Summary of Survival Data from Juvenile Coho Salmon 

in the Klamath River, Northern California, 2006

Open-File Report 2007–1023

Prepared in cooperation with the Bureau of Reclamation

U.S. Department of the Interior

U.S. Geological Survey
Cover: Photograph of Klamath River looking downstream near its confluence with the 

Salmon River, northern California. (Photograph taken by Philip Haner, U.S. Geological 

Survey, Cook, Washington, 2006.)
Summary of Survival Data from Juvenile 

Coho Salmon in the Klamath River, 

Northern California, 2006

By John W. Beeman

Prepared in cooperation with the

Bureau of Reclamation

Open-File Report 2007–1023

U.S. Department of the Interior

U.S. Geological Survey
U.S. Department of the Interior

DIRK KEMPTHORNE, Secretary

U.S. Geological Survey

Mark D. Myers, Director

U.S. Geological Survey, Reston, Virginia: 2007

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Suggested citation:

Beeman, J.W., 2007, Summary of survival data from juvenile coho salmon in the Klamath River, northern California, 

2006: U.S. Geological Survey Open-File Report 2007-1023, 6 p.
iii

Contents

Abstract...........................................................................................................................................................1

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

Survival of Juvenile Coho Salmon from Iron Gate Hatchery to the Shasta River...............................4

Survival of Juvenile Coho Salmon Through River Reaches ...................................................................5

Summary..........................................................................................................................................................6

Acknowledgments.........................................................................................................................................6

References cited............................................................................................................................................6

Figures

Figure 1. Map showing study area of the Klamath River juvenile coho salmon survival

study, northern California, 2006 ............................................................ 2

Figure 2. Schematic of the paired-release-survival model for the Klamath River juvenile

coho study, northern California ............................................................ 3

Tables

Table 1. Estimated relative apparent survivals, standard errors, and 95-percent

confidence intervals of radio-tagged juvenile coho salmon in each of the first

three study reaches in the Klamath River, northern California, spring 2006 ......... 4

Table 2. Model summary from analyses of apparent survival and capture probabilities 

to estimate reach survivals ............................................................... 5

Table 3. Estimated apparent survivals and profile likelihood confidence intervals of

radio-tagged juvenile coho salmon in five study reaches of the Klamath River,

northern California, spring 2006............................................................ 6
iv

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Abstract

Little is known about the survival of ESA-listed juvenile 

coho salmon during their seaward migration in the lower 

Klamath River. In 2006, the Bureau of Reclamation funded a 

study to estimate the survival of radio-tagged juvenile coho 

salmon in the Klamath River downstream of Iron Gate Dam. 

A series of models were evaluated to determine if survival 

varied between hatchery and wild fish and among several river 

reaches between the dam river kilometer 33, a total distance of 

276 kilometers. The results from 2006, the first year of study, 

indicated little support for differences in survival between 

hatchery and wild fish and lower survival in the most upstream 

reach than in those farther downstream. This document is a 

brief summary of survival results to date.

Introduction

In 2006, the U.S. Geological Survey (USGS) participated 

in a cooperative study to estimate survival of juvenile coho 

salmon in the lower Klamath River, northern California. The 

purpose of the study was to provide information about the 

relation between survival of juvenile coho salmon and river 

discharge in the Klamath River downstream of Iron Gate Dam 

(river kilometer [rkm] 310). The study fish were part of the 

Southern Oregon/Northern California Coasts Evolutionary 

Significant Unit of coho salmon listed as Threatened under 

the Endangered Species Act in 1997. The study was a 

collaboration among the USGS and, listed in alphabetical 

order, the Fish and Wildlife Service, the Karuk Tribe of 

California, and the Yurok Tribe. The work was funded by 

the Bureau of Reclamation, Klamath Falls Basin Office. This 

report is a brief summary of the survival results to date. 

We estimated apparent survivals of radio-tagged juvenile 

coho salmon in the Klamath River downstream of Iron Gate 

Dam, northern California in 2006 using paired-release and 

single-release methods; both are based on Cormack-JollySeber capture-mark-recapture models (Cormack, 1964; Jolly, 

1965; Seber, 1965). Apparent survival is the probability that an 

animal remains available for recapture. In the context of this 

study, apparent survival is the joint probability that the animal 

is both alive and migrates through the study area. As such, fish 

that stop migrating, or travel to areas outside the mainstem 

Klamath River and do not return during the study are counted 

as mortalities. All references to ‘survival’ in this report refer to 

apparent survival.

To review 2006 activities, we released radio-tagged 

juvenile coho salmon (Oncorhynchus kisutch) of wild 

and hatchery origin separated into treatment and control 

experimental groups. The wild fish were obtained at the rotary 

trap in the Shasta River operated by the California Department 

of Fish and Game and the hatchery fish came from Iron 

Gate Hatchery. The treatment groups were released into the 

Klamath River at the hatchery (rkm 309) and the control 

groups were released into the Shasta River near its confluence 

with the Klamath River (rkm 288; fig. 1). 

The purpose of the two experimental groups was to 

enable us to estimate survival of fish in the Klamath River 

from near Iron Gate Dam to the Shasta River, the first major 

tributary, without the potential effects of latent tagging and 

handling mortality. The paired-release design permits this and 

is described in detail in Burnham and others (1987). Latent 

mortality from tagging and handling, if present and expressed 

shortly after release, is included in overall mortality in other 

designs, and can result in an overestimate of the mortality 

associated with the treatment of interest. Relative estimates of 

survival were calculated using the paired-release design from 

the two experimental groups of wild and hatchery origin fish 

in each of the first three reaches. The survival estimates are 

“relative,” because they are calculated as the treatment survival 

divided by the control survival, hence they are the treatment 

survival relative to the control survival. In the first reach, the 

relative estimate reflects the survival of the treatment group 

from release at Iron Gate Hatchery to the release point of the 

control group at the Shasta River, a distance of 21 km, and 

is based on the survival of each group from release to the 

Scott River detection site (fig. 2). In the next two reaches, the 

estimates are the survival of the treatment group divided by 

the control group over the entire reach, because both groups 

traveled the same distance. These can be useful to determine 

if there are tagging and handling effects that are not expressed 

within the first reach.

Summary of Survival Data from Juvenile Coho Salmon 

in the Klamath River, Northern California, 2006

by John W. Beeman
Trinity River

rkm 69

Blake’s Riffle

rkm 13

Steelhead

Lodge

rkm 33

Salmon River

rkm 107

Indian

Creek

rkm 178

Scott

River

rkm 234

Shasta

River

rkm 288

C

T

56

71

36 38

54 & 75

Figure 1. Study area of the Klamath River juvenile coho salmon survival study, northern California, 2006.

Locations of treatment (T) and control (C) releases are indicated by arrows and detection sites are indicated 

by ☼. Bold numbers indicate the lengths of each reach in kilometers. Figure modified from U.S Fish and 

Wildlife Service, Arcata, CA., 2006.

   Summary of Survival Data from Juvenile Coho Salmon in the Klamath River, northern California, 2006
Figure 2. Schematic of the paired-release-survival model for the Klamath River juvenile coho study, northern California. 

Test fish released near Iron Gate Dam (IDG) were paired with control fish released near the Shasta River. The location of 

the control fish release is based on the definition of the reach of interest; the Shasta River was used in 2006. Survival from 

release near the dam to the Shasta River (Sreach) was measured relative to the control groups released near the Shasta River 

(Rc), canceling out effects of survival due to tagging and handling. Survival from there to and between the other sites, other 

than the last one, can be estimated as well, with the method depending on the assumptions that can be satisfied. Only the 

joint probability of capture and survival (λ) can be estimated in the last reach. 

St1

Sc1 IGD to Shasta River reach 

Rt

Rc

Scott River 

Indian Creek

Other sites, etc. 

St3

St2

Sc1

Sc3

Sc2

Sreach=

pt1

pt2 pc2

pc1

Last site downstream 

λt λc

ptn pcn

St1

Sta

Stb

Introduction 
Survival of Juvenile Coho Salmon from 

Iron Gate Hatchery to the Shasta River

A series of models was created and ordered in terms of 

parsimony using the program MARK (White and Burnham, 

1999). The analysis included a suite of models describing 

capture probabilities and survival of fish from the two 

experimental groups in each of the first three reaches. The 

models were ranked using Akaike Information Criterion (AIC) 

methods to determine the models that were best supported 

by the data. Estimates of capture probabilities and survivals 

were obtained via multimodel averaging, because several 

models were supported by the data. In multimodel averaging, 

models are weighted according to their AIC values and those 

with greater weights (for example, more supported by the 

data) contribute more to the result. The general methods 

are described in Burnham and Anderson (1998). Tests of 

model fit indicated moderate overdispersion in the data, 

which commonly is caused by heterogeneity. Overdispersion 

indicates that the variance may be underestimated. We 

therefore used a variance inflation factor, “c-hat”, of 1.305 to 

correct for the over dispersion in the data from hatchery fish 

and 1.536 in the data from wild fish (derived with program 

MARK using the median c-hat procedure). This is a common 

issue and does not indicate a problem with the fit of the model 

to the data.

The relative survival estimates and their confidence 

intervals are included in table 1. Each of the estimates is near 

1.0 and their confidence intervals overlap 1.0 considerably. 

We can conclude from this that the survival of the treatment 

groups from release to the Shasta River was high, but the 

confidence intervals around the estimates are wide. The 

estimates in reaches two and three also are near 1.0, and the 

current data do not support differential tagging and handling 

mortality being expressed in treatment and control fish 

through these reaches. Thus, examination of reaches further 

from the release sites was not warranted.

Table 1. Estimated relative apparent survivals, standard errors, and 95-percent confidence intervals of radio-tagged juvenile 

coho salmon in each of the first three study reaches in the Klamath River, northern California, spring 2006. 

[Data are from 157 wild fish and 116 hatchery fish released from April 25 through May 16, 2006. Results are based on the ratio of treatment group 

survival divided by the control group survival within each reach. Treatment fish were released at Iron Gate Hatchery (rkm 309) and control fish were 

released at the confluence of the Klamath and Shasta Rivers (rkm 288). As such, the first reach represents survival of the treatment group from Iron 

Gate Hatchery to the control release site. Both groups traveled the same distance through the remaining reaches. These are preliminary estimates 

generated on December 26, 2006, by John Beeman, U.S. Geological Survey, Western Fisheries Research Center]

Reach Description Reach 

length (km)

Relative 

apparent 

survival

Standard 

error

95-percent 

confidence interval

Lower Upper

Wild Origin

1 Iron Gate Hatchery to Shasta River 21 1.101 0.123 0.860 1.343

2 Scott River to Indian Creek (rkm 178) 56 0.987 0.088 0.815 1.160

3 Indian Creek to Salmon River (rkm 107) 71 1.000 0.055 0.892 1.109

Hatchery Origin

1 Iron Gate Hatchery to Shasta River 21 0.995 0.079 0.840 1.149

2 Scott River to Indian Creek (rkm 178) 56 0.986 0.053 0.882 1.091

3 Indian Creek to Salmon River (rkm 107) 71 0.999 0.041 0.918 1.079

 Summary of Survival Data from Juvenile Coho Salmon in the Klamath River, northern California, 2006
Survival of Juvenile Coho Salmon 

Through River Reaches

Survivals through each of the first five reaches and over 

them all were estimated using the single-release design. There 

were four objectives in this analysis. They were to determine 

if survival differed (1) between wild and hatchery fish, (2) 

between treatment and control experimental groups, (3) 

among reaches and, (4) to estimate the survival over the entire 

study area. The modeling approach was similar to that used 

for the paired-release analyses. In this analysis, the models 

were ranked and assessed based on the order of the ranking 

and by the error associated with their slopes describing the 

various effects (for example, the effect of origin on survival). 

The capture probabilities of nearly all models were specified 

similarly and were allowed to vary between origins and among 

reaches.

Four of the seven models evaluated were reasonably 

supported by the data (table 2). Similar support of several 

models indicated uncertainty in model selection. Model 

selection uncertainty means the “best” model from this 

analysis might not remain the “best” model if the experiment 

were repeated, and indicates that the models, given these 

data, are insufficient to distinguish among the various factors, 

and/or the factors are trivially different. Tests of model fit 

indicated moderate overdispersion in the data. We therefore 

used a variance inflation factor “c-hat” of 1.348 to correct for 

this (derived with the program MARK using the median c-hat 

procedure). 

The top four models included those in which survival 

could vary by various combinations of reach, group, and 

origin. The model with the most support received about twice 

the weight of the second, three times the weight of the third, 

and five times the weight of the fourth (see QAICc weights 

in table 2). The last two models received less than 20 times 

the weight of the first and are essentially not supported by 

the data. The model with the largest weight allowed survival 

to vary among reaches, but not by origin or group. The next 

three models included reach and various additive effects 

of experimental group in the first reach (GroupAcute in 

table 2), origin, and a combination of all three. However, the 

coefficients within these models were imprecise, indicating 

the effects they described were poorly supported by the 

models given the data available. Consequently, results from 

this first year of study show little support for differences 

between experimental groups in the first reach, or differences 

in survival between wild and hatchery fish. We therefore 

estimated the survival within each reach, and subsequently 

over all reaches, using the output from the most supported 

model (the top row in table 2). An alternative method would 

be to generate estimates of reach survivals for each of the four 

combinations of origin and group after multimodel averaging, 

but the estimates from the two methods are essentially 

identical in this case.

Table 2. Model summary from analyses of apparent survival and capture probabilities to estimate reach survivals. 

[Models are based on data from 157 wild fish and 116 hatchery fish released from April 25 through May 16, 2006. Model descriptions include factors allowed 

to vary within apparent survival (Phi) and capture probabilities (P), including reach, group (treatment or control), and origin (wild or hatchery). GroupAcute 

denotes a model factor for an acute group effect in the first reach only. Rankings are based on QAICc, a modification of Akaike Information Criterion for 

small samples and adjustments of extra binomial variation. A ‘+’ between factors indicates an additive effect, ‘*’ denotes a multiplicative effect. The global 

model includes multiplicative effects of all factors. Number of parameters denotes the number of estimable parameters in the model + 1 for the overdispersion 

adjustment]

Model QAICc Delta 

QAICc

QAICc 

weights

Model 

likelihood

Number of 

parameters

QDeviance

{Phi(Reach), P(Reach +Origin)} 1201.57 0.00 0.45 1.00 13 172.12

{Phi(GroupAcute + Reach), P(Reach + Origin)} 1202.67 1.10 0.26 0.58 14 171.17

{Phi(Reach + Origin), P(Reach + Origin)} 1203.58 2.01 0.17 0.37 14 172.08

{Phi(Reach + Origin + GroupAcute), P(Reach + Origin)} 1204.69 3.12 0.10 0.21 15 171.13

{Phi(Group*Origin + Reach), P(Reach + Origin)} 1207.46 5.89 0.02 0.05 16 171.83

{Phi(Origin*Group*Reach), P(Reach + Origin)} 1220.68 19.12 0.00 0.00 28 159.97

{global model} 1243.80 42.24 0.00 0.00 45 146.49

Survival of Juvenile Coho Salmon Through River Reaches   
The overall (pooling origins and groups) estimates of 

survival were similar in most reaches (table 3). The point 

estimates ranged from 0.837 to 1.000 and the 95-percent 

confidence intervals were approximately ±5 percent. The 

lowest point estimate was from the first reach (0.837, 95-

percent CI 0.776 to 0.893), which also is the reach fish spent 

the most time within (release to Scott River). The highest 

point estimate was in the fourth reach, Salmon River to Trinity 

River (1.000, 95-percent CI 0.966 to 1.000), a reach fish spent 

little time in. The overall estimate of survival from rkm 309 to 

rkm 33, taken as the product of the individual reach estimates, 

was 0.684 (95-percent CI 0.613 to 0.756). It is important to 

realize the estimates for each reach were not scaled by the 

length of each reach and are therefore not directly comparable 

to one another. These estimates are the first available for 

juvenile salmonids in the lower Klamath River and as such 

there are no others for direct comparison. However, the overall 

estimate is similar to those of juvenile salmonids migrating in 

the Columbia and Snake rivers on a “per kilometer” basis.

Summary

The apparent survival of radio-tagged juvenile coho 

salmon in the lower Klamath River in 2006 was estimated 

using mark-recapture methods. This was the first year of a 

multi-year study. No latent effects of tagging and handling on 

survival were evident. The current data and models indicate 

little support for a survival difference between hatchery and 

wild fish in 2006, but considerable model uncertainty exists. 

Survival was lower in the reach from Iron Gate Hatchery to the 

Scott River than in reaches farther downstream. The overall 

estimate of survival from Iron Gate Dam to river kilometer 33 

was 0.684 (95-percent CI 0.613 to 0.756).

Acknowledgments

I would like to express my thanks to the California 

Department of Fish and Game rotary trap crew at the Shasta 

River and the staff at Iron Gate Hatchery for providing sources 

of study fish. Eric Janney provided valuable assistance during 

the analysis. 

Table 3. Estimated apparent survivals and profile likelihood confidence intervals of radio-tagged juvenile coho salmon in five 

study reaches of the Klamath River, northern California, spring 2006. 

[Results are based on data from 157 wild fish and 116 hatchery fish released from April 25 through May 16, 2006. Results are based on pooling 

fish of hatchery and wild origin and treatment and control groups. Data for the overall result was calculated as the product of the reach estimates 

with variance estimated using the delta method. Length of reach 1 was 54 km for the control group and 75 km for the treatment group. Data are 

preliminary estimates from December 21, 2006, by John Beeman, U.S. Geological Survey, Western Fisheries Research Center]

Reach Description Reach length 

(km)

Apparent 

survival

Standard 

error

95-percent 

confidence interval

Lower Upper

1 Release to Scott River (rkm 234) 54 and 75 0.837 0.026 0.776 0.893

2 Scott River to Indian Creek (rkm 178) 56 0.916 0.024 0.854 0.961

3 Indian Creek to Salmon River (rkm 107) 71 0.938 0.019 0.887 0.973

4 Salmon River to Trinity River (rkm 69) 38 1.000 7.3E-07 0.966 1.000

5 Trinity River to Steelhead Lodge (rkm 33) 36 0.951 0.025 0.886 0.997

Overall Release to Steelhead Lodge 276 0.684 0.037 0.613 0.756

References Cited

Burnham, K.P., and Anderson, D.R., 1998, Model selection 

and multimodel inference: A practical information-theoretic 

approach: Springer Verlag, New York, 488 p.

Burnham, K.P., Anderson, D.R., White, G.C., Brownie, C.,

and Pollock, K.H., 1987, Design and analysis methods 

for fish survival experiments based on release-recapture: 

American Fisheries Society Monograph 5, American 

Fisheries Society, Bethesda, Maryland, 737 p.

Cormack, R.M., 1964, Estimates of survival from the sighting 

of marked animals: Biometrika, v. 51, no. 3/4, p. 429-438.

Jolly, G.M., 1965, Explicit estimates from capture-recapture 

data with both death and immigration-stochastic model: 

Biometrika, v. 52, no. 1/2, p. 225-247.

Seber, G.A.F., 1965, A note on the multiple-recapture census: 

Biometrika, v. 52, no. 1/2, p. 249-259. 

White, G.C., and Burnham, K.P., 1999, Program MARK: 

survival estimation from populations of marked animals: 

Bird Study 46 Supplement, p. 120-138.

   Summary of Survival Data from Juvenile Coho Salmon in the Klamath River, northern California, 2006
For more information concerning the research in this report, contact the 

Director, Western Fisheries Research Center

U.S. Geological Survey, 6505 NE 65th Street

Seattle, Washington 98115

http://wfrc.usgs.gov/
OFR 2007–1023 Beeman

Summary of Survival Data from Juvenile Coho Salmon in the 

Klamath River, northern California, 2006