Prepared in cooperation with the U.S. Army Corps of Engineers

Analyses of Potential Factors Affecting Survival of 

Juvenile Salmonids Volitionally Passing Through 

Turbines at McNary and John Day Dams, Columbia River

U.S. Department of the Interior

U.S. Geological Survey

Open-File Report 2011–1227

Analyses of Potential Factors Affecting Survival 

of Juvenile Salmonids Volitionally Passing 

Through Turbines at McNary and John Day Dams, 

Columbia River

By John Beeman, Hal Hansel, and Russell Perry, U.S. Geological Survey; and Eric Hockersmith 

and Ben Sandford, National Oceanic and Atmospheric Administration Fisheries

Prepared in cooperation with the U.S. Army Corps of Engineers

Open-File Report 2011-1227

U.S. Department of the Interior

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

KEN SALAZAR, Secretary

U.S. Geological Survey

Marcia K. McNutt, Director

U.S. Geological Survey, Reston, Virginia: 2011

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Suggested citation:

Beeman, J.W., Hansel, H., Perry, R.W., Hockersmith, E., and Sanford, B., 2011, Analyses of 

potential factors affecting survival of juvenile salmonids volitionally passing through turbines 

at McNary and John Day Dams, Columbia River: U.S. Geological Survey Open-File Report 

2011-1227, 124 p.

Any use of trade, product, or firm names is for descriptive purposes only and does not imply 

endorsement by the U.S. Government.

Although this report is in the public domain, permission must be secured from the individual 

copyright owners to reproduce any copyrighted material contained within this report.
iii

Contents

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

Introduction .......................................................................................................................................3

Methods ............................................................................................................................................4

Results of Analyses from Studies at John Day Dam.......................................................................13

Yearling Chinook Salmon ............................................................................................................13

Environmental Conditions........................................................................................................13

Survival....................................................................................................................................15

Key Findings in Data from Yearling Chinook Salmon at John Day Dam..................................21

Subyearling Chinook Salmon ......................................................................................................21

Environmental Conditions........................................................................................................21

Survival....................................................................................................................................22

Key Findings in Data from Subyearling Chinook Salmon at John Day Dam............................26

Results of Analyses from Studies at McNary Dam..........................................................................30

Yearling Chinook Salmon ............................................................................................................30

Environmental Conditions........................................................................................................30

Survival....................................................................................................................................30

Key Findings in Data from Yearling Chinook Salmon at McNary Dam.....................................37

Juvenile Steelhead ......................................................................................................................43

Environmental Conditions........................................................................................................43

Survival....................................................................................................................................45

Key Findings in Data from Juvenile Steelhead at McNary Dam...............................................49

Subyearling Chinook Salmon ......................................................................................................52

Environmental Conditions........................................................................................................52

Survival....................................................................................................................................54

Key Findings in Data from Subyearling Chinook Salmon at McNary Dam...............................58

Discussion.......................................................................................................................................63

Acknowledgments...........................................................................................................................69

References Cited ............................................................................................................................69

Appendix A. Summaries of Covariate Values from Data used in Studies of Yearling Chinook 

Salmon at John Day Dam in 2002 and 2003...................................................................................74

Appendix B. Capture History Summary of Yearling Chinook Salmon from data used in studies at 

John Day Dam in 2002 and 2003....................................................................................................76

Appendix C. Model Summary from Analyses of Recapture Probabilities (p) of Yearling Chinook 

Salmon from data used in studies at John Day Dam in 2002 and 2003..........................................77

Appendix D. Summaries of Covariate Values of Subyearling Chinook Salmon from data used in 

studies at John Day Dam in 2002 and 2003....................................................................................78

Appendix E. Capture History Summary of Subyearling Chinook Salmon from data used in studies 

at John Day Dam in 2002 and 2003................................................................................................80

Appendix F. Model Summary from Analyses of Recapture Probabilities (p) of Subyearling Chinook 

Salmon from data used in studies at John Day Dam in 2002 and 2003..........................................81

Appendix G. Summaries of Covariate Values from Yearling Chinook Salmon from data used in 

studies at McNary Dam from 2002–2009........................................................................................82

Appendix H. Capture History Summary of Yearling Chinook Salmon from Data Used in Studies at 

McNary Dam in 2002–2005, and 2009............................................................................................88
iv

Appendix I. Correlation Analyses of Yearling Chinook Salmon from Data Used in Studies at 

McNary Dam in 2002–2005, and 2009............................................................................................89

Appendix J. Model Summary from Analyses of Recapture Probabilities (p) of Yearling Chinook 

Salmon from Data Used in Studies at McNary Dam in 2002–2005, and 2009................................91

Appendix K. Model-selection Results from Radio- and Acoustic-tagged Yearling Chinook Salmon 

from Data Used in Studies at McNary Dam in 2002–2005, and 2009. ............................................92

Appendix L. Beta (Slope) Coefficients of Estimable Survival Parameters of Yearling Chinook 

Salmon from Data Used in Studies at McNary Dam in 2002–2005, and 2009................................93

Appendix M. Capture History Summary of Yearling Chinook Salmon from Data Used in Studies at 

McNary Dam in 2002–2005, and 2009............................................................................................94

Appendix M. Capture History Summary of Yearling Chinook Salmon from Data Used in Studies at 

McNary Dam in 2002–2005, and 2009............................................................................................94

Appendix N. Model Summary from Analyses of Recapture Probabilities (p) of Yearling Chinook 

Salmon from Data Used in Studies at McNary Dam in 2002–2005, and 2009................................95

Appendix O. Summaries of Covariate Values of Juvenile Steelhead from Data Used in Studies at 

McNary Dam in 2004–2009.............................................................................................................96

Appendix P. Capture History Summary of Juvenile Steelhead from Data Used in Studies at McNary 

Dam in 2004–2005 and 2009........................................................................................................102

Appendix Q. Results of Correlation Analyses of Juvenile Steelhead from Data Used in Studies at 

McNary Dam in 2004–2005 and 2009...........................................................................................103

Appendix R. Model Summary from Analyses of Recapture Probabilities (p) of Juvenile Steelhead 

from Data Used in Studies at McNary Dam in 2004–2005 and 2009. ...........................................105

Appendix S. Model-selection Results from Radio- and Acoustic-tagged Juvenile Steelhead from 

Data Used in Studies at McNary Dam in 2004–2005 and 2009. ...................................................106

Appendix T. Beta (Slope) Coefficients of Estimable Survival Parameters of Juvenile Steelhead 

from Data Used in Studies at McNary Dam in 2004–2005 and 2009. ...........................................107

Appendix U. Capture History Summary of Juvenile Steelhead from Data Used in Studies at McNary 

Dam in 2004–2005 and 2009........................................................................................................108

Appendix V. Model Summary from Analyses of Recapture Probabilities (p) of Juvenile Steelhead 

from Data Used in Studies at McNary Dam in 2004–2005 and 2009. ...........................................109

Appendix W. Summaries of Covariate Values of Subyearling Chinook Salmon from Data Used in 

Studies at McNary Dam in 2004–2009..........................................................................................110

Appendix X. Capture History Summary of Subyearling Chinook Salmon from Data Used in Studies 

at McNary Dam in 2004–2009.......................................................................................................116

Appendix Y. Results of Correlation Analyses Subyearling Chinook Salmon from Data Used in 

Studies at McNary Dam in 2004–2005 and 2009..........................................................................117

Appendix Z. Model Summary from Analyses of Recapture Probabilities (p) of Subyearling Chinook 

Salmon from Data used in Studies at McNary Dam in 2004–2005 and 2009................................119

Appendix AA. Model-selection Results from Radio- and Acoustic-tagged Subyearling Chinook 

Salmon from Data used in Studies at McNary Dam in 2004–2005 and 2009................................120

Appendix AB. Beta (Slope) Coefficients of Estimable Survival Parameters of Subyearling Chinook 

Salmon from Data used in Studies at McNary Dam in 2004–2005 and 2009................................121

Appendix AC. Capture History Summary of Subyearling Chinook Salmon from Data Used in 

Studies at McNary Dam in 2004–2009..........................................................................................122

Appendix AD. Model Summary from Analyses of Recapture Probabilities (p) of Subyearling 

Chinook Salmon from Data used in Studies at McNary Dam in 2004–2009 .................................123
v

Figures

Figure 1. Graph showing turbine unit discharges during yearling Chinook salmon 

passage (bars) and turbine efficiency (solid line) from data used in studies at John Day 

Dam in 2002 and 2003....................................................................................................................13

Figure 2. Graph showing daily-averaged covariate values for yearling Chinook salmon 

from data used in studies at John Day Dam in 2002 and 2003.......................................................14

Figure 3. Graph showing number of yearling Chinook salmon passing through each

turbine by year (bars) and the percentage of time each turbine was operated (line) from 

data used in studies at John Day Dam in 2002 and 2003 ...............................................................15

Figure 4. Graph showing estimated effects of water temperature (upper plate) and tag burden 

(lower plate) on apparent survival of yearling Chinook salmon from data used in studies at John 

Day Dam in 2002 and 2003.............................................................................................................20

Figure 5. Graph showing turbine unit discharges during subyearling Chinook salmon 

passage (bars) and turbine efficiency (solid line) from data used in studies at John Day 

Dam in 2002 and 2003....................................................................................................................22

Figure 6. Graph showing daily-averaged covariate values for subyearling Chinook 

salmon used in analyses of survival from data used in studies at John Day Dam in 2002 

and 2003 ..................................................................................................................................23

Figure 7. Graph showing number of subyearling Chinook salmon passing through 

each turbine by year (bars) and the percentage of time each turbine was operated (line) 

from data used in studies at John Day Dam in 2002 and 2003.......................................................24

Figure 8. Graph showing estimated effects of water temperature in 2002 (upper plate) and 2003 

(middle plate) and turbine discharge (lower plate) on apparent survival of subyearling Chinook 

salmon from data used in studies at John Day Dam in 2002 and 2003 ..........................................29

Figure 9. Graph showing turbine unit discharges during yearling Chinook salmon 

passage (bars) and turbine efficiency (solid line) from data used in studies at McNary 

Dam in 2002–2005 and 2009..........................................................................................................31

Figure 10. Graph showing daily-averaged covariate values for yearling Chinook salmon 

from data used in studies at McNary Dam in 2002–2009................................................................32

Figure 11. Graph showing number of yearling Chinook salmon passing through each turbine by 

year (bars) and overall percentage of time each turbine was operating (line) from data used in 

studies at McNary Dam in 2002–2005 and 2009 ............................................................................33

Figure 12. Graph showing estimated effects of head on apparent survival of yearling 

Chinook salmon at McNary Dam in 2002–2009..............................................................................39

Figure 13. Graph showing estimated effects of water temperature on apparent survival of 

yearling Chinook salmon from data used in studies at McNary Dam in 2002–2009........................41

Figure 14. Graph showing estimated effects of tag burden on apparent survival of yearling 

Chinook salmon from data used in studies at McNary Dam in 2002–2009 .....................................42

Figure 15. Graph showing turbine unit discharges during juvenile steelhead passage (bars) and 

turbine efficiency (solid line) from data used in studies at McNary Dam in 2004–2009...................43

Figure 16. Graph showing daily-averaged covariate values for juvenile steelhead from data 

used in studies at McNary Dam in 2004–2009................................................................................44

Figure 17. Graph showing number of juvenile steelhead passing through each turbine by 

year (bars) and overall percentage of time individual turbine units were operating (line) from 

data used in studies at McNary Dam in 2004, 2005, and 2009.......................................................45
vi

Figure 18. Graph showing estimated effects of head (upper plate) and spill percentage 

(lower plate) on apparent survival of juvenile steelhead at McNary Dam 2004–2009 .....................51

Figure 19. Graph showing turbine unit discharges during subyearling Chinook salmon 

passage (bars) and turbine efficiency (solid line) from data used in studies at McNary 

Dam in 2004–2009..........................................................................................................................52

Figure 20. Graph showing daily-averaged covariate values for subyearling Chinook 

salmon from data used in studies at McNary Dam in 2004–2009 ...................................................53

Figure 21. Graph showing number of subyearling Chinook salmon passing through each 

turbine by year (bars) and overall (line) from data used in studies at McNary Dam in 2004, 

2005, and 2009 ...............................................................................................................................54

Figure 22. Graph showing estimated effects of water temperature on apparent survival of 

subyearling Chinook salmon from data used in studies at McNary Dam in 2004–2009..................61

Figure 23. Graph showing estimated effects of spill percentage on apparent survival of 

subyearling Chinook salmon from data used in studies at McNary Dam in 2004–2009..................62

Tables

Table 1. Dam operations during studies used in the analysis of factors affecting survival of 

tagged fish passing turbines............................................................................................................. 6

Table 2. Variables used in analyses of the survival of fish passing turbines...................................10

Table 3. A priori order of covariate evaluations ..............................................................................12

Table 4. Correlation indices of data from yearling Chinook salmon from the turbine group 

from data used in studies at John Day Dam in 2002 and 2003.......................................................17

Table 5. Correlation indices of data from yearling Chinook salmon from the control group 

from data used in studies at John Day Dam in 2002 and 2003.......................................................18

Table 6. Model-selection results of data from radio-tagged yearling Chinook salmon used in 

studies at John Day Dam in 2002 and 2003....................................................................................19

Table 7. Beta (slope) coefficients of estimable survival parameters of yearling Chinook salmon 

from data used in studies at John Day Dam in 2002 and 2003.......................................................20

Table 8. Correlation indices of data from subyearling Chinook salmon from the turbine group 

from data used in studies at John Day Dam in 2002 and 2003.......................................................25

Table 9. Correlation indices of data from subyearling Chinook salmon from the control group 

from data used in studies at John Day Dam in 2002 and 2003.......................................................26

Table 10. Model-selection results of data from radio-tagged subyearling Chinook salmon 

used in studies at John Day Dam in 2002 and 2003.......................................................................27

Table 11. Beta (slope) coefficients of estimable survival parameters of subyearling Chinook 

salmon from data used in studies at John Day Dam in 2002 and 2003 ..........................................28

Table 12. Table of correlation indices of data from yearling Chinook salmon from the 

turbine group from data used in studies at McNary Dam in 2002–2009..........................................35

Table 13. Table of correlation indices of data from yearling Chinook salmon from the 

control group from data used in studies at McNary Dam in 2002–2009..........................................36

Table 14. Model-selection results from radio- and acoustic-tagged yearling Chinook 

salmon from data used in studies at McNary Dam in 2002–2009 ...................................................38

Table 15. Beta (slope) coefficients of estimable survival parameters of yearling Chinook 

salmon from data used in studies at McNary Dam in 2002–2009 ...................................................40

Table 16. Table of correlation indices of data from juvenile steelhead from the turbine 

group from data used in studies at McNary Dam in 2004–2009......................................................47
vii

Table 17. Table of correlation indices of data from juvenile steelhead from the control 

group from data used in studies at McNary Dam in 2004–2009......................................................48

Table 18. Model-selection results from radio- and acoustic-tagged juvenile steelhead 

from data used in studies at McNary Dam in 2004–2009................................................................50

Table 19. Beta (slope) coefficients of estimable survival parameters of juvenile steelhead 

from data used in studies at McNary Dam in 2004–2009................................................................51

Table 20. Table of correlation indices of data from subyearling Chinook salmon from the 

turbine group from data used in studies at McNary Dam in 2004–2009..........................................56

Table 21. Table of correlation indices of data from subyearling Chinook salmon from the 

control group from data used in studies at McNary Dam in 2004–2009..........................................57

Table 22. Model-selection results from radio- and acoustic-tagged subyearling Chinook 

salmon from data used in studies at McNary Dam in 2004–2009 ...................................................59

Table 23. Beta (slope) coefficients of estimable survival parameters of subyearling 

Chinook salmon from data used in studies at McNary Dam in 2004–2009 .....................................60
viii

Conversion Factors, Datums, and Abbreviations and Acronyms

Conversion Factors

Inch/Pound to SI

Multiply By To obtain

foot (ft) 0.3048 meter (m)

cubic foot per second (ft3/s) 0.02832 cubic meter per second (m3/s)

SI to Inch/Pound

Multiply By To obtain

kilometer (km) 0.6214 mile (mi)

Temperature in degrees Celsius (°C) may be converted to degrees Fahrenheit (°F) as follows:

°F=(1.8×°C)+32.

Datums

Horizontal coordinate information is referenced to the World Geodetic System of 1984 (WGS84).

Vertical coordinate information is referenced to the National Geodetic Vertical Datum of 1929 (NGVD 29).

Abbreviations and Acronyms

AICc Akaike Information Criterion adjusted to reflect the effects of sample size 

BIOP Biological opinion

FCRPS Federal Columbia River Power System 

NOAA National Oceanic and Atmospheric Administration 

rkm river kilometer

USACE U.S. Army Corps of Engineers

USGS U.S. Geological Survey
1

Analyses of Potential Factors Affecting Survival 

of Juvenile Salmonids Volitionally Passing 

Through Turbines at McNary and John Day Dams, 

Columbia River

By John Beeman, Hal Hansel, and Russell Perry, U.S. Geological Survey; and Eric Hockersmith 

and Ben Sandford, National Oceanic and Atmospheric Administration Fisheries

Executive Summary

This report describes analyses of data from radio- or acoustic-tagged juvenile 

salmonids passing through hydro-dam turbines to determine factors affecting fish

survival. The data were collected during a series of studies designed to estimate passage 

and survival probabilities at McNary (2002–09) and John Day (2002–03) Dams on the 

Columbia River during controlled experiments of structures or operations at spillways.

Relatively few tagged fish passed turbines in any single study, but sample sizes generally 

were adequate for our analyses when data were combined from studies using common 

methods over a series of years. We used information-theoretic methods to evaluate 

biological, operational, and group covariates by creating models fitting linear (all 

covariates) or curvilinear (operational covariates only) functions to the data. Biological 

covariates included tag burden, weight, and water temperature; operational covariates 

included spill percentage, total discharge, hydraulic head, and turbine unit discharge; and 

group covariates included year, treatment, and photoperiod. Several interactions between 

the variables also were considered. Support of covariates by the data was assessed by 

comparing the Akaike Information Criterion of competing models. The analyses were 

conducted because there was a lack of information about factors affecting survival of fish 

passing turbines volitionally and the data were available from past studies. The depth of 

acclimation, tag size relative to fish size (tag burden), turbine unit discharge, and area of 

entry into the turbine intake have been shown to affect turbine passage survival of 

juvenile salmonids in other studies.
2

This study indicates that turbine passage survival of the study fish was primarily 

affected by biological covariates rather than operational covariates. A negative effect of 

tag burden was strongly supported in data from yearling Chinook salmon at John Day and 

McNary dams, but not for subyearling Chinook salmon or juvenile steelhead. The 

negative effect of tag burden in data we examined from yearling Chinook salmon 

supports the recent findings from laboratory studies of barotrauma effects. A curvilinear 

(quadratic) effect of turbine unit discharge was weakly supported in data from 

subyearling Chinook salmon at John Day Dam. The maximum survival from those data 

was estimated to occur at a discharge of 15.9 thousand cubic feet per second, but the 

estimate was imprecise (95 percent confidence interval of -1.7–33.7 thousand cubic feet 

per second). This estimate is within the range of 1 percent of peak turbine operating 

efficiency (12.0–21.6 thousand cubic feet per second), but is lower than the 17.2 

thousand cubic feet per second discharge at peak operating efficiency (at a head of 102 

feet near the median in the data we examined). Effects of water temperature were 

supported in four of the five examined data sets and were strongly supported in all but 

one. Spill percentage, head, and total discharge received weak or moderate support in 

some cases.

The results are consistent with those of several controlled field experiments of 

turbine discharge. Studies based on the Hi-Z Turb’N tag (balloon tag) often show small, 

generally statistically insignificant, differences in survival at different turbine discharge 

levels. Some studies also show that a quadratic equation can be well fit to the relation of 

survival and turbine unit discharge. The lack of support for the operational covariates in 

most of the data sets we examined may be due to the small effect turbine discharge has 

even in controlled studies, the observational nature of the data we used, and the 

evaluation method. We assessed support of the data for models of linear and quadratic 

effects, whereas controlled experiments often statistically compare the point estimates of 

survival from each operational treatment studied. The results of our analyses suggest tag 

burden should be minimized or controlled for in analyses of future studies of passage

survival and that water temperature also should be considered as a factor. This study may 

be the first to use data from juvenile salmonids entering turbines volitionally to assess 

factors affecting their turbine passage survival. Analyses of other data sets from fish with 

similar attributes should be conducted to corroborate these results.
3

Introduction

Hydroelectric dams are often cited as one cause of reductions in populations of 

anadromous salmonids (National Research Council, 1996). Adult anadromous fish in 

rivers with hydroelectric dams often must cross dams as they migrate upstream to spawn 

and their offspring must cross them as they migrate to the ocean to rear. The use of fish 

ladders generally has been a successful means of providing upstream passage for adult 

salmonids, resulting in little passage delay and high passage survival (Keefer and others,

2004). Cumulative survival of juveniles during their downstream migration, however, is 

lower, and has been a focus area for improvements (Muir and others, 2001; Williams and 

others, 2001). As a result, a recent biological opinion (BIOP) for the Federal Columbia 

River Power System (FCRPS) set minimum standards for dam passage survival of 

juvenile salmonids (National Oceanic and Atmospheric Administration’s National 

Marine Fisheries Service, 2008).

Actions to improve dam passage survival of juvenile salmonids in the FCRPS 

have traditionally focused on reducing passage through routes with low survival and 

increasing passage through routes with high survival. Generally, juvenile salmonid 

survival is highest through spillways, intermediate through turbine bypass systems, and 

lowest through turbines (Muir and others, 2001). As such, efforts to improve survival of 

juvenile salmonids since about 1995 have primarily focused on improving the probability 

of passage and survival through the spillways at FCRPS dams (Swan and others, 1997;

Hansel and others, 2004; Johnson and others, 2005; Beeman and others, 2010).

Little effort has been directed toward improving survival of juvenile salmonids 

passing turbines relative to the other routes. This is unfortunate, because it may be more 

cost-effective to make improvements in turbine design or operation than to structures or 

operations of bypass systems or spillways. Turbines at several FCRPS dams are nearing 

their replacement age, and new fish-friendly designs may be beneficial to both fish and 

power generation (Odeh, 1999; Cada, 2001; Cada and others, 2006). Causes of mortality 

during turbine passage include exposure to shear, strike, and rapid pressure changes.

Odeh (1999) and Cada (2001) provide descriptions of potential sources of mortality 

during turbine passage.

One management action intended to maximize turbine passage survival is the 

BIOP mandate to operate Kaplan turbines within 1 percent of their peak efficiency. This 

is based on data from Bell (unpub. data), suggesting this would provide the greatest 

survival. Several studies conducted to test this premise have shown that the peak survival 

does not always coincide with the “1 percent rule”, and is often associated with higher 

discharges (Mathur and others, 2000; Skalski and others, 2002a; Normadeau Associates 

and others, 2003, 2008). These results, and supporting results from physical models of 

turbines, have prompted further research into the relation between turbine operating 

conditions and fish survival. The goal of this research is to determine the turbine 

operating criteria, or “operating point,” that optimizes survival of juvenile salmonids

passing through them. Such information could be used to design new turbine operating 

conditions and potentially new turbine designs.

Most studies of juvenile salmonid turbine passage survival have been based on 

surface-acclimated fish fitted with the Hi-Z Turb’n tag (balloon tag; Heisey and others, 

1992; Mathur and others, 1996, 2000; Normadeau Associates and others, 2003, 2008).
4

These studies were based on juvenile salmonids, often taken directly from a hatchery, 

fitted with an externally attached radio transmitter and an externally attached small 

inflatable balloon. The fish are passed through a hose directly into the turbine intake or 

runner after injecting the balloon with a liquid to cause it to inflate shortly after release.

The balloon facilitates recapture following passage after locating fish visually and with

radio telemetry. These studies have been useful for testing the effects of various turbineoperating conditions on fish survival. However, results from these studies show that the 

elevation of entry into the turbine intake can affect turbine passage survival, and results 

from Brown and others (2009), and Carlson and others (2010) show that depth of 

acclimation is also an important factor. Therefore, it is beneficial to have data from 

depth-acclimated volitionally passing fish from which to draw inference. This report 

describes analyses of such data.

Data from volitionally passing juvenile salmonids are available from many studies 

conducted to estimate dam passage and survival probabilities. These studies are common 

in the FCRPS and typically are conducted to assess changes in operations or structures at 

passage routes other than turbines (see Skalski and others, 2002b; Axel and others,

2004a, 2004b; Counihan and others, 2006a, 2006b; Adams and Liedtke, 2010; Beeman 

and others, 2010). Fish with attached negatively buoyant transmitters must add air to their 

swim bladders to regain neutral buoyancy, a process that may take several hours (Fried 

and others, 1976). The fish in the studies we used were held 12–24 hours after tagging 

and were released into the Columbia River about 10–20 km upstream from the dams and 

are assumed to be neutrally buoyant at the time of release. Few fish from individual 

studies pass turbines, due to the structures and operations designed to minimize turbine 

passage, and thus individual annual studies are not likely to be suitable for analyses of 

factors affecting survival of turbine-passing fish. For example, in one study, 185 of 2,400 

yearling Chinook salmon released in the reservoir upstream from McNary Dam 

(Columbia River kilometer [rkm] 470), were estimated to have passed the 14-unit 

powerhouse through the turbines (Adams and others, 2010). However, sample sizes 

increase when a suite of annual studies based on similar methods is considered together, 

which is the approach we describe in this report.

We had several hypotheses: (1) fish survival would be related to operational 

covariates, (2) fish survival would be higher during conditions of open geometry (that is, 

similar [aligned] wicket gate and stay vane angles and higher unit discharges), and (3) tag 

burden would pose a negative effect on survival. The latter hypothesis was based on 

results from Brown and others (2009) and Carlson and others (2010), indicating that tag 

burden was one of several important factors determining mortal injury of tagged fish in 

controlled laboratory experiments of simulated turbine passage.

Methods

Data from previous studies of dam passage survival were used to determine if 

several factors of interest affected survival of fish passing through turbines. The original 

purpose of the studies was to estimate the passage proportions and apparent survival of 

tagged yearling Chinook salmon (Oncorhynchus tshawytscha), subyearling Chinook 

salmon, and juvenile steelhead (O. mykiss) relative to structural or operational changes 

designed to improve passage survival of juvenile salmonids. Many of the changes in 

structure or operation were adaptively altered over the years of study.
5

None of the studies was designed specifically to determine the factors affecting 

survival of fish passing turbines, but the data needed for doing so were available in most 

cases. For example, in many of the studies, the date, time, and turbine unit of passage 

were determined for most fish and the physical, biological, and operational covariates at 

that time were known. However, there was no experimental operation of the turbines 

during these studies, such as changing head or turbine discharge on a predetermined 

schedule. A summary of the dam operations during the years used in analyses is by dam, 

year, and season (spring or summer) is shown in table 1.

Analyses of data from John Day Dam (rkm 347) were based on studies in 2002 

and 2003 (table 1). Data from John Day Dam were selected for analysis due to the wide 

range of unit discharges for these turbines within the 1 percent rule. Unit discharges 

within the 1 percent rule at John Day Dam at a typical head of 102 ft range from 12.1 to 

21.6 thousand ft3/s with a peak efficiency at 17.2 thousand ft3/s (Wittinger and others, 

2010). For comparison, unit discharges within the 1 percent rule at McNary Dam at a 

typical head of 72 ft range from 7.9 to 12.4 thousand ft3/s with a peak efficiency at 10.0

thousand ft3/s (Wittinger and others, 2010). Percentage of spill at John Day Dam during 

spring 2002 and 2003 was varied to evaluate juvenile fish passage and survival during 

12- and 24-hour spill. In 2002, the treatments were 24-hour 30 percent spill compared to

0 percent day spill with 60 percent night spill. In 2003, there was no planned spill during 

the day and the treatments were 45 percent night spill compared to 60 percent night spill. 

In each year, the treatments were alternated for 3 days each within 6-day blocks 

following a randomized block design, with changes between day and night operations at 

0600 and 1800 hours. The study designs are described in more detail in Hansel and others 

(2004), Beeman and others (2006), and Counihan and others (2006a, 2006b).

Analyses of data from McNary Dam were based on studies conducted from 2002

to 2009. Data from McNary Dam were selected for analysis due to the many years of data 

available resulting in attractive sample sizes of fish passing through turbines. Various

planned spill operations occurred at McNary Dam during the study years. Percentage of

spill during spring at McNary Dam from 2002 through 2004 was dominated by night spill 

to the gas cap operations (that is, until a regionally approved limit of total dissolved gas 

supersaturation was reached downstream; “fish passage plan spill”). During 2005 through 

2007, fish-passage plan spill compared to 24-hour spill and other spill tests associated 

with the installation and performance of temporary spillway weirs were investigated. In 

2008 and 2009, there were no specific spill treatments. During summer 2005, an 

involuntary spill was followed by a court-ordered spill, and in 2006–07, a 24-hour 40

percent spill compared to a 24-hour 60 percent spill was evaluated. There were no 

planned spill treatments during the summers in 2004 and 2009. For more specific

information on yearly study designs and spill operations at McNary Dam see Axel and 

others (2004a, 2004b), Perry and others (2006), Adams and others (2008), Adams and 

Counihan (2009), and Adams and Liedtke (2009, 2010).
6

Table 1. Dam operations during studies used in the analysis of factors affecting survival of tagged 

fish passing turbines.

Dam Year Season Operating conditions

Dates of turbine 

passage Reference

John Day 2002 Spring 24-h 30 percent spill vs. 60 percent

night spill

Apr. 30–May 31 Counihan and others, 

2006a

Summer 24-h 30 percent spill vs. 60 percent

night spill

June 25–July 16 

2003 Spring 45 percent night spill vs. 60 percent

night spill

Apr. 30–June 6 Counihan and others, 

2006b

Summer 24-h 30 percent spill vs. 60 percent

night spill

June 23–July 25 

McNary 2002 Spring Night spill to gas cap May 8–June 5 Axel and others, 

2004a

2003 Spring Night spill to gas cap May 2–June 9 Axel and others, 

2004b

2004 Spring Night spill to gas cap Apr. 24–May 25 Perry and others, 

Summer No treatments July 1–July 31 2006

2005 Spring 12-h vs. 24-h Apr. 23–June 2 Perry and others, 

Summer Involuntary spill then Court- 2007

ordered spill

June 23–Aug. 1 

2006 Spring Fish Passage Plan vs. 2006 test spill Apr. 27–June 4 Adams and others, 

Summer 24-h 40 percent spill vs. 24-h 60 2008

percent spill

June 20–July 27 

2007 Spring 2007 test spill vs. Modified 2006 

test spill

Apr. 19–June 7 Adams and 

Counihan, 2009

Summer 40 percent spill vs. 60 percent spill June 20–July 28 

2008 Spring No treatments Apr. 20–June 4 Adams and Liedtke, 

Summer 40 percent spill vs. 60 percent spill June 20–Aug. 2 2009

2009 Spring No treatments Apr. 18–June 4 Adams and Liedtke, 

Summer No treatments June 20–Aug. 9 2010

The studies were based on fish tagged with radio or acoustic transmitters and 

incorporated means of detection suitable for determining time spent in the river and 

forebay upstream from the dam, assigning route-specific passage at the dam, as well as 

detections downstream from which to estimate dam passage survival. For the purposes of 

these analyses, the date, time, and turbine unit of passage and at least two detection sites 

downstream were required. The locations of the sites downstream varied slightly over the 

years of study at McNary Dam, but were the same during both years at John Day Dam. 

Studies at McNary Dam used 2–7 detection sites downstream during any 1 year of study, 

ranging from 11 to 161 km downstream from the dam. Six downstream detection sites 

ranging from 10 to 74 km downstream from the dam were used in the studies at John Day 

Dam. 

The data from the tagged fish were compiled from databases created during the 

original studies and added to environmental and operational data. The environmental and 

operational data were provided by the U.S. Army Corps of Engineers (Jon Renholds, 
7

written commun.) either during the original studies, or in some cases, specifically for this 

analysis. Dam operations data from John Day Dam in 2000 were not available on a 

turbine-unit-specific basis and few tagged fish passed through turbines during studies that 

year, so the data from 2000 were omitted from analyses.

The spatial resolution of the fish data was usually sufficient to assign a specific 

turbine unit of passage, but in some years at McNary Dam passage was assigned to a 

group of turbine units. At McNary Dam, unit-specific resolution was available only in 

data from yearling Chinook salmon during 2002–05 and 2009 and in data from juvenile 

steelhead and subyearling Chinook salmon during 2004, 2005, and 2009. Therefore, 

analyses of these years was conducted prior to all-year analyses to determine if the 

potential effects of turbine unit discharge would be affected by the resolution of the 

passage assignments. If turbine unit discharge was not supported as a factor affecting 

turbine passage survival in these analyses, the full data set was used for subsequent 

analyses of all covariates. The most resolute data available were used to assign operations 

data to the time of passage for analyses of the all-year McNary data, but a south (units 1–

7) or north (units 8–14) assignment was used for turbine unit location, as this was the 

only resolution common to all years. The average of the unit discharges of the operating 

units to which fish passage was assigned was used as the passage unit discharge when 

unit-specific passage data were not available. Unit-specific passage data at John Day 

Dam were available for all years and were used to obtain operating conditions at the time 

of passage, but the variable of turbine unit location was grouped into south (units 1–8) or 

north (units 9–16) areas to reduce the number of parameters in the analysis, because 

relatively few fish were in the data set. The chronological resolution of the operations 

data was hourly at McNary Dam in 2002 and 2003 and at John Day Dam in 2002 and 

until noon on May 1, 2003. All other operations data were available at 5-minute intervals.

The data from the nearest period available were used as the condition at the time of 

turbine passage.

Apparent survival was estimated using Cormack-Jolly-Seber capture-recapture 

methods (Cormack, 1964; Jolly, 1965; Seber, 1965). Apparent survival is the probability 

that an animal survives and remains available for recapture. In the context of this study, 

fish that lose their tags leave the study area and do not return, or cease migrating between 

detection sites are assumed to be mortalities. All references to survival in this report refer 

to apparent survival.

The probability of detection at a site is the product of the probability of survival to 

the site and the probability of recapture at the site, so these parameters must be separately 

estimated. Thus, models contain parameters to estimate recapture probability and to 

estimate survival, although only those used to estimate survival are typically of interest.

Capture histories were created from the data for use in models of recapture and 

survival probabilities. A capture history is a series of values representing if tagged 

animals were alive when released and if they were detected passing each detection site or 

recapture occasion. In most studies used in these analyses, treatment fish were released 

upstream from the dam and control fish were released downstream from the dam, because 

relative survival was estimated in the original studies using methods such as the routespecific survival model (Skalski and others, 2002b). The only exception was the studies 

at McNary Dam in 2002 and 2003, which did not include a control group. We used data 

from the control group to represent riverine conditions present during the studies apart 
8

from powerhouse operations by assessing the effects of total river discharge on the 

survival of this group. All estimates of survival were based on single-release models and 

represented the survival from turbine passage to the first downstream detection site. In 

analyses of data from McNary Dam, the distance between these points was used as a 

model covariate to account for differences in site placements among years and the same 

values were used for control and turbine fish. The site locations were identical in each 

year of study at John Day Dam.

The goal of this study was to determine effects of the factors of interest on inriver survival between turbine passage and the nearest downstream detection site, so data 

from subsequent downstream detection sites were combined. For example, at John Day 

Dam in 2002, there were detection sites at rkms 337, 324, 309, 287, and 273, but data 

from sites downstream from rkm 337 were pooled into a single occasion. This resulted in 

a three-occasion data structure for analysis, including release, the first site downstream 

from the dam, and all sites downstream from the first.

The variables used in the analyses included group and individual covariates and

were selected based on results of a meeting of biologists and engineers from U.S. 

Geological Survey (USGS), National Oceanic and Atmospheric Administration (NOAA), 

and the U.S. Army Corps of Engineers (USACE) held at the USACE Portland District 

office on April 13, 2010. The meeting resulted in a list of biological, physical, and 

operational covariates to use as covariates in a priori models of the survival of tagged fish 

passing turbines.

The variables can be classified into group and individual covariates describing 

operational or biological factors (table 2). Group covariates included treatment, year, 

photoperiod (day or night based on civil twilight at the time of turbine passage or release 

of the control group), and river reach. Operational variables included head (forebay 

elevation minus tailwater elevation, in feet), spill percentage, turbine discharge, total dam 

discharge, and turbine location (the unit number, or bivariate division by north or south).

Discharge variables were in units of thousand cubic feet per second (thousand ft3

/s). 

Biological variables included tag burden percentage (tag weight in air * 100/fish weight

in air) and water temperature at the regional tailrace water-quality measurement site. 

Several interactions between variables also were included. The turbine location and 

photoperiod interaction was used to account for potential differences in predation in the 

tailrace, assuming that the location of turbine of passage may affect predation 

downstream and be influenced by the ambient light. Total discharge was applied to data 

from fish in the control group as a potential measure of overall effects of discharge, but 

was not applied to data from fish in the turbine group because it was highly correlated 

with hydraulic head and the latter variable was thought to be more pertinent for fish 

passing turbines. Bivariate and multivariate collinearity was assessed using Pearson’s r 

and variance inflation factor prior to survival analyses to avoid using highly correlated 

variables in models together. Using correlated or collinear variables together in models 

makes it difficult to separate their separate influence on the response variable, which in 

our analyses was survival of fish passing through turbines. This is indicated when 

Pearson’s r is greater than an absolute value of about 0.8 (|0.8|), and generally as variance 

inflation factors increase (Belsley and others, 1980).
9

The effects of the covariates on fish survival were evaluated using an informationtheoretic approach. In this approach, mathematical models representing hypotheses are 

compared based on the principle of parsimony. Parsimony is the balance between bias 

and variance of prediction. The square of bias is reduced as parameters are added to a 

model, but this increases the variance (Burnham and Anderson, 2002). Thus, the principle 

of parsimony attempts to find a balance between the fit of the model and the number of 

parameters required. Several measures of parsimony can be used for this assessment. We

selected the commonly used Akaike Information Criterion with an adjustment to reflect 

the effects of sample size (AICc). Models are compared based on the differences in the 

AICc values. Unlike in the null hypothesis testing statistical framework, there is no strict 

cutoff representing “significance” between models, and in fact, the method does not 

determine significance at all. Alternatively, support for differences between hypotheses, 

based on the data and the models, increases with difference in AICc between competing 

models. Burnham and Anderson (2002) suggest that when AICc values differ by less than 

2 units the support for one hypothesis over another is not meaningfully different based on 

the data and models considered. They also suggest that differences of 4–7 indicate 

considerably less support for the model with the greater AICc and those greater than 10 

indicate essentially no support for the model with the greater AICc. We will use the terms 

“no” or “weak” support, “moderate” support, and “strong” support for models differing 

by no more than 2 units, more than 2, and as much as 7 units, or more than 7 units, 

respectively.
10

Table 2. Variables used in analyses of the survival of fish passing turbines. 

[The Application column indicates which of the treatment groups the variables were applied to. Fish weight 

was used as a secondary variable instead of tag burden after all other variables were evaluated, due to their 

close association. The first model evaluated (global model) included all possible interactions among group 

covariates plus the other variables and interactions listed. A linear function between survival and each 

variable was used except for head and turbine discharge, for which linear and quadratic functions were 

used. km, kilometer; yyyy 4-digit year format; Trt, treatment; Turq, turbine discharge; Persp, percentage

spill; Turbloc, turbine unit location]

Type Name Definition Application Note

Group Photo Day (0) or night (1) Both

Group Gated Distance to first detection site (km) Both

Group Year yyyy Both

Group Trt Control (0) or turbine (1) Both

Group Reach River reach Both

Operational Totq Total discharge Control

Operational Head (linear) Forebay elevation minus tailwater elevation Turbine Linear

Operational Head (quadratic) Forebay elevation minus tailwater elevation Turbine Quadratic

Operational Turq (linear) Unit discharge Turbine Linear

Operational Turq (quadratic) Unit discharge Turbine Quadratic

Operational Turbloc Unit number, or south (0) & north (1) Turbine

Operational Persp (Spill discharge / total discharge) * 100 Both

Biological Tagb Tag burden percent Both Primary

Biological Weight Fish weight Both Secondary

Biological Temp Tailrace water temp Both

Interaction Turbloc*photo Turbloc*photo Turbine Predation

Interaction Trt*photo Trt*photo Both

Interaction Persp*trt Persp*trt Both

Interaction Tagb*year Tagb*year Both

Interaction Tagb*trt Tagb*trt Both

Interaction Temp*trt Temp*trt Both

Interaction Temp*yr Temp*yr Both

Interaction Other All possible group interactions Both Only in 

global model 
11

One must cautiously evaluate models when AICc differences are within about 0–2 

units per unit difference in parameter number, because the larger-parameter model may

seem to have support from the data only because it is similar to the supported reducedparameter model. As indicated in equation 1, in the absence of a change in the deviance 

( ) ˆ − 2log L(Θ ), which represents the fit of the model to the data, AICc increases by 2 for 

each added parameter. In these cases, the additional variable is sometimes called a 

“pretender” variable. The analyses in this report contain many comparisons of models 

differing by one parameter, which are simple to evaluate in this context. The AICc is 

calculated as 

1

2 ( 1) ) 2 ˆ 2log ( − −+ = − Θ + +

n K

K K AICc L K

(1)

where ) ˆ L(Θ is the maximized likelihood for the model, K is the number of estimable 

parameters in the model, and n is the sample size.

The analyses were done using Program MARK (White and Burnham, 1999). A 

recaptures-only data type with a logit link was used in each analysis. Each analysis began 

with a “full model” consisting of all group covariates and interactions among them, plus 

the full suite of individual covariates and interactions listed in table 2. Survival and 

recapture probabilities are inseparable in the last reach, although in the MARK software 

their joint probability (λ) is divided between estimates of survival and recapture. We 

fixed the value of the survival estimate in the last reach to 1.0 so that an estimate of λ was 

reflected in the estimate of recapture probability. We also fixed survival or recapture 

probabilities to 1.0 and reduced the number of estimated parameters accordingly in cases 

where the data indicated all fish in the sample survived or were detected. 

The full model was used as a basis for modifications of parameters describing 

recapture probabilities to determine the most parsimonious model of recapture 

probabilities for use in all other comparisons. Five models of recapture probabilities were 

evaluated including models with group, reach, multiplicative and additive combinations 

of group and reach, and the intercept only. In the event that more than one model of 

recapture probability was supported by the data, we selected the most parameterized 

model for use in subsequent analyses.

The analyses were conducted following an a priori order of variable removal and 

evaluation (table 3). This strategy is consistent with the principles of information 

theoretic analyses and parsimony. The premise behind the order was to evaluate for 

removal the interaction effects and as many group and biological covariates as possible 

prior to evaluating the operational covariates, so that the effects of the operational 

covariates would not be affected by evaluation within a series of potentially over-fitted 

models. The exception to this convention was the covariate of tag burden and the 

treatment*tag burden interaction, which we purposely left in the models to control for 

any effects until after the operational covariates were evaluated. This decision was based 

on laboratory results of Brown and others (2009) indicating tag burden was an important 

factor in survival and injury of tagged fish after simulated turbine passage.
12

Table 3. A priori order of covariate evaluations.

[Group covariates included treatment, photoperiod, and year. Individual covariates included tag burden, 

spill percentage, turbine passage location, turbine discharge, head, and total discharge. Interactions between 

treatment and tag burden and spill percentage were used to examine the potential differential effects of tag 

burden and spill percentage on turbine and control fish. The effect of total discharge was applied only to 

control fish (treatment = 0) and the effects of turbine location, head, and turbine unit discharge were 

applied only to turbine fish (treatment = 1). A tag burden and year interaction was included to address the

potential effect of different tag types on the tag burden effect. A turbine passage location and photoperiod 

interaction was included to determine potential effects of photoperiod on the effect of passage location that 

might be related to predation. Each covariate or interaction was evaluated in the order listed]

Group covariates and all possible interactions, plus individual covariates and selected interactions.

Tag burden and year interaction.

Temperature and year interaction.

Year effect.

Turbine passage location and photo period interaction.

Photoperiod and treatment interaction.

Temperature and treatment interaction.

Photoperiod effect.

Temperature effect.

Spill percentage and treatment interaction.

Total discharge effect.

Main spill percentage effect.

Main turbine passage location effect.

Linear head effect.

Quadratic head effect.

Linear turbine unit discharge effect.

Quadratic turbine unit discharge effect.

Tag burden and treatment interaction.

Distance to first gate effect (McNary only).

Tag burden effect.
13

Results of Analyses from Studies at John Day Dam 

Yearling Chinook Salmon

Environmental Conditions

The ranges of the individual covariates at the times of fish passage were similar 

between years. The turbines were usually operated within 1 percent of the peak turbine 

operating efficiency during the studies. The turbine unit discharge ranged from 11.4 to 

22.2 thousand ft3/s (fig. 1). A summary of covariate values at the times of fish passage is

shown in appendix A and covariate daily averages are presented in figure 2. Total 

discharge ranged from 138.9 to 372.4 thousand ft3/s, with a median of 227.7 thousand 

ft3

/s. The hydraulic head ranged from 97.0 to 104.5 ft, with a median of 101.6 ft. Spill 

percentages were generally according to the designed operation tests in each year, but 

were as high as 73.7 percent. Tag burden ranged from 1.23 to 8.92 percent, with a median 

of 4.53 percent. Water temperature ranged from 9.70 to 15.44 °C, with a median of 

12.17 °C.

Figure 1. Graph showing turbine unit discharges during yearling Chinook salmon passage (bars) 

and turbine efficiency (solid line) from data used in studies at John Day Dam in 2002 and 2003. 

The discharges bounded by the dashed line are within 1 percent of the peak turbine efficiency at a 

head of 102 feet.
14

Figure 2. Graph showing daily-averaged covariate values for yearling Chinook salmon from data 

used in studies at John Day Dam in 2002 and 2003.
15

Figure 3. Graph showing number of yearling Chinook salmon passing through each turbine by year 

(bars) and the percentage of time each turbine was operated (line) from data used in studies at 

John Day Dam in 2002 and 2003.

Fish passage was present at most turbine units in at least 1 year except for unit 13 

(fig. 3). Fewer fish passed through higher-numbered units (northern) than lower 

numbered units (southern), particularly in 2003, indicating that passage was generally

higher in units near the Oregon shoreline. Fish passage location generally coincided with 

unit operation. Similar numbers of fish passed turbines in 2002 (N = 120) and 2003 (N = 

126).

Survival

The analyses of factors affecting survival were based on 246 fish in the turbine 

group and 2,973 fish in the control group. Nearly three times as many fish were in the 

control group at night in 2003 (N = 1,562) than in the other groups of year, treatment, and 

photoperiod (appendix B).

Correlation analyses indicated that several variables were highly related. Pearson 

correlation coefficients greater than an absolute value of 0.8 (|0.8|) indicated that the 

separate influences of several pairs of variables could be difficult to determine if they 

were used together (tables 4 and 5; Belsley and others, 1980). These include the pairs 

head and total discharge, head and turbine discharge, tag burden and fish weight, 

percentage of spill and powerhouse discharge, and percentage of spill and photoperiod. 

The last pair was expected to be correlated because the dam operations were being tested 

during the original studies. Analyses of multicollinearity indicated that few dependencies 

among the variables would result from these correlations, although there would be some 

inflation of parameter variances if total discharge and head were used together. However, 

we had planned to apply only total discharge to the control group and head to the turbine 

group, so no difficulties were expected from these correlations. Fish weight and tag 

burden were not examined for multicollinearity because they likely would not be used 
16

together due to their high bivariate correlation coefficient (>|0.9|). Based on these results, 

tag burden and fish weight were not used in models together. If the data and models 

supported an effect of tag burden, it was replaced with fish weight during post-hoc 

analyses to determine which factor was better supported.

A single model of recapture probabilities was supported by the data. The 

multiplicative model of group and reach (model 1 in appendix C) received more than 99

percent of the AICc weight, indicating that it was the only model supported by the data. 

This model of recapture probabilities was used in all comparisons of effects on survival. 

Visual examination of the capture histories (appendix B) indicated all fish in the turbine 

group passing the dam during the night in 2002 and 2003 were detected at the first 

downstream site, so these parameters were fixed to 1.0 in the analyses. In subsequent 

analyses (model 17 from table 6), the recapture probabilities at the first downstream site 

ranged from 0.666 (SE 0.020) to 0.870 (SE 0.009), and averaged 0.761. The λ term

ranged from 0.708 (SE 0.056) to 1.0 (manually fixed for analysis), and averaged 0.980.

Few of the covariates examined were supported as determinants of survival in 

these data. Only water temperature and tag burden were supported by the data and

models (table 6). The operational covariates contributed little to the fit of the models, as 

indicated by the similarities in deviances between competing models (for example, model 

12 with total discharge compared to model 11 without it). Additionally, most models 

differed by a single parameter and in every case the difference in AICc values between 

models with and without each operational covariate changed by 0–2 units for each unit 

difference in the number of parameters, indicating that the covariates added little to the 

model fit. Linear effects require one parameter to describe and two parameters for those 

with a quadratic effect (the linear term and the squared term); therefore, for a factor with 

even a small effect one would expect a delta AICc of at least 2 for a linear effect (2 times 

the number of parameters to describe the effect) and at least 4 for a factor with a 

quadratic effect. For example, the AICc of the model with a linear effect of head (model 

14) was 1.6 greater than the model without a linear effect of head (model 15) and the 

model with the quadratic effect of head (model 14a) was 3.7 greater than the model 

without that parameter. The AICc of the model with a linear effect of turbine discharge 

(model 15) was 1.6 greater than the model without that effect (model 16) and the AICc of 

the model with a quadratic effect of turbine unit discharge (model 15a) was 3.5 greater 

than the model without turbine unit discharge. These results indicated that effects of the 

operational covariates were not supported. The only model of survival supported by the 

data included the group covariates of treatment and year plus the individual covariates of 

water temperature and tag burden (model 17 in table 6).

A positive effect of water temperature on survival was supported. When water 

temperature was removed, the delta AICc increased by 10 units (model 9 compared to

model 10 in table 6), indicating that it was strongly supported. The model slopes indicate 

a greater temperature effect on turbine fish than control fish (table 7, fig. 4). The 

estimated survival of the control group was higher than the turbine group, as expected.
17

Table 4. Correlation indices of data from yearling Chinook salmon from the turbine group from data 

used in studies at John Day Dam in 2002 and 2003.

[Pearson correlation coefficients are listed above the probabilities of obtaining a greater value under the 

hypothesis that Rho = 0. Sample size is 246; <, less than; see table 2 for variable name definitions]

A negative effect of tag burden was also strongly supported. The a priori order of 

variable assessment would have resulted in model 16 being the best-supported model, but 

close inspection indicated it was over parameterized. The tag burden and tag 

burden*treatment interaction in model 16 were of similar size, but of opposite sign, 

indicating the net effect may have been only on the control group. Model 17 includes a 

tag burden effect only on the control fish, is more supported than model 16 by a 

difference of 2 AICc units, and differs by a single parameter. This indicates the 

treatment*tag burden interaction term in model 16 is not contributing to the fit of the 

model, and model 17 is better supported. Model 17 represents the hypothesis that tag 

burden is a factor only for the control group. Removing this effect results in an increase 

in AICc of more than 20 units (model 17compared with model 18), indicating it is a 

strongly supported effect. It also indicates that the effect of tag burden on survival of the 

control group is negative (table 7, fig. 4).

TAG

TOTQ PER_SPI HEAD TURQ UNITLOC PHOTO TEMP WEIGHT BURDEN

TOTQ 1.0000 -0.0831 -0.8584 0.5075 -0.0374 0.1081 0.4566 -0.0089 0.0234

0.1938 <0.0001 <0.0001 0.5593 0.0907 <0.0001 0.8901 0.7147

PER_SPI 1.0000 0.4017 -0.6509 -0.0157 -0.8185 0.1107 0.1678 -0.1389

<0.0001 <0.0001 0.8070 <0.0001 0.0831 0.0083 0.0294

HEAD 1.0000 -0.6930 0.1055 -0.4002 -0.3908 0.0619 -0.0670

<0.0001 0.0987 <0.0001 <0.0001 0.3336 0.2949

TURQ 1.0000 -0.0328 0.5749 0.1515 -0.1399 0.1033

0.6089 <0.0001 0.0175 0.0283 0.1062

UNITLOC 1.0000 -0.0791 -0.1024 0.0749 -0.1032

0.2166 0.1091 0.2417 0.1063

PHOTO 1.0000 -0.0502 -0.1790 0.1648

0.4333 0.0049 0.0096

TEMP 1.0000 0.0206 0.0055

0.7476 0.9316

WEIGHT 1.0000 -0.9225

<0.0001
18

As a final comparison, model 17 was altered by replacing the tag burden covariate 

with fish weight. This model (19) differed from model 17 by an increase of nearly 9 

AICc units, has the same number of parameters, and is not supported. Thus, despite the 

high correlation between tag burden and fish weight (r = -0.9225), the data and models 

strongly support the effect on survival being due to tag burden.

Table 5. Correlation indices of data from yearling Chinook salmon from the control group from data 

used in studies at John Day Dam in 2002 and 2003.

[Pearson correlation coefficients are listed above the probabilities of obtaining a greater value under the 

hypothesis that Rho = 0. Sample size is 2,973; <, less than; see table 2 for variable name definitions]

TAG

TOTQ PER_SPI PHOTO TEMP WEIGHT BURDEN

TOTQ 1.0000 -0.0538 0.0095 0.5916 -0.0165 0.0408

0.0034 0.6046 <0.0001 0.3697 0.0261

PER_SPI 1.0000 -0.8768 0.0442 -0.0295 0.0301

<0.0001 0.0159 0.1077 0.1007

PHOTO 1.0000 -0.0272 0.0036 0.0026

0.1380 0.8461 0.8858

TEMP 1.0000 -0.0449 0.0852

0.0144 <0.0001

WEIGHT 1.0000 -0.9190

<0.0001
19

Table 6. Model-selection results of data from radio-tagged yearling Chinook salmon used in studies at John Day Dam in 2002 and 2003. 

[Presence of a factor in a model is indicated by an 'x' in the column for that factor. Model 1 was a global model including all group covariates and their 

interactions (g) as well as all individual covariates and interactions listed. All models shared a common g*reach model of recapture probability. K 

indicates the number of parameters. The tag burden covariate was applied only to the control group in model 17. An asterisk after the model number 

indicates the best-supported model of the suite. See table 2 for variable name definitions]

Individual covariates

Group covariates Biological Operational Model selection results

Model 

No.

g*reachtrtyrphototrt*yrtrt*photoyr*phototrt*yr*photoreachwttagbtrt*tagbyr*tagbtemptrt*tempyr*temppersptrt*persplinear turqquadratic turqlinear headquadratic headturlocturloc*photototq

AICc K Deviance

1 x x x x x x x x x x x x x x x x x x x x x x 4505.9 35 4435.4

2 x x x x x x x x x x x x x x x x x x x x x 4491.7 28 4435.4

3 x x x x x x x x x x x x x x x x x x x x 4490.6 27 4436.6

4 x x x x x x x x x x x x x x x x x x x 4488.5 26 4436.3

5 x x x x x x x x x x x x x x x 4484.7 22 4440.6

6 x x x x x x x x x x x x x x 4483.6 21 4441.4

7 x x x x x x x x x x x x x 4482.5 20 4442.4

8 x x x x x x x x x x x x 4482.8 19 4444.6

9 x x x x x x x x x x x 4481.2 18 4445.1

10 x x x x x x x x x x 4491.2 17 4457.1

11 x x x x x x x x x x 4479.3 17 4445.2

12 x x x x x x x x x 4477.8 16 4445.8

13 x x x x x x x x 4476.3 15 4446.2

14 x x x x x x x 4474.9 14 4446.9

14a x x x x x x x 4477.0 15 4446.9

15 x x x x x x 4473.3 13 4447.3

15a x x x x x x 4475.2 14 4447.2

16 x x x x x 4471.7 12 4447.7

17* x x x x 4469.7 11 4447.7

18 x x x 4490.0 10 4470.0

19 x x x x 4478.5 11 4456.5
20

Table 7. Beta (slope) coefficients of estimable survival parameters of yearling Chinook salmon from 

data used in studies at John Day Dam in 2002 and 2003. 

[The data are from model 17 in table 6; Beta, slope coefficient]

Figure 4. Graph showing estimated effects of water temperature (upper plate) and tag burden (lower 

plate) on apparent survival of yearling Chinook salmon from data used in studies at John Day Dam

in 2002 and 2003. Predictions (thick lines) and 95 percent confidence intervals (thin lines) from 

model 17 in table 6 are plotted. Note that the effect of tag burden was only supported for fish in the 

control group.

 Standard 95 percent confidence

Parameter Beta error Lower Upper

Intercept 1.959324 1.180059 -0.353590 4.272239

Treatment group -3.862740 0.603389 -5.045380 -2.680100

Tag burden for control group -0.480580 0.103616 -0.683670 -0.277490

Temperature 0.333017 0.090592 0.155456 0.510577
21

Key Findings in Data from Yearling Chinook Salmon at John Day Dam

• The data set included 246 fish in the turbine group and 2,973 fish in the 

control group.

• Most data were collected at turbine discharges within 1 percent of peak 

unit efficiency.

• Operational covariates were not supported as factors affecting turbine 

passage survival.

• A positive effect of water temperature on survival was strongly supported.

• A negative effect of tag burden on survival was strongly supported for the 

control group. There was strong support that this effect was due to tag 

burden rather than fish weight. An effect of tag burden was not supported 

for the turbine group.

Subyearling Chinook Salmon 

Environmental Conditions

The environmental conditions occurring during passage of subyearling Chinook 

salmon at John Day Dam differed between years. The differences between years were 

related to discharge and water temperature. As in the spring, the turbines were generally 

operated within 1 percent of peak efficiency during fish passage (fig. 5). Overall turbine 

unit discharge ranged from 9.7 to 22.7 thousand ft3/s with a median of 14.7 thousand ft3/s

and was higher in 2003 than in 2002. The turbine unit discharge ranged from 11.9 to 22.7 

thousand ft3/s in 2002 and 9.7 to 20.9 thousand ft3/s in 2003. Covariate values at the time 

of passage are summarized in appendix D and daily averages are shown in fig. 6. The 

median head was 102.70 ft (range 97.00 to 105.65 ft) and was similar between years. The 

median total discharge was 194.70 thousand ft3/s (range 89.90 to 396.20 thousand ft3/s), 

but differed between years. In 2002, the median total discharge was 253.90 thousand ft3

/s

(range 157.70 to 396.20 thousand ft3/s) and in 2003 it was 152.20 (range 89.90 to 237.40 

thousand ft3/s). Additionally, total discharge was 7 percent greater during the day than at 

night in 2002 and 6 percent greater during the day than at night in 2003. The percentage 

of spill also differed between years per the planned studies in 2002 and 2003. The median 

tag burden was 5.35 percent (range 1.67 to 7.33 percent) and was similar between years 

and day/night periods. The water temperature was higher in 2003 than in 2002, 

particularly in July. The medians were 17.60 °C (range 15.90 to 20.30 °C) in 2002 and 

18.44 °C (range 16.33 to 21.61 °C) in 2003. The data included fish passing through all 16 

units (fig. 7). In 2002, the passage was similar among units, but in 2003, most passage 

was through units 1–5. Location of passage coincided with unit operation. There were 

249 fish in the turbine group in 2002 and 547 in 2003, so most fish passage in the overall 

data set was through units 1–5.
22

Figure 5. Graph showing turbine unit discharges during subyearling Chinook salmon passage (bars) 

and turbine efficiency (solid line) from data used in studies at John Day Dam in 2002 and 2003.

The discharges bounded by the dashed line are within 1 percent of the peak turbine efficiency at a 

head of 102 feet.

Survival 

Analyses of survival were based on 796 fish in the turbine group and 5,463 fish in 

the control group. Sample sizes among groups of treatment, year, and photoperiod were 

generally similar within treatment groups, with 115–318 treatment fish and 1,150–1,499 

control fish per group (appendix E). Results of bivariate correlation and multicollinearity 

analyses were similar to those from yearling Chinook salmon (tables 8 and 9). Total 

discharge was applied only to the control group, head was applied only to the treatment 

group, and tag burden and fish weight were not used in models together.

Two of the five models of recapture probabilities were supported by the data and 

the more general of the two was selected for use in subsequent analyses (appendix F).

The full model, which allows recapture probabilities to vary among all combinations of 

group and reach, and the additive model of group and reach in which recapture 

probabilities vary among groups and reach in a similar manner, were the only models 

supported by the data. Their AICc values were identical and were at least 909 units 

smaller than those of the other models evaluated. The recapture probabilities at the first 

downstream site estimated from the more general model (model 18 in table 10) ranged 

from 0.466 (SE 0.015) to 0.957 (SE 0.015) and averaged 0.757. The λ term ranged from 

0.948 (SE 0.006) to 0.993 (SE 0.002), and averaged 0.972.
23

Figure 6. Graph showing daily-averaged covariate values for subyearling Chinook salmon used in 

analyses of survival from data used in studies at John Day Dam in 2002 and 2003.
24

Figure 7. Graph showing number of subyearling Chinook salmon passing through each turbine by 

year (bars) and the percentage of time each turbine was operated (line) from data used in studies 

at John Day Dam in 2002 and 2003.

Survival effects of several group covariates and one individual covariate were 

supported by the data and the models. Effects of treatment, year, photoperiod, reach, 

temperature, several interactions between these variables, and a quadratic effect of 

turbine unit discharge were supported (table 10). Models 5–5d evaluated several 

hypotheses about the effects of year. The models with linear and quadratic effects of head 

had AICc values 1.3 and 1.4 units greater than models without head, indicating the 

effects were not supported (models 14 and 14a compared to model 15). The model with a 

linear effect of turbine unit discharge (model 15) had an AICc value 2.0 greater than the 

model without turbine unit discharge (model 16), indicating that it was not a supported 

effect.

An effect of water temperature was supported. The model with the 

year*temperature interaction term (model 3 in table 10) had an AICc value about 22 units 

smaller than the AICc value of the model without this term (model 4) indicating that this 

effect was strongly supported by the data. The treatment* temperature interaction term 

was weakly supported by the data, as indicated by the 1-unit AICc reduction when the 

term was in the model (model 7 compared to model 8). Model 9, with the temperature 

main effect, had an AICc value about 4 units lower than model 10 without the effect, 

indicating moderate support for the factor. The most parsimonious model, model 18 in 

table 10, indicates that the effects of temperature were positive for control and turbine 

fish in 2002, had little effect on control fish in 2003, and were negative for turbine fish in 

2003. Figure 8 depicts the effects of temperature on survival of subyearling Chinook 

salmon based on the coefficients in table 11. The different effects between the years may 

be due to the lower discharge and higher temperatures during 2003 compared to 2002.

Additionally, the study season ended later in 2003 than in 2002.
25

Table 8. Correlation indices of data from subyearling Chinook salmon from the turbine group from 

data used in studies at John Day Dam in 2002 and 2003.

[Pearson correlation coefficients are listed above the probabilities of obtaining a greater value under the 

hypothesis that Rho = 0. Sample size is 796; <, less than; see table 2 for variable name definitions]

TAG

TOTQ PER_SPI HEAD TURQ TURLOC PHOTO TEMP WEIGHT BURDEN

TOTQ 1.0000 0.1668 -0.9308 0.4006 0.3314 -0.0218 -0.5238 0.0002 -0.0064

<0.0001 <0.0001 <0.0001 <0.0001 0.5388 <0.0001 0.9946 0.8562

PER_SPI 1.0000 0.0289 -0.3981 -0.0555 -0.5664 -0.1202 -0.0407 0.0208

 0.4156 <0.0001 0.1180 <0.0001 0.0007 0.2520 0.5572

HEAD 1.0000 -0.5006 -0.3198 -0.0998 0.4721 -0.0263 0.0206

<0.0001 <0.0001 0.0048 <0.0001 0.4594 0.5620

TURQ 1.0000 0.0610 0.3598 -0.1304 0.0578 -0.0329

 0.0855 <0.0001 0.0002 0.1032 0.3542

TURLOC 1.0000 -0.0499 -0.1759 -0.0057 -0.0051

0.1592 <0.0001 0.8725 0.8849

PHOTO 1.0000 0.0697 0.0183 0.0017

 0.0495 0.6071 0.9610

TEMP 1.0000 0.2641 -0.2849

<0.0001 <0.0001

WEIGHT 1.0000 -0.9600

<0.0001

A quadratic model of turbine unit discharge was weakly supported by the data. 

The model with the quadratic effect of turbine unit discharge (model 15a in table 10) had 

an AICc value 1.3 units smaller than the model without the effect (model 16), despite 

having two additional parameters. The model coefficients indicate an intermediate 

maximum survival at 15.9 thousand ft3

/s, with a 95 percent confidence interval (95

percent CI) of -1.7–33.7 thousand ft3

/s (fig. 8). The confidence interval spans more than 

the entire operating range of the turbines at John Day Dam. The range of discharges 

within 1 percent of peak turbine operating efficiency at John Day Dam is 12.0 to 21.6 

thousand ft3

/s and the peak operating efficiency is at 17.2 thousand ft3/s (at a head of 102 

ft near the median in the data we examined).
26

Table 9. Correlation indices of data from subyearling Chinook salmon from the control group from 

data used in studies at John Day Dam in 2002 and 2003. 

[Pearson correlation coefficients are listed above the probabilities of obtaining a greater value under the 

hypothesis that Rho = 0. Sample size is 5,463]

TAG

TOTQ PER_SPI PHOTO TEMP WEIGHT BURDEN

TOTQ 1.0000 0.0428 0.0855 -0.5063 -0.0692 0.0759

0.0015 <0.0001 <0.0001 <0.0001 <0.0001

PER_SPI 1.0000 -0.6701 -0.0487 -0.0070 0.0156

<0.0001 0.0003 0.6045 0.2480

PHOTO 1.0000 0.0462 -0.0016 0.0030

0.0006 0.9080 0.8275

TEMP 1.0000 0.2791 -0.3140

<0.0001 <0.0001

WEIGHT 1.0000 -0.9636

<0.0001

Key Findings in Data from Subyearling Chinook Salmon at John Day Dam

• The data set included 796 fish in the turbine group and 5,463 fish in the 

control group.

• Most data were collected primarily at turbine discharges within 1 percent 

of peak unit efficiency.

• Turbine discharge was the only operational covariate supported as a factor 

affecting turbine passage survival. A curvilinear fit to the data indicated 

maximum turbine passage survival was at 15.9 thousand ft3/s, but the 

estimate was imprecise and had a 95 percent confidence interval of -1.7–

33.7 thousand ft3

/s.

• Water temperature was supported as a factor affecting survival. A 

difference in the effect of water temperature between the 2 years was 

strongly supported. The data and models indicated moderate support for a 

positive effect for control and turbine groups in 2002 and a negative effect 

for the turbine group in 2003.

• An effect of tag burden on survival was not supported.
27

Table 10. Model-selection results of data from radio-tagged subyearling Chinook salmon used in studies at John Day Dam in 2002 and 2003. 

[Presence of a factor in a model is indicated by an 'x' in the column for that factor. Model 1 was a global model including all group covariates and their 

interactions (g) as well as all individual covariates and interactions listed. All models shared a common g*reach model of recapture probability. K indicates the 

number of parameters. An asterisk after the model number indicates the best-supported model of the suite. See table 2 for variable name definitions]

Individual covariates

Group covariates Biological Operational Model selection results

Model 

No. g

trtyrphototrt*yrtrt*photoyr*phototrt*yr*photoreachtagbtrt*tagbyr*tagbtemptrt*tempyr*temppersptrt*persplinear turqquadratic turqlinear headquadratic headturlocturloc*photototq

AICc K Deviance

1 x x x x x x x x x x x x x x x x x x x x x x 9175.0 37 9100.7

2 x x x x x x x x x x x x x x x x x x x x x 9160.9 30 9100.7

3 x x x x x x x x x x x x x x x x x x x x 9159.0 29 9100.9

4 x x x x x x x x x x x x x x x x x x x 9181.4 28 9125.3

5 x x x x x x x x x x x x x x x x 9194.3 25 9144.2

5a x x x x x x x x x x x x x x x x x x x 9157.0 28 9100.9

5b x x x x x x x x x x x x x x x x x x 9157.0 27 9102.8

5c x x x x x x x x x x x x x x x x x x 9181.1 26 9128.9

5d x x x x x x x x x x x x x x x x x 9183.9 26 9131.8

6 x x x x x x x x x x x x x x x x x 9155.0 26 9102.8

7 x x x x x x x x x x x x x x x x 9154.4 25 9104.3

8 x x x x x x x x x x x x x x x 9155.5 24 9107.4

9 x x x x x x x x x x x x x x x 9152.7 24 9104.6

10 x x x x x x x x x x x x x x 9156.9 23 9110.8

11 x x x x x x x x x x x x x x 9152.1 23 9106.0

12 x x x x x x x x x x x x x 9151.5 22 9107.4

13 x x x x x x x x x x x x 9150.4 21 9108.3

14 x x x x x x x x x x x 9148.9 20 9108.9

14a x x x x x x x x x x x 9149.0 21 9106.9

15 x x x x x x x x x x 9147.6 19 9109.5

15a x x x x x x x x x x 9144.3 20 9104.3

16 x x x x x x x x x 9145.6 18 9109.5

17 x x x x x x x x x 9142.8 19 9104.7

18* x x x x x x x x 9141.3 18 9105.2
28

Table 11. Beta (slope) coefficients of estimable survival parameters of subyearling Chinook salmon from 

data used in studies at John Day Dam in 2002 and 2003. 

[The data are from model 18 in table 10; Beta, slope coefficient]

 Standard 95 percent confidence

Parameter Beta error Lower Upper

Intercept -1.9540 1.4886 -4.8715 0.9636

treatment -13.6919 4.7556 -23.0128 -4.3710

year 16.1561 3.3910 9.5097 22.8026

treatment*year -3.0346 0.5684 -4.1488 -1.9205

temperature 0.2752 0.0851 0.1084 0.4420

temperature*year -0.7767 0.1755 -1.1206 -0.4328

temperature*treatment 0.2842 0.1769 -0.0626 0.6309

turbine unit discharge 1.0694 0.4497 0.1880 1.9509

turbine unit discharge ^2 -0.0334 0.0139 -0.0607 -0.0062
29

Figure 8. Graph showing the estimated effects of water temperature in 2002 (upper plate) and 2003 

(middle plate) and turbine discharge (lower plate) on apparent survival of subyearling Chinook 

salmon from data used in studies at John Day Dam in 2002 and 2003. Predictions (thick lines) and 

95 percent confidence intervals (thin lines) from model 18 in table 10 are plotted.
30

Results of Analyses from Studies at McNary Dam

Yearling Chinook Salmon

Environmental Conditions

The environmental conditions occurring during fish passage differed among years

available for analysis (2002–2009). The turbines were primarily operated within 1 percent 

of peak efficiency during fish passage (fig. 9). Covariate values at the time of fish passage 

are summarized in appendix G and daily averages are plotted in fig. 10. Overall turbine 

unit discharge ranged from 7.80 to 17.27 thousand ft3

/s with a median of 11.90 thousand 

ft3

/s. The maximum turbine unit discharges were higher in 2002–2005 (16.30–17.27 

thousand ft3/s) than in 2006–2009 (12.42–13.11 thousand ft3/s). The median head was 

72.13 ft (range 67.47 to 75.91 ft) and was slightly lower in 2006 (median 69.92 ft) than in 

the other years (medians ranging from 71.63 to 73.12 ft). The total project discharge, 

which was applied only to fish in the control group, ranged from 90.30 to 421.09 thousand 

ft3

/s and had a median of 255.60 thousand ft3/s. Percentage of spill varied among years and 

photoperiod according to annual study designs and environmental conditions (see table 1). 

Spill percentage spill ranged from 0.00 to 78.84 over the years of studies. The median tag 

burden was 4.35 percent (range 0.86 to 9.78 percent) and was similar in all years except 

2003. In 2003, the tag burden was higher than in the other years, with a median of 7.06 

percent and range of 3.47 to 9.78 percent. In 2003, a larger size transmitter was used to 

reduce regurgitation after gastric implantation. The median water temperature ranged from 

10.72 °C in 2009 to 12.83 °C in 2004. Water temperature ranged from 8.11 to 15.78 °C 

among years with a median of 12.33 °C.

The data included fish passing through all turbine units (fig. 11). The distribution of 

the unit of passage was similar among years and overall was slightly greater in lowernumbered units (closer to the Oregon shore). This distribution generally reflects the 

percentage of time individual turbines were operating (fig. 11). Sample sizes for the 

turbine group were smaller in 2002 (N = 33) and 2003 (N = 95) than in the other years (N = 

162–287). 

Survival

Two separate analyses were completed using data from McNary Dam due to the 

inconsistent resolution of the turbine unit of passage among years. An analysis of a data set 

restricted to 2002, 2003, 2004, 2005 and 2009, years with unit-specific passage 

assignments, was conducted first followed by analyses based on the complete data set from 

2002–2009.
31

Figure 9. Graph showing turbine unit discharges during yearling Chinook salmon passage (bars) and 

turbine efficiency (solid line) from data used in studies at McNary Dam in 2002–2005 and 2009. The 

discharges bounded by the dashed line are within 1 percent peak turbine efficiency at a head of 72.5 

feet.

The restricted analyses of survival at McNary Dam were based on 770 fish in the 

turbine group and 3,286 fish in the control group. Sample sizes varied among groups of 

treatment, year, and photoperiod and ranged from 114 to 1,219 per group for control fish 

and 12 to 189 per group for turbine fish (appendix H). There were no control fish in the 

studies during 2002 or 2003.

Correlation analyses indicated several variables were moderately related. Pearson 

correlation coefficients for fish weight and tag burden and total discharge and head were 

about |0.80| indicating that the separate influence of these variables might not be reliably 

determined if used together (appendix I). Analyses of multicollinearity indicated no 

dependencies among the variables would result from these correlations. The correlations 

between head and total discharge would not be problematic in the analysis, because head 

was only applied to the turbine group and total discharge was only applied to the control 

group. As in analyses of data from John Day Dam, tag burden and fish weight were not 

used in models together. Rather, tag burden was used as a covariate and, if supported as a 

factor affecting survival, it was replaced with fish weight during post-hoc analyses to 

determine which was more supported as the causal factor.

A model of recapture probabilities based on a multiplicative effect of group and 

reach was best supported by the data and used for all survival models for the reduced data 

set. The AICc of this model was 67 units less than the next best-supported model (model 1 

compared to model 2, appendix J) and received greater than 99.9 percent of the model 

weight. Thus, there was little evidence to support the other models of recapture probability 

evaluated.
32

Figure 10. Graph showing daily-averaged covariate values for yearling Chinook salmon from data used 

in studies at McNary Dam in 2002–2009.
33

Figure 11. Graph showing number of yearling Chinook salmon passing through each turbine by year 

(bars) and overall percentage of time each turbine was operating (line) from data used in studies at 

McNary Dam in 2002–2005 and 2009. Unit-specific passage assignments were not made as part of 

the studies in 2002–2005 and 2009.

Effects on survival of five of the covariates examined were supported by the data 

and models from the reduced data set (appendixes K and L). These included tag burden, 

head, percentage spill, water temperature, and total discharge. The linear model of head 

received only weak support with an AICc value 0.7 less than the model without head 

(model 13 compared to 14a), whereas the quadratic model had an AICc 0.3 greater than the 

model with no head effect and was not supported (model 14b compared to 14a). Both 

linear and quadratic models of turbine unit discharge had AICc values about 3 units greater 

than the model without turbine unit discharge and therefore were not supported (model 14b 

and 15b compared to 15). The model containing water temperature, percentage spill, and 

total project discharge (model 9) had AICc values 2.8 to 12 units less than the alternative 

models without these covariates (models 10, 11, and 12) indicating that they were 

moderately to strongly supported. Tag burden also received moderate support relative to 

the model without tag burden (model 16 compared to model 17). Because there was no 

evidence of an effect of turbine unit discharge, further analyses were conducted based on 

all the years of data (2002–2009). 

The analyses of factors affecting survival of yearling Chinook salmon at McNary 

Dam using all the data were based on 1,419 fish in the turbine group and 6,737 fish in the 

control group (appendix M). Numbers of fish in the turbine and control groups were 

similar among years except in 2002 and 2003. In these years, there were no control groups 

and there were fewer fish in the turbine groups (N = 33 in 2002 and N = 95 in 2003) than in 

other years (N = 163–287).

Correlation analyses indicated that several variables in the full data set were 

related. As in the analysis of the smaller data set, Pearson correlation coefficients for fish 

weight and tag burden and total discharge and head were greater than or equal to |0.79| 

indicating that the separate influence of these variables might not be separable when used 

together (tables 12 and 13). Analyses of multicollinearity indicated that only minor 

dependencies among the variables would result from these correlations and variance 
34

inflation factors were less than 5. As in the previous analysis, the correlation between head 

and total discharge would not be problematic in the analysis, because head was applied 

only to the turbine group and total discharge was applied only to the control group. Tag 

burden and fish weight also were treated as in the previous analysis. The unit-specific 

turbine of passage variable (turbloc) was replaced by a north or south passage location 

(unitloc) in the analyses of all years, because it was the only resolution common to all 

years.

A multiplicative recapture probability model of group and reach was supported by 

the data and used in all comparisons among survival models. This model received most of 

the AICc weight. The AICc value was 23 units less than the next best-supported model, 

indicating that it was the only model supported relative to the others evaluated (appendix 

N). Visual examination of the capture histories (appendix M) indicated that all fish in the 

sample from the turbine night group in 2009 were detected, so the capture probability was 

fixed to 1.0 for the first downriver reach. Similarly, the λ for the turbine night group in 

2003 in the second downriver reach was also fixed to 1.0. Capture histories also indicated 

that no mortality occurred in the sample from the turbine night group in 2002, so it was 

fixed to 1.0 for analysis. Recapture probabilities at the first downriver site ranged from 

0.309 (SE 0.0.062) to 1.0 (manually fixed for analysis) and averaged 0.717. The λ 

parameter ranged from 0.461 (SE 0.050) to 1.0 (manually fixed for analysis), and averaged 

0.849.

Few of the individual covariates examined were supported as determinants of 

survival for the turbine group. Only tag burden, water temperature, total discharge, and 

head were supported by the data and models (table 14). The total discharge covariate,

which was applied only to control fish, had a slightly positive effect on survival, and was 

included in models to account for environmental conditions apart from those related to 

powerhouse operation.

The operational covariates contributed little to the fit of the survival models 

examined with the exception of head. The model with a linear effect of head had an AICc 

value 1.4 units greater than the model without head and was not supported (model 13

compared to 14a). The quadratic model of head received moderate support compared to the 

model with no head effect as evidenced by an AICc that was 3.6 units lower (model 14a

compared to 14b). That model simulates an intermediate maximum survival at a head of 

71.2 ft, with a 95 percent confidence interval of 70.7–71.8 ft (fig. 12, table 15). Models 

with a linear or quadratic effect of turbine unit discharge had AICc values 1.8 and 2.1 

greater than the model without turbine unit discharge and were not supported by the data 

(models 14b and 15b compared to model 15a). Similarly, models with percentage spill and 

a percentage spill by treatment interaction were not supported compared to the model 

without percentage spill (models 8 and 10 compared to model 12). The interaction effect of 

water temperature and year was strongly supported (model 1) with an AICc value about 8 

units less than the model without this interaction (model 2). The effect of tag burden was 

also strongly supported with an AICc value nearly 11 units less than the alternative model 

without it (model 17 compared to model 16). Following the systematic evaluation of the 

individual and group covariates the best supported model contained only treatment, 

photoperiod, year, their interactions, and the individual covariates of tag burden, water 

temperature, total discharge, and a quadratic effect of head (model 16 in table 14). The 

post-hoc evaluation using fish weight in place of tag burden in the best-supported model 

indicated that weight was the better supported of the two correlated variables with an AICc 

value 3.4 units less than the model with tag burden (model 18 vs. model 16).
35

Table 12. Table of correlation indices of data from yearling Chinook salmon from the turbine group from 

data used in studies at McNary Dam in 2002–2009. 

[Pearson correlation coefficients are listed above the probabilities of obtaining a greater value under the hypothesis 

that Rho = 0. Sample size is 1,419; <, less than; see table 2 for variable name definitions]

TAG

TOTQ PER_SPI HEAD TURQ UNITLOC PHOTO TEMP WEIGHT BURDEN

TOTQ 1.0000 0.6082 -0.8693 0.2371 -0.1919 0.1939 0.3038 -0.0892 0.1022

<0.0001 <0.0001 <0.0001 <0.0001 <0.0001 <0.0001 0.0008 0.0001

PER_SPI 1.0000 -0.3156 -0.2626 -0.1579 0.4278 -0.0121 0.0425 -0.1181

<0.0001 <0.0001 <0.0001 <0.0001 0.6502 0.1098 <0.0001

HEAD 1.0000 -0.3915 0.1523 -0.0870 -0.3601 0.0754 -0.1496

<0.0001 <0.0001 0.0010 <0.0001 0.0045 <0.0001

TURQ 1.0000 0.1253 -0.0816 0.3595 -0.0778 0.1902

<0.0001 0.0021 <0.0001 0.0034 <0.0001

UNITLOC 1.0000 0.0167 0.1332 -0.0061 -0.0460

0.5293 <0.0001 0.8188 0.0832

PHOTO 1.0000 -0.0227 -0.0080 -0.0425

0.3936 0.7625 0.1097

TEMP 1.0000 -0.2044 0.1692

<0.0001 <0.0001

WEIGHT 1.0000 -0.7917

<0.0001

Low and high values of head and high values of water temperature and tag burden 

had negative effects on survival in most years. Values of head that were in the mid-range 

near 71 ft had higher rates of survival than those that were in the lower or higher part of the 

range of observed values (fig. 12). The model slopes generally indicate a greater 

temperature effect on turbine fish during the day than on turbine fish at night or control 

groups during day or night (table 15). A negative effect of water temperature on survival 

was supported for all years except for 2006 in which the effect was positive (fig. 

13). Post-hoc analyses indicated this anomaly was caused by a treatment, year, temperature 

interaction, which did not affect the interpretation of the important factors. Survival 

estimates of the control groups generally were higher than for the turbine groups, as 

expected. Tag burden had a negative effect on survival in all years, but it was more 

pronounced for the turbine group than the control group (fig. 14). A positive effect of total 

discharge was also supported.
36

Table 13. Table of correlation indices of data from yearling Chinook salmon from the control group from 

data used in studies at McNary Dam in 2002–2009. 

[Pearson correlation coefficients are listed above the probabilities of obtaining a greater value under the 

hypothesis that Rho = 0. Sample size is 6,737; <, less than; see table 2 for variable name definitions]

 TAG

 TOTQ PER_SPI PHOTO TEMP WEIGHT BURDEN

TOTQ 1.0000 0.5873 -0.1071 0.2913 -0.1141 0.1996

<0.0001 <0.0001 <0.0001 <0.0001 <0.0001

PER_SPI 1.0000 0.2342 0.0597 -0.0321 0.0219

<0.0001 <0.0001 0.0085 0.0721

PHOTO 1.0000 -0.1809 0.0858 -0.1292

<0.0001 <0.0001 <0.0001

TEMP 1.0000 -0.1742 0.1617

<0.0001 <0.0001

WEIGHT 1.0000 -0.8487

<0.0001
37

Key Findings in Data from Yearling Chinook Salmon at McNary Dam

• Initial analyses were based on a subset of the data because turbine unitspecific passage location was not available in all years. Unit-specific 

discharge was not supported as a factor on survival in these data (from 2002

to 2008 and 2009), so inferences were based on the full 2002–2009 data set 

and a “north-south” assignment for unit passage location.

• The full data set included 1,419 fish in the turbine group and 6,737 fish in 

the control group.

• Most data were collected at turbine discharges within 1 percent of peak unit 

efficiency.

• A positive effect of total discharge on survival was moderately supported 

(this covariate was applied only to the control group).

• Head was moderately supported as a factor affecting turbine passage 

survival. A curvilinear fit to the data indicated maximum turbine passage 

survival at a head of 71.2 ft with lower survival at greater or lesser values.

• Water temperature was supported as a factor affecting turbine passage 

survival. A difference in the effect of water temperature among years was 

strongly supported: the effect of water temperature was positive in 2006 and 

negative in all other years. 

• A negative effect of tag burden was strongly supported. There was 

moderate support for the alternative hypothesis that this was due to fish 

weight rather than tag burden.
38

Table 14. Model-selection results from radio- and acoustic-tagged yearling Chinook salmon from data used in studies at McNary Dam in 2002–

2009.

[Presence of a factor in a model is indicated by an 'x' in the column for that factor. Model 1 was a global model including all group covariates and their 

interactions (g) as well as all individual covariates and interactions listed. All models shared a common g*reach model of recapture probability. K 

indicates the number of parameters. An asterisk after the model number indicates the best-supported model of the suite]

Individual covariates

Group covariates Biological Operational Model selection results

Model 

No. g

trtyrphototrt*yrtrt*photoyr*phototrt*yr*photogatedwttagbtrt*tagbyr*tagbtemptrt*tempyr*temppersptrt*persphead linearhead quadraticturq linearturq quadraticturlocturloc*photototq

AICc K Deviance

1 x x x x x x x x x x x x x x x x x x x x x 14694.8 89 14515.6

2 x x x x x x x x x x x x x x x x x x x x 14702.9 82 14537.9

3 x x x x x x x x x x x x x x x x x x x x 14687.1 82 14522.1

4a x x x x x x x x x x x x x x x x 14694.7 65 14564.1

4b x x x x x x x x x x x x x x x x x 14691.4 75 14540.6

4c x x x x x x x x x x x x x x x x x 14690.4 76 14537.5

4d x x x x x x x x x x x x x x x x 14690.2 70 14549.4

5 x x x x x x x x x x x x x x x x x x 14685.6 81 14522.6

6 x x x x x x x x x x x x x x x x x 14687.0 80 14526.0

7 x x x x x x x x x x x x x x 14702.0 72 14557.2

8 x x x x x x x x x x x x x x x x x 14684.0 80 14523.0

9 x x x x x x x x x x x x x x x x 14684.4 79 14525.5

10 x x x x x x x x x x x x x x x x 14682.4 79 14523.4

11 x x x x x x x x x x x x x x x 14684.5 78 14527.6

12 x x x x x x x x x x x x x x x 14680.8 78 14523.9

13 x x x x x x x x x x x x x x 14679.9 77 14525.0

14a x x x x x x x x x x x x x 14678.5 76 14525.6

14b x x x x x x x x x x x x x x 14674.9 78 14518.0

15a x x x x x x x x x x x x x 14673.1 77 14518.2

15b x x x x x x x x x x x x x x 14675.2 79 14516.2

16* x x x x x x x x x x x x 14671.8 76 14519.0

17 x x x x x x x x x x x 14682.7 75 14531.8

18 x x x x x x x x x x x x 14668.4 76 14520.8
39

Figure 12. Graph showing estimated effects of head on apparent survival of yearling Chinook salmon 

at McNary Dam in 2002–2009. Predictions (thick lines) and 95 percent confidence intervals (thin 

lines) from model 16 in table 14 are plotted.
40

Table 15. data used in studies at McNary Dam in 2002–2009. 

[The data are from model 16 in table 14]

 

Standard 95 percent confidence

Parameter Beta error Lower Upper

intercept 6.7960 2.7932 1.3214 12.2705

treatment -384.8641 2.1281 -389.0352 -380.6930

photo 1.0985 0.9047 -0.6747 2.8717

2005 1.4746 3.0765 -4.5553 7.5045

2006 -7.9079 3.0029 -13.7936 -2.0223

2007 -0.9634 2.9527 -6.7508 4.8240

2008 -0.4017 3.3019 -6.8734 6.0700

2009 -2.4378 2.8305 -7.9857 3.1100

2002 -1.9472 7.6035 -16.8501 12.9558

2003 2.5164 5.1175 -7.5139 12.5466

treatment*photo -1.2107 0.6779 -2.5395 0.1181

treatment*2005 -0.5280 0.5670 -1.6392 0.5833

treatment*2006 -0.5468 0.6364 -1.7942 0.7006

treatment*2007 -0.9346 0.6615 -2.2311 0.3619

treatment*2008 -0.7543 0.7552 -2.2345 0.7259

treatment*2009 0.6700 0.5831 -0.4730 1.8129

photo*2005 -1.3721 1.0370 -3.4046 0.6604

photo*2006 1.0762 0.7204 -0.3358 2.4881

photo*2007 484.2001 0.0000 484.2001 484.2001

photo*2008 1.2204 0.9388 -0.6197 3.0605

photo*2009 0.1860 0.7605 -1.3046 1.6765

photo*2003 -1.7392 1.1979 -4.0871 0.6088

treatment*photo*2005 2.0918 0.9478 0.2341 3.9494

tag burden -0.2462 0.0704 -0.3841 -0.1082

head 10.8140 0.0000 10.8140 10.8140

head^2 -0.0759 0.0003 -0.0766 -0.0753

totq 0.0058 0.0020 0.0018 0.0098

temp -0.3519 0.2134 -0.7701 0.0664

temp*2005 -0.0304 0.2381 -0.4970 0.4362

temp*2006 0.6758 0.2373 0.2107 1.1410

temp*2007 0.1479 0.2287 -0.3003 0.5961

temp*2008 0.1143 0.2659 -0.4069 0.6354

temp*2009 0.1547 0.2232 -0.2827 0.5921

temp*2002 0.1837 0.6169 -1.0254 1.3929

temp*2003 -0.0925 0.4110 -0.8981 0.7130
41

Figure 13. Graph showing estimated effects of water temperature on apparent survival of yearling 

Chinook salmon from data used in studies at McNary Dam in 2002–2009. Predictions (thick lines) 

and 95 percent confidence intervals (thin lines) from model 16 in table 14 are plotted.
42

Figure 14. Graph showing estimated effects of tag burden on apparent survival of yearling Chinook 

salmon from data used in studies at McNary Dam in 2002–2009. Predictions (thick lines) and 95

percent confidence intervals (thin lines) from model 16 in table 14 are plotted.
43

Juvenile Steelhead

Environmental Conditions

The environmental conditions during passage of juvenile steelhead differed 

among the years analyzed (2004–2009). The turbines were operated primarily within 1 

percent of peak efficiency during fish passage (fig. 15). Covariate values at the time of 

fish passage are summarized in appendix P and daily averages are plotted in fig. 16.

Overall turbine unit discharge ranged from 7.90 to 16.60 thousand ft3/s with a median of 

11.90 thousand ft3/s. The maximum turbine unit discharges were higher in 2004 and 2005 

(16.30–16.60 thousand ft3/s) than in 2006–2009 (12.28–12.94 thousand ft3/s). The 

median head was 71.98 ft (range 67.36 to 75.64 ft) and it was lower in 2006 (70.11 ft) 

than during the other years (range in medians 71.32 to 73.76 ft). The total project 

discharge, which was applied as a covariate only to the control group, ranged from 90.90

to 418.52 thousand ft3/s and had a median of 235.92 thousand ft3/s. Spill percentage 

varied among years and photoperiod according to annual study designs and 

environmental conditions (see table 1). Spill percentage ranged from 0.00 to 78.49 for the 

years analyzed. The median tag burden was 1.89 percent (range 0.60 to 6.41 percent) and 

was similar for all years (range of medians 1.49 to 2.12 percent). The median water 

temperature ranged from 10.72 °C in 2008 and 2009 to 13.03 °C in 2007. Daily water 

temperature ranged from 8.11 to 15.67 °C among years with a median of 11.72 °C.

Figure 15. Graph showing turbine unit discharges during juvenile steelhead passage (bars) and 

turbine efficiency (solid line) from data used in studies at McNary Dam in 2004–2009. The 

discharges bounded by the dashed line are within 1 percent of the peak turbine efficiency at a head 

of 72.5 feet.
44

Figure 16. Graph showing daily-averaged covariate values for juvenile steelhead from data used in 

studies at McNary Dam in 2004–2009.

The passage data included fish passing through all turbine units (fig. 17). In 2004 

and 2005, most fish passed through turbine units 1–7 (closer to the Oregon shore) where 

the turbines were operating a higher percentage of the time. In 2009, the median total 

discharge was higher than the other 2 years and passage tended to be more evenly 

distributed across the powerhouse.
45

Figure 17. Graph showing number of juvenile steelhead passing through each turbine by year (bars) 

and overall percentage of time individual turbine units were operating (line) from data used in 

studies at McNary Dam in 2004, 2005, and 2009. Unit-specific passage assignments were not 

made as part of the studies in 2006–2008.

Survival

As in analyses of Chinook salmon at McNary Dam, two separate analyses of data 

from juvenile steelhead were conducted due to differences in turbine unit specificity 

when assigning turbine passage among years. First an analysis restricted to years having 

unit-specific passage locations (2004, 2005, and 2009) was performed, followed by an 

analysis of all years, 2004–2009. 

The restricted analysis was based on 158 fish in the turbine group and 1,531 fish 

in the control group. Turbine and control groups contained similar numbers of fish among 

years, except 2005 when there were no control fish (appendix P). Pearson correlation

coefficients ranged from |0.75| to |0.84| for the covariate pairs of fish weight and tag 

burden and total discharge and head (appendix Q). Analyses of multicollinearity 

indicated moderate dependencies associated with total discharge and head for the turbine 

group (variance inflation factor: total discharge = 9.2, head = 7.5), but no other serious 

dependencies were indicated for the turbine or control groups. As in previous analyses, 

we applied head only to the turbine group and total discharge to the control group and we 

used tag burden for all analyses, with post-hoc replacement with fish weight if a tag 

burden effect was supported by the data.
46

In the restricted analysis, a multiplicative model of recapture probabilities by 

group and reach was supported by the data and used in all comparisons among survival 

models (appendix R). The AICc for this model was about 54 units lower than the next 

best model indicating a much better fit to the data than the other models of recapture 

probability. Of the individual covariates examined, tag burden was weakly supported and 

spill percentage was moderately supported by the data and models as determinants of 

survival for the turbine group. In addition to these variables, total discharge was weakly 

supported for the control group (appendixes S and T). Models with linear and quadratic 

effects of head (models 13 and 14b) had AICc values 1.6 and 3.3 greater than the model 

without head (model 14a). Similarly, models with linear and quadratic effects of turbine 

unit discharge (models 14a and 15b) had AICc values 2.0 and 3.7 greater than the model 

with no turbine discharge effect (model 15a). These results indicate weak or no support 

for head or turbine unit discharge on turbine survival. Because an effect of turbine unit 

discharge on survival was not supported by these data, further analyses were based on the 

full 2004–2009 data set.

The analyses of factors affecting survival based on data from all years were based 

on 351 fish in the turbine group and 2,316 fish in the control group (appendix U).

Numbers of fish in the turbine group ranged from 47 to 79 fish among years, whereas 

control fish numbers ranged from 746 to 785 for years in which control releases were 

made. No juvenile steelhead control releases were made during 2005–2007.

Correlation analyses indicated that the relation between two pairs of the 

individual covariates was moderately high in the data from all years. Pearson correlation 

coefficients for fish weight and tag burden were |0.82| for turbine and control groups and 

the coefficient for head and total discharge for the turbine group was |0.9262| (tables 16 

and 17). The variance inflation factors for total discharge and head were 14.4 and 10.8 for

the turbine group also indicating moderately high dependencies between the two 

covariates; total discharge and head therefore were used in the manner described

previously. The location of the turbine unit of passage used in the restricted data set was 

replaced by a north or south passage location for all years, because that resolution was 

common to all years.

A multiplicative recapture probability model of group and reach was supported by 

the data for all years and was used in all comparisons among survival models.

Examination of data in appendix U indicated all fish from several control and turbine 

groups were detected at one or more of the downstream sites, so their recapture or λ

parameters were fixed to 1.0 in the analyses. The AICc for this model was 116 units 

smaller than the next best model indicating a better fit to the data than the other models of 

recapture probability (model 1 in appendix table V). Recapture probabilities at the first 

downriver site ranged from 0.250 (SE 0.108) to 1.000 (fixed for analysis) and averaged 

0.739. The λ parameters ranged from 0.774 (SE 0.079) to 1.000 (fixed for analysis) and 

averaged 0.908.
47

Table 16. Table of correlation indices of data from juvenile steelhead from the turbine group from data 

used in studies at McNary Dam in 2004–2009. 

[Pearson correlation coefficients are listed above the probabilities of obtaining a greater value under the 

hypothesis that Rho = 0. Sample size is 351; <, less than; see table 2 for variable name definitions]

TAG

PER_SPI HEAD TURQ UNITLOC PHOTO TEMP WEIGHT BURDEN

TOTQ 0.5179 -0.9262 0.3740 -0.2733 -0.0678 0.3287 -0.1260 0.1567

<0.0001 <0.0001 <0.0001 <0.0001 0.2051 <0.0001 0.0182 0.0033

PER_SPI 1.0000 -0.2959 -0.0231 -0.1321 0.3337 0.0753 -0.1340 0.0566

<0.0001 0.6664 0.6664 <0.0001 0.1591 0.0120 0.2899

HEAD 1.0000 -0.4112 0.2532 0.1455 -0.3065 0.1053 -0.1847

<0.0001 <0.0001 0.0063 <0.0001 0.0487 0.0005

TURQ 1.0000 0.0074 -0.1057 0.2747 -0.0328 0.2044

0.8908 0.0478 <0.0001 0.5407 0.0001

UNITLOC 1.0000 0.0961 0.0534 0.0333 0.0094

0.0721 0.3188 0.5341 0.8608

PHOTO 1.0000 -0.1413 -0.0044 -0.0871

0.0080 0.9348 0.1033

TEMP 1.0000 0.0010 0.1346

0.9856 0.0116

WEIGHT 1.0000 -0.8252

<0.0001

Head and spill percentage were the only individual covariates that were supported 

by the data and models for all years as having an effect on turbine passage survival (table 

18). The final model after all group and individual covariates had been systematically 

evaluated included the effects of treatment, total discharge for the control group, 

photoperiod for the turbine group, unique spill percentage effects for the turbine and 

control groups, and a quadratic effect of head (model 18 in table 18). The model with a 
48

Table 17. Table of correlation indices of data from juvenile steelhead from the control group from data 

used in studies at McNary Dam in 2004–2009. 

[Pearson correlation coefficients are listed above the probabilities of obtaining a greater value under the 

hypothesis that Rho = 0. Sample size is 2,316; <, less than; see table 2 for variable name definitions]

 TAG

 PER_SPI PHOTO TEMP WEIGHT BURDEN

TOTQ 0.5872 -0.0296 0.2583 -0.1312 -0.0228

<0.0001 0.1539 <0.0001 <0.0001 0.2736

PER_SPI 1.0000 0.2614 -0.0659 -0.0886 -0.0601

<0.0001 0.0015 <0.0001 0.0038

PHOTO 1.0000 -0.1096 0.0426 -0.0627

<0.0001 0.0402 0.0025

TEMP 1.0000 0.0427 0.2171

 0.0398 <0.0001

WEIGHT 1.0000 - 0.8160

<0.0001

linear effect of head (model 13) was only weakly supported with an AICc 1.2 less than 

the model without head. The quadratic model of head (model 14b) received moderate

support, with an AICc value 5.7 less than the model without head (model 14a). That this 

effect for the turbine group. Survival of the control group was higher than survival of the 

turbine group and survival of the turbine group was higher at night than during the day. 

An effect of photoperiod (day/night) on survival of the control group was not supported.
49

Key Findings in Data from Juvenile Steelhead at McNary Dam

• Initial analyses were based on a subset of the data because turbine unitspecific passage location was not available in all years. Unit-specific 

discharge was not supported as a factor on survival in these data (from 

2004, 2005, and 2009), so inferences were based on the full 2004–2009 

data set and a “north-south” assignment for unit passage location.

• The full data set included 351 fish in the turbine group and 2,316 fish in 

the control group.

• Most data were collected at turbine discharges within 1 percent of peak 

unit efficiency.

• Head was moderately supported as a factor affecting turbine passage 

survival. A curvilinear fit to the data indicated minimum turbine passage 

survival at a head of 73.1 ft with higher survival at greater or lesser values. 

This effect is in the opposite direction as the effect supported by data from 

yearling Chinook salmon at McNary Dam.

• Spill percentage was supported as a factor affecting survival. A negative 

effect of spill percentage was moderately supported as a factor affecting 

passage survival and a different effect of fish in turbine and controls 

groups was weakly supported. The final model described a smaller 

negative effect of spill percentage on control fish than on turbine fish.

• An effect of photoperiod was supported on survival of fish in the turbine 

group, but not those of the control group. The data and models indicated 

greater turbine passage survival at night than during the day.

• An effect of tag burden on survival was not supported from the full (2004–

2009) data set, but a negative effect was weakly supported in the restricted 

data set (2004, 2005, and 2009).
50

Table 18. Model-selection results from radio- and acoustic-tagged juvenile steelhead from data used in studies at McNary Dam in

2004–2009. 

[Presence of a factor in a model is indicated by an 'x' in the column for that factor. Model 1 was a global model including all group covariates and their 

interactions (g) as well as all individual covariates and interactions listed. All models shared a common g*reach model of recapture probability. K 

indicates the number of parameters. An asterisk after the model number indicates the best-supported model of the suite]

Individual covariates

Group covariates Biological Operational Model selection results

Model 

No. g

trtyrphototrt*yrtrt*photoyr*phototrt*yr*photogatedtagbtrt*tagbyr*tagbtemptrt*tempyr*temppersptrt*persphead linearhead quadraticturq linearturq quadraticturlocturloc*photototq

AICc K Deviance

1 x x x x x x x x x x x x x x x x x x x x x 4806.9 62 4681.2

2 x x x x x x x x x x x x x x x x x x x x 4799.5 57 4684.0

3 x x x x x x x x x x x x x x x x x x x 4793.5 52 4688.2

4 x x x x x x x x x x x x x x x 4787.6 39 4709.0

5 x x x x x x x x x x x x x x 4785.9 38 4709.3

6 x x x x x x x x x x x x x 4791.4 37 4716.7

7 x x x x x x x x x x x x x 4784.1 37 4709.5

8 x x x x x x x x x x x x 4783.5 36 4711.0

9 x x x x x x x x x x x 4783.1 35 4712.5

10 x x x x x x x x x x 4783.5 34 4715.0

11 x x x x x x x x x x 4790.7 34 4722.2

12 x x x x x x x x x x 4787.9 34 4719.4

13 x x x x x x x x x x 4781.1 34 4712.6

14a x x x x x x x x x 4782.3 33 4715.8

14b x x x x x x x x x x 4776.7 35 4706.1

15a x x x x x x x x x 4776.6 34 4708.1

15b x x x x x x x x x x 4778.6 36 4706.0

16 x x x x x x x x 4774.7 33 4708.2

17 x x x x x x x 4772.9 32 4708.4

18* x x x x x x 4770.8 31 4708.9
51

Figure 18. Graph showing estimated effects of head (upper plate) and spill percentage (lower plate) 

on apparent survival of juvenile steelhead at McNary Dam 2004–2009.

Table 19. Beta (slope) coefficients of estimable survival parameters of juvenile steelhead from data 

used in studies at McNary Dam in 2004–2009. 

[The data are from model 18 in table 18]

Standard 95 percent confidence

Parameter Beta error Lower Upper

intercept 2.14319 0.44930 1.26255 3.02382

treatment 725.04850 3.69852 717.79939 732.29761

treatment*photo 0.80499 0.33321 0.15189 1.45809

totq 0.00516 0.00173 0.00177 0.00855

persp -0.01687 0.00695 -0.03049 -0.00326

persp*trt 0.00992 0.01124 -0.01210 0.03194

head -19.88829 0.05170 -19.98962 -19.78695

head^2 0.13610 0.00068 0.13477 0.13744
52

Subyearling Chinook Salmon

Environmental Conditions

The environmental conditions occurring during passage of subyearling Chinook 

salmon varied among years due to the natural hydrograph and annual evaluations at 

McNary Dam. The turbines usually were operated within 1 percent of peak efficiency and 

the data primarily were collected during turbine unit discharge from 8 to 13 thousand

ft3/s (fig. 19). Covariate values at the times of fish passage are summarized in appendix Y

and daily averaged values are plotted in fig. 20. Turbine unit discharge was slightly lower 

during 2006, 2007, and 2009 than in 2004, 2005, and 2008. Head ranged from 69.04 to 

76.60 ft, with a median of 73.53 ft. Total project discharge ranged from 55.41 to 355.44 

thousand ft3/s with a median of 192.58 thousand ft3/s, and decreased over the study 

periods of most years. Spill percentage varied among years based on annual study 

objectives and the natural runoff, and ranged from 0.00 to 77.82 percent. Tag burden was 

generally similar among years, ranging from 0.68 to 7.01 percent with a median of 4.57 

percent. The median tag burden was lowest in 2005 (3.82 percent) and highest in 2004 

(5.12 percent). Water temperature increased throughout the study period in each year, 

ranging from 14.56 to 22.39 °C over the years, with a median of 18.81 °C. Water 

temperature was slightly lower in 2008 than in the other years.

Figure 19. Graph showing turbine unit discharges during subyearling Chinook salmon passage (bars) 

and turbine efficiency (solid line) from data used in studies at McNary Dam in 2004–2009. The 

discharges bounded by the dashed line are within 1 percent of the peak turbine efficiency at a head 

of 72.5 feet.
53

Figure 20. Graph showing daily-averaged covariate values for subyearling Chinook salmon from data 

used in studies at McNary Dam in 2004–2009.

Overall fish passage was similar among most turbine units, but annual differences 

existed. In 2004, one of the years with the largest sample sizes, most passage was through 

units 2–10 (fig. 21). In 2009, the pattern was nearly the opposite, with most passage

occurring through units 9–14. Passage in 2005 followed a pattern similar to 2004, but the 

sample size was smaller. Unit-specific passage assignments were not made during the 

studies from 2006–2008.
54

Figure 21. Graph showing number of subyearling Chinook salmon passing through each turbine by 

year (bars) and overall (line) from data used in studies at McNary Dam in 2004, 2005, and 2009. 

Unit-specific passage assignments were not made as part of the studies in 2006–2008.

Survival

As in analyses of yearling Chinook salmon and juvenile steelhead at McNary 

Dam, two separate analyses of data from subyearling Chinook salmon were 

performed due to the inconsistent resolution of the turbine unit of passage. Data from

2004, 2005, and 2009, years with unit-specific passage assignments, were analyzed first 

followed by analyses based on the complete data set from 2004–2009.

The analyses using years with unit-specific passage assignments were based on 

890 fish in the turbine group and 2,998 fish in the control group. The turbine group in 

2004 contained 2–4 times as many fish as the turbine groups in 2005 and 2009, and the 

control group in 2004 contained fewer fish than the other years (appendix W). Pearson 

correlation coefficients for fish weight and tag burden and total discharge and head 

ranged from |0.47| to |0.71| (appendix Y). Analyses of multicollinearity did not indicate 

any serious dependencies. As in previous analyses, we applied head only to the turbine 

group and total discharge to the control group. Tag burden was also treated in a similar to 

the other analyses, with post-hoc replacement with fish weight if an effect of tag burden 

was supported by the data.

A multiplicative recapture probability model of group and reach was supported 

by the data and used in all comparisons among survival models. This model received 

essentially 100 percent of the AICc weight, indicating it was the only model supported

among those considered (model 1 in appendix Z).
55

Four of the covariates examined were supported by the data and models as 

determinants of survival for the turbine group. These included tag burden, spill 

percentage, turbine passage location, and water temperature (appendixes AA and AB). 

Models with a linear or quadratic effect of head (models 13 and 14b) had AICc values 5 

and 6 units greater than the model having no head effect (model 14a) indicating no 

support for these models. Similarly, models with linear or quadratic effects of turbine unit 

discharge (models 14a and 15b) had AICc values 2 and 3 units greater than the model 

without turbine unit discharge (model 15a). Because an effect of turbine unit discharge on 

survival was not supported, further analyses were based on the complete 2004–2009 data 

set.

The analyses of factors affecting survival for all years (2004–2009) were based on 

1,912 fish in the turbine group and 6,547 in the control group (appendix AC). Numbers of 

fish in the turbine groups ranged from 117 to 500 fish among years, whereas annual 

control fish numbers ranged from 763 to 1,191. No control fish were released at night in 

2006 or 2008.

Correlation analyses indicate that several variables were moderately related.

Pearson correlation coefficients ranged from |0.63| to |0.72| for fish weight and tag burden 

and was |0.69| for total discharge and head (tables 20 and 21). The correlation coefficient 

for total discharge and water temperature was |0.69|. We applied the head covariate only 

to the turbine group and total discharge only to the control group. Tag burden was applied 

to turbine and control groups. As in analyses of yearling Chinook salmon at McNary 

Dam, specific turbine unit passage location used in the reduced data set was replaced by a 

north or south passage location for all years, because that was the only resolution 

common to all years.

A multiplicative recapture probability model of group and reach was supported by 

the data and used in all comparisons among survival models. This model received greater 

than 99.9 percent of the AICc weight, indicating that it was the only model supported

among those considered (model 1 in appendix AD). Recapture probabilities at the first 

downriver site ranged from 0.345 (SE 0.095) to 0.996 (SE 0.004) and averaged 0.779. 

The λ parameter ranged from 0.573 (SE 0.043) to 0.953 (SE 0.045) and averaged 0.796.

Survival effects of spill percentage and water temperature were the only individual 

covariates supported by the data and models (table 22). Operational covariates other than 

spill percentage contributed little to the fit of the survival models. The linear and 

quadratic models of head (model 13 and 14b) had AICc values 1.8 and 3.8 greater than 

the model with no head effect (model 14a) indicating no support for this covariate. 

Turbine unit discharge was also not supported; with linear and quadratic models having

AICc values 2 and 4 units greater than the model without turbine unit discharge (models 

14a and 15b compared to model 15a). Among the models examined, the model 

containing treatment, photoperiod, year, 2-way interactions, and the individual covariates

of water temperature and spill percentage were supported (model 17 in table 22).
56

Table 20. Table of correlation indices of data from subyearling Chinook salmon from the turbine group 

from data used in studies at McNary Dam in 2004–2009. 

[Pearson correlation coefficients are listed above the probabilities of obtaining a greater value under the 

hypothesis that Rho = 0. Sample size is 1,912; <, less than; see table 2 for variable name definitions]

TAG

TOTQ PER_SPI HEAD TUQ UNITLOC PHOTO TEMP WEIGHT BURDEN

TOTQ 1.0000 0.4719 -0.6881 0.3034 -0.1285 -0.3848 -0.6972 -0.2939 0.0607

<0.0001 <0.0001 <0.0001 <0.0001 <0.0001 <0.0001 <0.0001 0.0079

PER_SPI 1.0000 -0.0623 -0.3898 -0.1087 -0.0955 -0.3069 -0.2425 -0.2020

0.0065 <0.0001 <0.0001 <0.0001 <0.0001 <0.0001 <0.0001

HEAD 1.0000 -0.3611 0.0391 0.3604 0.5204 0.2378 -0.0674

<0.0001 0.0877 <0.0001 <0.0001 <0.0001 0.0032

TUQ 1.0000 0.0573 -0.2433 -0.2106 0.0336 0.0740

0.0122 <0.0001 <0.0001 0.1421 0.0012

UNITLOC 1.0000 0.0050 0.0441 0.0029 0.0129

0.8275 0.0540 0.8979 0.5718

PHOTO 1.0000 0.2242 0.1092 -0.0255

<0.0001 <0.0001 0.2654

TEMP 1.0000 0.3102 -0.0909

<0.0001 <0.0001

WEIGHT 1.0000 -0.7196

<0.0001
57

Table 21. Table of correlation indices of data from subyearling Chinook salmon from the control group 

from data used in studies at McNary Dam in 2004–2009. 

[Pearson correlation coefficients are listed above the probabilities of obtaining a greater value under the 

hypothesis that Rho = 0. Sample size is 6,547; <, less than; see table 2 for variable name definitions]

TAG

TOTQ PER_SPI PHOTO TEMP WEIGHT BURDEN

TOTQ 1.0000 0.2798 -0.2329 -0.6861 -0.2086 0.1625

<0.0001 <0.0001 <0.0001 <0.0001 <0.0001

PER_SPI 1.0000 -0.0436 -0.1374 -0.2374 -0.2019

0.0004 <0.0001 <0.0001 <0.0001

PHOTO 1.0000 0.1202 0.0094 -0.1284

<0.0001 0.4493 <0.0001

TEMP 1.0000 0.2608 -0.2156

<0.0001 <0.0001

WEIGHT 1.0000 -0.6296

<0.0001

A negative effect of water temperature was moderately supported for fish in 

turbine and control groups and a negative effect of spill percentage was weakly supported 

for fish in the turbine group. A negative effect of water temperature on survival was 

supported for all years except for 2005 in which the effect was positive (table 23, fig. 22). 

The model slopes generally indicate a greater temperature effect on the turbine group 

than the control group. Survival estimates of the control group were higher than for the 

turbine group, as expected. Spill percentage had a negative effect on survival of the 

turbine group in all years (fig. 23). The effect of photoperiod varied among years, with 

some years having higher survival during the day than at night, and other years with the 

opposite trend.
58

Key Findings in Data from Subyearling Chinook Salmon at McNary Dam

• Initial analyses were based on a subset of the data because turbine unitspecific passage location was not available in all years. Unit-specific 

discharge was not supported as a factor on survival in these data (from 

2004, 2005, and 2009), so inferences were based on the full 2004–2009 

data set and a “north-south” assignment for unit passage location.

• The full data set included 1,912 fish in the turbine group and 6,547 fish in 

the control group.

• Most data were collected at turbine discharges within 1 percent of peak 

unit efficiency.

• A negative effect of spill percentage was weakly supported as a factor 

affecting turbine passage survival.

• An effect of water temperature on survival was moderately supported. The 

effect was positive in 2005 and negative in all other years.

• An effect of tag burden on survival was not supported.
59

Table 22. Model-selection results from radio- and acoustic-tagged subyearling Chinook salmon from data used in studies at McNary Dam in 2004–2009. 

[Presence of a factor in a model is indicated by an 'x' in the column for that factor. Model 1 was a global model including all group covariates and their interactions (g) as well as all 

individual covariates and interactions listed. All models shared a common g*reach model of recapture probability. K indicates the number of parameters. An asterisk after the model 

number indicates the best-supported model of the suite]

Individual covariates

Group covariates Biological Operational Model selection results

Model No. g

trtyrphototrt*yrtrt*photoyr*phototrt*yr*photogatedtagbtrt*tagbyr*tagbtemptrt*tempyr*temppersptrt*persphead linearhead quadraticturq linearturq quadraticturlocturloc*photototq

AICc K Deviance

1 x x x x x x x x x x x x x x x x x x x x x 17789.84 85 17618.8

2 x x x x x x x x x x x x x x x x x x x x 17765.37 80 17604.4

3 x x x x x x x x x x x x x x x x x x x 17789.25 75 17638.4

4a x x x x x x x x x x x x x x x x 17803.94 65 17673.3

4b x x x x x x x x x x x x x x x x x x 17763.18 77 17608.3

4c x x x x x x x x x x x x x x x x x 17777.38 72 17632.6

4d x x x x x x x x x x x x x x x x x 17760.67 72 17615.9

5 x x x x x x x x x x x x x x x x 17759.29 71 17616.6

6 x x x x x x x x x x x x x x x 17758.88 70 17618.2

7 x x x x x x x x x x x x x x 17757.15 69 17618.5

8 x x x x x x x x x x x x x 17761.43 68 17624.8

9 x x x x x x x x x x x x x 17759.84 68 17623.2

10 x x x x x x x x x x x x x 17757.46 68 17620.8

11 x x x x x x x x x x x x x 17755.38 68 17618.7

12 x x x x x x x x x x x x 17753.49 67 17618.8

13 x x x x x x x x x x x 17751.55 66 17618.9

14a x x x x x x x x x x 17749.70 65 17619.1

14b x x x x x x x x x x x 17753.57 67 17618.9

15a x x x x x x x x x 17747.73 64 17619.1

15b x x x x x x x x x x 17751.71 66 17619.1

16 x x x x x x x x 17747.29 63 17620.7

17* x x x x x x x 17746.75 62 17622.2
60

Table 23. Beta (slope) coefficients of estimable survival parameters of subyearling Chinook salmon from data 

used in studies at McNary Dam in 2004–2009. 

[The data are from model 17 in table 22]

Standard 95 percent confidence

Parameter Beta error Lower Upper

intercept 6.46134 1.91771 2.70263 10.22004

treatment -0.92842 0.15768 -1.23748 -0.61937

photo -0.51201 0.18596 -0.87649 -0.14753

2005 -7.14920 2.69855 -12.43835 -1.86005

2006 4.65938 2.39320 -0.03129 9.35005

2007 1.45289 2.74781 -3.93282 6.83860

2008 3.43575 2.41183 -1.29143 8.16293

2009 6.13040 2.23710 1.74567 10.51512

photo*2005 0.68992 0.31715 0.06831 1.31153

photo*2006 0.67572 0.31164 0.06490 1.28654

photo*2007 -0.41557 0.33937 -1.08073 0.24960

photo*2008 1.30430 0.39638 0.52739 2.08120

photo*2009 0.28627 0.25838 -0.22015 0.79269

persp*treatment -0.00756 0.00353 -0.01448 -0.00063

temp -0.22686 0.09441 -0.41191 -0.04181

temp*2005 0.37577 0.13996 0.10145 0.65008

temp*2006 -0.23237 0.12016 -0.46789 0.00315

temp*2007 -0.05709 0.13775 -0.32707 0.21289

temp*2008 -0.19011 0.12272 -0.43064 0.05043

temp*2009 -0.29683 0.11036 -0.51313 -0.08053
61

Figure 22. Graph showing estimated effects of water temperature on apparent survival of subyearling Chinook 

salmon from data used in studies at McNary Dam in 2004–2009. Predictions (thick lines) and 95 percent

confidence intervals (thin lines) from model 17 in table 22 are plotted.
62

Figure 23. Graph showing estimated effects of spill percentage on apparent survival of subyearling Chinook 

salmon from data used in studies at McNary Dam in 2004–2009. Predictions (thick lines) and 95 percent

confidence intervals (thin lines) from model 17 in table 22 are plotted.
63

Discussion

Results of our analyses indicate the survival of tagged fish passing turbines was primarily 

affected by factors unrelated to turbine operation. Effects of water temperature were supported in 

four of the five data sets and were strongly supported in all but one. Tag burden was strongly 

supported in data from yearling Chinook salmon, but not in data from subyearling Chinook 

salmon or juvenile steelhead. Spill percentage, head, and turbine unit discharge received weak or 

moderate support in some cases. These findings are similar to results from several other studies 

of juvenile salmonids passing through turbines in the Columbia River Basin. Studies of turbine 

passage in the Columbia River Basin have most commonly been controlled field experiments 

based on fish fitted with balloon tags (Heisey and others, 1992). These studies generally find 

small and often statistically insignificant differences among fish survival at different turbine unit 

discharges, yet some show small, but statistically significant differences. 

Our results are similar to those of Ferguson and others (2006), who reported estimates of 

survival of turbine-passed fish from concurrent studies of controlled turbine unit discharges 

based on radio telemetry and balloon tags at McNary Dam. They reported that both methods 

found small, statistically insignificant, differences between survival of juvenile salmonids 

passing turbine unit 9 operated at discharges of 11.2 thousand ft3/s and 16.4 thousand ft3/s. 

Results based on balloon tags, which incorporate primarily direct mortality sources, were 0.930

(SE 0.021) at the lower discharge and 0.946 (SE 0.019) at the higher discharge. Examples of 

direct mortality sources from turbine passage include strike, shear, and barotrauma (Cada, 2001). 

Estimates of survival based on the radio-telemetry method, incorporating direct and indirect 

mortality sources from turbine passage to the release point of a control group of fish 2 km 

downstream, were 0.871 (SE 0.016) and 0.856 (SE 0.011) at the lower and higher discharge 

levels, respectively. Examples of indirect, or delayed, mortality include predation on dead, 

moribund, or healthy fish (Mesa and others, 1994). Predaceous fish pose a significant source of 

mortality of juvenile salmonids in the Columbia River Basin (Rieman and others, 1991; Ward 

and others 1995). Faler and others (1988) determined that northern pikeminnow (Ptychocheilus 

oregonensis) were opportunistic predators in the tailrace of McNary Dam, moving quickly into 

near-dam areas as dam operations changed. Avian predators are also important predators (Ryan 

and others, 2001). Ferguson and others (2006) suggested that delayed mortality comprised 46–70 

percent of the total estimated juvenile salmon mortality from turbine passage at McNary Dam. 

Our methods are similar to those of Ferguson and others (2006) in that we used data from studies 

incorporating direct and indirect sources of mortality, but differ from their methods by not 

controlling turbine discharges. The methods also differ analytically: we examined what may be 

considered observational data for specific trends, such as linear or quadratic fits, and Ferguson 

and others (2006) estimated survival at specific operating points from a controlled experiment.

Our finding of infrequent support for the turbine operation factors on survival is 

consistent with results of most controlled experiments. Evaluations of specific turbine discharges 

often find a numerical optimum in terms of fish survival, but the ranges in survival across test 

discharges are small and generally not statistically different. For example, Normandeau 

Associates and others (2003) estimated direct survival of balloon-tagged fish released into 

turbine intakes at McNary Dam and found no significant differences among estimates of survival 

of fish when the turbine was operated at four discrete levels from 8.0 to 16.4 thousand ft3

/s, with 

survival estimates ranging from 0.930 to 0.983. Similar results were found at other Columbia and 

Snake River dams (Mathur and others, 2000; Skalski and others, 2002a; Normandeau Associates 

and others, 2008a, 2008b). Additionally, the ranges of survival in these controlled studies are 
64

small. In four studies at Columbia or Snake River dams, Skalski and others (2002a) determined 

that estimates of fish survival generally differed by less than 5 percent over the range of unit 

discharges tested. In our analyses, a quadratic model of turbine unit discharge was weakly 

supported for subyearling Chinook salmon passing turbines at John Day Dam, but linear or 

quadratic effects were not supported for any other group. The effect size from lowest to highest 

survival from the relation at John Day Dam over the range of turbine discharges we examined 

was 11.2 to 13.9 percent (that is, a difference in survival probabilities of 0.112–0.139) for fish 

passing during the day and 20.5–24.5 percent for those passing at night. We estimated the peak 

survival of subyearling Chinook salmon at John Day Dam occurred at a turbine discharge of 15.9 

thousand ft3/s, but the 95 percent confidence interval ranged from -1.7 to 33.7 thousand ft3/s, 

indicating the estimate was imprecise. This may be due to the broad range of turbine discharges 

within 1 percent of peak unit efficiency at John Day Dam.

Results from this study likely will be compared to the studies of turbine survival based on 

balloon tags, but the methods used in studies we examined differ from balloon tag studies in five

primary ways. First, the fish used in this work were released into the Columbia River about 10–

20 km upstream from the dams and are assumed to be depth-acclimated by the time they reach 

the dam. That depth, assumed to be the depth of neutral buoyancy, is not known, but Beeman 

and Maule (2006) estimated mean in-situ migration depths of radio-tagged juvenile Chinook 

salmon to be 3.2 m and juvenile steelhead to be 2.3 m in McNary Reservoir slightly upstream 

from McNary Dam. The fish used in studies based on balloon tags are acclimated to near-surface 

depths, because they are removed directly from a shallow tank, fitted with the balloon and other 

tags, and released into a hose leading to the turbine intake or runner. Brown and others (2009) 

and Carlson and others (2010) determined that in controlled laboratory conditions simulating 

pressure changes that may occur during turbine passage that the depth of acclimation (that is, 

neutral buoyancy) was an important factor in subsequent signs of mortal injury. They determined

that signs of mortal injury increased with acclimation depth, suggesting that data from studies 

using balloon-tags will underestimate passage mortality and the data we examined would be 

more representative of run-of-river fish.

Second, the data we examined were based on fish volitionally entering turbine intakes 

and data from balloon tag studies were based on fish passed into turbine intakes or runners 

through hoses. This is an important distinction, because the elevation of entry into a turbine 

intake may affect area of turbine passage and fish survival. Normandeau Associates and others 

(1996) as reported in Skalski and others (2002a) detected significantly different survival of fish 

from releases made at different depths within the turbine intakes at Wanapum Dam on the 

Columbia River. Conversely, Mathur and others (1996, 2000) detected no statistically significant 

difference in survivals when releasing fish into turbine intakes at different elevations at other 

dams. Thus, interpretations of results from studies based on fish released through hoses may be 

affected by potential differences between fish release locations and location of passage of the 

untagged population. The vertical distribution of fish volitionally entering turbines is not known, 

but is likely different from the distribution of fish released from a hose. The availability of data 

from fish volitionally entering turbine intakes was one of the reasons our analyses were

conducted.
65

Third, mortality in studies based on balloon tags only address direct effects and our 

analyses included direct and indirect effects. By recapturing fish floated to the surface shortly 

after turbine passage, studies using balloon tags do not generally incorporate indirect effects of 

turbine passage, such as predation by fishes or birds. The estimates of survival in our analyses 

therefore are expected to be lower than those of studies based on balloon tags, which is 

consistent with our results. Ferguson and others (2006) also detected lower survival in groups 

incorporating direct and indirect sources of mortality compared to those from a balloon tag study 

at McNary Dam. The inclusion of indirect effects may dilute the effects of turbine discharge 

sometimes found in controlled studies of direct survival.

Fourth, studies based on balloon tags are carefully designed and controlled studies of 

turbine unit discharge, whereas turbine unit discharges were not controlled during collection of 

the data we used. The data we used were collected during studies controlling structures or 

operations at the spillway rather than at the powerhouse and were collected primarily during 

operation within one percent of the peak turbine efficiency (the “1 percent” rule). The 

ramifications of reliance on data collected predominantly within the 1 percent rule vary 

depending on the efficiency curve of the turbines being studied. For example, at John Day Dam 

the generator limit (21.3 thousand ft3

/s at a head of 102 ft) is near the upper end of the 1 percent 

rule (21.6 thousand ft3/s at a head of 102 ft), but at McNary Dam considerable operational range 

exists between the upper end of the 1 percent rule (12.4 thousand ft3

/s at a head of 73 ft) and the 

generator limit (16.2 thousand ft3/s at ahead of 73 ft). The uncontrolled nature of the turbine 

discharges represents an important difference between the studies, and was one reason we 

selected the information-theoretic method of analysis.

Fifth, our results are based on fish carrying transmitters internally and the balloon-tag 

studies are based on fish carrying balloon tags and transmitters externally. There is evidence 

from this study and others that the method of tag attachment (internal or external) is likely to 

affect the effect of tag burden on survival of fish passing turbines due to the mechanism of injury 

from barotrauma. A common cause of injury in juvenile salmonids exposed to rapid 

decompression, such as that during turbine passage, is from the expansion of the swim bladder 

and gas-laden tissues causing trauma to the swim bladder and internal organs (Brown and others,

2009). This is exacerbated as the volume of the swim bladder prior to exposure increases and as

the space it can expand into decreases. Swim bladder volume increases with acclimation depth 

and tag burden, regardless of tag attachment method, so this effect is similar in both study types 

with similar tag burdens. However, the space the swim bladder can expand into is reduced by the 

use of internal placement of transmitters and is different in studies of balloon tags (external 

attachment) and the data we examined (internal attachment). Brown and others (2009) found this 

to be true for transmitters placed internally with either gastric or surgical methods, both of which 

are present in the data we examined. This suggests that the turbine-passage survival of fish with 

internal transmitters will be lower than fish with external transmitters, which is consistent with 

empirical data (for example Ferguson and others, 2006). These results support the commonlyheld hypothesis that one of the differences between results of balloon tag studies and active-tag 

studies of dam-passage survival is the inclusion of indirect sources of mortality in results from 

active-tag studies, but indicates that some part of what has been called “indirect mortality”

actually may be direct plus indirect mortality caused by the method of tag attachment. Our 

analyses support this premise for yearling Chinook salmon at McNary Dam and potentially at 

John Day Dam. 
66

We used information-theoretic methods to determine which factors produced effects 

supported by the data rather than statistical null-hypothesis testing with strict “significance” 

cutoffs. We created models representing a priori hypotheses and used information-theoretic 

methods to determine the strength of evidence from the data, given the models, to determine 

which factors were supported as affecting survival of tagged fish passing turbines. Our analyses 

were not based on controlled experiments manipulating the operational factors while controlling 

for others and thus frequentist statistics were not appropriate (Burnham and Anderson, 2002). 

There is no strict cutoff of importance in information-theoretic methods, which is one of the 

reasons we selected the method. Rather, differences in AICc (or other measures of parsimony) 

represent a continuous scale of the support of models (hypotheses) by the data. Our use of this 

method was more dichotomous than in some applications, and might be considered akin to a 

series of stepwise comparisons. However, the factors considered and the order of model 

comparisons were determined a priori through consultation of experts in turbine design and 

operation, fishery management, and fishery research, and thus our use was consistent with the 

information-theoretic approach. Our goal in this study was to determine if the selected factors 

were supported as having effects on survival, which is not logically a “yes” or “no” question. 

We did not estimate overdispersion, but varying the overdispersion parameter (ĉ) did not 

appreciably alter the primary conclusions from the analyses. Mark-recapture data are based on 

theoretical models assuming subjects behave as individuals rather than as groups. An estimate of 

ĉ is 1 if individuals behave independently, 2 if they behave as pairs (for example, breeding pairs 

of Canada geese), 3 if they behave as triplets, and so on. A ĉ of 3 would be considered high 

(Burnham and Anderson, 2002). Estimates of ĉ are generally based on some form of deviance 

divided by the degrees of freedom and a chi-square goodness of fit test based on groups of 

individuals with like capture histories. However, in the presence of individual covariates, the 

typical analyses are not possible, because all individuals can be uniquely identified, and thus 

there are no groups. Pollock (2002) and White (2002) discuss this problem and suggest the 

estimation of ĉ in the presence of individual covariates as a topic requiring further research. We 

selected the approach used by Devries and others (2003), and examined the effects on the study 

conclusions over hypothetical ĉ values of 1 and 3. An adjustment to the AICc and parameter 

variances favoring models with fewer parameters is made when ĉ is greater than 1. This

adjustment can affect interpretation of the support for modeled hypotheses, so is usually of 

primary importance. The primary conclusions from analyses of data from John Day Dam 

remained similar at ĉ values of 1 and 3, although the level of support was reduced at the higher 

value. For example, the change in AICc when removing the strongly supported tag burden effect 

in the yearling Chinook salmon analyses was -18.3 when ĉ was 1 and -14.9 when it was 3.

However, the delta AICc of the weakly supported quadratic effect of turbine unit discharge in the 

subyearling Chinook salmon analyses was -1.3 when ĉ was set to 1 and +2.2 when it was 3, 

changing the conclusion from weakly supported to not supported (recall the quadratic effect 

requires two parameters, so a delta AICc of 2–4 would be required to indicate no support). The 

primary conclusions from McNary Dam were also changed only slightly at a ĉ value of 3. The

most supported conclusion, that tag burden affected survival of yearling Chinook salmon, was 

unchanged. Increasing ĉ to 3 reduced or removed support for factors that were weakly or 

moderately supported in the original analyses, such as year, photoperiod, spill percentage, and

head.
67

Our results suggest tag burden is an important factor affecting survival of yearling 

Chinook salmon at John Day and McNary dams. Data from John Day Dam strongly supported an 

effect of tag burden on control fish and data from McNary Dam strongly supported an effect on 

control and turbine fish. The lack of support for an effect on yearling Chinook salmon turbine 

fish at John Day Dam may be from the sparseness of the data: there were 246 turbine fish and 

2,973 control fish in the data set from John Day Dam and 1,419 turbine fish and 6,737 control 

fish at McNary Dam. The simulated effect on control fish was similar between dams and was

much less than the simulated effect on turbine fish at McNary Dam.

We detected little evidence to suggest tag burden affects survival of turbine passing 

juvenile steelhead or subyearling Chinook salmon. Effects of tag burden on turbine passage 

survival of juvenile steelhead and subyearling Chinook salmon at McNary Dam received weak to 

moderate support in analyses of the restricted set of years from McNary Dam (2004, 2005, and 

2009), indicating some evidence for an effect, but when the entire 2004–2009 data set was 

examined an effect of tag burden was not supported in these groups. The effect may be initially 

expected to be greatest in subyearling Chinook salmon, because they are physically smaller than 

the other fish studied, but the tag burden was similar in yearling and subyearling Chinook salmon 

due to different tags sizes used in each group. Therefore, there is no basis for a greater effect in 

subyearling Chinook salmon based on differences in tag burden. However, Brown and others 

(2009) reported more frequent mortality and signs of injury in radio-tagged subyearling Chinook 

salmon than in yearling Chinook salmon after simulated turbine passage and suggested the 

difference was due to the differences in fish sizes. Perhaps the lower turbine-passage survival of 

subyearling Chinook is primarily due to factors apart from tag burden, such as the effects of fish 

size and barotrauma described by Brown and others (2009) or other environmental factors. As in 

data we examined, tag burdens in the yearling and subyearling Chinook salmon groups studied 

by Brown and others (2009) were similar because different size tags were used in the two 

groups. A lack of support for the tag burden effect in juvenile steelhead might be expected, 

because their large size relative to the Chinook salmon resulted in a lower tag burden (median 

1.89 percent) than the other groups (median 4.35 percent or greater). Turbine passage survival 

could also vary due to differences in the pressures along the paths different species or races of 

fish take as they pass through turbines.

The negative effects of tag burden supported in our analyses are generally consistent with 

those of the laboratory experiments of Brown and others (2009) and Carlson and others (2010).

However, Carlson and others (2010) likely overestimated the effect of tag burden when using 

data from field-based studies to illustrate the potential effect of tag burden on survival. The 

source of mortality in their laboratory study of simulated turbine passage was barotrauma. 

However, the mortality of turbine-passing fish in field studies includes mortality from 

barotrauma, strike, shear, and other direct effects of turbine passage as well as indirect effects of 

turbine passage affecting predation after passage. Thus, one cannot use survival estimates from 

field studies of turbine-passing fish to correctly back-calculate the likely pressure history during 

turbine passage using results of Carlson and others (2010) without separating the mortality from 

barotrauma and mortality from other causes. Failing to do so overestimates the log ratio of 

pressure change during turbine passage described by Carlson and others (2010), which will then 

overestimate the mortality of tagged fish relative to untagged fish. The bias in using data from 

field studies of turbine passage to illustrate the effects of tag burden from the laboratory 

experiments of Carlson and others (2010) increases with tag burden. The proportion of turbinepassage mortality that may be attributed to sources other than barotrauma following passage is 
68

likely to be an important component of the total mortality. Petersen (1994) and Ward and others 

(1995) found that much of the reservoir-wide predation of juvenile salmonids by predaceous 

fishes occurs in the relatively small spatial area near hydro dams, and predation by avian 

predators is also high in these areas.

We were not able to separate effects of tag burden and fish weight using the data 

available. Tag burden and fish weight were inextricably confounded in our analyses, preventing 

us from determining their independent effects. Replacing tag burden with fish weight in models 

of yearling Chinook salmon at John Day and McNary dams resulted in ambiguous results, 

suggesting weight was the more supported factor in one case and tag burden was the more 

supported factor in the other. However, results from the controlled laboratory experiments of 

Carlson and others (2010), indicated fish weight was not an important contributor to the fit of 

models describing an index of mortal injury, lending support to tag burden as the causative factor 

in our analyses.

Additional controlled field experiments of factors affecting juvenile salmonid are needed 

to assess turbine survival. We feel most studies have been too narrowly focused to add 

substantially to the knowledge base on the subject. For example, most studies have examined 

turbine passage survival relative to the 1 percent rule and thus often only have three turbine 

discharge levels in their design (see Skalski and others [2002a] for a description of four studies).

These studies aid the quest for information about survival relative to the 1 percent rule, but do 

little to answer what we see as the larger question, which is whether there is a reproducible 

pattern between turbine discharge and survival. We suggest future studies be designed with at 

least four discharge levels spanning the entire operating range of turbine discharge and that the 

results be examined relative to a priori hypotheses such as linear or curvilinear patterns, rather 

than tests of statistical significance among operating points. The study conducted by 

Normandeau and Associates and others (2008a) exemplifies this approach. They estimated 

survival at each of five turbine discharge levels at Ice Harbor Dam on the Snake River. They 

concluded no statistical difference existed in survival among the five levels (although the data 

from the peak discharge was not used in the analysis due to a single test condition), but there was 

a clear curvilinear relation with a maximum at the intermediate discharge level. Their effect sizes 

were insufficient to result in statistically significant differences in survival, but a quadratic model 

provided a good fit to the relation between survival and discharge. Further studies of this type, 

despite being conducted using surface acclimated fish released through hoses, could be used to 

determine if there is a consistent relation between survival and turbine operation within turbine 

families (turbines of similar design) or at different dams. This level of information is needed if 

turbines are to be operated to achieve the greatest fish survival, as Skalski and others (2002a) 

recommend.

In summary, our results indicate that few operational covariates were supported as factors 

affecting turbine passage survival of juvenile salmonids at McNary or John Day dams. Support 

for linear or quadratic effects of head or turbine unit discharge was not common. Potential 

reasons the operational factors were generally not supported include the uncontrolled nature of 

the experiments and the small effect sizes common to even carefully controlled experiments of 

turbine discharge. Tag burden and water temperature were well-supported factors affecting the 

survival of juvenile salmonids passing turbines at these dams, and generally corroborate results 

of other field and laboratory studies. The results suggest tag burden should be minimized in 

studies of turbine passage, or that factor should be included as an explanatory variable in 

analyses. Additionally, effects of water temperature on survival were supported in several 
69

analyses suggesting it should be considered in designs or analyses of studies. The design of 

existing turbines at McNary Dam is unique to the Columbia River Basin, but those at John Day 

are similar to turbines at three of the four lower Snake River dams (Wittinger and others, 2010). 

This study identified several factors affecting the survival of fish passing turbines, but it is the 

only study we know of that examined data from tagged fish volitionally passing through turbines

for this purpose. It may be prudent to examine similar data from past studies at other FCRPS 

dams to corroborate these results.

Acknowledgments

This work was made possible by a suite of people and organizations responsible for the 

design, conduct, reporting, and funding of the studies that collected the data we used in analyses. 

These include staff at the U.S. Geological Survey (USGS), Western Fisheries Research Center 

office in Cook, Washington, National Oceanic and Atmospheric Administration (NOAA),

Northwest Fisheries Science Center office in Pasco, Washington, and the U.S. Army Corps of 

Engineers, Portland District located in Portland, Oregon, and Walla Walla District located in 

Walla Walla, Washington. The contracts for this study were overseen by Michael Langeslay, 

George Medina, and Dennis Schwartz of the Portland District U.S. Army Corps of Engineers.

Gordon Axel of NOAA Fisheries and Amy Braatz, Scott Brewer, Scott Evans, Gabriel Hansen of 

USGS, and Christopher Walker, formerly of USGS, assisted with the compilation of the data 

sets. Jon Renholds with the Walla Walla District Corps of Engineers provided much of the 

operations data. Reviews by Paul Heisey, Toby Kock, and staff of the U.S. Army Corps of 

Engineers improved the document. This work was completed under contract numbers 

W66QKZ00712046 and W66QKZ00712056.

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74

Appendix A. Summaries of Covariate Values from Data used in Studies of 

Yearling Chinook Salmon at John Day Dam in 2002 and 2003.

Table A1 — Summary statistics of turbine unit discharge (thousand ft3/s) during yearling Chinook salmon 

passage from data used in studies at John Day Dam in 2002 and 2003.

[N, number of observations; Min, minimum; Max, maximum; SD, standard deviation; SE, standard error]

Year N Min Max Mean Median SD SE

Overall 2002 120 11.90 22.10 15.33 15.00 2.33 0.21

2003 126 11.40 22.20 15.48 15.10 2.86 0.25

Overall 246 11.40 22.20 15.41 15.05 2.61 0.17

Day 2002 46 12.30 22.10 16.66 15.85 2.73 0.40

2003 59 11.50 22.20 17.52 17.00 2.70 0.35

Night 2002 74 11.90 18.30 14.51 14.60 1.57 0.18

2003 67 11.40 17.30 13.69 13.30 1.44 0.18

Table A2 — Summary statistics of head (feet) at John Day Dam during yearling Chinook salmon passage 

from data used in studies at John Day Dam in 2002 and 2003.

[N, number of observations; Min, minimum; Max, maximum; SD, standard deviation; SE, standard error]

Year N Min Max Mean Median SD SE

Overall 2002 120 98.00 104.10 101.61 101.60 1.19 0.11

2003 126 97.00 104.49 101.27 101.53 1.64 0.15

Overall 246 97.00 104.49 101.44 101.57 1.44 0.09

Day 2002 46 98.00 103.50 101.32 101.50 1.31 0.19

2003 59 97.00 102.61 100.34 100.50 1.53 0.20

Night 2002 74 99.50 104.10 101.79 101.80 1.08 0.13

2003 67 99.11 104.49 102.09 102.12 1.26 0.15

Table A3 — Summary statistics of total project discharge (thousand ft3/s) during yearling Chinook salmon 

passage from data used in studies at John Day Dam in 2002 and 2003.

[N, number of observations; Min, minimum; Max, maximum; SD, standard deviation; SE, standard error]

Year N Min Max Mean Median SD SE

Overall 2002 871 150.30 318.20 226.96 228.00 38.94 1.32

2003 2102 138.90 372.40 230.75 226.50 50.24 1.10

Overall 2973 138.90 372.40 229.64 227.70 47.24 0.87

Day 2002 301 160.10 316.50 215.81 217.50 43.02 2.48

2003 540 166.20 372.40 238.46 221.20 52.50 2.26

Night 2002 570 150.30 318.20 232.85 234.00 35.24 1.48

2003 1562 138.90 344.30 228.08 226.90 49.18 1.24
75

Table A4 — Summary statistics of spill percentage during yearling Chinook salmon passage from data 

used in studies at John Day Dam in 2002 and 2003.

[N, number of observations; Min, minimum; Max, maximum; SD, standard deviation; SE, standard error]

Year N Min Max Mean Median SD SE

Overall 2002 991 0.00 61.67 33.08 30.13 19.03 0.60

2003 2228 0.00 73.69 39.15 46.13 23.98 0.51

Overall 3219 0.00 73.69 37.28 45.54 22.74 0.40

Day 2002 347 0.00 43.12 15.83 18.89 14.47 0.78

2003 599 0.00 48.25 1.13 0.00 4.56 0.19

Night 2002 644 26.12 61.67 42.37 31.34 14.06 0.55

2003 1629 43.88 73.69 53.13 54.17 7.19 0.18

Table A5 — Summary statistics of tag burden (percent) of yearling Chinook salmon from data used in 

studies at John Day Dam in 2002 and 2003.

[N, number of observations; Min, minimum; Max, maximum; SD, standard deviation; SE, standard error]

 N Min Max Mean Median SD SE

Overall 2002 991 1.30 8.92 4.66 4.67 1.33 0.04

2003 2228 1.23 7.78 4.42 4.46 1.28 0.03

Overall 3219 1.23 8.92 4.49 4.53 1.30 0.02

Day 2002 347 2.03 8.24 4.83 4.86 1.35 0.07

2003 599 1.23 7.69 4.34 4.36 1.26 0.05

Night 2002 644 1.30 8.92 4.56 4.59 1.30 0.05

2003 1629 1.35 7.78 4.44 4.49 1.28 0.03

Table A6 — Summary statistics of temperature during yearling Chinook salmon passage from data used in 

studies at John Day Dam in 2002 and 2003.

[N, number of observations; Min, minimum; Max, maximum; SD, standard deviation; SE, standard error]

Year N Min Max Mean Median SD SE

Overall 2002 991 9.70 14.30 11.88 11.80 1.38 0.04

2003 2228 10.56 15.44 12.56 12.17 1.40 0.03

Overall 3219 9.70 15.44 12.35 12.17 1.43 0.03

Day 2002 347 9.90 14.10 11.76 11.80 1.36 0.07

2003 599 10.56 15.22 12.59 12.17 1.41 0.06

Night 2002 644 9.70 14.30 11.94 12.20 1.40 0.06

2003 1629 10.61 15.44 12.55 12.17 1.40 0.03
76

Appendix B. Capture History Summary of Yearling Chinook Salmon from 

data used in studies at John Day Dam in 2002 and 2003.

[Occ. represents the Occasion number after release. R(i) represents numbers released and j=2 and 3 indicate the 

released number detected at each downstream site]

Group 1 control day 2002

Occ. R(i) j=2 j=3 Total

1 301 208 79 287

2 208 203 203

Group 2 control day 2003 

Occ. R(i) j=2 j=3 Total

1 540 401 127 528

2 401 398 398

Group 3 control night 2002 

Occ. R(i) j=2 j=3 Total

1 570 366 174 540

2 366 349 349

Group 4 control night 2003

Occ. R(i) j=2 j=3 Total

1 1562 1332 195 1527

2 1332 1304 1304

Group 5 turbine day 2002

Occ. R(i) j=2 j=3 Total

1 46 31 9 40

2 31 30 30

Group 6 turbine day 2003

Occ. R(i) j=2 j=3 Total

1 59 38 12 50

2 38 38 38

Group 7 turbine night 2002 

Occ. R(i) j=2 j=3 Total

1 74 47 19 66

2 47 46 46

Group 8 turbine night 2003

Occ. R(i) j=2 j=3 Total

1 67 53 10 63

2 53 53 53
77

Appendix C. Model Summary from Analyses of Recapture Probabilities (p) 

of Yearling Chinook Salmon from data used in studies at John Day Dam in 

2002 and 2003.

[Models of p include those in which values can vary in various combinations of detection site (t) and group 

(treatment, year, and photoperiod). A '*' indicated a multiplicative effect, a '+' indicates an additive effect, and a '.' 

indicates a common value fitted to all groups and reaches. A multiplicative model (g*t) of apparent survival (phi) 

was used in all models. K indicates the number of estimable parameters]

 Delta AICc Model

Model AICc AICc Weights Likelihood K Deviance

{01 phi(g*t), p(g*t)} 4521.89 0.00 1.00 1.00 24 4473.67

{02 phi(g*t), p(g+t)} 4536.05 14.17 0.00 0.00 24 4487.84

{03 phi(g*t), p(g} 5069.96 548.07 0.00 0.00 24 5021.75

{04 phi(g*t), p (t)} 4639.80 117.92 0.00 0.00 17 4605.69

{05 phi(g*t), p (.)} 5178.08 656.20 0.00 0.00 17 5143.97
78

Appendix D. Summaries of Covariate Values of Subyearling Chinook 

Salmon from data used in studies at John Day Dam in 2002 and 2003.

Table D1 — Summary statistics of turbine unit discharge (thousand ft3/s) during subyearling Chinook 

salmon passage from data used in studies at John Day Dam in 2002 and 2003.

[N, number of observations; Min, minimum; Max, maximum; SD, standard deviation; SE, standard error]

Year N Min Max Mean Median SD SE

Overall 2002 249 11.90 22.70 15.64 15.20 2.75 0.17

2003 547 9.70 20.90 14.58 14.40 1.72 0.07

Overall 796 9.70 22.70 14.91 14.70 2.15 0.08

Day 2002 115 12.00 22.70 17.13 16.50 3.04 0.28

2003 318 9.70 20.90 15.07 15.00 1.63 0.09

Night 2002 134 11.90 18.70 14.36 13.70 1.62 0.14

2003 229 10.70 19.80 13.89 13.50 1.59 0.11

Table D2 — Summary statistics of head (feet) during subyearling Chinook salmon passage from data used 

in studies at John Day Dam in 2002 and 2003.

[N, number of observations; Min, minimum; Max, maximum; SD, standard deviation; SE, standard error]

Year N Min Max Mean Median SD SE

Overall 2002 249 97.00 104.00 100.61 100.40 1.33 0.08

2003 547 99.50 105.65 103.12 103.18 0.91 0.04

Overall 796 97.00 105.65 102.34 102.70 1.57 0.06

Day 2002 115 97.00 103.80 100.26 100.30 1.47 0.14

2003 318 99.50 105.31 102.89 102.91 0.93 0.05

Night 2002 134 98.30 104.00 100.92 100.90 1.13 0.10

2003 229 100.58 105.65 103.43 103.41 0.79 0.05

Table D3 — Summary statistics of total project discharge (thousand ft3/s) during subyearling Chinook 

salmon passage from data used in studies at John Day Dam in 2002 and 2003.

[N, number of observations; Min, minimum; Max, maximum; SD, standard deviation; SE, standard error]

Year N Min Max Mean Median SD SE

Overall 2002 2649 157.70 396.20 264.62 253.90 54.19 1.05

2003 2814 89.90 237.40 153.77 152.20 33.12 0.62

Overall 5463 89.90 396.20 207.52 194.70 71.12 0.96

Day 2002 1150 182.90 396.20 282.45 269.40 51.44 1.52

2003 1392 89.90 230.60 157.52 156.00 36.69 0.98

Night 2002 1499 157.70 369.40 250.93 252.10 52.24 1.35

2003 1422 90.80 237.40 150.11 146.80 28.77 0.76
79

Table D4 — Summary statistics of spill percentage during subyearling Chinook salmon passage from data 

used in studies at John Day Dam in 2002 and 2003.

[N, number of observations; Min, minimum; Max, maximum; SD, standard deviation; SE, standard error]

Year N Min Max Mean Median SD SE

Overall 2002 2898 0.00 67.93 33.18 30.36 17.51 0.33

2003 3361 0.00 64.87 28.66 29.80 21.04 0.36

Overall 6259 0.00 67.93 30.76 29.93 19.61 0.25

Day 2002 1265 0.00 61.21 21.13 28.54 14.54 0.41

2003 1710 0.00 61.03 14.28 0.00 14.92 0.36

Night 2002 1633 27.28 67.93 42.52 33.08 13.45 0.33

2003 1651 0.00 64.87 43.56 31.74 15.30 0.38

Table D5 — Summary statistics of tag burden (percent) of subyearling Chinook salmon from data used in 

studies at John Day Dam in 2002 and 2003.

[N, number of observations; Min, minimum; Max, maximum; SD, standard deviation; SE, standard error]

Year N Min Max Mean Median SD SE

Overall 2002 2898 1.67 7.33 5.13 5.28 0.81 0.01

2003 3361 2.24 7.20 5.31 5.45 0.78 0.01

Overall 6259 1.67 7.33 5.22 5.35 0.80 0.01

Day 2002 1265 1.95 7.33 5.13 5.28 0.82 0.02

2003 1710 2.24 6.54 5.30 5.45 0.78 0.02

Night 2002 1633 1.67 6.75 5.13 5.28 0.79 0.02

2003 1651 2.28 7.20 5.31 5.41 0.78 0.02

Table D6 — Summary statistics of temperature during subyearling Chinook salmon passage from data 

used in studies at John Day Dam in 2002 and 2003.

[N, number of observations; Min, minimum; Max, maximum; SD, standard deviation; SE, standard error]

Year N Min Max Mean Median SD SE

Overall 2002 2898 15.90 20.30 17.82 17.60 1.18 0.02

2003 3361 16.33 21.61 18.74 18.44 1.43 0.02

Overall 6259 15.90 21.61 18.31 18.00 1.40 0.02

Day 2002 1265 16.20 20.30 17.97 17.60 1.13 0.03

2003 1710 16.33 20.89 18.69 18.44 1.40 0.03

Night 2002 1633 15.90 20.30 17.69 17.40 1.21 0.03

2003 1651 16.33 21.61 18.79 18.61 1.45 0.04
80

Appendix E. Capture History Summary of Subyearling Chinook Salmon 

from data used in studies at John Day Dam in 2002 and 2003.

[Occ. represents the Occasion number after release. R(i) represents numbers released and j=2 and 3 indicate the 

released number detected at each downstream site]

Group 1 control day 2002 

Occ. R(i) j=2 j=3 Total

1 1150 504 565 1069

2 504 496 496

Group 2 control day 2003 

Occ. R(i) j=2 j=3 Total

1 1392 1122 255 1377

2 1122 1114 1114

Group 3 control night 2002

Occ. R(i) j=2 j=3 Total

1 1499 919 499 1418

2 919 890 890

Group 4 control night 2003 

Occ. R(i) j=2 j=3 Total

1 1422 1328 75 1403

2 1328 1259 1259

Group 5 turbine day 2002

Occ. R(i) j=2 j=3 Total

1 115 66 36 102

2 66 64 64

Group 6 turbine day 2003

Occ. R(i) j=2 j=3 Total

1 318 223 49 272

2 223 217 217

Group 7 turbine night 2002

Occ. R(i) j=2 j=3 Total

1 134 96 26 122

2 96 93 93

Group 8 turbine night 2003 

Occ. R(i) j=2 j=3 Total

1 229 183 8 191

2 183 179 179
81

Appendix F. Model Summary from Analyses of Recapture Probabilities (p) 

of Subyearling Chinook Salmon from data used in studies at John Day 

Dam in 2002 and 2003.

[Models of p include those in which values can vary in various combinations of detection site (t) and group 

(treatment, year, and photoperiod). A '*' indicated a multiplicative effect, a '+' indicates an additive effect, and a '.' 

indicates a common value fitted to all groups and reaches. A multiplicative model (g*t) of apparent survival (phi) 

was used in all models. K indicates the number of estimable parameters]

Delta AICc Model

Model AICc AICc Weights Likelihood K Deviance

{1 phi(g*t), p(g*t)} 9182.65 0.00 0.50 1.00 24 9134.54

{2 phi(g*t), p(g+t)} 9182.65 0.00 0.50 1.00 24 9134.54

{3 phi(g*t), p (t)} 10092.45 909.80 0.00 0.00 17 10058.39

{4 phi(g*t), p(g} 10828.06 1645.41 0.00 0.00 24 10779.94

{5 phi(g*t), p (.)} 11560.39 2377.74 0.00 0.00 17 11526.34
82

Appendix G. Summaries of Covariate Values from Yearling Chinook 

Salmon from data used in studies at McNary Dam from 2002–2009.

Table G1 — Summary statistics of turbine unit discharge (thousand ft3/s) during yearling Chinook salmon 

passage from data used in studies at McNary Dam in 2002–2009.

[N, number of observations; Min, minimum; Max, maximum; SD, standard deviation; SE, standard error]

Year N Min Max Mean Median SD SE

Overall 2002 33 7.93 16.40 11.12 11.48 1.46 0.25

2003 95 8.14 17.27 11.85 12.07 1.01 0.10

2004 173 7.90 17.10 12.54 12.10 1.65 0.13

2005 287 7.80 16.30 11.15 11.80 1.51 0.09

2006 213 7.99 13.11 12.13 12.15 0.56 0.04

2007 273 8.41 12.46 10.77 10.82 1.14 0.07

2008 163 8.12 12.42 10.37 10.21 1.34 0.10

2009 182 7.83 12.43 11.34 12.01 1.14 0.08

Overall 1419 7.80 17.27 11.38 11.90 1.43 0.04

Day 2002 12 8.67 11.86 10.73 11.51 1.21 0.35

2003 14 8.71 12.34 11.33 12.06 1.23 0.33

2004 32 7.90 16.60 12.56 12.05 1.96 0.35

2005 98 7.90 16.30 10.48 10.05 1.77 0.18

2006 107 8.71 12.94 12.19 12.21 0.59 0.06

2007 55 8.41 12.31 10.39 10.09 1.10 0.15

2008 56 8.12 12.42 10.57 10.31 1.41 0.19

2009 67 7.83 12.36 11.30 12.04 1.26 0.15

Night 2002 21 7.93 16.40 11.35 11.37 1.57 0.34

2003 81 8.14 17.27 11.94 12.07 0.95 0.11

2004 141 10.00 17.10 12.54 12.10 1.58 0.13

2005 189 7.80 16.20 11.50 12.00 1.22 0.09

2006 106 7.99 13.11 12.06 12.14 0.53 0.05

2007 218 8.50 12.46 10.87 10.88 1.13 0.08

2008 107 8.33 12.33 10.27 10.16 1.29 0.12

2009 115 7.92 12.43 11.37 11.95 1.06 0.10
83

Table G2 — Summary statistics of head (feet) during yearling Chinook salmon passage from data used in 

studies at McNary Dam in 2002–2009.

[N, number of observations; Min, minimum; Max, maximum; SD, standard deviation; SE, standard error]

 Year N Min Max Mean Median SD SE

Overall 2002 33 69.50 74.20 71.98 72.10 1.01 0.18

2003 95 69.78 73.97 72.06 72.01 1.07 0.11

2004 173 69.06 75.91 72.98 72.99 0.99 0.08

2005 287 69.85 75.31 73.15 73.02 1.19 0.07

2006 213 67.47 72.69 69.98 69.92 0.99 0.07

2007 273 69.93 74.28 72.19 72.10 0.98 0.06

2008 163 67.81 75.41 72.53 73.12 1.97 0.15

2009 182 69.40 75.43 71.75 71.63 1.23 0.09

Overall 1419 67.47 75.91 72.12 72.13 1.58 0.04

Day 2002 12 70.30 74.20 71.99 71.75 1.05 0.30

2003 14 69.93 72.27 70.95 70.86 0.84 0.23

2004 32 69.06 75.91 73.18 73.35 1.53 0.27

2005 98 69.85 75.31 73.18 72.93 1.59 0.16

2006 107 67.47 71.47 69.97 69.93 0.98 0.09

2007 55 70.08 74.28 72.38 72.43 1.04 0.14

2008 56 68.30 75.16 72.45 73.02 2.24 0.30

2009 67 70.07 75.43 71.91 71.67 1.26 0.15

Night 2002 21 69.50 73.40 71.97 72.20 1.01 0.22

2003 81 69.78 73.97 72.25 72.17 0.99 0.11

2004 141 70.21 75.04 72.93 72.96 0.82 0.07

2005 189 70.92 75.08 73.14 73.15 0.92 0.07

2006 106 67.57 72.69 69.98 69.92 1.00 0.10

2007 218 69.93 74.18 72.14 72.07 0.96 0.06

2008 107 67.81 75.41 72.57 73.16 1.81 0.18

2009 115 69.40 74.43 71.65 71.49 1.21 0.11
84

Table G3 — Summary statistics of total project discharge (thousand ft3/s) during yearling Chinook salmon 

passage from data used in studies at McNary Dam in 2002–2009.

[N, number of observations; Min, minimum; Max, maximum; SD, standard deviation; SE, standard error. 

* This variable was only applied to fish of the control group, but there was no control group in 2002 or 2003. Data 

summaries for 2002 and 2003 are based on fish of the turbine group, but are not included in the Overall row]

Year N Min Max Mean Median SD SE

Overall *2002 33 163.40 399.10 239.30 238.20 56.70 9.87

*2003 95 148.32 358.34 222.56 175.64 62.68 6.43

2004 755 130.20 291.50 183.84 158.10 48.18 1.75

2005 1575 90.30 358.40 215.62 228.90 52.26 1.32

2006 1213 166.68 399.28 327.24 343.69 48.58 1.39

2007 1310 177.02 289.06 255.44 257.24 26.89 0.74

2008 949 157.03 421.09 285.46 275.62 83.74 2.72

2009 935 141.43 356.09 262.79 261.27 51.01 1.67

Overall 6737 90.30 421.09 256.28 255.60 69.41 0.85

Day *2002 12 203.90 312.10 256.12 255.60 30.48 8.80

*2003 14 230.36 326.54 293.97 302.15 26.34 7.04

2004 114 130.20 291.50 231.35 234.90 55.47 5.19

2005 356 90.30 358.40 199.64 188.20 65.93 3.49

2006 139 285.08 378.74 344.77 351.64 34.50 2.93

2007 92 194.39 283.84 238.53 233.32 31.30 3.26

2008 116 170.77 369.03 230.57 220.67 65.91 6.12

2009 244 141.43 350.88 244.34 236.17 59.59 3.82

Night *2002 21 163.40 399.10 229.70 211.90 66.08 14.42

*2003 81 148.32 358.34 210.22 173.88 58.80 6.53

2004 641 140.90 283.90 175.39 157.30 41.45 1.64

2005 1219 92.30 297.80 220.28 229.70 46.54 1.33

2006 1074 166.68 399.28 324.97 335.88 49.67 1.52

2007 1218 177.02 289.06 256.72 257.45 26.11 0.75

2008 833 157.03 421.09 293.10 279.78 83.13 2.88

2009 691 177.02 356.09 269.31 266.63 45.92 1.75
85

Table G4 — Summary statistics of spill percentage during yearling Chinook salmon passage from data 

used in studies at McNary Dam in 2002–2009.

[N, number of observations; Min, minimum; Max, maximum; SD, standard deviation; SE, standard error]

 Year N Min Max Mean Median SD SE

Overall 2002 33 0.00 68.09 35.67 49.60 25.11 4.37

2003 95 0.00 62.64 19.00 0.02 21.71 2.23

2004 928 0.00 78.52 21.30 0.00 30.66 1.01

2005 1862 0.00 78.84 36.30 35.82 21.96 0.51

2006 1426 0.00 63.66 47.72 50.27 9.67 0.26

2007 1583 36.80 42.41 40.58 40.70 0.61 0.02

2008 1112 38.92 59.56 46.15 41.18 7.46 0.22

2009 1117 38.77 59.13 42.97 40.85 4.01 0.12

Overall 8156 0.00 78.84 39.47 40.77 17.77 0.20

Day 2002 12 41.19 68.09 55.32 54.80 7.33 2.12

2003 14 36.30 62.64 46.65 45.59 6.21 1.66

2004 146 49.44 78.52 65.06 63.79 5.90 0.49

2005 454 32.79 78.84 53.16 56.37 14.29 0.67

2006 246 39.94 63.66 49.79 51.20 4.85 0.31

2007 147 36.80 42.41 40.87 40.78 0.58 0.05

2008 172 39.65 59.49 43.48 41.19 5.19 0.40

2009 311 39.98 54.30 42.54 40.93 3.33 0.19

Night 2002 21 0.00 62.61 24.44 19.44 24.81 5.41

2003 81 0.00 56.92 14.22 0.00 19.76 2.20

2004 782 0.00 71.29 13.14 0.00 26.16 0.94

2005 1408 0.00 73.56 30.86 33.80 21.23 0.57

2006 1180 0.00 61.65 47.29 50.06 10.34 0.30

2007 1436 37.39 41.83 40.55 40.68 0.61 0.02

2008 940 38.92 59.56 46.64 41.18 7.70 0.25

2009 806 38.77 59.13 43.13 40.85 4.23 0.15
86

Table G5 — Summary statistics of tag burden (percent) of yearling Chinook salmon from data used in 

studies at McNary Dam in 2002–2009.

[N, number of observations; Min, minimum; Max, maximum; SD, standard deviation; SE, standard error]

 Year N Min Max Mean Median SD SE

Overall 2002 33 2.12 4.35 3.35 3.28 0.54 0.09

2003 95 3.47 9.78 6.96 7.06 1.17 0.12

2004 928 1.42 6.96 4.86 4.97 1.24 0.04

2005 1862 1.33 5.69 3.78 3.80 0.84 0.02

2006 1426 2.52 6.64 4.93 4.95 0.84 0.02

2007 1583 1.90 6.52 4.66 4.69 0.91 0.02

2008 1112 1.96 6.52 4.39 4.36 0.96 0.03

2009 1117 0.86 5.17 3.60 3.69 0.84 0.03

Overall 8156 0.86 9.78 4.37 4.35 1.10 0.01

Day 2002 12 2.65 4.35 3.44 3.22 0.61 0.18

2003 14 3.92 8.57 6.83 7.13 1.31 0.35

2004 146 1.85 6.87 4.76 4.93 1.31 0.11

2005 454 1.33 5.53 3.85 3.94 0.88 0.04

2006 246 3.02 6.49 4.78 4.77 0.83 0.05

2007 147 1.97 6.05 4.25 4.29 0.85 0.07

2008 172 1.96 6.33 4.03 3.95 0.86 0.07

2009 311 0.86 5.08 3.64 3.75 0.83 0.05

Night 2002 21 2.12 4.04 3.29 3.33 0.51 0.11

2003 81 3.47 9.78 6.98 7.06 1.15 0.13

2004 782 1.42 6.96 4.88 4.98 1.23 0.04

2005 1408 1.54 5.69 3.76 3.77 0.83 0.02

2006 1180 2.52 6.64 4.96 4.98 0.84 0.02

2007 1436 1.90 6.52 4.70 4.75 0.90 0.02

2008 940 2.18 6.52 4.46 4.44 0.96 0.03

2009 806 1.26 5.17 3.59 3.68 0.85 0.03
87

Table G6 — Summary statistics of temperature during yearling Chinook salmon passage from data used in 

studies at McNary Dam in 2002–2009.

[N, number of observations; Min, minimum; Max, maximum; SD, standard deviation; SE, standard error]

 Year N Min Max Mean Median SD SE

Overall 2002 33 10.00 14.30 11.80 11.80 1.12 0.20

2003 95 10.50 15.33 12.04 11.78 1.14 0.12

2004 928 10.22 13.72 12.51 12.83 0.84 0.03

2005 1862 9.89 15.00 12.48 12.56 1.21 0.03

2006 1426 9.50 14.60 12.49 12.60 1.39 0.04

2007 1583 8.83 15.78 12.24 12.50 1.97 0.05

2008 1112 8.28 13.56 10.96 11.33 1.66 0.05

2009 1117 8.11 15.00 10.96 10.72 1.94 0.06

Overall 8156 8.11 15.78 12.01 12.33 1.69 0.02

Day 2002 12 10.00 13.50 11.55 11.50 0.89 0.26

2003 14 10.83 15.17 12.39 11.78 1.34 0.36

2004 146 10.83 13.56 12.56 12.72 0.71 0.06

2005 454 9.89 14.94 12.04 12.22 1.08 0.05

2006 246 10.10 14.60 12.07 11.80 1.23 0.08

2007 147 9.06 15.50 10.63 10.22 1.52 0.13

2008 172 8.33 13.33 10.03 9.50 1.56 0.12

2009 311 8.33 14.94 10.81 10.00 1.95 0.11

Night 2002 21 10.00 14.30 11.95 12.10 1.23 0.27

2003 81 10.50 15.33 11.97 11.72 1.10 0.12

2004 782 10.22 13.72 12.50 12.83 0.86 0.03

2005 1408 10.06 15.00 12.62 12.56 1.22 0.03

2006 1180 9.50 14.60 12.58 12.80 1.41 0.04

2007 1436 8.83 15.78 12.40 12.56 1.94 0.05

2008 940 8.28 13.56 11.13 11.44 1.62 0.05

2009 806 8.11 15.00 11.02 10.89 1.94 0.07
88

Appendix H. Capture History Summary of Yearling Chinook Salmon from 

Data Used in Studies at McNary Dam in 2002–2005, and 2009.

[Occ. represents the Occasion number after release. R(i) represents numbers released and j=2 and 3 indicate the 

released number detected at each downstream site]

 Group 1 control day 2004 Group 9 turbine day 2004

Occ. R(i) j=2 j=3 Total Occ. R(i) j=2 j=3 Total

1 641 299 162 461 1 141 56 28 84

2 299 163 163 2 56 33 33

Group 2 control day 2005 Group 10 turbine day 2005

Occ. R(i) j=2 j=3 Total Occ. R(i) j=2 j=3 Total

1 1219 1015 156 1171 1 189 132 28 160

2 1015 913 913 2 132 124 124

Group 3 control day 2009 Group 11 turbine day 2009

Occ. R(i) j=2 j=3 Total Occ. R(i) j=2 j=3 Total

1 691 641 10 651 1 115 97 3 100

2 641 598 598 2 97 92 92

Group 4 control night 2004 Group 12 turbine night 2002

Occ. R(i) j=2 j=3 Total Occ. R(i) j=2 j=3 Total

1 114 59 22 81 1 12 10 2 12

2 59 29 29 2 10 8 8

Group 5 control night 2005 Group 13 turbine night 2003

Occ. R(i) j=2 j=3 Total Occ. R(i) j=2 j=3 Total

1 356 295 47 342 1 14 4 4 8

2 295 269 269 2 4 4 4

Group 6 control night 2009 Group 14 turbine night 2004

Occ. R(i) j=2 j=3 Total Occ. R(i) j=2 j=3 Total

1 244 233 6 239 1 32 14 4 18

2 233 220 220 2 14 9 9

Group 7 turbine day 2002 Group 15 turbine night 2005

Occ. R(i) j=2 j=3 Total Occ. R(i) j=2 j=3 Total

1 21 15 3 18 1 98 77 11 88

2 15 14 14 2 77 71 71

Group 8 turbine day 2003 Group 16 turbine night 2009

Occ. R(i) j=2 j=3 Total Occ. R(i) j=2 j=3 Total

1 81 38 18 56 1 67 59 0 59

2 38 17 17 2 59 54 54
89

Appendix I. Correlation Analyses of Yearling Chinook Salmon from Data 

Used in Studies at McNary Dam in 2002–2005, and 2009.

Table I1. Table of correlation indices of data from yearling Chinook salmon from the turbine group at 

McNary Dam in 2002–2005 and 2009.

[Pearson correlation coefficients are listed above the probabilities of obtaining a greater value under the hypothesis 

that Rho = 0. Sample size is 770; <, less than; see table 2 for variable name definitions]

TAG

TOTQ PER_SPI HEAD TURQ TURLOC PHOTO TEMP WEIGHT BURDEN

TOTQ 1.0000 0.5980 -0.7568 0.0105 0.1995 0.2288 0.1362 0.1116 -0.0791

<0.0001 <0.0001 0.7714 <0.0001 <0.0001 0.0001 0.0019 0.0282

PER_SPI 1.0000 -0.1566 -0.3468 0.0338 0.5888 -0.0901 0.1169 -0.2090

<0.0001 <0.0001 0.3487 <0.0001 0.0124 0.0012 <0.0001

HEAD 1.0000 -0.2068 -0.2034 -0.0005 -0.1870 -0.1325 -0.0170

<0.0001 <0.0001 0.9893 <0.0001 0.0002 0.6377

TURQ 1.0000 -0.0145 -0.2136 0.1912 0.0193 0.1448

0.6878 <0.0001 <0.0001 0.5933 <0.0001

TURLOC 1.0000 -0.0616 -0.2044 0.0422 0.0397

0.0875 <0.0001 0.2426 0.2708

PHOTO 1.0000 -0.0912 0.0223 -0.1044

0.0114 0.5371 0.0037

TEMP 1.0000 -0.1309 0.0780

0.0003 0.0305

WEIGHT 1.0000 -0.7305

<0.0001
90

Table I2. Table of correlation indices of data from yearling Chinook salmon from the control group at 

McNary Dam in 2002–2005 and 2009.

[Pearson correlation coefficients are listed above the probabilities of obtaining a greater value under the hypothesis 

that Rho = 0. Sample size is 3,265; <, less than; see table 2 for variable name definitions]

 TAG

 TOTQ PER_SPI PHOTO TEMP WEIGHT BURDEN

TOTQ 1.0000 0.5410 -0.0163 0.2874 0.1694 -0.1926

<0.0001 0.3529 <0.0001 <0.0001 <0.0001

PER_SPI 1.0000 0.3768 0.0059 0.0549 -0.1419

<0.0001 0.7353 0.0017 <0.0001

PHOTO 1.0000 -0.1241 0.0118 -0.0311

<0.0001 0.4997 0.0759

TEMP 1.0000 -0.1200 0.0812

<0.0001 <0.0001

WEIGHT 1.0000 -0.7973

<0.0001
91

Appendix J. Model Summary from Analyses of Recapture Probabilities (p) 

of Yearling Chinook Salmon from Data Used in Studies at McNary Dam in 

2002–2005, and 2009.

[Models of p include those in which values can vary in various combinations of detection site (t) and group 

(treatment, year, and photoperiod). A '*' indicated a multiplicative effect, a '+' indicates an additive effect, and a '.' 

indicates a common value fitted to all groups and reaches. A multiplicative model (g*t) of apparent survival (phi) 

was used in all models. K indicates the number of estimable parameters]

 AICc

Delta

AICc

AICc 

Weights

Model 

Model Likelihood

 

K

 

Deviance

{1 Phi(g*t), p(g*t)} 7216.47 0.00 1.00 1.00 48 7119.80

{2 Phi(g*t), p(g+t)} 7283.83 67.36 0.00 0.00 48 7187.16

{3 Phi(g*t), p(g)} 7298.73 82.27 0.00 0.00 48 7202.07

{4 Phi(g*t), p(t)} 8004.71 788.24 0.00 0.00 33 7938.39

{5 Phi(g*t), p(.)} 8037.00 820.53 0.00 0.00 33 7970.68
92

Appendix K. Model-selection Results from Radio- and Acoustic-tagged Yearling Chinook Salmon from Data 

Used in Studies at McNary Dam in 2002–2005, and 2009.

[Presence of a factor in a model is indicated by an 'x' in the column for that factor. Model 1 was a global model including all group covariates and their interactions (g) as well 

as all individual covariates and interactions listed. Distance to the first downriver gate (gated) was only used when year was present in the model. All models shared a 

common year*reach model of recapture probability. K indicates the number of parameters.]

Individual Covariates

Group Covariates Biological Operational Model Selection Results

Model 

Number g

trtyrphototrt*yrtrt*photoyr*phototrt*yr*photogatedwttagbtrt*tagbyr*tagbtemptrt*tempyr*temppersptrt*persphead linearhead quadraticturq linearturq quadraticturlocturloc*photototq

AICc K Deviance

1 x x x x x x x x x x x x x x x x x x x x x 7216.4 64 7087.2

2 x x x x x x x x x x x x x x x x x x x x x 7212.9 60 7091.8

3 x x x x x x x x x x x x x x x x x x x 7206.0 56 7093.0

4a x x x x x x x x x x x x x x x 7215.7 45 7125.2

4b x x x x x x x x x x x x x x x x x 7205.6 54 7096.8

4c x x x x x x x x x x x x x x x x 7203.2 52 7098.4

4d x x x x x x x x x x x x x x x 7204.0 48 7107.3

5 x x x x x x x x x x x x x x x 7201.8 51 7099.0

6 x x x x x x x x x x x x x x 7200.4 50 7099.6

7 x x x x x x x x x x x x x 7198.7 49 7100.0

8 x x x x x x x x x x x x 7197.3 48 7100.6

9 x x x x x x x x x x x 7195.3 47 7100.7

10 x x x x x x x x x x 7207.3 46 7114.7

11 x x x x x x x x x x 7198.1 46 7105.5

12 x x x x x x x x x x 7201.0 46 7108.3

13 x x x x x x x x x x 7194.9 46 7102.3

14a x x x x x x x x x 7195.6 45 7105.0

14b x x x x x x x x x x 7195.9 47 7101.2

15a x x x x x x x x x 7192.9 45 7102.3

15b x x x x x x x x x x 7195.9 47 7101.3

16* x x x x x x x x 7191.3 44 7102.8

17 x x x x x x x 7196.1 43 7109.6

18 x 7196.5 44 7102.9
93

Appendix L. Beta (Slope) Coefficients of Estimable Survival 

Parameters of Yearling Chinook Salmon from Data Used in Studies at 

McNary Dam in 2002–2005, and 2009.

[The data are from model 16 in appendix L]

Standard 95% Confidence

Parameter Beta Error Lower Upper

intercept 5.403126 0.880395 3.677551 7.128701

treatment 14.439400 8.404396 -2.033210 30.912020

2005 0.836723 0.290310 0.267715 1.405731

2009 -0.443710 0.367891 -1.164770 0.277360

2002 0.259362 0.743256 -1.197420 1.716145

2003 1.709109 1.345273 -0.927630 4.345844

photo*2005 0.040509 0.361362 -0.667760 0.748779

photo*2009 0.743644 0.331634 0.093642 1.393646

photo*2003 -2.505620 1.473538 -5.393760 0.382511

tag burden -0.214470 0.084410 -0.379920 -0.049030

persp 0.005215 0.004853 -0.004300 0.014726

head -0.201670 0.112947 -0.423040 0.019711

totq 0.005538 0.002532 0.000577 0.010500

temp -0.259040 0.066728 -0.389820 -0.128250
94

Appendix M. Capture History Summary of Yearling Chinook Salmon 

from Data Used in Studies at McNary Dam in 2002–2005, and 2009. 

[Occ. represents the Occasion number after release. R(i) represents numbers released and j=2 and 3 indicate 

the released number detected at each downstream site]

Group 1 control day 2004 Group 10 control night 2007 Group 19 turbine day 2008

Occ. R(i) j=2 j=3 Total Occ. R(i) j=2 j=3 Total Occ. R(i) j=2 j=3 Total

1 641 299 162 461 1 92 39 42 81 1 107 80 12 92

2 299 163 163 2 39 35 35 2 80 73 73

Group 2 control day 2005 Group 11 control night 2008 Group 20 turbine day 2009

Occ. R(i) j=2 j=3 Total Occ. R(i) j=2 j=3 Total Occ. R(i) j=2 j=3 Total

1 1219 1015 156 1171 1 116 98 17 115 1 115 97 3 100

2 1015 913 913 2 98 92 92 2 97 92 92

Group 3 control day 2006 Group 12 control night 2009 Group 21 turbine night 2002

Occ. R(i) j=2 j=3 Total Occ. R(i) j=2 j=3 Total Occ. R(i) j=2 j=3 Total

1 1074 923 107 1030 1 244 233 6 239 1 12 10 2 12

2 923 840 840 2 233 220 220 2 10 8 8

Group 4 control day 2007 Group 13 turbine day 2002 Group 22 turbine night 2003

Occ. R(i) j=2 j=3 Total Occ. R(i) j=2 j=3 Total Occ. R(i) j=2 j=3 Total

1 1218 386 715 1101 1 21 15 3 18 1 14 4 4 8

2 386 334 334 2 15 14 14 2 4 4 4

Group 5 control day 2008 Group 14 turbine day 2003 Group 23 turbine night 2004

Occ. R(i) j=2 j=3 Total Occ. R(i) j=2 j=3 Total Occ. R(i) j=2 j=3 Total

1 833 623 187 810 1 81 38 18 56 1 32 14 4 18

2 623 589 589 2 38 17 17 2 14 9 9

Group 6 control day 2009 Group 15 turbine day 2004 Group 24 turbine night 2005

Occ. R(i) j=2 j=3 Total Occ. R(i) j=2 j=3 Total Occ. R(i) j=2 j=3 Total

1 691 641 10 651 1 141 56 28 84 1 98 77 11 88

2 641 598 598 2 56 33 33 2 77 71 71

Group 7control night 2004 Group 16 turbine day 2005 Group 25 turbine night 2006

Occ. R(i) j=2 j=3 Total Occ. R(i) j=2 j=3 Total Occ. R(i) j=2 j=3 Total

1 114 59 22 81 1 189 132 28 160 1 107 80 13 93

2 59 29 29 2 132 124 124 2 80 78 78

Group 8 control night 2005 Group 17 turbine day 2006 Group 26 turbine night 2007

Occ. R(i) j=2 j=3 Total Occ. R(i) j=2 j=3 Total Occ. R(i) j=2 j=3 Total

1 356 295 47 342 1 106 70 11 81 1 55 17 32 49

2 295 269 269 2 70 65 65 2 17 15 15

Group 9 control night 2006 Group 18 turbine day 2007 Group 27 turbine night 2008

Occ. R(i) j=2 j=3 Total Occ. R(i) j=2 j=3 Total Occ. R(i) j=2 j=3 Total

1 139 91 45 136 1 218 70 89 159 1 56 31 21 52

2 91 76 76 2 70 63 63 2 31 30 30

Group 28 turbine night 2009

Occ. R(i) j=2 j=3 Total

1 67 59 0 59

2 59 54 54
95

Appendix N. Model Summary from Analyses of Recapture 

Probabilities (p) of Yearling Chinook Salmon from Data Used in 

Studies at McNary Dam in 2002–2005, and 2009. 

[Models of p include those in which values can vary in various combinations of detection site (t) and group 

(treatment, year, and photoperiod). A '*' indicated a multiplicative effect, a '+' indicates an additive effect, 

and a '.' indicates a common value fitted to all groups and reaches. A multiplicative model (g*t) of apparent 

survival (phi) was used in all models. K indicates the number of estimable parameters]

Model AICc

Delta 

AICc

AICc 

Weights

Model 

Likelihood K Deviance

{1 Phi(g*t) p(g*t)} 14736.09 0.00 1.00 1.00 84 14567.04

{2 Phi(g*t) p(g+t)} 14759.35 23.26 0.00 0.00 84 14590.31

{3 Phi(g*t) p(g)} 15908.43 1172.34 0.00 0.00 84 15739.38

{4 Phi(g*t) p(t)} 16562.16 1826.07 0.00 0.00 57 16447.68

{5 Phi(g*t) p(.)} 17414.50 2678.41 0.00 0.00 57 17300.02
96

Appendix O. Summaries of Covariate Values of Juvenile Steelhead 

from Data Used in Studies at McNary Dam in 2004–2009.

Table O1 — Summary statistics of turbine unit discharge (thousand ft3/s) during juvenile steelhead

passage from data used in studies at McNary Dam in 2004–2009.

[N, number of observations; Min, minimum; Max, maximum; SD, standard deviation; SE, standard error]

 Year N Min Max Mean Median SD SE

Overall 2004 47 10.50 16.60 12.69 12.00 1.66 0.24

2005 57 7.90 16.30 10.69 10.70 1.54 0.20

2006 79 8.33 12.94 11.97 12.12 0.89 0.10

2007 48 8.13 12.28 10.72 11.17 1.40 0.20

2008 66 8.31 12.30 10.40 10.18 1.25 0.15

2009 54 8.65 12.56 11.32 11.97 1.12 0.15

Overall 351 7.90 16.60 11.29 11.90 1.51 0.08

Day 2004 19 11.40 16.60 13.22 12.20 1.88 0.43

2005 32 7.90 12.20 10.13 9.90 1.21 0.21

2006 39 8.33 12.94 12.12 12.19 0.83 0.13

2007 23 8.49 12.24 10.82 11.16 1.30 0.27

2008 31 8.37 12.30 9.92 9.48 1.15 0.21

2009 27 8.65 12.39 11.05 11.59 1.20 0.23

Night 2004 28 10.50 16.40 12.33 12.00 1.41 0.27

2005 25 7.90 16.30 11.40 12.00 1.66 0.33

2006 40 8.80 12.94 11.82 12.06 0.92 0.15

2007 25 8.13 12.28 10.62 11.23 1.51 0.30

2008 35 8.31 12.18 10.83 11.29 1.19 0.20

2009 27 9.34 12.56 11.59 12.05 0.98 0.19
97

Table O2 — Summary statistics of head (ft) during juvenile steelhead passage from data used in 

studies at McNary Dam in 2004–2009.

[N, number of observations; Min, minimum; Max, maximum; SD, standard deviation; SE, standard error]

 Year N Min Max Mean Median SD SE

Overall 2004 47 69.22 75.35 72.86 72.80 1.15 0.17

2005 57 70.05 75.64 73.72 73.76 1.18 0.16

2006 79 67.36 71.89 70.00 70.11 1.11 0.12

2007 48 70.02 74.82 72.23 72.46 1.11 0.16

2008 66 68.12 75.19 71.94 72.08 2.30 0.28

2009 54 69.42 74.06 71.58 71.32 1.25 0.17

Overall 351 67.36 75.64 71.90 71.98 1.89 0.10

Day 2004 19 70.81 75.35 73.12 72.74 1.25 0.29

2005 32 71.62 75.64 74.03 74.24 1.20 0.21

2006 39 67.47 71.47 69.86 69.86 1.01 0.16

2007 23 70.02 74.82 72.08 71.86 1.29 0.27

2008 31 68.27 75.19 73.01 73.18 1.86 0.33

2009 27 69.64 74.01 71.83 71.67 1.19 0.23

Night 2004 28 69.22 74.04 72.68 72.83 1.06 0.20

2005 25 70.05 75.09 73.34 73.64 1.06 0.21

2006 40 67.36 71.89 70.13 70.54 1.19 0.19

2007 25 70.63 74.15 72.37 72.51 0.92 0.18

2008 35 68.12 74.91 71.00 69.89 2.26 0.38

2009 27 69.42 74.06 71.33 71.02 1.28 0.25
98

Table O3 — Summary statistics of total project discharge (thousand ft3/s) during juvenile steelhead

passage from data used in studies at McNary Dam in 2004–2009.

[N, number of observations; Min, minimum; Max, maximum; SD, standard deviation; SE, standard error]

 Year N Min Max Mean Median SD SE

Overall 2004 746 130.40 318.60 190.74 172.10 44.24 1.62

2005 57 90.90 347.90 189.69 172.70 54.88 7.27

2006 79 248.99 396.37 329.67 342.01 40.98 4.61

2007 48 171.95 288.34 245.99 253.14 29.87 4.31

2008 785 157.03 418.52 267.59 260.99 79.21 2.83

2009 785 141.43 356.09 263.88 262.87 50.68 1.81

Overall 2500 90.90 418.52 243.26 235.92 70.28 1.41

Day 2004 123 184.40 253.50 237.21 250.10 23.25 2.10

2005 32 90.90 301.10 193.01 182.90 46.53 8.22

2006 39 271.28 389.22 334.02 346.50 34.66 5.55

2007 23 171.95 288.34 248.00 255.59 33.15 6.91

2008 104 170.77 369.03 223.95 220.67 49.41 4.85

2009 200 141.43 350.88 244.15 242.40 60.41 4.27

Night 2004 623 130.40 318.60 181.57 163.50 41.55 1.66

2005 25 92.80 347.90 185.43 158.00 64.80 12.96

2006 40 248.99 396.37 325.43 310.03 46.39 7.33

2007 25 177.23 283.38 244.14 248.09 27.08 5.42

2008 681 157.03 418.52 274.25 267.49 80.79 3.10

2009 585 177.02 356.09 270.62 268.91 45.01 1.86
99

Table O4 — Summary statistics of spill percentage during juvenile steelhead passage from data 

used in studies at McNary Dam in 2004–2009.

[N, number of observations; Min, minimum; Max, maximum; SD, standard deviation; SE, standard error]

 Year N Min Max Mean Median SD SE

Overall 2004 793 0.00 78.49 28.23 0.32 31.74 1.13

2005 57 0.00 75.09 36.65 45.43 24.08 3.19

2006 79 36.09 64.43 48.79 50.65 6.77 0.76

2007 48 39.81 46.67 40.82 40.72 0.94 0.14

2008 851 39.42 60.52 45.17 40.82 7.09 0.24

2009 839 38.77 59.13 43.03 40.89 4.01 0.14

Overall 2667 0.00 78.49 39.31 40.82 19.71 0.38

Day 2004 142 48.88 78.49 67.47 68.43 4.20 0.35

2005 32 32.83 75.09 51.21 48.39 11.59 2.05

2006 39 40.10 64.43 49.23 50.68 5.80 0.93

2007 23 39.81 41.46 40.71 40.77 0.41 0.08

2008 135 40.02 59.80 42.37 40.89 4.15 0.36

2009 227 40.11 54.30 42.61 41.00 3.39 0.22

Night 2004 651 0.00 75.48 19.67 0.00 28.53 1.12

2005 25 0.00 55.71 18.02 0.00 23.13 4.63

2006 40 36.09 61.91 48.36 50.60 7.65 1.21

2007 25 39.87 46.67 40.93 40.69 1.24 0.25

2008 716 39.42 60.52 45.69 40.79 7.40 0.28

2009 612 38.77 59.13 43.18 40.85 4.20 0.17
100

Table O5 — Summary statistics of tag burden (percent) during juvenile steelhead passage from 

data used in studies at McNary Dam in 2004–2009.

[N, number of observations; Min, minimum; Max, maximum; SD, standard deviation; SE, standard error]

 Year N Min Max Mean Median SD SE

Overall 2004 793 0.76 6.41 2.19 2.08 0.73 0.03

2005 57 0.85 4.96 1.62 1.49 0.63 0.08

2006 79 0.66 4.84 2.22 2.12 0.82 0.09

2007 48 0.94 4.00 2.04 1.95 0.73 0.10

2008 851 0.60 5.60 2.01 1.95 0.64 0.02

2009 839 0.69 4.63 1.73 1.67 0.53 0.02

Overall 2667 0.60 6.41 1.98 1.89 0.67 0.01

Day 2004 142 0.95 4.71 2.15 2.05 0.65 0.05

2005 32 1.01 2.90 1.62 1.51 0.46 0.08

2006 39 0.66 4.66 2.03 1.93 0.70 0.11

2007 23 0.94 3.39 2.02 1.87 0.74 0.15

2008 135 0.95 4.90 1.91 1.84 0.56 0.05

2009 227 0.72 4.63 1.74 1.68 0.56 0.04

Night 2004 651 0.76 6.41 2.20 2.09 0.74 0.03

2005 25 0.85 4.96 1.63 1.41 0.81 0.16

2006 40 1.04 4.84 2.40 2.34 0.89 0.14

2007 25 1.17 4.00 2.07 1.97 0.73 0.15

2008 716 0.60 5.60 2.03 1.98 0.65 0.02

2009 612 0.69 4.20 1.73 1.66 0.53 0.02
101

Table O6 — Summary statistics of water temperature during juvenile steelhead passage from data 

used in studies at McNary Dam in 2004–2009.

[N, number of observations; Min, minimum; Max, maximum; SD, standard deviation; SE, standard error]

 Year N Min Max Mean Median SD SE

Overall 2004 793 10.33 14.00 12.64 12.83 0.80 0.03

2005 57 10.06 14.94 11.83 11.39 1.08 0.14

2006 79 10.00 14.50 12.39 12.40 1.41 0.16

2007 48 9.33 15.67 12.77 13.03 1.98 0.29

2008 851 8.28 13.56 10.74 10.72 1.59 0.05

2009 839 8.11 15.00 10.98 10.72 1.92 0.07

Overall 2667 8.11 15.67 11.49 11.72 1.74 0.03

Day 2004 142 10.67 13.00 12.30 12.83 0.76 0.06

2005 32 10.06 14.33 11.78 11.61 0.90 0.16

2006 39 10.10 14.50 12.53 12.40 1.41 0.23

2007 23 10.44 15.28 12.74 12.39 1.80 0.38

2008 135 8.44 12.67 9.73 9.50 1.18 0.10

2009 227 8.33 14.94 10.85 10.33 1.94 0.13

Night 2004 651 10.33 14.00 12.71 12.89 0.79 0.03

2005 25 10.11 14.94 11.89 11.39 1.30 0.26

2006 40 10.00 14.50 12.26 12.40 1.41 0.22

2007 25 9.33 15.67 12.80 13.28 2.17 0.43

2008 716 8.28 13.56 10.93 11.33 1.59 0.06

2009 612 8.11 15.00 11.02 10.89 1.91 0.08
102

Appendix P. Capture History Summary of Juvenile Steelhead from 

Data Used in Studies at McNary Dam in 2004–2005 and 2009. 

[Occ. represents the Occasion number after release. R(i) represents numbers released and j=2 and 3 indicate 

the released number detected at each downstream site]

 Group 1 control day 2004 Group 6 turbine day 2005

Occ. R(i) j=2 j=3 Total Occ. R(i) j=2 j=3 Total

1 623 397 142 539 1 25 14 4 18

2 397 334 334 2 14 12 12

Group 2 control day 2009 Group 7 turbine day 2009

Occ. R(i) j=2 j=3 Total Occ. R(i) j=2 j=3 Total

1 585 548 2 550 1 27 19 0 19

2 548 517 517 2 19 19 19

Group 3 control night 2004 Group 8 turbine night 2004

Occ. R(i) j=2 j=3 Total Occ. R(i) j=2 j=3 Total

1 123 91 14 105 1 19 14 2 16

2 91 84 84 2 14 11 11

Group 4 control night 2009 Group 9 turbine night 2005

Occ. R(i) j=2 j=3 Total Occ. R(i) j=2 j=3 Total

1 200 185 0 185 1 32 21 3 24

2 185 168 168 2 21 21 21

Group 5 turbine day 2004 Group 10 turbine night 2009

Occ. R(i) j=2 j=3 Total Occ. R(i) j=2 j=3 Total

1 28 14 5 19 1 27 23 0 23

2 14 13 13 2 23 23 23
103

Appendix Q. Results of Correlation Analyses of Juvenile Steelhead

from Data Used in Studies at McNary Dam in 2004–2005 and 2009.

Table Q1. Table of correlation indices of data from juvenile steelhead from the turbine group from 

data used in studies at McNary Dam in 2004, 2005, and 2009 .

[Pearson correlation coefficients are listed above the probabilities of obtaining a greater value under the 

hypothesis that Rho = 0. Sample size is 158; <, less than; see table 2 for variable name definitions]

TAG

TOTQ PER_SPI HEAD TURQ TURBLOC PHOTO TEMP WEIGHT BURDEN

TOTQ 1.0000 0.4610 -0.8358 0.2063 0.0956 0.0662 0.1317 0.0836 -0.0137

<0.0001 <0.0001 0.0093 0.2322 0.4088 0.0991 0.2961 0.8645

PER_SPI 1.0000 -0.0449 -0.0582 -0.0929 0.6055 -0.0355 -0.0871 -0.0293

0.5755 0.4675 0.2455 <0.0001 0.6576 0.2763 0.7147

HEAD 1.0000 -0.2839 -0.1596 0.2075 -0.0850 -0.1414 -0.0441

0.0003 0.0451 0.0089 0.2882 0.0764 0.5825

TURQ 1.0000 -0.0618 -0.1779 0.3206 -0.0164 0.2995

0.4407 0.0253 <0.0001 0.8381 0.0001

TURBLOC 1.0000 -0.0439 -0.2326 -0.0956 0.0646

0.5838 0.0033 0.2324 0.4197

PHOTO 1.0000 -0.2778 -0.0658 -0.0832

0.0004 0.4117 0.0298

TEMP 1.0000 0.0474 0.1779

0.5546 0.0254

WEIGHT 1.0000 -0.7478

<0.0001
104

Table Q2. Table of correlation indices of data from juvenile steelhead from the control group from 

data used in studies at McNary Dam in 2004, 2005, and 2009.

[Pearson correlation coefficients are listed above the probabilities of obtaining a greater value under the 

hypothesis that Rho = 0. Sample size is 1,531; <, less than; see table 2 for variable name definitions ]

 TAG

 TOTQ PER_SPI PHOTO TEMP WEIGHT BURDEN

TOTQ 1.0000 0.6132 0.1143 0.0466 -0.0667 -0.1793

<0.0001 <0.0001 0.0683 0.0090 <0.0001

PER_SPI 1.0000 0.3654 -0.1099 -0.0412 -0.1102

<0.0001 <0.0001 0.1070 <0.0001

PHOTO 1.0000 -0.0917 0.0011 -0.0453

0.0003 0.9651 0.0767

TEMP 1.0000 0.0512 0.2124

0.0451 <0.0001

WEIGHT 1.0000 -0.8071

<0.0001
105

Appendix R. Model Summary from Analyses of Recapture 

Probabilities (p) of Juvenile Steelhead from Data Used in Studies at 

McNary Dam in 2004–2005 and 2009. 

[Models of p include those in which values can vary in various combinations of detection site (t) and group 

(treatment, year, and photoperiod). A '*' indicated a multiplicative effect, a '+' indicates an additive effect, 

and a '.' indicates a common value fitted to all groups and reaches. A multiplicative model (g*t) of apparent 

survival (phi) was used in all models. K indicates the number of estimable parameters]

Delta AICc Model

Model AICc AICc Weights

Likelihoo

d K Deviance

{1 Phi(g*t), p(g*t} 2773.45 0.00 1.00 1.00 25 2723.02

{2 Phi(g*t), p(g+t} 2830.40 56.95 0.00 0.00 25 2779.97

{3 Phi(g*t), p(g)} 2865.30 91.85 0.00 0.00 25 2814.87

{4 Phi(g*t), p(t)} 2994.67 221.22 0.00 0.00 16 2962.49

{5 Phi(g*t), p(.)} 3011.59 238.14 0.00 0.00 16 2979.41
106

Appendix S. Model-selection Results from Radio- and Acoustic-tagged Juvenile Steelhead from Data 

Used in Studies at McNary Dam in 2004–2005 and 2009.

[Presence of a factor in a model is indicated by an 'x' in the column for that factor. Model 1 was a global model including all group covariates and their interactions 

(g) as well as all individual covariates and interactions listed. Distance to the first downriver gate (gated) was only used when year was present in the model. All 

models shared a common year*reach model of recapture probability. K indicates the number of parameters.]

Individual Covariates

Group Covariates Biological Operational Model Selection Results

Model 

Numbe

r g

trtyrphototrt*yrtrt*photoyr*phototrt*yr*photogatedwttagbtrt*tagbyr*tagbtemptrt*tempyr*temppersptrt*persphead linearhead quadraticturq linearturq quadraticturlocturloc*photototq

AICc

 

K

Devianc

e

1 x x x x x x x x x x x x x x x x x x x x x 2790. 38 2713.0

2 x x x x x x x x x x x x x x x x x x x x 2792. 36 2719.5

3 x x x x x x x x x x x x x x x x x x x x 2800. 36 2728.0

4 x x x x x x x x x x x x x x x x x 2781. 33 2715.2

5 x x x x x x x x x x x x x x x x 2779. 32 2715.2

6 x x x x x x x x x x x x x x x 2779. 31 2716.7

7 x x x x x x x x x x x x x x 2778. 30 2717.7

8 x x x x x x x x x x x x x 2776. 29 2717.7

9 x x x x x x x x x x x x 2774. 28 2717.7

10 x x x x x x x x x x x 2776. 27 2722.2

11 x x x x x x x x x x x 2774. 27 2720.0

12 x x x x x x x x x x x 2778. 27 2724.1

13 x x x x x x x x x x x 2773. 27 2719.3

14a x x x x x x x x x x 2772. 26 2719.7

14b x x x x x x x x x x x 2775. 28 2718.9

15a x x x x x x x x x 2770. 25 2719.7

15b x x x x x x x x x x 2773. 27 2719.4

16 x x x x x x x x 2768. 24 2720.4

17* x x x x x x x 2766. 23 2720.4

18 x x x x x x 2767. 22 2722.6

19 x x x x x x x 2765. 23 2719.5
107

Appendix T. Beta (Slope) Coefficients of Estimable Survival 

Parameters of Juvenile Steelhead from Data Used in Studies at 

McNary Dam in 2004–2005 and 2009.

[The data are from model 17 in appendix S]

 Standard 95% Confidence

Parameter Beta Error Lower Upper

intercept 2.38540 0.56300 1.28191 3.48889

treatment -1.09401 0.64970 -2.36741 0.17940

tag burden -0.23449 0.15202 -0.53246 0.06348

totq 0.00427 0.00273 -0.00108 0.00962

persp -0.01389 0.00563 -0.02492 -0.00286

persp*trt 0.02231 0.01025 0.00222 0.04240

temp*2009 -0.01401 0.05052 -0.11303 0.08500

temp*2005 -0.06593 0.08709 -0.23662 0.10476

tag burden*2009 0.18442 0.25036 -0.30629 0.67512

tag burden*2005 0.40273 0.56854 -0.71161 1.51706
108

Appendix U. Capture History Summary of Juvenile Steelhead from 

Data Used in Studies at McNary Dam in 2004–2005 and 2009. 

[Occ. represents the Occasion number after release. R(i) represents numbers released and j=2 and 3 indicate 

the released number detected at each downstream site]

Group 1 control day 2004 Group 7 turbine day 2004 Group 13 turbine night 2004

Occ. R(i) j=2 j=3 Total Occ. R(i) j=2 j=3 Total Occ. R(i) j=2 j=3 Total

1 623 397 142 539 1 28 14 5 19 1 19 14 2 16

2 397 334 334 2 14 13 13 2 14 11 11

Group 2 control day 2008 Group 8 turbine day 2005 Group 14 turbine night 2005

Occ. R(i) j=2 j=3 Total Occ. R(i) j=2 j=3 Total Occ. R(i) j=2 j=3 Total

1 681 428 215 643 1 25 14 4 18 1 32 21 3 24

2 428 399 399 2 14 12 12 2 21 21 21

Group 3 control day 2009 Group 9 turbine day 2006 Group 15 turbine night 2006

Occ. R(i) j=2 j=3 Total Occ. R(i) j=2 j=3 Total Occ. R(i) j=2 j=3 Total

1 585 548 2 550 1 40 23 8 31 1 39 27 7 34

2 548 517 517 2 23 17 17 2 27 23 23

Group 4 control night 2004 Group 10 turbine day 2007 Group 16 turbine night 2007

Occ. R(i) j=2 j=3 Total Occ. R(i) j=2 j=3 Total Occ. R(i) j=2 j=3 Total

1 123 91 14 105 1 25 6 9 15 1 23 4 12 16

2 91 84 84 2 6 5 5 2 4 4 4

Group 5 control night 2008 Group 11 turbine day 2008 Group 17 turbine night 2008

Occ. R(i) j=2 j=3 Total Occ. R(i) j=2 j=3 Total Occ. R(i) j=2 j=3 Total

1 104 67 28 95 1 35 15 6 21 1 31 13 14 27

2 67 62 62 2 15 14 14 2 13 12 12

Group 6 control night 2009 Group 12 turbine day 2009 Group 18 turbine night 2009

Occ. R(i) j=2 j=3 Total Occ. R(i) j=2 j=3 Total Occ. R(i) j=2 j=3 Total

1 200 185 0 185 1 27 19 0 19 1 27 23 0 23

2 185 168 168 2 19 19 19 2 23 23 23
109

Appendix V. Model Summary from Analyses of Recapture 

Probabilities (p) of Juvenile Steelhead from Data Used in Studies at 

McNary Dam in 2004–2005 and 2009. 

[Models of p include those in which values can vary in various combinations of detection site (t) and group 

(treatment, year, and photoperiod). A '*' indicated a multiplicative effect, a '+' indicates an additive effect, 

and a '.' indicates a common value fitted to all groups and reaches. A multiplicative model (g*t) of apparent 

survival (phi) was used in all models. K indicates the number of estimable parameters]

Model AICc Delta AICc

AICc 

Weights

Model 

Likelihood K Deviance

{1 Phi (g*t), p(g*t)} 4799.74 0.00 1.00 1.00 47 4704.74

{2 Phi (g*t), p(g+t)} 4915.38 115.64 0.00 0.00 47 4820.38

{3 Phi (g*t), p(g)} 5071.73 271.99 0.00 0.00 47 4976.74

{4 Phi (g*t), p(t)} 5159.27 359.53 0.00 0.00 30 5098.86

{5 Phi (g*t), p(.)} 5330.28 530.54 0.00 0.00 30 5269.87
110

Appendix W. Summaries of Covariate Values of Subyearling Chinook 

Salmon from Data Used in Studies at McNary Dam in 2004–2009.

Table W1 — Summary statistics of turbine unit discharge (thousand ft3/s) during subyearling 

Chinook salmon passage from data used in studies at McNary Dam in 2004–2009.

[N, number of observations; Min, minimum; Max, maximum; SD, standard deviation; SE, standard error]

Year N Min Max Mean Median SD SE

Overall 2004 500 7.80 12.50 11.07 11.70 1.33 0.06

2005 117 7.92 16.60 10.95 12.00 1.96 0.18

2006 435 6.20 12.95 9.94 9.61 1.30 0.06

2007 276 7.85 12.24 9.78 9.48 1.24 0.07

2008 308 5.05 12.43 10.57 10.65 1.58 0.09

2009 273 7.87 12.35 10.02 9.87 1.26 0.08

Overall 1909 5.05 16.60 10.39 10.32 1.48 0.03

Day 2004 245 7.80 12.50 10.63 11.10 1.50 0.10

2005 41 7.92 12.30 9.75 8.74 1.77 0.28

2006 114 7.96 12.53 9.15 9.10 0.76 0.07

2007 94 7.88 12.24 9.54 9.20 1.29 0.13

2008 79 5.05 12.43 9.97 9.57 1.72 0.19

2009 113 7.87 11.86 9.44 9.24 1.12 0.11

Night 2004 255 7.80 12.40 11.50 11.90 0.97 0.06

2005 76 8.10 16.60 11.61 12.10 1.74 0.20

2006 321 6.20 12.95 10.22 9.94 1.33 0.07

2007 182 7.85 12.20 9.91 9.65 1.20 0.09

2008 229 7.08 12.39 10.77 11.02 1.48 0.10

2009 160 8.17 12.35 10.42 10.38 1.19 0.09
111

Table W2 — Summary statistics of head (feet) during subyearling Chinook salmon passage from 

data used in studies at McNary Dam in 2004–2009.

[N, number of observations; Min, minimum; Max, maximum; SD, standard deviation; SE, standard error]

Year N Min Max Mean Median SD SE

Overall 2004 500 71.60 76.19 74.01 73.98 1.01 0.04

2005 117 70.72 76.47 72.67 72.78 1.24 0.11

2006 435 69.09 75.74 72.77 72.58 1.41 0.07

2007 276 71.26 75.90 73.96 73.90 0.90 0.05

2008 308 69.04 75.59 72.35 71.99 1.51 0.09

2009 273 70.59 76.60 74.28 74.73 1.31 0.08

Overall 1909 69.04 76.60 73.41 73.53 1.45 0.03

Day 2004 245 71.71 76.12 74.28 74.33 0.97 0.06

2005 41 71.22 76.47 73.44 73.52 1.23 0.19

2006 114 69.49 75.51 73.92 74.30 1.32 0.12

2007 94 71.73 75.77 74.31 74.49 0.87 0.09

2008 79 69.39 75.59 72.87 72.82 1.32 0.15

2009 113 70.80 76.60 74.82 75.03 0.99 0.09

Night 2004 255 71.60 76.19 73.76 73.56 0.97 0.06

2005 76 70.72 74.91 72.25 71.82 1.03 0.12

2006 321 69.09 75.74 72.36 72.09 1.20 0.07

2007 182 71.26 75.90 73.77 73.74 0.86 0.06

2008 229 69.04 75.38 72.17 71.85 1.54 0.10

2009 160 70.59 76.32 73.90 74.13 1.37 0.11
112

Table W3 — Summary statistics of total project discharge (thousand ft3/s) during subyearling 

Chinook salmon passage from data used in studies at McNary Dam in 2004–2009.

[N, number of observations; Min, minimum; Max, maximum; SD, standard deviation; SE, standard error]

Year N Min Max Mean Median SD SE

Overall 2004 763 73.40 214.40 146.51 154.30 25.33 0.92

2005 1048 150.69 225.69 190.98 192.20 18.25 0.56

2006 1191 146.33 333.97 236.52 224.55 46.50 1.35

2007 1182 146.45 231.21 188.59 187.44 22.29 0.65

2008 1176 132.12 355.44 238.43 221.37 74.59 2.17

2009 1187 55.41 298.39 182.54 175.53 49.08 1.42

Overall 6547 55.41 355.44 200.64 192.58 54.58 0.67

Day 2004 173 73.40 169.70 138.88 160.10 36.83 2.80

2005 314 166.99 218.90 191.38 191.00 18.59 1.05

2006 NA NA NA NA NA NA NA

2007 30 157.86 157.86 157.86 157.86 0.00 0.00

2008 NA NA NA NA NA NA NA

2009 299 104.24 278.15 158.50 142.12 43.35 2.51

Night 2004 590 110.40 214.40 148.74 152.20 20.29 0.84

2005 734 150.69 225.69 190.81 192.55 18.11 0.67

2006 1191 146.33 333.97 236.52 224.55 46.50 1.35

2007 1152 146.45 231.21 189.39 187.88 22.02 0.65

2008 1176 132.12 355.44 238.43 221.37 74.59 2.17

2009 888 55.41 298.39 190.64 188.25 48.26 1.62
113

Table W4 — Summary statistics of spill percentage during subyearling Chinook salmon passage 

from data used in studies at McNary Dam in 2004–2009.

[N, number of observations; Min, minimum; Max, maximum; SD, standard deviation; SE, standard error]

Year N Min Max Mean Median SD SE

Overall 2004 1263 0.00 22.24 0.23 0.00 2.23 0.06

2005 1165 0.00 77.82 56.08 70.95 27.39 0.80

2006 1626 0.72 63.71 47.71 41.64 8.81 0.22

2007 1458 37.15 62.66 51.18 42.68 10.12 0.27

2008 1484 0.19 62.61 51.12 51.59 8.73 0.23

2009 1460 0.00 67.85 51.18 51.25 5.22 0.14

Overall 8456 0.00 77.82 43.57 50.79 22.14 0.24

Day 2004 418 0.00 0.00 0.00 0.00 0.00 0.00

2005 355 10.09 77.82 59.27 70.89 24.30 1.29

2006 114 39.76 63.47 46.99 41.71 8.94 0.84

2007 124 37.15 62.66 46.49 41.18 9.28 0.83

2008 79 37.76 62.45 50.64 44.50 9.47 1.07

2009 412 49.52 67.13 51.79 51.57 1.92 0.09

Night 2004 845 0.00 22.24 0.34 0.00 2.72 0.09

2005 810 0.00 77.53 54.68 71.07 28.54 1.00

2006 1512 0.72 63.71 47.77 41.64 8.80 0.23

2007 1334 39.58 62.22 51.62 57.43 10.09 0.28

2008 1405 0.19 62.61 51.15 51.59 8.69 0.23

2009 1048 0.00 67.85 50.94 51.17 6.03 0.19
114

Table W5 — Summary statistics of tag burden (percent) of subyearling Chinook salmon from data 

used in studies at McNary Dam in 2004–2009.

[N, number of observations; Min, minimum; Max, maximum; SD, standard deviation; SE, standard error]

Year N Min Max Mean Median SD SE

Overall 2004 1263 1.32 7.01 5.03 5.12 1.19 0.03

2005 1165 1.66 5.00 3.75 3.82 0.68 0.02

2006 1626 1.78 5.93 4.75 4.88 0.76 0.02

2007 1458 1.34 6.25 4.73 4.88 0.83 0.02

2008 1484 0.68 6.67 4.86 4.94 0.85 0.02

2009 1460 1.38 5.93 4.18 4.32 0.91 0.02

Overall 8456 0.68 7.01 4.57 4.65 0.97 0.01

Day 2004 418 1.86 7.01 5.00 4.98 1.19 0.06

2005 355 2.06 5.00 3.76 3.82 0.68 0.04

2006 114 2.45 5.80 4.59 4.69 0.72 0.07

2007 124 1.81 5.93 4.71 4.86 0.87 0.08

2008 79 2.95 6.67 5.00 5.10 0.85 0.10

2009 412 1.58 5.93 4.18 4.32 0.91 0.04

Night 2004 845 1.32 7.01 5.05 5.18 1.19 0.04

2005 810 1.66 5.00 3.75 3.82 0.69 0.02

2006 1512 1.78 5.93 4.76 4.91 0.77 0.02

2007 1334 1.34 6.25 4.73 4.88 0.83 0.02

2008 1405 0.68 6.67 4.85 4.94 0.84 0.02

2009 1048 1.38 5.93 4.18 4.32 0.90 0.03
115

Table W6 — Summary statistics of temperature during subyearling Chinook salmon passage from 

data used in studies at McNary Dam in 2004–2009.

[N, number of observations; Min, minimum; Max, maximum; SD, standard deviation; SE, standard error]

Year N Min Max Mean Median SD SE

Overall 2004 1263 18.83 21.94 20.12 20.06 0.82 0.02

2005 1165 17.11 21.06 18.76 19.06 1.08 0.03

2006 1626 15.70 21.60 18.54 18.80 1.45 0.04

2007 1458 16.28 20.78 18.70 19.28 1.47 0.04

2008 1484 14.56 20.06 17.84 18.28 1.55 0.04

2009 1460 16.22 22.39 19.10 19.06 1.71 0.04

Overall 8456 14.56 22.39 18.81 19.17 1.55 0.02

Day 2004 418 18.83 21.78 20.10 19.89 0.84 0.04

2005 355 17.17 21.06 18.92 19.22 1.08 0.06

2006 114 16.30 21.30 19.58 19.80 1.03 0.10

2007 124 16.50 20.78 19.08 19.39 1.06 0.10

2008 79 15.33 20.00 18.22 18.33 1.19 0.13

2009 412 16.33 22.22 19.28 19.33 1.72 0.08

Night 2004 845 18.89 21.94 20.13 20.11 0.81 0.03

2005 810 17.11 20.78 18.69 18.83 1.08 0.04

2006 1512 15.70 21.60 18.47 18.70 1.45 0.04

2007 1334 16.28 20.78 18.66 19.28 1.50 0.04

2008 1405 14.56 20.06 17.82 18.28 1.56 0.04

2009 1048 16.22 22.39 19.03 19.00 1.70 0.05
116

Appendix X. Capture History Summary of Subyearling Chinook 

Salmon from Data Used in Studies at McNary Dam in 2004–2009.

[Occ. represents the occasion number after release. R(i) represents numbers released and j=2 and 3 indicate 

the released number detected at each downstream site]

Group 1 control day 2004 Group 7 turbine day 2004

Occ. R(i) j=2 j=3 Total Occ. R(i) j=2 j=3 Total

1 590 466 30 496 1 255 157 14 171

2 466 283 283 2 157 95 95

Group 2 control day 2005 Group 8 turbine day 2005

Occ. R(i) j=2 j=3 Total Occ. R(i) j=2 j=3 Total

1 734 462 149 611 1 76 37 16 53

2 462 370 370 2 37 29 29

Group 3 control day 2009 Group 9 turbine day 2009

Occ. R(i) j=2 j=3 Total Occ. R(i) j=2 j=3 Total

1 888 789 19 808 1 160 116 1 117

2 789 658 658 2 116 92 92

Group 4 control night 2004 Group 10 turbine night 2004

Occ. R(i) j=2 j=3 Total Occ. R(i) j=2 j=3 Total

1 173 105 14 119 1 245 125 19 144

2 105 65 65 2 125 70 70

Group 5 control night 2005 Group 11 turbine night 2005

Occ. R(i) j=2 j=3 Total Occ. R(i) j=2 j=3 Total

1 314 230 44 274 1 41 19 12 31

2 230 192 192 2 19 18 18

Group 6 control night 2009 Group 12 turbine night 2009

Occ. R(i) j=2 j=3 Total Occ. R(i) j=2 j=3 Total

1 299 265 1 266 1 113 69 2 71

2 265 216 216 2 69 48 48
117

Appendix Y. Results of Correlation Analyses Subyearling Chinook 

Salmon from Data Used in Studies at McNary Dam in 2004–2005 and 

2009.

Table Y1. Table of correlation indices of data from subyearling Chinook salmon from the turbine 

group from data used in studies at McNary Dam in 2004, 2005, and 2009.

[ Pearson correlation coefficients are listed above the probabilities of obtaining a greater value under the 

hypothesis that Rho = 0. Sample size is 890; <, less than; see table 2 for variable name definitions]

TAG

TOTQ PER_SPI HEAD TURQ TURLOC PHOTO TEMP WEIGHT BURDEN

TOTQ 1.0000 0.4428 -0.7172 0.2668 0.0977 -0.3370 -0.6506 -0.2352 -0.1389

<0.0001 <0.0001 <0.0001 0.0035 <0.0001 <0.0001 <0.0001 <0.0001

PER_SPI 1.0000 0.0987 -0.4328 0.1989 -0.0186 -0.2085 -0.1835 -0.3585

0.0032 <0.0001 <0.0001 0.5794 <0.0001 <0.0001 <0.0001

HEAD 1.0000 -0.4883 0.0585 0.3116 0.5662 0.1904 0.0287

<0.0001 0.0811 <0.0001 <0.0001 <0.0001 0.3925

TURQ 1.0000 -0.1302 -0.3232 -0.2785 0.0185 0.0931

<0.0001 <0.0001 <0.0001 0.5807 0.0054

TURLOC 1.0000 0.0343 0.0364 0.0186 -0.0295

0.3066 0.2786 0.5805 0.3793

PHOTO 1.0000 0.1445 0.0682 0.0238

<0.0001 0.0421 0.4781

TEMP 1.0000 0.2297 0.1108

<0.0001 0.0009

WEIGHT 1.0000 -0.6328

<0.0001
118

Table Y2. Table of correlation indices of data from subyearling Chinook salmon from the control 

group from data used in studies at McNary Dam in 2004–2005 and 2009.

[Pearson correlation coefficients are listed above the probabilities of obtaining a greater value under the 

hypothesis that Rho = 0. Sample size is 2,998; <, less than; see table 2 for variable name definitions]

 TAG

TOTQ PER_SPI PHOTO TEMP WEIGHT BURDEN

TOTQ 1.0000 0.3941 -0.1364 -0.6318 -0.2725 -0.0937

<0.0001 <0.0001 <0.0001 <0.0001 <0.0001

PER_SPI 1.0000 0.0631 -0.1137 -0.2930 -0.4022

0.0005 <0.0001 <0.0001 <0.0001

PHOTO 1.0000 0.0036 -0.0380 -0.0373

0.8421 0.0374 0.0412

TEMP 1.0000 0.2450 0.0250

<0.0001 0.1720

WEIGHT 1.0000 -0.4751

<0.0001
119

Appendix Z. Model Summary from Analyses of Recapture 

Probabilities (p) of Subyearling Chinook Salmon from Data used in 

Studies at McNary Dam in 2004–2005 and 2009.

[Models of p include those in which values can vary in various combinations of detection site (t) and group 

(treatment, year, and photoperiod). A '*' indicated a multiplicative effect, a '+' indicates an additive effect,

and a '.' indicates a common value fitted to all groups and reaches. A multiplicative model (g*t) of apparent 

survival (phi) was used in all models. K indicates the number of estimable parameters]

Delta

AICc

AICc 

Weights

Model 

Model AICc Likelihood K

 

Deviance

{1 Phi(g*t), p(g*t)} 8445.31 0.00 1.00 1.00 36 8307.72

{2 Phi(g*t), p(g+t)} 8645.42 200.10 0.00 0.00 36 8573.02

{3 Phi(g*t), p(g)} 8792.06 346.75 0.00 0.00 36 8719.66

{4 Phi(g*t), p(t)} 8817.73 372.41 0.00 0.00 25 8767.53

{5 Phi(g*t), p(.)} 8964.37 519.05 0.00 0.00 25 8914.17
120

Appendix AA. Model-selection Results from Radio- and Acoustic-tagged Subyearling Chinook Salmon 

from Data used in Studies at McNary Dam in 2004–2005 and 2009.

[Presence of a factor in a model is indicated by an 'x' in the column for that factor. Model 1 was a global model including all group covariates and their interactions 

(g) as well as all individual covariates and interactions listed. Distance to the first downriver gate (gated) was only used when year was present in the model. All 

models shared a common g*reach model of recapture probability. K indicates the number of parameters. Unlike other analyses in this report, a treatment and weight 

interaction (trt*wt) was tested post hoc here instead of the weight main effect because the treatment and tag burden interaction (trt*tagb) was supported rather than 

the tag burden main effect in this data set]

Individual Covariates

Group Covariates Biological Operational

Model Selection 

Results

Model

Numbe

r g

trtyrphototrt*yrtrt*photoyr*phototrt*yr*photogatedtrt*Wttagbtrt*tagbyr*tagbtemptrt*tempyr*temppersptrt*persphead linearhead quadraticturlocturq linearturq quadraticturloc*photototq

AICc K

Devianc

e

1 x x x x x x x x x x x x x x x x x x x x x 8986. 4 8888.0

2 x x x x x x x x x x x x x x x x x x x x 8283. 4 8188.6

3 x x x x x x x x x x x x x x x x x x x 8303. 4 8212.4

4a x x x x x x x x x x x x x x x x 8306. 3 8227.5

4b x x x x x x x x x x x x x x x x x x 8282. 4 8191.8

4c x x x x x x x x x x x x x x x x x 8279. 4 8193.0

4d x x x x x x x x x x x x x x x x 8281. 4 8198.8

5 x x x x x x x x x x x x x x x x 8277. 4 8193.1

6 x x x x x x x x x x x x x x x 8285. 4 8203.0

7 x x x x x x x x x x x x x x x 8276. 4 8193.7

8 x x x x x x x x x x x x x x 8277. 4 8196.7

9 x x x x x x x x x x x x x x 8277. 4 8197.0

10 x x x x x x x x x x x x x x 8278. 4 8197.6

11 x x x x x x x x x x x x x x 8274. 4 8194.0

12 x x x x x x x x x x x x x 8272. 3 8194.0

13 x x x x x x x x x x x x 8273. 3 8196.9

14a x x x x x x x x x x x x 8268. 3 8194.0

14b x x x x x x x x x x x x x 8274. 3 8196.1

15a x x x x x x x x x x x 8266. 3 8194.1

15b x x x x x x x x x x x x 8269. 3 8193.3

16 x x x x x x x x x x 8267. 3 8197.5

17* x x x x x x x x x x 8264. 3 8194.1

18 x x x x x x x x x x 8267. 3 8196.7
121

Appendix AB. Beta (Slope) Coefficients of Estimable Survival 

Parameters of Subyearling Chinook Salmon from Data used in 

Studies at McNary Dam in 2004–2005 and 2009. 

[The data are from model 17 in appendix AA]

Standard 95% Confidence

Parameter Beta Error Lower Upper

Intercept 6.064139 1.900079 2.339984 9.788295

treatment 0.376022 0.462350 -0.530190 1.282228

photo -0.738320 0.206600 -1.143260 -0.333390

2005 -6.999290 2.680197 -12.252500 -1.746100

2009 6.903824 2.236789 2.519718 11.287930

photo*2005 0.847542 0.316948 0.226325 1.468760

photo*2009 0.351506 0.253333 -0.145030 0.848038

tag burden*treatment -0.201000 0.079477 -0.356770 -0.045220

spill percentage*treatment -0.010710 0.004455 -0.019440 -0.001980

turbine location -0.044660 0.026510 -0.096620 0.007298

turbine location*photo 0.045399 0.025110 -0.003820 0.094615

temp -0.206850 0.093677 -0.390460 -0.023240

temp*2005 0.367133 0.139097 0.094503 0.639763

temp*2009 -0.333630 0.110448 -0.550100 -0.117150
122

Appendix AC. Capture History Summary of Subyearling Chinook 

Salmon from Data Used in Studies at McNary Dam in 2004–2009.

[Occ. represents the Occasion number after release. R(i) represents numbers released and j=2 and 3 indicate 

the released number detected at each downstream site]

Group 1 control day 2004 Group 9 control night 2007 Group 17 turbine night 2004

Occ. R(i) j=2 j=3 Total Occ. R(i) j=2 j=3 Total Occ. R(i) j=2 j=3 Total

1 590 466 30 496 1 30 9 16 25 1 245 125 19 144

2 466 283 283 2 9 8 8 2 125 70 70

Group 2 control day 2005 Group 10 control night 2009 Group 18 turbine night 2005

Occ. R(i) j=2 j=3 Total Occ. R(i) j=2 j=3 Total Occ. R(i) j=2 j=3 Total

1 734 462 149 611 1 299 265 1 266 1 41 19 12 31

2 462 370 370 2 265 216 216 2 19 18 18

Group 3 control day 2006 Group 11 turbine day 2004 Group 19 turbine night 2006

Occ. R(i) j=2 j=3 Total Occ. R(i) j=2 j=3 Total Occ. R(i) j=2 j=3 Total

114 1191 936 150 1086 1 255 157 14 171 1 74 7 81

74 936 801 801 2 157 95 95 2 63 63

Group 4 control day 2007 Group 12 turbine day 2005 Group 20 turbine night 2007

Occ. R(i) j=2 j=3 Total Occ. R(i) j=2 j=3 Total Occ. R(i) j=2 j=3 Total

1 1152 382 567 949 1 76 37 16 53 1 94 31 19 50

2 382 317 317 2 37 29 29 2 31 29 29

Group 5 control day 2008 Group 13 turbine day 2006 Group 21 turbine night 2008

Occ. R(i) j=2 j=3 Total Occ. R(i) j=2 j=3 Total Occ. R(i) j=2 j=3 Total

1 1176 961 95 1056 1 321 202 32 234 1 79 61 5 66

2 961 851 851 2 202 172 172 2 61 50 50

Group 6 control day 2009 Group 14 turbine day 2007 Group 22 turbine night 2009

Occ. R(i) j=2 j=3 Total Occ. R(i) j=2 j=3 Total Occ. R(i) j=2 j=3 Total

1 888 789 19 808 1 182 64 64 128 1 113 69 2 71

2 789 658 658 2 64 50 50 2 69 48 48

Group 7 control night 2004 Group 15 turbine day 2008

Occ. R(i) j=2 j=3 Total Occ. R(i) j=2 j=3 Total

1 173 105 14 119 1 232 156 13 169

2 105 65 65 2 156 137 137

Group 8 control night 2005 Group 16 turbine day 2009

Occ. R(i) j=2 j=3 Total Occ. R(i) j=2 j=3 Total

1 314 230 44 274 1 160 116 1 117

2 230 192 192 2 116 92 92
123

Appendix AD. Model Summary from Analyses of Recapture 

Probabilities (p) of Subyearling Chinook Salmon from Data used in 

Studies at McNary Dam in 2004–2009. 

[Models of p include those in which values can vary in various combinations of detection site (t) and group 

(treatment, year, and photoperiod). A '*' indicated a multiplicative effect, a '+' indicates an additive effect, 

and a '.' indicates a common value fitted to all groups and reaches. A multiplicative model (g*t) of apparent 

survival (phi) was used in all models. K indicates the number of estimable parameters]

Model AICc Delta AICc AICc Weights Model Likelihood K Deviance

{1 Phi(g*t), p(g*t)} 17951.17 0.00 1.00 1.00 66 17818.54

{2 Phi(g*t), p(g)} 18907.49 956.33 0.00 0.00 66 18774.86

{3 Phi(g*t), p(g+t)} 18921.35 970.19 0.00 0.00 66 18788.73

{4 Phi(g*t), p(t)} 19677.74 1726.57 0.00 0.00 45 19587.44

{5 Phi(g*t), p(.)} 19692.38 1741.21 0.00 0.00 45 19602.08
124

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 Beeman and others—Analyses of Potential Factors Affecting Survival of Juvenile Salmonids Volitionally Passing Through Turbines at McNary and John Day Dams, Columbia River—Open-File Report 2011-1227