery (Figure 2). Lookingglass Fish 

Hatchery (LFH) serves as the adult holding, spawning, incubation, and rearing facility for the 

program. Smolts are transported from LFH to the Catherine Creek acclimation ponds for a short 

period of acclimation in the spring prior to release. Annual adult mitigation, smolt production, and 
131 

brood year specific smolt-to-adult return goals were developed for the Catherine Creek program 

to represent 16.67% of the total Grande Ronde River basin goals (Table 1). 

The implementation has been guided by nine priority management objectives: 1) Prevent 

extinction of the Catherine Creek Chinook salmon population; 2) Establish adequate broodstock 

to meet annual production needs; 3) Establish an annual return of hatchery fish to the 

compensation area; 4) Provide a demographic foundation to rebuild from after the key limiting 

factors and threats are addressed; 5) Maintain and enhance natural production while maintaining 

long term fitness; 6) Maintain genetic and life history characteristics of the natural population; 7) 

Operate the hatchery program so that the genetic and life history characteristics of hatchery fish 

mimic wild fish; 8) Re-establish historical tribal and recreational fisheries; 9) Maintain endemic 

wild populations of spring Chinook salmon in the Minam and Wenaha rivers – minimize straying. 

Figure 1. Natural-origin adult spawner abundance in Catherine Creek spring Chinook 

salmon population. 

Run year

1953 1960 1967 1974 1981 1988 1995 2002 2009

Natural adults

0

1000

2000

3000

4000
132 

Figure 2. Map of the Catherine Creek Chinook salmon hatchery facilities. 

Table 1. Lower Snake River compensation plan mitigation goals for Oregon’s Catherine 

Creek spring Chinook salmon hatchery program. Adult and survival goals are 

expressed for returns to the compensation area. 

Category Goal

Annual smolt goal 150,000 smolts 

Annual adult goal 970 adults 

Brood year smolt-to-adult return rate 0.65% 

A comprehensive research, monitoring and evaluation program had been underway with the 

primary objectives to: 1) Document and assess fish culture and hatchery operation practices and 

performance; 2) Determine optimum rearing and release strategies; 3) Determine total catch and 

escapement, smolt survival, smolt-to-adult survival, and assess if adult production meets 

mitigation goals; 4) Compare recruits-per-spawner (R/S) for hatchery and natural origin fish; 5) 

Assess response in natural population abundance and productivity (adult R/S, smolts-perspawner) to supplementation; 6) Assess and compare life history characteristics (age structure, 

run timing, sex ratio, smolt migration, fecundity) of hatchery and natural fish; 7) Determine the 

success of maintaining genetic integrity of endemic wild spring Chinook salmon in the Minam and 

Wenaha rivers; 8) Assess success in restoring fisheries. 
133 

Program Assessment 

When co-managers developed supplementation program strategies for Grande Ronde River 

basin spring Chinook salmon populations they adopted a spread the risk strategy. The Catherine 

Creek population was selected to represent a conservative hatchery intervention program. The 

sliding scale management framework is somewhat simple, with only three escapement 

management zones. When the predicted escapement of natural and hatchery fish combine 

exceeds 500, the criteria reaches the most conservative level where no more than 50% of the fish 

released to spawn naturally can be natural-origin and 30% or more of the broodstock must be 

natural-origin (Table 2). No returning captive broodstock progeny are retained for hatchery 

broodstock. 

Table 2. Catherine Creek spring Chinook salmon sliding scale broodstock management 

plan. H = Hatchery and N = Natural. 

Escapement 

level (H & N) 

Maximum % natural 

retained for broodstock 

% hatchery 

above weir 

Minimum % of natural- origin 

broodstock 

< 250 40 d d 

251-500 20 ≤ 70 ≥ 20 

> 500 ≤ 20 ≤ 50 ≥ 30 

d = No constraint 

The captive broodstock program adults served as the only source of broodstock for the 1998-

2000 spawn years. From 2001-2004, captive broodstock adults and natural-origin adults collected 

in Catherine Creek were the broodstock sources. Conventional hatchery produced adults, captive 

broodstock, and natural-origin adults all contributed to production for 2005-2009. The number of 

natural-origin females spawned was low in all years (Table 3). Conventional hatchery adults and 

natural adults are spawned together and captive broodstock adults are always spawned 

separately. Conventional and captive offspring are reared separately and uniquely marked to 

allow identification at the adult stage. No Catherine Creek hatchery fish spawned naturally until 

2001. Hatchery fish have comprised a high proportion of natural spawners since 2002 (49.7-

82.8%). The Proportionate Natural Influence (PNI) has been low the past five years, ranging from 

0.183 to 0.328 (Table 4). 

During the early years of operation and broodstock collection, a substantial proportion of the run 

escaped the weir un-trapped (Figure 3). Prespawning mortality of fish collected and held for 

broodstock at LFH has been at or below 10% for all years (Figure 4). Green egg-to-smolt survival 

has been consistently high for all brood years except 2001 and 2009. The smolt production goal 

was originally established at 250,000 and then changed in 2006, when co-managers agreed to 

reduce the goal to 150,000 and shift production to increase releases into Lookingglass Creek. 

Smolt production goals have not been met, however production has approached the 150,000 goal 

in recent years (Figure 5). Hatchery smolt survival to Lower Granite Dam is lower than the survival 

of natural smolts and it is the lowest of all NE Oregon Chinook hatchery programs (Figure 6). The 

smolt migration pattern of hatchery smolts at Lower Granite Dam is significantly different than 

natural smolts. Initial arrival timing is similar, however the hatchery smolts have a compressed 

distribution with an earlier date of completion, while natural fish have a prolonged migration period 

(Figure 7). 

 
134 

Table 3. Hatchery broodstock history for the Catherine Creek spring Chinook salmon 

hatchery program. 

Spawn year 

Number of females in 

broodstock Percent natural 

origin adults in 

broodstock 

Number of 

Captive 

Broodstock 

Natural Hatchery females 

1998 0 0 0 69 

1999 0 0 0 162 

2000 0 0 0 177 

2001 29 0 100 153 

2002 20 0 100 128 

2003 28 0 100 160 

2004 9 0 100 77 

2005 8 9 29.4 44 

2006 8 29 30.8 83 

2007 14 31 37.3 79 

2008 11 21 31.6 81 

2009 13 30 35.0 69 

Adult returns to the compensation area have been well below the reduced goal of 970 adults 

(Figure 8). Two factors have resulted in these poor returns: smolt production well below the goal 

and poor SARs. SARs have been consistently below the goal of 0.65% (Figure 9). Hatchery SARs 

have been lower than SARs for natural smolts (Figure 10). 

Catherine Creek Chinook salmon are exploited at low rates in all fisheries. On average, 78.3% of 

hatchery adults produced escape to Catherine Creek. The highest exploitation rate occurs in the 

Lower Columbia River sport fisheries, which has exceeded 14% in recent years (Table 5). 

Stray rates are generally low and a majority of the strays return to LFH where the fish were reared. 

Unlike past years, when large numbers of Carson and Rapid River stock hatchery fish strayed 

into the Minam and Wenaha rivers, few Catherine Creek strays have been recovered in these 

populations. Most of the hatchery adults that returned to Catherine Creek have been passed 

above the weir to spawn naturally, used for broodstock, or outplanted into Lookingglass and 

Indian creeks for reestablishment of natural production (Figure 11). 
135 

Table 4. Vital statistics for natural spawning spring Chinook salmon in Catherine Creek. PNI 

= Proportionate Natural Influence. 

Spawn 

year 

Total Number 

spawning in nature 

Percent hatchery 

spawning in nature 

Percent natural retained 

for broodstock PNI 

1998 101 0 0 

1999 48 0 0 

2000 58 0 0 

2001 557 22.6 5.5 0.716

2002 457 49.7 14.5 0.420

2003 487 58.7 20.9 0.449

2004 215 82.8 32.7 0.305

2005 152 74.3 20.4 0.183

2006 282 63.1 16.8 0.274

2007 171 71.3 36.3 0.256

2008 216 64.8 19.1 0.227

2009 287 54.0 21.0 0.328

Total adult spawners in nature has varied considerably since supplementation was initiated. When 

compared with the 1995-2000 time period, we have seen a significant increase in total spawners 

from 2002-2009. Hatchery fish have comprised over 50% of the natural spawners in each year 

since 2002 (Figure 12). Natural-origin spawner abundance has remained relatively low in recent 

years, similar to the low spawner abundance observed in the late 1990s. The adult R/S for 

conventional hatchery fish has exceeded 1.0 in all four completed brood years. The hatchery R/S 

for Catherine Creek tends to be the lowest of all NE Oregon spring Chinook hatchery programs. 

The R/S for natural spawning fish was low for the 2001-2004 brood years, ranging from 0.1-0.4 

(Figure 13). The hatchery is providing a significant full life cycle survival advantage due to the 

extremely low R/S for natural spawning fish. 

Natural smolt production was highly variable in both the pre- and post-supplementation periods. 

We have observed a slight increase in natural smolt abundance since supplementation was 

initiated (Figure 14). Smolts-per-spawner has decreased since supplementation started in the 

early 2000s (Figure 15). We found a significant negative relationship between adult spawner 

abundance and smolts-per-spawner (Figure 16). 
136 

Figure 3. Estimated proportion of Chinook salmon run trapped at the Catherine Creek weir. 

Figure 4. Prespawn mortality of broodstock collected at the Catherine Creek weir and held 

at Lookingglass Hatchery and green egg-to-smolt survival.

Return year

19971998

19992000200120022003200420052006

2007

20082009

Proportion of run trapped

0.0

0.1

0.2

0.3

0.4

0.5

0.6

0.7

0.8

0.9

1.0

Brood Year

2001 2003 2005 2007 2009

Prespawn mortality

0.0

0.2

0.4

0.6

0.8

1.0

Green egg-to-smolt survival

0.0

0.2

0.4

0.6

0.8

1.0 Prespawn mortality

Egg-to-smolt survival

No data
137 

Figure 5. Chinook salmon smolt releases into Catherine Creek, 1998-2008 brood years.

Figure 6. Catherine Creek spring Chinook salmon conventional hatchery- and natural-origin 

smolt survival to Lower Granite Dam, 1998-2007 brood years.

Brood Year

1998 2000 2002 2004 2006 2008

Number of smolts (thousands)

0

50

100

150

200

250

Captive 

Conventional 

Release Goal

Brood Year

1998 1999 2000 2001 2002 2003 2004 2005 2006 2007

0

20

40

60

80

100 Hatchery

Natural

% Survival to

Lower Granite Dam (+ 95% CI)
138 

Figure 7. Migration timing at Lower Granite Dam of conventional hatchery and natural-origin 

Catherine Creek smolts, mean 2003-2009.

Figure 8. Adult returns to the LSRCP compensation area for Catherine Creek spring 

Chinook salmon, includes captive broodstock F1 and conventional returns.

Date

4/1 5/1 6/1 7/1

Proportion

0.0

0.2

0.4

0.6

0.8

1.0

Hatchery

Natural

Run year

2001 2002 2003 2004 2005 2006 2007 2008 2009

Escapement to LGD

0

200

400

600

800

1000

1200

1400

1600

1800

Mitigation goal 1617 

970 
139 

Figure 9. Smolt-to-adult survival (SAS) and return (SAR) rates for conventional hatchery 

Catherine Creek spring Chinook salmon, 2001-2006 brood years. Note: the 2005 

and 2006 brood years include only ages 3 and 4 and age 3 returns, respectively. 

Figure 10. Conventional hatchery- and natural-origin smolt-to-adult return (SAR) for 

Catherine Creek spring Chinook salmon, 1993-2006 brood years. Note: the 2005 

and 2006 brood years include only ages 3 and 4 and age 3 returns, respectively. 

Brood year

2001 2002 2003 2004 2005 2006

SAR/ SAS

0.0

0.1

0.2

0.3

0.4

0.5

0.6

0.7

SAR

SAS

SAR mitigation goal

Brood year

1994 1996 1998 2000 2002 2004 2006

SAR

0.0

0.5

1.0

1.5

2.0

2.5

3.0

Hatchery

Natural
140 

Table 5. Catch and escapement distribution (%) for captive F1 and conventional Catherine 

Creek spring Chinook salmon. 

 Brood Year 

 2001 2002 2003 2004 Mean 

Ocean 0.0 1.7 0.0 0.0 0.4 

Columbia River Harvest 

Tribal 0.0 0.0 0.0 10.7 2.7 

Sport 12.5 0.0 14.3 14.0 10.2 

Commercial Net 0.4 0.0 2.4 7.0 2.4 

Snake River 

Stray below LGD 0.0 0.0 0.0 2.7 0.7 

Stray above LGD 8.3 4.2 6.2 1.7 5.1 

Sport above LGD 0.0 0.7 0.0 0.0 0.2 

Tribal above LGD 0.0 0.0 0.0 0.0 0.0 

Escapement to River 78.8 93.4 77.1 64.0 78.3 

Figure 11. Escapement disposition of Catherine Creek spring Chinook salmon from the 2001-

2004 brood years. Data include captive broodstock F1 and conventional fish.
141 

Figure 12. Adult spawner abundance in the Catherine Creek and Minam River populations. 

Spawners include both natural and hatchery-origin fish. 

Figure 13. Catherine Creek Chinook recruits-per-spawner (jacks omitted) for hatchery 

spawned adults and natural spawning hatchery- and natural-origin adults, 2001-

2004 brood years. 

ICTRT Viability Threshold 

ReturnYear

1995

1996

1997

1998

1999

2000

2001

2002

2003

2004

2005

2006

2007

2008

2009

Adult spawners in nature

0

200

400

600

800

Natural

Hatchery

Minam River

Brood year

2001 2002 2003 2004

Recruits-per-spawner

(adults only)

0

1

2

3

4

5

Hatchery

Natural

ICTRT

Viability

Criterion
142 

Figure 14. Catherine Creek Chinook salmon natural-origin smolt abundance, 1993-2007 

brood years.

Figure 15. Catherine Creek Chinook salmon naturally produced smolts-per-spawner, 1997-

2007 brood years. 

Brood year

1994 1996 1998 2000 2002 2004 2006

Number of smolts

0

5000

10000

15000

20000

25000

30000

Pre-supplementation Post-supplementation

Brood year

1998 2000 2002 2004 2006

Smolts / spawner

0

5 0

100

150

200

250

Pre-supplem entation Post-supplem entation

First hatchery

spaw ners in

nature (jacks)
143 

Figure 16. Relationship between adult spawner abundance and smolts-per-spawner for 

Catherine Creek Chinook salmon, 1995-2007 spawn years. 

Similar to what we observed in the Upper Grande Ronde River population, the estimated smoltsper-spawner dropped to low levels at much lower escapement levels than anticipated based on 

prior Ecosystem Diagnosis Treatment modeling and recent historical escapements. We observed 

depressed productivity at adult spawner abundance levels of less than 200. We did not find a 

significant relationship between percent hatchery-origin spawners and smolts-per-spawner. 

There is high variability in smolts-per-spawner among years when no hatchery fish were present. 

The smolts-per-spawner values were all low when the percent hatchery spawners was ≥ 50%. 

(Figure 17). From 2005-2009 we observed a similar pattern of early age-at-return of hatchery fish, 

but differences between hatchery and natural adult age composition are only significant for age 5 

due to the small sample size of four brood years (Figure 18). Adult migration timing at the 

Catherine Creek weir is similar for hatchery and natural fish (Figure 19). There was complete 

overlap in the range of spawning between natural and hatchery-origin females, however natural 

females have higher proportions in the lower reaches and hatchery females are concentrated in 

the reaches near the release location (Figure 20). 

Adult spaw ners

0 100 200 300 400 500

Smolts / spawner

0

50

100

150

200

250

P = 0.0003

r

2

 = 0.6891
144 

Figure 17. Relationship between percent hatchery-origin adults in nature and smolts-perspawner for Catherine Creek Chinook salmon, 1995-2007 spawn years. 

Figure 18. Mean age-at-return distribution for hatchery- and natural-origin Catherine Creek 

Chinook salmon, 2001-2004 brood years.

% Hatchery origin adults in nature

0.0 0.2 0.4 0.6 0.8 1.0

Smolts / spawner

20

40

60

80

100

120

140

160

180

200

Age class

Age 3 Age 4 Age 5

Proportion

0.0

0.2

0.4

0.6

0.8

1.0

Natural

Hatchery

P=0.354

P=0.403

P=0.010
145 

Figure 19. Adult migration timing of hatchery- and natural-origin fish at the Catherine Creek 

Weir, mean 2005-2009 run years. 

Figure 20. Spawning distribution of hatchery- and natural-origin females in Catherine Creek.

Date

Apr May Jun Jul 

Proportion

0.0

0.2

0.4

0.6

0.8

1.0

Hatchery

Natural

Survey section (upstream )

1234567

Proportion of female carcasses

0.00

0.05

0.10

0.15

0.20

0.25

0.30

0.35

0.40

Hatchery

Natural

Acclimation
146 

The proportion of natural spawners in the Minam and Wenaha rivers that were hatchery strays 

has been low since 2002. In the most recent years hatchery strays have comprised less than 5% 

of the spawners in these two populations (Figure 21). These recent proportions of hatchery strays 

are much reduced from the high proportions (over 50%) observed from 1986-1994 when Carson 

and Rapid River hatchery stock were used in the program. The small number of hatchery strays 

that were recovered in the Minam and Wenaha rivers originated from Lostine River, Catherine 

Creek and Lookingglass Creek releases (Figure 22). 

Figure 21. The proportion of total carcasses recovered in the Minam and the rivers that were 

hatchery-origin strays, 2001-2009.

Run Year

2001 2002 2003 2004 2005 2006 2007 2008 2009

Proportion of hatchery carcasses

0.0

0.2

0.4

0.6

0.8

1.0

Minam River

Wenaha River

1986-1994 mean

1986-1994 mean
147 

Figure 22. Origin of hatchery strays in the Minam and Wenaha rivers, 2002-2009.

SUMMARY AND CONCLUSIONS 

Broodstock Development and Management 

We have completed a successful transition from non-local broodstock to local Catherine Creek 

broodstock, but we have encountered a number of challenges during the transition process. The 

low abundance of natural-origin returns to Catherine Creek has limited broodstock availably for 

the conventional program. In addition, low abundance of natural-origin adults results in high 

proportions of hatchery fish in nature and in broodstock. The high contribution of hatchery 

spawners produces PNIs that are well below levels considered desirable. 

In-Hatchery Performance 

Pre-spawning mortality has been low and green egg-to-smolt survival has been high for most 

years. Although we did not present green egg-to-smolt survival for the 2009 brood year, (migration 

year 2011) the survival rate for this brood year will be very low due to the catastrophic mortality 

of parr in the Canadian Troughs on 3, June 2009. The mortality event was attributed to high 

precipitation that created unseasonably high turbid water, a severed water line, and a clogged 

drum filter that stopped water flow to the troughs. 
148 

Production, Survival, and Adult Production Performance 

The smolt production goal has not been reached in any year due to the availability of adults in 

Catherine Creek and variability in the performance of the captive broodstock program. Smolt 

survival to Lower Granite Dam is the lowest of all NE Oregon hatchery produced smolts. Adult 

returns to the compensation area have not shown an increasing trend, which is inconsistent with 

other NE Oregon Chinook hatchery programs. These low adult returns are a result of poor SARs 

in all years and low smolt production releases in some years. Few Catherine Creek adults are 

harvested and the majority of adults produced escape to Catherine Creek. Stray rates of 

Catherine Creek Chinook salmon are generally low and few have been found in the Minam or 

Wenaha rivers. We have been unable to open mark-selective sport fisheries targeting Catherine 

Creek fish because of the depressed status of natural-origin returns. The natural-origin 

abundance has only exceeded the critical abundance threshold in two of the past fifteen years. 

Supplementation: Life History and Spawning Characteristics 

We have not observed differences in age-at-return between hatchery natural-origin adults; all 

other life history characteristics are similar. We have few years of data for comparisons so our 

conclusions are considered preliminary. 

Supplementation: Abundance and Productivity 

We have increased the total number of natural spawning fish with the addition of substantial 

numbers of hatchery returns to the spawning grounds. Natural-origin smolt abundance is higher 

for the post-supplementation time period. We have not observed an increase in natural-origin 

adult abundance. The number of smolts-per-spawner declined substantially since 

supplementation was initiated. Density dependence appears to be a significant factor influencing 

smolts-per-spawner in the post-supplementation time period. Recruits-per-spawner for natural 

spawners has been very low since supplementation was initiated with all values below 0.5. 

The hatchery program is providing a demographic boost that appears to be critical in preventing 

the population from going extinct. The very low R/S values for natural spawners in recent years 

provide no resilience. Significant full life cycle survival improvements, that will allow natural R/S 

rates to consistently exceed 1.0, are needed in order for this population to persist without 

continued hatchery intervention. 

FUTURE PROGRAM CHALLENGES AND NEEDS 

The low productivity of naturally spawning fish and low abundance of natural-origin adults are 

significant challenges limiting the success of this program. These factors limit smolt production, 

limit the ability to improve the PNI, and prohibit targeted harvest on hatchery fish. There are no 

short-term or simple solutions for improving productivity. Productivity can only be enhanced by 

improving survival across the entire life cycle. These types of improvements in tributary and 

mainstem migratory habitat will take many salmon generations. 

Two significant challenges faced by this program include low smolt-to-adult survival and high 

smolt morality between the release location and Lower Granite Dam. Work is underway to identify 

the location and potential causes of mortality that occurs in the Grande Ronde Valley low gradient 

habitat. 
149 

Our lack of understanding about why natural productivity is so low and why supplementation has 

not produced more natural fish, limits our ability to make adaptive changes. Work is underway to 

better understand relationships between habitat conditions and Chinook salmon production, 

relative reproductive success of natural spawning hatchery fish, and density dependent 

mechanisms. The continuation of these investigations along with supplementation and hatchery 

effectiveness monitoring will provide essential information needed to better manage the program 

and understand biological responses in the future. 

ODFW Response to ISRP Comments – Catherine Creek 

Key Findings 

ISRP comment page 48: “Are hatchery smolts larger than natural smolts?” 

Response: Hatchery smolts are released at a larger size than natural origin smolts. Typical mean 

length at release for hatchery smolts is 115 mm while the natural fish average 87 mm. 

ISRP comment page 48: “Are some fish migrating downstream as subyearlings in the fall and 

winter? How does early emigration affect survival rates? Are early emigrants less successful after 

accounting for their young age compared with smolts?” 

Response: We have observed that about 40% of parr produced in Catherine Creek migrate 

downstream into the Grande Ronde Valley low gradient habitat in the fall and early winter for the 

1993-2007 brood years. The fall migrants overwinter in Catherine Creek and the Grande Ronde 

River and begin seaward migration in the spring. Significant overwinter mortality occurs for both 

life history types, those that redistribute downstream and those that remain in upper Catherine 

Creek. We have not observed a consistent significant survival advantage to the smolt stage at 

Lower Granite for either life history type. 

ISRP comment page 48: “What percentage of propagated releases are visually marked or 

tagged?” 

Response: We attempt to mark/tag 100% of the releases. A small proportion (less than 3%) has 

poor marks at release and may not be recognizable at return. 

ISRP comment page 48: “Is broodstock the sole reason for lower straying?” 

Response: We hypothesize that the broodstock origin and release strategies (tributary locations 

and acclimation) are all factors that have contributed to reduced straying. 

ISRCP comment page 48: “Is Catherine Creek a situation where interbreeding of hatchery and 

wild fish reduces survival of the spawning fish but continued introduction?” 

Response: We have too few years of information to conclude that the interbreeding of hatchery 

and wild fish is reducing productivity. However, early results of the relative reproductive success 

indicate hatchery fish are performing about 75% as well as natural origin fish. We did conclude in 

our paper, “We have increased the total number of natural spawning fish with the addition of 

substantial numbers of hatchery returns to the spawning grounds. The hatchery program is 
150 

providing a demographic boost that appears to be critical in preventing the population from going 

extinct.” 

ISRP comment page 48: “Is the decline in smolts per spawner associated with reduced growth of 

smolts suggesting food limitations?” 

Response: There is a significant negative relationship between parr abundance and parr-to-smolt 

survival, thus the decline in smolts per spawner does appear to be strongly associated with parr 

abundance. We also observed a significant negative relationship between parr abundance and 

fall migrant size and fall migrant size and survival to smolt. Although we are uncertain of the 

mechanisms driving these relationships, the food availability hypothesis seems very reasonable. 

ISRP comment pages 48-49: “If hatchery females carry fewer eggs, on average, to what extent 

does this influence the smolts per spawner relationship in Fig. 16? What influence does average 

female age have on Fig. 16? Is fecundity at age available for this stock? 

Response: Hatchery females do not have lower fecundity at age; however, since their average 

age is slightly less than natural fish the average fecundity is slightly lower. Age composition of 

females varies considerably from year to year; however, average age of female spawners is 

reduced slightly in this supplementation program. The overall influence on smolts per spawner is 

minimal because the denominator is all adult spawners and the decreased fecundity is not great. 

We are collecting fecundity by origin and age. To date sample sizes are limited; however, Age 5 

females have greater fecundity than Age 4 and we have not seen a difference by origin. 

ISRP comment page 49: “Hatchery strays have been quite low in the Minam and Wenaha rivers 

since 2002. How does the survival of smolts from these two systems (to LGD and overall) 

compare with that of Catherine Creek and the Upper Grande Ronde where supplementation is 

high?” 

Response: We do not have smolt survival data for the Wenaha to use for comparisons. We 

recently completed a comparison of survival rates and provide the results comparing Catherine 

Creek and the Minam River to address the above comment. These results are from the 2000-

2005 brood years for SARs and 2000-2008 brood years for egg-smolt. 

 Minam River Catherine Creek 

Egg-to-summer parr 32.7% 24.4% 

Parr-to-tributary smolt 23.0% 19.4% 

Tributary smolt-to-LGD smolt 56.0% 41.8% 

SAR-tributary smolt-to-spawner 1.4% 0.5% 

Survival in Catherine Creek is lower than the Minam for all life stages. Of specific concern is the 

lower survival for the smolts from the tributary to Lower Granite Dam and smolt-to-adult spawner. 

We are uncertain of the mechanisms driving these differences. However, we believe that 

environmental conditions and predation in the migratory route, distance to Lower Granite Dam, 

smolt size, as well as smolt condition are all factors influencing smolt-to smolt survival and SARs. 

We have initiated focused investigations to better understand the key factors influencing the poor 

performance for Catherine Creek. 

ISRP comment page 49: “Do these two rivers (Minam and Wenaha) show strong density 

dependence relationships? Is the ratio of recruits per spawner greater than 1? How do these 

populations persist when so few hatchery fish spawn in the rivers? 
151 

Response: We do not have adequate data to assess density dependence in the Wenaha River. 

We have not observed a strong signal of density dependence for any life stage in the Minam River 

population. The ratio of recruits per spawner has averaged below 1.0 for the most recent ten 

completed brood years for the Minam and Wenaha populations. However, there have been some 

years in the time series that have been well above 1.0. The populations are on a slow long-term 

decline with the high productivity years boosting the populations up periodically. Overall the 

productivity of the Minam River and Wenaha River populations is primarily limited by smolt-toadult survival, which is regulated by dam and reservoir mortality as well as ocean survival. 

 
152 

LOSTINE RIVER SUPPLEMENTATION PROGRAM (1997 – 2009)

Peter Cleary 

Nez Perce Tribe 

500 Main Street 

Joseph, Oregon 

ABSTRACT 

Efforts to rebuild Lostine River Chinook salmon (Oncorhynchus tshawytscha) in Oregon’s Grande 

Ronde Basin were undertaken with two supplementation programs. A captive broodstock program 

began collecting Lostine River juvenile parr for broodstock in 1995 and a conventional program 

began collecting Lostine River adult broodstock in 1997. Smolts from the supplementation 

programs were acclimated and volitionally released during the spring. Hatchery Chinook salmon 

were monitored as smolts and returning adults using coded-wire tags, PIT tags, redd counts, and 

mark-recapture escapement estimates. Survival estimates for natural Chinook salmon smolts 

from 1999 to 2009 were higher than for hatchery Chinook salmon smolts in all years except 2002. 

Spawner abundance from 1997 to 2000 never exceeded 250 spawners. Spawner abundance 

increased to 270 to 1,055 spawners from 2001 to 2009 with returning hatchery origin females 

beginning in 2001. Hatchery origin spawners comprised 29% to 80% of all adult spawners. 

Hatchery Chinook salmon had significantly more age 3, and fewer age 5 adult returns than natural 

Chinook salmon for brood years 1997 to 2004. Natural progeny-to-parent ratios declined from 

brood year 1999 to brood year 2003. Supplementation has increased the overall abundance of 

Lostine River Chinook salmon and provided harvest opportunities but adult recruitment needs to 

increase if supplementation is to be a successful strategy for rebuilding the natural population. 

INTRODUCTION 

This program is funded by the Bonneville Power Administration who chose to fund M&E and O&M 

as a package back in 1997. The funding provided by BPA allows NPT to work cooperatively with 

state and federal agencies for field activities such as pre-release sampling, and spawning ground 

surveys. It also allows NPT to participate in annual production planning for the Lower Snake River 

Compensation Plan (LSRCP). The Lostine River is considered to be part of the larger 

Wallowa/Lostine River Spring Chinook salmon population area as defined by NOAA (Figure 1). 

This definition is used when evaluating population status (ICTRT 2006). However, when 

supplementation began in the Lostine River the population area was not defined and the Lostine 

River was managed as its own population. Therefore, the results presented for the purpose of 

this review are limited to the Lostine River. 

The Lostine River watershed drains an area of 236 km2 in the Grande Ronde Subbasin and 

originates from an elevation of 2,225 m. The majority of the stream above the acclimation facility, 

at river kilometer 21, is within US Forest Service lands and majority of the stream below the 

acclimation facility is contained within agricultural farm lands. The majority of the Chinook salmon 

spawning habitat in the Lostine River is located upstream of the town of Lostine at river kilometer 

9. 
153 

Figure 1. A map showing the Grande Ronde Basin spring Chinook salmon populations in 

northeast Oregon. 

PROGRAM OVERVIEW 

Supplementation in the Lostine River began in response to a decline in redd counts. Lostine River 

supplementation is part of the Grande Ronde Basin Endemic Spring Chinook Supplementation 

Program (GRESP 1998). This program began in 1995 as a cooperative project between comanagers. In 2006 a formal monitoring and evaluation plan for supplementation (Hesse et al. 

2006) was completed and reviewed by the ISRP. Two approaches were taken for 

supplementation in the Lostine River. A captive broodstock program was chosen for one approach 

because it did not require the use of returning adults for broodstock. The second approach was a 

conventional broodstock program. The two approaches had two major differences. The captive 

broodstock program used all wild origin broodstock whereas the conventional program 

incorporated hatchery origin fish as part of the broodstock. The second major difference was that 

the captive broodstock program collected juvenile parr as broodstock to obtain eggs for smolt 

production. This meant that it took longer to start up the program because the parr had to be 

raised to the adult life stage to obtain eggs. The conventional program collected returning adults 

as broodstock for smolt production so it took less time to obtain eggs. 

The program objectives for Lostine River supplementation were first stated in the NEOH Master 

plan in 2000 (Ashe et al. 2000) and were divided into short, mid, and long term objectives. These 

objectives are as follows: 

 Short term goal - Preservation of population by maintaining an annual escapement of 250 

adults. 

 Midterm – Restoration of population by achieve an annual escapement of 500 natural 

adults. 

 Long term – Reestablish historical escapement and harvest by maintaining natural selfsustaining population of 1,716 adults and achieve the LSRCP hatchery-origin goal of 

1,625 adults. 
154 

The short term objective was established with the mindset that loss of Lostine Chinook salmon 

was a real possibility. The midterm objective for natural escapement was established to work 

towards a self sustaining population of Lostine River Chinook salmon. The long term objective 

was the original goal for the LSRCP in the Lostine River and included a component for harvest. 

Program objectives required that the captive and conventional supplementation programs release 

250,000 smolts. It was planned that the number of captive broodstock smolts produced would be 

reduced as the population of Chinook salmon in the Lostine River increased and that the captive 

broodstock smolt production would eventually be replaced by smolts produced by the 

conventional broodstock program. The goal of 250,000 smolts was chosen because at a 0.1% 

smolt-to-adult return rate it was expected to return 250 adults. Two hundred and fifty adults was 

a minimum number of adults returns that co-managers thought would prevent the loss of Chinook 

salmon in the Lostine River as stated in the short term goal. 

As with any supplementation program, there are risks as well as benefits. The risks that comanagers were most concerned with were that natural and hatchery life history traits could 

diverge over time and that productivity of the stock could decrease due to a decreased fitness in 

hatchery origin fish. The benefits that were expected with supplementation were higher egg-tosmolt survival and harvest opportunities. 

RESULTS 

Prior to the first adult returns from the supplementation, the catch at the weir from 1997 to 2000 

did not exceed 100 fish. Escapement of hatchery Chinook salmon met the desired minimum adult 

return of 250 Chinook salmon beginning in 2001. But not all returning fish are captured at the 

weir. Escapement at the Lostine River weir is estimated using a mark-recapture technique (Cleary 

and Edwards 2009). Figure 2 shows the catch from 1997 to 2009 with total escapement (age 3-

5) shown by the dotted line. Only in 2007 has there been a census count at the weir. But the point 

to be made is that escapement since 2001 has been greater than 500 Chinook salmon. However, 

the mid-term goal was to return 500 natural origin Chinook salmon. This goal was reached only 

recently in 2008 and 2009 (Figure 3). 

The majority of the escapement since 2001 has been comprised of hatchery origin adult returns. 

The abundant returns of hatchery origin Chinook salmon have contributed to both sport and tribal 

fisheries below Lower Granite Dam, and in the Wallowa River and Lostine River. The terminal 

tribal fishery and distribution of fish at the weir for food banks occurred on and off from 2001 to 

2009. The sports fishery was re-established in the Wallowa River in 2008 and continued in 2009. 

The majority of the harvest (Figure 4) occurred in 2009 from the tribal distribution at the weir. The 

Nez Perce Tribe was required to remove these hatchery fish at the weir under an existing 

agreement with co-managers to limit the influence of hatchery origin spawners (Ashe et al. 2000) 
155 

Figure 2. The catch of natural and hatchery Chinook salmon at the Lostine River weir from 

1997 to 2009 and the total escapement (age 3-5) as shown by the dotted line. 

Figure 3. The estimated escapement of Lostine River Chinook salmon that occurred from 

1997 to 2009. 

0

500

1,000

1,500

2,000

2,500

3,000

3,500

Chinook Salmon (n)

Return Year

Natural Hatchery Total Escapement

0

500

1000

1500

2000

2500

3000

3500

Escapement

Return Year

Natural Hatchery
156 

Figure 4. The number of Lostine River Chinook salmon harvested by fishery and the percent 

of harvest accomplished by each fishery. 

During the first four years of the program it was not possible to meet the goal of 250,000 smolts. 

Adult returns were so poor in brood years 1998 and 1999 that no broodstock was taken for the 

conventional supplementation program and we relied entirely on smolts produced from the captive 

broodstock program for juvenile releases in 2000 and 2001. However, with the exceptions of 2005 

and 2008, the smolt production goal of 250,000 smolts was reached and by 2005, 75% of the 

smolt production was accomplished by the conventional broodstock program (Figure 5). Prerelease sampling at Lookingglass Fish Hatchery showed that smolts ranged in size from 109 to 

128 mm. The smolts were acclimated and volitionally released from two temporary structures. 

The facility had a combined capacity for 125,000 smolts. This meant that when smolt production 

reached 250,000 smolts in 2003 the single acclimated volitional release had to be split into two 

acclimated volitional release that occurred in the early and late spring. As a single release group, 

these hatchery smolts were significantly larger than their natural smolt counterparts when 

compared side by side at the Lostine River screw trap and all differences were significant (Figure 

6). Hatchery smolts did not survival as well as natural smolts from the Lostine River screw trap to 

Lower Granite Dam (Figure 7). And natural smolts tended to have a more prolonged migration 

time to Lower Granite Dam and arrive a bit later than their hatchery counterparts (Figure 8). 

However, arrival timing may have been influenced in some years by the early acclimated volitional 

release group of hatchery Chinook salmon smolts. 

0

500

1,000

1,500

2,000

2,500

Number Harvested

Return Year

Terminal Tribal Fishery

Distribution at Weir

Terminal Sports Fishery

Sport and Tribal Harvest Below 

Lower Granite Dam

62.8%

15.6%

0.6%

21.0%

Overall Percent 

Harvested by Fishery
157 

Figure 5. The number of Lostine River Chinook salmon smolts produced from 1999 to 2009 

by the conventional and captive broodstock programs. 

Figure 6. Length at emigration as compared at the Lostine River screw trap from 1999 to 

2009. No data was available for 2004. 

0

50,000

100,000

150,000

200,000

250,000

300,000

Smolts Released

Year Released

Conventional Captive

Goal

0

30

60

90

120

150

180

Fork Length (mm)

Migration Year

Natural Hatchery

NA
158 

Figure 7. The survival of Lostine River natural and hatchery Chinook salmon from the 

Lostine River screw trap to Lower Granite Dam from 1999 to 2009. 

Figure 8. Average smolt migration timing to Lower Granite Dam from 1999 to 2009. 

Returning natural origin adults out performed hatchery origin adults, both as surviving adults and 

to the tributary. But in all years the hatchery smolt to adult return rate exceeded the rate of 0.1% 

used originally in planning the releases of 250,000 smolts (Figure 9). So predictably spawner 

abundance increased with escapement but the majority of the spawners were hatchery origin 

Chinook salmon (Figure 10). The number of smolts per spawner ranged from 56 smolts per 

spawner to 312 smolts per spawner from brood years 1997 to 2007 but there was no decisive 

trend (Figure 11). However, natural recruits per adult spawner showed a decrease in productivity 

from 1997 to 2000 prior to the return of age 4 hatchery females. Once age 4 hatchery females 

began returning in 2001 the number of recruits per spawner decreased below 1.0 (Figure 12). But 

this may be just a coincidence caused by poor migratory or ocean conditions. 

0%

20%

40%

60%

80%

100%

Survival from the Lostine River 

Screw Trap to Lower Granite Dam

Year Released

Natural Hatchery

0%

20%

40%

60%

80%

100%

Cumulative Frequency

Date

Natural (1999 - 2009) Hatchery (1999 - 2009)

P < 0.05
159 

Figure 9. Lostine River natural and hatchery smolt-to-adult returns and smolt to adult 

survival from brood years 1997 to 2004. 

Figure 10. Adult age 4 and 5 spawner abundance by origin in the Lostine River from 1997 to 

2009. 

0%

2%

4%

6%

8%

10%

Return Rate

Brood Year

Natural

SAR SAS

NA

0%

2%

4%

6%

8%

10%

Return Rate

Brood Year

Hatchery

SAR SAS

0

200

400

600

800

1,000

1,200

Spawners

Return Year

Natural Origin Spawners Hatchery Origin Spawners
160 

Figure 11. Natural smolts per spawner in the Lostine River from brood years 1997 to 2007. 

Figure 12. Lostine River natural Chinook salmon progeny per parent ratios from brood years 

1997 to 2004. 

No differences were observed in the size at return of age four natural and hatchery females. 

Natural age 5 females were statistically larger than age 5 hatchery females but the difference is 

probably not biologically significant (Figure 13). There was no significant difference between the 

average fecundity of age 4 or age 5 natural and hatchery Chinook salmon females from 2004 to 

2009 (Figure 14). But there were significantly fewer age 5 hatchery Chinook salmon and 

significantly more age 3 hatchery Chinook salmon returning per brood year than natural Chinook 

salmon (Figure 15). No significant differences (p > 0.05) were found between the cumulative 

percent of natural and hatchery female carcasses recovered by survey section in the Lostine 

River (Figure 16). 

0

50

100

150

200

250

300

350

Smolts per Spawner

Brood Year

NA

0.00

0.50

1.00

1.50

2.00

2.50

3.00

3.50

4.00

Adult Recruits per Spawner

Brood Year
161 

Figure 13. Average size at return of natural and hatchery Lostine River Chinook salmon from 

brood years 1997 to 2004. 

Figure 14. Average fecundity of natural and hatchery Lostine River Chinook salmon from 

1997 to 2009. 

0

20

40

60

80

100

Age 4 Females Age 5 Females

Fork Length (cm)

Natural Hatchery

P = 0.682

P = 0.037

0

1,000

2,000

3,000

4,000

5,000

6,000

Age 4 Females Age 5 Females

Natural Hatchery

P = 0.464

P = 0.401
162 

Figure 15. The average percent of Lostine River natural and hatchery Chinook salmon returns 

by age from brood year 1997 to 2004. 

Figure 16. The average and cumulative percentage and frequency of natural and hatchery 

female carcasses recovered by sections surveyed from 2001 to 2009. 

0%

20%

40%

60%

80%

100%

Age 3 Age 4 Age 5

Brood Year Returns

Natural Hatchery

P = 0.323

P = 0.030

P = 0.015
163 

Coded wire tag recoveries revealed that some of the Lostine River hatchery fish did stray. But 

stray rates were less than 3% of the smolts released and most of the straying occurred above 

Lower Granite Dam. The loss of Lostine River Chinook salmon at Lookingglass Fish Hatchery 

due to bacterial kidney disease (Renibacterium salmoninarum) was relatively minor from 1999 to 

2009 and ranged from 0 to 3,800 fish. An outbreak of infectious hematopoietic necrosis (IHN) in 

2005 forced hatchery personnel to euthanize an entire raceway but IHN occurred only in 2005 

and 2006 and IHN was not detected in any other years. 

SUMMARY 

It appears that supplementation has increased the overall abundance of Lostine River Chinook 

salmon and provided harvest opportunities. The increase in overall abundance and harvest 

opportunities has occurred because the production goal of 250,000 smolts has been met by the 

program. However, there are differences in life history traits, such as fewer returning age 5 

hatchery Chinook salmon. And there has been a decrease in adult recruit per spawner ratios but 

it is not possible to say whether this is due to differences in life history traits or other out-of-basin 

factors such as poor ocean conditions. 

LITERATURE CITED: 

Ashe, B., K. Concannon, D.B. Johnson, R.L. Zollman, D. Bryson, G. Alley. 2000. Northeast 

Oregon hatchery spring Chinook master plan. Bonneville Power Administration. Project 

No. 198805305, April 2000. DOE/BP-3267. 

Cleary, P.J. and M. Edwards. 2009. Evaluation of Spring Chinook Salmon Oncorhynchus 

tshawytscha Supplementation in the Lostine River, Oregon, 2008 Annual Report (January 

2008 to December 2008). BPA Project Number 199800702, Contract Number 00035952. 

Bonneville Power Administration. Portland, Oregon. 

GRESP. 1998. Grande Ronde Basin endemic spring Chinook salmon supplementation program: 

Preliminary Environmental Assessment (DOE/EA – 1173). Bonneville Power 

Administration, Portland, Oregon. February 1998. 

Hesse, J.A., J.R. Harbeck, and R.W. Carmichael. 2006. Monitoring and Evaluation Plan for 

Northeast Oregon Hatchery Imnaha and Grande Ronde Subbassin Spring Chinook 

Salmon. Nez Perce Tribe Dept. of Fisheries Resources Management. Box 365. Lapwai, 

Idaho. 

ICTRT. 2006. Interior Columbia Basin TRT: Viability Criteria for Application to Interior Columbia 

Basin Salmonid ESUs. Interior Columbia Basin Technical Recovery Team. July 2005. 

 
164 

 

REINTRODUCTION OF SPRING CHINOOK SALMON IN LOOKINGGLASS CREEK: 

ANALYSIS OF THREE STOCKS OVER TIME 

Steve Boe, Carrie Crump, Rey Weldert, and Jeremy Wolf 

Confederated Tribes of the Umatilla Indian Reservation 

203 Badgley Hall, Eastern Oregon University 

La Grande, Oregon 

Gene Shippentower and Gary James 

Confederated Tribes of the Umatilla Indian Reservation 

46411 Ti’Mine Way 

Pendleton, Oregon 

This work is collaborative with comanagers Oregon Department of Fish and Wildlife and Nez 

Perce Tribe, funded by the Bonneville Power Administration, and administered by the Lower 

Snake River Compensation Plan. 

ABSTRACT 

We compared natural production between an endemic spring Chinook salmon (Oncorhynchus 

tshawytscha) population that is locally extinct with two different supplementation stocks used in 

Lookingglass Creek, a tributary of the Grande Ronde River located in northeast Oregon. Habitat 

in Lookingglass Creek has been relatively unaltered over this 3-stock study period from the 1960’s 

to present. Spring Chinook salmon were once abundant in Lookingglass Creek and supported 

significant tribal and sport fisheries. Intensive monitoring of natural production occurred 

throughout the 1960’s which provided benchmark productivity data for this study. Dam 

construction on the Columbia and Lower Snake Rivers was probably a major factor in the decline 

of the native Lookingglass stock in the late 1970’s. The construction of Lookingglass Hatchery 

and weir in 1982 caused further stock reduction and extirpation. From 1992 to 1999, a nonendemic Rapid River (Idaho) stock with a history of hatchery domestication was introduced to reestablish a spring Chinook population. The weir and trap at the hatchery and outmigrant trap 

allowed for precise monitoring of fish in and fish out for this comparison study. Rapid River stock 

showed results that were generally similar to the endemic stock but with some variation across 

the metrics evaluated (redd distribution, spawn timing, fish per redd, outmigrants per redd, and 

outmigration timing within Lookingglass Creek and in the Columbia River hydrosystem). A switch 

to a local Grande Ronde River Basin stock (Catherine Creek captive broodstock progeny) began 

with juvenile releases in 2001 and returning adults placed above the weir beginning in 2004. The 

Catherine Creek stock has a much shorter history of hatchery domestication than Rapid River. 
165 

Hatchery- and natural-origin adults have returned to Lookingglass Creek and are successfully 

reproducing upstream of the hatchery. As was the case with comparison of the first two stocks, 

the current Catherine Creek stock is also beginning to show similar or increased productivity and 

similar life history. Results indicate striking potential for hatchery reintroduction/supplementation 

success for spring Chinook salmon. Continued work will evaluate the productivity of progeny from 

captive Catherine Creek broodstock that spawn naturally versus those that are subjected to 

another “hatchery cycle” and used for broodstock in the Lookingglass Creek reintroduction 

project. 

INTRODUCTION 

The preceding goals and objectives are consistent with the overall mission statement of the 

CTUIR Department of Natural Resources: 

“To protect, restore, and enhance the First Foods; water, salmon, deer, cous, and huckleberry - 

for the perpetual cultural, economic, and sovereign benefit of the CTUIR. We will accomplish this 

utilizing traditional ecological and cultural knowledge and science to inform: 1) population and 

habitat management goals and actions; and 2) natural resource policies and regulatory 

mechanisms.” 

Similarly, the CTUIR DNR Fisheries Program mission statement is: 

“To provide sustainable harvest opportunities for aquatic species of the first food order by 

protecting, conserving and restoring native aquatic populations and their habitats.” 

The tribal goals fit within the framework of mitigation goals established for the Lower Snake River 

Compensation Plan by the hatchery releases used to supplement any natural returns. Annual 

reports describing the historical efforts at reestablishing natural production of spring Chinook 

salmon in Lookingglass Creek are available at 

http://www.fws.gov/lsnakecomplan/Reports/CTUIRreports.html. 

The native Lookingglass Creek stock of spring Chinook salmon was extirpated within a few years 

after establishment of Lookingglass Hatchery (LH) in 1982. Prior to 1982, Lookingglass Creek 

had the second highest number of redds in the Basin (Figure 1). Lookingglass Creek is within the 

“usual and accustomed” areas of gathering for the Confederated Tribes of the Umatilla Indians 

(CTUIR). The start-up of Lookingglass Hatchery represented the beginning of large-scale 

hatchery intervention in the Grande Ronde River Basin, with the exceptions of the Wenaha and 

Minam rivers that remain wild fish only. CTUIR, along with comanagers, began efforts in the early 

1990s to reestablish natural production of spring Chinook salmon in Lookingglass Creek. Several 

stocks, including remnants of the endemic stock, Imnaha River, Wind River (Washington), Carson 

Hatchery (Washington), and Rapid River (Idaho) were used before comanagers selected Rapid 

River. The Rapid River stock was replaced with Catherine Creek stock (native to the Grande 

Ronde River Basin) beginning in 2001. The present management goal is to reintroduce spring 

Chinook salmon into Lookingglass Creek using Catherine Creek captive brood stock to support 

natural population restoration, tributary harvest, and maintain genetic diversity of a gene bank for 

the Catherine Creek stock. 
166 

Figure 1. Percent of total redds by stock (tributary) in the Grande Ronde River Basin 

(LGC=Lookingglass Creek, CC=Catherine Creek UGR=Upper Grande Ronde R., 

LOS=Lostine R. , WEN=Wenaha R., MIN=Minam R.). 

Lookingglass Creek provides a unique study opportunity to observe and evaluate natural 

production from an endemic stock vs two different supplementation treatments. The reference 

condition (endemic stock) and two treatments in this unplanned experiment occur in the same 

stream over different time periods. The study takes place in a stream within a relatively healthy 

watershed with much less effect from human activities (e.g. grazing, water withdrawals, mining, 

and logging) that are common to other streams in the Basin. The Lookingglass Hatchery weir 

affords near complete control over fish that move upstream to spawn. In addition to this project 

on Lookingglass Creek, other supplementation projects in the Grande Ronde River Basin using 

local stocks include the Upper Grande Ronde River, the Lostine River, and Catherine Creek. 

Burck (1993) studied the endemic stock (control) from late 1963 through late 1974 (Study Era 1). 

Metrics from juvenile and adult life history and production were reported. Rapid River stock 

(supplementation treatment 1) were used in a reintroduction effort from 1992-2000 (Study Era 2). 

The Rapid River stock was used in several streams in the Basin. Metrics similar to Burck (1993) 

were contained in annual reports that can be accessed at 

http://www.fws.gov/lsnakecomplan/Reports/CTUIRreports.html. Catherine Creek captive 

broodstock progeny (supplementation treatment 2) have been used since 2001 (Study Era 3). 

Rapid River stock were replaced with Catherine Creek stock because Catherine Creek stock were 

local, had characteristics similar to the extirpated endemic stock, and surplus was available. It 

also afforded an opportunity to study performance of captive broodstock in the natural 

environment. Captive broodstock are collected in the natal stream as parr, reared in the hatchery 

until maturity, and spawned. Their progeny are hatchery-reared, marked, and released, usually in 

the spring as smolts. 

Current spring Chinook salmon management (Appendix 1) for Lookingglass Creek (developed 

with comanagers) includes a sliding scale for disposition of hatchery- and natural-origin adults 

Stock

LGC CC UGR LOS WEN MIN

Percent of Total Redds

0

5

10

15

20

25

30

1965-1981 

1982-1991 
167 

collected at the Lookingglass Hatchery trap and holding returns for either outplanting above the 

trap or use as conventional broodstock at the hatchery. Both marked (F1) and unmarked (F2) 

returns are outplanted and used as hatchery broodstock. This is unique in the Grande Ronde 

Basin, as returning adults used for conventional broodstock from Catherine Creek, the Lostine 

River, and the Upper Grande Ronde River exclude any marked (F1) captive broodstock progeny 

due to their extended rearing time in the hatchery environment. 

The supplementation sequence for Catherine Creek captive broodstock progeny into 

Lookingglass Creek began with the first liberation of juveniles from brood year 2000 in September 

2001. The first substantial returns of Catherine Creek captive broodstock (F1) occurred in 2004. 

This was the first year of Study Era 3 when adults were released above the Lookingglass Hatchery 

to spawn naturally. The first age 4 unmarked returns (F2) occurred in 2008. 

Our Research Goal is to conduct monitoring and evaluation studies to inform managers 

concerning use of a local spring Chinook salmon broodstock (Catherine Creek) for reintroduction 

into Lookingglass Creek. Specific objectives are to 1)compare performance across three time 

periods of two reintroduced stocks (Rapid River, Catherine Creek) with the extirpated endemic 

stock of spring Chinook salmon in Lookingglass Creek, and 2)evaluate use of Catherine Creek 

F1 captive broodstock progeny for natural spawning and hatchery production. 

STUDY AREA 

The Lookingglass Creek watershed is in the Blue Mountains of northeast Oregon with the 

headwaters at an elevation of 1,484 m above sea level (Figure 2). Flow is to the southeast for 25 

river km (rkm) through the Umatilla National Forest then through private land before entering the 

Grande Ronde River at rkm 137, at an elevation of 718 m above sea level. Lookingglass Creek 

has five major tributaries: Lost Creek, Summer Creek, Eagle Creek, Little Lookingglass Creek, 

and Jarboe Creek. Nearly all spring Chinook salmon spawning occurs in Lookingglass Creek and 

Little Lookingglass Creek. Lookingglass Hatchery is located at approximately rkm 4.0 on 

Lookingglass Creek. 
168 

Figure 2. Lookingglass Creek watershed. 

METHODS 

Standard methods for fish sampling and data collection to evaluate performance measures 

(metrics) for spring Chinook salmon followed Burck 1993, Hesse et al. 2006 and Johnson et al. 

2007. In summary, these included adult trapping, spawning ground surveys, parr collection, and 

outmigrant sampling with a 1.5 m rotary screw trap. Units for spawning ground surveys (Figure 3) 

were modified from Burck (1993). Metrics used to evaluate stock performance for adult life history 

and production included spawner abundance, percent hatchery/natural origin spawners, redd 

distribution, adults/redd, and prespawning mortality, smolt-to-adult ratio, and progeny per parent 

(recruits/spawner). Metrics used for juvenile life history and production included first-year growth, 

survival to Lower Granite Dam and migration timing to McNary Dam, total outmigrants, 

outmigrants/redd and outmigration by season. Detailed descriptions of methods used are in 

annual reports accessible at http://www.fws.gov/lsnakecomplan/Reports/CTUIRreports.html. 

Comparisons with other populations in the Grande Ronde Basin made use of unpublished data 

provided by ODFW Fish Research, La Grande, Oregon, and published data from completed 

reports available at http://www.fws.gov/lsnakecomplan/Reports/ODFWreports.html and 

http://efw.bpa.gov/searchpublications. Natural-origin spring Chinook salmon data for Grande 

Ronde Basin stocks were obtained from Favrot et al. (2010). We obtained SAR and progeny-perparent data by visually estimating data from figures in Carmichael et al. 2011a and Carmichael et 

al. 2011b (both this volume) and Cleary (2011, this volume). We attempted to include the time 

frame from 1992-present when including other streams for comparison with Lookingglass Creek. 
169 

Figure 3. Spawning ground survey unit designations and river miles for Lookingglass Creek 

(modified from Burck 1993). 

RESULTS 

Comparisons of different populations follow stream name (e.g. LGC=Lookingglass Creek, 

WEN=Wenaha River). Comparisons for Study Eras 1 and 2 include L-E (Lookingglass Creek, 

endemic stock), L-R F1 and L-R F2 (Lookingglass Creek, Rapid River stock, F1 (brood years 1992-

1994) and F2 generations (brood years 1996-1997). Comparisons for Study Era 3 include L-C F1

and L-C F2 (Lookingglass Creek, Catherine Creek captive broodstock, F1 (brood years 2004-2006) 

and F2 generations (brood years 2008-2009). 

Population estimates of spawners above the Lookingglass Hatchery weir showed little variation 

from the number released, indicating a large portion of the fish spawning upstream were handled 

at the trap (Figure 4). The numbers of spawners during Study Eras 2 and 3 have been much lower 

than Study Era 1 (endemic), a result of the low numbers of juveniles released; 2008 was the first 

year when spawners and redds began to approach endemic (Study Era 1) levels. 
170 

Figure 4. Average numbers of adults released above the Lookingglass Hatchery weir to 

spawn naturally. 

Adult spring Chinook salmon released above Lookingglass Hatchery to spawn naturally during 

Study Eras 2 and 3 ranged from 47 to 188. The percentages of hatchery- and natural-origin 

returns released have been variable, usually dominated by hatchery-origin (Table 1). Spawner 

composition of both reintroduction periods has shifted from hatchery-origin to higher fractions of 

natural-origin. Brood years 1996-1997 (L-R F2) saw the fewest hatchery-origin returns spawning 

in nature. 

Table 1. Hatchery- and natural-origin releases to spawn naturally above Lookingglass 

Hatchery, brood years 1992-2009. 

BY # Hatchery-origin # Natural-origin Total Released % Hatchery-origin 

1992 128 5 133 96 

1993 99 0 99 100 

1994 73 39 112 65 

 

1996 0 50 50 0 

1997 2 75 77 3 

2004 101 0 101 100 

2005 57 0 57 100 

2006 47 0 47 100 

2007 67 6a 73 92 

 

2008 150 38 188 80 

2009 40 63 103 39 

a all age 3

Stock

Endemic L-R L-C

Number

0

100

200

300

400

500

Released 

Population Estimate 
171 

Most spawning above Lookingglass Hatchery occurs in Unit 3 (Figure 5). Differences in the 

release time and location for upstream spawners can affect redd distribution If outplanting occurs 

late in the season, and above Little Lookingglass Creek, few redds are found in that tributary. 

Outplanting earlier in the season and below Little Lookingglass Creek will afford more natural 

conditions for mate selection and redd location. 

Figure 5. Lookingglass Creek redds by unit and study era. 

Fish/redd values for Study Era 3 have been less than 2 (Figure 6), lower than both Study Era 2 

(2.5-3) and Study Era 1 (endemic stock). Fish/redd values for Study Era 3 were also lower than 

for Catherine Creek, the Upper Grande Ronde River, or the Lostine River. Prespawning mortality 

was typically less than 5% for Lookingglass Creek, but may be much higher in some years if 

headburn is a problem on fish arriving at the trap. Prespawning mortality has been a frequent 

problem at the Upper Grande Ronde River due to high water temperatures, but this is rarely a 

problem at Lookingglass Creek. Flow in Lookingglass Creek during the summer months is 

primarily from springs in the upper reaches and much of the stream is well-shaded with a steeply 

incised channel and abundant riparian vegetation. The timing of natural spawning in Lookingglass 

Creek has varied little during four decades, typically beginning in mid-August and concluding by 

mid-September. This is the same general period for other Grande Ronde Basin stocks. 

Stock/Unit

Endemic L-R L-C

Percent of Total Redds

0

20

40

60

80

Unit 1 

Unit 2 

Unit 3 

Unit 4 
172 

Figure 6. Fish/redd for various stocks in the Grande Ronde Basin. 

During Study Eras 2 and 3, total outmigrant production was low, the result of low numbers of 

spawners above the weir compared to Study Era 1. The first year with a substantial number of 

adults spawning above the weir was 2008. Outmigrants per redd for Lookingglass Creek during 

Study Eras 2 and 3 were higher than the endemic era (Table 2). Outmigrants/redd for 

Lookingglass Creek appeared to be higher with lower numbers of redds across the three eras 

(Figure 7). Outmigrants/redd has been higher for Lookingglass Creek during the reintroduction 

periods than for other Grande Ronde Basin stocks (Figure 8). 

 

Stock

End L-R F1 L-R F2 L-C F1 L-C F2 CC UGR LOS

Fish/redd

0

2

4

6

8

10

12
173 

Table 2. Outmigrants/redd for spring Chinook salmon from Lookingglass Creek. 

BY Outmigrantsa Redds Outmigrants/redd 

1965 33,437 99 338 

1966 55,315 279 198 

1967 31,036 120 259 

1968 29,076 133 219 

1969 33,148 276 120 

 

1992 8,715b 49 178 

1993 46,536 132 353 

1994 6,388 40 160 

 

1996 14,625 24 609 

1997 13,330 24 555 

 

2004 16,344 49 334 

2005 11,500 29 397 

2006 12,502 28 447 

2007 7,796 32 244 

 

2008 59,942 104 576 a Usually from August of brood year +1 through June of brood year+2. For example, the 

outmigration period for BY 1965 would be from August of 1966 through June of 1967. 

b trap operated beginning in November 1993 

Figure 7. Log10 regression of redds on outmigrants/redd for Lookingglass Creek spring 

Chinook salmon. 

Log Redds

1.2 1.4 1.6 1.8 2.0 2.2 2.4 2.6

Log Outmigrants/Redd

2.0

2.2

2.4

2.6

2.8

3.0

Log Outmigrants/Redd = 3.023-Log Redds*0.301

F = 4.79, P = 0.048
174 

Figure 8. Average outmigrants/redd for various Grande Ronde Basin spring Chinook salmon 

stocks. 

Some outmigration occurs throughout the year. Most outmigrants >60 mm FL leave Lookingglass 

Creek during the fall after emergence, designated the “early” period. Smaller numbers leave 

during the following spring, or “late” period). All three study eras showed similar patterns, with 80-

87% “early” migrants, compared to an average of 71% “early” migrants for Catherine Creek 

(Favrot et al. 2010). Most Upper Grande Ronde River outmigrants leave in the spring (Favrot et 

al. 2010). 

Growth of juveniles sampled in the screw trap during both reintroduction eras was similar, 

reaching greater lengths than the endemic stock (Figure 9). This pattern may have been related 

to the higher density of juveniles during the endemic era. Summer growth of parr had two periods 

of rapid growth separated by a period of slower growth during Study Eras 1 and 3, but only one 

period of rapid growth during summer was evident for parr during Study Era 2. 

Stock

End L-R F1 L-R F2 L-C F1 L-C F2 CC UGR LOS

Average outmigrants/redd

0

100

200

300

400

500

600

700
175 

Month

Apr May Jun Jul Aug Sep Oct

Mean FL (mm)

30

40

50

60

70

80

90

100

Endemic 

LGC-RR 

LGC-CC 

Figure 9. Mean FL of Lookingglass Creek spring Chinook salmon parr. 

Survival probabilities to Lower Granite Dam for parr PIT-tagged in late July-early August in the 

primary nursery areas upstream of Lookingglass Hatchery were usually between 0.10-0.30 

(Figure 10). Survival probabilities for stocks with the most years of data (Catherine Creek and the 

Lostine and Minam rivers) varied 5-6 fold. Arrival timing of juvenile outmigrants at McNary Dam 

was compressed into a shorter time frame for Study Era 1 than either Study Eras 2 or 3 (Figure 

11). McNary Dam was used instead of Lower Granite Dam because some mark (freeze brand) 

data were available from the endemic era. 

 
176 

Figure 10. Parr survival probabilities to Lower Granite Dam. 

Figure 11. Arrival timing of Lookingglass Creek spring Chinook salmon outmigrants to 

McNary Dam. 

Progeny-per-parent ratios for Lookingglass Creek natural spawners were greater than 1 

(replacement) for only 2 of 7 years (Table 3). Progeny-per-parent ratios for Grande Ronde Basin 

stocks show considerable variation between stocks and brood years (Figure 12). 

Stock

L-R F1 L-R F2 L-C F1 CC UGR LOS WEN MIN

Survival Probability

0.00

0.05

0.10

0.15

0.20

0.25

0.30

0.35

Week

3/25 4/1 4/8 4/15 4/22 4/29 5/6 5/13 5/20 5/27 6/3 6/10 6/17 6/24 7/1 7/8

%

0

5

10

15

20

25

30

Endemic 

LGC-RR 

LGC-CC 
177 

Table 3. Progeny-per-parent (recruits/spawner) by brood year for natural-origin spring 

Chinook salmon from Lookingglass Creeka. 

BY Spawners Age 4 

returns 

Age 5 

returns 

Progeny:parent 

1992 186 94 30 0.67 

1993 286 83 27 0.38 

1994 113 30 4 0.30 

 

1996 47 48 15 1.34 

1997 67 38 4 0.63 

2004 96 45 14 0.61 

2005 42 63 8 1.69 a ages 4/5 only, adjusted for prespawning mortality 

Figure 12. Progeny-per-parent for Grande Ronde Basin stocks. 

Smolt-to-adult ratios (SAR, Table 4) for 5 of 7 brood years were below the range of 2-6% that is 

the objective for anadromous salmon and steelhead in the Columbia Basin (Northwest Power and 

Conservation Council 2009). Median values for natural-origin SAR have been below 2% for 4 

Grande Ronde Basin stocks (Figure 13). 

 

Stock

LGC CC UGR LOS WEN MIN

Progeny-per-parent (R/S)

0

1

2

3

4
178 

Table 4. Smolt-to-adult (SAR) ratios for natural-origin spring Chinook salmon from 

Lookingglass Creek. 

BY Seq* Age 4 

Returns 

Age 5 Returns SAR(%) 

1992 2,457 94 30 5.0 

1993 8,895 83 27 1.2 

1994 1,748 30 4 1.9 

 

1996 6,401 48 15 1.0 

1997 4,338 38 4 1.0 

 

2004 2,962 45 14 2.0 

2005 4,957 63 8 1.4 

* Seq for a brood year is the sum by season (fall, winter, spring) of the product of 

outmigrants and survival probability to Lower Granite Dam. 

Figure 13. SARs for Grande Ronde Basin stocks. 

CONCLUSIONS 

Performance measures were variable but generally similar between the extirpated endemic stock 

and both introduced stocks. Parr growth was higher for both of the reintroduced stocks and 

outmigrants per redd was higher for some brood years of the reintroduced stocks. Juvenile and 

adult abundance measures for the endemic stock were greater than either of the reintroduced 

stocks. There were minor differences in most performance measures between Lookingglass 

Creek natural spawners from 2004-present and Catherine Creek natural spawners for the same 

period. The data suggest a potential for successful reintroduction/supplementation of spring 

Chinook salmon in Lookingglass Creek using captive broodstock as the donor stock. 

Stock

LGC CC UGR LOS

SAR (%)

0

1

2

3

4

5

6

7
179 

These results should be viewed as preliminary since only short time series (<10 brood years) are 

available for the three study eras. Further complicating comparisons is the unplanned nature of 

the experiment and the confounding effect of time. Any observed differences in life history or 

production may result not from stock differences but, for example, from environmental conditions 

in the ocean during the evaluation period. 

The apparent density-dependent relationship for outmigrants/redd and redd warrants further 

investigation. This pattern is surprising since there has been relatively little habitat deterioration 

since extirpation of the endemic stock. 

Future work will include evaluating the productivity of captive Catherine Creek broodstock 

progeny that spawn naturally compared to those subjected to another “hatchery cycle” and used 

for broodstock in the Lookingglass Creek reintroduction project. We will also compare the 

performance of Lookingglass Creek and Catherine Creek conventional broodstocks (Objective 

2b). 

REFERENCES 

Burck, W. A. 1993. Life history of spring Chinook salmon in Lookingglass Creek, Oregon. 

Information Reports Number 84-1. Oregon Department of Fish and Wildlife, Fish Division. 

Portland, Oregon. 

Carmichael, R. W., Hoffnagle, T., Feldhaus, J., Eddy, D., and N. Albrecht. 2011a. Catherine Creek 

Spring Chinook Salmon Hatchery Program Review. Lower Snake River Compensation Plan 

Spring Chinook Salmon Program Review. U. S. Fish and Wildlife Service, Boise, Idaho. 

Carmichael, R. W., Hoffnagle, T., Feldhaus, J., Eddy, D., and N. Albrecht. 2011b. Upper Grande 

Ronde River Spring Chinook Salmon Hatchery Program Review. Lower Snake River 

Compensation Plan Spring Chinook Salmon Program Review. U. S. Fish and Wildlife Service, 

Boise, Idaho. 

Cleary, P. 2011. Lostine River Supplementation Program (1997-2009). Lower Snake River 

Compensation Plan Spring Chinook Salmon Program Review. U. S. Fish and Wildlife Service, 

Boise, Idaho. 

Favrot, S. D. and eight coauthors. 2010. Investigations into the early life history of naturally 

produced spring Chinook salmon and summer steelhead in the Grande Ronde River Subbasin. 

Annual report by the Oregon Department of Fish and Wildlife to the Bonneville Power 

Administration. Project Number 1992-026-04. 

Hesse, J. A., Harbeck, J. R., and R. W. Carmichael. 2006. Monitoring and evaluation plan for 

Northeast Oregon hatchery Imnaha and Grande Ronde Subbasin spring Chinook salmon. 

Prepared for Bonneville Power Administration, Portland Oregon. 

Johnson, D. H., Shrier, B. M., O’Neal, J. S., Knutzen, J. A., Augerot, X., O’Neill, T. A., Pearsons, 

T. A. and 37 additional contributing authors. 2007. Salmonid Field Protocols Handbook: 

Techniques for Assessing Status and Trends in Salmon and Trout Populations. American 

Fisheries Society, Bethesda. 
180 

Northwest Power and Conservation Council. 2009. Columbia River Basin Fish and Wildlife 

Program 2009 Amendments. Council Document 2009-09. Available at 

http://www.nwcouncil.org/library/2009/2009-09.pdf. 

ACKNOWLEDGMENTS 

We would like to thank Scott Marshall, Steve Yundt, Joe Krakker, Tammy Froscher, Margaret 

Anderson, and Chris Starr (LSRCP) for program support, administration, and review, and advice. 

We thank Julie Burke and Celeste Reeves for program assistance and Nicole Novak and Stacy 

Schumacher for GIS assistance (CTUIR). We thank Mike McLean, Laurie Hewitt and Ryan 

Seeger for field assistance (CTUIR). We thank Roger Elmore, Scott Patterson, and the many 

other ODFW staff that have helped with field assistance and coordination. Our thanks to ODFW 

Fish Research, La Grande, for providing unpublished data. We thank the private landowners 

along Lookingglass Creek and tributaries, including Forest Capital LLC, that have kindly provided 

us to access their properties to conduct this work over the years. We thank Dave Crabtree and 

Darlene Robison (Umatilla National Forest) for field assistance and supply of water temperature 

and other data. 

 
181 

Appendix 1. Draft Lookingglass Creek Spring Chinook Salmon Management Plan (being 

reviewed by comanagers, October 2010) 

Lookingglass Creek is co-managed by the Confederated Tribes of the Umatilla Indian Reservation 

(CTUIR), the Nez Perce Tribe (NPT), and Oregon Department of Fish and Wildlife (ODFW). The 

primary objective of this plan is to coordinate the restoration of spring Chinook into Lookingglass 

Creek using Catherine Creek stock and utilizing two hatchery programs; the Lower Snake River 

Compensation Plan (LSRCP) mitigation program and the Bonneville Power Administration (BPA) 

captive broodstock program. Activities in Catherine Creek will be outlined as they relate to the 

Lookingglass Creek restoration effort. 

Program Goal 

The goal of the Lookingglass Creek Spring Chinook Hatchery Program is to reintroduce spring 

Chinook into Lookingglass Creek using the Catherine Creek stock to support natural population 

restoration, tributary harvest, and maintenance of a gene bank for the Catherine Creek stock. 

Adult Return Goals 

There are no LSRCP or Tribal Recovery Plan (TRP) hatchery and natural adult return goals 

identified specifically for Lookingglass Creek. However, LSRCP does have a specific 

spring/summer Chinook goal of 58,700 hatchery adults for the Snake River and 5,820 hatchery 

adults into the Grande Ronde Basin. The TRP return goal for the Grande Ronde Basin is 16,000 

adults. Restoration of a genetically independent Lookingglass spring Chinook population to a 

“viable status” is not necessary to achieve viable status of the Grande Ronde Major Population 

Group (MPG). 

Historically, Lookingglass Creek abundance exceeded 1,000 adults based on redd count data 

from 1950s-1970s. The Interior Columbia Technical Recovery Team (ICTRT) has designated 

Lookingglass Creek as a “Basic Population” with a Minimum Abundance Threshold (MAT) of 500 

natural adults. 

Juvenile Production and Releases 

To meet the LSRCP Grande Ronde Basin adult mitigation goal, a juvenile production target of 

900,000 fish at 20 fish per pound with an estimated return rate of 0.87% was originally identified. 

In 2002, the Grande Ronde Spring Chinook Hatchery Management Plan (GRSCHMP) was 

developed which outlined more specific hatchery production goals for each tributary in the basin. 

The GRSCHMP identified an initial production target of 150,000 yearling smolts for Lookingglass 

Creek and 250,000 yearling smolts for Catherine Creek. After the captive brood evaluations were 

completed, the release goal for Lookingglass Creek was to be increased to 250,000 with a 

corresponding decrease to 150,000 for Catherine Creek. These changes have occurred and 

current production as listed in Table B1 of the 2009-2017 United States v. Oregon Management 

Agreement is outlined in Table 1. 

 
182 

Table 1. Lookingglass Creek and Catherine Creek production outlined in Table B2 of 2009-

2017 US v. Oregon Management Agreement. 

Release 

Site 

Rearing 

Facility Stock 

Life 

Stage

Target 

Release 

Number 

Primary 

Program 

Purpose Funding 

LGC LOOH/CB CC Smolt 250,000 Fishery/Reintroduction LSRCP/

BPA 

CC LOOH/CB CC Smolt 150,000 Supplementation/Fishery LSRCP/

BPA 

LGC=Lookingglass Creek, CC=Catherine Creek 

LOOH=Lookingglass Hatchery, CB=Captive Broodstock 

LSRCP=Lower Snake River Compensation Plan 

BPA=Bonneville Power Administration 

The BPA captive brood program for Catherine Creek was established in response to low 

escapements in the mid to late 1990’s. Production from this program not needed in Catherine 

Creek is available to meet any production shortfalls in the Lookingglass Creek program. However, 

this program is being phased out with brood year 2005. The last spawn of Catherine Creek captive 

adults should be 2010 with the last production available in 2012. Returns from this program would 

be expected through 2015 

Releases for the Lookingglass Creek program occur on-station from Lookingglass Hatchery. Fish 

will be volitionally released for at least one week prior to force out in mid-April. Size at release 

goal is 20 fish per pound. Any changes in size or release strategies will be coordinated through 

the Lookingglass Hatchery Annual Operating Plan (AOP).

Marking 

Marking for the Lookingglass Creek program has been outlined in Attachment C of the 2009-2017 

United States v. Oregon Management Agreement. Conventional brood releases will be 100% Ad 

clipped with representative coded-wire-tag (CWT) groups. Captive brood releases will be 100% 

AdCWT. 

Weir Management 

All Lookingglass Creek adults arriving at the at the Lookingglass Hatchery intake weir prior to July 

4 will be ponded into the adult holding ponds. Disposition of these adults will occur in early July 

according to the guidelines in Table 2 and adults designated to be passed upstream will be 

outplanted at that time. Disposition of Lookingglass Creek adults arriving after July 4 will be based 

on the percentages outlined in Table 2. All adults passed upstream will have genetic samples 

taken. 

 
183 

Table 2. Pass:Keep Disposition 

Escapement 

Level 

% Passed Above % Keep for Brood 

150 67 33 

200 60 40 

250 55 45 

300 50 50 

>300 Adjustments will be based on brood 

needs. If brood need has been met 

remainder to be released upstream. 

Adults arriving at the weir that are identifiable as Upper Grande Ronde or Lostine fish will be 

ponded into their respective brood ponds. Catherine Creek adults may be retained if needed for 

brood or spawning escapement or recycled into lower Lookingglass Creek 

Broodstock Management 

Broodstock for the program will be collected from returns to either the Lookingglass Hatchery weir 

or the Catherine Creek weir. Either conventional or captive hatchery adults may be used for brood. 

The goal for broodstock composition will be to incorporate 30% natural origin adults to maintain 

genetic diversity and counteract domestication selection in the program. In addition, no more than 

25% of the returning natural origin adults shall be retained for brood. The broodstock collection 

goal will not be constrained by the 25% cap on natural adult collection. If a shortage of natural 

adults occurs, then additional hatchery adults will be collected in order to meet the brood target. 

It is estimated that 158 adults (47 natural origin and 111 hatchery origin) will be required for brood 

to meet the 250,000 smolt production level. 

Escapement 

The ICTRT has established a MAT of 500 adults for Lookingglass Creek population in order to 

reach viable status with an estimated 90% of the historical habitat located upstream of the current 

weir site. Other documents have suggested that historically the full seeding level is much higher 

that this figure. In the near term, Lookingglass Creek in the reach above the weir will be managed 

for an escapement goal of 1,000 adults. 

Jack Management 

Hatchery jacks will be incorporated into the broodstock at a target rate of one for every 10 adult 

males collected (8 fish). All natural jacks will be released upriver. No hatchery jacks will be 

released upriver. All CWT hatchery jacks will be sacrificed for tag recovery. Other hatchery jacks 

will either be sacrificed with carcasses provided to the Tribes or food banks or recycled into lower 

Lookingglass Creek for harvest benefits. 

Surplus Production 

Every attempt will be made to adhere to the production goals. However, surplus production may 

occur due to higher than anticipated fecundities or survival rates. Any production above the 

identified goals will be reared to full term yearling smolts if hatchery space is available. If space 

is not available, surplus production will be outplanted as fry or fingerlings in the fall into lower 

Lookingglass Creek. These fish would be 100% marked to indicate hatchery origin. 

 
184 

Fish Health 

The Lookingglass Creek artificial production programs included within this management plan will 

follow the Integrated Hatchery Operations Team (IHOT) policies and procedures for fish health. 

Bacterial Kidney Disease (BKD) is of special management concern within the spring Chinook 

program. Eggs from individual females will be incubated separately and eggs from females with an 

ELISA value of 0.8 or higher will be culled from the program. If a production surplus does occur, eggs 

from females with an ELISA reading higher that 0.4 may be culled rather than reared. 

Harvest 

It is anticipated that the run composition into Lookingglass Creek in the next few years will be 

heavily skewed toward hatchery origin adults. Large returns of hatchery origin spring Chinook 

may provide opportunities for harvest. Management details for harvest of spring Chinook in 

Lookingglass Creek and will be outlined in Tribal Resource Management Plans (TRMP), Fishery 

Management and Evaluation Plan (FMEP) and/or under the 4d Rule. 

 
185 

IMNAHA RIVER SPRING/SUMMER CHINOOK SALMON 

HATCHERY PROGRAM REVIEW 

Richard W. Carmichael 

Tim Hoffnagle 

Joseph Feldhaus 

Debra Eddy 

Nick Albrecht 

Oregon Department of Fish and Wildlife 

203 Badgley Hall, EOU 

One University Blvd 

La Grande OR 97850 

 

This program is a cooperative effort of the Oregon Department of Fish and Wildlife, the Nez Perce 

Tribe and the Confederated Tribes of the Umatilla Indian Reservation. The program is funded by 

the Bonneville Power Administration and administered by the United States Fish and Wildlife 

Service under the Lower Snake River Compensation Plan. 

INTRODUCTION AND BACKGROUND 

This paper provides background information, program development history, and an assessment 

of program performance for the Imnaha River spring/summer Chinook salmon Oncorhynchus

tshawytscha hatchery program. We cover the period from program initiation in 1982 to the present 

(2010). 

The Imnaha River basin historically supported an abundant run of spring/summer Chinook 

salmon. Tribal and recreational fisheries occurred throughout the basin. Recreational fisheries 

were closed in the mid-1970s due to the depressed status of the population and tribal fishing was 

limited in many years. 

The Imnaha River basin is located in Northeastern Oregon. The basin originates in high elevation 

areas of the Eastern Wallowa Mountains and the plateau between the Wallowa River drainage 
186 

and Hells Canyon. The Imnaha River enters the Snake River at rkm 309.9. Historically, the 

primary production areas included the upper mainstem of the Imnaha River and Big Sheep Creek. 

The Lower Snake River Compensation Plan (LSRCP) Imnaha River spring/summer Chinook 

hatchery program was initiated in 1982 in response to severe abundance declines that occurred 

in the mid-1970s (Figure 1). 

Figure 1: Natural-origin adult abundance of Imnaha River spring/summer Chinook salmon 

population, 1949-2009. 

Table 1. Lower Snake River Compensation Plan mitigation goals for Oregon’s 

spring/summer Chinook salmon in the Imnaha River basin. Adult and survival 

goals are expressed for returns to the compensation area and total catch and 

escapement. 

Category Goal 

Compensation Area 

Annual smolt goal

Annual pounds of production

Annual adult goal

Broodyear smolt–to-adult return rate (SAR)

 

Total Catch & Escapement 

Annual adult goal

Brood year smolt-to-adult survival rate (SAS)

490,000 Smolts(360,000 interim)

24,500 lbs.

3,210 Adults

0.65%

16,050 Adults

3.25%

Run year

1950 1960 1970 1980 1990 2000

Natural adults

0

1000

2000

3000

4000

5000

6000

Pre-supplementation Post-supplementation
187 

Annual adult mitigation, brood year specific smolt-to-adult return and total survival rates, and 

annual smolt production goals were established to compensate for the estimated annual loss of 

48% of the adult production (Table 1). 

The adult return and smolt-to-adult return rate goals for the compensation area represent the 

required performance to the area above Lower Granite Dam. The total adult and smolt-to-adult 

survival rate goals were determined based on an assumed catch to escapement ratio of four-toone that existed prior to construction of the dams. An interim smolt production goal of 360,000 

has been adopted due to rearing space limitations and preferred density criteria at Lookingglass 

Fish Hatchery (LFH). 

The implementation of LSRCP Imnaha Chinook salmon hatchery program has been guided by 

five priority management objectives: 1) establish an annual supply of broodstock capable of 

meeting production goals; 2) maintain and enhance natural production while maintaining long 

term fitness of the natural population; 3) re-establish historic tribal and recreational fisheries; 4) 

establish a total return number of spring Chinook salmon that meets the LSRCP compensation 

goal; 5) operate the hatchery program to maintain the genetic and life history characteristics of 

the natural population and have hatchery fish characteristics mimic wild fish, while achieving 

management objectives. 

Figure 2. Map of the Grande Ronde Imnaha river basins including the Imnaha weir / 

acclimation site and Lookingglass Fish Hatchery. 

The Imnaha River juvenile acclimation and adult weir/trapping facility is located at rkm 85 on the 

mainstem of the Imnaha River (Figure 2). The Imnaha weir/ acclimation site is operated as a 

satellite of LFH, which serves as the adult holding, spawning, incubation and rearing facility for 
188 

the Imnaha Chinook program. A temporary facility was operated on the Imnaha River from 1982-

1988 and a permanent facility was constructed in 1989. 

A comprehensive research, monitoring, and evaluation (RM&E) program has been underway 

since 1984. The primary objectives of the RM&E are: 1) document and assess fish culture and 

hatchery operation practices and performance; 2) determine optimum rearing and release 

strategies that will produce maximum survival to adult; 3) determine total catch and escapement, 

smolt survival, and smolt-to-adult survival, and assess if adult production meets mitigation goals; 

4) assess and compare recruits-per-spawner of hatchery and natural origin fish; 5) assess 

response in natural population abundance and productivity (adult recruits-per-spawner, smoltsper-spawner) to supplementation; 6) assess and compare life history characteristics (age 

structure, run and spawn timing, sex ratios, smolt migration, fecundity) of hatchery and natural 

fish; and 7) assess success in restoring fisheries. 

PROGRAM ASSESSMENT 

The uniqueness of the Imnaha spring/summer Chinook salmon population was recognized prior 

to the initiation of the hatchery program. This recognition led to the decision to use only endemic 

local broodstock for the hatchery program. Wild adults were collected for broodstock beginning in 

1982. Natural-origin adults comprised a majority of the broodstock from 1982-1988. In recent 

years natural-origin adults have represented only a small proportion of the annual broodstock 

(Table 2). 

Table 2. Hatchery broodstock history for the Imnaha River spring/summer Chinook salmon 

hatchery program. 

Spawn years 

Number of females in broodstock

Natural Hatchery Percent natural origin adults in broodstock 

1982-1988 10-91 0-10 100-82.2 

1989-2002 6-48 9-168 7.1-71.4 

2003-2009 19-34 72-87 19.1-26.4 

Few hatchery fish spawned naturally from 1982-1988. Hatchery fish have represented a high 

proportion of natural spawners in recent years and the Proportionate Natural Influence (PNI) has 

been low, ranging from 0.218-0.279 (Table 3). A sliding scale broodstock management plan has 

been used throughout most of the implementation time frame. The sliding scale has been modified 

through time and the current sliding scale management plan (Table 4).

Table 3. Vital statistics for natural spawning spring/summer Chinook salmon in the Imnaha 

River. 

Spawn years 

Total number 

spawning in nature

Percent hatchery 

spawning in 

nature 

Percent natural 

retained for 

broodstock PNI 

1982-1988 539-1715 0-15.4 2.3-28.8 1-0.881 

1989-2002 291-4643 24.4-75.8 3.0-28.9 0.161-0.781 

2003-2009 804-3164 49.3-86.2 3.9-21.2 0.235-0.362 
189 

Table 4. Sliding scale broodstock and natural escapement management plan for the 

Imnaha River spring/summer Chinook salmon hatchery program. 

Total escapement 

to river 

Maximum % natural 

retained for broodstock 

 % Hatchery 

above weir 

Minimum % of naturalorigin broodstock 

>15 0 NA NA 

15-159 50 NA NA 

150-299 40 70 20 

300-499 40 60 25 

500-999 30/40* 50 30 

1000-1499 30/40* 40/30* 40 

1500-1999 25 25 50 

>2000 25 <10* 100 

* 3 consecutive years with Minimum Abundance Threshold ≥ 1000 

One of the significant challenges that this program has faced is trapping adults throughout the 

entire run. The weir can be safely installed only when river discharge is ≤ 28 m 3 / 5. There have 

been many years that a large proportion of the return has passed by the weir prior to weir 

installation (Figure 3). In addition, significant spawning occurs below the weir location. 

Prespawning mortality of broodstock has been variable with some high mortality rates early in the 

program implementation. In recent years, prespawning mortality has been low (Figure 4). Green 

egg-to-smolt survival rates have been consistently high through time. The smolt production goal 

of 490,000 has not been achieved in any year. Since 2000, when the interim smolt production 

goal was adopted, the smolt production has met or exceeded the goal in six of nine years (Figure 

5). Smolt survival to Lower Granite Dam has been relatively high (greater than 65%) for most 

recent brood years (Figure 6). The smolt migration pattern for hatchery fish is different than natural 

fish. Hatchery fish have a compressed distribution with later arrival timing and earlier migration 

completion (Figure 7). 
190 

Figure 3. Estimated proportion of the Chinook salmon run trapped at the Imnaha River weir, 

1997-2009. 

Figure 4. Prespawn mortality of broodstock collected and held for spawning and green eggto-smolt survival, 1982-2009 brood years. 

Return year

1997

1998

1999

2000

2001

2002

2003

2004

2005

2006

2007

2008

2009

Proportion of run trapped

0.0

0.1

0.2

0.3

0.4

0.5

0.6

0.7

0.8

0.9

1.0

Hatchery

Natural

Brood Year

1986 1991 1996 2001 2006

Prespawn mortality

0.0

0.2

0.4

0.6

0.8

1.0

0.0

Green egg-to-smolt survival

0.2

0.4

0.6

0.8

1.0 Prespaw n m ortality 

Egg-to-sm olt survival 

* No data

* *
191 

Figure 5. Chinook salmon hatchery smolt releases in the Imnaha River basin, 1996-2008 

brood years. 

Figure 6. Mean Imnaha River hatchery smolt survival to Lower Granite Dam, 1991-2007 

brood years. 

B rood Y ear

1996 1998 2000 2002 2004 2006 2008

Number of smolts (thousands)

0

100

200

300

400

500 R e le a s e G o a l (4 9 0 ,0 0 0 )

In terim P ro d u ctio n

G o a l (3 6 0 ,0 0 0 )

Brood Year

1991 1993 1995 1997 1999 2001 2003 2005 2007

0

1 0

2 0

3 0

4 0

5 0

6 0

7 0

8 0

9 0

100

% Survival to

Lower Granite Dam (+ 95% CI)
192 

Figure 7. Mean migration timing at Lower Granite Dam of natural and hatchery-origin 

Imnaha River smolts, 1995-2009 migration years. 

Prior to 2001, adult returns to the compensation area were well below the mitigation goal of 3,210. 

We reached the goal for the first time in 2001 and have met or exceeded the goal in three of the 

last nine years (Figure 8). One of the primary reasons we have not achieved adult return goals is 

because smolt production has been below the original goal of 490,000. One key measure of 

performance is the SAR relative to the program goal of 0.65%. Over the past 10 years the SAR 

has ranged from 0.03% to 2.5%. The SAR goal has been met or exceeded in eight of the last 10 

years (Figure 9). 

Imnaha River Chinook salmon are exploited at very low rates in the ocean, Columbia River and 

tributaries fisheries. On average, 88.3% of the adults produced escape to the Imnaha River (Table 

5). 

Date

4/1 5/1 6/1 7/1

Proportion

0.0

0.2

0.4

0.6

0.8

1.0

Hatchery

Natural
193 

Figure 8. Adult returns to the LSRCP compensation area for hatchery-origin Imnaha River 

spring/summer Chinook salmon, 1985 – 2009 run years. 

Figure 9. Smolt-to-adult survival (SAS) and return (SAR) rates for Imnaha River hatchery 

Chinook salmon, 1982 – 2006 brood years. 

Run year

1985 1990 1995 2000 2005

Escapement to LGD

0

1000

2000

3000

4000

5000

6000

M itigation goal

Brood year

1985 1990 1995 2000 2005

SAR / SAS

0.0

0.5

1.0

1.5

2.0

2.5

3.0

SAR 

SAS 

SAR

M itigation

goal
194 

Table 5. Catch and escapement distribution (%) of Imnaha River hatchery spring/summer 

Chinook salmon. 

Recovery Location Percent of total 

 Brood Year 

 2001 2002 2003 2004 Mean 

Ocean 0.6 0.2 0.1 0.4 0.3 

Columbia River Harvest 

 Tribal 1.3 3.5 7.4 1.5 3.4 

 Sport 3.0 12.1 4.5 4.6 6.1 

 Commercial net 0.8 2.0 0.6 0.3 0.9 

Snake River 

 Stray below LGD 0.3 0.2 0.4 0.6 0.4 

 Stray above LGD 0.0 0.4 0.3 0.1 0.2 

 Sport above LGD 0.2 1.3 0.0 0.0 0.4 

 Tribal above LGD 0.0 0.0 0.0 0.0 0.0 

Escapement to River 93.9 80.2 86.7 92.5 88.3

Imnaha River hatchery Chinook that return to the Imnaha River have a diverse disposition profile. 

A high proportion of the returns spawn naturally, are outplanted to the Big Sheep Creek drainage 

or are used for broodstock. Smaller proportions are harvested in tribal and recreational fisheries 

or are distributed to Oregon food banks or for tribal consumption (Figure 10). 

One of the key indicators of the magnitude of full life cycle survival advantage that is provided by 

hatchery supplementation programs is the hatchery-to-natural ratio in adult recruits-per-spawner 

(R/S). For the ten most recent brood years the R/S for hatchery spawned fish averaged 9.3 and 

1.4 for natural spawning fish. Natural spawner recruits-per-spawner exceeded 1 in only four of 

the last ten brood years and was below 0.5 for five most recent brood years (Figure 11). 
195 

Figure 10. Disposition of Imnaha River hatchery Chinook salmon that returned to the Imnaha 

River, 2001-2004 return years. 

We have consistently observed differences in run timing between hatchery and natural adults. 

Hatchery fish pass through the Lower Snake River dams later that natural fish and also have a 

later run timing distribution at the weir (Figure 12). This difference in timing is likely a result of 

broodstock collection that selects the later returning fish in most years. Consistent with later run 

timing for hatchery females we have also observed a later spawn timing for hatchery females. We 

have observed complete overlap in spawning range, however the hatchery fish distribution is 

concentrated more downstream around the release location (Figure 13). Hatchery fish return at 

an earlier age than natural-origin fish with a very high proportion of age 3 males and few age 5 

fish (Figure 14). Age 3 males make up about 50% of the males that return for a brood year. 

Tribal 

distribution 

9%

Food bank

3%

Sport

2%

Tribal harvest

6%

Kept for

Hatchery

12%

Outplants

20%

Fish in river

48%
196 

Figure 11. Imnaha River Chinook salmon recruits-per-spawner (jacks omitted) for hatchery 

spawned adults and natural spawning (natural-origin and hatchery-origin) adults, 

1982-2004 brood years. 

Figure 12. Run timing of hatchery and natural-origin Imnaha River Chinook salmon at the 

Imnaha River Weir, 2001-run year. 

Hatchery

1985 1990 1995 2000

0

5

10

15

20

25

Natural

Brood year

1985 1990 1995 2000

Recruits-per-spawner

(adults only)

0

1

2

3

4

5

ICTRT Viability Criterion

2001: All Fish

P < 0.0001

Week of the year

23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38

Percent of run

0

5

10

15

20

25

30

35

Cumulative percent

0

10

20

30

40

50

60

70

80

90

100

Hatchery

Natural
197 

Figure 13. Spawning distribution of hatchery and natural-origin females in the Imnaha River. 

 

Figure 14. Mean age-at-return distribution for hatchery and natural-origin Imnaha River 

Chinook salmon, brood years 1982-2004. 

Reach

123456789

Proportion of run

0

5

10

15

20

25

30

35

40

Cumulative percent

0

20

40

60

80

100

Hatchery 

Natural

Cumulative hatchery

Cumulative natural

Weir

RKm 86

Downstream Upstream

RKm 58 RKm 104

Age class

Age 3 Age 4 Age 5

Proportion

0.0

0.1

0.2

0.3

0.4

0.5

0.6

0.7

Natural

Hatchery

P<0.001

P=0.923

P<0.001
198 

The most common accepted definition of supplementation was developed by Regional 

Assessment of Supplementation Project (RASP) many years ago: “the use of artificial propagation 

to maintain or increase natural production to maintain long-term fitness of the target population 

...”We have estimated the abundance of natural spawning hatchery and natural origin fish for 

many years (Figure 15). However, this information alone provides little insight into the 

effectiveness of supplementation. For supplementation to be successful, natural-origin 

abundance must increase to levels above that which would have occurred without 

supplementation and productivity must not decrease. Approaches to assessing supplementation 

success are challenging, primarily due to the lack of availability of data for reference populations 

that are unsupplemented. The compilation of long-term abundance and productivity datasets by 

IDFG, ODFW, and the ICTRT for Snake River spring/summer Chinook salmon populations 

provided the unsupplemented reference population data to allow us to conduct a unique 

comprehensive analyses of the Imnaha Chinook supplementation program.

Figure 15. Abundance of naturally spawning hatchery and natural-origin adults in the Imnaha 

River Chinook salmon population, 1982-2009. 

To assess the natural-origin abundance and productivity response of the Imnaha River population 

we acquired and compiled adult spawners and recruit abundance and productivity (R/S) time 

series datasets for the supplemented Imnaha River population and eight unsupplemented Idaho 

Salmon River basin populations (Figure 16). We determined the level of correlation (Pearson’s) 

in abundance and productivity (R/S) between the Salmon River basin and Imnaha River 

ReturnYear

1982198519881991199419972000200320062009

Total adult spawners in nature

0

500

1000

1500

2000

2500

3000

Natural

Hatchery

ICTRT

Viability

Criterion
199 

populations for the pre-supplementation time period (late 1950s-1985 for abundance and late 

1950s-1981 for productivity) to evaluate the adequacy of the Salmon River populations as 

reference populations. We calculated year-specific and mean year-specific pre-and posttreatment ratios (Imnaha / reference population) for total spawners, natural-origin spawners, and 

productivity. We conducted t-tests to compare means for pre-and post-time-periods. We designed 

our analysis to test the following assumptions and hypotheses: 

1) Total spawner abundance should increase. Therefore, the post-supplementation total 

abundance ratio should be greater than the pre-supplementation ratio. 

2) Natural-origin spawner abundance should increase. Therefore, the post-supplementation 

abundance ratio should be greater than the pre-supplementation ratio. 

3) Productivity should remain the same. Therefore, the post-supplementation R/S ratio should be 

equal to or greater than the pre-supplementation ratio. 

Figure 16. Map showing the locations of Snake River basin spring/summer Chinook salmon 

populations used for analyzing supplementation responses in the Imnaha River. 

We found a high degree of correlation between the Imnaha river population and Salmon River 

reference populations for natural-origin abundance and adult R/S in the pre-supplementation time 

period (Table 6). We have provided time series comparisons (examples) between the Imnaha 

River and the Bear Valley Creek populations for total spawners, natural-origin spawner 

abundance, and R/S as well as year specific ratios, (Figures 17-22). 

Imnaha River Big

Creek

Imnaha River

Sulphur Creek

Lemhi 

River

Bear Valley 

Creek

Camas

Creek

Loon

Creek

Valley

Creek
200 

Table 6. Pre-supplementation natural-origin abundance correlations, Imnaha population vs. 

Idaho populations. 

 Natural origin abundance Recruits per spawner 

Idaho stream rho P-value rho P-value 

Bear Valley Creek 0.56501 0.0026 0.47290 0.0262 

Big Creek 0.53876 0.0026 0.36653 0.0715 

Camas Creek 0.67431 0.0004 0.65674 0.0023 

Lemhi River 0.47824 0.0087 0.40587 0.0441 

Loon Creek 0.64394 0.0002 0.60903 0.0016 

Marsh Creek 0.62440 0.0003 0.53570 0.0058 

Sulphur Creek 0.52331 0.0043 0.35625 0.0805 

Valley Creek 0.75378 <0.0001 0.58447 0.0027 

Mean total spawner abundance ratio increased from the pre-to the post-time period for all eight 

pairwise comparisons. Three of the eight increases were significant (Table 7). The response in 

natural-origin abundance was much more variable. Natural-origin abundance ratios increased in 

three and decreased in five comparisons, with no consistent pattern in the response (Table 8). 

There was a consistent response pattern in the R/S ratio. The mean R/S ratio showed a significant 

reduction for all eight pairwise comparisons indicating a significant reduction in productivity for 

the post-supplementation time period (Table 9). 

Figure 17. Abundance of total spawners for the Imnaha River and Bear Valley Creek Chinook 

salmon populations, 1960-2009. 

Spawn year

1960 1970 1980 1990 2000

Total adult spawners

0

1000

2000

3000

4000

Imnaha River

Bear Valley Creek

Supplementation Starts 
201 

Figure 18. Total Chinook salmon spawner abundance ratios (Imnaha River / Bear Valley 

Creek), 1960-2009. 

Figure 19. Abundance of natural-origin spawners in the Imnaha River and Bear Valley Creek 

Chinook salmon populations, 1960-2009. 

Spaw n year

1960 1970 1980 1990 2000

IR / BVC total abundance ratio

0

2

4

6

8

1 0

1 2 U nsupplem ented S upplem ented

Spawn year

1960 1970 1980 1990 2000

Natural adult spawners

0

1000

2000

3000

4000

Im naha River

Bear Valley Creek

Supplementation Starts 
202 

Figure 20. Chinook salmon ration of natural-origin abundance (Imnaha River / Bear Valley 

Creek), 1960-2009. 

Figure 21. Recruits-per-spawner (spawner-to-spawner) for the Imnaha River and Bear Valley 

Creek Chinook salmon populations, 1960-2004. 

Spawn year

1960 1970 1980 1990 2000

IR / BVC

natural abundance ratio

0

2

4

6

8

1 0

1 2 U nsupplem ented Supplem ented

Spaw n year

1960 1970 1980 1990 2000

Recruits / spawner

0

2

4

6

8

Im naha R iver

B ear V alley C reek
203 

Figure 22. Chinook salmon ratio of recruits-per-spawner (Imnaha River R:S / Bear Valley 

Creek R:S), 1960-2003 brood years. 

Table 7. Total Chinook salmon spawner abundance ratios (Imnaha abundance / reference 

abundance) for pre-and post-supplementation time periods. P values represent ttest results. 

 Mean 

Stream Pre-supplementation 

Postsupplementation Difference P-value 

Bear Valley Creek 3.02 3.24 0.22 0.568 

Big Creek 7.54 9.89 2.35 0.796 

Camas Creek 10.18 27.76 17.58 0.007 

Lemhi River 2.84 10.84 8.01 <0.001 

Loon Creek 14.23 29.17 14.94 0.065 

Marsh Creek 3.77 5.80 2.03 0.146 

Sulphur Creek 10.92 21.05 10.13 0.096 

Valley Creek 13.74 16.65 2.90 0.002 

 

Spawn year

1960 1970 1980 1990 2000

IR / BVC R:S ratio

0

1

2

3

4

5 Unsupplem ented Supplem ented
204 

Table 8. Natural-origin Chinook salmon spawner abundance ratios (Imnaha abundance / 

reference abundance) for pre-and post-supplementation time periods. P values 

represent t-test results. 

 Mean 

Stream 

Presupplementation Postsupplementation Difference P-value 

Bear Valley Creek 3.02 1.72 -1.30 0.013 

Big Creek 7.54 5.68 -1.85 0.006 

Camas Creek 10.18 16.08 5.90 0.783 

Lemhi River 2.84 4.49 1.65 0.019 

Loon Creek 14.24 16.66 2.42 0.437 

Marsh Creek 3.77 2.84 -0.93 0.049 

Sulphur Creek 10.92 9.79 -1.13 0.337 

Valley Creek 13.74 8.45 -5.29 0.318 

Table 9. Chinook salmon recruit-per-spawner ratios (Imnaha R/S / reference R/S) for preand post-supplementation time periods. P values represent t-test results. 

 Mean 

Stream 

PreSupplementation Postsupplementation Difference P-value 

Bear Valley Creek 1.86 0.63 -1.23 <0.001 

Big Creek 1.71 0.81 -0.90 0.012 

Camas Creek 1.94 1.48 -0.45 0.062 

Lemhi River 1.72 1.04 -0.68 0.005 

Loon Creek 2.32 1.44 -0.87 0.002 

Marsh Creek 1.56 1.15 -0.41 0.026 

Sulphur Creek 2.13 1.54 -0.59 0.031 

Valley Creek 1.66 0.85 -0.81 <0.001 

One important management objective for this program is to restore and sustain tribal and 

recreational fisheries. Recently, a harvest management framework has been adopted to guide 

annual tributary harvest decisions. Essential elements of the tributary harvest management 

strategy include the following: 1) Allowable natural origin impact is conservative and scaled 

relative to “critical and viable levels”; 2) Each population is considered separately in fishery 

decisions; 3) Fishery protects any population below “critical” threshold from impact; 4) Generally, 

hatchery fish harvest is limited by resulting incidental impact on natural origin adults; 5) Hatchery 

fish escapement must meet broodstock and supplementation needs; 6) Monitoring allows impact 

tracking and in-season adjustment. 

The critical and viable thresholds for the Imnaha River population are listed in (Table 10). Tribal 

and recreational fisheries are regulated based on allowable impact on the margin of natural-origin 

fish between the run prediction and the critical abundance threshold. The maximum natural-origin 

allowable sport fishing impact ranges from 0% at 300 natural-origin adults to 5.5% at 2000 naturalorigin adults allowable tribal allocations are higher at each escapement level. The sport fishery 

has been managed for marked selective harvest and catch-release for all unmarked fish. The 

tribal fishery has been non-selective. 
205 

Table 10. List of Grande Ronde / Imnaha Chinook MPG salmon populations and associated 

interim critical and viable thresholds. 

Natural Population 

Critical abundance 

threshold Viable abundance threshold 

Wallowa/ 

Lostine Rivers 225 adults/yr 750 adults/yr 

Catherine Creek 150 adults/yr 500 adults/yr 

Upper Grande Ronde River 150 adults/yr 500 adults/yr 

Imnaha River 300 adults/yr 1000 adults/yr 

Wenaha River 225 adults/yr 750 adults/yr 

Minam River 225 adults/yr 750 adults/yr 

Figure 23. Number of hatchery fish harvested and natural-origin fish caught and released in 

the Imnaha River Chinook salmon sport fishery (ODFW Wallowa Fish District). 

As stated previously, the recreational fishery was closed from the late 1970s through 2000. Sport 

fisheries have occurred in eight of the last ten years. The number of fish harvested has generally 

been below the historical value, however harvest in 2009 exceeded the 1959-69 mean value 

(Figure 23). Catch rates have been highly variable since the fishery was reopened. Season length 

has also been variable, but well below the traditionally season length in the 1960s (Figure 24). 

The tribal fishery has been conducted on a more regular basis than the sport fishery. 

R etu rn Y ear

Number of Chinook caught

0

200

400

600

800

1000 H atch ery 

N a tu ra l 

No Fishery

No Fishery

M ile s o p e n 42 45 1959-69 1979-00 No Fishery

M e a n A n n u a l 

A d u lt H a rve s t 2001

20022003200420052006200720082009

0
206 

Figure 24. Catch rate and season length for the Imnaha River Chinook salmon recreational 

fishery. 

SUMMARY AND CONCLUSIONS 

Broodstock Development and Management 

The low abundance of natural-origin adults limited program success throughout the early years 

and to some extent in recent years. Smolt production goals were not reached due to availability 

of natural-origin broodstock. The low abundance of natural-origin returns has resulted in a high 

proportion of hatchery-origin fish in the broodstock and spawning naturally, resulting in low PNIs. 

The inability to install the weir prior to arrival of the first fish and resulting selective broodstock Hours/Chinook

0

5

1 0

1 5

2 0

2 5

No Fishery

No Fishery

R eturn Y ear

Number of fishing days

0

1 0

2 0

3 0

4 0

5 0

6 0

No Fishery

No Fishery

2001 2002 2003 2004 2005 2006 2007 2008 2009

1959-69

1979-00 No Fishery

No DataNo Fishery

2001 2002 2003 2004 2005 2006 2007 2008 2009

1959-69

1979-00
207 

collection of late returning fish has created significant problems for the program. Uncontrolled 

escapement of hatchery fish occurs for the early part of the run in many years, resulting in high 

hatchery proportions on the spawning grounds. 

In-Hatchery Performance 

Pre-spawning mortality and egg-to-smolt survival rates have been variable. However, prespawning mortality is generally low and egg-to-smolt survival has been high. With the exception 

of a few years, in-hatchery performance has not limited program success.

Production, Survival and Adult Return Performance 

We have reached our interim smolt production goal of 360,000 in most of the recent years. Smolt 

survival to Lower Granite Dam is among the highest observed for Oregon’s Snake River hatchery 

programs. Adult returns have improved substantially in the past ten years and we have reached 

our return goal to the compensation area in 30% of the recent years. Smolt-to-adult return rates 

have also improved greatly and we have met the return rate goal of 0.65% in 80% of the recent 

years. Although we have seen improvement in total smolt-to-adult survival rates, we are a long 

way from reaching the original goal of 3.25%. 

Imnaha River hatchery Chinook salmon are exploited at very low rates. Few fish are harvested in 

ocean or mainstem Columbia River fisheries. Greater than 80% of the adults produced escape to 

the Imnaha River basin. We have observed very low stray rates consistently through time. In 

recent years stray rates have not exceeded 2% in any year. Recreational fishing opportunity has 

been restored to the Imnaha River in recent years. Although seasons are short and harvest rates 

are low in most years, the fishing is a welcome and popular addition to recreational opportunities 

in N.E. Oregon. Tribal fishing now occurs on a consistent and regular basis. 

Supplementation: Life History and Spawning Characteristics 

 Hatchery fish return at an earlier age than natural-origin fish with far more age 3 males and fewer 

age 5 adults. Adult return timing to the weir is later for hatchery fish compared to natural-origin 

fish and hatchery fish spawn later. The run timing and spawn timing differences are likely a result 

of unintentional selective broodstock collection. The spawning distribution of hatchery females is 

distributed more downstream than natural females, concentrated near the release location. We 

have not observed differences in size-at-age or age specific fecundity between hatchery and 

natural-origin fish. 

Supplementation: Abundance and Productivity 

The Imnaha hatchery program has demonstrated a significant full life cycle survival advantage 

over naturally spawning fish with a R/S advantage of over 10:1. We have not observed an 

increasing trend in natural-origin abundance since we started the hatchery program. R/S for mixed 

hatchery and natural-origin fish spawning naturally has averaged less that 1.0 and has only 

exceeded 1.0 in 5 of the last 20 complete brood years. We have significantly increased the total 

number of spawners, but it does not appear that we have increased the number of natural-origin 

recruits. The natural productivity of mixed hatchery and natural-origin spawners in the Imnaha 

River population has decreased significantly since supplementation was initiated. 

We have conducted an initial qualitative assessment to assess potential reasons why we have 

not seen an increase in natural-origin abundance and why productivity has declined. 
208 

1) Poor reproductive success of hatchery fish: We do not have any direct measures of 

relative reproductive success. Given the results of other studies, the low PNI for this 

program, selective broodstock collection, and divergent life history characteristics (spawn 

timing and younger age at return) it is likely that hatchery fish have reduced reproductive 

success. 

2) Competitive and other ecological effects: We have no information to assess these types 

of effects. Therefore, we are highly uncertain of the implications. 

3) Other genetic and ecological effects: Given the combination of selective broodstock 

collection, high proportion of hatchery fish spawning naturally, differences in spawn timing 

and spawning distribution, unnaturally high proportions of jacks spawning naturally and 

potential weir effects on adult distribution, we hypothesize that these effects may be 

important. 

4) Density dependent effects of increased total spawners: We demonstrated that the 

hatchery program significantly increased total spawners, and increased spawner density. 

This increase could result in decreased observed productivity; however, we have a 

substantial number of low spawner abundance years in the post-supplementation time 

period and post-supplementation abundance has not reached historical abundance levels. 

Although density may be a factor depressing observed productivity, it does not provide 

any explanatory power for the lack of response in natural-origin abundance. 

FUTURE PROGRAM CHALLENGES AND NEEDS 

The Imnaha River Chinook salmon hatchery program could benefit greatly from a new weir and 

adult collection system that would allow adult collection across the entire run. A new weir would 

provide be better application of the sliding scale management plan, improved PNI, and 

improvement in similarity of life history characteristic between hatchery and natural fish. 

The low productivity of natural spawning fish as well as the low abundance of natural-origin adults 

are major challenges for achieving management objectives. These factors limit the ability to 

improve PNI and also limit access to harvest of surplus hatchery fish, which is regulated based 

on natural-origin fish impacts. 

The lack of detailed understanding of why productivity has declined and why more natural-origin 

fish have not been produced by supplementation limits our ability to make sound decisions on 

how best to modify the program. We will continue studies to better understand how hatchery 

operations, density dependence, life history divergence, and hatchery fish performance are 

influencing overall program success. 

ODFW Response to ISRP Comments – Imnaha River 

Key Findings 

ISRP comment page 53: “A final conclusion on the effect of the program on natural adult 

abundance and productivity is not provided.” 

Response: The supplementation program and the RM&E are ongoing. Adaptive management 

actions are proposed to improve the effectiveness of the program, thus final conclusions regarding 

program success would be premature. However, we believe the conclusions we provided do 
209 

reflect final conclusions regarding the program performance to date. Relevant to this ISRP 

comment are the following conclusions from the report: 

“The Imnaha hatchery program has demonstrated a significant full life cycle survival advantage 

over naturally spawning fish with a R/S advantage of over 10:1. We have not observed an 

increasing trend in natural-origin abundance since we started the hatchery program. R/S for mixed 

hatchery and natural-origin fish spawning naturally has averaged less that 1.0 and has only 

exceeded 1.0 in 5 of the last 20 complete brood years. We have significantly increased the total 

number of spawners, but it does not appear that we have increased the number of natural-origin 

recruits. The natural productivity of mixed hatchery and natural-origin spawners in the Imnaha 

River population has decreased significantly since supplementation was initiated.” 

In addition to the above conclusions, we provided extensive conclusions related to life history and 

spawning characteristic comparisons (see page 26 in the report). 

ISRP comment page 53: “A section summarizing HSRG and USFWS hatchery review findings 

and how they are reflected in project management would improve the presentation.” 

Response: We did include such a summary in the presentation but did not include it in the report. 

Following is the summary we provided in the presentation. 

Imnaha River HSRG and HRT Recommendations 

 Program Goals: HSRG – Maintain current interim 360,000 smolt goal, divide program into 

integrated conservation and stepping stone harvest and improve PNI 

HRT – Maintain current 350,000 smolt goal, modify sliding scale so that pHOS does not exceed 

pNOB to improve PNI and establish natural origin escapement goal where pHOS is 0 

Response: Maintain current 360,000 smolt goal and improve PNI, however construction and 

operation of new weir is essential to achieve these recommendations. 

 Facility Rearing Capacities: HSRG – Improve the weir so it can trap across the run 

HRT – Expand early rearing and smolt rearing capacities by modification of Lookingglass or 

construction of Lostine NEOH facility, install new more efficient weir 

Response: New weir currently planned for implementation when funds secured other new 

facilities planned by co-managers. 

 Rearing-Release Strategies: HSRG – Increase smolt size at release 

Response: Not considered beneficial for survival or age-at-return. 

 Define More Specific Goals for Big Sheep Creek: HRT - Co-managers establish quantifiable 

and measurable goals for outplanting hatchery-origin Chinook adults into Big Sheep Creek 

Response: Co-managers currently considering this recommendation, with expansion of 

monitoring under NEOH additional assessment of outplanting effectiveness will be possible. 

 
210 

SIZE-AT-RELEASE OF IMNAHA RIVER CHINOOK SALMON HATCHERY SMOLTS: 

DOES SIZE MATTER? 

Joseph Feldhaus 

Tim Hoffnagle 

Richard Carmichael 

Debra Eddy 

Oregon Department of Fish and Wildlife 

203 Badgley Hall 

Eastern Oregon University 

La Grande, OR 

This program is a cooperative effort of the Oregon Department of Fish and Wildlife, the 

Confederated Tribes of the Umatilla Indian Reservation and the Nez Perce Tribe. The program is 

funded by the Bonneville Power Administration and administered by the United States Fish and 

Wildlife Service under the Lower Snake River Compensation Plan. 

INTRODUCTION 

The Imnaha River Chinook salmon (Oncorhynchus tshawytscha) population has been 

supplemented with hatchery salmon since the 1982 brood year, when wild Imnaha River adults 

were first captured and spawned in captivity. This supplementation program has been operated 

under the auspices of the U.S. Fish and Wildlife Service’s Lower Snake River Compensation Plan 

(LSRCP) program. This Imnaha River Chinook salmon hatchery supplementation program has 

been operated by the Oregon Department of Fish and Wildlife (ODFW) with the following 

production and program objectives: 

 Prevent extinction of Imnaha River salmon populations and ensure a high probability of 

population persistence into the future. 

 Establish adequate broodstock to meet annual production needs and to meet the longterm mitigation goal of 490,000 smolt releases. 

 Meet the LSRCP mitigation goal of 3,210 hatchery adult returns to the Imnaha Basin. 

 Reestablish historic tribal and recreational fisheries. 

 Minimize impacts of the hatchery program on resident stocks. 
211 

 Maintain genetic and life-history characteristics of natural Chinook salmon populations in 

the Imnaha River. 

 Operate the hatchery program so that genetic and life history characteristics of hatchery 

Chinook mimic those of wild Chinook, while achieving mitigation goals. 

Data collected from research and monitoring activities are used to design and adapt culture 

practices to most effectively meet these management objectives. Based on the age structure of 

hatchery and natural spring Chinook adults from the 1982-1987 brood year returns captured at 

the Imnaha River weir, there was evidence that age composition differed between hatchery and 

natural adults (Figure 1). This finding suggested that the Imnaha River hatchery spring Chinook 

program was failing to meet the objective that genetic and life history characteristics of hatchery 

Chinook mimic those of wild Chinook. 

Figure 1. Age structure of adult hatchery and natural spring Chinook adults from the 1982-

1987 brood years captured at the Imnaha River weir. 

Based on these findings, a long term study was initiated to determine if smaller smolts could better 

meet the program objective of producing hatchery fish that mimic the life history characteristics of 

naturally produced Imnaha River spring Chinook salmon. The first study objective was to compare 

life history characteristics (e.g., age and size at maturity and run timing) between large and small 

smolts. A second study objective, that directly addresses the mitigation goal requirement, was to 

identify optimum rearing and release strategies that will produce the maximum survival to 

adulthood for hatchery-produced Chinook salmon smolts. We determined and compared the 

following performance metrics between large and small smolts: juvenile survival rates to Lower 

Granite Dam (LGD), smolt-to-adult return (SAR) rate to LGD, harvest rate, stray rate, smolt-toadult survival (SAS) rate, and the number of adults produced per 10 kg of smolts released. 

STUDY AREA AND METHODS 

The smolts used for this study were offspring of hatchery- and natural-origin adults collected at 

the Imnaha River Weir/Acclimation Site, located at rkm 85. The Imnaha River Supplementation 

Program uses endemic Imnaha River Chinook salmon. The adults were spawned and reared at 

Lookingglass Fish Hatchery (LFH), located on Lookingglass Creek, a tributary of the Grande 

Ronde River at rkm 138. At smoltification, the smolts were transported to the Imnaha River 

Age 3

43%

Age 4

41% Age 5

16%

Age 3

13%

Age 4

51%

Age 5

36%

Hatchery Natural
212 

Acclimation Site in April, nearly two years after their parents were collected, and released to 

migrate to the ocean and return upon maturation (Figure 2). 

Figure 2. Map of the Grande Ronde and Imnaha River Basins and locations of the Imnaha 

Weir/Acclimation Site and Lookingglass Hatchery. 

Experimental treatments were conducted with paired releases of large and small smolts from 

brood years (BY) 1988-1998. The 1991 BY was excluded because of high mortality due to 

bacterial kidney disease. The target size varied among BYs - for large smolts the target was 30 

or 38 g/fish (12 or 15 fish/lb) and 18 or 23 g/fish (20 or 25 fish/lb) for small smolts. The 38 g large 

smolt target consisted of brood years 1988 and 1990 and the 30 g large smolt target was from 

BYs 1989 and 1992-1998. The 23 g small smolt target was for BYs 1988-1990, and the 18 g small 

smolt target was for BYs 1992-1998. 

Additionally, rearing density varied among BYs due to low returns and the resulting reduced 

availability of adults for broodstock during some return years. We accounted for these differences 

in rearing density by separating the BYs into high density (> 40,000 smolts/raceway, or >14.5 

kg/m3) and low density (< 30,000 smolts/raceway, or < 9 kg/m3) years (Table 1). Outdoor 

raceways at LFH are 30.5 m X 3 m and 1 m deep (95 m3). High density smolt releases were 

conducted with BYs 1988-1993 and low density smolt releases occurred with BYs 1994-1998. 

The number of smolts/raceway in the high density release years ranged from 44,346-85,796 

smolts and 6,613-26,796 smolts for the low density releases. 

Smolt survival to LGD was based on detections of passive integrated transponder (PIT) tags and 

was limited to the 1992-1998 BYs because PIT tag technology was not available prior to 1992. 

Recovery information for each coded-wire tag (CWT) code group was obtained from the Regional 

Mark Information System (RMIS) CWT recovery database (Pacific States Marine Fisheries 
213 

Commission). The observed and estimated number of hatchery salmon from each CWT code 

recovered in ocean and mainstem river fisheries, as well as the fish collected in sport, commercial 

and tribal harvests, strays collected in and out of the Snake River Basin, and those returning to 

their expected spawning or collection location were summarized from the RMIS database. 

Estimated CWT recoveries in the RMIS database were expanded from observed recoveries 

based on sampling rates at each recovery location. The RMIS database does not expand for 

recoveries observed in the Imnaha Basin. Therefore, we estimated total CWT marked hatchery 

adults from each code group (observed from weir collections and spawning ground recoveries) 

returning to the Imnaha River based on total escapement to each stream, sampling rate, and the 

proportion of each cohort marked with CWTs. Smolt-to-adult survival (SAS) rate was defined as 

the total estimated number of adults from a BY release group that were harvested, strayed, and/or 

returned to the LSRCP compensation area above LGD. The smolt-to-adult return (SAR) was 

defined as the estimated total number of adults returns from a BY release group that returned to 

the LSCRP compensation area over LGD. Age composition (% maturing at ages 3, 4 and 5) was 

calculated from all CWT recoveries. We defined strays as any fish captured outside of its direct 

migration route to its expected spawning or collection location. The number of smolts/10 kg was 

calculated by using the mean weight of the smolts at liberation. 

RESULTS AND DISCUSSION 

The first step in our analysis was to compare the performance of paired releases of large and 

small smolts without the density effect. There was no difference in downstream survival to LGD 

between large and small smolts (P = 0.07; Figure 3). Large smolts survived at a mean rate of 

67.4% and small smolts at a mean rate of 65.6%. Survival to LGD varied significantly among BYs 

(P < 0.0001; Figure 4). 

Table 1. Spring Chinook salmon release metrics for each raceway of large and small smolts 

reared at high or low density and released from the Imnaha River Acclimation site, 

1988-1998 brood years. 
214 

Brood year 

Density 

group 

Size 

group 

Rearing 

pond 

Target 

fish/ 

pound

Mean 

weight 

(g) 

Rearing 

density 

(kg/m3) 

Number 

of 

CWT's 

released 

Total 

smolts 

released

1988 High Large 12 12 36.6 22.3 51,281 51,669 

 13 12 35.5 21.7 51,597 52,013 

 Small 14 20 25.1 21.6 56,611 73,337 

 15 20 24.4 21.8 56,514 76,018 

1989 High Large 16 15 29.9 18.1 41,582 51,557 

 17 15 28.0 18.7 40,770 56,848 

 Small 14 20 20.5 19.3 42,804 79,654 

 15 20 20.5 19.2 42,834 79,611 

1990 High Large 17 12 41.3 21.5 43,315 44,346 

 18 12 40.2 21.4 45,075 45,256 

 Small 16 20 21.6 21.8 85,110 85,796 

1992 High Large 14 15 29.9 18.3 49,471 52,075 

 Small 15 25 17.6 17.4 81,997 84,013 

 16 25 18.9 18.7 80,404 83,900 

1993 High Large 13 15 26.1 15.4 49,576 50,222 

 14 15 25.8 14.8 47,084 48,723 

 Small 9 25 20.4 18.7 77,200 77,952 

 16 25 20.8 17.9 72,015 72,959 

1994 Low Large 3 15 25.5 4.2 13,635 13,839 

 4 15 27.9 4.6 13,376 13,890 

 Small 5 25 23.8 3.0 10,695 10,877 

 6 25 23.3 6.3 22,643 22,915 

 7 25 22.3 6.0 22,069 22,840 

1995 Low Large 6 15 30.7 3.6 9,742 9,896 

 7 15 32.9 2.6 6,390 6,613 

 Small 3 25 22.6 3.4 12,749 12,834 

 4 25 20.1 5.1 20,782 21,568 

1996 Low Large 1 15 29.3 2.4 6,619 6,997 

 2 15 30.3 5.0 12,670 14,022 

 3 15 31.7 5.3 13,328 14,171 

 Small 4 25 19.9 2.2 9,000 9,494 

 5 25 20.0 4.5 18,028 19,056 

 6 25 19.6 2.2 8,596 9,513 

 7 25 19.9 4.7 18,691 19,874 

 
215 

Table 1. continued 

Brood year 

Density 

group 

Size 

group 

Rearing 

pond 

Target 

fish/ 

pound

Mean 

weight 

(g) 

Rearing 

density 

(kg/m3) 

Number 

of 

CWT's 

released 

Total 

smolts 

released

1997 Low Large 10 15 28.9 4.6 11,942 13,395 

 11 15 28.6 4.7 12,287 13,997 

 12 15 27.9 8.8 24,570 26,796 

 13 15 27.9 4.6 12,756 13,997 

 14 15 26.5 4.2 12,051 13,308 

 15 15 27.9 4.9 12,992 14,872 

 Small 8 25 18.5 4.9 21,239 22,385 

 9 25 18.7 4.8 20,212 21,787 

1998 Low Large 7 15 27.0 6.0 18,097 18,894 

 10 15 28.9 6.0 15,972 17,590 

 Small 2 25 23.0 4.1 14,880 15,245 

 3 25 22.1 4.8 18,232 18,600 

 4 25 21.3 4.7 18,178 18,624 

 5 25 21.1 4.6 17,659 18,618 

 6 25 22.1 4.9 18,207 18,617 

 8 15 24.7 5.1 16,948 17,581 

 9 15 24.9 5.2 16,108 17,585 

 16 25 21.9 4.8 18,001 18,633 

Small smolts tended to return at an older age than larger smolts, with a lower percentage of 

smaller smolts returning at ages 3 and 4 and a greater percentage returning at age 5. However, 

there was no statistical difference in age composition of adult returns between treatment groups 

(P ≥ 0.22; Figure 5). 

Although mean survival rates were consistently higher for smaller smolts, size at release did not 

result in significant differences in harvest, stray, SAR or SAS rates between release groups (P > 

0.23; Table 2). Among brood years, there was highly significant annual variation in SAS rates 

(Figure 6). The 1989-1994 BYs had mean SAS rates that ranged from 0.02-0.26%, well below 

that LSRCP SAR goal of 0.65%. Mean SAS rates for the 1988 and 1995-1998 BYs ranged from 

0.60-2.67. This overall variation and pattern in brood year SAS rates was similar to that seen in 

other Snake River Chinook salmon hatchery programs, including Rapid River stock released from 

LFH, indicating regional causes for the poor survival years of the late 1980s and early 1990s. 
216 

Figure 3. Mean percent survival to Lower Granite Dam (LGD) of large and small PIT-tagged 

Chinook salmon smolts released from the Imnaha River Acclimation Site, 1992-

1998 brood years. 

Figure 4. Mean annual percent survival to Lower Granite Dam of large and small smolts 

released from the Imnaha River Acclimation Site (LGD), 1992-1998 brood years. 

Smolt Size Group

Large Small

Percent survival to LGD (+ 1 SD)

0

10

20

30

40

50

60

70

80

90

100

Brood Year

1992 1993 1994 1995 1996 1997 1998

Percent survival to LGD (+ 1 SD)

0

10

20

30

40

50

60

70

80

90

100

Large smolts

Small smolts
217 

Figure 5. Age composition of age 3-5 adult returns from large and small smolt releases of 

Chinook salmon into the Imnaha River. 

Table 2. Smolt-to-adult survival (SAS) rate (%) for large and small smolt releases from 

brood years 1988-1990 and 1992-1998. 

Rate 

Large smolts 

(mean 30 g/fish) 

Small smolts 

(mean 21 g/fish) P-value 

Harvest 0.027 0.060 0.23 

Stray 0.013 0.016 0.97 

SAR 0.780 1.10 0.42 

Total SAS 0.82 1.17 0.43 

A mean of 2.8 adults returned for every 10 kg of smolts released from the large release group 

and 5.5 adults returned / 10 kg released from the small smolt release group (P = 0.02; Figure 7). 

This is consistent with the finding that there were no significant differences in survival rates 

between large and small smolt releases. If a larger number of small smolts are released than 

large smolts, and SAS is similar, it is logical that equal weight (= greater numbers) of small smolts 

released would result in a larger number of adult returns. 

Next, we compared large and small smolt releases within the high density (BY 1988-1993) and 

low density (BY 1994-1998) rearing years. Smolt survival estimates, based on PIT tag detections, 

from the Imnaha River acclimation site to LGD for the high density experimental phase were 

limited to BY 1992-1993 (Figure 8). There were no significant differences in smolt survival rates 

between large and small smolt releases for either the high or low density release years (P ≥ 0.21). 

Age 3 Age 4 Age 5

Percentage (+ 1 SD)

0

10

20

30

40

50

60

70

80

90

100 Large

Small
218 

Figure 6. The percent smolt-to-adult survival (SAS) for large and small smolt releases, 1988-

1998 brood years. 

Figure 7. Adult returns per 10 kg of large and small smolts released, 1988-1998 brood years. 

Brood Year 1988

1989199019911992199319941995199619971998

Percent SAS rate (+ 1 SD)

0.0

0.5

1.0

1.5

2.0

2.5

3.0 Large

Small

No data

Smolt Size Group

Large Small

Adults/10 kg of smolts released

0

2

4

6

8

10

12
219 

Figure 8. Percent survival of PIT-tagged large and small smolts from the Imnaha River 

acclimation site to Lower Granite Dam during high (1992-1993) and low density 

(1994-1998) rearing years. 

There were no significant differences in adult age composition for either the high density release 

years (Figure 9) or the low density release years (P ≥ 0.09; Figure 10). Similarly, mean SAS rates 

were not significantly different between large and small smolts from either the high or low density 

releases (Figure 11). 

There was significant variation in SAS rates among brood years for smolt release groups during 

both the high and low density rearing years (P < 0.001; Figure 12). The SAS rates for high density 

rearing years (BY 1988-1993) were lower than SAS rates observed during the low density 

experimental rearing years (BY 1994-1998). The overall pattern observed in our data for SAS 

rates from 1988-1998 was similar to data presented by the Idaho LSRCP program at the 2010 

LSRCP review over the same time period, in Rapid River stock smolt releases from LFH, and is 

similar to trends observed for Chinook populations in the entire Columbia Basin, suggesting that 

regional variables (e.g., survival in the Columbia River, ocean conditions) are significant factors 

influencing the observed SAS patterns. 

For both the high and low density rearing years, there were no significant differences in harvest, 

stray, or SAR rates between large and small smolts (P > 0.30). For all experimental groups, 

harvest and stray rates were less than 0.1%. The SAR rates for smolt release groups from the 

high density rearing years were less than half the SAR rates for the low density release groups 

(Table 3). Within each of the high and low density rearing years, there were significant differences 

in harvest, stray, and SAR rates among brood years (P < 0.001). 

High ( BY 1992-1993) Low ( BY 1994-1998)

Percent survival to LGD (+ 1 SD)

0

20

40

60

80

100 Large 

Small

Density
220 

Figure 9. Age composition of adult returns from large and small smolt releases during high 

density rearing years, 1988-1993. 

Figure 10. Age composition of adult returns from large and small smolt releases during low 

density rearing years, 1994-1998. 

Age 3 Age 4 Age 5

Percentage (+ 1 SD)

0

10

20

30

40

50

60

70

80

90

100

Large

Small 

Age 3 Age 4 Age 5

Percentage (+ 1 SD)

0

10

20

30

40

50

60

70

80

90

100

Large

Small 
221 

Figure 11. Smolt-to-adult survival (SAS) rates of large and small smolt releases during the 

high (BY 1988-1993) and low (BY 1994-1998) density rearing years. 

Figure 12. Smolt-to-adult survival (SAS) for large and small smolt releases during high (BY 

1988-1993) and low (BY 1994-1998) density rearing years. 

Table 3. Harvest, stray, smolt-to-adult return (SAR) and total smolt-to-adult survival (SAS) 

rates for large and small smolts released during high and low density rearing years. 

Density

High 1988-1993 Low 1994-1998

Smolt-to-adult survival (+ 1 SD)

0.0

0.5

1.0

1.5

2.0

2.5

3.0

Large

Small

Brood Year

1988

1989

1990

1991

1992

1993

1994

1995

1996

1997

1998

Percent SAS survival (+ 1 SD)

0.0

0.5

1.0

1.5

2.0

2.5

3.0 Large

Small

No data

High Density (1988-1993)

Low Density (1994-1998)
222 

High density 

BY 1988-1993 

Low density 

BY 1994-1998 

Rate 

Large 

smolts 

Small 

smolts P-value 

Large 

smolts 

Small 

smolts P-value 

Harvest 0.001 0.002 0.37 0.042 0.087 0.31 

Stray 0.007 0.005 0.51 0.017 0.021 0.97 

SAR 0.281 0.209 0.58 1.082 1.525 0.30 

SAS 0.288 0.216 0.51 1.142 1.633 0.31 

For the high density rearing years there was no difference in the number of adults that returned 

per 10 kg of smolts released for either size of smolt (P = 0.5); 0.89 adults returned per 10 kg of 

large smolts and 0.96 adults returned per 10 kg of small smolt (Figure 13). However, for the low 

density rearing years, there was a significantly greater number of adult returns per 10 kg of smolts 

released from the small smolt releases (7.60 adults / 10 kg released) than for the large smolts 

(3.98 adults / 10 kg released; P = 0.01). 

Figure 13. Adult returns per 10 kg of smolts released for experimental releases of large and 

small smolts from high (BY 1988-1993) and low (BY 1994-1998) density rearing 

years of Imnaha River Chinook salmon. 

 

Smolt Density

High (BY 1988-1993) Low (BY 1994-1998)

Adults/10 kg of smolts released

0

2

4

6

8

10

12

14

Large

Small
223 

SUMMARY AND CONCLUSIONS 

We found that PIT-tagged smolts survived at a similar rate to LGD, regardless of release size or 

rearing density. Differences in size-at-release or rearing density did not result in observed 

differences in age composition, harvest, stray, SAR, or SAS rates. For all experimental groups, 

brood year (or smolt migration year) had a greater effect on the response variables than smolt 

size or rearing density. For this study, similar SAR and SAS rates between smolt size release 

groups resulted in about twice as many adult returns/kg from the small smolt releases compared 

to large smolt releases. Additionally, Imnaha River hatchery spring Chinook appear to have a very 

low stray rate. 

From a management perspective, these findings reconfirm the importance of annual variation on 

smolt and adult survival metrics. Based on these results, which appear to be unique to the Imnaha 

River spring Chinook salmon program, in space poor and egg rich years, like those we expect to 

continue experiencing at Lookingglass Hatchery, one potential strategy for maximizing the 

number of adult returns is to release more small smolts rather than fewer, large smolts. However, 

it is important to consider that this study occurred during a time when smolts migrating through 

the Columbia River hydrosystem were experiencing maximum transport (i.e., barged). Until a 

consistent “spread-the-risk” strategy is adopted, where half of the migrating smolts are 

transported and half migrate in-river, the best overall release strategy may be to spread the risk 

and release both large and small smolts. 

ODFW Response to ISPR Comments – Size at Release - Imnaha River Smolts 

Below are our responses to comments made by the ISRP regarding the presentation on size at 

release of Chinook salmon into the Imnaha River. 

I. Introduction 

ISRP Comment: “The introduction does not provide an explanation for why there is an objective 

of having a hatchery program that mimics the life-history characteristics of the natural population. 

The objective of maintaining the genetic and life-history characteristics of the natural population 

are not explained either, but are largely self-evident: as a first principle, long-term viability of the 

natural population is presumed to require maintaining the evolutionary potential of the population. 

Superimposing a hatchery program on the population will influence the state of the evolutionary 

potential, and conducting the program in such a way that it does not critically compromise the 

potential for future evolution is important. One way to limit deleterious effects is believed to be 

maintaining genetic similarity between the hatchery and natural population.”

Response: In the future, we will strive to provide a more thorough explanation and justification for 

the LSRCP program objectives. These comments will be used to improve the manuscript from 

this study that will be submitted to a refereed journal. 

ISRP Comment: “While the observation of earlier age of maturation is interesting and worthy of 

study, it is not explained how this alteration affects the dynamics of either the hatchery program 

or the natural population.” 

Response: One concern with early maturation is lower female fecundity. A second concern is 

lower fitness benefits, and therefore poor survival, for offspring from early maturing fish. We are 
224 

conducting ongoing research to understand the effects of early maturation on the hatchery and 

natural Imnaha River Chinook population. 

ISRP Comment: “An essential issue is whether the age structure difference is being accompanied 

by underlying genetic modification of the hatchery population, and to what extent the natural 

population may be modified by interbreeding between natural-origin and hatchery-origin adults, 

both in the hatchery and in the natural settings. The experimental design employed in these 

investigations is unable to provide insight into this important issue. It would be helpful to briefly 

elaborate on these concepts in the introduction.” 

Response: We will use this constructive insight for the manuscript we plan on publishing about 

this study. 

IV. Outlook and Recommendations 

ISRP Comment: “It is not evident how hatchery practices are modified to produce a specific mix 

of large and small smolts or how managers are integrating the findings into specific actions. It 

would be useful to indicate whether this research is being continued. “ 

Response: We are working with co-managers to replicate this study. 

ISRP Comment: “The ISRP encourages the authors to submit the findings for publication. This 

may require additional replication.” 

Response: Our goal is to submit a manuscript of this study for publication. 

 
225 

GRANDE RONDE BASIN SPRING CHINOOK 

SALMON CAPTIVE BROODSTOCK PROGRAM: 

F1 GENERATION PERFORMANCE

Tim Hoffnagle 

Rich Carmichael 

Joseph Feldhaus 

Deb Eddy 

Nick Albrecht 

Sally Gee 

Oregon Department of Fish and Wildlife 

203 Badgley Hall 

Eastern Oregon University 

La Grande, OR 97850

This program is a cooperative effort of the Oregon Department of Fish and Wildlife, the 

Confederated Tribes of the Umatilla Indian Reservation and the Nez Perce Tribe. The program is 

funded by the Bonneville Power Administration and administered by the United States Fish and 

Wildlife Service under the Lower Snake River Compensation Plan. 

INTRODUCTION 

This paper summarizes a presentation given at the Lower Snake River Compensation Plan 2010 

Spring Chinook Hatchery Program Review Symposium held on 30 November - 2 December 2010. 

This presentation provided background and history, along with preliminary results of data 

collected for monitoring the F1 generation of the Grande Ronde Basin Spring Chinook Salmon 

Captive Broodstock Program and discussed three main topics: 

1) Background - what got us here? 

2) Captive Broodstock Rearing - basically, what worked and what didn’t for rearing the 

salmon in captivity. This is a summary of important results pertaining to production 

parameters for the captive rearing phase of the Captive Broodstock Program. This phase 

lasts from parr collection through maturity and spawning. 

3) Comparing the Captive Broodstock (CBS) Program with the Conventional Hatchery 

Program (CHP) and natural salmon – preliminary results regarding hatchery rearing to 

smolt and survival after release into nature. 
226 

PROGRAM BACKGROUND 

The Grande Ronde Basin of northeast Oregon historically supported multiple large populations of 

spring Chinook salmon Oncorhynchus tshawytscha, including Catherine Creek, the Lostine River 

and Upper Grande Ronde River populations. Annual escapement varied, however, there was a 

steady decline from 1960 through the mid-1990s, when populations reached severely low levels 

(Figure 1). Recreational fisheries were closed in 1974 and tribal fisheries were curtailed or closed, 

as well. Natural origin abundance declined to zero in the Upper Grande Ronde River in 1989 and 

in Catherine Creek in 1990. Natural escapement was less than 70 spawners for five of seven 

years (1989-1995) for the Lostine River. 

This steady decline in Grande Ronde Basin spring Chinook salmon escapement necessitated 

hatchery intervention. The Lower Snake River Compensation Plan (LSRCP) was initiated in the 

late 1970s and hatchery programs began in Oregon in 1982. Initially, non-endemic Carson (BY 

1982-1987) and Rapid River (BY 1986-1996) stocks were used for supplementation. However, 

neither stock performed well in the Grande Ronde Basin, having low survival and high stray rates. 

Snake River spring Chinook salmon were listed as threatened under the Endangered Species Act 

in 1992 and the last releases of these non-endemic stocks occurred in 2000 (1999 BY). Since the 

Grande Ronde Basin streams still had genetically distinct populations, the co-managers (Oregon 

Department of Fish and Wildlife, Confederated Tribes of the Umatilla Indian Reservation and Nez 

Perce Tribe) began to manage for naturally reproducing populations of native stocks. The Grande 

Ronde Basin Spring Chinook Salmon Captive Broodstock Program began in 1995 with the 

collection of 1994 brood year natural parr from each of the three program streams: Catherine 

Creek, Lostine River and Upper Grande Ronde River. Conventional Hatchery programs 

(collecting returning adults) have been operating continuously in the Lostine River since 2000 

(starting in 1997 but skipping 1998 and 1999) and since 2001 in Catherine Creek and the Upper 

Grande Ronde River. 
227 

Figure 1. Natural Chinook salmon escapement to Catherine Creek, the Lostine River and 

Upper Grande Ronde River in northeast Oregon, 1960-1995. 

The Oregon LSRCP Chinook salmon program has production goals and nine management 

objectives for the program populations in the Grande Ronde Basin to guide the program: 

 Prevent extinction of Catherine Creek Chinook salmon population 

 Establish adequate broodstock to meet annual production needs 

 Establish an annual return of hatchery fish to the compensation area 

 Provide a demographic foundation to rebuild from after the key limiting factors and 

threats are addressed 

 Maintain and enhance natural production while maintaining long term fitness 

 Maintain genetic and life history characteristics of the natural population 

 Operate the hatchery program so that the genetic and life history characteristics of 

hatchery fish mimic wild fish 

 Re-establish historical tribal and recreational fisheries 

 Maintain endemic wild populations of spring Chinook salmon in the Minam and Wenaha 

rivers – minimize straying. 

The CBS Program was designed to quickly increase total escapement, thereby increasing the 

total adults spawning in nature, by greatly increasing the survival advantage that hatchery fish 

possess over naturally produced salmon - even more so than for conventional hatchery programs. 

It does so by holding fish in captivity for just over one complete life cycle (parr of the F0 generation 

through smolt of the F1 generation), greatly reducing the smolt-to-adult mortality rate. The overall 

goal of the CBS program is to increase the number of natural origin adults returning to spawn in 

the target populations. Therefore, the success of the Program will be determined by changes in 

natural origin adult abundance (the F2 generation). 

The CBS program was integrated with LSRCP production. Eggs produced (F1 generation) from 

the Captive Broodstock Program are incorporated into the LSRCP production, as needed. In the 

early years of the CBS, it comprised the entirety of the LSRCP smolt production. As the CHPs in 

these streams developed, CBS production became less important and these programs were 

mostly terminated. The last CBS spawn for the Catherine Creek and the Lostine River populations 

Run year

1960 1970 1980 1990

Escapement

0

1000

2000

3000

4000

5000

Total 

Catherine Creek

Lostine River

Upper Grande Ronde River
228 

occurred in 2010 (BY 2005). The Upper Grande Ronde River population is the most severely 

depressed and its CBS Program is transitioning to a Safety Net Program, beginning with BY 2009. 

The final CBS spawn for the Upper Grande Ronde River will occur in 2013 (BY 2008). Thereafter, 

the Safety Net Program salmon will be spawned only when needed to supplement CHP 

production. Otherwise, the mature adults will be released into unseeded Upper Grande Ronde 

River tributaries to spawn naturally. 

Like the LSRCP, the CBS Program has specific objectives aimed at the overall goal of restoring 

natural populations of Chinook salmon and minimizing impacts on wild populations: 

 Prevent extinction of the native Catherine Creek, Lostine River and Upper Grande Ronde 

River Chinook salmon populations. 

 Maintain genetic diversity of indigenous artificially propagated Chinook salmon 

populations. 

 Maintain the genetic diversity in wild, endemic Chinook salmon populations in the Minam 

and Wenaha rivers. 

 Provide a future basis and methodologies to reverse declines in stock abundance and 

ensure a high probability of population persistence until causes of population declines 

have been addressed. 

 Establish an annual supply of spring Chinook salmon broodstock capable of meeting 

annual hatchery production goals. 

 Restore and maintain naturally spawning populations of spring Chinook salmon. 

The CBS Program is also an experimental program, with the charge of developing recommended 

strategies for future captive broodstock/rearing programs. As such, monitoring and evaluation are 

integral components with their own set of objectives: 

 Monitor, assess and compare the effects of pre- and post-smolt rearing treatments. 

 Develop and evaluate the effectiveness of innovative methodologies for rearing, spawning 

and disease treatment and prevention. 

 Monitor and compare aspects of life history and production performance between Captive 

and Conventional broodstock programs. 

 Monitor and assess the performance of captive broodstock offspring (F1 generation) in 

captivity (pre-smolt) and in nature (post-smolt) and their offspring (F2 generation). 

 Assess our ability to achieve the genetic conservation goals and production benchmarks. 

 Develop and maintain a comprehensive database for the program. 

There are also specific experimental rearing, spawning and disease treatment/prevention 

strategies that were implemented and must be evaluated. Some of these evaluations (e.g., rearing 

regimes and spawning protocols) were part of the original program design, while others (e.g., 

disease treatment/prevention and early sex and maturation determination) were developed in 

response to issues that developed as the program developed. 
229 

Figure 2. Life history of Chinook salmon in the Grande Ronde Basin Spring Chinook Salmon 

Captive Broodstock Program. 

Captive broodstock salmon were collected as natural parr from each of the populations and reared 

in captivity in separate tanks, for each stock and cohort, from collection through maturity (Figure 

2). Rearing to smolt was conducted first at Lookingglass Hatchery and later at Wallowa Hatchery 

(Figure 3). 

At smoltification, approximately half of the smolts were sent to Manchester Research Station 

(NOAA Fisheries), on Puget Sound, for rearing in saltwater and the other half to Bonneville 

Hatchery (ODFW) for freshwater rearing. Upon maturation, saltwater-reared salmon were 

transported to Bonneville Hatchery for spawning within stocks. The resulting offspring 

(incorporated into the LSRCP production) were reared to smoltification at Lookingglass Hatchery, 

at which time they were transported to acclimation sites on the natal streams of their parents. 

After a period of acclimation, they were released to complete their life cycles (including spawning) 

in nature – CBS salmon were visibly differentially marked so that they were not collected for 

broodstock upon their return. 

 

Collect Wild Parr

Rear to Smolt

Post-smolt Rearing (Freshwater or Saltwater) 

Spawn Within Stocks 

Rear F1 Generation to Smoltification 

Release F1 Generation in Parent’s Natal Stream 

Returning Adults Allowed to Spawn in Nature 
230 

Figure 3. Program populations, hatcheries and acclimation sites used by the Grande Ronde 

Basin Spring Chinook Salmon Captive Broodstock Program. Note: LFH = 

Lookingglass Hatchery, WFH = Wallowa Hatchery, MRS = Manchester Research 

Station and BOH = Bonneville Hatchery. 

CAPTIVE BROODSTOCK RESULTS 

The CBS had specific performance targets for the captive rearing phase of the program. These 

were developed based on assumptions that were made when the program was designed. Here, 

we assess program success by comparing actual performance with these performance targets. 

We were generally able to collect the goal of 500 parr / stream / brood year, except for three years 

for the Upper Grande Ronde River (Table 1). In 1995 we were able to collect only 110 BY 1994 

parr and were unable to collect any BY 1995 or BY 1999 parr in 1996 and 2000, respectively, due 

to extremely low abundance of natural spawners (20 and 4 salmon in 1995 and 1999, 

respectively). Our sex ratio was nearly 1F:1M, as expected. Growth was much slower than 

expected, with adults being approximately 35% smaller (at age) than naturally reared adults (the 

expected size). Survival was slightly better than expected, particularly from parr to smolt. 

Males matured much earlier than expected, with 89% maturing at ages 2 or 3 and only 1% at age 

5 (Table 2). Nearly all (88%) females matured at age 4, making their age composition much closer 

to that expected than the males. This actually worked well for the program, as it made it easy for 

us to avoid sibling mating. There was little overlap in spawn timing between the CBS and CHP or 

naturally spawning salmon. CBS spawn timing was about 3 weeks later than salmon in nature or 

in the CHP at Lookingglass Hatchery. Fecundity was less than half of that expected, due to the Grande

Ronde

River

Snake

Imnaha

River

Wallowa River

Catherine

L

ostin

e

Riv

e

r

km

0 8 16

Creek

River
231 

small size of the females. Approximately 20% (range: 0-77% for a given stock and spawn year) 

of all eggs collected were culled to prevent vertical transmission of bacterial kidney disease (BKD) 

– effective fecundity was 38% of expected. 

Table 1. Assumptions/targets and results for captive rearing of the F0 generation of the 

Grande Ronde Basin Spring Chinook Salmon Captive Broodstock Program. 

Parameter Assumption/target Result 

Parr collection 500 Yes, except GR 1994, 

1995 and 1999 

Sex ratio 1F:1M 1F:1.08M 

Growth Similar to natural ~35% smaller 

Survival Parr-smolt 90% 97% 

 Smolt-adult 55% 55% 

 Parr-adult 50% 53% 

Mean fertility (green egg-to-eyed egg survival) and eyed egg-to-smolt survival rates of the F1

generation were higher than expected (Table 3). However, this was not enough to overcome low 

fecundity and eggs lost due to BKD culling. Mean smolt-to-adult return rate (SAR) was 0.35%, 

250% higher than expected for the CBS Program (0.1%), but well below the Oregon LSRCP goal 

of 0.65%. Age composition of the F1 generation was younger than expected, but typical for 

Northeast Oregon spring Chinook hatchery programs. 

Table 2. Assumptions/targets and results for maturation and spawning of the F0 generation 

of the Grande Ronde Basin Spring Chinook Salmon Captive Broodstock Program. 

 Age 2 Age 3 Age 4 Age 5 

Sex Target Result Target Result Target Result Target Result 

Females 0% 0% 6% 1% 78% 88% 16% 11% 

Males 2% 20% 35% 69% 48% 10% 15% 1% 

 

 Expected Result 

Spawn timing ~ 15 August - 15 September ~ 6 September - 21 October 

Fecundity Age 3 Age 4 Age 5 

Predicted 1200 3000 4000 

Actual 1232 1715 1588 

 
232 

Table 3. Assumptions/targets and results of the F1 generation of the Grande Ronde Basin 

Spring Chinook Salmon Captive Broodstock Program. 

Parameter Target Result 

Fertility (green-to-eyed egg) 75% 85% 

Eyed egg-smolt survival 80% 83% 

Smolt production 150,000 78,720 

Return rate (SAR) 0.1% 0.35% 

 

 Age at maturation 

Age Composition Age 3 Age 4 Age 5 

Target 10% 60% 30% 

Result 15% 71% 14% 

The CBS Program’s annual smolt production goal was 150,000 smolts per population, which 

would result in a targeted return of 150 adults at an SAR of 0.1%. Actual smolt production was 

highly variable but seldom attained the goal of 150,000 smolts (Figure 4). This was mostly due to 

the lower than expected fecundity and the unexpectedly high rate of culling for BKD prevention. 

The Catherine Creek and Lostine River stocks had more consistent production than the Upper 

Grande Ronde River stock, which had the lowest and highest smolt production numbers. The first 

two production years for the Upper Grande Ronde River were very low due to few parr being 

collected for BY 1994 and none for BY 1995. After that, smolt production in the Upper Grande 

Ronde River varied from zero smolts in 2008 (BY 2006 – we had a large Conventional Hatchery 

Program production) to 210,637 smolts in 2003 (BY 2001) and 190,531 smolts in 2010 (BY 2008). 

In 2006, we released only 76 Upper Grande Ronde River CBS smolts because we euthanized 

the remaining 2000 brood year salmon in 2004 due to the development of oral tumors of an 

unknown cause. 

The smolt-to-adult return rate for the CBS Program F1 generation was generally above the 

expected rate of 0.1% (Figure 5). However, the numbers of smolts released were generally below 

the target of 150,000. subsequently, adult escapement rarely exceeded the goal of 150 

adults/stream. 

As the Program progressed, issues arose that impeded our ability to reach our smolt production 

goals. To begin with, we were unable to collect 500 parr each year in the Upper Grande Ronde 

River, due to dramatically low escapement in several years. The salmon reared in saltwater were 

smaller at maturity than those reared in freshwater, which resulted in lower fecundity. We initially 

had a hard time detecting all maturing salmon during our spring sorting for maturing adults, leaving 

many salmon in saltwater longer than they would be naturally. Green egg-to-smolt survival for the 

CBS program was not as high as that of the CHP. We have also had the beneficial problem of 

smolt production in excess of the CBS target (150,000) in some years (Catherine Creek BY 200 

and 2003; Upper Grande Ronde River BY 2001 and 2008). Bacterial kidney disease was the most 

pressing issue, as over half of all captive broodstock mortalities were caused by BKD and up to 

77% of the eggs collected for a given stock and spawn year were culled to prevent vertical 

transmission of the bacterium that causes BKD. We also found that the spawn timing of the CBS 

adults at Bonneville Hatchery was 3-4 weeks later than that of salmon spawning in nature or at 

Lookingglass Hatchery, which removed the option of releasing CBS adults into nature to spawn 

with naturally spawning salmon. 
233 

Figure 4. F1 generation smolts released into Catherine Creek, the Upper Grande Ronde 

River and Lostine River from the Grande Ronde Basin Spring Chinook Salmon 

Captive Broodstock Program, 1998-2008 brood years. 

Figure 5. Escapement of F1 generation Chinook salmon from the Grande Ronde Basin 

Spring Chinook Salmon Captive Broodstock Program to Catherine Creek and the 

Upper Grande Ronde River, 1998-2004 brood years. 

Catherine Creek

1998 2000 2002 2004 2006 2008

Number of smolts

0

50000

100000

150000

200000

250000 Upper Grande Ronde River

Brood year

1998 2000 2002 2004 2006 2008

Lostine River

1998 2000 2002 2004 2006 2008

Captive

Broodstock

Target

Catherine Creek

Brood year

1998 1999 2000 2001 2002 2003 2004

Adult escapement to stream

0

100

200

300

400

500

600

700

Actual returns

Return goal

Upper Grande Ronde River

Brood year

1998 1999 2000 2001 2002 2003 2004

Captive Broodstock

Target
234 

We have addressed and continue to address many of these issues. To improve our ability to 

detect maturing salmon (and thereby move them from saltwater to freshwater at a more natural 

time) and determine their sex, we tested both ultrasound and near infrared spectroscopy and 

found that ultrasound was the more practical method. When we had excess F1 generation 

production from the CBS Program, we released them as eggs or as parr into pre-designated outlet 

streams (unseeded tributaries of their parents’ natal stream). For BKD, we tested vaccines and 

drugs to prevent and treat the disease. We found that the vaccines did not work and the drugs 

were of limited use. Additionally, we are looking for new ways to detect BKD in salmon, before 

they exhibit externally visible symptoms, and from samples of raceway water, in order to treat 

them sooner and use fewer prophylactic drugs treatments. We are also testing new methods for 

the detection of BKD in adult salmon for predicting the likelihood of vertical transmission. This will 

reduce the rate of culling, as it appears that using the enzyme-linked immunosorbent assay for 

this purpose may have caused us to cull more eggs than were necessary. We suspect that the 

water temperature in Tanner Creek (the water source for the adult holding ponds at Bonneville 

Hatchery) did not get sufficiently cold at an early date (Tanner Creek is at least 1,000 m lower 

elevation) for the CBS salmon to ripen as early as they would in northeast Oregon. 

COMPARISONS OF CAPTIVE, CONVENTIONAL AND NATURAL SALMON 

Here we compare the performance of the Captive Broodstock F1 generation with that of the 

Conventional Hatchery Program and both groups of hatchery offspring with natural origin salmon, 

when data for natural salmon are available. We also evaluate whether the CBS Program met its 

F1 generation goals and whether we met the LSRCP production and smolt-to-adult survival (SAR) 

goals. 

Mean eyed egg-to-smolt survival of CBS salmon was 78%, below the CBS Program goal of 80% 

(Figure 6). Eyed egg-to-smolt survival for the CBS Program was also worse than that of the 

Conventional Hatchery Program, which achieved 96%. Mean eyed egg-to-smolt survival for both 

programs greatly exceeded that of natural salmon in these streams, which averages 

approximately 8% (ODFW Early Life History Project, unpublished data). 

Smolt releases for the CBS Program rarely reached the CBS target of 150,000 smolts/stream and 

never reached the LSRCP release goal of 250,000 smolts (Figure 7). However, increased adult 

escapement, in part due to the CBS Program, allowed us to collect sufficient adults for the CHP. 

As a result, smolt release numbers have begun to achieve the target for each stream (the 

Catherine Creek LSRCP target was reduced to 150,000 in 2005) and are likely to continue 

achieving the release goal. The Lostine River program consistently approached the LSRCP 

production goal and will greatly exceed the LSRCP target for BY 2010 due to overcollection of 

adults for the CHP. 
235 

Figure 6. Mean (+1 SD) eyed egg-to-smolt survival for the F1 generation of the Captive 

Broodstock Program and Conventional Hatchery Program in Catherine Creek, the 

Lostine River and Upper Grande Ronde River. 

Figure 7. Number of F1 smolts released from the Captive Broodstock and Conventional 

Hatchery programs into Catherine Creek and the Lostine and Upper Grande 

Ronde rivers, 1997-2010 brood years. Note: smolt numbers for the 2009 and 2010 

brood years are estimates, based on parr and eggs, respectively, on hand as of 

November 2010. 

Eyed egg-to-smolt survival

0.0

0.2

0.4

0.6

0.8

1.0

Captive Broodstock

Conventional Broodstock

Catherine

Creek

Upper Grande

Ronde River

Lostine

River

natural

rate

CBS

goal

Catherine Creek

1998 2000 2002 2004 2006 2008 2010

Number of smolts

0

50000

100000

150000

200000

250000

300000

Captive

Conventional

Upper Grande Ronde River

Brood year

1998 2000 2002 2004 2006 2008 2010

Lostine River

1998 2000 2002 2004 2006 2008 2010

CBS

target

LSRCP

release goal
236 

We monitored downstream migration survival and timing of smolt using PIT tag detections at the 

outflow of the acclimation ponds and at Snake and Columbia river dams. Downstream migration 

survival to Lower Granite Dam was usually better for the CHP smolts than for CBS smolts but not 

significantly so (P=0.319; Figure 8). Natural smolts generally survived better than smolts from 

either hatchery program, but not significantly so (P=0.317). 

We measured length of returning adults at weirs, at Lookingglass Hatchery and on spawning 

ground surveys. Size at maturity for the CBS F1 generation and CHP salmon was similar to that 

of natural salmon for both sexes (Figure 9). The F1 generation was much larger than their parents, 

which were reared from parr to adult in captivity. CBS parents were approximately 35% smaller 

and had less than half the fecundity of their offspring, which had their post-smolt rearing in nature. 

It seems that something integral is missing in the post-smolt captive rearing regime of the CBS 

Program. 

The Upper Grande Ronde River CBS salmon seem to be closer to mimicking the natural age 

composition than the CHP salmon (Figure 10). In Catherine Creek, the CBS salmon demonstrate 

the more typical hatchery age composition of greater numbers of age 3 and fewer age 5 adults. 

CHP salmon demonstrate the typical hatchery age composition in both streams. 

We estimated run timing by the arrival time of salmon at the weirs. Unfortunately, due to periods 

of high stream discharge, the weirs could not always be installed before the first salmon arrived 

or operated continuously thereafter, resulting in an incomplete picture of the true run timing at 

each stream. Adult arrival at the weir seems to be similar to that of the natural salmon but 

compressed for both hatchery programs (Figure 11). 

Figure 8. Downstream migration survival to Lower Granite Dam for natural and F1 generation 

Captive Broodstock Program and Conventional Hatchery Program Chinook 

salmon smolts, 1997-2007 brood years. 

Upper Grande Ronde River

Brood year

1998 2000 2002 2004 2006

Catherine Creek

1998 2000 2002 2004 2006

Survival to Lower Granite Dam

0.0

0.2

0.4

0.6

0.8

Natural

Captive

Conventional

Lostine River

1998 2000 2002 2004 2006
237 

Figure 9. Mean (+1 SD) fork length at maturity of male and female natural and F1 generation 

Captive Broodstock Program and Conventional Hatchery Program Chinook 

salmon. 

Figure 10. Age composition of Catherine Creek and Upper Grande Ronde River natural and 

F1 generation Captive Broodstock Program and Conventional Hatchery Program 

Chinook salmon. 

 

Females

Age

4 5

Fork length (mm, + 1 SD)

400

500

600

700

800

900

1000

Captive Broodstock

Conventional Broodstock

Natural

Males

Age

345

Catherine Creek

Age class

345

Proportion

0.0

0.1

0.2

0.3

0.4

0.5

0.6

0.7

0.8

Natural

Captive

Conventional

Upper Grande Ronde River

Age class

345
238 

Figure 11. Representative run timing (arrival at weir) to Catherine Creek (2006 run year) and 

the Upper Grande Ronde River (2005 run year) for natural and F1 generation 

Captive Broodstock Program and Conventional Hatchery Program Chinook 

salmon 

We defined strays as any salmon collected outside of the direct migration route to its expected 

spawning or collection location. Mean stray rates were 5.0% and 5.2% for the Catherine Creek 

and Upper Grande Ronde River populations, respectively, right at the accepted maximum of 5%, 

and ranged from 0-12.5% (Figure 12). However, a closer look at the data shows that straying is 

not a big problem for either of these programs. Nearly all of the strays for both programs were 

recovered within the Grande Ronde Basin – and nearly all of those returned to Lookingglass 

Hatchery (where they were reared and which they had to swim past on their way to their parents’ 

natal stream, where they were released and where we hoped they would return. 

We determined spawning distribution in nature based on the locations of female carcasses 

recovered during spawning ground surveys. Acclimation sites in all three streams are located 

reasonably high in the spawning area and/or in areas of good spawning habitat (especially the 

Lostine River). Spawning distributions of both CBS and CHP adults tended to focus around the 

acclimation sites, although there is complete overlap with the natural salmon spawning 

distributions in all three populations (Figure 13). The Lostine River acclimation site is located in 

some of the best spawning gravel in the river. As a result, spawning distributions in of the CBS 

and CHP salmon in the Lostine River is similar to that of natural salmon. In Catherine Creek, 

natural Chinook salmon are more evenly distributed, whereas adults from both hatchery programs 

are more likely to spawn in the reaches directly below the acclimation site. The Upper Grande 

Ronde River acclimation site is located in the reach furthest upstream and >70% of the hatchery 

salmon spawn that reach, whereas natural salmon are more evenly distributed throughout the 

total spawning area. 

Catherine Creek - 2006

Week of the year

22 23 24 25 26 27 28 29 30 31

Proportion of run

0.0

0.1

0.2

0.3

0.4

0.5

Natural

Captive

Conventional

Upper Grande Ronde River - 2005

Week of the year

22 23 24 25 26 27 28 29 30 31
239 

Figure 12. Stray rates for Catherine Creek and Upper Grande Ronde River F1 generation 

Chinook salmon, 1998-2004 brood years. 

CBS salmon usually met the CBS SAR target - mean SAR for BY 1998-2004 was 0.300 (Figure 

14). However, the CBS program was only was able to meet the LSRCP SAR target of 0.65 twice 

and the CHP reached this goal only once. Mean SAR for the natural salmon (BY 1998-2004) in 

CC and GR was 0.64%. For the brood years for which we have data from natural salmon and the 

CBS and CHP programs (BY 2001-2004), mean SARs were 0.40%, 0.32% and 0.24% for the 

three origins, respectively. 

Annual adult escapement for the CBS program has often reached the CBS escapement goal of 

150 adults to each stream, particularly in the early years (Figure 15). However, escapements for 

the combined CBS and CHP programs have not approached LSRCP goals of 970 and 1,617 

adults above LGD for the Catherine Creek and the Upper Grande Ronde River populations, 

respectively. The largest hatchery returns over LGD were 601 salmon from Catherine Creek and 

888 adults from the Upper Grande Ronde River, both in 2009. 

It may be that the LSRCP SAR target of 0.65% is unrealistic. Mean SAR for the 1998-2004 brood 

years of natural salmon in Catherine Creek and the Upper Grande Ronde River was 0.64%, nearly 

achieving the LSRCP goal. However, the SAR for the natural salmon exceeded the LSRCP goal 

in only one of those brood years (1.834 for BY 1998, which dramatically increased the mean) and 

ranged from 0.247 - 0.639 for the remaining BYs, 1999-2004). Given this and that the mean SARs 

for either hatchery program are well below the LSRCP target of 0.65%, it may be that neither the 

SAR nor the adult return goal are consistently attainable for these streams in their present 

condition and/or that of their migration corridor. 

 

Catherine Creek

Brood year

1998 1999 2000 2001 2002 2003 2004 2005

Stray rate 

0

2

4

6

8

10

12

14

Captive

Conventional

Upper Grande Ronde River 

Brood year

1998 1999 2000 2001 2002 2003 2004 2005
240 

Figure 13. Spawning distributions (based on locations of female carcass recoveries) of 

natural and F1 generation Captive Broodstock Program and Conventional 

Hatchery Program Chinook salmon for all spawn years in which hatchery salmon 

were present in Catherine Creek (2002-2009), the Lostine River (2001-2009) and 

Upper Grande Ronde River (2004-2009). 

Lower fecundity (due to small size of females), fertility and survival to smolt have resulted in the 

CBS Program having much lower R:S than the CHP, often <1 (Figure 16). Mean R:S for the CBS 

Program was 1.5 recruits / female parent (BY 1998-2005), compared to 14.3 recruits / female 

parent for the CHP (BY 2001-2006). 

However, these data are not a completely accurate comparison of the two hatchery programs. 

We compared adult spawner production for natural salmon with those of the CBS and CHP 

programs using mean rates for the natural salmon and each hatchery program to estimate the 

number of adults that would be produced, based on the 500 natural parr that were collected for 

each CBS Program cohort (natural rates included estimates from the ODFW Early Life History 

Program, B. Jonasson, personal communication; Table 4). For each rearing strategy, the data in 

Table 4 begin with 500 parr, the number of natural parr collected for the CBS Program. Working 

backwards, it takes 0.44 females spawning in nature to produce 500 natural parr (to rear in nature 

Catherine Creek

1234567

0.0

0.1

0.2

0.3

0.4

0.5

0.6

Natural

Captive Broodstock

Conventional

Weir Acclimation

Lostine River

12345678

Proportion of female carcasses 0.0

0.1

0.2

0.3

0.4

0.5

0.6

Upper Grande Ronde River

Reach (upstream )

1234

0.0

0.2

0.4

0.6

0.8

Weir Acclimation

Current Acclimation

Weir

Pre-2005

Weir
241 

or in the CBS Program) and 0.14 females to produce 500 CHP parr. Moving forward from the 500 

parr, we find that CBS parents (F0 generation) have a huge survival advantage while being reared 

in captivity: >50% parr-to-adult survival, compared to <0.5% for the CHP and ~0.2% for natural 

salmon. This results in a greater number of F1 generation spawners on the spawning ground per 

500 F0 generation parr from the CBS Program over either the CHP or natural salmon. We get 

nearly 2 adults in the next generation of natural salmon and approximately 18 F1 generation adults 

from the CHP. In contrast, the CBS program produces approximately 370 F1 generation adults, 

about 20 times more adults than the CHP and nearly 200 times more than natural rearing. 

Figure 14. Smolt-to-adult return (SAR) rates for natural, F1 generation Captive Broodstock 

Program and Conventional Hatchery Program Chinook salmon from Catherine 

Creek and the Upper Grande Ronde River, 1998-2004 brood years. 

Catherine Creek

Brood year

1998 2000 2002 2004

SAR (to stream)

0.0

0.2

0.4

0.6

0.8

1.0

1.2

1.4 Upper Grande Ronde River 

Brood year

1998 2000 2002 2004

2.4

LSRCP

Target

Captive

Broodstock

Target

Natural

Captive

Conventional
242 

Figure 15. Total escapement to Catherine Creek and the Upper Grande Ronde River for the 

F1 generation of the Captive Broodstock and Conventional Hatchery programs, 

1998-2006 brood years. Note: 2006 brood year escapement is for ages 3 and 4 

adults, only. 

Figure 16. Recruits-per-female spawner ratios for F1 generation Captive Broodstock Program 

and Conventional Hatchery Program Chinook salmon from Catherine Creek and 

the Upper Grande Ronde River, 1998-2004 brood years. 

Catherine Creek

LSRCP Goal = 970

Brood year

1998 2000 2002 2004 2006

Total escapement to stream

0

100

200

300

400

500

600

700 Upper Grande Ronde River

LSRCP Goal = 1,617

Brood year

1998 2000 2002 2004 2006

Captive

Broodstock

Target

Captive Broodstock 

Conventional 

Natural 

Catherine Creek

Brood year

1998 1999 2000 2001 2002 2003 2004

R:S (total offspring / female parent)

0

5

10

15

20

25

Captive

Conventional

Upper Grande Ronde River 

Brood year

1998 1999 2000 2001 2002 2003 2004
243 

SUMMARY AND CONCLUSIONS 

Smolt production for the Captive Broodstock Program rarely achieved the CBS F1 generation 

production goals but often reached its total escapement goal for the program populations. 

However, the combined CBS and CHP programs rarely achieved the LSRCP production goal until 

recently, when sufficiently large escapements made it possible to attain full LSRCP production in 

each of the Grande Ronde Basin programs. Egg-to-smolt and downstream migration survival 

rates to Lower Granite Dam were better in the Conventional Hatchery Program than for the 

Captive Broodstock Program F1 generation. Escapement of CBS F1 generation back to the 

program streams often met the CBS Program escapement and SAR goals but the combined 

CBS/CHP programs rarely met the LSRCP SAR goal and never met the LSRCP escapement 

goal. Size at maturity for both programs was similar to that of natural salmon at each age, which 

was the expectation. Age composition of mature salmon in both the CBS and CHP was generally 

typical for hatchery programs, having more age 3 and less age 5 adults than natural salmon. Stray 

rates were higher than desired for both programs but the straying occurred nearly completely 

within the Grande Ronde Basin and was largely a result of adults straying to Lookingglass 

Hatchery (where they were raised), instead of the streams into which they were released as 

smolts. Run timing and spawning distribution were similar between programs and with natural 

salmon. Recruits-per-spawner ratios were higher in the Conventional Hatchery Program. Smolt 

production and R:S ratios were low for the CBS F1 generation due to low fecundity and fertility of 

the CBS parents and culling for BKD prevention. 

Table 4. Production comparison among natural Chinook salmon, a Conventional Hatchery 

Program and a Captive Broodstock Program, based on 500 parr, the number 

collected for captive rearing in the Captive Broodstock Program. Note: shaded 

areas indicate parts of the life cycle occurring in nature. 

 Natural CHP CBS 

Parameter Units Rate Number Rate Number Rate Number

Fecundity Females 4,141 0.44 3,977 0.14 4,141 0.44 

Fertility Green Eggs 0.906 1,840 0.891 570 0.906 1,840 

Eyed-to-Parr Eyed Eggs 0.3 1,667 0.965 508 0.3 1,667 

Number of parr Parr 500 500 500 

Parr-to-Smolt Smolts 0.13 65 0.98 490 0.97 485 

Smolt-to-Adult Adults 0.019 1.2 0.005 2.3 0.55 227 

Sex Ratio Females 0.5 0.6 0.5 1.1 0.5 133 

Fecundity Green Eggs 4,141 2,492 3,977 4,492 1,795 

239,40

8 

Fertility Eyed Eggs 0.906 2,258 0.891 4,002 0.811 

194,16

0 

BKD culling Eyed Eggs 0 2,258 0.01 3,962 0.8 

155,32

8 

Eyed-to-Smolt Smolts 0.039 88 0.965 3,824 0.688 

106,86

6 

Smolt-to-Adult Adults 0.019 2 0.005 18 0.003 370 

The Grande Ronde Basin Spring Chinook Salmon Captive Broodstock Program was successful 

in increasing the numbers of adults spawning in nature in each of the program streams, its primary 

goal. However, there are issues that must be addressed for future captive broodstock programs. 
244 

Slow growth and the resulting low fecundity were the prime causes for not reaching the smolt 

production goals of the CBS Program. Disease (particularly bacterial kidney disease) caused us 

to barely achieve our parr-to-adult survival goal. Worse, culling to prevent vertical transmission of 

BKD further reduced our smolt production, often dramatically (up to 77%). The F1 generation also 

did not perform very well in the hatchery, having lower fertility and hatching success than the 

Conventional Hatchery Program. Lastly, gene amplification and domestication are potential 

hazards to any hatchery program but are particularly risky to captive broodstock programs. 

Figure 17. Total escapement for Chinook salmon to Catherine Creek, the Lostine River and 

Upper Grande Ronde River, 1960-2009 run years. 

CBS F1 generation adults first returned in 2001 (BY 1998). The first CHP adults returned to the 

Lostine River in 2000 and to Catherine Creek and the Upper Grande Ronde River in 2004. As 

expected, total escapement to the Grande Ronde Basin has increased since the inception of the 

CBS and CHP programs (Figure 17). The Lostine River population had the greatest increase, 

while the Upper Grande Ronde River population had boom and bust years and was more 

dependent upon hatchery production than the other two populations. 

We have always considered that the ultimate measure of the success or failure of the CBS 

Program would hinge on an increase in the number of natural adults returning to and producing 

offspring in each of the program streams. Although the numbers of total adults returning to these 

streams have increased, we are seeing little evidence of an increase in the numbers of natural 

adults being produced in the program populations (Figure 18). This is the ultimate goal of the CBS 

and CHP programs and we cannot say that they have succeeded in attaining that goal. 

Run year

1960 1970 1980 1990 2000

Escapement

0

1000

2000

3000

4000

5000 Total 

Catherine Creek

Lostine River

Upper Grande Ronde River

First F1 generation returns

LR 

CHP

CBS

CC & GR

CHP
245 

Figure 18. Combined total and hatchery escapement for Chinook salmon and percent of the 

run comprised of natural salmon in Catherine Creek, the Lostine River and Upper 

Grande Ronde River of the Grande Ronde Basin, 1960-2009 run years. Note: nonendemic Rapid River and Carson stock Chinook salmon produced the 1986-1994 

hatchery returns. Endemic stock Chinook salmon comprised the 2000 - 2009 

hatchery returns. 

ODFW RESPONSE TO ISRP COMMENTS – Grande Ronde Captive Broodstock 

Below are our responses to comments made by the ISRP regarding the presentation on the F1

generation of the Grande Ronde Basin Spring Chinook Salmon Captive Broodstock Program. 

Several of the responses are needed to clarify some comments made by the ISRP. 

I. Introduction 

ISRP comment: “2010 was the last year of CBS; the work transfers now to a Safety Net Program.” 

Response: 2010 was not the last year of the Captive Broodstock Program. It was the last year for 

the Catherine Creek and Lostine River portions of the program but the Upper Grande Ronde River 

portion will continue until the last of the BY 2008 salmon are spawned in 2013. We are in the 

process of moving the Upper Grande Ronde River program to a Safety Net Program (SNP). The 

SNP is funded by Accord money from the Confederated Tribes of the Umatilla Indian Reservation. 

It is intended to insure that a sufficient number of hatchery smolts are produced in years in which 

an insufficient number of adults are captured for the Conventional Hatchery Program. 

ISRP comment: “The Captive Brood Program in the Grande Ronde subbasin was designed to 

increase survival of hatchery-spawned parr“ 

Run year

1960 1970 1980 1990 2000

Escapement

0

1000

2000

3000

4000

5000

Percent natural

0

20

40

60

80

100

Total 

Hatchery

Natural

% natural
246 

Response: The Captive Broodstock Program was designed to increase survival of the naturallyspawned (not hatchery-spawned, as was stated in the ISRP review) parr from capture to 

adulthood and their offspring from egg to smolt. 

II. Data 

ISRP comment: “It is not clear if genetic analyses will be included.” 

Response: Yes, genetic analyses were always part of the plan for the Captive Broodstock 

Program. However, they were not funded until FY 2011. We have begun to examine the 

relatedness of the natural parr collected for the captive broodstock and the spawning success of 

the Captive Broodstock F1 generation in nature. The latter study is being done in collaboration 

with NOAA Fisheries. 

ISRP comment: “Methods were not described in detail but summary reports provided a description 

of methods, which may also be found elsewhere (a reference is required).” 

Response: Methods for the Captive Broodstock Program can be found in annual reports and 

annual operating plans submitted to BPA and in the program’s 1995-2002 status report (Hoffnagle 

et al. 2003. Grande Ronde Basin Spring Chinook Salmon Captive Broodstock Program, 1995 - 

2002 Project Status Report, Fish Research and Development Project, Oregon. Northeast Region, 

Oregon Department of Fish and Wildlife, La Grande.). Methods for monitoring and evaluating the 

F1 and F2 generations can be found in annual reports and annual operating plans submitted to 

LSRCP. 

III. Key Findings 

ISRP comment: “F1 fish showed an overall lower than expected percentage of older fish. F1 

fertility and eyed egg-smolt survival were slightly lower than expected, but the main problem was 

a much lower SAR than assumed (0.1% versus 0.35%).” 

Response: The ISRP got the target and actual SAR values reversed. The target SAR for the 

Captive Broodstock F1s is 0.1%. We exceeded that in the program, having a mean of 0.35%. 

However, this was well below the LSRCP SAR goal of 0.65%. 

ISRP comment: “Of particular note were BKD (impact was not excessive)...” 

Response: BKD caused over half of the mortalities for 8/10 brood years (1994-2003) and killed 

more than half of the total fish collected for two of those years. It was, by far, the greatest source 

of mortality in the program. 

ISRP comment: “Table 1. Please provide SD or SE along with mean survival and an indication of 

the number of years that data is available.” 

Response: We’re not sure to which table this comment is referring – all results were provided in 

figures and the survival figures did contain standard deviation. We agree that this information is 

useful to readers and will be sure to continue to provide it in the future. 

ISRP comment: “Growth was 35% smaller — was this for same age of fish, or does this value 

reflect earlier age at maturation?” 
247 

Response: This was a growth comparison of fish of the same age. 

ISRP comment: “Table 2. The low fecundity in the captive fish, especially among the older age 

fish is an interesting finding. There was no mention of whether eggs were smaller or larger than 

natural or conventional hatchery fish.” 

Response: We do not know what “Table 2” refers to. The dramatically lower fecundity of the 

Captive Broodstock fish was mostly due to the smaller size (see the comment above) of the 

females reared in captivity. Egg weight of CBS females was similar to that of natural salmon from 

these populations. 

ISRP comment: “There was good comparison of smolt-to-LGD survival among natural, CBS and 

CHP smolts. It appears survival was very low (~40%), and it is not clear from the report(s) why 

was survival of fish from the Lostine River higher than from Catherine and Upper Grande Ronde.” 

Response: See Monzyk et al. 2009. Migration characteristics of hatchery and natural spring 

Chinook salmon from the Grande Ronde River Basin, Oregon, to Lower Granite Dam on the 

Snake River. TAFS 138:1093-1108. Smolts from the Upper Grande Ronde River and Catherine 

Creek have to negotiate a long stretch of slow moving water through the Grande Ronde Valley, 

which the Lostine River salmon do not. 

IV. Outlook and Recommendations 

ISRP comment: “The test that is needed is a comparison of NOR vs. CBS relative reproductive 

success through F2 and beyond.” 

Response: We agree and hope to do that in conjunction with the Relative Reproductive Success 

Study being conducted by NOAA Fisheries. 

ISRP comment: “Here, as in all LSRCP projects, there is more emphasis required on the limits to 

production outside of the subbasin, including ocean effects and harvest.” 

Response: We agree but this is beyond the scope of our funding. 

ISRP comment: “The fecundity issue by itself seems like a problem that perhaps could be 

effectively addressed with a more productive feeding regimen.” 

Response: We have discussed this issue with experts in salmon feeding and nutrition, who are 

equally perplexed. The Salmon River (Idaho) Chinook salmon captive rearing program has similar 

issues with small size of captive-reared adults. We are open to suggestions on this issue and may 

be able to evaluate them using the Safety Net Chinook salmon. 

ISRP comment: “Although the captive program has functioned with some success at the original 

stages or the rebuilding process, the long-term prognosis of meeting LSRCP mitigation objectives 

remains less clear.” 

Response: The Captive Broodstock Program was not designed to meet the LSRCP mitigation 

objectives. It was designed to increase the numbers of salmon returning to the program 

populations, at which time Conventional Hatchery Programs could be started to meet the LSRCP 

mitigation objectives. The CBS Program has met this objective. 
248 

 
249 

MANAGEMENT OF BACTERIAL KIDNEY DISEASE IN CHINOOK SALMON HATCHERIES 

BASED ON BROODSTOCK TESTING BY ENZYME-LINKED IMMUNOSORBENT ASSAY 

(ELISA): A MULTI-YEAR STUDY 

A. Douglas Munson1, Diane G. Elliott2 and Keith Johnson1

1. Idaho Department of Fish and Game 

Eagle Fish Health Laboratory 

Eagle, ID 83616 USA 

2. Western Fisheries Research Center 

U.S. Geological Survey 

6505 N.E. 65th Street 

Seattle, WA 98115-5016 USA 

This article can be viewed at: 

North American Journal of Fisheries Management 30:940-955, 2010 

CopyRight of the American Fisheries Society 2010 

DOI:10.1577/M09-044.1 

 
250 

GENETIC ANALYSIS OF NATURAL-ORIGIN SPRING CHINOOK AND COMPARISON TO 

SPRING CHINOOK FROM AN INTEGRATED SUPPLEMENTATION PROGRAM AND 

CAPTIVE BROODSTOCK PROGRAM IN THE TUCANNON RIVER 

by 

Todd W. Kassler and Cheryl A. Dean 

Prepared for: 

U.S. Department of Energy 

Bonneville Power Administration 

P.O. Box 3621 

Portland, OR 97283-3621 

Project Number 2000-019-00 

Primary Contract Number 40744 

October 2010

Washington Department of Fish and Wildlife, Molecular Genetics Laboratory 

600 Capitol Way N, Olympia, WA 98501 

This report can b e wiewed at: 

HTTP://WWW.FWS.GOV/LSNAKECOMPLAN/REPORTS/WDFW/EVAL/TUCANNON%20SP

%20CHINOOK%20GENETICS%20REPORT%20CONSENSUS.PDF 
251 

PREVALENCE OF BACTERIAL KIDNEY DISEASE IN NATURAL VS. HATCHERY-REARED 

ADULT CHINOOK SALMON SPAWNED IN A HATCHERY AND IN NATURE 

Timothy L. Hoffnagle 

Northeast Region Fish Research 

Oregon Department of Fish and Wildlife 

203 Badgley Hall 

Eastern Oregon University 

La Grande, Oregon 

 Glenda O’Connor 

Northeast Region Fish Health 

Oregon Department of Fish and Wildlife 

217 Badgley Hall 

Eastern Oregon University 

La Grande, Oregon 

Richard W. Carmichael and Sally Gee 

Northeast Region Fish Research 

Oregon Department of Fish and Wildlife 

203 Badgley Hall 

Eastern Oregon University 

La Grande, Oregon 

September 2009 

Funds supplied by: 

Lower Snake River Compensation Plan, U. S. Fish and Wildlife Service 

This Report can be viewed at: 

http://www.fws.gov/lsnakecomplan/Reports/ODFW/Eval/BKD%20in%20Wild%20and%20H

atchery%20Chinook%20Salmon.18%20SEP%202009.Information%20Report.Final.pdf
252 

ODFW RESPONSE TO ISRP COMMENTS – BACTERIAL KIDNEY DISEASE 

Below is the only comment that we found to address for the presentation on bacterial kidney 

disease in hatchery and natural salmon in the Grande Ronde and Imnaha river basins. 

ISRP comment: “Again, it would be useful to summarize the fish health program of the LSRCP.” 

Response: We agree but this is beyond the scope of our present funding with LSRCP. 

 
253 

THE USE OF PASSIVE INTEGRATED TRANSPONDER (PIT) TAGS AS A TOOL TO 

MONITOR AND MANAGE ADULT CHINOOK SALMON RETURNS TO IDAHO 

John D. Cassinelli 

Idaho Department of Fish and Game 

1414 East Locust Lane, Nampa, Idaho 

BACKGROUND 

In 2006, the Idaho Department of Fish and Game (IDFG) began increasing the number of Passive 

Integrated Transponder (PIT) tags injected into hatchery spring/summer Chinook salmon smolts 

to gain the ability to use the tags to monitor and quantify adult returns (for the purpose of this 

report, “adult” includes jacks). By release year 2008 (BY 2006), all hatchery Chinook salmon smolt 

releases from IDFG-operated hatcheries contained a representative group of PIT tags with the 

exception of off-site releases of Rapid River Chinook salmon into the Little Salmon River and in 

the Snake River at Hells Canyon Dam. Currently, over 230,000 PIT tags are implanted into 

Chinook salmon leaving IDFG hatcheries annually (Figure 1). 

ADULT MONITORING 

Starting in 2009, adult PIT tag detections have been monitored throughout the return at 

Bonneville, McNary, Ice Harbor, and Lower Granite dams. These PIT tag detections are expanded 

by the juvenile tagging rate for run-at-large (monitor mode) tags from the separation-by-code 

process. The expanded detections are used to generate daily in-season return estimates by 

hatchery, release site, and age at each dam. These daily updates are posted to a shared website 

(https://research.idfg.idaho.gov/PublicDocuments/Forms/AllItems.aspx) Monday through Friday 

throughout the adult run. Also throughout the run, weekly teleconference calls are held to discuss 

the updated run projections, run status, harvestable shares, hatchery operations and fishery 

status. Participation in these weekly calls typically includes, but is not limited to, IDFG, Oregon 

Department of Fish and Wildlife, Washington Department of Fish and Wildlife, U.S. Fish and 

Wildlife Service, Nez Perce Tribe, Shoshone Bannock Tribe, and Idaho Power Company. This 

coordinated process enables the most up to date in-season estimates to be available to all parties 

and for real time management decisions to be made. 
254 

The use of PIT tags to monitor adult returns typically provides us with a more accurate return 

estimate than we get from pre-season forecasts that are based on simple sibling regression 

models. Figure 2 shows a comparison of two- and three-ocean adult return forecasts versus inseason return estimates from expanded PIT tags in 2010. As you can see, while the forecasts for 

the Clearwater River were close to the PIT tag estimates, the Salmon River forecasts were much 

higher than the actual return based off of PIT tag estimates. Figures 3 and 4 compare an inseason estimate that is very close to a preseason forecast (Figure 3, South Fork Clearwater 2010) 

versus an in-season estimate that is a lot lower than the preseason forecast (Figure 4, South Fork 

Salmon River 2010). This emphasizes the value of having a tool that can be used to generate inseason stock and age specific return estimates as these more accurate numbers enable more 

precise management. In addition to in- and post-season return estimates, adult return monitoring 

also provides more robust stock and age specific data for inter-dam conversion rates, run timing, 

fallback with reascension rates, and after hour’s passage rates at each dam. All of these are 

important monitoring and evaluation metrics that aid in run reconstruction. 

Figure 3. 
255 

ADDRESSING ISSUES 

While PIT tag expansions provide valuable adult return data, there are some shortcomings 

associated with using PIT tags to estimate adult returns. In looking at historic adult return 

estimates, there was evidence that expanding PIT tagged adults by juvenile tagging rates was 

underestimating the return. This was likely due to issues such as unaccounted for tag shedding 

and differential survival post release. While evidence for this exists, historically it has been difficult 

to estimate rates of PIT tags in adult returns because hand scanning at hatchery racks is not 100 

percent efficient. To get at the true tagged proportions within the adult returns, we had in-ladder 

detection arrays installed in both the South Fork Salmon River (Figure 5) and the Sawtooth Fish 

Hatchery adult traps. The South Fork array was installed prior to trapping in 2009 and the 

Sawtooth array prior to trapping in 2010. These array systems have repeat antennas which allow 

us to get detection efficiencies which in turn, allow us to get at the true proportion of PIT tags in 

the adult return, by age class. We can then correct the expasions rates and use the corrected 

expasions to adjust our estimates downriver at in-stream arrays and at the dams. However, these 

adjustments can only be done post-season and cannot be used to adjust in-season return 

estimates. Figure 6 shows an example of these adjusted expansions for the South Fork Salmon 

River at Lower Granite Dam for the 2010 return. Using these corrected expansions, we have 

found in-season stock specific estimates range from 11 – 37 percent low and that the level of 

underestimation varies across years, locations, and between age classes. However, despite this 

level of underestimation, return estimates can still be corrected post-season for locations that we 

have in-ladder arrays and in-season numbers are still more accurate than relying on preseason 

forecasts. 

Figure 4. 
256 

In addition to monitoring adults at these array systems, we are midway through a double marking 

study at the Powell Satellite Facility. Brood Year 2006 Chinook salmon from Clearwater Fish 

Hatchery destined to be released at the Powell Satellite in 2008 were part of a double marking 

study designed to investigate shed rates of PIT tags from release to adult return and to estimate 

if PIT-tagged fish exhibit differential survival from non-PIT tagged fish. Prior to the release of these 

fish, the water intake for the pond froze over, resulting in a loss of water into the pond and the 

mortality of about half or the release group. The surviving fish from this study returned as oneocean jacks in 2009 and two-ocean adults in 2010. All returning fish were thoroughly double 

scanned with both a CWT wand and handheld PIT tag reader to confirm the presence or absence 

of tags. Eight treatment fish and 12 control fish returned to Powell in 2009 as jacks. Of these eight 

treatment fish, one was missing a PIT tag (12.5% shed rate). In 2010, 36 treatment fish and 31 

control fish returned. Of these 36 treatment fish 11 had lost their PIT tags (30.6%) shed rate. Also, 

at some facilities we have started experimenting with a pump array system to get at the true 

number of PIT tagged fish as they are loaded onto trucks for release to get a better idea of true 

on-station shedding/survival. 

SUMMARY 

Having representative PIT tag groups in the majority of our releases provides a tool to get real 

time in-season estimates of adult returns at four of the eight lower Columbia and Snake River 

dams. These estimates are distributed and discussed through a shared website and weekly 

Figure 6. 

Figure 5. 
257 

teleconference calls throughout the adult return which allows for more accurate and timely 

management and coordination. While these in-season estimates provide more accurate stockand age-specific estimates than preseason forecasts, tag shedding and mortality cause these 

estimates to be low. However, in-ladder array systems allow us to correct these estimates at some 

of our facilities for run reconstruction purposes post-season. We will continue to monitor the rates 

at which PIT tagged adults return and continue to evaluate, and hopefully quantify, possible 

causes of these differential return rates. 

IDFG RESPONSE TO ISRP COMMENTS – PIT tags 

ISRP Comments: 

The value of this paper would be greatly enhanced if it reviewed all available literature in an effort 

to determine PIT tag shed rates for each age class of salmon. What factors contribute to tag loss? 

Are there methods to minimize tag loss? Continued research into tag loss is critical because many 

decisions in the Basin are based on PIT tag data. High and variable tag loss could introduce 

significant error in survival rate estimates, leading to the misinterpretation of data from 

hydrosystem and supplementation experiments, and from harvest management. 

IDFG Response to ISRP comments: 

Very little literature exists in regards to adult age- or sex- specific PIT tag retention. At this time, 

there are two papers that cover this topic to some degree. 

Prentice, E. F., D. J. Maynard, S. L. Downing, D. A. Frost, M. S. Kellett, D. A. Bruland, P. SparksMcConkey, F. W. Waknitz, R. N. Iwamoto, K. McIntyre, and N. Paasch. 1994. Comparison 

of long-term effects of PIT tags and CW tags on coho salmon (Oncorhynchus kisutch). 

Pages 123–137 in A study to determine the biological feasibility of a new fish tagging 

system. Bonneville Power Administration Annual report for 1990–1993, BPA Report 

DOE/BP-11982-5, Portland, Oregon. 
258 

Knudsen, C., M. Johnston, S. Shroder, W. Bosch, D. Fast, and C. Strom. 2009. Effects of Passive 

Integrated Transponder Tags on smolt-to-adult recruit survival, growth, and behavior of 

hatchery spring Chinook salmon. NAJFM 29:658-669. 

In the Prentice et al. paper, it was determined through double tagging (PIT and CWT) that tag 

loss was higher in returning age 2 and 3 female Coho salmon than in returning age 2 and 3 males. 

Adult females showed a 47.9% loss of tags while males only lost 11.3% of their tags (data from 

two return years). This tag loss appeared to occur primarily during late maturation and it was 

concluded that females have a much higher rate of tag loss near full maturation due to the fact 

that female Salmonids drop eggs into their body cavity prior to being expelled through the 

ovipositor. Because fish are PIT tagged in the body cavity, the PIT tag would be free floating 

among the eggs and could be expelled as an irritant. 

Similarly, we have found through investigations at the South Fork Salmon River ladder array, that 

there are differential tag loss rates between males and females. For brood years 2005 and 2006 

combined, overall tag loss for males was 24.3% while for females it was 52.5% (Figure 7.) 

To further investigate, all fish returning in 2011 to the SFSR trap with a PIT tag are being externally 

marked. When these fish are ripe and removed on spawning days, they will be checked again for 

tags to see what the rate of PIT tag shedding is in sexually maturing fish that have made it back 

to hatchery holding. If the majority of tag loss does occur primarily during late maturation as 

Prentice et al. suggest, then correcting PIT tag expansions at lower Snake River and Columbia 

River dams based off of adjusted adult tag rates at time of terminal trapping may not be valid and 

unadjusted expansions at these dams may be more accurate. 

 1 and 2-Ocean Male Returns 2-Ocean Female Returns

Brood 

Year 

Return 

Year Trap 

Males 

Trapped 

Expected 

CSS/BDL 

PIT 

Recoveries

Actual 

CSS/BDL 

PIT 

Recoveries

Estimated

PIT Loss

Females 

Trapped

Expected 

CSS/BDL 

PIT 

Recoveries 

Actual 

CSS/BDL 

PIT 

Recoveries

Estimated 

PIT Loss

2005 2008 SFSR 1,957 93 70 24.85% 

2005 2009 SFSR 1,480 70 53 24.77% 2,170 103 62 39.98% 

2006 2009 SFSR 5,295 258 196 23.99% 

2006 2010 SFSR 1,686 82 62 24.49% 3,286 160 63 60.63% 

Figure 7. Estimated PIT tag loss for brood year 2005 and 2006 SFSR male and female 

Chinook salmon. Not enough tag recoveries were made to include the 3-ocean 

component from each brood year. 

The Knudsen paper did not investigate tag loss by sex but instead looked at tag loss across age 

classes and over time, using double tagging with PITs and CWT as well. This paper showed that 

average tag loss was 2.0% in juveniles prior to release, and 18.4% for fish returning 6 months to 

4 years after release. This study indicated that most PIT tag loss had occurred within the first 6 

months post-release, as no significant loss was observed in older fish. However, fish were 

examined prior to full development of gametes. The study also showed that due to tag loss and 

lowered survival of tagged fish, that SARs based on PIT tagged fish were 25% lower than SARs 

based off of CWT. 
259 

Preliminary data from these two papers coupled with preliminary data from IDFG could suggest 

that there is a differential survival/tag loss resulting in a 25% lower number of PIT tagged fish 

within the first six months and additional tag loss, up to 35%, occurs in females pre spawn. 

However, data supporting this conclusion is preliminary and additional years of monitoring are 

needed. 

IDFG agrees that “Continued research into tag loss is critical because many decisions in the Basin 

are based on PIT tag data.” And we are currently in the process of adding in-trap array systems 

to the three Clearwater Fish Hatchery satellite facilities (Powell, Red River, Crooked River) so 

that we can expand our ability to monitor differential return rates of PIT tagged fish and further 

investigate potential causes and timing of tag loss and differential survival. Once tag loss is better 

understood, methods to minimize it will be more attainable. 

 
260 

2010 LSRCP SPRING/SUMMER CHINOOK PROGRAM REVIEW ROLLUP 

Symposium Summary

Mark Schuck

Mark Schuck is Evaluations Project leader for Washington Department of Fish and Wildlife. He 

has worked within the LSRCP program evaluations since 1982 when he began steelhead 

evaluations at Lyons Ferry Hatchery. He became project leader for all salmon and steelhead 

evaluations in 1995. 

 
261 

Slide 2 

Roll Up Presentation

 What am I going to tell you?

 Metrics – as agreed upon by Cooperators

 Generalizations (everything is combined)

 Observations/take homes

 Program strengths and Data gaps

 How did I summarize the data?

 Cooperators provided Metric Summaries

 Tried to roll‐up into general overview take‐homes.

 I did not comprehensively re‐analyze data.

The roll-up presentation was meant to encapsulate the results that had been presented over the 

two-day symposium. The hope was that it would remind and emphasize to attendees the notable 

consistencies or exceptions that had been highlighted in the project presentations. As noted in 

this slide, I did not complete an exhaustive re-analysis of Cooperator’s data, rather I combined 

common data sets that had been provided to me to show general program performance (i.e. – at 

a LSRCP program level, how had the performance compared with expectations, where did the 

program succeed, and where did it fail). This was to include recognition of evaluation studies’ data 

gaps that prevented adequate or complete evaluation of program performance. 

 
262 

Slide 3 

Roll Up Presentation

 Remember

 The data represent the hard work of a large hatchery network

and their staff (production) to meet challenging goals and

objectives.

 The data are a result of close collaboration among

cooperators (hatchery + M&E), and represent estimates of

performance within the limitations of time, money and

management direction at the time.

 Production and evaluations have been as adaptive as possible

while attempting to retain the continuity of purpose that is

necessary for anadromous fish mitigation. Currently 100%

marked production for accounting and assessment.

This is a disclaimer both for the ability to achieve and evaluate program goals, and the inability to 

summarize at too fine a detail without confusing attendees. Production and evaluation staffs work 

closely to monitor the program both within and across political boundaries, but long term studies 

are expensive and have had to be adaptive to stay current with relevant fisheries science. 

Substantial marking occurs annually to enable evaluations of these programs. 

 
263 

Slide 4 

LSRCP Goals/Assumptions

 Smolt production (assumed 0.87% SAR)

 6,750,000

 Adult Numbers (escapement)

 58,700 to Snake Basin

 Harvest (somewhere downriver)

 58,700 sport harvest

 176,100 commercial harvest

Goals and assumptions for the Spring/Summer Chinook programs as documented in the original 

1975 Corps of Engineers document1. The escapement number was to the Project Area (Generally 

the Snake River basin, more particularly for most of the cooperators to above Lower Granite Dam) 

and harvest from that escapement was assumed. The downriver harvest portions of the program 

have had little mention in past LSRCP program reviews and are notable for their magnitude. 

---------------------------- 

1Special Report: Lower Snake River Compensation Plan, Lower Snake river Washington and 

Oregon, June 1975. U.S. Corps of Engineers, Walla Walla, Washington. 95 pp plus appendices. 

 
264 

Slide 5 

LSRCP Summary Goals

 Objectives changed as a result of ESA or production or

management goals changed by the Cooperators.  Progress

toward goals or objectives presented here reflect those changes

overtime.

 Postrelease survival (to LGD and SAR/SAS)

 Population level changes (age structure, return timing,

productivity)

 Fisheries

 Focus period (BY1996‐2004)

Reviewers should remember that progress toward achieving LSRCP goals and the Cooperator’s 

management objectives are relative in this roll up presentation: i.e. – where production or survival 

targets have been changed by the management entity, their progress toward achieving that new 

target is captured here and may be greater or less than in the original LSRCP document. The 

summary goals presented herein are those for which roll-up metrics could be reasonably 

summarized to inform attendees. Many of the metrics presented did not capture the entire 

program duration, but data extending back to the early 1980’s is often included to provide context 

and better show trends. 

 
265 

Slide 6 

 
266 

Slide 7 

Brood stock Acquisition

 In general mitigation programs are typically meeting

brood stock objectives.  Other programs face

challenges.

 Mature supplementation programs are also mostly

successful in brood collection.

 New supplementation programs have experienced

challenges with brood stock:

 Low abundance of NOR

 Low abundance of early hatchery releases

 Supplementation programs can face challenges

collecting representative brood stock and achieving

desired PNI.

Brood stock is the cornerstone of production programs. The conventional hatchery mitigation 

programs in LSRCP have generally been successful at meeting brood needs. Supplementation 

programs, especially newer ones, have been challenged in meeting broodstock needs where 

constraints are in place to control pNOB, pHOS and PNI, or where low abundance of natural fish 

has simply prevented reaching brood stock needs. The recent upturn in spring/summer Chinook 

abundance has positively affected these programs. 

 
267 

Slide 8 

Egg to smolt survival: Goal = 70%

50%

55%

60%

65%

70%

75%

80%

85%

90%

95%

100%

1989 1993 1997 2001 2005 2009

Release Year

LSRCP Goal

This summarizes survival for all programs combined, by release year since 1989. The LSRCP 

assumption/goal was that properly operated hatchery programs should achieve an eyed egg to 

smolt (release) survival of 70%. As the accompanying graph depicts, the program has achieved 

that level of performance in most years, and nearly so in two of the three years where survival 

was below the goal. These data represent hatchery performance only for programs that collected 

their own eggs. Total smolt production often included eyed-egg transfers from other established 

hatcheries, especially in early years. For years with no percentage plotted, there were incomplete 

hatchery data to calculate a collective performance. Individual hatchery data sets will contain 

more information from which specific survival estimates could be derived. 

 
268 

Slide 9 

Disease Considerations

 BKD control has been effective

 Prophylactic treatments of adult females are used

commonly.  Juvenile treatments are used, but more/less

aggressively by agency protocol.

 Culling of eggs from high ELISA value females is used

by some hatcheries –not universally.

 Prevalence has dropped.

 ODFW not seen increase in natural populations.

 Standard Disease monitoring is closely followed

throughout the Program

 Presently disease is not limiting production.

Disease within a hatchery can devastate populations and seriously degrade the beneficial 

hatchery effect of high egg to release survival. BKD is a prevalent disease of Chinook that was, 

and continues to be, a focus of control efforts. The cooperators continue to utilize adult broodstock 

injections to control the disease prior to spawning, which has effectively controlled its incidence. 

Each cooperator differentially practices disease control within their hatchery. There is no general 

treatment regime such as culling of eggs from high ELISA values females, or prophylactic 

administration of medicated feed to juveniles. 

Standard disease monitoring and control efforts from the Pacific Northwest are employed 

throughout the program and there is general agreement that disease does not currently limit 

production at any facility. 

 
269 

Slide 10 

Smolt production : LSRCP total

0%

20%

40%

60%

80%

100%

120%

1987 1991 1995 1999 2003 2007

% Annual Goal

Release Year

LSRCP Goal = 6.75 M

This slide depicts the percent of the program production goal annual smolt releases have met. It 

does not include parr releases, but does include smolt releases that came from hatcheries outside 

the basin to boost production releases toward the goal. The severe decrease in smolt releases in 

the mid 1990’s was directly related to adult abundance. 

Since that time adult abundance has greatly improved and smolt production responded. However, 

failure to reach 100% of the goal since those low abundance years has resulted from changes to 

the program in response to ESA listings, recommendations that arose from new studies on the 

effects of hatchery fish on natural populations, hatchery review recommendations, management 

decisions to limit production releases in some areas to limit hatchery fish abundance, and low 

returns of conventional hatchery, natural origin, or endemic origin hatchery fish to support 

mitigation and supplementation programs. 

 
270 

Slide 11 

 
271 

Slide 12 

Smolt Survival: Release to LGD

0%

10%

20%

30%

40%

50%

60%

70%

80%

90%

100%

1993 1996 1999 2002 2005 2008

Survival

Release Year

Knox Br.

Sawtooth

Lochsa

SF Clearwater

Imnaha

UGR

Smolt survival to Lower Granite Dam (LGD) has been a key monitoring metric of cooperators. 

Although at first glance this appears a jumble – there is some synchrony among programs 

between years despite the within year survival differences among the releases. This diversity 

between migration years and among programs may be strongly affected by environmental and 

river conditions in the year of release. 

 
272 

Slide 13 

Mean Survival to LGD

y = ‐0.0002x + 0.6247

R2 = 0.0887

0%

10%

20%

30%

40%

50%

60%

70%

80%

0 100 200 300 400 500 600 700 800

Survival

Distance to LGD (km)

In developing the symposium, many metrics were discussed that might represent relative 

performance of hatcheries and stocks across a large program like the LSRCP. One possible factor 

affecting smolt performance, in this case survival from release to LGD, was distance traveled. I 

plotted survival by facility (or release site) and distance to LGD but found no strong relationship. 

It appears that other factors play a more important role in juvenile survival than distance traveled. 

(Note: these data points were developed from the same survivals used in the previous slide.) 

 
273 

Slide 14 

SARs for Primary Rivers

0.00%

0.50%

1.00%

1.50%

2.00%

2.50%

1994 1997 2000 2003

Brood year

SAR

Salmon

Grande Ronde

Clearwater

Imnaha

Tucannon

LSRCP Assumption = 0.87%

The LSRCP hatchery program was sized for production based on an assumed SAR*of 0.87%. 

Performance by river system was summed for all releases by brood year. Despite the diversity 

among programs there is substantial synchrony among years, which suggests that the migration 

corridor and ocean are very important drivers of program success. The programs are not 

achieving the assumed SAR in most years, which also suggests that either the original 

assumption of survival was in error, or productivity is being driven down by factors other than the 

hatchery environment. 

----------------------- 

•SAR = Smolt to adult returns (includes jacks) to the project area. 

•The Grande Ronde line includes Captive Brood smolt release performance, which has lagged 

Conventional Hatchery Program fish performance. 

 
274 

Slide 15 

Brood Year

LSRCP Design Goal = 0.87%

0.00%

0.20%

0.40%

0.60%

0.80%

1.00%

1.20%

1.40%

1994 1995 1996 1997 1998 1999 2000 2001 2002 2003

Mean SAR for LSRCP by Brood Year

10 yr. Mean = 0.52%

This is a further depiction of collective survival by brood year for the entire program. In 80% of 

brood years the SAR is below the assumed LSRCP goal, with the 10 year mean being only 60% 

of the target 0.87% SAR. 

 
275 

Slide 16 

Return Timing

 Hatchery and natural population run timing does not

appear to have significantly changed over time.

 Although there tends to be slight deviations between

H & N at LGD, with slightly prolonged natural arrival.

 Spring and summer populations retain their different

timing.

Each program evaluated the return timing of their adults and often compared them to natural 

populations. No significant changes in run timing were noted for any program, although there may 

be a slightly longer immigration period for the natural fish. 

 
276 

Slide 17 

Age at return

1‐Ocean

28%

2‐Ocean

61%

3‐Ocean

10%

Salmon River Hatchery

1‐Ocean

18%

2‐Ocean

53%

3‐Ocean

29%

Salmon River Natural

Age at return is evaluated to assess the impact of hatchery rearing environment on population 

age structure. Examining age structure over time and in comparison with natural population age 

structure is more instructive in attempting to understand if the effects are cumulative. Hatchery 

fish tended to return younger than their naturally rearing cohort. Each program reported age at 

return and when all the data were examined, a consistent increase in 1-ocean (age 3) returns 

(almost entirely jacks) was noted among all the programs. Moreover the increased return of 1-

ocean fish was normally offset by a commensurate decrease in 3-ocean (age 5) fish, while 2-

ocean (age 4) fish (the dominant age class in all cases) remained relatively constant. This and 

the following slide provide examples of the common shift in age structure noted in all the other 

programs. They were not all presented here as that served no purpose in describing the general 

response to hatchery rearing. 

(Continued on next slide) 
277 

Slide 18 

Age at Return

Age 3

16%

Age 4

77%

Age 5

7%

Grande Ronde Hatchery

Age 3

5%

Age 4

65%

Age 5

30%

Grande Ronde Natural

Interestingly, while cooperators noted the presence of mini-jacks (mature males that were 

adfluvial or fluvial) in some rivers, they did not appear to be a significant problem in any of the 

rivers. On the contrary, where sampling for mini-jacks had occurred on the Tucannon River, the 

mini-jacks captured were entirely of natural origin. Cooperators concluded that there was 

insufficient data to suggest that mini-jacks were an issue or concern (i.e. – no indication of 

excessive natural expression). 

Possibly more important was that there was no identifiable trend in any of the populations 

(hatchery or natural) over time toward a steadily increasing number of younger fish. This suggests 

that age structure response in hatchery fish is environmentally driven and may not be affecting 

natural age structure because of domestication effects expressed into the natural population. 

 
278 

Slide 19 

Hatchery Fish Progeny/Parent Performance (w/o jacks)

0

5

10

15

20

25

1994 1995 1996 1997 1998 1999 2000 2001 2002 2003 2004

Recruits/Spawner

Brood Year

Clearwater

Imnaha

Grande Ronde

Tucannon

Salmon

Progeny per parent ratios (Recruits/spawner) were examined for all hatchery programs to 

measure survivals relative to expectations (can programs sustain themselves), and in some cases 

to compare against natural population performance (see slides following). Highly variable 

performance over time among all the programs shows clearly in the above graph. Highs and lows 

appear to be driven by SARs (see previous) that are dependent upon river migration and ocean 

conditions. 

 
279 

Slide 20 

Hatchery and Natural Fish R/S Performance

(w/o jacks)

0

1

2

3

4

5

6

7

8

9

1985 1987 1989 1991 1993 1995 1997 1999 2001 2003 2005

Recruits/Spawner

Brood Year

Hatchery Wild

Tucannon River

The Tucannon is a supplementation program where R/S has been monitored for both hatchery 

and natural populations since its inception. Similar annual fluctuations occur across the years 

shown above for both populations, however the hatchery consistently recruits more adults from 

each spawner as should be expected based on the early life history survival advantage provided 

by the hatchery. The natural population recruited above the replacement level (1.0) in only 5 of 

20 years shown in the chart, and there was no clear negative relationship between the presence 

of hatchery fish over time and R/S performance. 

 
280 

Slide 21 

R/S Performance

 All the programs increased spawners in their

respective rivers.

 There is uncertainty about whether supplementation

programs will provide an abundance boost in natural

populations.

 The Imnaha has seen reduced R/S performance since

supplementation began.

More supplementation efforts were begun after the critically low abundance levels of 

spring/summer Chinook in the mid 1990’s. Because of that the data series on many LSRCP 

supplementation programs are relatively short. There were consistencies among all the programs 

that are captured here (including the Tucannon on previous slide). Supplementation remains 

experimental and there is not sufficient weight of evidence to conclude that they are benefiting 

natural populations. Further, there is evidence that in some rivers, natural population performance 

has been depressed by the presence of hatchery supplementation fish. 

 
281 

Slide 22 

Spatial Distribution of Spawners

 Problems with weirs (flow, poor design, improper

water source for attraction, poor ladder design) in

some cases rectified by acclimation or facility changes.

 Hatchery Fish concentrate near release area for their

focal spawning area.  This can affect their success if

significant habitat quality variation occurs in the river.  

However there could also be density dependent

effects.

 In most cases there is complete spatial overlap of

hatchery and natural spawners.

Hatchery fish releases occur directly from hatcheries, from remote acclimation facilities and from 

trucks directly into receiving waters. Because of these varying approaches, distribution of 

returning adults has been monitored. As noted above, hatchery fish may tend to congregate near 

release sites with slightly less diverse distribution then their natural cohort, but in general spawn 

in target rivers in similar locations. 

 
282 

Slide 23 

% of LSRCP Adult Goal Achieved

0%

10%

20%

30%

40%

50%

60%

70%

80%

90%

100%

1987 1991 1995 1999 2003 2007

Return Year

Project Area Goal = 58,700

Total Fish Goal = 293,500

As previously mentioned there are two distinct parts to the LSRCP mitigation goal (escapement 

to the Snake River Project Area and below Project harvest contribution) that must be considered 

additively to represent the whole. The above chart depicts the collective LSRCP accounted adults 

and jacks, expressed as a % of the project area and total adult goals. Clearly in the early years 

of the program adult returns were poor, only returning more than 10% of the project area goal in 

2 of the first 12 years. More recent performance has improved greatly with one year approaching 

90% of the Project area goal. Performance is of course directly related to SARs and production 

levels. Total program returns (shown in red) lag far behind, barely exceeding 20% of the program 

goal in one year. The average contribution to the goal is less than 10% for the years shown. 

Reaching the total fish goals may never occur. Factors contributing to this may include an over 

estimate of Snake River fish to historical fisheries and an overly optimistic assumed SAR (0.87%) 

for the program. 

 
283 

Slide 24 

Catch / Escapement

0%

10%

20%

30%

40%

50%

60%

70%

80%

90%

100%

% of Accounted Fish

Return Year

Harvest Below LGD Escapement to LGD

This chart simply depicts the data presented in the previous slide in a different fashion. Downriver 

catch was assumed to have represented four times (4x) the escapement to the Snake during the 

1960s when the baseline contributions for the LSRCP were negotiated. As this clearly shows, 

current downriver harvest is a fraction of Snake River escapement. It is important to understand 

that restrictions currently in place to protect ESA listed Snake River spring/summer Chinook 

populations may prevent fisheries of their historical magnitude of occurring prior to recovering and 

delisting under ESA. The affect this has on expectations for LSRCP to meet its original harvest 

goal is unknown and presently not being actively discussed. 

 
284 

Slide 25 

0.0%

1.0%

2.0%

3.0%

4.0%

5.0%

6.0%

7.0%

8.0%

Stray Rates

McCall

Sawtooth

Clearwater

Imnaha River

Catherine Ck

Catherine Ck ‐ CB

Lookingglass Ck

UGR River

UGR River ‐ CB

Tucannon

Lostine

Dworshak 96‐06

Dworshak 2000‐06

Stray rates are calculated based on the Oregon definition of straying which is: Captured or caught 

outside of its normal migration pathway. As the chart shows there is a broad diversity of stray 

rates from barely measurable to approaching 8%. There is also substantial variability in straying 

across years. For example, early stray rates from the Dworshak program were high (10-20%), 

driving the mean stray rate for the reporting period 1996-2006 to over 6%, however recent straying 

(2000-06 in chart) averages only about 2%. 

These data may also be limited by the cooperators’ ability to collect or document straying in all 

locations. For example the stray rate for Tucannon Chinook based on recovery of coded wire tags 

averages less than 2% for the reporting period, but recent detections of PIT tagged Tucannon 

Chinook showed more than 25% of detected fish passing above Lower Granite Dam and not 

returning to the Tucannon River. Such unidentified behavior contributes to a substantial 

underestimate of straying and SAR. Technological advancements can help better understand 

these variables and possibly their cause. 

 
285 

Slide 26 

Fisheries (w/in Snake Basin)

 During the 1975‐1995 period there was nearly

complete lack of fisheries.

 Since late 1990’s fisheries reestablished:

 8.7% of historical harvest

 31% of historical mileage open

 15.9% of historical days

 Still a long way to go, but recent fisheries have shown

the potential economic and cultural value fisheries

possess.

Fisheries have been identified as a high priority goal for all state and tribal entities involved with 

the LSRCP program from the beginning. The near total lack of fisheries within the Snake for over 

20 years severed cultural and social ties to Chinook fisheries. The resurgence of fisheries starting 

in the late 1990’s was greeted substantial enthusiasm, and the fisheries have developed in the 

intervening years with gradually increasing opportunity (miles, days and harvest) across the basin. 

The value of fisheries to local communities and Tribal culture will continue to keep those fisheries 

a high priority for LSRCP cooperators as long as ESA listed natural fish can be protected. 

 
286 

Slide 27 

Effects of supplementation

 Natural Origin abundance – can be increased in short

term

 Run/spawn timing and spatial distribution doesn’t

seem affected.

 Can preserve genetic and life history resources

 However risks have been identified and answers must

be pursued.

 Data are difficult to generate and require a long time

frame.  Current results not conclusive (+/‐)within

work already completed.

These are general conclusions for supplementation programs currently in effect within the LSRCP 

program. As noted above there are insufficient results to conclude broadly about the effectiveness 

of supplementation. With implementation of hatchery review recommendations, use of local brood 

stocks and supplementation is being pursued. While there are often clear short term benefits from 

these programs, these efforts need continued monitoring and research to ensure the presumed 

long term benefits occur. 

 
287 

Slide 28 

Adaptive Management of program

 New or integrated brood stocks – programs have used to

maintain the genetics and life history patterns of source

populations

 Captive brood stock = used short term and possibly prevented

population extinction in some cases.

 Acclimation = 3 new facilities

 Reduced production – implemented to improve survival,

address concerns on hatchery densities.

 Active adult management(exclusion or mgmt for pHOS or

pNOB) is used as a result of co‐managerdiscussions and joint

decisions.

 Disease – Management and control is carefully implemented

and has been successful in controlling BKD.

Adaptation has been constant within the program. From adopting different size, time or type of 

release to improve survivals, to reducing rearing densities to reduce disease prevalence and 

severity, to utilizing captive brood stocks to prevent extirpation of populations. The LSRCP 

cooperators have applied a broad array of changes to the program during its life span. 

Recent adaptations have been the adoption and development of endemic brood stock programs, 

often including agreement among the managers to actively manage hatchery and wild fish 

numbers escaping above program facilities to control hatchery fractions spawning in nature. 

To achieve such flexibility and implement often unproven management concepts, the cooperators 

have engaged in continuous coordination and negotiation efforts such as annual operation plan 

(AOP) development and the joint development of Hatchery and Genetic Management Plans and 

regional research plans (see next slide). 

 
288 

Slide 29 

Adaptive Management of program

 Fisheries – Tribal and Sport have been closely coordinated and

implemented within management agreements both locally and

regionally.

 Improved documentation to be responsive to data requests,

collaborative data management and dissemination, and

evaluations to address critical questions.

 AOP process

 Regional harvest and Manager discussions

 Weekly conference calls

 Annual LSRCP meetings or Symposia.

Such communication has greatly improved inter-agency cooperation. The continual demand for 

research and monitoring data has encouraged the development of regional data bases to facilitate 

sharing. These efforts, often coupled with weekly manager conference calls have kept 

cooperators engaged with each other and often working more closely toward shared priorities. 

Certainly the annual LSRCP cooperator meetings and regular program symposia, such as this 

one, have helped share LSRCP successes and failures and invited critical review of production 

and research. 

 
289 

Slide 30 

Adaptive Management of program

 HSRG/HRT suggestions – They were complex and diverse

but some commonalities were:

 Move away from non‐local stocks to endemics and integrated

brood.

 Decrease pHOS and increase pNOB – move toward more

natural

 Reduce production and acclimate

 These suggestions may or may not be valid but are under,

or have been considered and decisions to implement may

take significant time and funding.

As previously mentioned, critical review of programs has been invited. Two such reviews in recent 

years by the HSRG and the US Fish and Wildlife Service’s HRT have prompted several common 

recommendations for LSRCP programs. 

These remain under consideration and a concerted effort has been made (at the request of 

LSRCP staff) by all cooperators to address these recommendations in HGMPs, which are being 

used to obtain the needed ESA consultation coverage for these programs. 

 
290 

Slide 31 

Data Gaps

 Natural fish SARs consistently surpass Hatchery fish SARs

– Why?

 Supplementation is still “Experimental” and we need to

understand why it isn’t generally improving natural fish

status.

 Why are river capacities seemingly lower than expected

(density dependence) and can factors be addressed to help

recovery?

 Accurate fish accounting – There is considerable

uncertainty in estimating hatchery and natural adult

abundance. Methods need to be developed to address.  

As programs mature and results from evaluation studies are completed, many questions are 

answered and adaptations made. However with expanding fishery knowledge and improvement 

in science technology, many answers remain elusive. In many cases the data collected are 

insufficient to provide conclusive results and will require further study, either for more years to 

understand natural variability or through implementation of altered approaches using different or 

more accurate methods. The LSRCP evaluation program remains committed to filling these data 

gaps with scientifically sound research and results. 

 
291 

Slide 32 

Monitoring and Evaluation

 Less intensely now within the hatcheries

 Complete suite of population metrics

 Focus early (or with new programs) on hatchery

performance

 Increased studies to improve survival

 Size and time of release

 Acclimation vs. Direct

 Endemic brood stocks

 Analysis of potential effects on Wild

 R/S

 Spatial distribution

 Smolts/spawner

 Genetics

Evaluation studies will have to be adaptable into the future as they have in the past, moving from 

a hatchery centric focus to ensure production was producing quality smolts to more survival 

studies that will improve survival of the hatchery product. The more recent emphasis on 

understanding the effects of hatchery fish on ESA listed natural populations arose from a desire 

by managers to protect critical natural populations while maintaining the mitigation benefits of 

downriver and within Snake basin fisheries. 

 
292 

Slide 33 

Monitoring and Evaluation

 Contribution to fisheries

 Affects on natural populations (ESA)

 Actively engaged within Columbia Basin efforts to

understand the pros/cons of hatcheries collaborative

scientific processes. (ASMS, AHSWG, ISS, CSS, ISEMP,

PNAMP, CRHEET........ And the LSRCP)

Regardless of the focus of studies in the Snake basin, LSRCP funded evaluation staff from all the 

cooperators often serve as crucial members to regional scientific processes. Staff members serve 

on a host of standing and Ad Hoc committees pursuing a better understanding of the effects of 

hatcheries at recovering ESA listed populations. This activity has been and will continue to be 

supported by the LSRCP administration. 

 
293 

Slide 34 

 
294 

Slide 35 

Take Home’s

 Neither mitigation nor supplementation programs

have achieved the juvenile production goal

(collectively)

 Brood stock collection challenges

 Conflicting management objectives

 Hatcheries have generally met size and fish quality

goals for releases.

 The program has not yet met its original adult

abundance targets – however abundance within the

Snake has risen.

 Some of original assumptions may be unreachable in

our current world.

Slide 36 

Take Home’s

 Substantial modifications have been made to

individual programs to meet changing expectations

(Adaptive for success and Redirected management

intent).

 New brood stocks

 Captive broodstock conservation programs

 Acclimation

 Hatcheries Affect Fish

 Some is good – persistence, fisheries

 Some is not so good – age at return, etc.

 Some remains unknown – will supplementation work?

 
295 

Slide 37 

Take Home’s

 Evaluations have actively pursued understanding the

potential effects of the programs on natural

populations

 Post release survival is highly variable and likely

dependent on migration (river) and ocean conditions.

 Hatchery fish return younger than Wild fish

(especially jacks)– but there hasn’t been a consistent

increase (trend) in younger fish for natural or

hatchery populations.

Slide 38 

Take Home’s

 Disease has generally not been a significant factor in

limiting program success

 Fisheries cannot always effectively access harvestable

hatchery fish while protecting the ESA listed Snake

River natural fish.

 Evaluations continue to look hard at what works, what

doesn’t, and helping ensure the programs are

responsive to developing fish science.

 Adaptive change is a management  paradigm within

the LSRCP program.
296 

Although the LSRCP program hasn’t met its goals the cooperators generally believe that the 

Snake basin spring / summer Chinook populations are probably better off with then than they 

otherwise would have been. 

 
297 

APPENDIX 1. 

AN INDEPENDENT SCIENTIFIC REVIEW PANEL RETROSPECTIVE REPORT 

Review of the Lower Snake River Compensation Plan’s Spring 

Chinook Program 

ISRP 2011-14 

May 27, 2011 

LSRCP_Spring_ Chinook_ Retro_27May 
298 

Independent Scientific Review Panel

for the Northwest Power & Conservation Council

851 SW 6th Avenue, Suite 1100

Portland, Oregon 97204

www.nwcouncil.org/fw/isrp

ISRP Members 

J. Richard Alldredge, Ph.D., Professor of Statistics at Washington State University.

Robert Bilby, Ph.D., Ecologist at Weyerhaeuser Company. 

Peter A. Bisson, Ph.D., Senior Scientist at the Olympia (Washington) Forestry Sciences 

Laboratory of the U.S. Forest Service’s Pacific Northwest Research Station. 

Charles Henny, Ph.D., Emeritus Research Scientist at the U.S. Geological Survey in Corvallis, 

Oregon, an expert in wildlife and environmental toxicology. 

Colin Levings, Ph.D., Emeritus Research Scientist and Past Section Head Marine Environment 

and Habitat Science Division, Department of Fisheries and Oceans, Canada. 

Eric J. Loudenslager, Ph.D., Hatchery Manager and Adjunct Professor of Fisheries Biology, 

Humboldt State University, California, an expert in genetics and fish culture. (ISRP Chair)

Katherine Myers, Ph.D., Principal Investigator of the High Seas Salmon Research Program at 

the School of Aquatic and Fishery Sciences, University of Washington.

Thomas P. Poe, M.S., Consulting Fisheries Scientist, an expert in behavioral ecology of fishes, 

formerly with the U.S. Geological Survey. 

Greg Ruggerone, Ph.D., Fisheries Scientist for Natural Resources Consultants (also an ISAB 

member). 

Dennis Scarnecchia, Ph. D., Professor of Fish and Wildlife Resources, University of Idaho, an 

expert in large river fisheries population dynamics, and salmon, trout and char.

Bruce Ward, Fisheries Scientist, formerly with the Ministry of Environment, Aquatic Ecosystem 

Science Section, University of British Columbia, Vancouver, B.C., Canada. 

Scientific Peer Review Group Members 

William Smoker, Ph.D., Professor of Fisheries Emeritus at the University of Alaska 

Fairbanks, School of Fisheries and Ocean Sciences. 

Richard Williams, Ph.D., Affiliated Research Scientist, Center for Salmonid and Freshwater 

Species at Risk, University of Idaho, an expert in population and evolutionary genetics, ecology. 

Staff 

Erik Merrill, J.D., Independent Science Program Manager, Northwest Power and Conservation 

Council. 

Cover photo from Yankee Fork Chinook Salmon Supplementation Program Presentation by Lytle 

Denny and Kurt Tardy, Shoshone-Bannock Tribes, LSRCP Program Review, November 30, 2010 
299 

Table of Contents 
300 

EXECUTIVE SUMMARY 

The Independent Scientific Review Panel (ISRP) conducted a review of the Spring Chinook 

Hatchery Program of the Lower Snake River Compensation Program at the request of the 

Northwest Power and Conservation Council and U.S. Fish and Wildlife Service, based on annual 

reports, summary oral presentations, and agency and tribal program reports prepared for the 

spring Chinook Symposium in November 2010 in Boise, Idaho. The format used to provide an 

independent retrospective evaluation of the accomplishments of the LSRCP spring Chinook 

program worked well. The ISRP believes the data, evaluations, and conclusions provided by the 

LSRCP spring Chinook program are applicable beyond the Columbia River Basin and Pacific 

Northwest and encourages use of the roll-up report as the foundation to develop a scientific paper 

on assessing hatchery performance. 

 

Overall, the performance and practices within the hatchery were acceptable and met stated goals. 

However, information was lacking on broodstock collection goals and no summary was given of 

differences among the hatcheries (or within years in a hatchery) in fish culture practices such as 

acclimation versus direct release, on-site versus satellite facility release, rearing densities, nor 

size and timing at release that might contribute to explaining differences in the performance of 

smolts after release. 

Fish performance post-release to return has been adequately reported. Post-release survival and 

abundance of hatchery fish has been below expectations. An analysis of survival of smolts after 

passing Lower Granite Dam was not included in the reports. Smolt to Adult Survival (SAS), and 

Smolt to Adult Return (SAR) goals (the primary mitigation goals) and the assumptions behind 

them were overly optimistic. The LSRCP spring Chinook program has not achieved adult 

production goals to the Columbia River mouth, or to the project area, in any year. 

Since the mid-1990s, the LSRCP has included conservation objectives using captive broodstock 

and supplementation protocols. Assessment of supplementation in the Imnaha River using a 

Before After Control Impact (BACI) analysis of the abundance of natural origin returns indicated 

that, when contrasted to nine unsupplemented reference locations, the Imnaha River spring 

Chinook showed decreased natural origin return abundance post-supplementation relative to five 

reference sites, and increased abundance post-supplementation relative to four reference sites. 

The BACI analysis found that productivity (recruits per spawner) in the Imnaha River had 

decreased relative to all nine unsupplemented sites. We recommend that the BACI method (or 

alternatives of similar statistical validity) be used at all locations that have programs that plan to 

use returning hatchery fish to spawn in the streams. 

Density-dependent survival in many of the LSRCP watersheds was a factor constraining the 

increase in smolt production that was expected from increased spawner abundance in the 

streams. Managers need to periodically evaluate the carrying capacity of the freshwater 

environment and adjust hatchery releases accordingly, with fewer releases when carrying 

capacity is diminished. Most of the hatchery programs were self-sustaining. At least one adult 

female returned to the hatchery or tributary weir from the spawning of an adult female in the 

hatchery. 

Recently, there has been a Hatchery Scientific Review Group (HSRG) review of the LSRCP 

hatchery programs. Although the LSRCP reports and presentations identified some HSRG 

recommendations, in general they did not elaborate sufficiently on the recommendations from 

those reviews and how they were being addressed by the co-managers. Several of the 

supplementation programs have moved to sliding-scale broodstock management, where the 

proportion of hatchery-origin adult fish used for broodstock and permitted on the spawning 
301 

grounds is increased in the absence or low abundance of wild broodstock. Implementing 

conservation/supplementation programs using sliding-scale broodstock management where, over 

the long-term (decades), the hatchery broodstock has little gene flow from the natural population, 

but the natural population has a large proportion of hatchery-origin adults, is inconsistent with the 

scientific framework guidance on the operation of an integrated hatchery program. Operating 

these programs using the sliding scale over many years carries a high risk that both abundance 

and productivity of naturally spawning stocks will decrease. 

The ISRP recommends that managers take action wherever needed to rapidly establish natural 

populations that are viable. The LSRCP needs to integrate information on the status of the natural 

populations and their habitat into an adaptive management framework that will inform what should 

or should not be done within the hatchery programs to enhance the natural populations. This may 

include reductions in hatchery releases that mix with natural populations or possible increases in 

hatchery production to mitigate harvest – a delicate balance. 

 
302 

LOWER SNAKE RIVER COMPENSATION PLAN SPRING CHINOOK PROGRAM2 

On November 22, 2010, the Northwest Power and Conservation Council (Council), in cooperation 

with the U.S. Fish and Wildlife Service, requested that the Independent Scientific Review Panel 

(ISRP) conduct a review of the Spring Chinook Hatchery Program of the Lower Snake River 

Compensation Plan (LSRCP). 

The LSRCP was authorized by Congress in 1976 to replace the lost fish and wildlife resources 

caused by the construction and operation of four hydroelectric dams on the Lower Snake River in 

Washington. The established goal for spring/summer Chinook salmon Oncorhynchus 

tshawytscha was to return 58,700 adult fish above Lower Granite Dam after providing 234,800 

adults to fisheries in the ocean and Columbia River below the project area. Spring Chinook for 

the LSRCP are reared at six hatcheries: Lookingglass (upper Grande Ronde River, Catherine 

Creek, Lostine River, and Imnaha programs), Lyons Ferry (Tucannon River program), Clearwater, 

Dworshak, McCall (South Fork Salmon River program), and Sawtooth (upper Salmon River and 

Yankee Fork programs) and acclimated and released at several other satellite facilities. The U.S. 

Fish and Wildlife Service (Service) owns these hatcheries and administers the program. State, 

federal, and tribal fish and wildlife agencies in the region operate the facilities and evaluate 

program success. 

The LSRCP has conducted two programmatic reviews since authorization. At the time of the first 

review (May 1990) each of the spring Chinook facilities reported success in developing a 

broodstock source and working to achieve smolt production goals. Although only a few years of 

adult returns had occurred, hatchery facilities reported large numbers of adults trapped in the mid 

1980’s (Figure 1). Overall, the participants judged progress to date as very successful in meeting 

initial goals of broodstock acquisition and smolt production (Herrig 19903). 

In 1992 NOAA Fisheries listed Snake River spring/summer Chinook as Threatened under the 

Endangered Species Act. In 1994 and 1995 the annual returns were so low (Figure 1) that some 

believed extinction may be imminent. The tone of the second symposium held in February 1998 

was very somber. A common theme was expressed in one of the reports: 

“If we cannot improve mainstem passage survival and increase natural productivity so that 

progeny-to-parent ratios consistently exceed 1.0, recovery will never occur. Natural populations 

will go extinct and only hatchery fish will remain.” (p. 95, Carmichael, Parker and Whitesel 19984) 

 

2 This description of the LSRCP spring Chinook program and review is taken from the Symposium 

Announcement provided by the U.S. Fish and Wildlife Service. 

3 Herrig, D.M. 1990. A Review of the Lower Snake River Compensation Plan Hatchery Program. 

U.S. FWS, LSRCP Boise Id. 47 pgs. 

4 Proceedings of the Lower Snake River Compensation Plan Status Review Symposium 1998. 
303 

Figure 1. Counts of Adult Hatchery and Wild spring/summer Chinook salmon crossing Lower 

Granite Dam 1979 - 20085

The dismal returns of the early to mid-1990s led state and tribal agencies to reconsider how to 

best redirect their individual LSRCP hatchery programs. By the time of the second program review 

in 1998, modifications were being implemented in many programs. Most notable among the 

changes were: 1) captive broodstock and rearing programs were being developed in Oregon, 

Washington, and Idaho, 2) the centralized releases of an out-of-basin stock was discontinued at 

Lookingglass Creek in favor of developing comprehensive endemic supplementation programs in 

the Grande Ronde basin, 3) sliding scale broodstock management was developed for the Imnaha 

program to control the genetic risks associated with the natural spawning of hatchery-origin fish 

and, 4) a basinwide study was funded by the Bonneville Power Administration (BPA) to rigorously 

test the efficacy of supplementation at LSRCP and other spring Chinook hatcheries in Idaho. 

While some facilities made major programmatic changes including a reorientation toward 

supplementation, others did not and continued to operate programs directed primarily at harvest 

mitigation. 

Over the 12-year period since the last LSRCP program review, new developments and scientific 

advances have occurred to inform managers and policy makers about options for the future 

direction of the LSRCP spring Chinook hatchery program. For example: 

 

 

5 Figure taken from USFWS Spring Chinook Symposium Announcement 
304 

 New information is available regarding the roles that system operations, barging of 

smolts, predation, climate and ocean conditions play in determining smolt- to-adult 

survival rates.6

 A new Columbia River Fishery Management Plan7 has been approved to guide 

harvest and production through 2017. 

 A Biological Opinion8 for the FCRPS has been approved to guide system operations 

and offsite mitigation. 

 Two scientific reviews (HSRG9 and HRT10) have been conducted of LSRCP hatchery 

programs. 

The Service organized a symposium held in Boise, Idaho from November 30 through December 

2, 2010 to evaluate the successes and failures of the LSRCP spring Chinook hatchery program 

since 1998 and to identify what changes in the LSRCP are warranted based on information and 

developments since 1998. 

ISRP REVIEW CHARGE 

The ISRP was created by the 1996 amendment to the 1980 Northwest Power Act and instructed 

by the U. S. Congress to review projects proposed for funding by the Council through BPA’s fish 

and wildlife budget. In 1998 the Senate-House Conference Report for the fiscal year 1999 Energy 

and Water Development Appropriations bill expanded the ISRP responsibilities to include review 

of projects in federal agency budgets that are reimbursed by BPA, using the same criteria as 

projects in the Council’s Fish and Wildlife Program. The LSRCP is a BPA-funded reimbursable 

program. 

The ISRP is directed by Congress to evaluate projects using four criteria: it is based on sound 

scientific principles, it benefits fish and wildlife, it has clearly defined objectives and outcomes, 

and it has adequate provisions for monitoring and evaluation of results. In 2002, the ISRP 

reviewed 26 individual LSRCP proposals as part of the Columbia Plateau, Blue Mountain and 

Mountain Columbia provincial reviews (ISRP 2002-6). In addition to individual project proposal 

reviews, the 1996 amendment directs the ISRP to conduct a retrospective review of project 

accomplishments. The Council’s 2009 Fish and Wildlife Program directs the ISRP to focus 

retrospective review on the measurable benefits to fish and wildlife made through projects funded 

by BPA and previously reviewed by the ISRP. The current ISRP review is an evaluation of the 

managers’ self-assessment of LSRCP spring Chinook program performance against the LSRCP 

goals and Fish and Wildlife Program artificial production principles, based on summary oral 

presentations, annual reports, and agency and tribal program reports prepared for the spring 

Chinook Symposium in November 2010. Consequently, the review is a retrospective evaluation 

of the collective individual program benefits to fish and wildlife and an assessment of how well 

 

6 See Williams et al. 2005. Effects of the Federal Columbia River Power System on Salmonid 

Populations. NOAA Tech. Memo., NMFS-NWFSC-63 

7 U.S. v. Oregon 2010 – 2017 

8 See 2010 Supplemental Biological Opinion for the 2008 FCRPS Biological Opinion 

9 HSRG 2009 – Columbia River Basin system-wide review: www.hatcheryreform.us

10 HRT: U.S. Fish and Wildlife Service (USFWS). 2011. Hatchery Review Team, Pacific Region. 

U.S. Fish and Wildlife Service, Portland, Oregon. Available at: 

http://www.fws.gov/Pacific/fisheries/hatcheryreview/reports.html 
305 

the LSRCP has addressed programmatic issues raised in the ISRP’s 2002 review of LSRCP 

program individual proposals. 

In addition to the Council’s request, the Service was especially interested in obtaining ISRP 

feedback on potential LSRCP program gaps, the appropriateness of underlying scientific 

assumptions guiding program activities, and the quality of the data collected and analyzed at the 

program and project levels. 

To conduct this review, the ISRP participated in the three-day Symposium of oral presentations. 

Following oral presentations by state and tribal LSRCP cooperators, ISRP reviewers were able 

to ask questions of presenters to clarify scientific points. The ISRP also used program summaries 

developed by agencies and tribes as part of the symposium and annual reports that are publicly 

available through the LSRCP. 

This report prepared by the ISRP is part of a continuing, periodic review of the LSRCP. 

Specifically, the Council, BPA, ISRP, and the Service agreed that ISRP review of LSRCP projects 

be incorporated in a three-year rolling programmatic review organized by species. In addition to 

the spring Chinook review in 2010/2011, the ISRP will review the steelhead program in winter 

2011/2012 and the fall Chinook program in 2012/2013. 

COLUMBIA RIVER BASIN HATCHERY PROGRAM ASSESSMENT 

Since the last LSRCP review in 1998, Congress has directed multiple reviews of salmon hatchery 

production programs through the Fish and Wildlife Program (NWPCC 1999-4, 1999-15, 2004-17, 

2005-11) and Hatchery Scientific Review Group (HSRG 2004, 200911) that established a scientific 

framework for implementing and evaluating of hatchery programs. Independent reviews have also 

provided guidance on specific monitoring and evaluation metrics and analyses consistent with 

this scientific framework (ISAB 2000-4, ISRP/ISAB 2005-15, ISRP 2008-7). 

Assessing hatchery programs requires information and performance measures for fish culture 

practices in three areas: 1) inside the hatchery, 2) for hatchery-produced fish after release, and 

3) the effect of hatchery-produced fish on wild stocks and other hatchery fish outside the hatchery 

(ISAB 2000-4). Information and assessment in these three areas is required to establish 

benchmarks for survival in the hatchery environment, to understand how practices in the hatchery 

influence post-release survival and performance, to establish post-release survival benchmarks 

for harvest management, and to establish quantitative estimates for benefits and risks to natural 

populations. 

The program presentation outline for each project in the LSRCP provided to the state and tribal 

co-managers by the Service is consistent with the ISAB recommendations for the design of 

 

11 HSRG 2004: Hatchery Scientific Review Group: Mobrand, Lars (chair), J. Barr, L. Blankenship, 

D. Campton, T. Evelyn, T. Flagg, C. Mahnken, R. Piper, P. Seidel, L. Seeb, and W. Smoker. 2004. 

Hatchery reform: Principles and Recommendations of the HSRG. Long Live the Kings, 1305 

Fourth Avenue, Suite 810, Seattle, WA 98101 (available from www.hatcheryreform.us). 

HSRG 2009: Hatchery Scientific Review Group: Paquet, P. (chair), A. Appleby, J. Barr, L. 

Blankenship, D. Campton, M. Delarm, T. Evelyn, D. Fast, T. Flagg, J. Gislason, P. Kline, G. 

Nandor, L. Mobrand, and S. Smith. 2009. Report to Congress on Columbia River Basin hatchery 

reform. 
306 

hatchery monitoring programs (ISAB 2000-4). Here, the ISRP is evaluating the sufficiency of the 

written reports and presentations in addressing the following questions, consistent with the 

program outline, ISAB hatchery monitoring guidelines, and the Council artificial production review 

(ISAB 1999-15): 

1. How are the project fish performing in the hatchery? 

 Are there unambiguous performance indicators and quantitative objectives for those 

indicators? 

 Are performance indicators for fish in the hatchery environment adequately 

measured, reported, and analyzed? 

 Are programs able to achieve the goals as planned? 

 Is fish culture performance within standards expected for salmonids? 

2. How are hatchery juveniles performing once released? 

 Are there unambiguous performance indicators and quantitative objectives for those 

indicators? 

 Are performance indicators for fish after release from the hatchery environment 

adequately measured, reported, and analyzed? 

 Are they able to achieve the goals of the projects as planned? 

3. What are the demographic, ecological, and genetic impacts of the programs on wild fish? 

 Are there unambiguous performance indicators and quantitative objectives for those 

indictors for natural and hatchery fish? 

 Is performance for ecological and genetic impacts adequately measured, reported, 

and analyzed? 

 Are they adequately evaluating supplementation (for example using the Ad Hoc 

Supplementation Work Groups’12 recommendations)? 

4. How are programs being modified and problems achieving objectives being addressed? 

REPORT ORGANIZATION 

The report is organized into two sections. The first section summarizes ISRP evaluation of 

individual programs in terms of the four questions posed above. The second section provides 

ISRP editorial suggestions and comments on the written summary reports for individual programs. 

The first section begins with a table with individual hatchery programs as columns and 

performance indicators arranged as rows under three categories of quantitative metrics: inhatchery fish performance, post-release fish performance, and impacts of the hatchery program 

on wild stocks and other hatchery fish. This table represents a snap-shot of the status of the 

individual programs as the ISRP understands them, based on the symposium presentations and 

reports. This snap-shot is followed by ISRP findings, answering the questions posed above based 

on the information in the snap-shot, presentations, and written summaries. Finally, the ISRP 

concludes the first section with recommendations for adaptive management. 

 

12 AHSWG: Ad Hoc Supplementation Work Group, Galbreath 2008. 
307 

Table 1. ISRP assessment of the reporting of objectives and performance metrics in individual hatchery progr

for the 2010 LSRCP Spring Chinook Program Review. 

A. Hatchery PerformanceMetric Sawtooth McCall Clearwater Dworshak Tucannon Imnaha

Grande Ronde 

CC

Broodstock Collection Goals 

NR1 NR NR NR 100 - 170 NR NR N

Years Achieved NR NR NR 9/10 NR NR NR NPre-spawning Mortality Goal 

<20% <20% <20% <20% <20% <20% <2

Years Achieved 9/10 8/10 10/10 1010 8/10 7/9 8/Egg to Smolt Goal >70% >70% >70% >70% >70% >70% >70% >7Years Achieved 10/10 10/10 9/10 NR 8/10 9/10 8/8 7/Smolt Release Goal 

1.5M 1.0M 1.4M - 

2.3M 

1.05 - 1.4M 0.13 - 

0.225M 

0.36M 0.25M 0

Years Achieved 2/10 10/10 4/10 2/10 5/10 6/10 1/10 0/B. Post-Release PerformanceSurvival to LGD Goal 

NR NR NR NR NR NR NR N

Survival to LGD2 >65% SAS Goal 4.35% 4.0 4.35% 4.35% 4.35% 3.25% 3.25% 3Years Achieved 0 0 0 0 0 0 0 0 Lower Col & Ocean Harvest Goal 

77,000 32,000 47,600 36,500 4,608 16,050 NR N

Years Achieved 0 0 0 0 0 0 SAR Goals 0.87% 0.80% 0.87% 0.87% 0.87% 0.65% 0.65% 0Years Achieved 0/10 7/10 2/10 0/10 8/10 1/6 Return to LGD Goal 

19,400 8,000 11,900 9,135 1,152 3,210 1,617 1
308 

Metric Sawtooth McCall Clearwater Dworshak Tucannon Imnaha

Grande 

Ronde 

C

Years Achieved 0 6 0 1 0 3 0 0 Tribal Harvest Goals 

NR NR NR NR NR NR NR N

Years Tribal Harvest 

6/10 9/10 2/10 10/10 NR NR NR N

Sport Harvest Goals 

NR NR NR NR NR NR NR N

Years of Sport Harvest 

2/10 10/10 9/10 10/10 NR NR NR N

Weir Abundance Goals 

NR NR NR NR NR NR NR N

Years Achieved 9/10 Spawning Escapement Goals 

NR NR NR NR 750 Nat 

Hatch NR 

NR NR N

Years Achieved 2/10 Nat C. Interaction Performance3Age Structure Yes Yes Yes NA Yes Yes Yes YRun Timing Yes Yes Yes NA Yes Yes Yes YNOR Abundance Yes Yes No No Yes Yes Yes YNOR Productivity Yes Yes No No Yes Yes Yes YBACI Assessment No No No No No Yes No N
309 

Metric Sawtooth McCall Clearwater Dworshak Tucannon Imnaha Grande 

Ronde 

CC

Other Supplementation Effectiveness Evaluation5 

No No No No No No Yes Y

RRS Assessment4

No No No No No No Y

Other Genetic Assessment 

No No No Yes No No N

1. NR – Not Reported. 2. A number of reports provided information on smolt survival to Lower Granite Dam, but the information is in a b

cannot actually determine what the estimates are. 

3. For interaction metrics Yes indicates that the data are being collected and reported, No indicates that the data a

(they may not be needed everywhere), NA – Not Applicable. 

4. RRS – relative reproductive study 5. Evaluations include effects of density-dependence, which could limit supplementation effectiveness if present 
310 

ISRP FINDINGS, CONCLUSIONS, AND RECOMMENDATIONS 

1. Review Approach and LSRCP Report Contents 

The snapshot provided by Table 1 gives an overview of performance across the LSRCP projects, 

summarizing performance metrics for each hatchery and the number of years that these have 

been achieved. Broodstock collection goals, which should be tied to ecological criteria such as 

carrying capacity and wild stock abundance, were not reported for any – an issue further 

addressed under findings and individual project reviews. As expected, within-hatchery production 

goals were largely met (pre-spawn mortality, egg-to-smolt survival). However, with few exceptions 

across the snapshot, smolt release goals and post-release survival goals were either not met for 

the most part, or if so, were not reported (NR), thus could not be evaluated. 

Interaction performance (Table 1) refers to the collection of information on the program used for 

evaluation of effects on natural populations. The table summarizes whether data was collected, 

reported, and analyzed. Most biological traits of interest (age, size, and timing) were tracked. 

Evaluation metrics and experimental design (e.g., BACI), information on supplementation 

effectiveness, and information on compliance with HSRG recommendations were available from 

only a few hatchery programs. Recommendations and detail on these overall performance metrics 

are included in findings below. Genetic assessments and relative reproductive success 

information is available for only two projects. 

Finding 1.1. The format used to provide an independent retrospective evaluation of the 

accomplishments of the LSRCP spring Chinook program worked well. Using the format, the 

program co-managers summarized the outcomes from implementing their individual program 

components and compared them to goals established in the LSRCP. Managers’ summaries were 

presented during a three-day symposium, followed by written reports. 

Recommendation. The LSRCP should proceed as planned in using this format to review the 

steelhead and fall Chinook components of the LSCRP in 2011/12, and 2012/13, respectively. The 

Council is encouraged to use this format for ISRP retrospective evaluation of Fish and Wildlife 

Program categorical and geographic projects. Having the project proponents develop a summary 

report that is evaluated by the ISRP would be more efficient and productive than attempting to 

extract summary information from proposal materials in TAURUS. 

Finding 1.2. The presentations and written reports generally provided enough information for the 

ISRP to verify conclusions of the co-managers. The reports, however, were inconsistent in their 

presentation and should be standardized for assembly into a symposium proceedings. There 

were a number of important goals and evaluation endpoints that were not clearly and consistently 

presented in each of the reports. Most of these are designated NR (not reported) or are blank in 

the ISRP summary table (Table 1). The ISRP believes most of these data have been collected, 

but were not summarized in a sufficiently clear format. Additional data and analyses beyond the 

framework metrics in the ISRP table were found in many reports. These data and analyses should 

remain in the reports. These unique analyses were very important, but sufficiently report-specific, 

that they could not be applied to all the hatchery programs and effectively captured in the ISRP 

summary table. Specific comments to the authors from the ISRP are found in the individual report 

reviews. 

Recommendation. The ISRP believes the data, evaluation, and conclusions provided by the 

LSRCP spring Chinook program is applicable beyond the Columbia River Basin and Pacific 

Northwest. We encourage the co-managers to use the roll-up report as the foundation to develop 
311 

a scientific paper for submission to a peer-reviewed fisheries, natural resource, or conservation 

journal. 

2. How are the project fish performing in the hatchery? 

2.1 Are there unambiguous performance indicators and quantitative objectives for those 

indicators? 

Finding 2.1. There were four primary unambiguous performance metrics for in-hatchery 

performance: broodstock collection, pre-spawning broodstock mortality (<20%), egg-to-smolt 

survival (>70%), and smolt release numbers. 

2.2. Are the performance indicators for fish in the hatchery environment adequately measured, 

reported, and analyzed? 

Finding 2.2. Performance goals and empirical results for pre-spawning mortality, egg-to-smolt 

survival, and smolt release numbers were reasonably reported. Broodstock goals were 

unambiguously presented for only one program (Dworshak). Even in that case it was a line on a 

bar graph, and the ISRP was unable to read what the actual numerical goal is. For pre-spawning 

mortality and egg-to-smolt survival, many of the reports used bar graphs, and it was impossible 

for the ISRP to actually determine what the range and mean values obtained were. It was possible 

to determine the number of years the programs met goals in some cases. 

2.3. Are individual programs able to achieve the goals of the projects as planned? 

Finding 2.3. Goals for pre-spawning mortality and egg-to-smolt survival were generally met within 

the program guidelines. The occasional years when pre-spawning mortality was high in specific 

facilities was usually associated with warmer water temperatures. In the last 10 years reported, 

egg-to-smolt survival failed to achieve the 70% standard only once, and in that instance it was 

just below 65%. The success in collecting broodstock was variable. Many of the established 

mitigation programs met collection goals (e.g., Dworshack), whereas some newer 

supplementation programs did not (e.g., Lostine). Spring Chinook smolt releases have never met 

the original LSRCP objectives. The causes of this deficiency have included difficulties in obtaining 

broodstock owing to poor adult survival (e.g., Sawtooth: upper Salmon River mainstem), 

reductions in program production effort to meet updated rearing density constraints (e.g., 

Dworshak), and inadequate water supplies at some hatchery facilities (e.g., Lookingglass 

Hatchery). 

2.4. Is fish culture performance within standards expected for salmonids? 

Finding 2.4. Yes, overall the in-hatchery performance was acceptable. 

Conclusions/Recommendations. Revisions to the hatchery reports should address the ambiguity 

in broodstock collection goals and evaluation of success in achieving the objectives. There was 

no summary of differences among the hatcheries (or within years in a hatchery) in the fish culture 

practices such as acclimation versus direct release, on-site versus satellite facility release, and 

rearing densities, size and timing at release that might contribute to explaining differences in the 

performance of smolts after release. 

3. How well are project fish performing once released? 
312 

3.1. Are there unambiguous performance indicators and quantitative objectives for those 

indictors? 

Finding 3.1. The primary indicators of fish performance following release were smolt survival from 

release to Lower Granite Dam (LGD) and adult production by release/broodyear measured back 

to the mouth of the Columbia River and to LGD. No goal has been established for juvenile survival 

to LGD. Adult abundance expressed both as numbers of fish and as rate of return was used as 

the adult life-stage performance metrics. The rate for return to the Columbia was smolt-to-adult 

survival (SAS) and rate for return to LGD was smolt- to-adult return (SAR). For a number of 

programs adult recruits-per-spawner was estimated for both hatchery and natural spawning adults 

and compared. This provided a measure of the full life-cycle benefit of hatchery rearing to total 

adult abundance. Information on harvest and straying was inconsistently presented across the 

reports. The hatchery reports also provided hatchery smolt arrival time at LGD compared to 

natural smolts, adult migration time, age class, and in some reports spawning distribution 

compared to natural fish. The ISRP discusses these migration timing, age class, and other lifehistory metrics below under the topic of hatchery:natural salmon interactions. 

3.2. Are performance indicators for fish after release from the hatchery environment adequately 

measured, reported, and analyzed? 

Finding 3.2. Adult SAS and SAR and actual abundance at the Columbia River mouth and LGD 

were adequately measured, reported, and analyzed. Smolt survival to LGD and comparison to 

natural smolt survival was difficult to interpret. In some instances bar graphs were used, making 

it difficult to determine the actual values for a project. Natural smolts will often leave the natal 

stream as parr, hold in larger streams, and then continue migration the following year. How a 

comparison of survival was made between this group and those released from a hatchery 

program was not clearly discussed. Since there were no standards for survival, the interpretation 

of the survival rate is ambiguous. There was no analysis of the factors that might affect smolt 

survival to LGD. The subdivision of the adults that do return from the ocean and reach LGD and 

then contribute to tribal harvest, sport harvest, broodstock, and natural spawning escapement 

was insufficiently presented for most projects. Some projects reported the number of years that 

harvest occurred for both tribal and sport fishing constituents, but others only mentioned that there 

had been fishing seasons some years. 

3.3. Are they able to achieve the goals of the projects as planned? 

Finding 3.3. No, the LSRCP spring Chinook program has not achieved adult production goals to 

the Columbia River mouth or to the project area. The LSRCP spring Chinook production was 

planned to return 293,500 fish to the mouth of the Columbia River and 58,700 fish to the project 

area (generally considered at LGD). Most years, the production to the mouth has been less than 

10% of the goal; the year with the largest returns (2001) produced just over 20% of the goal. 

Production to the project area has been variable over the last 10 years. In 2001 nearly 90% of the 

58,700 fish goal was achieved, in 2005 it was less than 20%. The LSRCP had an SAR to LGD of 

0.87% as a planning assumption which also assumed substantial harvest in the lower Columbia 

River. The 10-year mean SAR was 0.52% with almost no harvest below the project area. A 

comparison of recruits-per-spawner for hatchery and natural spawning adults did reveal a 

substantial full-life cycle benefit from the LSRCP. There are many more adult fish as a 

consequence of the hatchery production. 

Recommendations/Conclusions. During the Boise symposium, LSRCP co-managers gave the 

ISRP the impression that they believed smolt survival from the hatchery or release locations to 
313 

LGD was reasonable and not an impediment to the program’s success. The ISRP believes that 

smolt survival to LGD needs to be better understood, and that improvements in this river reach 

might lead to greater numbers of returning adults. The tributary programs with the largest survival 

to LGD, South Fork of the Clearwater and Imnaha, yielded adult production closer to LSRCP 

goals and supported fisheries. The written reports should clarify how the returning adults 

originating from individual tributaries or hatcheries are intended to be used for tribal and sport 

fisheries, hatchery broodstock, and natural spawning escapement, the number of years that 

harvest seasons have been allowed, and the extent to which objectives have been achieved. This 

information was lacking. 

4. What are the demographic, ecological, and genetic impacts of the programs on wild 

fish? 

4.1. Are there unambiguous performance indicators and quantitative objectives for those indictors 

for natural and hatchery fish? 

Finding 4.1. There were no easily-obtained, unambiguous, scientifically-justifiable indicators for 

evaluating the ecological (predation and competition) or genetic (fitness effects of interbreeding 

between hatchery and natural-origin fish) impacts of hatchery programs on wild salmon 

populations. The LSRCP is not alone in having challenges in developing indicators to quantify 

and evaluate these vitally important uncertainties. There was no apparent explicit evaluation of 

the impact of hatchery smolts on the parr and smolt populations that are resident at the time of 

releases, including potential residualism of hatchery smolts. Genetic effects were indirectly 

investigated by comparing age of return of hatchery and natural fish, and tracking the trend in this 

life-history characteristic in natural fish. Adult females from hatchery-reared spring Chinook 

cohorts produced more three-year-old fish and fewer five-year-old fish than their natural 

counterparts. It is not known the extent to which this alteration in life-history may involve selection 

for specific genotypes. By monitoring the trend through time, the rationale is that if the trend in 

hatchery fish increased over time it might have a considerable genetic component. If the trend in 

the natural population started to indicate that younger age fish were increasing, it would support 

the idea that interbreeding between the hatchery and natural salmon was leading to changes in 

the genetics of natural populations. The collection of this information is important, but the 

interpretation is fraught with complications. 

The trends over time in both the hatchery and natural populations need to be contrasted to an 

unsupplemented reference population that is carefully monitored. Without that contrast, trends in 

the natural population and hatchery population may reflect natural selection to a changing 

environment. Analysis of the current data does not permit identifying the genetic component of 

any change or any environmental causes. 

There is an ongoing relative reproductive success investigation at Catherine Creek that should 

provide a better understanding of the effect on population demography from supplementation. 

Stray rates were estimated for some programs, but this metric was not uniformly presented in the 

reports. In some streams, the distribution of natural and hatchery spawners (breeding locations) 

were monitored. Natural- and hatchery-origin salmon spawning distribution is worth continuing 

and may provide insight into differences in natural and hatchery fitness in the wild. 

4.2. Are performance for ecological and genetic impacts adequately measured, reported, and 

analyzed? See response to 4.1. 
314 

Finding 4.2. The information on age structure, migration timing, and spawning distribution was 

reasonably collected, presented, and analyzed. 

4.3. Are they adequately evaluating supplementation (for example using AHSWG 

recommendations)? 

Finding 4.3. The Before-After-Control-Impact (BACI) model used to evaluate supplementation in 

the Imnaha River is a method that the ISRP believes is scientifically valid. We recommend that 

this method (or alternatives of similar validity) be used at all locations that have programs that 

plan to use returning hatchery fish to spawn in the streams. No other program besides the Imnaha 

evaluates supplementation for the critical endpoint, i.e., a gain in natural-origin adult salmon 

abundance as a consequence of spawning by hatchery fish. In a stream that is being 

supplemented, the primary treatment of interest is the natural spawning by hatchery adults and 

the endpoint of interest is production of adult offspring from the hatchery fish that adds, not 

replaces, natural production in the stream. The second critical endpoint, the density independent 

recruits-per-spawner (R/S, productivity) as a measure of the fitness of the natural spawning 

population, is also evaluated with this BACI model. The analysis of natural-origin return (NOR) 

abundance evaluates the demographic benefit of supplementation; the analysis of R/S evaluates 

the fitness cost of supplementation. 

Finding 4.4. The BACI analysis of NOR abundance indicated that when contrasted to nine 

unsupplemented reference locations, the Imnaha River showed decreased abundance postsupplementation relative to five sites, and increased abundance post-supplementation relative to 

four sites. The BACI analysis found that productivity in the Imnaha River had decreased relative 

to all nine unsupplemented sites. Based on this analysis and inspection of the trends in NOR 

abundance in the other supplementation projects, the ISRP concludes that a conservation benefit 

in terms of NOR abundance is unlikely from supplementation. Based on the analysis of 

productivity loss in the Imnaha River, the ISRP concludes that costs to population fitness are 

likely. Quantification of supplementation effects on abundance and productivity needs to be 

evaluated at the other locations to establish whether this is a case-specific finding or a general 

one. 

Finding 4.5. Relative reproductive success investigations in Catherine Creek established that 

hatchery-origin adult spring Chinook produced progeny that survived and returned as adults. 

Hatchery-origin adults spawning in the stream produced parr at slightly higher rates than naturalorigin fish (1.03:1), produced smolts at an equal rate (1:1), but produced adults at a lower rate 

(0.77:1). 

Finding 4.6. Inspection of smolts-per-spawner yield in the Lostine River and analyses from 

Catherine Creek and the upper Grande Ronde River strongly suggest density dependence in 

smolt production. Density-dependent survival in these watersheds was a factor that appeared to 

be restricting the increase in smolt production that was expected from increased spawner 

abundance in the streams. 

Finding 4.7. Most of the hatchery programs were self-sustaining. At least one adult female 

returned to the hatchery or tributary weir from the spawning of an adult female in the hatchery. 

On this basis, the program might maintain an important genetic lineage that otherwise would 

become extirpated. Over the long-term, however, hatchery-dominated programs that are 

implemented to reduce extinction risk will result in genetic changes owing to domestication 

selection and drift that are likely to offset any demographic benefit. 
315 

Recommendation/Conclusions. Analysis of abundance and productivity in the supplemented 

locations, especially those tributaries where there is a conservation objective in the management 

plan, is urgently required. The ISRP concludes that there is an absence of empirical evidence 

from the ongoing projects to assign a conservation objective other than preventing extinction. The 

supplementation projects as they are currently conducted with high proportions of hatchery fish 

in the hatchery broodstock and on the natural spawning grounds are likely compromising the longterm viability of the populations. Evaluation of most supplementation projects would benefit from 

a more thorough comparison with life-stage specific productivity of salmon from unsupplemented 

reference streams. All programs should evaluate the potential influence of density-dependent 

effects and investigate why density-dependence was occurring at such low population levels in 

those streams where it has been observed. In other words, is the capacity of spawning and/or 

rearing habitat restricting production of smolts when additional adults reach the spawning 

grounds? 

5. How are programs being modified and problems achieving objectives being 

addressed? 

Finding 5.1. Recently, there has been an HSRG and a Service HRT review of the LSRCP hatchery 

programs. This represents the best available science related to the hatchery programs and their 

evaluations. Although the LSRCP reports and presentations identified some HSRG 

recommendations, in general they did not elaborate sufficiently on the recommendations from 

those reviews and how they were being addressed by the co-managers. For example, for the 

Sawtooth program (to be split into a segregated mitigation program and an integrated 

conservation program), quantitative objectives for the integrated program were not provided, nor 

was there any evidence presented that habitat conditions were suitable for a conservation 

program. Each report should be specific and provide sufficient detail on the response to the HSRG 

and USFWS HRT recommendations. 

Finding 5.2. The LSRCP analysis and discussion of smolt survival needs to be expanded to 

incorporate available survival information to the mouth of the Columbia River and to consider 

transport, hydrosystem passage, and losses to avian, mammal, and piscivorous predators. 

LSRCP smolts are PIT-tagged at the hatcheries and again at Lower Granite Dam to provide the 

fish used in the Fish and Wildlife Program Comparative Survival Studies, NOAA survival studies, 

and the Corp Anadromous Fish Evaluation Program (ACE AFEP) investigations. The insights on 

juvenile salmon survival from these investigations do not appear to be integrated into the planning 

to address the inability of the LSRCP spring Chinook program to achieve the SAS and SARs 

necessary to mitigate for the four lower Snake River dams. In other words, how much additional 

survival during each life-stage is needed to provide some anticipated level of abundance or 

harvest (not the original LSRCP goals, which were unrealistic)? A more thorough examination of 

the life-stage and migration-stage survivals might reveal key limitations and suggest where 

additional survival benefits are required and may be possible. 

CONCLUSIONS AND RECOMMENDATIONS 

Conclusion 1. Available evidence suggests that the SAS, SAR, and overall mitigation goals 

established and the assumptions behind them were overly optimistic. The goals are probably 

unobtainable even with substantial improvements in Snake and Columbia River environmental 

conditions. 
316 

Recommendation 1. A scientifically-justified (ecologically-based) approach is needed to develop 

empirical guidance on a realistic harvest mitigation level that might be attainable at some specific 

time in the future. 

Conclusion 2.a. The observation that most hatchery programs have self-sustaining broodstocks 

supports the argument that these programs may reduce the risk of complete population 

extirpation. However, the risk of functional extirpation of the natural spawning population is 

unlikely to be reduced by these programs. 

Conclusion 2.b. The BACI analysis from the Imnaha River and inspection of data and trends from 

other programs with a supplementation design indicate that these programs are not yielding an 

increase in natural-origin adults over unsupplemented reference locations. There is an absence 

of support for the argument that these programs provide a conservation benefit by reducing 

demographic risk. Some analyses suggest habitat improvement is needed in the watersheds 

before benefits from supplementation might be realized. 

Conclusion 2.c. Implementing conservation/supplementation programs using the sliding-scale 

broodstock management where, over the long-term, the hatchery broodstock has little gene flow 

from the natural population, and the natural population has a large proportion of hatchery-origin 

adults, is inconsistent with the scientific framework guidance on the operation of an integrated 

hatchery program. Operating these programs using the sliding scale over many years carries a 

high risk that both abundance and productivity will decrease. 

Recommendation 2. Take action wherever needed to rapidly establish natural populations that 

are viable. The LSRCP needs to integrate information on the status of the natural populations into 

adaptive management of what can or should be done within the hatchery programs to enhance 

the natural populations. 

To ensure that the LSRCP spring Chinook program is conducted using the best scientific 

information available, it needs to be consistent with the Council’s APR (NPCC 1999-15), HSRG 

scientific framework (HSRG 2004) and HSRG Columbia River basin findings (HSRG 2009). 

The 2009 NPCC Fish and Wildlife Program generally adopted the HSRG framework of integrated 

and segregated hatchery programs, with conservation and harvest mitigation purposes. While the 

ISRP concludes that conservation purposes beyond reducing extinction risk are unsupportable 

with the available empirical evidence, we recognize that integrated and segregated harvest 

mitigation is possible. It is generally accepted that more fish for harvest can be provided using 

segregated hatchery programs. There are also some examples – spring Chinook in the Deschutes 

River reared at the Warm Springs Hatchery – of functioning integrated harvest programs (Olson 

et al. 200413). 

The HSRG has argued, and the ISRP concurs, that scientific foundations from population genetics 

and demography demonstrate that integrated harvest programs require a natural population that 

is replacing itself, a program where the size of the natural population exceeds the size of the 

hatchery population, and a situation where gene flow is greatest from the natural population to 

the hatchery population (HSRG 2004). 

 

13 Olson, D. E., B. Spateholts, M. Paiya, and D. E. Campton. 2004. Salmon hatcheries for the 

21st century: A model at Warm Springs National Fish Hatchery. American Fisheries Society 

Symposium 44:585-602. 
317 

The original, and a primary ongoing, purpose of the LSRCP is to provide harvest mitigation for 

fish losses attributable to the Snake River dams. Achieving this goal, at any scale, using hatchery 

production managed consistent with conservation of natural populations will require improving the 

viability of the natural populations. 
318 

ISRP COMMENTS ON INDIVIDUAL PROGRAM SUMMARIES 

1. Salmon River 

A. Yankee Fork 

I. INTRODUCTION 

The Yankee Fork Chinook Salmon Supplementation (Yankee Fork) Program was initiated in 2006 

(Intro of written report says 2006, but later (p.11) says 2008). Chinook in the Yankee Fork are one 

of the nine populations of Snake River spring/summer Chinook salmon within the Upper Salmon 

Major Population Group. The ICTRT currently rates the Yankee Fork Chinook population at high 

risk of extinction; the population is not replacing itself and the geometric mean abundance of 13 

spawners is far from the recommended 500 spawners. 

In 1977, when Chinook salmon runs across Idaho began to dwindle, the Tribes established 

sanctuary areas in the Salmon River to allow rebuilding to occur. At the time, the Yankee Fork, 

along with several other tributaries were designated as permanent areas for Tribal fishing. 

Hatchery fish from three different Salmon River sources were released to support Tribal fishing; 

however, once the ESA listing of Chinook occurred in 1992, hatchery fish were not released into 

Yankee Fork to support Tribal fishing opportunity. 

The Tribe’s goal is to use hatchery supplementation as a short-term option for increasing Chinook 

abundance to meet harvest and conservation objectives. The Tribes are working to achieve the 

long-term goal of returning 2,000 naturally spawning Chinook salmon to the Yankee Fork; 

consequently, the program will focus on providing natural spawning escapement. Long-term 

management strategies also include restoring habitat, managing harvest, and monitoring and 

evaluating fisheries activities to learn adaptively. 

The Tribe’s long-term adult goal for the Yankee Fork system is divided into four objectives: 1) 

provide 750 adults for natural spawning (Conservation); 2) provide up to 1,000 adults for harvest 

in Columbia, Snake, Salmon, and Yankee Fork fisheries (Harvest); 3) allow Tribal harvest using 

traditional hunting methods including spear fishing, netting, and snagging; and 4) smolt releases 

of 200,000 – 400,000 initially, until Crystal Springs Fish Hatchery is online, then increase to 

~600,000 smolts. 

The Tribe’s first phase is to develop a locally-adapted Chinook salmon run. Because there are 

very few natural-origin adults returning to Yankee Fork, the sponsors will release of up to 1,500 

pre-spawn adults and 200,000 – 400,000 smolts per year, obtained from Sawtooth Fish Hatchery. 

Sawtooth hatchery fish will be crossbred with the naturally returning Yankee Fork adults. Once 

the locally-adapted run is developed, broodstock will be collected entirely from the natural-origin 

adults returning to Yankee Fork. 

Historical data. It would be helpful to provide information in the history/background section on the 

adult returns and harvest that was achieved during the 1977 – 1991 period when many spring 

Chinook were stocked into the Yankee Fork. 

Genetic and Stock Background. One issue not discussed in the report is the conservation 

planning for the Yankee Fork independent population of the Upper Salmon MPG. How is it that a 

Yankee Fork independent population is identified as having persisted at very small adult 

abundance after having Mackay, Pahsimeroi, and Sawtooth populations introduced into the 

stream? If there is an independent Yankee Fork population, how can the Sawtooth hatchery 
319 

population, which is the primary component of a different independent population, be used to 

establish the locally adapted stock? 

The small redd counts and TRT analysis provide ample evidence that the Yankee Fork spring 

Chinook population is at high risk of extirpation. The background section emphasizes a nonnormal distribution of adult spawning abundance measured as redd counts across years as 

additional evidence. There is no citation that this criterion serves as an indicator of population 

risk. Such citation should be provided. If none is available, it would be better to just use the TRT 

analysis. Otherwise, this criterion will sneak into the grey literature and potential gain usage that 

is not based on thorough analysis. 

It would also be useful to provide a brief discussion of the use of Yankee Fork for Idaho 

Supplementation Studies (ISS) and Captive Brood projects, and confirm how any conflicts 

between the projects have been considered and whether these conflicts (if any) are resolved. 

Goals and Objectives. The 2,000 adult spring Chinook goal should be partitioned into hatchery 

and natural-origin goals, and these returning adults should be further partitioned into fish for 

harvest, fish for hatchery broodstock, and fish for natural spawning. From the second paragraph 

it appears that 750 adults will escape to spawn, 1000 harvested, but the balance is not allocated 

to hatchery broodstock. It is not transparent that 250 fish can provide the needed adult returns 

given existing SARs. There should be a table that summarizes the natural and hatchery smolt 

production, assumed SARs, adult returns and disposition from each group of fish. This table 

should also provide the mix of hatchery fish permitted on the spawning grounds, and the natural 

and hatchery-origin fish used in the hatchery broodstock. 

Monitoring and Evaluation. The Yankee Fork project plans on releasing both smolts and adults to 

provide “supplementation.” The monitoring section states that a BACI design will be used for 

evaluation, which is welcome, but the details of the methods and the sufficiency of the tagging 

rates and recovery of fish is not thorough enough to reach a conclusion on the robustness of the 

plan. 
320 

II. DATA 

The Tribes plan to use a treatment and control study design to monitor and evaluate the program. 

Select treatment tributaries such as the South Fork Salmon River, Upper Salmon River, 

Pahsimeroi River, and Johnson Creek will be used to evaluate supplementation. Control streams 

will be selected from streams already being evaluated for supplementation under the ISS, since 

data are already being collected. The study design intends to assess performance of multiple 

groups of fish within the Yankee Fork and compare their performance to salmon in natural-only 

control streams. 

The Tribe’s Monitoring and Evaluation program is largely conceptual at this point as presented in 

the written project report. Details of the M&E and genetic parentage analysis need to be 

developed and documented within the project report in order to provide a baseline implementation 

document. Project cooperators intend to manage adaptively; consequently, it is very important at 

a project’s initiation to describe the project assumptions, field and lab methods in adequate detail, 

as well as M&E data collection and analytical protocols. Some (or many of these) may change 

over the course of the project to adjust to environmental and biological variability encountered in 

dynamic salmon systems. Long-term evaluation of the project’s goals and the efficacy of 

supplementation will be compromised (or impossible) without the development of detailed 

baseline data and protocols. 

The rotary screw trap data on page 10 would be more usefully presented as the results of fish 

production and emigration from specific management actions – either smolt stocking or natural 

production from the release of adults the previous autumn. The initial rotary screw trap data 

indicates challenges and difficulties in actually operating the trap and producing estimates of 

watershed production. Some discussion of what is needed to resolve these problems is 

warranted. Finally it would be helpful to show the location of screw trap on a map. Are hatchery 

fish released above this area, and if so, are hatchery fish enumerated separately from naturallyproduced salmon? 

In many Idaho streams spring Chinook leave the spawning stream in three pulses – first spring 

YOY, fall parr, and the second spring smolts (yearlings). The explanation of how all this is going 

to be sorted out is not transparent. At what life-stage are there going to be production metrics 

used for evaluation: spring fingerlings, fall parr, yearling smolts? How are sponsors going to figure 

out which group actually produced most of the returning adults? This seems to be a point of 

important discussion in some Idaho spring Chinook systems. Are the sponsors going to try to 

convert fingerling and parr numbers into smolt equivalents for analysis and estimation of SARs 

etc? 

Explanation of estimates of the numbers of individuals that passed the weir undetected, and 

spawned below the weir is needed (adult trapping, outplants, and redds; Table 3). What methods 

are used, and will the sizable numbers of fish spawning below the weir and passing undetected 

compromise analysis of the experiment. It is not evident how to account for the 381 fish return 

from the 2004 broodyear release of 135,934 smolts in 2006, since only 205 hatchery-origin adults 

are accounted for in table 3. 

 
321 

III. KEY FINDINGS 

The Yankee Fork Chinook Salmon Supplementation Program appears to be its initiation phase 

(started in either 2006 or 2008). The project is linked with other ongoing Chinook supplementation 

and research projects in the geographic area. 

Early data, which the sponsors discuss, showed a small run-timing shift for hatchery fish when 

compared with wild fish. Both show bimodal return peaks, with the hatchery-origin fish run shifted 

about two weeks later than the wild fish. The largest peak for wild fish occurred about mid-July, 

whereas the main peak for hatchery fish occurred during the first week of September. These life 

history differences may have adaptive and reproductive differences that will hopefully be 

elucidated by the parentage analysis and reproductive success studies. 

Long-term goals of the project are also tied to a proposed expansion and improvement of the 

Crystal Springs Fish Hatchery. The Crystal Springs Fish Hatchery proposal also includes plans 

for constructing adult trapping and holding facility in Yankee Fork, as well as an improved weir. 

This project report did not describe any details of the weir and would have benefited if some of 

those details had been included. 

Other missing details 

Screw Trap: The data that was presented needs to be clarified. There needs to be a definition of 

fry versus parr (i.e., specific lengths or age of each life history). A time series of captured fish by 

life stage would help clarify the presentation given that sampling was intermittent over time and 

total abundance estimates could not be generated. Provide how many fish were PIT-tagged or 

stained for mark-recapture and the results of the mark-recapture efforts. Provide the length at age 

of fish over time. Indicate if the goals were reached. Given that problems were encountered (e.g., 

high water), describe how will sampling be improved so that objectives can be achieved 

Smolt release: Provide the location and date of release, mean size at release and how those 

metrics compare with naturally produced smolts individuals. 

Adult trapping: In text, please present annual values, rather than cumulative values since 2008. 

The sponsors might combine the adult trapping section with the spawning ground section and 

provide a comprehensive view of fish entering and spawning in the watershed. 

Run Timing: Provide the year do these values represent (run timing graphs). It will be interesting 

to see if the timing pattern of natural and hatchery salmon continues in future years, and to 

evaluate whether supplementation affects timing characteristics. 

Harvests: Please include a table of annual harvests of hatchery versus natural salmon. 

Spawning Ground Surveys: Need to provide caption for Fig. 16. Continue to document hatchery 

versus natural origin spawners. The chart should also show the proportion of fish that are natural. 

 
322 

IV. OUTLOOK AND RECOMMENDATIONS 

The Shoshone-Bannock Tribes’ Yankee Fork program is in the initiation stage, and MOA 

supplementation project Supplementation, Monitoring, and Evaluation Program (BPA project 

#2008-95-00) and Crystal Springs Hatchery Master Plan are related to the LSRCP program. 

The final Yankee Fork program should reflect and serve the conservation, harvest, and cultural 

traditions of the Shoshone-Bannock Tribes. Before determining the final program design, the 

recovery plan and ESA status of spring Chinook in the Yankee Fork needs to be established. The 

Interior Columbia River Technical Recovery Team (ICTRT) classifies the Yankee Fork as an 

independent population, but also concludes that genetic evidence suggests past introgression 

with Rapid River hatchery spring Chinook. In the period from 1980 to 2000 more than 2 million 

juvenile spring Chinook from Pahsimeroi and Sawtooth hatcheries were stocked into the Yankee 

Fork watershed. The ICTRT currently rates the Yankee Fork spring Chinook population at high 

risk of extinction; the population is not replacing itself (20 year geometric mean R/S is 0.80) and 

the geometric mean abundance of 13 spawners is far from the 500 recommended. Further, the 

ICTRT concludes that the upper Salmon River spring Chinook MPG can be recovered without the 

Yankee Fork achieving “viable” status (a natural population with 500 individuals and a BevertonHolt productivity of 1.9). 

If the Yankee Fork spring Chinook are a unique independent population the ISRP does not 

understand how a program based on salmon from a different independent population (Upper 

Salmon River mainstem (Sawtooth segregated hatchery stock)) can be consistent with 

conservation and recovery plan objectives. If the Yankee Fork spring Chinook are a mixture of 

Upper Salmon River spring Chinook stocks and not essential for delisting, the ISRP does not 

understand why a program with a substantial conservation objectives that requires rigorous 

supplementation protocols and M&E is desirable. Consequently, the ISRP wonders if a more 

realistic management strategy for the Yankee Fork would be to simply manage Yankee Fork 

spring Chinook as a terminal Tribal fishery designed to avoid interactions with other stocks in the 

area. That is, management of the Yankee Fork population should be designed and implemented 

so it does not impede the recovery of other Salmon River Chinook populations. 

The Yankee Fork is a small-intermediate size watershed that could lend itself to this discrete 

management strategy. The combination of the watershed’s size with the collection and sorting 

weirs at the Pole Flats and Five Mile locations, offer an opportunity to achieve harvest and cultural 

objectives while testing the potential for population expansion following habitat restoration. 

Planning: A summary of the HSRG recommendations (sliding scale) for this program should be 

included, and a discussion of how the recommendations are being considered in the development 

of the program. 

Monitoring and Evaluation: The investigators recognized the limitations of their brief investigation. 

They indicated the need for parentage studies as a means to evaluate supplementation efforts. 

However, they should also provide recommendations for improving monitoring of smolts and 

adults. Detailed tables and graphs should be developed for the project and these should be 

updated annually as new data are collected. 

The Results section did not provide information on the “treatment and control” study that was 

identified in the study design. 
323 

The project report should provide more details, evaluation of the monitoring and findings, and 

recommendations for improvement in order to better achieve project objectives. The report should 

comment on observed status versus the production goals that were stated in the Introduction. If 

natural productivity is exceptionally low, what in-river modifications might be made to improve 

survival? There was no mention of habitat quality in the Yankee Fork and whether or not quality 

and quantity of habitat was affecting survival. Are there habitat projects in the watershed? If so, 

they should be integrated into this effort. 

B. South Fork Salmon River 

I. INTRODUCTION 

The South Fork Salmon River (SFSR) summer Chinook salmon mitigation program was 

established to provide in-kind mitigation for summer run Chinook salmon losses associated with 

the four lower Snake River hydroelectric dams. The McCall Fish Hatchery is responsible for all 

the incubation and rearing for this program. The hatchery and the associated satellite facility were 

constructed in 1980. 

The natural populations of Chinook salmon in the SFSR were listed as threatened in 1992 and 

the hatchery population was added to the listing in 2005. The ICTRT (2005) status assessment 

of the SFSR natural population indicates the population is not viable, is at a high risk for 

abundance and productivity, and is at moderate risk for spatial structure and diversity. 

The LSRCP adult mitigation goal for the McCall Fish Hatchery is 8,000 adult Chinook salmon 

above Lower Granite Dam (LGD) and 32,000 adults available for downriver (Columbia and lower 

Snake rivers) commercial and sport harvest. The release goal is 1 million smolts and is based on 

a 0.80% smolt-to-adult survival rate applied to the LGD mitigation objective of 8,000 adults. All 

smolts are transported from the McCall Fish Hatchery and released directly into the upper SFSR 

at Knox Bridge (RKm 115). 

Management Objectives for the SFSR Chinook salmon program are to meet the LSRCP adult 

mitigation objectives, to restore and maintain natural populations of Chinook salmon in the SFSR, 

to restore and maintain recreation and tribal Chinook salmon fisheries, and to minimize the impact 

of the McCall Fish Hatchery and SFSR Trap. 

Monitoring and evaluation (M&E) objectives for the SFSR include monitoring production, 

productivity, and life history characteristics of hatchery and natural populations, and to evaluate 

broodstock and rearing strategies to increase and maximize adult returns. M&E activity on the 

SFSR is a cooperative effort between the Idaho Department of Fish and Game (IDFG) and the 

Nez Perce Tribe (NPT). 

The broodstock history for the SFSR has been continually changing since the program’s 

inception. This has made it impossible to estimate the contributions of the several founding stocks 

and difficult to evaluate the program. In recent years, the program has swung from focusing on 

segregated hatchery origin broodstock (1995-2009) to an integrated stepping-stone broodstock 

protocol, which was initiated in 2010. 

Management and Monitoring/Evaluation Objectives. It is not clear how the actions in this program 

contribute to the objective “restore and maintain natural populations of Chinook salmon in the 

SFSR,” or how the program is being implemented to “minimize the impact of the hatchery program 

on the natural Chinook populations in the SFSR.” The sentences on monitoring and evaluation 
324 

do not identify the individual metrics that are being used to evaluate the various program 

objectives. Some are self-evident, e.g., adult abundance, harvest, etc, but other objectives are 

not, e.g., restore and maintain natural populations and minimize impacts. It would be helpful to 

identify how the information is being gathered. For example, are estimates of adult abundance 

determined from CWT data collected at LGD or the hatchery rack? Is there representative PITtagging and CWT-tagging? 

Status of Natural Population. Additional specific details would enhance this section. The section 

states that the SFSR mainstem is part of a SFSR major population group that has four 

independent populations. Identify the ESU, the names and number of MPGs in the ESU, and then 

name the SFSR MPG independent populations and perhaps provide a map with their geographic 

distribution. There should be a description of where this hatchery program interacts with other 

spring Chinook populations, and the nature of the interaction. For example, genetic interactions 

may occur in tributaries where hatchery fish stray. It would be helpful to include a figure showing 

the trends in abundance of natural stocks and the viability assessment/recovery plan thresholds 

for viability. 

II. DATA 

The written and Power Point reports both presented many trend figures that were interesting. The 

results and performance of the SFSR program appear typical of many that we saw at the 

symposium – consistent problems in the early years with survival, within-hatchery mortality, and 

failure to reach program level goals for juvenile release numbers, while results for the last decade 

or so document programs that have addressed within-hatchery issues and are mostly reaching 

juvenile release numeric goals. 

Adult returns. SFSR hatchery returning salmon have reached the program SAR goal of 0.80% in 

only 7 of 35 years (20%; Figure 6). SARs for ISS smolts in general are lower than those recorded 

for smolts produced by SFSR adults, but have also only reached the 0.80% goal about 20% of 

the years. 

A description of how adults at LGD partitioned into the different Snake/Salmon river MPGs and 

independent populations would be useful. Are there hypotheses on how/why juvenile survival 

from release to LGD is greater for hatchery than wild smolts, yet SARs are lower for hatchery fish 

from smolt to adult? 

Life history characteristics and age composition. It is not clear from the text and figures whether 

the age composition data is estimated for a “run” year or a “brood” year. Given the variation in 

survival from brood year to brood year, it seems that should be how age classes are reported, not 

on run years. As an aside, in the figure showing age composition (comparing 1-ocean to 2-ocean 

and 3-ocean fish), it would have been easier to see trends using a stacked bar graph than 3 

separate line graphs. 

III. KEY FINDINGS 

Like many of the LSRCP hatcheries, the SFSR hatchery has made admirable progress over its 

roughly 30-year history toward solving in-hatchery production problems and achieving withinhatchery survival, and occasionally, production goals, depending upon broodstock availability. 

However, the mixed pedigree of the broodstock, the ever-changing broodstock management 

strategy, and the shifting nature of the supplementation strategy (from segregated to integrated 

stepping-stone over the last few years) creates uncertainty about what we can expect to learn 
325 

from the SFSR supplementation experiment, as well as uncertainty about its future performance. 

A constantly shifting program becomes difficult to track and assess due to shifting goals and 

shifting data baselines. 

While methods were not described, key metrics were presented in the report and presentation. It 

would be helpful if the data reporting were summarized as explicit statements reflecting the 

managers’ self-evaluation of how well the program is achieving the objectives established. 

Smolt survival. Please comment on why survival of hatchery smolts to LGD is consistently higher 

than that of natural smolts given that survival to adult stage of hatchery smolts is consistently 

lower. Does high early survival of hatchery smolts reflect distance or size? This finding is opposite 

that of Upper Salmon River spring Chinook. 

Smolt-to-adult survival of natural smolts is much higher than that of hatchery fish. If available add 

the adult return per spawner for natural spawner to the report. If it is not available summarize the 

information from the ICTRT viability assessment. Discuss if their habitat characteristics in the 

watershed that could be improved as a means to enhance spawner-to-smolt survival. 

The presentation of life history data of hatchery and natural Chinook was helpful. Older age of 

maturation by natural Chinook is important because older fish produce more numerous and larger 

eggs and therefore contribute to higher adult returns per spawner. Are there any differences in 

mean length-at-age of hatchery versus natural Chinook (ANOVA test)? It is difficult to tell from 

graphs given the Y-axis scale. 

Stray rate. Indicate if the reported values estimated the percentage of the hatchery return that 

stray to streams. Provide any information on the fraction of natural spawners that are hatchery 

strays. If there is natural spawning near the weir site, provide what fraction are hatchery fish. 

IV. OUTLOOK AND RECOMMENDATIONS 

The TRT concluded that the natural population was not viable. What is needed to make it viable? 

What is the annual return per spawner of natural Chinook? Can tributary habitat or mainstem river 

conditions be improved sufficiently to allow a viable natural population? Or is hatchery production 

essential in the next decade or so in order to maintain fish returning to this region? What is needed 

to meet the management objectives that were stated in the introductory comments? Are 

management objectives realistic or should they be re-evaluated? 

The “Summary and Outlook for the Future” section of the written report describes in broad brush 

the future direction of the program including the implementation of Parental Based Tagging (PBT), 

which along with CWTs, will be used to monitor catch contribution and stock identification. This 

section should also include a brief summary of the findings from the USFWS hatchery review and 

the HSRG review, and how the program is addressing those findings. 

The Summary section also describes the integrated stepping-stone approach to supplementation 

that includes maintaining two broodstocks (integrated and segregated). Returns from the 

integrated brood will be used to supplement the natural-origin population above the hatchery weir 

and produce the next generation of integrated broodstock. Weir and broodstock management will 

be based on a sliding scale approach. There is text indicating that this program will initiate 

supplementation above the existing weir. The management and monitoring of that program should 

be summarized. 
326 

While this may be a very pragmatic approach to managing the SFSR Chinook stock, it (coupled 

with the mixed artificial production history of the stock) is one that encompasses significant 

uncertainty with respect to rebuilding a natural population and the fitness effects of such a 

strategy. The detailed methods of this approach and consideration of the uncertainties associated 

with it are not addressed in the written document and deserve greater discussion and scrutiny. It 

is our recommendation that the SFSR plans that design the dual programs be reviewed by the 

ISRP or an equivalent body when it is available. 

C. Upper Salmon River

I. INTRODUCTION 

The natural population of Chinook salmon in the Upper Salmon River was listed as threatened in 

1992, and the hatchery population was added to the listing in 2005. From 1991 to 2009, the 

estimated natural-origin adult abundance in the Upper Salmon River mainstem population has 

ranged from 18 to 1,431 fish. The Interior Columbia Technical Recovery Team (ICTRT) concluded 

that the USR natural population is not currently viable, is at a high risk for abundance and 

productivity measures, and is at moderate risk for spatial structure and diversity. 

The Upper Salmon River (USR) spring Chinook salmon program was established in 1985 to 

provide in-kind mitigation for losses of spring run Chinook salmon associated with the construction 

and operation of the four lower Snake River hydroelectric dams. The Sawtooth Fish Hatchery is 

located on the Salmon River approximately seven miles upstream from the town of Stanley, Idaho. 

All adult trapping, spawning, incubation and rearing occurs at this facility. Currently, this facility is 

used to monitor adult abundance of the natural population and no broodstock is collected at this 

site. 

The LSRCP adult mitigation goal for the USR spring Chinook program is 19,400 adult Chinook 

salmon above Lower Granite Dam (LGD) and 77,000 adults available for downriver sport and 

commercial harvest. The original release target of 2.3 million yearling smolts was based on an 

assumed 0.87% smolt-to-adult survival rate applied to the LGD mitigation objective; however, due 

to limitations with well water availability and ice thickness in outdoor rearing containers during the 

winter months, the actual facility capacity was adjusted down to 1.7 million yearling smolts. 

Currently, the release strategy is for 1.5 million smolts released directly into the Salmon River at 

Sawtooth Fish Hatchery and 200,000 smolts released into the Yankee Fork as part of the 

Shoshone Bannock Tribe supplementation program. 

Initial broodstock for the USR program was collected at a temporary weir in the Upper Salmon 

River from 1981 to 1984. It was estimated that approximately 50% of the two-ocean broodstock 

collected in 1981 were from the release of Rapid River hatchery smolts in 1979. A similar 

proportion of the three-ocean returns in 1982 were assumed to be from the same hatchery 

release. Since 1983, all broodstock have been of USR origin. Because mass marking was not 

initiated until brood year 1991, the origin of adult returns (hatchery or natural) could not be 

distinguished until 1995. 

The broodstock history and AP strategy for the USR has changed several times since the 

program’s inception. This has made it impossible to estimate the contributions of the USR and 

Rapid River founding stocks and difficult to evaluate the program. Prior to 1995 the program was 

a de facto integration/supplementation program with both hatchery- and natural-origin adults 

incorporated into the broodstock and also released above the weir to spawn naturally. In recent 
327 

years, the program has swung from focusing on segregated hatchery origin broodstock (1995-

2009) to an integrated stepping-stone broodstock protocol, which was initiated in 2010. 

Management and Monitoring/Evaluation Objectives. It is not clear how the actions in this program 

contribute to the objective “restore and maintain natural populations of Chinook salmon in the 

USR,” or how the program is being implemented to “minimize the impact of the hatchery program 

on the natural Chinook populations in the USR.” The sentences on monitoring and evaluation do 

not identify the individual metrics that are being used to evaluate the various program objectives. 

Some are self-evident (e.g., adult abundance, harvest) but other objectives are not (e.g., restore 

and maintain natural populations and minimize impacts). It would be helpful to identify how the 

information is being gathered. For example, are estimates of adult abundance determined from 

CWT data collected at LGD or the hatchery rack? Is there representative PIT tagging and CWT 

tagging? 

A table summarizing the planning assumptions for this program would help. See table 1 in the 

Imnaha report for an example. 

Broodstock History. This section notes that broodstock collected in 1981 (and 1982) likely 

included adults from Rapid River smolts released into the upper Salmon River in 1979. It appears 

to be appropriate and necessary to provide an expanded explanation of Chinook salmon smolt 

releases in the upper Salmon River in the years preceding the development of this program. 

Status of Natural Population. Additional specific details would enhance this section. The section 

states that the USR mainstem is part of a USR major population group that has nine independent 

populations. The sponsors should identify the ESU, the names and number of MPGs in the ESU, 

and then name USR MPG independent populations, and provide a map with their geographic 

distributions. There should be a description of where the USR hatchery program interacts with 

other spring Chinook populations, and the nature of the interaction. For example, genetic 

interactions may occur in tributaries where hatchery fish stray. It would be helpful to include a 

figure showing the trends in abundance of natural stocks and the viability assessment/recovery 

plan thresholds for viability. 

The USR written report contains adequate background information and project objectives, but the 

format should be standardized with that of the other spring Chinook hatchery reports. This 

summary was consistent with that presented for the South Fork Salmon, but it was quite different 

from the summary of the Yankee Fork investigation, which is relatively new. 

II. DATA 

Methods were not described, but key metrics were presented. Greater detail, or references to key 

documents where the methods are adequately described, would be of benefit to the report. 

Hatchery survival and production. A comparison of the observed pre-spawning mortality, 

fecundity, egg take, and egg–to-smolt survival to the planning assumptions would improve the 

presentation. 

Adult returns LGD. An explanation of how adults at LGD are partitioned into the different 

Snake/Salmon river MPGs and independent populations; whether they are these based on CWT 

or PIT tag data, and the precision of the estimates would improve the report. How robust are the 

estimates? 
328 

Life history characteristics. The figures showing age composition (comparing 1-ocean to 2-ocean 

and 3-ocean fish) should use a stacked bar graph rather than 3 separate line graphs. 

III. KEY FINDINGS 

Like many of the LSRCP hatcheries, the USR hatchery has made admirable progress over its 26-

year history toward solving in-hatchery production problems and achieving within-hatchery 

survival, and occasionally, production goals, depending upon broodstock availability. The mixed 

pedigree of the broodstock and the shifting nature of the supplementation strategy (from 

segregated to integrated stepping-stone over the last few years) create uncertainty about what 

we can expect to learn from the USR hatchery program, as well as uncertainty about its future 

performance. A constantly shifting program becomes difficult to track and assess due to shifting 

goals and shifting data baselines. 

Data Reporting. It would be helpful if the data reporting were summarized as explicit statements 

reflecting the managers’ self-evaluation of how well the program is achieving the objectives 

established in the background. 

Smolt Survivals. Why is release to LGD survival higher here for natural versus hatchery smolts, 

a pattern that is opposite that for the South Fork? 

Survival of subyearling releases was determined to be too low. Can this information be applied to 

the natural Chinook; do natural Chinook also have high mortality? If so, what is needed to improve 

survival of natural Chinook while rearing in the watershed? 

Adult Survival. Please provide adult return per spawner data for the natural component, if 

possible, and evaluate sustainability, including the degree to which survival must improve to 

provide sustainability and sustained harvest. Can sustainability of natural runs be achieved with 

ongoing actions to improve survival, or is “sustainability” totally dependent on highly favorable 

environmental conditions that are not likely to persist? 

Adult timing. The high degree of synchrony of hatchery and natural Chinook return timing 

suggests that time cannot be used to reduce bycatch of natural Chinook. Harvests of hatchery 

Chinook were presented (Note: two Figure 10s were shown). How many natural Chinook were 

harvested? 

Straying. Are the presented values the percentage of hatchery fish on the spawning grounds or 

fraction of hatchery return that were found in streams? If the former, it would be good to present 

information on the locations sampled and level of effort. If the former, it is surprising that only 

0.59% of the spawners were hatchery origin given that hatchery fish tend to stray, harvest rates 

are low, and natural fish abundance is very low. 

IV. OUTLOOK AND RECOMMENDATIONS 

The TRT concluded that the natural population was not viable. The “Summary and Outlook for 

the Future” section of the written report describes in broad brush the future direction of the 

program including the implementation of Parental Based Tagging (PBT), which, along with CWTs, 

will be used to monitor catch contribution and stock identification. This section should also include 

a brief summary of the findings from the USFWS hatchery review and the HSRG review, and how 

the program is addressing those findings. The project sponsors also indicate that development of 
329 

an HGMP is underway. It is our recommendation that the USR HGMP be reviewed by the ISRP 

or an equivalent body when it is available. 

The Summary section also describes the integrated stepping-stone approach to supplementation 

that includes maintaining two broodstocks (integrated and segregated). Returns from the 

integrated brood will be used to supplement the natural-origin population above the hatchery weir 

and produce the next generation of integrated broodstock. Weir and broodstock management will 

be based on a sliding scale approach. There is text indicating that this program will initiate 

supplementation above the existing weir. The management and monitoring of that program should 

be summarized. 

The program anticipates being split with a portion being conducted as a segregated program and 

a portion implemented as an integrated program. The integrated program will produce adults to 

supplement the natural population above the hatchery. As designed by the HSRG (2005) an 

integrated artificial production program requires a natural population that is above replacement. 

It is not clear to the ISRP that abundance and productivity of the natural population are sufficient 

to implement an integrated program. Given the response in natural abundance from other 

supplementation programs for spring Chinook it is not evident that additional natural adults will be 

produced to provide the foundation for an integrated program. These issues should be carefully 

discussed and considered in the summary section. It is our recommendation that the USR plans 

that design the dual programs be reviewed by the ISRP or an equivalent body when it is available. 

Analysis of the hatchery and natural Chinook data should lead back to objectives. What is needed 

to achieve the objectives (or are objectives unreasonable given current conditions)? Are there 

habitat issues that need to be addressed? Where are the major bottlenecks for survival and which 

bottlenecks might be altered to improve survival. For example, if sufficient natural spawner data 

are available, one could calculate smolts per spawner and smolt survival to LGD. Are these values 

high or low, and can survival during these life stages be improved? Or is it essential that smolt 

survival through the hydropower system be improved. Low, moderate and high survival at sea 

should be considered when evaluating survival requirements during each life stage. 

2. Clearwater and Tucannon

A. Clearwater 

I. INTRODUCTION 

The Clearwater Fish Hatchery near Ahsakha, Idaho and its three outlying facilities (Powell, Red 

River, and Crooked River) comprise the largest hatchery complex constructed by the Army Corp 

of Engineers under the LSRCP. Construction began in 1986 with the Red River satellite facility 

and ended in 1991 with the completion of the main Clearwater Hatchery. The three satellite 

facilities function variously for trapping, spawning, rearing, and acclimation. The Idaho 

Department of Fish and Game (IDFG) operates the hatchery. 

As described by IDFG, “The main hatchery consists of two separate incubation facilities, 24 

outdoor raceways for steelhead rearing, 11 outdoor raceways for Chinook rearing, an adult 

holding and spawning area... [The hatchery] receives its water through a uniquely designed 

pipeline. Two pipelines pass through 25 feet of solid concrete in the middle of the Dworshak Dam. 

Water is carried 1.8 miles downstream where energy is dissipated through a hydroelectric plant. 

The water then continues through the two separate pipelines delivering water of two different 

temperatures to the rearing facility. The delivery of two separate water temperatures allows 
330 

Clearwater Hatchery to raise spring Chinook salmon ... at optimum rearing temperatures” 

(http://fishandgame.idaho.gov/fish/hatcheries/clearwater.cfm). Since the 1990s, the spring 

Chinook program has used locally adapted stocks. Since 2005, the program has moved primarily 

toward smolt releases because of low survival of parr. 

II. DATA 

Data presented to evaluate success consisted of broodstock performance (% prespawn 

mortality), in-hatchery survival, number released, percent (parr or smolt) survival to LGR, number 

of adult returns to the Lower Columbia River, number of adult returns to LGR, smolt-to-adult 

survival rate (SAS), smolt to adult return (SAR), and in-river state and tribal harvest. Life history 

data for assessing hatchery and wild differences include run timing, age composition, length-atage, spawning timing, and fecundity. Known strays of adults were also assessed above and below 

LGR. 

III. KEY FINDINGS 

1. Fish performance in the hatchery is documented and appears to be adequate and 

consistent with standards of other rearing operations in the basin. There is demonstrated 

success at producing apparently healthy fish at release. There was little information 

presented to indicate if and how other aspects of smolt quality are being significantly 

improved upon or evaluated in the hatchery at this time. 

2. The shift to native broodstock and to releases of full term smolts, rather than parr, has 

been justified based on post-release survival performance; however, the management 

change appears to have also resulted in increased production of jacks. 

3. Although performance of fish in the hatchery is measured based on survival, and inhatchery survival rates appear to be adequate to the smolt stage (generally 70% and 

above except for the South Fork in 2008), survival as measured by SASs and SARs is 

not. With low SAR and SAS results, the hatchery is not producing adult returns that meet 

its mitigation goals. The program is averaging 5% of mitigation goals to the mouth of the 

Columbia and a maximum success of only 18.5% of its mitigation goals. 

4. Released smolts are showing erratic and low survival rates. Measures of these survival 

rates and other life history aspects (size, age at return, etc.) seem appropriate, although 

the information provided is not sufficient to provide much insight as to why overall 

survival is so low. 

5. The ecological and genetic impacts of the programs on wild fish are shown primarily 

through comparisons of life history characteristics between hatchery and wild fish. 

Although in the presentation it was concluded that impacts to wild fish were not 

significant, we note that the percentage of jacks among hatchery fish returns has 

increased in BY 2002 and 2003, and that returns of jacks were higher in 2007, 2008, and 

2009, and returns of 3 SW fish were lower. 

6. Survival rates of smolts have declined from the mid-1990s as numbers of smolts 

released has increased. The causes of this undesirable pattern are not identified. 

7. Evaluation of supplementation could be improved. In particular, it was not clarified why 

survival rates of wild smolts exceeded hatchery smolts in 1994-1996, but not in any 

recent years except 2007 (by a narrow margin). Has the quality (or size) of hatchery 

smolts risen sufficiently or is there some unknown interaction of released fish and wild 

fish? 
331 

8. It is unclear why survival to Lower Granite Dam is only 60-70%, whereas it is higher for 

releases from Powell. What are the primary factors affecting survival of both the 

hatchery and wild smolts, and how well is that understood? 

9. No information was provided on the possibility of residualization of precocious males 

(mini-jacks) from these increasingly large smolt releases and potential effects on wild 

fish. This issue may deserve study and discussion among LSRCP entities. 

IV. OUTLOOK AND RECOMMENDATIONS 

The low SARs indicate that existing approaches for rearing and releasing smolts do not result in 

fish capable of returning as adults to the Columbia River and Lower Granite Dam in numbers 

sufficient for meeting existing LSRCP mitigation goals. Under existing conditions, the long-term 

outlook for successfully meeting project area mitigation objectives is not favorable and appears 

unlikely. The overall mitigation goals of returning 59,500 fish to Columbia River mouth and 11,900 

adults above Lower Granite do not appear achievable within the foreseeable future. No actions 

proposed seem to provide much likelihood of an improved outlook. The main benefit of the 

program as of 2010 has been to provide modest state recreational and tribal harvest fisheries, 

which, from any perspective beyond satisfying immediate harvest demands, do not seem 

justifiable unless it is shown that those fish, if not harvested and allowed to spawn, would result 

in reproductive success leading to a density dependent suppression of the natural production 

potential of the basin. The genetic and long-term fitness implications of the harvest are not 

evaluated. A science-based plan for deciding the most goal-oriented disposition of returning 

adults (harvest, allow to spawn naturally, broodstock, etc.) was not provided. A key question is 

how many fish should be used to meet longer-term mitigation goals before immediate harvest is 

pursued. At present, the only realistic prognosis for this program is to provide the modest fishery 

well below its mitigation goals. 

In addition, it would be useful to have the information presented in terms of the Interior Columbia 

River Technical Recovery Team (ICTRT) goals and findings on VSPs, as well as HRSG review 

and recommendations, and a description of how the program releases are justified when the these 

recommendations are considered. 

B. Dworshak 

I. INTRODUCTION 

Dworshak Hatchery is located at the confluence of the North Fork and the mainstem Clearwater 

River, Idaho, below Dworshak Dam. LSRCP spring Chinook salmon goals are 9,135 adults above 

LGD after an expected 36,500 combined harvest in ocean, Columbia River, and Lower Snake 

River fisheries (45,635 fish), and a production goal of 1.05 million smolts. Hatchery objectives are 

to provide recreational and tribal fish for harvest, return sufficient broodstock to meet annual 

production needs, minimize impacts to natural populations, and assist other programs in the 

Clearwater basin. The hatchery is not located in a natural spawning area. 

II. DATA 

Data presented to evaluate success consisted of broodstock performance (% prespawn 

mortality), , in-hatchery survival, number released, percent (parr or smolt) survival to LGR, number 

of adult returns to the LGD, number of adult returns to LGD, smolt-to-adult survival rate (SAS), 

smolt to adult return (SAR), and in-river state and tribal harvest. Life history data for assessing 
332 

hatchery and wild differences include run timing, age composition, length-at-age, spawning 

timing, and fecundity, but without comparisons to wild fish for reference. Known strays of adults 

were also assessed above and below LGD. 

III. KEY FINDINGS 

1. Fish performance in the hatchery is well-documented and appears to be adequate. 

2. The shift to native broodstock and to releases of full term smolts rather than parr has 

been justified. One result, however, has been an increase in the production of jacks. 

3. Although performance of fish in the hatchery is measured based on survival, and inhatchery survival rates appear to be adequate to the smolt stage (mean 83.2%), there 

was little information presented to indicate that other aspects of smolt quality are being 

significantly improved upon at the hatchery at this time. 

4. Fish culture performance is within expected standards; however, survival as measured 

by SASs and SARs is not. 

5. Released smolts are showing erratic and low survival rates. Measures of these survival 

rates and other life history aspects (size, age at return, etc.) seemed appropriate, 

although the information provided is not sufficient to provide much insight as to why 

overall survival is so low. 

6. The ecological and genetic impacts of the programs on wild fish are not evaluated in the 

material provided. As in the Clearwater hatchery, we note that the percentage of jacks 

among hatchery fish returns has increased in 2007, 2008, and 2009 return years. 

7. It is also clear that survival rates have declined from the mid-1990s. The causes of this 

undesirable pattern are not discussed. 

8. The program is operating well below expectations in terms of mitigation goals. It has met 

or exceeded its upriver goal only in 2001; over the period 2005-2009 returns above LGD 

have not exceeded 45% of the goal of 9,135 fish. Return to the Columbia River has been 

less than 10% of total adult fish goals for the most two recent years. 

IV. OUTLOOK AND RECOMMENDATIONS 

Under existing conditions the long-term outlook for successfully meeting project area mitigation 

objectives is not favorable. It does not appear that overall goals are achievable within the 

foreseeable future. No actions proposed seem to provide much likelihood of an improved outlook. 

The main benefit of the program as of 2010 (and the prognosis) is to provide continued State 

recreational and Tribal harvest fisheries well below mitigation goals. A science-based plan for 

deciding the most goal-oriented disposition of returning adults (harvest, allow to spawn naturally, 

broodstock, etc.) was not provided. This analysis should be linked to LSRCP activities at the 

Clearwater hatchery. To an outside evaluator, the close proximity of the Clearwater and Dworshak 

LSRCP programs suggests that the programs should be combined and administered jointly with 

an overall goal-setting process. A key question is how many fish should be used to meet longerterm mitigation goals before immediate harvest is pursued. 

C. Tucannon 

I. INTRODUCTION 
333 

The Tucannon Hatchery functions jointly with Lyons Ferry Hatchery as a rearing facility. Fish for 

broodstock are trapped at the Tucannon Hatchery (excess fish marked and released above the 

trap), trucked to Lyons Ferry Hatchery and held until spawning. Rearing through the fingerling 

stage is at the Lyons Ferry Hatchery, when the fish are transported to the Tucannon Hatchery for 

rearing. Pre-smolts are moved to Curl Lake for acclimation before release as smolts. 

It was estimated during mitigation negotiations that 2,400 Chinook salmon historically returned to 

the Tucannon River, and that the mitigation goal for the two Snake River dams below the river 

would consist of a goal of 1,152 returning adult fish. It was also assumed that 4,608 adult salmon 

(1,152 x 4) would be harvested below the project area. The expected SAS was 0.87%, so that 

132,000 smolts would be needed for the program to meet LSRCP mitigation goals. 

II. DATA 

Data presented to evaluate success consisted of broodstock performance (% prespawn 

mortality), in-hatchery plus acclimation survival, number of smolts produced and released, redd 

counts above and below weir, percent of the run that is natural fish, hatchery origin and natural 

escapement to the Tucannon River, strays and recoveries in various downriver and ocean 

fisheries, run timing of hatchery and natural adults, smolt emigration timing, smolt-to-adult survival 

rate (SAS), smolt to adult return (SAR) by origin (natural, hatchery), percent survival of smolts 

versus fish size at release, and progeny per parent ratio (hatchery and natural). Comparisons of 

hatchery versus natural versus captive broodstock fish were made for several life history traits, 

including age composition, fecundity, egg size, and reproductive effort. Several correlative 

analyses were also conducted in an effort to assess density dependence and factors leading to 

the suppressed natural production. 

III. KEY FINDINGS 

1. Fish performance in the prespawn, hatchery, and presmolt acclimation phases was 

documented and appears to be adequate. It was all native broodstock; marked strays 

were removed from the system. Pre-spawn mortality of adults has been greatly reduced 

(<10%) by holding the fish at Lyons Ferry Hatchery. Eyed egg-to-smolt survival from 2005 

to 2008 has exceeded 90%. The number of smolts produced has approached the 132,000 

goal but is well below the revised 225,000 goal designed to meet mitigation losses at 

existing SAS rates. There was some information presented to indicate that smolt survival 

may improve by releasing larger smolts. Disease issues were not a major impediment. 

2. Although fish culture performance was within expected standards, survival of hatchery fish 

as measured by SASs and SARs was not. Although SARs met the 0.87% goal in 1997, 

SARs over the most recent 5-year period has ranged from approximately 0.10-0.30%. 

Natural SARs were several times higher than hatchery SARs. 

3. The program was operating well below expectations in terms of mitigation goals. At current 

mean survival rate of 0.21%, it would theoretically take more than 500,000 smolts to meet 

the mitigation goal of 1,152 fish. 

4. Released smolts were showing erratic and low survival rates. Measures of these survival 

rates and other life history aspects (size, age at return, etc.) seems appropriate, although 

the information provided was not sufficient to provide much insight as to why overall 

survival was so low. 
334 

5. The ecological and genetic impacts of the programs on wild fish are shown primarily 

through comparisons of life history characteristics between hatchery and wild fish. The 

percentage of precocious males may reduce adult returns. Adult hatchery fish had a 

younger age composition and earlier migration timing than wild fish. 

6. Information was provided on the possibility of residualization and male precocity from the 

increasingly large smolt releases and potential effects on wild fish. Residualization (minijacks) is an issue deserving more study. Effects of mini-jacks on SARs should be 

evaluated. 

IV. OUTLOOK AND RECOMMENDATIONS 

Under existing habitat conditions, the long-term outlook for successfully meeting project area 

mitigation objectives is not favorable. While fish culture performance was within standards 

expected for salmonids in general, the low SARs indicate that existing approaches for rearing and 

releasing smolts do not result in fish capable of returning as adults to the Columbia River and 

Lower Granite Dam in numbers sufficient for meeting existing LSRCP mitigation goals. Although 

releasing more and larger smolts may provide returns closer to goals, the much lower SARs for 

hatchery fish than wild fish are causes for concern (and even the wild fish are not replacing 

themselves in most years). Releasing larger smolts may also increase residualization of the 

incidence of min-jacks. The lack of adult replacement along with the bimodal (biseasonal) 

emigration timing of wild fish suggests that their historical life history may have involved some of 

the stock rearing to smolt size in the Tucannon River, but another segment, and perhaps the 

larger portion, emigrating early and rearing in the Snake River mainstem for several months or 

more prior to smoltification. The reduction in this life history (low survival in response to mainstem 

modifications) may be the cause of wild fish remaining below replacement in most years. 

Proposed instream habitat improvements may improve survival of natural fish to some extent. 

Field evaluation of potential density dependence should be included in the evaluation of this effort. 

D. Genetic Analysis of Tucannon 

I. INTRODUCTION 

The Tucannon River is a tributary of the Snake River in southeastern Washington. In 1985, the 

spring Chinook supplementation program was initiated in the Tucannon River by capturing wild 

endemic adults and spawning them at the Tucannon River Hatchery. By 1989, the hatchery was 

integrating natural and hatchery-origin spring Chinook in the broodstock and both natural and 

hatchery-origin spring Chinook were naturally spawning in the river. 

Spring Chinook in the Snake River basin (including the Tucannon River) were listed as 

Endangered in 1992 by NMFS; however, the status was changed to Threatened in 1995. Adult 

returns declined precipitously during the mid-1990s and a captive brood program was proposed 

by WDFW and the co-managers in addition to the supplementation program that began in 1985. 

The captive broodstock program began in 1997. 

The hatchery programs in the Tucannon River (supplementation and captive brood) are being 

conducted with the possibility that artificial propagation may have negative effects on the genetic 

profile of spring Chinook in the Tucannon River. The genetic effects could result in fitness loss 

and reduced reproductive success. 
335 

This study used microsatellite DNA analysis to evaluate spring Chinook from three spawner 

groups (in-river spawners; supplementation spawners, and the captive brood program). Analyses 

of natural- and hatchery-origin fish were also used to determine the impacts of spawner group in 

addition to spawner origin. Analysis was conducted on collections from 1986, 1997 – 1998, and 

2000 – 2008. The collection from 1986 was prior to the return of Chinook that were produced by 

the supplementation program and was therefore a collection of the wild endemic stock. Analysis 

of the 1986 collection provided a baseline measure of the genetic diversity of Tucannon River 

spring Chinook prior to the supplementation program and allowed evaluation of genetic changes 

over 12 years including the time of the captive brood program in the Tucannon River. 

II. DATA 

Data and methods were adequate for the questions being addressed in the project. A total of 

2,545 samples were analyzed at 14 microsatellite loci (13 coastwide GAPS loci plus Ssa-197). 

Eight different groupings of samples were analyzed to determine if there were genetic differences 

among hatchery or natural-origin samples, in-river, or supplementation samples, and the captive 

brood, as long as for differences among brood years or collection years. 

III. KEY FINDINGS 

The results of the genetic analysis in the Tucannon River suggested that genetic diversity of spring 

Chinook salmon has not changed as a result of supplementation or the captive brood program. 

While the initial analysis showed many significant differences among the various Chinook 

samples from the different collections, variation occurred primarily around the year of collection 

and did not show patterns of change over time. 

Analysis was conducted on the supplementation and in-river collections by collection year and by 

brood year to determine if genetic changes were a result of individuals from different brood years 

spawning together. Overall, there were no differences between the analysis of the collection years 

and brood years (one locus for one collection not in Hardy-Weinberg equilibrium and low number 

of loci comparisons with significant linkage disequilibrium). 

Hatchery and natural-origin samples were also analyzed to determine if there were any genetic 

differences that resulted between individuals that had different origins. The results of the analysis 

by collection year and brood year did not reveal any patterns in the genetic differences among 

collections that could be attributed to differential survival of the genetic ancestries. The differences 

that were detected were from differences that occurred among the collection years. 

Finally, the factorial correspondence plots of mean values for the temporal in-river and 

supplementation collections with the natural origin collection from 1986 showed that the 

collections were differentiated, but that the results for the collection from 1986 laid between the 

groups of the other temporal collections. The genetic diversity of these collections has therefore 

not been altered from the 1986 natural-origin collection but maintained a genetic difference that 

existed among years. This suggests that the supplementation and captive brood program have 

not homogenized any of the spawner groups because they remain grouped with the collections 

based on their spawner group or origin. 

IV. OUTLOOK AND RECOMMENDATIONS 

This study documented a thorough and systematic examination of the genetic profile of the 

natural-origin Chinook stock based on 1986 samples, prior to initiation of the supplementation or 
336 

captive brood programs, and in-river, supplementation, and captive brood lines after the 

program’s start. While the analyses documented many differences among the different groups, 

differences appeared to be primarily related to broodyear or year of collection and not to the 

genetic divergence of the three groups. 

Consequently, from this point forward, a reduced genetic sampling program (reduced in scale, 

frequency, and perhaps relying on key genetic markers) should be sufficient to monitor the 

program and detect divergence among the three groups, should that start to occur. 

Adult returns of Chinook salmon and smolt-to-adult return rates (SARs) to the Tucannon River 

appeared to be following the same patterns observed elsewhere in the Salmon and Clearwater 

systems. Programs appeared to be producing adequate numbers of smolts, but failed to return 

adequate numbers of adults. This study is of limited value in addressing the perplexing question 

of why recruitment of natural adults remains below replacement or why SARs are so much lower 

for hatchery fish than natural fish. 

3. Grande Ronde 

A. Grande Ronde Spring Chinook Captive 

I. INTRODUCTION 

The introduction and background information clearly defined the stock status and history, and the 

experimental approach where parr were collected as captive broodstock (three streams). Success 

will be determined by a positive change in natural origin returns. That stage has not yet been 

reached. Natural origin abundance declined to zero in some of the tributaries prior to the study – 

no reason was given, where there should have been. Trends in Chinook abundance indicated a 

clear delineation of the 1976/1977 and 1989 ocean regime shifts as likely causes in the trends in 

abundance (this was not discussed). Nine management objectives were tabled which related to 

the captive brood stock (CBS) work. 2010 was the last year of CBS; the work transfers now to a 

Safety Net Program (not well defined or referenced, and should be). 

The Captive Brood Program in the Grande Ronde subbasin was designed to increase survival of 

hatchery-spawned parr to adulthood by retaining the fish in captivity through maturation and 

spawning instead of releasing them through the hydrosystem, thereby assuring that sufficient fish 

would be available (“return”) for broodstock for transitional development of a conventional 

hatchery program. It was designed to prevent extinction of the Catherine Creek, Upper Grande 

Ronde, and Lostine populations. Other objectives were to maintain genetic diversity of the 

artificially propagated fish and of the indigenous wild fish in the Minam and Wenaha Rivers. The 

approach was used to develop and refine these methods for rapid recovery in situations where 

extinction is imminent and until causes of the precipitous natural declines can be identified. 

II. DATA 

Appropriate data for these analyses has been collected and reported, including metrics on 

numbers, size, sex ratio, fecundity, and recruitment. It is not clear if genetic analyses will be 

included. Methods were not described in detail but summary reports provided a description of 

methods, which may also be found elsewhere (a reference is required). 
337 

III. KEY FINDINGS 

Issues, both prophylactic and husbandry, related to collection of parr as brood stock and following 

through to adults, spawning and release of CBS smolts, then adult returns were addressed. Of 

particular note were BKD (impact was not excessive), lower fecundity (small size by 35%), and 

early-maturing males. This lower fecundity (57% of expected for age-4 and 40% of expected for 

age-5) led to fewer than projected numbers of smolts. Thus, smolt goals (150,000) were rarely 

obtained, and subsequent adult returns rarely exceeded the goal of 150 adults/stream. There was 

much lower recruits-per-spawner in CBS (1.5) than conventional hatchery returns (14.3). F1 fish 

showed an overall lower than expected percentage of older fish. F1 fertility and eyed egg-smolt 

survival were slightly lower than expected, but the main problem was a much lower SAR than 

assumed (0.1% versus 0.35%). Overall, fish performance was documented and appeared 

adequate. 

The program, with its combination of captive brood plus conventional hatchery, is operating well 

below expectations in terms of mitigation goals. Adult returns to Catherine Creek and the Upper 

Grande Ronde have not reached half of overall return goals in any brood years since 1998; in 

most years the return rate is a third or less of LSRCP goals. It does not appear that overall goals 

are achievable within the foreseeable future. 

While their fish culture performance were within standards expected for salmonids in general, the 

low SARs indicated that existing approaches for rearing and releasing smolts did not result in fish 

capable of returning as adults to the Columbia River and Lower Granite Dam in numbers sufficient 

for meeting existing LSRCP mitigation goals. Released smolts showed erratic and low survival 

rates. Measures of these survival rates and other life history aspects (size, age at return, etc.) 

seemed appropriate, although the information provided was not sufficient to give much insight as 

to why overall survival of natural, conventional hatchery, and captive derived smolts was so low. 

The ecological and genetic impacts of the programs on wild fish were not evaluated in the material 

provided. Please refer to programmatic comments for these issues. 

More detailed comment: 

Table 1. Please provide SD or SE along with mean survival and an indication of the number of 

years that data is available. Growth was 35% smaller — was this for same age of fish, or does 

this value reflect earlier age at maturation? 

Table 2. The low fecundity in the captive fish, especially among the older age fish is an interesting 

finding. There was no mention of whether eggs were smaller or larger than natural or conventional 

hatchery fish. 

There was good comparison of smolt-to-LGD survival among natural, CBS and CHP smolts. It 

appears survival was very low (~40%), and it is not clear from the report(s) why was survival of 

fish from the Lostine River was higher than from Catherine and Upper Grande Ronde. 

IV. OUTLOOK AND RECOMMENDATIONS 

This work must follow through to F2 to determine if CBS returns spawn successfully and contribute 

to smolt yield and adult return, as they acknowledge. The test that is needed is a comparison of 

NOR vs. CBS relative reproductive success through F2 and beyond. It is not clear that this is 

covered (requires genetic samples), although there is recognition of the need to measure through 
338 

to F2. Here, as in all LSRCP projects, there is more emphasis required on the limits to production 

outside of the subbasin, including ocean effects and harvest. 

Although this program did not meet smolt production objectives, overall it functioned as intended 

to stave off extirpation and get to the point where the conventional program could replace it. Its 

effectiveness in producing sufficient naturally produced adults (150) is not yet clear in the Upper 

Grande Ronde, but successes in Catherine Creek and the Lostine River suggest that meeting 

this goal is within range. 

Lower fecundity of captive fish might be addressed with better understanding of factors affecting 

growth of captive-reared versus fish in nature. The fecundity issue by itself seems like a problem 

that perhaps could be effectively addressed with a more productive feeding regimen. 

Although the captive program has functioned with some success at the original stages or the 

rebuilding process, the long-term prognosis of meeting LSRCP mitigation objectives remains less 

clear. 

B. Grande Ronde early years 

I. INTRODUCTION 

A brief, well-written introduction to the issues of Chinook in the Grande Ronde basin was provided. 

This is background historical material for related projects (detail provided in these elsewhere) and 

defines the monitoring and evaluation, which seems very much in order and capable of assessing 

problems and successes associated with the initial development of the Lookingglass Hatchery 

and Rapid River broodstock. 

Of note, the assumed harvest rate (80%, i.e., 4:1 catch to escapement ratio) prior to construction 

of dams seems much too high, at least on a long-term sustainable basis, even in a pristine 

watershed. This assumption and associated production goals were thus unrealistic. 

II. DATA 

The history of releases, returns, and survivals of spring Chinook salmon broodstock sources used 

in the Grande Ronde basin was well represented in graphs and tables for the spring Chinook 

hatchery program, 1978-1997 brood years. Shifts in the program and rearing strategy shifts away 

from parr and broodstock changes were well documented. 

III. KEY FINDINGS 

Recruits-per-spawner for all three populations were above 0.5 in only two of the eight years; a 

consensus was reached to move to native brood stock, including wild fish refugia and captive 

brood stock experiments. 

Conclusions were succinctly presented, for example: 

 Prior supplementation failed as indicated by low natural origin abundance. 

 Extinction risk was high based on population growth rate trends, low abundance of 

natural origin spawners, and low productivity. 

 There was significant genetic differentiation between hatchery and natural populations 

and between the Minam, Wenaha, Upper Grande Ronde, Lostine, and Catherine Creek 

natural populations. 
339 

 Hatchery programs using endemic broodstock should be initiated immediately in 

Catherine Creek, the Upper Grande Ronde, and Lostine river populations. 

 Given the uncertainties associated with use of artificial propagation to enhance natural 

production, they suggest a diversified approach (lower to higher risk) and maintain the 

Minam and Wenaha river basins as wild-fish management areas. 

A long history of non-local Chinook brood stock is reported. If there are samples available to 

evaluate how genetic characteristics of the natural stock may have changed over time, perhaps 

from tissue remaining on scale samples, this should be explored. Of interest is the question of

similarity or difference among the natural stock, the present hatchery stock, and the Rapid River 

stock. 

Fig. 7. Please define how the stray rates were calculated, or provide reference to these methods. 

Can hatchery practices be improved to improve homing and to reduce straying? 

IV. OUTLOOK AND RECOMMENDATIONS 

As they noted: “Preliminary results of the new hatchery programs are presented in separate 

papers. The true measure of success of these programs will be determined by the response of 

the natural populations, smolt survival, adult returns, and the ability to restore and sustain tribal 

and sport fisheries in the future.” 

This is a multi-agency project that seems well coordinated with an established monitoring and 

evaluation framework that has been effectively utilized towards appropriate adaptations, and 

should continue. 

Under existing habitat conditions the long-term outlook for successfully meeting project area 

mitigation objectives does not appear favorable. Adult returns have not exceeded one-fourth of 

the goals for the basin (5,820). Although releasing more smolts may provide returns closer to 

goals, the much lower SARs for hatchery fish than wild fish are causes for concern. 

C. Upper Grande Ronde Supplementation 

I. INTRODUCTION 

Objectives were clearly laid out. History and data trends were presented and interpreted. This 

was a good background description and listing of program objectives, including research and 

monitoring objectives. The program would benefit from having a habitat component so that habitat 

issues could be evaluated and addressed as needed to improve salmon survival rather than 

simply relying upon supplementation and hatchery production. These runs are severely 

depressed and all approaches for recovering the populations should be considered. 

 
340 

II. DATA 

No specific comments 

III. KEY FINDINGS 

In summary: 

1. Goals for smolt production have not been met because of low numbers of adult fish. 

2. Adult returns are less than 50% of goals. 

3. A strong relationship was found between number of spawners and smolts per spawner. 

4. Age structure of hatchery adults shifted toward younger fish compared to natural 

spawners 

5. Mean smolt survival to LGR was lower than desired for both hatchery and natural fish. 

The causes were not explored. 

Density dependent relationships at these low spawner abundances suggests habitat capacity 

issues exist. Fig. 15 suggests strong density-dependence: a sharp decline in smolts per spawner 

with increasing spawner abundance. This relationship should be followed carefully in the coming 

years. The report mentioned that EDT analysis did not predict density dependence at these low 

numbers. However, EDT is usually based on “expert” opinion. These data indicate additional effort 

is needed to evaluate habitat quantity and quality in the watershed. Is the decline in smolts per 

spawner associated with reduced growth of smolts, suggesting food limitation? Or is the decline 

related to early emigration of fry and fingerlings, suggesting limited habitat availability? These 

data highlight the need to include a habitat component in the Program, rather than simply relying 

on hatchery supplementation to “fix” the problem. Supplementation is only a short-term solution 

to be used when abundance is extremely low. 

Return per spawner of natural Chinook is exceptionally low. What fraction of this low ratio is 

related to smolts per spawner versus adults per smolt? If low productivity is indicated by low 

smolts per spawner, what measures might be taken to improve habitat? What is the size of smolts 

(and earlier fingerling migrants)? What is the timing of juveniles leaving the watershed? Is it 

associated with return per spawner? 

IV. OUTLOOK AND RECOMMENDATIONS 

It was concluded that there was no benefit apparent to natural smolt migration abundance or 

smolts per spawner (see slides 34 and 35, and recommendations listed in slide 36). 

This, and Catherine Creek, are comprehensive research programs with appropriate monitoring 

and adaptations as required that are managed effectively, with good reporting, and require 

continuation. Out-of-basin comments apply, and reasons for low survival of smolts to LGD 

warrants further research, along with further exploration of freshwater capacity. 

Based on the evidence presented, the supplementation program has not been successful and 

shows little sign of leading to increased abundance of natural fish. The decline in smolts per 

spawners as the number of spawners (mostly hatchery fish) has increased suggests that habitat 

in the river for this species is limited even at the low densities of fish present and that recovery is 

predicated on increasing instream productivity (see programmatic comments). The causes of this 

apparent density relationship are not explored. It is also of concern that inasmuch as the number 

of hatchery-reared fish allowed to move above the weir is not limited, that the remaining wild fish 

may have been compromised to no benefit. 
341 

The summary noted high pre-spawning mortality associated with the weir. Please report this 

annual mortality. Are these mortalities included as successful returns when calculating return per 

spawner and SAR? Has habitat degradation led to increased water temperature? Can anything 

be done to reduce high water temperature? Are cool water refuges available for spawners? 

The ISRP was pleased to see that the summary section stating that research has been initiated 

to better understand habitat characteristics that are affecting Chinook productivity. However, it 

would have been worthwhile to present the sampling approach for these studies so they could be 

considered in our review. It is good that the program realizes that hatchery supplementation is 

not the solution to the problem, rather factors affecting low survival of natural salmon must be 

identified and fixed if the natural run is to persist and eventually provide harvest. 

D. Catherine Creek Supplementation 

I. INTRODUCTION 

We compliment the presenters on excellent work. There was good background description and 

listing of program objectives, including research and monitoring objectives. The program would 

benefit from having a habitat component so that habitat issues could be evaluated and addressed 

as needed to improve salmon survival rather than simply relying upon supplementation and 

hatchery production. These runs are severely depressed and all approaches for recovering the 

populations should be considered. Factors such as limited overwinter habitat have the ability to 

generate density dependent responses (Van Dyke et al. 200914). The relation between fish 

responses and habitat issues should be explored more closely. 

III. KEY FINDINGS 

In summary:

1. Goals for smolt production were close to being met. 

2. Adult returns were less than 50% of goals. 

3. A strong inverse relationship was found between number of spawners and smolts per 

spawner. Also a strong inverse relationship between percent hatchery fish and smolts 

per spawner. 

4. Age structure of hatchery adults was shifted toward younger fish compared to natural 

spawners. 

5. Mean smolt survival to LGR was much lower than desired for both hatchery and natural 

fish. The causes were not explored. 

Smolt-to-LGD survival was lower in Catherine Creek compared with all other stocks, and this 

needs further exploration. The report mentions that timing of hatchery smolts is somewhat earlier 

than natural smolts. Are hatchery smolts larger than natural smolts? It would be good to compare 

length frequency distributions of hatchery and natural smolts in Catherine Creek and in other 

watershed. Are some fish migrating downstream as subyearlings in fall and winter? If so, these 

findings should be described. How does early emigration affect survival rates? Are early 

emigrants less successful after accounting for their younger age compared with smolts? 

 

14 Erick S. Van Dyke, D.L. Scarnecchia, B. C. Jonasson, and R. W. Carmichael. 2009. 

Relationship of winter concealment habitat quality on pool use by juvenile spring Chinook salmon 

in the Grande Ronde River Basin, Oregon USA. Hybrobiologia 625:27-42. 
342 

What percentage of propagated releases are visually marked or tagged? 

Straying into the Minam and Wenaha rivers declined significantly after switching from non-local 

to local broodstock. Is broodstock the sole reason for lower straying? Methods to reduce straying 

are important. 

The ratio of recruits per spawner of natural Chinook is well below 1, indicating that the natural run 

is declining. Continued natural spawning by hatchery fish perhaps keeps the natural run from 

perishing. On the other hand, a number of studies indicate interbreeding of hatchery and natural 

spawners leads to reduced fitness of the natural stock. Is Catherine Creek a situation where 

interbreeding of hatchery and wild fish reduces survival of the spawning fish but continued 

introduction of hatchery fish into the spawning areas maintains the less-fit natural population? 

This is an important question that should be addressed soon. 

Fig. 16 suggests strong density-dependence: a sharp decline in smolts per spawner with 

increasing spawner abundance. This relationship should be followed carefully in the coming 

years. Density dependent relationships at these low spawner abundances suggests habitat 

capacity issues. These data indicate additional effort is needed to evaluate habitat quantity and 

quality in the watershed. Is the decline in smolts per spawner associated with reduced growth of 

smolts, suggesting food limitation? Or is the decline related to early emigration of fry and 

fingerlings, suggesting limited habitat availability? These data highlight the need to include a 

habitat component to the Program, rather than simply relying on hatchery supplementation to “fix” 

the problem. It is also possible that interbreeding of hatchery and wild salmon has lowered the 

survival of natural spawners (e.g., Fig. 17). An experimental approach may be necessary to 

evaluate whether smolts per spawner declines with increasing contributions of hatchery 

spawners. 

Fig. 18. Please report age composition for male and female salmon because females tend to be 

older on average and these larger fish carry more eggs. If hatchery females carry fewer eggs, on 

average, to what extent does this influence the smolts per spawner relationship in Fig. 16? What 

influence does average female age have on Fig. 16? Is fecundity at age available for this stock? 

Fig. 21. Hatchery strays have been quite low in the Minam and Wenaha rivers since 2002. How 

does survival of smolts from these two systems (to LGD and overall) compare with that of 

Catherine Creek and Upper Grande Ronde where supplementation is high? Do these two river 

show strong density-dependence relationships? Is the ratio of recruits per spawner greater than 

1? It is important to monitor, evaluate, and compare these rivers where supplementation has been 

much less. How do these populations persist when so few hatchery fish spawn in the rivers? Is 

habitat quality better? If so, and the natural population is sustainable, then a key step for rebuilding 

populations in Upper Grande Ronde and Catherine Creek would seem to be habitat rehabilitation. 

What efforts are being made to address habitat issues in the basin and how does the hatchery 

supplementation program integrate and coordinate their actions with habitat efforts? Alternatively, 

these populations are limited largely by survival from smolt-to-adult. These life stage survival limits 

require further attention. 

IV. OUTLOOK AND RECOMMENDATIONS 

Based on the evidence presented, the supplementation program has not been successful and 

shows little sign of leading to increased abundance of natural fish. The decline in smolts per 

spawners as the number of spawners (mostly hatchery fish) has increased suggests that habitat 

in the river for this species is very limited even at the low densities of fish present, and that 
343 

recovery is predicated on increasing instream production. The potential for sufficiently increasing 

instream production is not clear. The causes of this apparent density relationship were not 

explored, and should be. Based on data presented, there is a serious supplementation bottleneck 

in this system that must be circumvented before gains will be made. 

The report should have provided more information on efforts to evaluate the effect of habitat 

conditions on Chinook productivity. More complete monitoring and evaluation of Minam and 

Wenaha rivers is needed because these rivers have received few hatchery fish since 2002. Is 

productivity also low in these two rivers? Although data were not presented, it appears that 

productivity is likely much higher in the Minam and Wenaha rivers simply because the populations 

are persisting without supplementation. More complete monitoring (e.g., spawner and smolt 

production) of these two rivers and comparisons with existing supplementation projects and 

habitat efforts may help evaluate key factors affecting survival of these populations in the Grande 

Ronde basin. 

4. Lostine and Imnaha 

A. Lostine Supplementation 

I. INTRODUCTION 

The introduction is clear in explaining the project relationship with the LSRCP, the watershed 

characteristics, and the use of artificial production technologies to increase adult spring Chinook 

abundance first by efforts to develop a Captive Brood Program to protect the stock from 

extirpation, and then shifting to a conventional hatchery program designed ultimately through 

supplementation to increase the number of natural spawners to 1,716. 

Suggestions for additions and clarification in the report follow: 

1. Program Overview: Provide the year(s) different artificial production activities began in 

the Lostine River. 1995 is mentioned, but it is not clear whether that is a first year of 

brood stock collection, release of smolts, capture of parr for the captive rearing, etc. 

2. There is a short-term goal of returning 250 adults from the hatchery program (page 2). 

The anticipated disposition of those fish in terms of natural spawning, retention for 

broodstock, and harvest should be provided. The report is not clear on whether there 

was anticipation that some natural production would also be taking place during this 

time-period. How was the transition from short-term abundance of 250 individuals to the 

mid-term abundance of 500 hypothesized to proceed? 

3. Page 3. “The benefits that were expected with supplementation were higher egg-tosmolt survival and harvest opportunities.” The higher egg-to-smolt survival is a measure 

of within hatchery performance of the program, and yield to harvest would be a measure 

of benefit after fish are released. Were there benefits anticipated from the natural 

spawning of an increased total abundance of adults as a consequence of the hatchery 

program? The background section reads as though there are conservation justifications 

for beginning the program, but the sentence on benefits does not seem to explicitly 

include any. 

II. DATA 

There is a good presentation of SARs, SASs, spawner abundance, natural smolts per spawner, 

recruits per spawner results to date, including graphs. 
344 

Suggestions for additions and clarification in the report follow: 

1. Figure 11. Natural smolts per spawner. This relationship should be expanded to consider 

smolts-per-spawner as a function of the number of female spawners. This would give a 

preliminary consideration of density dependence in this tributary population. Is there 

evidence of sufficient smolt rearing capacity in the Lostine River to anticipate 

restoration? Is return year on figure 10 equivalent to brood year on figure 11? If so, 

inspection suggests the years of increased total spawning abundance (2001 – 2005) 

produced fewer smolts per spawner than years with fewer adults (2000 and 2004). 

2. Figure 12. Adult recruits per spawner. It is not clear whether this is female to female or 

total adult abundance to total adult abundance. The critical relationship would be egg to 

egg, but female to female would be sufficient. Adult recruits per spawner appear to be 

fewer in years with more adults spawning. This river system may already be exhibiting 

density dependence. 

3. Provide a summary of the percent hatchery and natural adults in the broodstock and in 

the spawning escapement for each brood year, and PNI for the program. Also, indicate 

the operating parameters for the program and whether the program has been able to 

meet that guidance. 

4. An analysis evaluating the supplementation similar to the Imnaha program analysis is 

required. 

III. KEY FINDINGS 

The midterm escapement goal was reached for hatchery fish. Smolt release targets were not 

reached in the first four years due to a lack of sufficient number of broodstock – reached by 2005. 

Recruits per spawner for wild spring Chinook has been less than one since the 2001 brood year. 

While there was a substantial survival difference between wild and hatchery smolts, there was no 

difference in adult size-at-age (what about within sex?) nor in spawning location. Stray rates of 

hatchery fish appeared low (3%) and disease issues were few and seemed minor. 

Natural fish survived at higher rates than both hatchery groups except in 2002. The number of 

adult returns was increased, allowing a harvest. It is not clear if wild fish were harvested 

incidentally or otherwise in the tribal, sport, or other fisheries. 

IV. OUTLOOK AND RECOMMENDATIONS 

A summary of the HSRG recommendations and program managers’ actions in response to those 

recommendations should be added. 

No analyses of natural production in response to the supplementation treatment (hatchery-origin 

adults spawning in the Lostine River) and this is required to assess benefits. There is no evidence 

of an increase in wild adult abundance that can be associated with supplementation. There is 

possibly a decline, but cannot separate ocean effects from supplementation effects in the 

analysis. Need to explore RRS, as well as mortality evident in the smolt migration to LGD and 

beyond – the key limit to population viability that likely cannot be fixed with a hatchery. Harvest 

issues may also require further exploration if wild stock are included. 

The main benefits to the Lostine River program have been the returns of sufficient fish to provide 

some Tribal harvest opportunities in the river and some below LGR. There was no information 

provided to indicate that the program is meeting LSRCP goals for rebuilding natural runs. 

Recruitment of natural fish remains well below LSRCP targets. 
345 

B. Imnaha Supplementation 

This report is well prepared and should serve as a format for other reports/programs that involve 

supplementation and reintroduction efforts.

I. INTRODUCTION 

No specific ISRP comments or suggestions. 

II. DATA 

No specific ISRP comments or suggestions. 

III. KEY FINDINGS 

1. Pre-spawn mortality and hatchery egg to smolt survival were within acceptable limits. 

2. Smolt production was near or exceeding goals in most years; smolt survival goals to 

LGR were high compared to other Grande Ronde and nearby areas. 

3. SARs sufficient for hatchery fish returning to provide tribal and sport fisheries. Even with 

the observed SARs, SASs was not sufficient to provide the LSRCP goals for ocean and 

lower Columbia River harvest. 

4. No observed trend in abundance of natural spawners since supplementation began; 

natural recruits per spawner remains low. Natural fish production decreasing since 

supplementation began. BACI analysis suggests that supplementation has not improved 

adult abundance. 

A final conclusion on the effect of the program on natural adult abundance and productivity is not 

provided. Arriving at reasonable inference on the program’s effects on these vital statistics is an 

important next step. This information would contribute to evaluating the programs effect on the 

viability of the natural population. The results that are presented are not encouraging and do not 

appear to provide empirical justification for expanded supplementation of spring Chinook. 

IV. OUTLOOK AND RECOMMENDATIONS 

A section summarizing the HSRG and USFWS hatchery review findings and how they are 

reflected in project management would improve the presentation. 

The analysis begs the question of whether hatchery production should be scaled to meet harvest 

needs only, and at the least, to the productive capacity of the system for freshwater rearing, since 

there is no evidence that wild production benefits from supplementation. 

The Imnaha hatchery program per se has been more effective in meeting many of the interim 

goals of the LSRCP than most other spring Chinook programs. Most of the other systems in the 

LSRCP have not even been able to meet hatchery production objectives, and some have resorted 

to captive brood programs. Unfortunately, the analysis to date also reveals that the 

supplementation efforts have not resulted in an increase in abundance of natural spawners. This 

is cause for concern about the prognosis of the entire supplementation strategy. Although several 

causes for the failure of the hatchery program to have been hypothesized, the specific causes 

remain unidentified for this system. Until these causes are indentified, the prognosis for the 

program meeting LSRCP objectives is not good. 
346 

C. Size at release Imnaha 

I. INTRODUCTION 

The Imnaha River has historically supported spring Chinook salmon with documented larger size 

and later age at maturity than neighboring stocks. One key objective of the LSRCP is to develop 

a program where returns of hatchery fish and natural supplemented fish mimic the age 

composition of the original wild population. The shift toward younger age at maturity and the desire 

to optimize size at release led to an evaluation of optimal size(s) at release. 

The Imnaha supplementation program has three objectives that pertain to the investigation in this 

report – minimize impacts of the hatchery program on resident stocks; maintain the genetic and 

life-history characteristics of natural Chinook salmon populations in the Imnaha River; and operate 

the hatchery program so that genetic and life-history characteristics mimic those of wild Chinook. 

Age composition in hatchery-origin spring Chinook salmon is typically different from the natural 

populations from which they were derived. Age of maturation is usually earlier (younger) in 

hatchery-origin salmon – resulting in more three-year old females and fewer five-year old females 

compared to the natural counterpart. 

The introduction does not provide an explanation for why there is an objective of having a hatchery 

program that mimics the life-history characteristics of the natural population. The objective of 

maintaining the genetic and life-history characteristics of the natural population are not explained 

either, but are largely self-evident: as a first principle, long-term viability of the natural population 

is presumed to require maintaining the evolutionary potential of the population. Superimposing a 

hatchery program on the population will influence the state of the evolutionary potential, and 

conducting the program in such a way that it does not critically compromise the potential for future 

evolution is important. One way to limit deleterious effects is believed to be maintaining genetic 

similarity between the hatchery and natural population. 

It is less self-evident why life-history characteristics of the hatchery population should mimic the 

natural population. Some characteristics, like run- and spawn-timing are likely essential for 

reproduction in the hatchery and natural environment, so these are very important. Similarly, 

characteristics like precocious male maturation, mini-jacks, and jacks, might strongly influence 

the total biological yield from the hatchery exercise. While the observation of earlier age of 

maturation is interesting and worthy of study, it is not explained how this alteration affects the 

dynamics of either the hatchery program or the natural population. 

An essential issue is whether the age structure difference is being accompanied by underlying 

genetic modification of the hatchery population, and to what extent the natural population may be 

modified by interbreeding between natural-origin and hatchery-origin adults, both in the hatchery 

and in the natural settings. The experimental design employed in these investigations is unable 

to provide insight into this important issue. It would be helpful to briefly elaborate on these 

concepts in the introduction. 

II. DATA 

Data measured included juvenile survival to Lower Granite Dam, age composition and survival of 

adults, SARs, SASs, and returns per 10 kg of smolts produced. 
347 

Smolts were divided into two size groups, large and small. However, page 4 text does not actually 

describe how groups of large and small smolts were established and does not describe how CWT 

groups are established. How CWT data was used is explained adequately. 

III. KEY FINDINGS 

1. Releasing larger smolts did not confer any advantage over releasing smaller smolts 

under existing habitat and transportation schemes. 

2. Size of smolt did not seem to be a factor influencing the age at maturity of the adults. 

3. For reasons of space and cost releasing more, smaller smolts results in a greater return 

of adult fish per weight of smolts produced. 

The ISRP has no concerns with the interpretation of the data or analysis. 

IV. OUTLOOK AND RECOMMENDATIONS 

A statement was provided on spreading the risk by releasing both large and small smolts. Based 

on their evaluation, their conclusion to not raise just larger smolts but to raise a broader range of 

smolts to spread the risk seemed appropriate. It is not evident how hatchery practices are modified 

to produce a specific mix of large and small smolts or how managers are integrating the findings 

into specific actions. It would be useful to indicate whether this research is being continued. 

The ISRP encourages the authors to submit the findings for publication. This may require 

additional replication (see Bilton et al. 198215). 

D. Reintroduction of Spring Chinook Salmon in Lookingglass Creek: Analysis of Three 

Stocks Over Time 

I. INTRODUCTION 

This was a well-prepared report that defined the issues, objectives, methods, and results for work 

involving re-introduction of spring Chinook. Adult returns were from smolt releases that were 

progeny from Catherine Creek captive broodstock (collected as parr), a stock that is likely more 

closely related to the extirpated population than the Rapid River hatchery stock used previously. 

Three comparisons of numerous population metrics were possible, including natural production 

from endemic stock (1963 to 1974), production from Rapid River broodstock (1992 to 2000), and, 

since 2001, Catherine Creek captive broodstock. Metrics for comparison were appropriate and 

included a full list: adult returns at the weir, spawning, parr, tissue samples for genetic analyses, 

parr to LGD survival, total outmigrants, outmigrants/redd by season, juvenile growth, survival, 

migration timing, progeny/parent ratios, and smolt/adult ratios. These results were nicely 

summarized in graphs and tables. The authors acknowledged that results were preliminary and 

that differences may have been also due to environmental conditions in the ocean (note that 

difference in freshwater conditions may also accompany regime shifts). 

Reintroduction of spring Chinook to Lookingglass Creek to establish a self-sustaining viable 

population was the long-term objective. The success will be a function of the productivity and 

 

15 Bilton, H. T., D. F. Alderdice, and J. T. Schnute (1982). Influence of time and size at release 

of juvenile coho salmon (Oncorhynchus kisutch) on returns at maturity. Canadian Journal of 

Fisheries and Aquatic Sciences 29: 426-447. 
348 

capacity of the freshwater environment, which was stated as healthy and unaltered over the study 

period. Specific comments: 

1. Figure 1: the percent of redds in different streams in the two time periods needs to reflect 

hatchery-origin adults in the later time period. The implication of the figure is that LGC had 

the second greatest redd counts in the 1965 – 1981 time period, but not in the 1982 – 

1991 period. And that this reduction represents loss to the entire system. However, if many 

of the redds in other locations are from hatchery fish spawning in unproductive habitat that 

do not yield progeny, the redd count observation is less useful in establishing what might 

be expected in the current environment. 

2. Abundance and productivity of the “endemic” stock during the 1960 – 1980 time period is 

more appropriately considered a “reference” rather than a control. In this particular data 

collection, two things are being evaluated: first is the potential of the environment in 

Lookingglass Creek to provide conditions for survival of adults to spawning, adequate 

spawning gravel, and conditions for juvenile rearing and growth; second is the 

performance of the Catherine Creek stock in this specific environment. The two elements 

are confounded experimentally. 

II. DATA 

While data collection from weirs and surveys was summarized and data to date was analyzed, 

the ISRP provides suggestions below that are intended improve an otherwise nicely-prepared 

report. 

Paragraph 2 page 5. Provide a table or figure with the numbers of hatchery and wild fish released 

above the weir for each year. This would clarify the first sentence that states that 56-66% of the 

fish have been natural-origin in later periods. 

Neither figure 2 or figure 4 identified the “Units” in Lookingglass Creek. Please identify these in 

figure 2 and present the data in figure 4. Reference to figure 4 should be to figure 5. Please 

elaborate and explain the statement: “Differences in release time and location for upstream 

spawners can affect redd distribution.” 

Provide the actual estimates of different classes of outmigrants that are discussed qualitatively 

on page 7 following figure 5. The comparison of smolt per redd across eras should be adjusted 

by spawner density. Rather than smolt per redd, develop a regression of smolts per redd or smolts 

per female, as a function of spawner (or female) abundance. This will facilitate establishing 

whether contemporary capacity is similar to capacity in the 1960s and 70s. 

Provide the actual data used to estimate the recruits per spawner. It would be useful to identify 

for each broodyear the numbers of fish released to spawn, their composition (natural and 

hatchery), the outmigrant production from that spawning (parr and smolts), and subsequent 

natural adult production. Are the recruits per spawner female to female? The Catherine Creek F1 

appears greater than one. If this is the case across multiple year-classes, the stock should rebuild 

without long-term supplementation. 

III. KEY FINDINGS 

The critical issue is whether the empirical data from the natural spawning of Catherine Creek 

adults suggests that habitat and environmental conditions in Lookingglass Creek are sufficient for 

reintroduction and reestablishing a self-sustaining population. Outmigrants/redd from the captive 

brood and supplementation experiment nearly matched previous endemic values, suggesting a 
349 

well-designed reintroduction might lead to reestablishment of a self-sustaining natural population. 

However, a look at the total spawners, comparing endemic versus Catherine Creek brood, 

suggests high numbers of spawners did not always yield high numbers of outmigrants. In other 

words, density dependence may be occurring at relatively low spawner density, and/or this value 

has changed over time. Regardless, a closer look at the time-stratified recruitment is required, a 

factor which may confound this analysis. Beyond the limits of the freshwater environment, and 

resulting a further lowering of parent:progeny ratios to values barely above replacement, SARs 

by 2004-5 were ~1.5%, indicating a limit in the ocean life stage. 

IV. OUTLOOK AND RECOMMENDATIONS 

The conclusion section should identify whether this program was reviewed by the HSRG or the 

USFWS hatchery review, and if it was, state how the program implementation reflects the 

recommendations of the reviews, or how it will do so in the future. The HSRG suggested the ESA 

status as extinct, but that the productivity and capacity of the habitat was 3 and 200, respectively. 

This suggests there is uncertainty about these estimates, since this report suggests 1.5 and 500. 

A review is required. They also suggest productivity could increase from 1.3 to 2.8 without 

hatchery fish, thus a viable population may result in the longer term. Projections into the impact 

of climate change may also be useful in planning around these values. 

Given the marginal nature of the recruitment in its current state, it is perhaps premature to suggest 

that there seems real potential for successful re-introduction with the captive brood 

supplementation. There will be need to adapt to a sliding-scale broodstock approach, which 

remains experimental. Continued hatchery production may provide tribal harvest, but this should 

be carefully managed such that “wild” production is not compromised. Continued and careful 

monitoring and broodstock selection will be necessary to confirm the development of a selfsustaining population. 

Limits to production are also evident below LGD, and are likely oceanic – SARs are lower than 

anticipated and currently limit returns. Despite relatively high yield of outmigrants, suggesting near 

capacity production of juveniles from the unaltered habitat (the outmigrant capacity is unclear at 

this point, and requires further analysis), adult returns remain low, and recruits per spawner are 

marginal, and only slightly >1. Sources of mortality below LGD should be explored more 

thoroughly. 

Although the comparisons used in this study may prove instructive, the issue of three “treatments” 

that did not occur not over the same time period poses some major problems for interpretation. 

No evidence was provided that supplementation with the Catherine Creek stock will result in any 

different responses than seen elsewhere in the Grande Ronde and Imnaha basins. The main 

issue in question seems to be how much of an increase or decrease in natural production can be 

seen with the captive brood approach compared to previous endemic values and use of hatchery 

brood fish, and that information was not presented in a convincing manner, nor could it be, due 

to the differences in time period. The important point is that there are now some natural-origin fish 

returning from which brood stock can be selected, and the program can move on using the sliding 

scale. 

Comments on Appendix 1. Draft Lookingglass Creek spring Chinook 

salmon management plan. 

Adult return goals. The statement that restoration of a genetically-independent Lookingglass 

Creek spring Chinook population to viable status is not necessary to achieve viable status of the 
350 

Grande Ronde Major Population Group should be attributed to a reference or identified as an 

assumption of the management plan. Discuss whether restoration of Lookingglass Creek with 

Catherine Creek Independent Population spring Chinook makes any difference in the status of 

the Grande Ronde MPG. 

Juvenile production and releases. The rationale for the release numbers in Lookingglass Creek 

should be based on habitat capacity and harvest goals, but we did not see this. Please provide a 

revised estimate of the estimated productive capacity of Lookingglass Creek and explain how it 

is reflected in the natural and hatchery management. 

Weir Management. Table 2, defining the pass or keep disposition of returning adults, should 

reflect the HSRG recommendations (or explain otherwise), and identify whether the fish kept or 

passed are hatchery or natural origin. Please indicate if this is the case. Do the fish that are 

recycled into lower Lookingglass Creek spawn, and if so, how would this complicate the 

assessment of the reintroduction program? We assume it does not – please correct if otherwise. 

Broodstock management. There are several biological uncertainties embedded in the program, 

and it would be beneficial to explicitly identify them and develop management guidance for 

addressing them in a short- and long-term adaptive management effort. The extent to which wild 

fish need to be parents in a broodstock for reintroduction is unknown. Whether the 30% guideline 

is too large or way too small is uncertain. The proportion of a natural population (either absolutely 

or at different levels of abundance) that can be removed to provide broodstock without 

compromising the viability of the population is not well investigated by the fisheries biology 

community. The 25% guidance may be too liberal, especially in years with small natural 

abundance. Finally, the strategy of backfilling a shortage of natural-origin adults with hatcheryorigin adults to maintain a target smolt production level has poorly investigated consequences for 

reintroduction success and for the primary biological characteristics of the integrated 

hatchery/natural population. Backfilling will likely slow down adaptation to the natural 

environmental conditions by having hatchery-adapted parents predominating in both the hatchery 

environment and the natural spawning aggregate. The current state of the science to deal with 

these uncertainties is via the HSRG review and recommendations. Please state how these 

recommendations will be incorporated into future plans. 

5. General Topics and Program Roll-Up 

A. Benefits of Culling for Bacterial Kidney Disease (BKD) 

Culling female Chinook salmon with high ELISA optical density scores (ELISA ODs) together with 

segregation of eggs and progeny from high ELISA OD females when culling is not 

demographically advisable has been satisfyingly successful in reducing Bacterial Kidney Disease 

as an impediment to hatchery production of healthy Chinook salmon smolts. Despite historical 

failures in developing vaccines and less than complete control of this intracellular bacteria with 

antibiotic, this application of ELISA-based detection of the pathogen (coupled with culling or 

segregation of the offspring of infested females has had worthwhile success in reducing incidence 

of the disease. In their report article the authors properly address the report on genetic effects (or 

lack thereof) of this culling (Hard et al. 200616); Hard’s recent personal communication (J Hard 14 

 

16 Hard, J. J., D. Elliot, R. Pascho, D. Chase, J Winton, and D. Campton. 2006. ELISA-based 

segregation for control of bacterial kidney disease in Chinook salmon (Oncorhynchus 

tshawytscha). Canadian Journal of Fisheries and Aquatic Sciences 63:2793-2808. 
351 

Apr 2011) is a little less sanguine, he retains some apprehension about the long-term effects on 

genetic variation for resistance to BKD following exposure to the causative bacteria 

Renibacterium salmoninarum (Rs). “The high heritability for resistance to Rs and the high 

frequency of returning adults with high ELISA titers suggest [that]: adults with high titers that 

survive to return to the hatchery may in fact be highly resistant to the disease; eliminating them 

from broodstock might erode resistance in the population over the long term. This risk is what 

needs to be weighed against the risk of an epizootic in the hatchery in the shorter term.” But given 

the unavoidable enhancement of stressors and thus the disease in hatcheries, even if there are 

deleterious evolutionary effects, the benefits of this practice probably outweigh them, particularly 

if they allow diminished use of antibiotics in the future. The report of this project is a peer-reviewed 

publication (NAJFM 30:940–955, 2010), which is an indication of the quality and importance of 

the work and a credit to the project team. 

Some basic questions are suggested by the project review. One is why a useful vaccine against 

Rs has been developed for Atlantic salmon when efforts for Pacific salmon have been frustrated. 

Another question is whether, despite the negative finding of Hard et al. (2006), the culling of veryhigh-titer females (which were not allowed in their experiments) may in the long term erode 

resistance in cultured stocks (pers comm J Hard 14 Apr 2011.). He indicates that USGS and 

NOAA are pursuing genomic research on Rs resistant and susceptible Chinook. 

A very useful addition to this report would be a summary of the LSRCP overall fish health program 

including a description of routine fish health monitoring, how epizootics are reported and 

managed, and how the program relates to responsible government agencies. 

B. Bacterial Kidney Disease Study: Natural vs. Hatchery 

The project team compared Rs prevalence over years (measured by ELISA) in four groups of 

stocks: captive broodstocks, supplementation broodstocks, natural populations receiving 

offspring of captive or supplementation broodstocks, and wilderness natural populations. They 

find no evidence that hatchery releases have caused an increase of Rs in natural populations 

which reduces concern that supplementation might increase disease risk for natural populations, 

but they wisely promise continued monitoring. In fish health/disease discussions, people often do 

not distinguish between the prevalence of the causative agent of a disease (e.g., ELISA detection 

of Rs, the agent causing BKD) and the prevalence of the disease. In this report, the two are 

conflated “we examine[d] the prevalence of BKD, based on...ELISA OD...” when actually the 

report is on the prevalence of Rs. It’s a useful distinction in a discussion of a disease like BKD: 

Rs is widely prevalent in nature, BKD isn’t. The problem of concern is the likely amplification of 

Rs in a captive broodstock program and the effect of the increased Rs infestation on natural 

populations into which the offspring of captive broodstocks are introduced. If the result is an 

increase of Rs in natural populations over the level naturally present, it might make the 

populations more susceptible to BKD in a stressful environment. It’s comforting that no increased 

prevalence has been found, but it is important to realize that little is known about the occurrence 

of BKD in natural populations. 

Again, it would be useful to summarize the fish health program of the LSRCP. 

C. Study: Use of PIT-Tags as a Tool to Monitor Adult Chinook Returns 

 
352 

PIT tags provide a critical tool for evaluating stock specific survival to each life stage, age 

composition, in-season estimates of abundance, and survival rates associated with specific 

projects such as transporting salmon in barges around dams. This brief paper indicated that 

shedding of PIT tags by salmon may be remarkably greater than previously believed, thereby 

introducing bias in critical metrics that rely upon PIT tags. For example, using double-tagged fish, 

the authors estimate that 12.5% of jack Chinook salmon (n = 8 fish total) and 30.6% of Chinook 

spending two years at sea shed their PIT tag (n = 36 fish). These preliminary findings suggest 

older salmon have a higher rate of tag loss. 

The value of this paper would be greatly enhanced if it reviewed all available literature in an effort 

to determine PIT tag shed rates for each age class of salmon. What factors contribute to tag loss? 

Are there methods to minimize tag loss? Continued research into tag loss is critical because many 

decisions in the Basin are based on PIT tag data. High and variable tag loss could introduce 

significant error in survival rate estimates, leading to the misinterpretation of data from 

hydrosystem and supplementation experiments, and from harvest management. 

D. Program Roll-Up 

This roll-up was a good summary, but additional analyses could and should be performed. A 

synthesis of findings across all watersheds is essential for review and adaptive management of 

this program. Detailed comparisons of individual programs can provide answers to questions that 

individual reports cannot. 

Program goals from 1975 have not been achieved. The original planning assumption that the 

affected natural populations would remain viable and produce approximately 50% of the pre-dam 

abundance was erroneously optimistic. The hatchery mitigation goals assumed a sustained 

harvest rate (80%) that is unrealistic even for a productive Chinook population in a pristine habitat. 

Assumed SAR values (0.87%) were also unrealistic based on observed values and current 

conditions in fresh and marine waters. 

A major concern is the apparent lower-than-anticipated production capability of natural salmonids 

in most of the LSRCP systems. Evidence of density dependence (e.g., reduced Imnaha recruits 

per spawner versus total spawners in nature) has occurred at lower numbers of spawners than 

forseen at the beginning of the program. Indications of density effects have arisen despite pristine 

habitat in many tributaries, and considerable habitat improvement work in others. 

Although disease is not a major problem in hatcheries, it may be worthwhile to use genomic 

technology to identify whether disease may significantly contribute to mortality of returning adults 

(Miller et al. 2011). See Science paper by Kristi Miller, CDFO, in 2011 (Fraser sockeye study).17

Additional research is needed to identify factors contributing to high mortality during the smolt-toLGD stage and from LGD to the ocean. A good time series has been developed but further 

analyses are warranted using all stocks. Distance is just one of many variables to be considered. 

Other variables for consideration include: (1) food availability, (2) predator abundance including 

exotic species, (3) agricultural crop acreage in drainages (and associated pesticide use), and (4) 

wastewater treatment plants (WWTPs) discharges of various products into watersheds. Although 

many of these rives are relatively small, WWTPs even with small discharges may have an adverse 

 

17 Genomic Signatures Predict Migration and Spawning Failure in Wild Canadian Salmon. 

Kristina M. Miller and others. Science 14 January 2011: 214-217. [DOI:10.1126/science.1196901] 
353 

effect because the river flow is also small and provides less ability to dilute the discharged 

contaminants (flame retardants, pharmaceuticals, personal care products, etc). 

Age at return: Reduced age at return (and size) of hatchery fish and lower fecundity lead to 

reduced productivity of populations that are supplemented with hatchery fish. Some attempt to 

model or measure this outcome is recommended. 

Mini-jacks: LSRCP managers suggested that few mini-jacks were produced in the hatcheries, 

whereas NMFS scientists estimated high numbers of mini-jacks (e.g., 52% in Lookingglass 

Hatchery, 2006 and 2007).18 This discrepancy should be evaluated. Please see mini-jack 

comment above in Grande Ronde section. 

SAR and R/S data for hatchery and natural fish should be used to evaluate factors in freshwater 

that might lead to high mortality of natural Chinook. A comprehensive examination of habitat and 

factors affecting productivity of natural salmon is needed. 

Stray rates. Most program reports were not adequate with regard to discussions of stray rates. It 

is difficult to monitor strays in all areas, therefore counts will be biased low. Nonetheless, how 

stray rates for each program are estimated, how they may be deficient, and what is needed to 

improve them, needs development. The Collaborative System Monitoring Evaluation Program 

(CSMEP) conducted initial surveys and analysis of hatchery stray rates in the Snake River system 

and bringing this information into the LSRCP is important. 

The shedding of PIT-tags, especially among older Chinook, is a critical observation that was not 

mentioned in the roll-up (see comment above in 5C). PIT tags are a key tool for monitoring and 

evaluation of many programs. Additional review and research is needed to determine if shed rates 

are, for example, 30% for Chinook spending two winters at sea versus 12% for Chinook spending 

only one winter. The presentations and reports are insufficient for an evaluation of the rigor and 

robustness of the counts of fish (slide 31). Data quality is a project-by-project, metric-by-metric 

exercise that would require a financial-audit-like analysis of the data for each project. The regional 

monitoring coordination for anadromous salmon has just begun to address these challenges. 

The most successful portion of the program has been the raising of smolts for release; there has 

been return in sufficient numbers in a few systems to provide modest tribal and non-tribal 

recreational fisheries. Very little evidence is presented of supplementation benefits and any 

positive effects of these higher returns in producing more natural fish. The consistently lower 

SARs for hatchery fish than natural fish also argues that even though fish health is good, physical 

performance of hatchery fish in the hydrosystem, estuary, and ocean (from release to return) 

remains lower than for wild (natural) fish 

The basis for concluding that natural-origin abundance can be increased is not justified. Whether 

or not genetic and life-history resources can be preserved is an open question. There have been 

no described extirpations of local natural-origin populations, but no clear evidence that population 

status was positively affected by the hatchery programs. The success in establishing a hatchery 

program using a local tributary broodstock that is self-sustaining is evidence that these programs 

 

18 Larsen, Donald A., Beckman, Brian R. and Cooper, Kathleen A. (2010) Examining the Conflict 

between Smolting and Precocious Male Maturation in Spring (Stream-Type) Chinook Salmon. 

Transactions of the American Fisheries Society, 139: 2, 564 — 578. First published on: 09 

January 2011 
354 

could prevent extinction of the lineage. It is not evidence that they could prevent extirpation from 

the natural environment. In many locations, it appears there is now a hatchery spring Chinook 

population with some natural production from feral hatchery fish. 

The importance of tributaries for rearing habitat of anadromous salmonids in large river systems 

is well known. The importance of lower river and mainstem rearing habitats later in their life cycle 

for fish that originated from tributaries is less well understood and appreciated. If combinations of 

growth and survivorship are such that higher fitness is obtainable from a migratory, anadromous 

life history, and genetic capability is present, anadromy can be adaptive and evolve. The same 

argument, minus the high costs of osmoregulatory change, can be made for a potamodromous 

(i.e., in-river migratory) life history. In this life history, Snake River spring Chinook spawn in upper, 

typically unproductive tributaries (often in granitic geologies), and move progressively downriver 

prior to smoltification to take advantage of increasingly productive freshwater habitats. In terms 

of productivity, the most historically productive freshwater habitats for salmonids were these 

mainstem and lower river “transitional” habitats. In the historical condition, density dependence 

within the tributary may still have occurred, but the overflow (well-documented emigration) of fish 

would have found higher quality habitat downriver in the transitional habitat. This hypothesis is 

consistent with the documented low success rates associated with parr releases from hatcheries, 

and the shift to exclusively smolts, released into tributary habitats. Consistently higher productivity 

downriver would have resulted in an adaptive, life history evolution toward progressive 

movements through transitional habitats prior to smoltification. 

However, mainstem impoundments, introductions of non-native, lentic-oriented species, and 

warmer waters have greatly reduced the amount of this transitional habitat favored by salmonids. 

Similar density dependence may occur in estuaries as numbers of smolts released increases. 

Potential natural production (as measured by adult returns) of the existing spring Chinook stocks 

based on historical stock sizes, and their use in defining appropriate LSRCP targets, may thus be 

substantially overestimated. This suggest a re-analysis of the capacity of the current freshwater 

environment may be in order, along with current life-stage survivals throughout the life cycle, and 

that LSRCP targets should be adjusted accordingly. 

 
355 

APPENDIX 2. LSRCP RESPONSE TO ISRP REPORT 2011-14 

The Lower Snake River Compensation Plan (LSRCP) thanks the Northwest Power and 

Conservation Council (NPCC) for their interest in the LSRCP Program, and the Independent 

Science Review Panel (ISRP) for their recently completed Program Review and Report of the 

Lower Snake River Compensation Plan’s Spring Chinook Program (ISRP Report). We support 

the ISRP conclusion that the symposium format used to facilitate LSRCP cooperator review and 

independent retrospective evaluation of LSRCP accomplishments worked well and we remain 

committed to implement this process for the steelhead and fall Chinook program components. 

We interpret ISRP’s statement that “Overall, the performance and practices within the hatchery 

were acceptable and met stated goals” to mean the LSRCP program fulfills the Congressional 

mandate that projects must be based on sound scientific principles, benefit wildlife, have clearly 

defined objectives and outcomes, and have adequate provisions for monitoring and evaluation of 

results. LSRPC believes the LSRCP program provides benefits to treaty and non-treaty fisheries, 

benefits to Snake Basin spring Chinook salmon populations, has clearly defined objectives, and 

is adequately monitoring and evaluating the results. We feel the symposium and associated 

reports helped identify areas which can be improved. We are committed to modifying the program 

in ways that move us closer to achieving LSRCP goals while enhancing or incurring only minimum 

impacts to ESA listed fish. 

Comments in the ISRP Report have been incorporated into the final reports for the LSRCP 2011 

Spring Chinook Program Review where appropriate. Comments in the ISRP Report have been 

and will continue to be useful as LSRCP develops the Steelhead Program Review for scheduled 

for March 19 and 20, 2012. LSRCP has incorporated ISRP comments on individual programs into 

the final reports for those individual programs, and the ISRP Report and this response are 

included with the final Spring Chinook Program Proceedings on the LSRCP website at 

http://www.fws.gov/lsnakecomplan/Reports/HGMPreports.htm. 

Since the November 2010 LSRCP Spring/Summer Chinook Program Review, Draft Hatchery 

Genetic Management Plans have been produced by program Cooperators and submitted to 

NOAA, and are available on the LSRCP website. It is unfortunate that these documents were not 

available at the time of the Program Review because they address in detail many of the comments 

and recommendations made in the ISRP report. Information in HGMPs addresses many of the 

ISRP comments and recommendations on original program goals and subsequent cooperator 

management goals, program change over time, broodstock goals, harvest goals and harvest 

levels, parent-progeny ratios, and response to hatchery reform (HSRG and USFWS Hatchery 

Review) recommendations, and will not be specifically addressed. 

While planning and organizing the review, LSRCP and Cooperators spent a significant amount of 

time standardizing format presentations for the individual programs for both oral presentations 

and written reports. As ISRP observed at the review overall program objectives were established 

initially in the COE Special Report. Subsequent to the establishment of program objectives, each 

cooperator incorporated additional objectives into individual programs. As a result, each program 

is quite different. The roll-up was our initial effort at standardizing reporting of metrics. We felt that 

the roll-up was effective, however, understand that it can be improved. We have begun the 

process of incorporating ISRP suggestions and a modified Table 1 (from the ISRP Report) into 

the planning of the Steelhead Program Review Process. We plan to have a fully filled out Table 

1, specific to the steelhead program, available at the beginning of the Steelhead Program Review. 

We are hopeful that will lead to improved standardization of metric reporting and a more useful 

roll-up. 
356 

ISRP commented that LSRCP primary mitigation goals established in the COE Special Report 

were based on overly optimistic survival assumptions. In the COE Special Report mitigation goals 

were based on an assumed 0.87% survival from smolt release back to the project area as adult, 

and that for each adult returning to the project area, four would be harvested in fisheries 

downstream of the project area. This equates to a smolt-to-adult survival of 4.35%. This smolt-toadult survival is within the 2-6% survival range established by the NPCC as being necessary to 

restore fish populations affected by development of the hydrosystem. If the COE 0.87% survival 

to the project area is optimistic, then so is the NPCC goal. The reality of existing conditions does 

not invalidate the original program goals or mitigation obligation. 

In their report, ISRP spent significant time on issues related to impacts of hatchery produced fish 

on naturally produced fish populations. LSRCP recognizes that this is an important issue. Since 

the beginning of the program, the LSRCP has focused on accounting for adults produced by the 

program. Much (but not all) of the work evaluating the impacts of hatchery releases on natural 

populations has been direct funded by BPA through the NPCC’s Fish and Wildlife Program. 

Perhaps this was not made as clear as it could have been at the LSRCP Program review. For 

example, Idaho Supplementation Studies (ISS) funded through the Fish and Wildlife Program has 

been evaluating supplementation effects since the early 1990’s. Many of the programs being 

evaluated by ISS use LSRCP produced fish. ISS did not report at the LSRCP Program Review. 

On the other hand, the Relative Reproductive Success study reported on by NOAA at the LSRCP 

review is not funded by LSRCP. The ‘spider web’ of interconnected studies evaluating effects of 

LSRCP produced fish and multiple funding sources caused difficulty in deciding what to include 

and what to exclude in the LSRCP review. The common thread between the presentations was 

juveniles produced and adults returned. 

ISRP recommended that the BACI (Before/After/Control Impact) analysis be used to evaluate 

supplementation effects. LSRCP agrees that the BACI approach is useful. Where appropriate, we 

will incorporate BACI analysis into LSRCP evaluation. Conducting BACI analysis will require 

additional coordination with the NPCC Fish and Wildlife Program, BPA, and perhaps others who 

fund the evaluation of impacts of LSRCP produced fish on naturally produced fish. 

ISRP commented that fresh water carrying capacity needed to be evaluated periodically to 

minimize effects of density dependence. Addressing carrying capacity issues has both ESA and 

US v. OR fish management implications and will require participation by NOAA, US v. OR parties, 

BPA, and NPCC. The impact of hatchery releases on listed natural populations is addressed as 

part of the development of Hatchery Genetic Management Plans and the ESA Hatchery permitting 

process. 

ISRP recommended that LSRCP and managers take action to rapidly establish natural 

populations that are viable. Much work is being done to supplement natural populations. However, 

as ISRP notes in several locations in their report, efforts to increase naturally spawning population 

size must not lead to decreased productivity of those populations. Work will continue to 

accomplish this, but how to do that is currently not clear. 

LSRCP was disappointed at the lack of emphasis of harvest and harvest opportunity provided by 

the LSRCP program in the ISRP Report. The LSRCP was developed to replace fish lost as a 

result of the hydrosystem. Over 80% of the adults that were to be provided were specifically for 

harvest. At the time of the previous LSRCP review ocean conditions were so poor program 

emphasis had shifted to increase abundance of ESA listed populations to prevent local 

extinctions, and little harvest opportunity was being provided. Since then ocean productivity has 
357 

improved, adult returns (particularly hatchery origin adults) have increased and reasonably 

consistent annual sport and tribal harvest opportunity is being provided. We believe that the 

LSRCP Program has taken significant steps toward achieving LSRCP Program goals. While adult 

return goals remain far from being met, in-hatchery survival goals are being met currently, 

broodstock and smolt production goals are close to being met in recent years, and harvest 

opportunity, particularly above the project area, has increased in the last 10 years. LSRCP 

acknowledges that, natural populations are not currently viable. 

ISRP Findings, Conclusions, and Recommendations 

1. Review and approach and LSRCP Report Comments (pp.10-11) 

LSRCP plans a similar format for the upcoming Steelhead and Fall Chinook Program Reviews. 

Planning is underway and efforts are being made to strengthen weaknesses and fill gaps noted 

by ISRP from the Spring Chinook Program Review. One of the obvious improvements will be 

preparation of a table similar to Table 1 from the Spring Chinook Review. We intend to use that 

table to guide preparation of the roll-up/summary presentation. Preparation of a peer reviewed 

article is under discussion with no decision at this point. 

2. How are the project fish performing in the hatchery? (pp. 11-12) 

ISRP notes that smolt release goals have never met the original LSRCP objectives. There are 

three reasons for that. First, few facilities currently have a release size goal of 15 fish per pound. 

Desire to increase SAR, precosity, mimicking the size of natural fish, and water temperature of 

hatchery water are all factors influencing hatchery manager decisions to adopt size of release 

goals different from 15 smolts per pound. Second, real world limitations at some hatcheries 

prevented achieving smolt production goals. For example, raceway ice cover over winter at 

Sawtooth Fish hatchery reduces rearing area and mandated a reduction in the hatchery 

production goal from 2.3 million to 1.3 million (subsequently increased to 1.7 million); inadequate 

water supply at Clearwater Fish Hatchery prevents operating the hatchery at full production. 

Clearwater Hatchery increased Chinook production at the expense of steelhead production, which 

meant leaving steelhead raceways dry because adequate water has never been available to 

operate the hatchery at full production. Third, broodstock availability has limited production at 

some facilities some years. For example, Sawtooth Fish Hatchery often struggles to return 

enough adults to achieve full production; ODFW management objective changes at Lookingglass 

Hatchery from Rapid River and Carson stock to endemic stock for releases in Lostine, Upper 

Grande Ronde, and Catherine Creek required rebuilding broodstock sources. While original goals 

have not been met, LSRCP believes significant progress has been made toward providing 

adequate brood at each facility to achieve egg and smolt production goals. Changes noted above 

suggest the need for additional metrics to monitor individual hatchery production goals. 

ISRP noted the lack of a summary of differences between hatcheries and years. LSRCP became 

aware of this shortcoming while putting the roll-up presentation together. We found that the 

complexity of the program and changes to the program during the last 12 years makes difficult 

making meaningful comparisons across hatcheries. LSRCP efforts will continue to develop 

meaningful metrics to compare hatcheries over time. 

3. How well are project fish performing once released? (pp. 12-13) 

ISRP suggested that better understanding of smolt survival to Lower Granite Dam could lead to 

increased adult return. LSRCP notes that the number of PIT tagged fish has increased 
358 

significantly in recent years. LSRCP cooperators currently Pit tag ~140,000 annually to better 

understand smolt survival to Lower Granite Dam and to the adult stage. Significant effort is ongoing elsewhere in the NPCC Fish and Wildlife Program to install additional Pit Tag detection 

arrays and to analyze smolt survival (e.g., CSS study) in the Snake River (and Tucannon River) 

basin to better understand Chinook life cycle survival. 

4. What are demographic, ecological, and genetic impacts of programs on wild fish? 

ISRP noted that there is “an absence of empirical evidence from the ongoing projects to assign a 

conservation objective other than preventing extinction”. As noted above in 1998, following the 

last LSRCP Program, ocean productivity had crashed and preventing extinction of local stocks 

was high priority. Captive broodstock programs were implemented in cooperation with NPCC to 

increase the number of returning adults to prevent local extinctions. Subsequently, ocean 

productivity has improved and the number returning adults has increased. HGMPs address 

management of hatchery origin adults in hatchery and natural production. 

5. How are programs being modified and problems achieving objectives being 

addressed? 

Responses to specific hatchery reform (HSRG and USFWS Hatchery Reform) recommendations 

are contained in HGMPs referenced above. 

ISRP suggested additional emphasis be put on evaluating smolt survival from release to the 

ocean. As noted above, significant effort to evaluate smolt survival within the Columbia Basin is 

currently occurring. In addition to studies mentioned above, studies the effect of pinnepeds, terns, 

introduced and native fish on smolts occur. Study on tributary and estuary rearing conditions also 

occur. LSRCP will coordinate with BPA and NPCC on additional study in these areas as gaps in 

current information are identified. 

Conclusions and Recommendations 

1. Develop realistic harvest mitigation levels that might be attainable at some time in the 

future. 

The smolt survival-to-adult goals (4.35%) that underlies the LSRCP Program is consistent with 

the NPCC goal of 2-6%. If this goal is unrealistic, the entire Columbia River basin adult return 

goal should be reevaluated also. The reality of existing conditions does not invalidate the original 

program goals or mitigation obligation. 

2. Take action necessary to rapidly establish natural populations that are viable. 

Following the previous Program Review in 1998, actions were taken to prevent extinction. Those 

efforts were generally successful, and extinction was avoided. Now, efforts need to turn to natural 

population recovery. NOAA is currently in the process of developing hatchery production permits 

that incorporate attempts to rebuild natural production based on recently submitted HGMPs. 

Those permits will incorporate natural population protection and rebuilding efforts as approved for 

the LSRCP Program.