Independent Scientific Advisory Board

for the Northwest Power and Conservation Council,

Columbia River Basin Indian Tribes, 

and National Marine Fisheries Service

 851 SW 6th Avenue, Suite 1100

Portland, Oregon 97204

ISAB@nwcouncil.org

Biological Effectiveness 

of 2005 Summer Spill 

ISAB 2006-1 

January 18, 2006 
ISAB Members 

Robert Bilby, Ph.D., Ecologist at Weyerhaeuser Company, an expert in riparian ecology. 

Susan Hanna, Ph.D., Professor of Agriculture and Resource Economics at Oregon State 

University (also an IEAB member). 

Nancy Huntly, Ph.D., Professor of Wildlife Biology at Idaho State University. 

Stuart Hurlbert, Ph.D., Professor of Biology and Director, Center for Inland Waters at 

San Diego State University. 

Roland Lamberson, Ph.D., Professor of Mathematics and Director of Environmental 

Systems Graduate Program at Humboldt State University. 

Colin Levings, Ph.D., Research Scientist and Past Section Head Marine Environment and 

Habitat Science Division, Department of Fisheries and Oceans, Canada (also an ISRP 

member). 

William Pearcy, Ph.D., Professor Emeritus of Oceanography at Oregon State University. 

Thomas P. Poe, M.S., Consulting Fisheries Scientist, an expert in behavioral ecology of 

fishes, formerly with the U.S. Geological Survey (also an ISRP member). 

Peter Smouse, Ph.D., Professor of Ecology, Evolution, and Natural Resources at Rutgers 

University, an expert in biometrics and population theory.
ISAB Review: Biological Effectiveness of 2005 Summer Spill 

Contents 

Executive Summary............................................................................................................ 1 

I. Background...................................................................................................................... 4 

II. Responses to Questions Posed by the Council, NMFS, and CRITFC........................... 4 

Questions 1 and 2. Studies Relevant to 2005 Spill Operations, Status of Data, and Data 

Analyses.......................................................................................................................... 4 

NMFS/USFWS PIT-tag Studies................................................................................. 5 

Fish Passage Center - Preliminary Survival Analysis for Subyearling Chinook 

Originating Above Lower Granite Reservoir ............................................................. 6 

Radio-tag Studies........................................................................................................ 7 

Question 3. How are the survival and passage metrics derived?.................................. 10 

Models....................................................................................................................... 10 

Estimates................................................................................................................... 10 

Passage Metrics......................................................................................................... 11 

Sample Sizes and Error Terms.................................................................................. 11 

Question 4. Potential Effects of 2005 Spill Operations on Fall Chinook “Reservoir 

Type” Juveniles............................................................................................................. 11 

Background on Chinook life history patterns........................................................... 11 

Potential Effects of the summer spill on reservoir-type Chinook............................. 12 

Question 5. What additional studies and monitoring would need to be implemented to 

provide the region with a more thorough evaluation of the potential benefits of summer 

spill in recovering listed Snake River fall Chinook? .................................................... 13 

III. Conclusions................................................................................................................. 15 

Acknowledgements........................................................................................................... 18 

Literature Cited ................................................................................................................. 18 

Appendix A. Background Life History Information on Juvenile Fall Chinook .............. 22 

Food Habits................................................................................................................... 22 

Overwinter Movements and Distribution ..................................................................... 22 

Lower River and Estuarine Distribution....................................................................... 23 

Attachment 1. Memorandum from the Northwest Power and Conservation Council, 

October 14, 2005............................................................................................................... 25 

Attachment 2. NMFS (NOAA Fisheries) and CRITFC Questions................................... 26 

i 
ISAB Review: Biological Effectiveness of 2005 Summer Spill 

Executive Summary 

In October 2005, the Independent Scientific Advisory Board (ISAB) received a request 

from the Northwest Power and Conservation Council (Council) to review the biological 

effectiveness of court-ordered summer spill operations in 2005 for benefit/recovery of 

ESA-listed Snake River fall Chinook. The National Marine Fisheries Service (NMFS) 

and the Columbia River Inter-Tribal Fish Commission (CRITFC) approved the ISAB’s 

assignment and added questions for the ISAB to consider in its review. 

The 2005 court-ordered spill began on June 20 at the four lower Snake River dams and 

continued through August 31. At McNary Dam on the Columbia River, court-ordered 

spill was initiated on July 1 and continued through August 31. A large majority of the 

subyearling fall Chinook hatchery production fish emigrated through the lower Snake 

River prior to initiation of the spill, but a majority of the wild subyearling fall Chinook 

were exposed to the spill. 

The ISAB found several studies relevant to the effect of the 2005 court-ordered summer 

spill on juvenile subyearling salmon survival, travel time, dam passage, and smolt to 

adult return rates (SARs). However, none of these studies was specifically designed to 

examine how summer spill may benefit recovery of ESA-listed Snake River fall Chinook, 

and none produced reports for review. 

PIT-tag studies 

• A joint study by the NMFS and the U.S. Fish and Wildlife Service (USFWS) was 

conducted in 2005 to compare smolt to adult survival rates (SARs) of Snake River 

fall Chinook under alternate transport and dam operational strategies. In order for 

this study to provide information relevant to the effectiveness of the 2005 spill it 

will be necessary to monitor the returning adults to establish SARs for the 2005 

cohort. Draft post-release performance results of reach survivals are available for 

Snake River groups, but data from Clearwater groups are not yet available. Nor 

do these estimates account for “reservoir type” fall Chinook. The post-release 

performance (i.e. passage timing, spill exposure history, travel rate, and joint 

probability of migrating and surviving) of wild subyearlings and Lyons Ferry 

hatchery surrogate subyearlings were similar. Compared with either wild or 

surrogate subyearlings, production subyearlings emigrated much earlier, 

experienced almost no spill, and had higher travel rates and survival. 

• The Fish Passage Center (FPC) used PIT-tag data from all tagged research, wild, 

and production fish to produce a preliminary 2005 reach survival estimate. This 

estimate may be a good indicator of a potential benefit of the 2005 summer spill 

for subyearling Chinook, but actual benefit cannot be assessed until SARs can be 

estimated. Most of the preliminary analyses focus on differences in survival 

estimates among years. These comparisons are of limited utility for direct 

1 
estimation of spill effects, given major variations in river hydrosystem spill 

operations among years and considerable interannual variation in migration 

timing and passage behavior of subyearling Chinook. Travel time estimates may 

be adequate for the entire population of migrating smolts but are inadequate for 

estimating travel times for wild fish and specific sub-groups of migrants (e.g. 

Clearwater fish). 

• The survival estimates presented represent the joint probability of migrating as a 

subyearling and surviving through the reach of interest. Thus any differences in 

estimated in survival estimates observed among years could be due to a change in 

survival, a change in the proportion of fish migrating as subyearlings as opposed 

to yearlings, or both. 

Radio-tag studies 

• Radio-tag studies provided very useful data to determine passage behavior and 

survival estimates of subyearling Chinook at each of the lower Snake River dams

and McNary dam during the court ordered spill. Data indicated that when 

provided with significant levels of summer spill subyearling fall Chinook 

juveniles passed through spillways at lower Snake River dams with little delay 

and high efficiency (96 to 99 % FPE). 

• Data also indicate that the removable spillway weirs (RSW) tested at Lower 

Granite and Ice Harbor dams were efficient in passing a large proportion of the 

subyearling Chinook with high survival rates. Except for the on/off RSW tests, 

only one primary spill condition was tested; spill on for 24 hr/day. Controlled 

tests, varying amounts and duration of spill, would have given a better evaluation 

of spill effects on passage behavior and survival.

• Radio-tag data are very useful for evaluating overall spill passage behavior and 

survival at specific dams but not for multi-reservoir reach survival estimates (e.g. 

Lower Granite Dam to McNary Dam), system-wide survival estimates, or SARs 

because of relatively short-lived tag duration. 

Subyearling fall Chinook Reservoir Type 

• The USFWS PIT-tag data on wild subyearling Chinook are not useful for 

evaluating immediate effects of summer spill. These studies are designed to 

determine long-term trends in SARs of wild populations. 

• The effects of 2005 summer spill on the proportions of “reservoir type” and 

“ocean-type” fall Chinook relative to the proportions observed in recent years 

may be observed in the spring of 2006 when reservoir-type fish migrate from the 

system. 

2 
• The larger size of the reservoir-type smolts likely confers a survival advantage 

over the ocean-type smolts, contributing to their higher representation among 

returning adults. The reservoir-type life history suggests that, for fall Chinook 

juveniles, getting to the estuary as fast as possible may reduce the chances of 

surviving. Emigrating at a slower rate, feeding, and reaching the estuary/ocean at 

a larger size may promote higher survival due to reduced predator vulnerability. 

Both increasing travel rates due to summer spill and transporting subyearling fall 

Chinook that might become reservoir-type may be detrimental to continuation of 

this life history type. 

ISAB Recommendations for Additional Research, Monitoring, and Evaluation 

Studies for Determining the Efficacy of Summer Spill for Protecting and Recovering 

Snake River fall Chinook 

• Replicate the studies of coordinated dam/spill operations for multiple years, to test 

for effects of spill on Snake River Chinook salmon over a range of variation in 

flow that occurs among years. 

 

• Substantially augment monitoring of tagged juveniles and adults throughout the 

system, to allow wider-scale assessments of competing hydrological options, 

including strategies related to transport of Snake River fall Chinook juveniles. 

• Evaluate the consequences of changing the spill regime for upriver movements of 

adult salmon and other species for which changes in summer spill are relevant, 

particularly steelhead trout, white sturgeon, and Pacific lamprey. 

• Increase the monitoring of reservoir-type fall Chinook, throughout the system, fall 

through winter, and over years. There is a need for both a better in-river tracking 

system for these fish and some sense of the extent to which this over-wintering 

behavior is genetically programmed. 

• Study survival of over-wintering reservoir-type Chinook salmon to estimate their 

mortality rates during reservoir residency and during passage downstream. Given 

the substantial proportion of returning adults produced by this life history type, an 

improved understanding of the factors impacting these fish may be critical to the 

recovery of Snake River fall Chinook salmon. 

3 
ISAB Review: Biological Effectiveness of 2005 Summer Spill 

I. Background 

On October 17, 2005, the Independent Scientific Advisory Board (ISAB) received a 

request from the Northwest Power and Conservation Council (Council) to review the 

biological effectiveness of spill operations in 2005 and provide a report by November 30, 

2005 (Attachment 1). On October 18, the ISAB’s Executive Committee, including Ex 

Officio members from the Council, National Marine Fisheries Service (NMFS), and the 

Columbia River Intertribal Fishery Commission (CRITFC), discussed the Council's 

request. NMFS and CRITFC approved the ISAB assignment with the understanding that 

the ISAB would consider their additional questions and comments (Attachment 2). The 

ISAB included those questions and synthesized all questions into the following set: 

(1) What studies were conducted in 2005 that are expected to provide data relevant to 

evaluate the effects of the Court ordered summer spill on juvenile salmonid survival, 

travel time (i.e. from Lower Granite Reservoir to the estuary), smolt to adult return rates, 

and smolt condition (i.e. physiological condition and disease)? 

(2) What is the status of data from such studies, are they adequate for analyses of the 

effects of spill, and which analyses are completed, ongoing, or still need to be 

undertaken? 

(3) How are each of the survival and passage metrics derived and are they statistically 

sound? 

(4) What are the potential effects of the 2005 summer spill on the fall Chinook “reservoir 

type” juveniles? 

(5) What additional studies and monitoring would need to be implemented to provide the 

region with a more thorough evaluation of the potential benefits of summer spill in 

recovering listed Snake River fall Chinook? 

II. Responses to Questions Posed by the Council, NMFS, and CRITFC 

Questions 1 and 2. Studies Relevant to 2005 Spill Operations, Status of 

Data, and Data Analyses 

 

The ISAB found several studies relevant to the effect of the 2005 Court ordered spill on 

juvenile subyearling salmon survival, travel time, dam passage, and smolt to adult return 

rates (SARs). For each study we give some background, objectives, results, and status of 

data and analyses. 

4 
NMFS/USFWS PIT-tag Studies 

Study Design 

The NMFS and U.S. Fish and Wildlife Service (USFWS) conducted a joint PIT-tag study 

(Marsh and Connor 2005) to compare smolt to adult return rates (SARs) of Snake River 

fall Chinook salmon under alternate transport and dam operational strategies. The three 

primary objectives for the study were to: (1) compare SARS of PIT-tagged wild and 

surrogate-sized (hatchery fall Chinook subyearlings reared to a size to match wild 

subyearlings) hatchery subyearling Chinook transported from Snake River dams to below 

Bonneville Dam with the SARs of PIT-tagged wild and surrogate hatchery subyearlings 

remaining in the river; (2) compare post-release performance of wild fall Chinook salmon 

subyearlings from the Snake and Clearwater rivers to hatchery fall Chinook subyearlings 

released in these rivers as surrogates for natural fish in transportation studies; and (3) in 

future years compare SARs of PIT-tagged production-sized hatchery-reared subyearling 

Chinook salmon transported from Snake River dams to below Bonneville Dam, with the 

SARs of PIT-tagged production hatchery-reared subyearling Chinook remaining in the 

river. 

Status of Data and Data Analysis 

• No reports regarding this study were available for review by the ISAB. 

• Only information labeled as preliminary or draft has been reviewed by the ISAB 

via presentations (Dec. 7 power point presentation by Connor and Smith). 

• Objectives (1) and (3) require SARs before results can be evaluated, and thus will 

not be addressed for several years. 

• Reach survival estimates for the lower Snake and to McNary Dam were 

calculated as the joint probability of migrating as a subyearling and surviving. 

• Draft results for Objective (2) were given for Snake River groups but data from

Clearwater groups were not yet available, at time of reporting. 

• The post-release performance (i.e. passage timing, spill exposure history, travel 

rate, and joint probability of migrating and surviving) of wild subyearlings and 

hatchery-reared surrogate subyearlings from Lyons Ferry were similar. 

• Compared with either wild or surrogate subyearlings, production subyearlings 

emigrated much earlier, experienced almost no spill, and had faster travel rates 

and higher survival. 

Adequacy of Data for Evaluating Effectiveness of 2005 Spill 

• Current information from this study does not enable evaluation of the 

effectiveness of 2005 spill, because it is necessary to monitor the returning adults 

in order to establish SARs for the 2005 cohort. This will require monitoring for 

another three to five years. 

• This study was originally designed to be conducted during alternating spill and 

non-spill river conditions with 2005 designated as a non-spill year. Detection of 

juvenile fish at the dams was much lower than anticipated, due to the 2005 spill 

5 
regime actually implemented under the court decision. As a consequence, the 

sample size of tagged fish treatment groups may have been too low for adequate 

numbers of fish to be collected for the transport treatment group (i.e. because 

most juveniles passed through the spillways and were unable to be collected for 

transport). 

• Also, in-river detections were probably too low for precise reach survival 

estimates (again because the great majority of fish passed via the spillways, where 

they are not detected). 

• The available data provide some preliminary indication of how wild subyearlings 

compared with surrogate and production hatchery subyearlings, but sample sizes 

were low, relative to the precision needed for Objective (2) above. 

• The survival estimates from this and all other analyses presented represent the 

joint probability of subyearling emigration and survival through the reach. Thus, 

differences among years in this estimate of survival could be due to a change in 

the proportion of juveniles emigrating as subyearlings vs. over-wintering 

yearlings, differences in survival, or a combination of the emigration and survival. 

Fish Passage Center - Preliminary Survival Analysis for Subyearling Chinook

Originating Above Lower Granite Reservoir 

Design of Analysis 

The Fish Passage Center (FPC) used data from all PIT-tagged wild, surrogate, and 

hatchery production smolts to estimate reach survival (from Lower Granite Dam tailrace 

to McNary Dam tailrace) and travel time. Two groups of PIT-tagged fish, the wild 

Clearwater River fish (n = 858) and hatchery surrogate Clearwater fish (n = 19,268) were 

not used, because of their late marking and migration timing. All other fish detected and 

returned to the river at Lower Granite Dam were used in the analysis. 

Three different preliminary analyses have been presented by the FPC in different forums

(including a presentation to the ISAB on December 7, 2005) and documented in memos 

dated September 12, October 25, and December 13, 2005. In the October 25, 2005 

analysis, subyearling migrants were separated into two groups to assess survival prior to 

(May 20-June 12) and after implementation (June 17-July 15) of the court-ordered 

summer spill in 2005. Similar groupings by date were created for each year, 2001 through 

2004, to allow comparisons among years. The December 7, 2005 analysis (power point 

presentation by Filardo and McCann) expanded the survival estimates to include the 

years 1998-2000, and the within year analysis comparison groups were expanded from 

two groups to four groups, each with a smaller time interval. The FPC subdivided the 

intervals, because shorter time intervals exhibit more consistent environmental conditions 

allowing finer distinctions in survival and travel time among river conditions (FPC memo 

dated December 13, 2005). 

6 
Status of Data and Data Analysis 

• No published reports were available for the ISAB to review for this evaluation. 

• As noted above, three different preliminary analyses have been presented in 

different forums and this is a strong indicator of the preliminary nature of the data 

analyses to date. 

• The final analysis will be completed and included in the FPC’s 2005 Annual 

Report due out in the spring of 2006. 

• Preliminary analysis yielded the following conclusions: (1) the 2005 point 

estimate for subyearling Chinook survival during the summer spill period was the 

highest recorded in recent years (1998-2004) in the reach from Lower Granite 

Dam to McNary Dam, and (2) travel time estimates of subyearling Chinook 

through the reach was the second fastest in recent years (2001-2004). 

Adequacy of Data Analysis for Evaluating Effectiveness of 2005 Spill 

• A majority of hatchery or production subyearling Chinook passed through the 

lower Snake River prior to initiation of the summer spill. Therefore the effect of 

the spill on this group was negligible. 

• The 2005 reach survival estimate may be a good indicator of a potential benefit of 

the 2005 summer spill for subyearling Chinook, but actual benefit cannot be 

determined until SARs can be estimated. 

• Most of the preliminary analyses focus on among year comparisons of survival 

estimates. These comparisons may be of limited utility because of major 

variations in hydrosystem spill operations among years (power point presentation 

by Skalski, December 7, 2005) and in view of considerable annual variation in 

migration timing and passage behavior of subyearling Chinook. 

• Travel time estimates may be adequate for the entire population of juvenile 

salmon but inadequate for wild fish and other specific sub-groups of migrants 

(e.g. Clearwater fish). 

• The latest, December 7 analysis, which used four rather than two groupings of 

fish further reduced an already small sample size and increased variability/error of 

the survival estimates. 

Radio-tag Studies 

The U.S. Geological Survey (USGS) and the NMFS were funded by the US Army Corps 

of Engineers (COE) to conduct radio-tag passage behavior and survival studies at the 

following hydroelectric dams during the 2005 summer spill season: Lower Granite, Little 

Goose, Lower Monumental, Ice Harbor dams on the Lower Snake River, and McNary 

Dam on the mainstem Columbia River. Evaluations of removable spillway weirs (RSW) 

at Lower Granite and Ice Harbor dams were also conducted during the court-ordered spill 

(Peters 2005). Different study designs, as well as passage and survival metrics, were used 

at each dam, so a brief summary of study design and preliminary results follows for each 

dam.

7 
Lower Granite – The study was conducted by the USGS from June 20 –July 22, 2005 

(Perry et al. 2005) and was designed to compare passage and survival of radio-tagged 

subyearling Chinook (run of the river fish) through a removable spillway weir (RSW) 

and the conventional spillbays. They used a randomized-block design. Two single-day 

treatments (either RSW on or RSW off/conventional spillbays) were randomized within 

sixteen 2-day blocks during the court ordered spill. The Paired-Release Recapture Model 

was used to estimate survival probabilities for passage through the RSW and 

conventional spillbays. 

• Dam survival was higher when the RSW was deployed (93.9% Standard Error 

(SE) = 4.3%) than when it was not (89.5% SE = 4.3%). 

• Fish Passage Efficiency (FPE), which is the percentage of fish passing the dam

through non-turbine routes, was 97.5% with the RSW deployed and 98% when it 

was not. 

• Estimated survival of fish passing through the RSW was 94.5% (SE = 2.5%) and 

was 90.2% (SE = 3.4%) through conventional spillbays. 

Little Goose – The study was conducted by the USGS from June 17 through August 1, 

2005 (Perry et al. 2005) and was designed to estimate survival probabilities of radiotagged subyearling Chinook (run of the river fish) passing through the spillway by use of 

the Single-Release Recapture Model. 

• Dam survival was estimated to be 91.6% (SE = 2.1%). 

• Fish passage efficiency was 97%. 

• Estimated spillway survival was 92.0% (SE = 2.2%). 

Lower Monumental – The study was conducted by the NMFS from July 6-16, 2005 

(Absolon et al. 2005) and was designed to estimate survival probabilities of radio-tagged 

subyearling Chinook (run of the river fish) passing through the spillway by use of a 

Paired-Release-Recapture design. 

• Dam survival was estimated to be 86.2% (Confidence Interval (CI) = 75.2-98.8). 

• Fish passage efficiency was 96%. 

• Estimated spillway survival was 90.5% (CI = 76.0-107.7) 

Ice Harbor – The study was conducted by the NMFS from June 10 –July 16, 2005 

(Ogden et al. 2005) and was designed to compare passage and survival of subyearling 

Chinook (run of the river fish) through a removable spillway weir (RSW) with that 

through the conventional spillbays. They used a randomized-block design with treatments 

(either RSW deployed or RSW not deployed/conventional spillbays) for 20 days during 

the court-ordered spill. The Paired-Release Recapture design was used to estimate 

survival probabilities for passage through both the RSW and through conventional 

spillbays. 

• Dam survival was slightly higher when the RSW was not deployed (99.6% CI = 

97.1-102.1) than when the RSW was deployed (98.0% CI = 95.3-100.7). 

• Fish passage efficiency was also slightly higher when the RSW was not deployed 

(99%) than when it was deployed (98%). 

8 
• Estimated spillway survival was higher when the RSW was not deployed (99.8% 

CI = 97.3-102.2) than when the RSW was deployed (95.9% CI = 91.2-100.5). 

McNary – The study was conducted by the USGS from July 1-August 10, 2005 (Perry et 

al. 2005) and was designed to estimate survival probabilities of radio-tagged subyearling 

Chinook (run of the river fish) passing through various passage routes of the dam by use 

of the Route-Specific Survival Model. 

• Dam survival was estimated to be 96.3% (SE = 1.4%). 

• Fish passage efficiency was 81%, which was low relative to Snake River dam

FPEs, but high compared to other lower Columbia River dams. 

• Estimated spillway passage survival was 102% (SE = 1.3%).

• Estimated turbine passage survival was 86% (SE = 3.8%). 

• Estimated juvenile bypass survival was 86% (SE = 2.9%). 

Status of Data and Data Analysis 

• No published reports regarding these studies were available for review by the 

ISAB. 

• Only information labeled as preliminary or draft has been reviewed by the ISAB 

via presentations (the Anadromous Fish Evaluation Program (AFEP) Annual 

Review November 14-17, 2005 and the December 7, 2005 power point 

presentations by Perry and Hockersmith). 

• While survival and passage estimates are not finalized in technical reports or peer 

reviewed documents, statements at the 2005 AFEP Review and in the Federal 

Columbia River Power System After-Action Report (October 2005) indicated that 

any final adjustments in the estimates would probably be slight. 

Adequacy of Data for Evaluating Effectiveness of 2005 Spill

• Data are very useful for evaluating overall spill passage survival at specific dams

but not for reach or system-wide survival.1

• Data indicated that when provided with significant levels of summer spill 

subyearling fall Chinook juveniles will readily pass through spillways at lower 

Snake River dams with high efficiency (96 to 99 % FPE) and with high rates of 

survival (90.2 to 99.8%).

• Data also indicated that RSWs tested at Lower Granite and Ice Harbor dams were 

efficient in passing a large proportion of the subyearling Chinook with high 

survival rates.

• Except for the on/off RSW tests, only one primary spill condition was tested, spill 

on for 24 hr/day. Controlled tests, varying amounts and duration of spill would 

have given a better evaluation of spill effects on passage behavior and survival.

 

1

 Confidence limits for survival percentages that are above 100% should be interpreted as “not statistically 

distinguishable from 100% at the upper end.” The limited inference is due to inadequate sample sizes. 

9 
Question 3. How are the survival and passage metrics derived? 

Models 

PIT-Tag Studies - The Cormack-Jolly-Seber (CJS) release-recapture model (Burnham et 

al. 1987) was used to estimate survival from release above Lower Granite Dam to 

downstream detection sites and between series of dams. The CJS method is based on 

mark release-recapture theory in which the subsequent detection histories on a known 

number of marked fish re-released at a particular dam is used to estimate the number of 

fish that pass that particular dam that are alive but undetected. 

 

Radio Tag Studies - Three major models are being used to estimate survival of downriver 

migrating smolts, the Single Release Model (SRM), the Paired Release Model (PRM), 

and the Route Specific Survival Model (RSSM). There are more elaborate models, such 

as the triple release model, but they are rarely used in such studies. All of the methods 

and metrics used are the regional standards for the field (Peven et al. 2005). 

The ISAB has examined the resulting estimates and sampling protocols. The 

caveats/limitations listed in this report represent reservations about limited sample sizes 

and detection of smolts passing through the spillways, not criticisms of the statistical 

models. 

Estimates 

The model employed depends on the design of the study and the particular question being 

addressed. Some of the typical applications for these models are: 

System-Wide Estimates – Obtainable from Single Release Model studies, with 

measurement from release point (above the first dam) and the final detection point at or 

below the final dam. It is also possible to use a long series of Paired Release Model 

studies to estimate the survival from each dam and reach, combining into a systemwide estimate at the end. 

Project/Dam Estimates – Project survival is measured from below an upstream (1st) 

dam to detection stations downriver from the next (2nd) dam. With a detector in the 

forebay of the 2nd dam, it is possible to separate project survival into pool and dam

survival components, respectively, using an augmented Paired Release Model 

treatment. 

Route Specific Survival Estimates – The Route Specific Survival Model is typically 

used to subdivide survival and passage efficiency among passage routes for a single 

project. The study design usually entails the placement of detection arrays in the 

forebay, above the mixing zones in the tailraces of different passage routes through the 

dam, and further downstream. Fish detected below the dam are compared with the fish

above the dam, and parceled out to various routes of passage through the project. 

10 
Passage Metrics 

• Spill Passage Efficiency – % of fish passing through the spillbays. 

• Fish Passage Efficiency – % of fish passing through non-turbine routes. 

• Spill Effectiveness – % of fish passing through the spillbays, divided by the % of 

water through the spillbays. 

• Fish Guidance Efficiency – % of fish successfully routed around the turbines to 

the bypass system by the screens. 

Sample Sizes and Error Terms 

The variances for estimates of survival fractions depend on the numbers of fish released 

(R) and on the detection probability (PD). A graphic analysis is provided in Figure 12 of 

Peven et al. (2005), as a joint function of R and PD. It is well understood that large 

sample sizes are required to document meaningful differences in survival rates. If the 

initial releases are divided among multiple categories, or if multiple routes of passage are 

to be evaluated, sample sizes must be quite a bit larger. The numbers of tagged fish 

released for Summer Spill 2005 studies would have been adequate for the original 

purposes, but were too small (in retrospect) to obtain the necessary precision for 

comparisons of multiple passage routes and alternative spill regimes. Time allowance for 

some advanced planning, along with some advance studies of the statistical power of the 

design chosen, will ensure adequate (larger) sample sizes and greater precision. 

Question 4. Potential Effects of 2005 Spill Operations on Fall Chinook 

“Reservoir Type” Juveniles 

Background on Chinook life history patterns 

Until recently, most Snake River fall Chinook were assumed to exhibit an “ocean-type” 

life history, entering the estuary during the summer. Connor et al. (2002, 2005), using 

scale analysis, identified another life history type displayed by Snake River fall Chinook. 

These fish, termed “reservoir-type” Chinook, over-winter in the lower Snake River 

reservoirs and possibly the lower Columbia River reservoirs, migrating to the estuary the 

following spring. The rate of expression of reservoir type life history is inversely 

proportional to water temperature and growth during rearing (Connor et al. 2002). Cooler 

temperatures resulting from cold water released from the Dworshak Dam and reduced 

food supply may increase the proportion of Snake River fall Chinook that exhibit the 

reservoir-type life history. (See Appendix A. for more detailed information on Chinook 

life history patterns.) 

The reservoir-type fall Chinook make an important contribution to returning fall Chinook 

salmon in the Snake River. In recent years, PIT-tagged reservoir-type Chinook have 

accounted for a larger percent of returning adults, especially females, than “ocean-type” 

Chinook (Connor 2005). High food availability in the reservoirs where these fish 

overwinter enable rapid growth, and reservoir-type Chinook smolts are much larger at the 

11 
time of entry into the ocean than ocean-type smolts (Tiffan and Connor 2005). (See 

Appendix A. for food habits information on juvenile fall Chinook). 

 

Potential Effects of the summer spill on reservoir-type Chinook 

Stimulation of migration from different flow patterns during spill - The migratory 

behavior of ocean-type subyearling Chinook through the Columbia River reservoirs has 

been described by several authors and is summarized by Coutant and Whitney (2005). 

The migratory routes are complex and include diurnal shifts in distribution to open water 

at night to shallow shoreline habitat in the daytime. The latter habitat was thought to be 

important for feeding. Most of fish were caught in the upper 3.6 m, with 80% in the upper 

1.8 m. Curet (1993) concluded that the subyearlings did not pass through Lower Granite 

Reservoir and Little Goose reservoir quickly, using the shorelines and open water areas 

of the reservoirs for rearing. This is consistent with observations of Chinook feeding in 

large lakes such as Shuswap Lake on the Fraser River system (e.g. Graham and Russell 

1979.). 

However, detailed data on the vertical and horizontal distribution and migratory behavior 

of large Chinook (e.g. > 200 mm) such as reservoir-type Chinook are not available for 

late summer, autumn, and winter. It is also not known whether reservoir-type Chinook 

are relatively more or less entrained in water moving downstream during a spill event, in 

comparison with other operational modes. As discussed in detail in Coutant and Whitney 

(2005), movement of salmonids through the reservoirs is not a simple function of water 

velocity or flow patterns. Factors such as fish size, temperature, and physiological state 

are involved and can influence current-mediated migration in the surface waters of the 

dam forebay. 

The larger size of the reservoir-type smolts likely confers a survival advantage over the

ocean-type smolts, contributing to their higher representation among returning adults. 

The reservoir-type life history suggests that for fall Chinook juveniles getting to the 

estuary as fast as possible may not be the best for chances of surviving. Emigrating at a 

slower rate, feeding, and reaching the estuary/ocean at a larger size may increase the 

probability of survival due to reduced predator vulnerability. However, until detailed inreservoir studies are conducted, it is uncertain if attaining a larger size in the reservoir per 

se confers significant survival benefits to reservoir-type smolts. Predation on other life 

history types of Chinook smolts by northern pike minnow (Shively et al. 1996) in the 

Clearwater River and by birds in the mid-river (Antolos et al. 2005) and estuary of the 

Columbia (Lyons et al. 2005) has been shown to be size and species specific. 

Physiological factors such as osmoregulatory ability are also involved. For example 

Beckman et al. (1999) investigated the possible role of a variety of factors on survival of 

hatchery-reared Chinook smolts on the Deschutes River OR. Spring growth rate, gill 

ATPase activity, and plasma IGF-I concentration showed significant relationships to 

SAR. 

 

12 
Are data available to determine if the 2005 spill caused significant changes in residency 

and number of subyearling wild and hatchery Chinook holding over in the upper river 

reservoirs and emigrating as yearlings in 2006? - No publications or data sets were 

found that provided a time series of population or residency estimates for overwintering 

Chinook in the reservoirs. Winter is a difficult season for sampling in the reservoirs 

because of ice conditions and possible changes in Chinook behavior due to low water 

temperatures. However, data were obtained during winter 2004-2005 (Tiffan et al. 2005), 

which might be compared with results of radio-tagging for winter 2005-2006, underway 

at present (see Appendix A). Winter 2004-2005 results showed residency times of up to

150 days but residency decreased in the spring, as fish resumed emigration. 

Change in food supply for reservoir-type - Effects of spills on ecosystem processes and 

food species dynamics in Columbia River reservoirs have yet to be documented, so 

effects on the food supply for reservoir-type Chinook are unknown. It is likely that some

of the likely potential prey species for reservoir-type Chinook, such as zooplankton and 

larval fishes, might be expected to be flushed into downstream reservoirs during spill 

events, which tend to take water off of the upper surface layers of the reservoir. Earlier 

studies showed that phytoplankton was flushed from the Columbia impoundments to 

estuarine habitats (Sherwood et al. 1990), but the likely impact of such flushing on 

production in the system has not yet been evaluated. 

Question 5. What additional studies and monitoring would need to be 

implemented to provide the region with a more thorough evaluation of the 

potential benefits of summer spill in recovering listed Snake River fall 

Chinook?

1) Experimental studies involving controlled and coordinated dam/spill operations for 

multiple years, to address the effects of spill over some reasonable range of variation in 

flow among years, are required to conclusively address to the effectiveness of spill on 

Snake River Chinook salmon. A single-year study will not be sufficient to evaluate the 

juvenile phase of the Chinook life cycle, and the spill regimes for the various dams in 

2005 were quite different, both relative to the timing of Snake River fall Chinook passage 

and in the physical conditions at each dam. 

A 2004 summer spill study, comparing survival of radio-tagged subyearling Chinook

salmon under two different 24 hour spill operations at Bonneville Dam (Counihan et al. 

2005, and Evans et al. 2005) is instructive for the design of studies of summer spill 

passage and survival in the lower Snake. The ISRP in their review of the proposal for this 

study2

 stated that, “Summer spill is currently a key issue, and this study starts to address 

some of the questions of the benefit of summer spill by providing real data, which 

provides rationale to move forward with this project. However, a primary issue the ISRP 

has identified in the review of the Anadromous Fish Evaluation Program (ISRP 2004-8) 

 

2

 ISRP 2004-5: Review of Summer Spill Study Proposal: Estimating the survival of sub-yearling Chinook 

salmon through Bonneville Dam during two spill operation scenarios using radio-telemetry. April 6, 2004. 

13 
is the need for a long-term plan for fish studies related to the hydrosystem with proposals 

developed as far in advance of implementation as feasible to allow for adequate planning, 

proposal development, and review.” 

2) Substantially augmented monitoring of tagged juveniles and adults throughout the 

system to allow wider-scale assessments of competing hydrological options, including 

strategies related to transport of Snake River fall Chinook juveniles. Consequently, the 

region’s assessments will need to be highly reliable (increased numbers of tagged fish), if

the region is to have any hope of contrasting divergent hydrological options, in terms of 

the mandate to protect and recover listed Snake River fall Chinook stocks. 

3) It is important to determine the connection between changes in the hydrological 

regime and those in life history strategy. It remains unclear whether the reservoir-type 

fall Chinook is better viewed as an evolutionary response to a major change in the 

hydrological regime of the Columbia Basin or as a developmentally plastic response to 

variable hydrological conditions. Regardless, it is almost surely responsive to a changing 

summer spill regime. The Basin will ultimately require both a better in-river tracking 

system for these fish and some indication of the extent to which the over-wintering 

behavior is genetically programmed, as opposed to environmentally responsive and 

plastic. Perhaps the recent paper by Brannon et al. (2004) is relevant. They surmise that 

Chinook life history genetics are conditioned by temperature (i.e. life history types are 

arrayed on a temperature continuum). 

The ISAB has emphasized that to resolve the very large uncertainties about the actual 

migration survival rates and the relative contributions of the two distinct life history types 

to the effective production of wild fall Chinook will require new data to be collected 

using a new study design. It will be especially important to collect scales from returning 

adults as they pass Lower Granite Dam to secure a large enough sample size to determine 

frequencies of the two life history types at that stage (ISAB 2004-2). 

4) Survival of over-wintering reservoir-type Chinook salmon is an area that deserves 

further research. Estimates of mortality rates of fall Chinook exhibiting this life history 

during reservoir residency and during passage downstream have been difficult to obtain. 

To date, relatively small sample sizes have precluded any accurate calculations of 

survival rates. (See Appendix A for details of ongoing winter migration and distribution 

study updates.) 

5) Data on fall and winter distribution of salmonids in other reservoirs, the tidal

freshwater river and the upper estuary are also required to understand the ecology of 

reservoir-type Chinook. In this regard the monitoring of juvenile Chinook in the upper 

estuary by Bottom et al. (2005) could be expanded further upriver to the extensive tidal 

freshwater reaches below Bonneville Dam.

6) Any change in spill regime can be expected to alter the migrational dynamics of 

various other salmonid and non-salmonid species of interest. Quite apart from the 

necessity to manage the hydrosystem for several competing human needs, there are 

14 
multiple fish species that need to be accommodated. The effect of spill on Pacific 

lamprey and white sturgeon, species that have been documented to have passage 

problems in the hydrosystem, clearly needs additional study. 

7) It will also be important to determine the consequences of changing the spill regime

for upriver movements of adult salmon and any other species for which changes in 

summer spill timing and volume are relevant. There is anecdotal information (NMFS 

Hydro Division) that adult passage counts decreased at Little Goose Dam during the 

summer spill and increased when spill was reduced from 70% of daily average flow to 

40% of average flow. Additional data/studies on adult salmon and steelhead passage

behavior at lower Snake dams are needed to determine if there are any significant effects 

of summer spill on passage delay, fall-back, straying rates, and pre-spawn mortality of

these migrants. 

III. Conclusions 

The ISAB found no studies specifically designed to evaluate the effectiveness of the 

court ordered spill on juvenile salmonid survival, travel time, smolt to adult return rates, 

or smolt condition. Some of the studies implemented on the river in 2005 may provide 

some information on the response of juvenile salmon to the increased spill. However, 

these results will not be complete until adult salmon from the 2005 cohort return. The 

data in hand suggest: 

PIT-tag Studies 

• NMFS/USFWS - It will be necessary to monitor the returning adults to establish 

SARs for the 2005 cohort, in order for this study to provide information relevant to 

the effectiveness of the 2005 spill. Adults from the 2005 cohort will return in three to

five years. Reach survival estimates for juvenile migrants will be available in the 

spring of 2006. Draft post-release performance results of reach survivals were 

presented to the ISAB for Snake River groups, but data from Clearwater groups were 

not yet available. Nor do these estimates account for reservoir-type fall Chinook. The 

post-release performance (i.e. passage timing, spill exposure history, travel rate, and 

joint probability of migrating and surviving) of wild subyearlings and Lyons Ferry 

hatchery surrogate subyearlings were similar. Compared with either wild or surrogate 

subyearlings, production subyearlings emigrated much earlier, experienced almost no 

spill, and had higher travel rates and survival. 

• FPC Analysis - The 2005 reach survival estimate may be a good indicator of a 

potential benefit of the 2005 summer spill for subyearling Chinook, but until SARs 

can be estimated it is only a potential benefit. Most of the preliminary analyses focus 

on survival estimates among years. These comparisons are of limited utility, given 

major variations in river hydrosystem spill operations among years and considerable 

annual variation in migration timing and passage behavior of subyearling Chinook 

from year to year. Travel time estimates may be adequate for the entire population of 

15 
migrating smolts but are inadequate for estimating travel times for wild fish and 

specific sub-groups of migrants (e.g. Clearwater fish). 

• The survival estimates presented represent the joint probability of migrating as a 

subyearling and surviving through the reach of interest. Any changes in survival 

estimates observed among years could be due to a change in survival or a change in 

the proportion of fish migrating as subyearlings as opposed to yearlings. 

Radio-tag Studies 

• Radio-tag studies provided very useful data to determine passage behavior and 

survival estimates of subyearling Chinook at each of the lower Snake River dams and 

McNary dam during the court ordered spill. Data indicated that when provided with 

significant levels of summer spill subyearling fall Chinook juveniles passed through 

spillways at lower Snake River dams with little delay and high efficiency (96 to 99 % 

FPE). 

• Data also indicate that the removable spillway weirs (RSW) tested at Lower Granite 

and Ice Harbor dams were efficient in passing a large proportion of the subyearling 

Chinook with high survival rates. Except for the on/off RSW tests, only one primary 

spill condition was tested; spill on for 24 hr/day. Controlled tests, varying amounts 

and duration of spill, would have given a better evaluation of spill effects on passage 

behavior and survival. 

• Radio-tag data are very useful for evaluating overall spill passage behavior and 

survival at specific dams but not for multi-reservoir reach survival estimates (e.g. 

Lower Granite Dam to McNary Dam), system-wide survival estimates, or SARs 

because of relatively short-lived tag duration. 

Subyearling fall Chinook Reservoir Type 

• PIT-tag data on wild subyearling Chinook are not useful for evaluating immediate 

effects of summer spill. These studies are designed to determine long-term trends in 

SARs of wild populations. 

• The effects of 2005 summer spill on the proportions of reservoir-type and ocean-type 

fall Chinook relative to the proptions observed in recent years may be observed in the 

spring of 2006 when reservoir-type fish migrate from the system. 

Recommended Research Studies 

• Replicate the studies of coordinated dam/spill operations for multiple years, to reflect 

some reasonable range of variation in flow among years, particularly as it impacts the 

effectiveness of spill on Snake River Chinook salmon. 

 

16 
• Substantially augment monitoring of tagged juveniles and adults throughout the entire 

system, to allow wider-scale assessments of competing hydrological options (i.e. 

transport vs. in-river strategies). 

• Monitor the autumn and winter distribution of salmonids in other reservoirs, the tidal 

freshwater river, and in the upper estuary, extending all the way to Bonneville Dam.

• Evaluate the consequences of changing the spill regime for upriver movements of 

adult salmon, steelhead, and other species for which changes in summer spill are 

relevant (e.g. white sturgeon, Pacific lamprey, and American shad). 

• Increase the monitoring of reservoir-type fall Chinook, throughout the system and 

over years. We will ultimately require both a better in-river tracking system for these

fish and some sense of the extent to which this behavior is genetically programmed. 

• Estimate survival of over-wintering reservoir-type Chinook salmon. In particular, 

estimates of mortality rates during reservoir residency and during passage 

downstream are needed.

17 
Acknowledgements 

The ISAB gratefully acknowledges the following scientists for their excellent 

presentations of study results and analyses related to the 2005 summer spill effects on 

Snake River subyearling fall Chinook: William P. Connor (USFWS), Steven G. Smith 

(NMFS), John Skalski (UW), Margaret Filardo and Jerry McCann (FPC), Rock Peters 

(COE), Russ Perry (USGS) and Eric Hockersmith (NMFS). These presentations were 

especially helpful, as the majority of the ISAB members were new to the Board. 

Literature Cited 

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Smith. 2005. Passage behavior and survival for radio-tagged subyearling Chinook at 

Lower Granite Dam, 2005. NOAA Fisheries. Abstract p. 75, in Proceedings 2005 

Anadromous Fish Evaluation Program, Walla Walla District/U S Army Corps of

Engineers. Maxey Hall, Whitman College, Walla Walla Washington. 

Antolos, M., Roby, D. D., Lyons, D. E.; Collis, K.,Evans, A.F. Hawbecker, M., and 

B.A.Ryan.2005 Caspian tern predation on juvenile salmonids in the mid-Columbia River

Transactions of the American Fisheries Society. 134:466-480.

 

Beckman, B. R., Dickhoff, W. W. Zaugg, W. S. ,Sharpe, C., Hirtzel, S., Schrock, R. 

Larsen, D.A., Ewing, R.D., Palmisano, A., Schreck, C.D., and C.V. W. Mahnken, 

1999.V. W. Growth, smoltification, and smolt-to-adult return of spring Chinook salmon 

from hatcheries on the Deschutes River, Oregon. Transactions of the American Fisheries 

Society. 128.1125-1150. 

 

Bottom, D.L., Jones, K.J., Cornwell, T.J., Gray, A., and C.A. Simenstad, 2005. Patterns 

of Chinook salmon migration and residency in the Salmon River estuary (Oregon). 

Estuarine Coastal and Marine Science 64: 79-93. 

Bottom, D., and 13 others 2005. Estuarine habitat and juvenile salmon: current and 

historic linkages in the Lower Columbia River and Estuary. Abstract p. 19-20 in 

Proceedings 2005 Anadromous Fish Evaluation Program, Walla Walla District/U S Army

Corps of Engineers. Maxey Hall, Whitman College, Walla Walla Washington. 

Brannon, E.L., M.S. Powell, T.P. Quinn, and A. Talbot. 2004. Population structure of 

Columbia River Basin Chinook Salmon and Steelhead Trout. Reviews in Fisheries 

Science 12:99-232. 

Burnham, K.P., D.R. Anderson, G.C. White, C. Brownie, and K.H. Pollock. 1987. Design 

and analysis methods for fish survival experiments based on release-recapture. American 

Fisheries Society Monograph 5. 

Connor, W.P. and S.G. Smith. 2005. Dec 7, 2005 power point presentation to the ISAB. 

18 
Connor, W.P. 2005. Tabulated data on run composition (% ocean type and % reservoir 

type) for wild fall Chinook salmon females and males collected from the adult fish 

bypass system at Lower Granite Dam (unpublished data distributed following 

presentation to ISAB on Dec 7, 2005). 

Connor, W.P. 2005. Investigating passage of ESA-listed juvenile fall Chinook salmon at 

lower granite dam during winter when the fish bypass system is not operated. Annual 

Report 2005. Prepared for: U.S. DOE Bonneville Power Administration Environment, 

Fish and Wildlife Department P.O. Box 3621 Portland, OR 97208-3621. Project Number 

200203200. www.efw.bpa.gov/Environment/EW/EWP/DOCS/REPORTS/GENERAL

Connor, W. P., Burgie, H.L., and R. Waitt, 2002. Juvenile life history of wild fall 

Chinook salmon in the Snake and Clearwater Rivers. North Amer J Fish Man 22: 703-

712. 

Connor, W.P., Sneva, J.G., Tiffan, K.F., Steinhorst, R.K., and D. Ross, 2005. Two 

alternative juvenile life history types for fall Chinook salmon in the Snake River basin. 

Trans Amer Fish Soc 134: 291-304. 

Counihan, T.D., J.M. Hardiman, C. Walker, and A. Puls. 2005. Subyearling Chinook 

salmon route-specific passage and survival probabilities associated with two 24-h spill 

operations at Bonneville Dam, 2004. USGS draft report submitted to the Bonneville 

Power Administration November 30, 2005. 

Coutant, C.C. and R.R. Whitney, 2005. Hydroelectric system development: effects on 

juvenile and adult migration. P. 249-324 in Williams, R.N. (Ed) 2005. Return to the 

River. Elsevier. 

Curet, T.S. 1993. Habitat use, food habits, and the influence of subyearling Chinook 

salmon in Lower Granite and Little Goose Reservoirs, Washington. Master’s thesis, 

University of Idaho, Moscow. 

Evans, S.D., L.S. Wright, R.E. Reagan, N.S. Adams, and D.W. Rondorf. 2005. Passage 

behavior of radio-tagged subyearling Chinook salmon at Bonneville Dam, 2004. USGS 

Annual Report submitted to the U.S. Army Corps of Engineers, November 5, 2005. 

Filardo, M.and J. McCann. 2005. Dec 7, 2005 power point presentation to the ISAB. 

Graham, C.C. and L.R. Russell, 1979. An investigation of juvenile salmonid utilization of 

the delta-lakefront area of the Adams River, Shuswap Lake. Canada Fisheries and Marine 

Service Manuscript Report 1508. 32 p. 

Gilbert, C.H. 1913. Age of maturity of the Pacific salmon Oncorhynchus. Bull US 

Bureau Fish 32: 1-22. 

19 
Higgs, D.A., J.S. Macdonald, C.D. Levings, and B. Dosanjh. 1995. Nutrition and 

feeding habits of Pacific salmon (Oncorhynchus spp.) in relation to life history stage 

p.161-315 . In Physiological ecology of Pacific salmon. Edited by Brett, R., Clarke, 

W.C., Groot, K., and L. Margolis. University of B.C. Press, Vancouver, B.C. 510 p. 

Hockersmith 2005 – Dec. 7 power point presentation. 

ISAB. 2004. ISAB findings from the Reservoir Operations/Flow Survival Symposium.

ISAB Report 2004-2. www.nwcouncil.org/library/isab/isab2004-2.htm 

ISRP. 2004. Review of Response to ISRP comments on Summer Spill Study Proposal: 

Estimating the survival of sub-yearling Chinook salmon through Bonneville Dam during 

two spill operation scenarios using Radio-Telemetry: 2004. ISRP 2004-5a. 

www.nwcouncil.org/library/isrp/isrp2004-5a.htm (See footnote above). 

Lyons, D.E., Roby, D. D. and K. Collis, Ken 2005. Foraging ecology of Caspian Terns in 

the Columbia River estuary, USA. Waterbirds. 28: 280-291. 

Mains, E.D., and J.M. Smith. 1964. The distribution, size, time, and current preferences 

of seaward migrant Chinook in the Columbia and Snake Rivers. Washington Dept. of 

Fisheries. Fisheries Research Papers 2 (3). March 1964, 43 pp. 

Marsh, D.M. and W.P. Connor. 2005. A study to compare SARs of Snake River fall 

Chinook salmon under alternative transportation and dam operational strategies. Research 

Proposal to the US Army Corps of Engineers. February 2005. 

Nightengale and Bennett 1996 (cited in Return to the River 2000 draft) 

(nwcouncil.org./library/return/ch5.pdf). 

Ogden, D.A., E.E. Hockersmith, G.A.Axel, R.F. Absolon, B.P. Sandford, S.G. Smith, and 

D.B.Dey. 2005. Passage behavior and survival for radio-tagged subyearling Chinook 

salmon at Ice Harbor Dam, 2005. Abstract p. 69, in Proceedings 2005 of the Anadromous 

Fish Evaluation Program, Walla Walla District/U S Army Corps of Engineers. Maxey 

Hall, Whitman College, Walla Walla Washington. 

Perry, R. 2005. Dec. 7, 2005 power point presentation to ISAB. 

Rich, W.H. 1920. Early history and seaward migration of Chinook salmon in the 

Columbia and Sacramento Rivers Bull US Bureau Fisheries 37:1-74. 

Peven, C., A. Giorgi, J. Skalski, M. Langesllay, A. Grassell, S.G. Smith, T. Counihan, R. 

Perry, and S. Bickford. 2005. Guidelines and recommended protocols for conducting, 

analyzing, and reporting juvenile salmonid survival studies in the Columbia River Basin.

Source of this document not evident. 

Reimers, P.E. 1973. The length of residence of juvenile fall Chinook salmon in Sixes 

River, Oregon. Research Reports of the Fish Commission of Oregon 4(2): 3-42. 

20 
Rondorf, D.W., Gray, G.A., and R.B. Fairley, 1990. Feeding ecology of subyearling 

Chinook salmon in riverine and reservoir habitats of the Columbia River. Transactions of 

the American Fisheries Society 119: 16-24. 

Sherwood, C.P., Jay, D.A., Harvey, R.B., Hamilton, P. and C.A. Simenstad 1990. 

Historical changes in the Columbia River estuary. Progress in Oceanography 25:299-352. 

Shively, R.S, Poe, T. P., and S.T.Sauter, 1996. Feeding response by northern squawfish 

to a hatchery release of juvenile salmonids in the Clearwater River, Idaho. Transactions 

of the American Fisheries Society. 125:230-236. 

Skalski, J. 2005. Dec . 7, 2005 power point presentation to ISAB. 

Tiffan, K, 2005. Passage of juvenile fall Chinook salmon at Lower Granite Dam during 

the winter when the juvenile bypass is not operated. Abstract p. 11 in Proceedings 2005 

Anadromous Fish Evaluation Program, Walla Walla District/U S Army Corps of

Engineers. Maxey Hall, Whitman College, Walla Walla Washington. 

Tiffan, K.F., Kock, T.J., Connor, W.P., Mullins, F., and J.G. Sneva, 2005. Investigating 

Passage of ESA-listed Juvenile Fall Chinook Salmon at Lower Granite Dam During 

Winter When the Fish Bypass System is not Operated. Chapter 1 in Tiffan, K. and 

Annual Report 2005. Prepared for: U.S. Department of Energy Bonneville Power 

Administration Environment, Fish and Wildlife Department P.O. Box 3621 Portland, OR 

97208-3621. Project Number 200203200: 

www.efw.bpa.gov/Environment/EW/EWP/DOCS/REPORTS/GENERAL 

Tiffan, K. and B. Connor, 2005 . Investigating passage of ESA-listed juvenile fall 

Chinook salmon at lower granite dam during winter when the fish bypass system is not 

operated. Annual Report 2005. Prepared for:U.S. Department of Energy Bonneville 

Power Administration Environment, Fish and Wildlife Department P.O. Box 3621 

Portland, OR 97208-3621. Project Number 200203200. 

www.efw.bpa.gov/Environment/EW/EWP/DOCS/REPORTS/GENERAL 

21 
Appendix A. Background Life History Information on Juvenile Fall 

Chinook

Food Habits 

The diet of Chinook subyearlings in reservoirs (lentic environment) is different than 

rivers and streams (lotic environment). In lotic environments (e.g. Hanford Reach on the 

Columbia River) subyearling Chinook (55-97 mm length) primarily ate aquatic insects, 

and in the lentic environment (reservoir Lake Wallula) switched to zooplankton, 

amphipods, and terrestrial insects (Rondorf et al. 1990). The corophiid amphipod 

Corophium salmonis is now abundant in Lower Granite reservoir and is also potentially 

available as food for reservoir-type Chinook (Nightengale and Bennett 1996 in Return to 

the River (2000 draft). However, as far as known subyearling Chinook do not feed on the 

amphipod (Curet 1993, cited in Coutant et al. (2005) (see also below)). The caloric 

benefit of the amphipod relative to zooplankton and insects has not been established 

(Chapter 5 (nwcouncil.org/library/return/ch5.pdf). However, aquatic insects, especially 

their larvae and pupae are known to have more fatty acids (Higgs et al. 1995) compared 

to amphipods. 

As mentioned above the only data on juvenile Chinook feeding in Lower Granite 

reservoir indicates that larger fish (> 86 mm) fed mainly on larval fish while smaller fish 

(< 86 mm) fed on ephemeropterans (mayflies), cladocerans (water fleas), and dipterans 

(midges) (Curet 1993). Age 0 reservoir-type Chinook passing Lower Granite or Little 

Goose dams in spring 1997 were larger (112-139 mm, Connor et al. 2005) than the fish 

that Curet (1993) studied and therefore might be expected to feed on larval fish and 

possibly amphipods or mysids. Age 1 reservoir-type Chinook were larger again (222-224 

mm; Connor et al. 2005). 

Overwinter Movements and Distribution 

In order to understand the effects of the 2005 spill on reservoir-type Chinook, data on 

SARs are required. There are good baseline data available on the sex ratio of returning 

reservoir-type Chinook for several years (Connor Dec 7, 2005 presentation to ISAB). The 

USGS is currently tagging and radio-tracking 2005 limited numbers of fall Chinook 

holdovers, which is a good start on an in-season assessment of reservoir-type Chinook 

which should tie with the SAR data when those become available. The following studies 

are in progress for the winter 2005-2006 (Tiffan pers. comm. to Tom Poe, Dec 14, 2005): 

• Collection and radio tagging of reservoir-type Chinook in Lower Granite 

reservoir. 25 juveniles were collected and tagged on 11/02/2005, 23 juveniles on 

12/06/05. It is hoped that another 25 can be tagged in January 2006. 

• From Lower Granite Reservoir beach seine sampling 25 juveniles were collected, 

tagged, and released 25 juveniles on 11/02/05, and 23 juveniles on 12/06/05. It is 

hoped to collect, tag and release another 25 juveniles early in Jan 2006. 

22 
• Radio-telemetry antenna arrays kept in place from the summer studies for 

detections of smolts (and maybe some mobile tracking) are now being used to 

collect data on over-winter movement and distribution history, as was done in 

2004. The tags being used have an estimated life of 139 days, but past history has 

shown that some have lasted over 150 days. 

• If efforts can be expanded by collecting and tagging more fish, it should be 

possible to conduct a meaningful study of overwinter survival for tagged fish. 

The ISAB looks forward to the results of these studies. Although the research planned is 

limited by budget concerns, the winter 2005-2006 data will be very useful to help assess 

survival status of reservoir-type Chinook, pending later SAR results. 

Winter passage survival of over-wintering juvenile fall Chinook at lower Snake River 

dams is also deserving of further research. Mortality resulting from turbine passage 

routes could result in significant decreases in detections of radio tagged fish. To date, 

limitations based on relatively small sample sizes have precluded meaningful estimates of 

survival probabilities for over-wintering fish that passed through turbines in dams on the 

lower Snake River. 

Lower River and Estuarine Distribution 

Data on autumn and winter distribution of salmonids in other reservoirs, the tidal

freshwater river and the upper estuary are also required to understand the ecology of 

reservoir-type Chinook. In this regard, the monitoring of juvenile Chinook in the upper 

estuary by Bottom et al. (2005) could profitably be expanded upriver to the extensive 

tidal freshwater reaches below Bonneville Dam. Results from the upper estuary habitats 

show Chinook are present during winter (Figure 1). If these fish remained in the habitats 

over the winter they would develop a freshwater check similar to reservoir-type Chinook, 

and therefore might be indistinguishable in returning adults. Long-term ecosystem studies 

in the reservoirs are also needed to understand the feeding ecology of reservoir-type 

Chinook and its effects on their survival. 

23 
Lo

g

10

CP

UE

J M M J S N J M M J S N J M M J S N J M M J S N

10

0.0

0.5

1.0

1.5

2.0

2.5

3.0

Estuarine Zone

Mouth

Mixing

Tidal Fresh

 

J M M J S N J M M J S N J M M J S N J M M J S N

10

0.0

0.5

1.0

1.5

2.0

2.5

3.0

Estuarine Zone

Mouth

Mixing

Tidal Fresh

Log10 CPUE

J M M J S N J M M J S N J M M J S N J M M J S N

0.0

0.5

1.0

1.5

2.0

2.5

3.0

Juvenile Chinook Salmon

J M M J

2002

S N J M M J S

2003

N J M M J S

2004

N J M M J S

2005

N

Estuarine Zone

Mouth

Mixing

Estuarine Zone

Mouth

Mixing

Tidal Fresh 3.0

2.5

2.0

1.5

1.0

0.5

0.0

Fig 1. Results of beach seine sampling for juvenile Chinook in three zones of 

the Columbia River estuary (graphic courtesy of Dr. Dan Bottom, NOAA Fisheries, 

Newport; OR. presented at the AFEP Annual Review Nov15 2005). 

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Attachment 1. Memorandum from the Northwest Power and 

Conservation Council, October 14, 2005 (letterhead removed) 

TO: ISAB Executive Committee and Administrative Oversight Panel

FROM: Melinda Eden, Council Chair

SUBJECT: Request for ISAB Review of 2005 Spill Effectiveness 

At its October 12, 2005 meeting, the Council agreed to request the Independent Scientific 

Advisory Board (ISAB) to review the biological effectiveness of spill operations in 2005. 

The Council’s 2003 mainstem amendments call for NOAA Fisheries, the federal 

operating agencies, and salmon managers to implement tests to examine the benefits of

the current summer spill program for outmigrating juvenile fall Chinook, and to 

determine whether the biological benefits can be achieved in a more effective and less 

costly manner. The 2005 operations amounted to an experiment beyond the envisioned 

spill program, of which the Council is highly interested in the results.

Specifically, the Council asks that the ISAB consider the full migration and spill season

and address the following questions: 

1. What was the effect of the spill operations, including the net effect of the courtordered spill, for juvenile survival over the various passage routes including the 

standard spillways, the removable spillway weirs, and other bypass routes? 

2. How does or should the fall Chinook reservoir life-history type factor into an 

analysis of the effectiveness of the 2005 operations?

In answering these questions, the Council understands that the ISAB will examine data 

collected and analyses conducted by Columbia River Basin fish and wildlife agencies 

such as the National Marine Fisheries Service, the Fish Passage Center, and others. The 

Council asks that the ISAB review these data and analyses for their scientific soundness 

and where appropriate, suggest ways in which the analyses may be improved; e.g. were a 

broad enough range of years or factors such as temperature adequately considered? The 

ISAB should also highlight uncertainties that affect the analyses. 

The Council values the fact that the ISAB serves not only the Council but also the 

National Marine Fisheries Service (NOAA Fisheries) and the Columbia River Basin 

Tribes. Consequently, the Council encourages NOAA Fisheries and the tribes to review, 

refine, and add questions to the Council’s request and to provide information necessary to 

ensure a thorough review. 

To be of greatest value, the Council requests that the ISAB complete the review by 

November 30, 2005. 

 

 

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Attachment 2. NMFS (NOAA Fisheries) and CRITFC Questions 

NMFS Questions 

1. Do sufficient data exist and do the analyses conducted to date provide an adequate 

evaluation of the effect of the 2005 summer spill program on: 

 a. Juvenile survival and travel time?

 b. Smolt-to-Adult return rates?

2. What are the potential affects of the summer spill program on fish of the “reservoirtype” life history compared to fish that migrate as subyearlings? 

3. Are studies currently in place or planned adequate to address these questions?

CRITFC Questions 

1. Can the ISAB provide comparisons of estimates of route-specific survival and passage 

rates (i.e. for turbines, RSW, bulk spill, screens and bypass system) by project and reach? 

2. Which stocks were likely to be most affected by the 2005 spill operations? 

3. What additional monitoring would be appropriate and desirable to discern other useful 

biological knowledge related to spill and other dam passage routes (e.g., physical 

monitoring metrics such as temperature in the migration corridor and in transportation 

facilities; physiological status of juveniles as they move downstream)? 

4. Can the ISAB relate the data available for interim analysis in the context of achieving 

recovery metrics for Snake River fall Chinook (e.g., meeting biological diversity, spatial 

structure and abundance)?

________________________________________ 

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