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

A Multi-Year Analysis of Spillway Survival for Juvenile 

Salmonids as a Function of Spill Bay Operations at 

McNary Dam, Washington and Oregon, 2004–09

Open-File Report 2012–1125

U.S. Department of the Interior

U.S. Geological Survey

A Multi-Year Analysis of Spillway Survival for Juvenile 

Salmonids as a Function of Spill Bay Operations at 

McNary Dam, Washington and Oregon, 2004–09

By Noah S. Adams, Hal C. Hansel, Russell W. Perry, and Scott D. Evans

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

Open-File Report 2012-1125

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: 2012

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Suggested citation:

Adams, N.S., Hansel, H.C., Perry, R.W., and Evans, S.D., 2012, A multi-year analysis of spillway survival for juvenile 

salmonids as a function of spill bay operations at McNary Dam, Washington and Oregon, 2004–09: U.S. Geological 

Survey Open-File Report 2012-1125, 68 p.
iii

Contents

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

Introduction.................................................................................................................................................................... 2

Description of Study Area.............................................................................................................................................. 2

River Conditions......................................................................................................................................................... 4

Methods......................................................................................................................................................................... 6

Data ........................................................................................................................................................................... 6

Survival Analysis.......................................................................................................................................................10

Results..........................................................................................................................................................................17

Yearling Chinook Salmon..........................................................................................................................................17

Survival Analysis ...................................................................................................................................................17

Juvenile Steelhead....................................................................................................................................................23

Survival Analysis ...................................................................................................................................................23

Subyearling Chinook Salmon....................................................................................................................................30

Survival Analysis ...................................................................................................................................................30

Sockeye Salmon.......................................................................................................................................................41

Survival Analysis ...................................................................................................................................................41

Discussion ....................................................................................................................................................................46

Spillway Survival.......................................................................................................................................................46

Bypass Survival ........................................................................................................................................................47

Spillway and Bypass Survival ...................................................................................................................................48

References Cited..........................................................................................................................................................49

Appendix A: All Candidate Models Examined for Spillway Survival..............................................................................52

Appendix B: All Candidate Models Examined for Bypass Survival ...............................................................................65

Figures

Figure 1. Map showing location of McNary Dam andother major hydroelectric projects on the Columbia and 

Snake Rivers, Washington and Oregon......................................................................................................................... 3

Figure 2. Hydrograph of mean daily project outflow during radio and acoustic telemetry study dates at 

McNary Dam, 2004–09, and the 10-year average, 2000–09. ........................................................................................ 4

Figure 3. Hydrograph of mean daily project spill during radio and acoustic telemetry study dates at 

McNary Dam, 2004–09, and the ten year average, 2000–09 ........................................................................................ 5

Figure 4. Hydrograph of mean daily water temperature of the Columbia River at McNary Dam during radio and 

acoustic telemetry study dates, 2004–09, and the 10-year average, 2000–2009.......................................................... 5

Figure 5. Percentage of spill discharge for each spill pattern during spring (a) and summer (b) study periods at 

McNary Dam, 2004–09................................................................................................................................................ 13

Figure 6. Schematic of the mark-recapture model used to estimate survival (ø) and detection probabilities (p) of 

juvenile salmonids passing through McNary Dam for releases during 2004–09.......................................................... 14

Figure 7. Survival of yearling Chinook salmon that passed through conventional spill bays (black plot) and the 

TSWs (gray plot) at McNary Dam in relation to spill bay discharge, 2004–09 ............................................................. 21

Figure 8. Spillway survival of yearling Chinook salmon in relation to total discharge for each spill pattern at 

McNary Dam, 2004–09................................................................................................................................................ 22

Figure 9. Spillway survival of juvenile steelhead in relation to spillway discharge at McNary Dam, 2004–09............. 27
iv

Figure 10. Spillway survival of juvenile steelhead in relation to total discharge for each spill pattern at 

McNary Dam, 2004–09................................................................................................................................................ 28

Figure 11. Spillway survival of subyearling Chinook salmon in relation to percent spill for each spill pattern 

at McNary Dam, 2004–09............................................................................................................................................ 35

Figure 12. Spillway survival of subyearling Chinook salmon in relation to total discharge for each spill pattern at 

McNary Dam, 2004–09................................................................................................................................................ 36

Figure 13. Spillway survival of subyearling Chinook salmon in relation to total discharge for each spill pattern at 

McNary Dam, 2004–09................................................................................................................................................ 37

Figure 14. Bypass survival of subyearling Chinook salmon in relation to total discharge, with an interaction 

between spill pattern and total discharge, for each spill pattern at McNary Dam, 2004–09......................................... 39

Figure 15. Bypass survival of subyearling Chinook salmon in relation to water temperature at 

McNary Dam, 2004–09................................................................................................................................................ 40

Figure 16. Spillway survival of sockeye salmon in relation to spillway discharge for each spillway passage

location at McNary Dam, 2004–09.............................................................................................................................. 44

Figure 17. Spillway survival of sockeye salmon in relation to total discharge for each spillway passage 

location at McNary Dam, 2004–09............................................................................................................................... 45

Tables

Table 1. Sample sizes of fish used in this analysis that passed through theMcNary Damspillway or 

bypass, 2004–09. .......................................................................................................................................................... 6

Table 2. Specifications of transmitters surgically implanted in juvenile salmonids, 2006–09......................................... 7

Table 3. Summary statistics of fork length and weight of acoustic-tagged juvenile salmonids released in 

the Columbia River, by release site, 2006–09. .............................................................................................................. 8

Table 4. Number of acoustic-tagged juvenile salmonids released in the Columbia River, number (and 

percentage of those released) that passed McNary Dam through any route, range of passage dates, and 

corresponding percentage spill of total project discharge over dates of passage at McNary Dam, 

by species, 2006–09...................................................................................................................................................... 9

Table 5. List of variables used in survival analyses of fish passing the McNary Dam spillway and 

bypass, 2004–09. ........................................................................................................................................................ 11

Table 6. Yearly resolution of spill bay passage location, Temporary Spillway Weir placement (T), 

and lateral division....................................................................................................................................................... 12

Table 7. Model selection results based on varying λ and p with respect to year for yearling 

Chinook salmon, 2004–09........................................................................................................................................... 17

Table 8. Model selection for fish that passed through the spillway at McNary Dam relating 

survival (ø) as a function of individual and group covariates using the fixed structure of the 

best model for p and λ parameters for yearling Chinook salmon, 2004–09. ................................................................ 19

Table 9. Slope (Beta) coefficients, standard error, and 95-percent confidence limits of model

parameters for yearling Chinook salmon passing McNary Dam, 2004–09. ................................................................. 20

Table 10. Model selection for fish that passed through the juvenile bypass system outfall at McNary Dam 

relating survival (ø) as a function of individual and group covariates using the fixed structure of the best 

model for p and λ parameters for yearling Chinook salmon, 2004–09......................................................................... 23

Table 11. Model selection results based on varying λ and p with respect to year for juvenile steelhead at 

McNary Dam, 2004–09................................................................................................................................................ 24
v

Table 12. Model selection for fish that passed through the spillway at McNary Dam relating 

survival (ø) as a function of individual and group covariates using the fixed structure of the best model 

for p and λ parameters for juvenile steelhead, 2004–09. ............................................................................................. 25

Table 13. Slope (Beta) coefficients, standard error, and 95-percent confidence limits of model parameters 

for juvenile steelhead passing McNary Dam, 2004–09................................................................................................ 26

Table 14. Model selection for fish that passed through the juvenile bypass system outfall at McNary Dam 

relating survival (ø) as a function of individual and group covariates using the fixed structure of the best 

model for p and λ parameters for juvenile steelhead, 2004–09 ................................................................................... 29

Table 15. Model selection results based on varying λ and p with respect to year for subyearling Chinook salmon, 

2004–09....................................................................................................................................................................... 31

Table 16. Model selection for fish that passed through the spillway at McNary Dam relating survival (ø) as a 

function of individual and group covariates using the fixed structure of the best model for p and λ parameters for 

subyearling Chinook salmon, 2004–09........................................................................................................................ 32

Table 17. Slope (β) coefficients, standard error, and 95-percent confidence limits of model parameters for 

subyearling Chinook salmon passing McNary Dam, 2004–09..................................................................................... 34

Table 18. Model selection for fish that passed through the juvenile bypass system outfall at McNary Dam relating 

survival (ø) as a function of individual and group covariates using the fixed structure of the best model for p and λ

parameters for subyearling Chinook salmon, 2004–09................................................................................................ 38

Table 19. Model selection results for sockeye salmon passing through the spillway based on varying λ and p with 

respect to year, 2004–09............................................................................................................................................. 41

Table 20. Model selection for fish that passed through the spillway at McNary Dam relating survival (ø) as a

function of individual and group covariates using the fixed structure of the best model for p and λ parameters for 

sockeye salmon, 2004–09........................................................................................................................................... 42

Table 21. Slope (β) coefficients, standard error, and 95-percent confidence limits of model parameters for 

sockeye salmon passing through the spillway at McNary Dam, 2004–09 ................................................................... 43
vi

Conversion Factors, Datums, Abbreviations, and Acronyms

Conversion Factors

Inch/Pound to SI

Multiply By To obtain

Flow rate

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

SI to Inch/Pound

Multiply By To obtain

Length

meter (m) 3.281 foot (ft)

kilometer (km) 0.6214 mile (mi)

Mass

gram (g) 0.03527 ounce, avoirdupois (oz)

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 (WGS 84).

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

Abbreviations and Acronyms

AIC Akaike’s Information Criterion

CJS Cormack-Jolly-Seber models

Kcfs 1,000 ft3/s

PIT passive integrated transponder

rkm river kilometer

TSW temporary spillway weir
1

A Multi-Year Analysis of Spillway Survival for Juvenile 

Salmonids as a Function of Spill Bay Operations at 

McNary Dam, Washington and Oregon, 2004–09

By Noah S. Adams, Hal C. Hansel, Russell W. Perry, and Scott D. Evans

Abstract 

We analyzed 6 years (2004–09) of passage and survival data collected at McNary Dam to 

examine how spill bay operations affect survival of juvenile salmonids passing through the spillway at 

McNary Dam. We also examined the relations between spill bay operations and survival through the 

juvenile fish bypass in an attempt to determine if survival through the bypass is influenced by spill bay 

operations. We used a Cormack-Jolly-Seber release-recapture model (CJS model) to determine how the 

survival of juvenile salmonids passing through McNary Dam relates to spill bay operations. 

Results of these analyses, while not designed to yield predictive models, can be used to help 

develop dam-operation strategies that optimize juvenile salmonid survival. For example, increasing total 

discharge typically had a positive effect on both spillway and bypass survival for all species except 

sockeye salmon (Oncorhynchus nerka). Likewise, an increase in spill bay discharge improved spillway 

survival for yearling Chinook salmon (Oncorhynchus tshawytscha), and an increase in spillway 

discharge positively affected spillway survival for juvenile steelhead (Oncorhynchus mykiss). The 

strong linear relation between increased spill and increased survival indicates that increasing the amount 

of water through the spillway is one strategy that could be used to improve spillway survival for 

yearling Chinook salmon and juvenile steelhead. However, increased spill did not improve spillway 

survival for subyearling Chinook salmon and sockeye salmon. Our results indicate that a uniform spill 

pattern would provide the highest spillway survival and bypass survival for subyearling Chinook 

salmon. Conversely, a predominantly south spill pattern provided the highest spillway survival for 

yearling Chinook salmon and juvenile steelhead. Although spill pattern was not a factor for spillway 

survival of sockeye salmon, spill bay operations that optimize passage through the north and south spill 

bays maximized spillway survival for this species. Bypass survival of yearling Chinook salmon could be 

improved by optimizing conditions to facilitate bypass passage at night, but the method to do so is not 

apparent from this analysis because photoperiod was the only factor affecting bypass survival based on 

the best and only supported model. Bypass survival of juvenile steelhead would benefit from lower 

water temperatures and increased total and spillway discharge. Likewise, subyearling Chinook salmon 

bypass survival would improve with lower water temperatures, increased total discharge, and a uniform 

spill pattern.
2

Introduction

As juvenile salmon Oncorhynchus spp. and steelhead O. mykiss migrate downriver to the ocean, 

they are subject to natural and human-induced mortality. Predators contribute to total natural mortality 

along with other factors (Vigg and others, 1991; Collis and others, 2001). Impoundments caused by 

hydroelectric dams on the Snake and Columbia Rivers may indirectly contribute to mortality by slowing 

the migration of juvenile salmonids (Raymond, 1968, 1979; Plumb and others, 2006), thereby 

increasing energy expenditure during migration and allowing greater opportunity for predation. Further, 

passage through dams can be a major source of direct mortality (Mesa 1994; Whitney and others, 1997) 

that is cumulative for populations negotiating multiple dams.

Studies monitoring fish movements near McNary Dam were conducted annually from 2004 to 

2009 to assess how dam operations or fish passage structures influence passage and survival of juvenile 

salmonids migrating through the hydroelectric system in a particular year. Although the McNary Dam

studies provided valuable information for developing management strategies, some important questions 

remain unanswered. Managers often are interested in understanding how rates of survival and passage 

vary with environmental conditions, such as total river discharge or distribution of discharge across 

possible passage routes. Consistently similar conditions are favorable when the goal is point estimation 

under a given condition, but understanding how survival or passage varies in response to dam 

operations requires data for a wide range of conditions. Studies conducted in a single year will only 

consider a narrow range of environmental conditions, due to natural year-to-year variation in the 

environment. Multi-year analyses are better suited for the development of quantitative relationships than 

single-year analyses, because operational and environmental variation typically will be higher over a 

period of 5–10 years than within any given year. Furthermore, multi-year analyses benefit from the 

large sample sizes over multiple years, which can reduce statistical uncertainty and help identify 

relations that otherwise might be statistically undetectable. We analyzed 6 years (2004–09) of passage 

and survival data collected at McNary Dam to examine how spill bay operations affect survival of 

juvenile salmonids passing through the spillway at McNary Dam. In addition, we examined relations 

between spill bay operations and survival through the juvenile fish bypass in an attempt to determine if 

survival through the bypass is influenced by spill bay operations.

Description of Study Area

McNary Dam is the fourth dam on the Columbia River (counting upriver from its terminus with 

the Pacific Ocean) located 470 river kilometers (rkm) upriver from the Pacific Ocean and 52 rkm 

downriver from the confluence of the Columbia and Snake Rivers (fig. 1). The reservoir formed by 

McNary Dam (Lake Wallula) extends 98 rkm upriver to the Hanford Reach of the Columbia River, and 

impounds 16 rkm of the Snake River downstream of Ice Harbor Dam. John Day Dam is located 123 

rkm downriver of McNary Dam and creates Lake Umatilla. Our study area extended from Hat Rock 

State Park, Oregon, 10 rkm upriver of McNary Dam, to Sundale, Washington, 92 rkm downstream of 

McNary Dam, where our last acoustic telemetry array was located.
3

McNary Dam is oriented perpendicular to the river channel and includes a navigation lock, 

spillway, powerhouse, and earthen dam. The spillway is 399 m long with 22 vertical lift-type spill gates 

that regulate discharge through the dam. The spillway discharges water at the ogee crest approximately 

14 m below the water surface. During the sampling seasons in 2007–09, temporary spillway weirs 

(TSWs) were installed as part of a strategy to improve fish passage at the dam. 

Figure 1. Map showing location of McNary Dam and other major hydroelectric projects on the Columbia and Snake 

Rivers, Washington and Oregon.

WA

OR

Chief Joseph Dam

Wells Dam

Rocky Reach Dam

Rock Island Dam

Wanapum Dam

Priest Rapids Dam

John Day Dam McNary Dam

Ice Harbor Dam

Lower Monumental Dam

N

Grand Coulee Dam

Little Goose Dam

W 120 ̊ W 119 ̊ W 118 ̊

N 46 ̊

N 47 ̊

N 48 ̊

Scale (km): 0 50 100
4

River Conditions

Average daily discharge throughout a season was variable depending upon year. The 10-year 

average (2000–2009) in mid-April was about 210 kcfs, with discharge increasing to greater than 250 

kcfs by late May (fig. 2). River-flows for the 10-year average decreased through June and July to less 

than 150 kcfs by August. Average daily spill at McNary Dam from 2000 to 2009 followed a similar 

trend to mean daily outflow (fig. 3). Mean daily spill in mid-April, at the start of the season, averaged 

80 kcfs and peaked in late May or early June at 125 kcfs for the 10-year average. During 2004 and 2005, 

flow through the dam was low compared to the 10-year average. In 2004, very little flow was 

discharged through the spillway during the summer season. More detailed information regarding 

average daily discharge, including how discharge varied during the day and night periods, can be found 

in the annual reports of research (Perry and others, 2006, 2007; Adams and others, 2008; Adams and 

Counihan, 2009; Adams and Liedtke, 2009, 2010).

Water temperature steadily increased during the study period, from 9°C in April to a peak of 

about 21°C in late July or early August (fig. 4). Water temperatures were slightly lower (1–2°C) in 2008 

than during the other 5 study years. For more detailed information on the environmental conditions and 

dam operations for individual years included in this analysis, please refer to Adams and Evans (2011).

Figure 2. Hydrograph of mean daily project outflow during radio and acoustic telemetry study dates at McNary 

Dam, 2004–09, and the 10-year average, 2000–09. Data obtained from Columbia River DART website: 

http://www.cbr.washington.edu/dart/river.html.

0

50

100

150

200

250

300

350

400

450

04/17 05/01 05/15 05/29 06/12 06/26 07/10 07/24

Discharge (1000 ft

3/s)

2000-09

2004

2005

2006

2007

2008

2009
5

Figure 3. Hydrograph of mean daily project spill during radio and acoustic telemetry study dates at McNary Dam, 

2004–09, and the ten year average, 2000–09. Data obtained from Columbia River DART website: 

http://www.cbr.washington.edu/dart/river.html.

Figure 4. Hydrograph of mean daily water temperature of the Columbia River at McNary Dam during radio and

acoustic telemetry study dates, 2004–09, and the 10-year average, 2000–2009. Data obtained from Columbia 

River DART website: http://www.cbr.washington.edu/dart/river.html.

0

50

100

150

200

250

300

04/17 05/01 05/15 05/29 06/12 06/26 07/10 07/24

Disharge (1000 ft

3/s)

2000-09

2004

2005

2006

2007

2008

2009

5

7

9

11

13

15

17

19

21

23

04/17 05/01 05/15 05/29 06/12 06/26 07/10 07/24

Temperature ( C)

2000-09 2004 2005 2006 2007 2008 2009
6

Methods

Data

We analyzed radio and acoustic telemetry data collected during the spring and summer of 2004–

09 to examine how spill bay operations affected survival of juvenile salmonids passing through the 

spillway and the juvenile fish facility bypass. Telemetry equipment was deployed upstream, at, and 

downstream of McNary Dam to monitor fish movements. During the years included in our analyses, 

more than 21,000 acoustic-tagged yearling Chinook salmon (Oncorhynchus tshawytscha), juvenile 

steelhead (Oncorhynchus mykiss), subyearling Chinook salmon (Oncorhynchus tshawytscha), and 

sockeye salmon (Oncorhynchus nerka) were detected passing through the McNary Dam spillway or 

juvenile bypass (table 1). Yearling Chinook salmon and juvenile steelhead were hatchery-reared,

although subyearling Chinook and sockeye salmon were of unknown origin. U.S. Geological Survey

personnel tagged and released all yearling and subyearling Chinook salmon and juvenile steelhead used 

for this analysis. Treatment fish were released 10 km upstream of McNary Dam and control fish were 

released about 0.5 km downstream of the dam. Sockeye salmon were released in the Mid-Columbia 

River by personnel from Hydroacoustic Technologies Incorporated, LGL Limited, Chelan County 

Public Utility District, and Grant County Public Utility District. Specifications for the acoustic 

transmitters used in the annual studies are provided in table 2. Numbers of each species released, release 

dates, release sites, passage dates, and percentage of spill during dates of passage are documented in 

tables 3 and 4. Other details describing tags, tagging, and data-collection methods are given in Adams 

and others (1998, 2008), Perry and others (2006, 2007), Adams and Counihan (2009), and Adams and 

Liedtke (2009, 2010).Methods used to tag sockeye salmon are described by Steig and others (2007, 

2008, 2009, 2010), Sullivan and others (2009), and Timko and others (2007, 2008, 2010). Survival 

estimates for all species were assessed from dam passage to a downstream array located from rkm 446

to 448. 

Table 1. Number of fish used in this analysis that passed through the McNary Dam spillway or bypass, 2004–09.

[NA, analysis not possible because sockeye salmon were not PIT tagged]

Route Yearling

Chinook salmon

Juvenile

steelhead

Subyearling

Chinook salmon

Sockeye

 salmon

Spillway 4,405 3,794 4,213 2,870

Bypass 2,864 1,390 1,835 NA
7

Table 2. Specifications of transmitters surgically implanted in juvenile salmonids, 2006–09.

[NA, not applicable]

Year Site Acoustic 

transmitter model

Average tag

dimensions

(millimeters)

Average tag

weight in air 

(grams)

Average tag life 

(days)

PIT tag 

model

Yearling Chinook salmon and juvenile steelhead

2006 Columbia 795-E 6.8 × 21.0 1.5 21 TX1411ST

2007 Columbia 795-E 6.8 × 21.0 1.5 21 TX1411ST

2008 Columbia 795-E 7.1 × 21.9 1.6 18 TX1411ST

2009 Columbia 795-LE 6.7 × 21.1 1.4 28 TX1411ST

Subyearling Chinook salmon

2006 Columbia 795-M 6.8 × 16.5 0.8 17 TX1411ST

2007 Columbia 795-M 6.8 × 16.5 0.8 17 TX1411ST

2008 Columbia 795-S 6.5 × 22.2 0.7 13 TX1411ST

2009 Columbia 795-LM 6.5 × 16.3 0.7 24 TX1411ST

Sockeye salmon

2006 Mid-Columbia 795-M 6.8 × 16.5 0.8 14 NA

2007 Mid-Columbia 795-M 6.8 × 16.5 0.8 14 NA

2008 Mid-Columbia 795-M 6.8 × 16.5 0.8 17 NA

2009 Mid-Columbia 795-Lm 5.0 × 17.5 0.7 22 NA
8

Table 3. Summary statistics of fork length and weight of acoustic-tagged juvenile salmonids released in the 

Columbia River, by release site, 2006–09.

[Species/age class: Y. Chinook, yearling Chinook salmon; Steelhead, juvenile steelhead; S. Chinook, subyearling Chinook 

salmon. Release site: HAT, near Hat Rock State Park, Oregon, approximately 10 kilometers upstream of McNary Dam; 

TAIL, 0.5 kilometers downstream of McNary Dam in the tailrace directly out from the downstream tip of the navigation 

wall; SAC, intentionally sacrificed fish released at the TAIL release site; RC, Rocky Reach Collector; RR, Rocky Reach 

Dam; RH, Rock Island Hydro Park; RI, Rock Island Dam; WA, Wanapum Dam; WE, Wells Dam. N, number of fish; Min, 

minimum; Max, maximum]

Species/

age class

Release

site

Release

dates N

Fork length, 

in millimeters Weight, in grams

Mean Min Max Mean Min Max

2006

Y. Chinook HAT 4/27–6/4 1,797 149 125 179 31.7 23.0 59.5

Y. Chinook TAIL 4/27–6/4 1,213 148 133 175 31.3 22.6 49.8

Y. Chinook SAC 4/30–6/1 49 148 134 174 31.7 23.0 48.7

Steelhead HAT 4/27–6/1 1,005 209 122 290 78.6 31.0 236.5

Steelhead SAC 5/4–5/31 50 205 158 267 73.3 30.1 152.6

S. Chinook HAT 6/20–7/19 1,794 120 104 155 17.5 12.5 44.8

S. Chinook TAIL 6/20–7/19 1,191 120 108 158 17.4 13.5 44.9

S. Chinook SAC 6/22–7/11 50 118 112 133 16.7 13.6 25.1

2007

Y. Chinook HAT 4/19–6/7 1,973 151 130 222 33.4 23.0 108.4

Y. Chinook TAIL 4/19–6/7 1,310 151 133 206 33.5 23.0 78.8

Y. Chinook SAC 4/27–6/4 53 151 135 179 33.2 23.7 49.9

Steelhead HAT 4/21–6/6 1,118 215 160 292 84.6 27.4 207.7

Steelhead SAC 4/28–6/2 50 223 178 279 93.4 43.7 166.8

S. Chinook HAT 6/20–7/25 1,771 118 105 166 17.8 13.2 55.2

S. Chinook TAIL 6/20–7/25 1,182 118 105 168 17.6 12.8 59.9

S. Chinook SAC 6/24–7/24 50 118 110 136 17.8 13.5 32.5

2008

Y. Chinook HAT 4/19–6/3 1,424 154 131 206 36.0 23.0 147.6

Y. Chinook TAIL 4/20–6/4 949 153 130 200 35.5 23.0 76.7

Y. Chinook SAC 4/22–5/31 50 151 134 189 34.2 24.1 63.6

Steelhead HAT 4/19–6/2 1,186 211 136 289 82.8 27.5 224.0

Steelhead TAIL 4/20–6/3 785 210 135 294 81.7 25.0 232.7

Steelhead SAC 4/22–5/31 50 213 171 270 87.2 38.3 179.2

S. Chinook HAT 6/19–7/28 1,752 116 102 158 17.1 11.8 46.8

S. Chinook TAIL 6/20–7/29 1,176 117 103 155 17.1 11.8 40.7

S. Chinook SAC 6/22–7/27 50 117 107 142 17.4 12.4 33.3

2009

Y. Chinook HAT 4/18–6/4 1,411 164 134 240 44.4 29.0 119.0

Y. Chinook TAIL 4/18–6/4 935 164 137 255 44.7 29.0 174.0

Y. Chinook SAC 4/20–5/29 51 161 143 195 41.9 30.4 75.2

Steelhead HAT 4/18–6/4 1,176 220 111 280 93.8 32.6 215.4

Steelhead TAIL 4/18–6/4 785 220 158 283 94.7 32.4 218.0

Steelhead SAC 4/23–5/29 51 216 156 254 87.4 31.5 130.0

S. Chinook HAT 6/20–7/30 1,784 121 105 158 20.2 13.5 47.0

S. Chinook TAIL 6/20–7/30 1,187 122 102 172 20.4 13.5 57.8

S. Chinook SAC 6/25–7/28 51 118 109 148 18.8 14.0 38.2
9

Table 4. Number of acoustic-tagged juvenile salmonids released in the Columbia River, number (and percentage

of those released) that passed McNary Dam through any route, range of passage dates, and corresponding 

percentage spill of total project discharge over dates of passage at McNary Dam, by species, 2006–09.

[Species/age class: Y. Chinook, yearling Chinook salmon; Steelhead, juvenile steelhead; S. Chinook, subyearling Chinook 

salmon. Percentage of spill: Percentage of project discharge spilled includes the water discharged through the temporary 

spillway weirs]

Species/age 

class

Number

released

Number (%) 

passed

First passage 

date 

Last passage 

date

Percentage of 

spill

2006

Y. Chinook 1,797 1,717 (96) 4/27/2006 6/5/2006 50

Steelhead 1,005 944 (94) 4/27/2006 6/2/2006 48

S. Chinook 1,791 1,638 (91) 6/20/2006 7/30/2006 49

Sockeye 3,493 1,339 (38) 5/10/2006 6/11/2006 52

2007

Y. Chinook 1,974 1,911 (97) 4/20/2007 6/9/2007 43

Steelhead 1,118 1,086 (97) 4/22/2007 6/9/2007 41

S. Chinook 1,771 1,631 (92) 6/21/2007 8/7/2007 52

Sockeye 2,500 1,224 (49) 5/11/2007 6/14/2007 41

2008

Y. Chinook 1,424 1,396 (98) 4/19/2008 6/8/2008 46

Steelhead 1,186 1,186 (100) 4/19/2008 6/3/2008 47

S. Chinook 1,752 1,646 (94) 6/20/2008 8/8/2008 51

Sockeye 2,002 1,084 (54) 5/18/2008 6/21/2008 57

2009

Y. Chinook 1,403 1,351 (96) 4/18/2009 6/8/2009 44

Steelhead 1,170 1,107 (95) 4/19/2009 6/4/2009 43

S. Chinook 1,772 1,602 (90) 6/20/2009 8/7/2009 51

Sockeye 3,974 3,578 (90) 5/18/2009 6/20/2009 50
10

Survival Analysis

We used release-recapture models developed by Cormack (1964), Jolly (1965), and Seber (1965) 

(hereafter referred to as CJS) to examine how environmental variables and dam operations affect 

survival of juvenile salmonids passing through the spillway and juvenile fish bypass at McNary Dam. A

logit link was used to relate individual and group covariates of environmental variables assigned at dam 

passage (table 5) to survival. Models were created and parameters estimated in the program MARK 

(White and Burnham, 1999).

Group covariates for photoperiod, year, passage location, spill bay type, and spill pattern were 

based on discrete time periods, passage structures, spillway locations, or spillway operations. For 

photoperiod, dark and light periods were determined using civil twilight for each day. Group covariates 

for passage location and spill bay type were defined based on consistencies across years so that fish 

were assigned as passing through a particular part of the spillway or spillway structure (table 6).

Spillway passage location generally was assigned as follows: north, spill bays 1–6; middle, bays 7–15; 

south, bays 16–22. In 2008 it was necessary to include bay 7 in the group of north bays and bay 16 in 

the group of middle bays. Spill bay type was defined as either a TSW or a standard vertical lift-type spill 

gate depending on a fish’s passage location.

Spill patterns were defined based on the percentage of total spill discharged through the north, 

middle, and south portions of the spillway during the spring and summer when the study fish passed the 

dam. The number of spill patterns and their characteristics were determined by cluster analysis using the 

FASTCLUS procedure in SAS® software (SAS Institute, 2008). Daily percentages of total spill 

discharged through each portion of the spillway were calculated for two 12-h intervals (0600–1759 and 

1800–0559). Because the percentages of total spill discharged through the north and south portions of 

the spillway were highly correlated, only the percentage of spill for the north and middle spillway were

used to create each cluster (spill pattern). The procedure was run repeatedly, allowing the total number 

of spill patterns defined in each sequential run to incrementally range from 2 to 10. The optimum 

number of patterns was determined by graphically examining the Cubic Clustering Criterion statistic for 

where it peaked, and the Approximate Overall R-Squared statistic for where its rate of increase began to 

level or taper off. Five spill patterns were used for both spring and summer for fish that passed through 

the spillway (fig. 5), and an additional no-spill category was added for the bypass survival analysis.

Twelve-hour intervals with very little total spill discharge (< 20 kcfs) were excluded from the spillway 

analysis and included in the no-spill category for the bypass analysis.

The individual spill bay discharge covariate for a fish’s passage location was determined using 

the highest resolution of passage location possible given the hydrophone configuration for each year 

(table 6). When a specific spill bay passage assignment was not possible for a fish passing through one 

of the standard spill gates, we averaged individual spill bay discharges across two to seven combined 

spill bays. To minimize measurement error associated with this covariate, we excluded fish if the 

difference in spill bay discharge among the combined bays was greater than 3 kcfs. As a result, we 

removed 15 percent of the yearling Chinook salmon, 10 percent of the juvenile steelhead, 7 percent of 

the subyearling Chinook salmon, and 7 percent of the sockeye from the analysis.
11

Table 5. List of variables used in survival analyses of fish passing the McNary Dam spillway and bypass, 2004–09.

Type Name Definition

Group Photoperiod Day, night

Group 1Year yyyy, year of study

Group Passage location North, middle, or south passage location at spillway

Group Bay type Type of spill bay (conventional or TSW)

Group Spill pattern Distribution of spill (north, south, or uniform)

Individual Temperature Average daily tailrace water temperature

Individual Total discharge Total river discharge at McNary Dam

Individual Spillway discharge Discharge through the spillway (all spill bays)

Individual Spill bay discharge Discharge through individual spill bays

Individual Percent spill Percentage of discharge through the spillway

Individual Fish weight Fish weight

Individual 2Tag burden Tag weight/fish weight

1

A secondary variable used to assess whether year could account for additional variation over and above the effect of other 

covariates. 

2

A secondary variable used in lieu of fish weight after all other variables were evaluated because of high correlation between 

tag burden and fish weight. 
12

Table 6. Yearly resolution of spill bay passage location, Temporary Spillway Weir placement (T), and lateral 

division.

Spill Bay Location

South Middle North

Year 22 21 20 19 18 17 16 15 14 13 12 11 10 9 8 7 6 5 4 3 2 1

2009 T Spring T

2009 T T Summer

2008 T T

2007 T T

2006

2005

2004
13

Figure 5. Percentage of spill discharge for each spill pattern during spring (a) and summer (b) study periods at 

McNary Dam, 2004–09. Black bars represent spill through south spill bays, white bars represent spill through 

middle spill bays, and gray bars represent spill through north spill bays. Numbers above bars represent percentage

of spill discharge.

78

55

47

39

27

22

41

36 34

40

0

4

17

27

33

0

10

20

30

40

50

60

70

80

90

1 2 3 4 5

Percent of spill discharge

Spill pattern

b

50

43

36

30

15

42

34 32

39

43

8

23

32 31

42

0

5

10

15

20

25

30

35

40

45

50

55

1 2 3 4 5

Percent of spill discharge

Spill pattern

a South Middle North

b
14

An initial step in the modeling process was to assign probabilities to detection histories that represent 

detections of fish downstream. For example, the possible histories for survival in this study included: 

111, 101, 110, and 100, where a 1 represents detection at a telemetry array and a 0 represents nondetection. The first digit represents a fish that was released or that passed through a particular passage 

route, the second digit represents the first downstream detection array, and the last digit represents 

detection at the last detection array. The probabilities of these capture histories were then incorporated 

into a multinomial probability model to estimate model parameters using maximum likelihood methods.

The model parameters included: ø, the probability of survival from dam passage through the spillway or 

bypass to the first downstream detection array; p, the probability of being detected at the first 

downstream detection array given the individual survived; and λ, the joint probability of surviving and 

being detected from the first downstream array to the next downstream array (fig. 6). The probabilities 

of the possible detection histories can be expressed as: 

P111: øpλ

P101: ø(1 – p)λ

P110: øp(1 – λ)

P100: (1 – ø) + ø(1 – p)(1 – λ), (1)

To express survival as a function of covariates, we used a logit link function, which models the 

logit of each parameter as a linear function of covariates. For example, a model of survival as a function 

of photoperiod and a continuous covariate, x, can be expressed as: 

ø(photo + xi) = exp(β0 + βphoto + β1 xi) / 1 + exp(β0 + βphoto + β1 xi), (2)

In this expression, β represents the intercept and slope coefficients. The logit link also was used 

for estimating our detection parameters. The logit link was used to estimate all model parameters 

because it constrains parameter estimates between 0 and 1, which is appropriate for probabilities. A 

quadratic term was included in models where there was potential for a unimodal curvilinear response of 

fish survival to a particular covariate. We found that adding this term to models never resulted in a 

significant effect, so we did not present the results. 

Passage Route

(Spill, Bypass)

Detection 

Array 1

Detection 

Array 2

ø

p

λ

Figure 6. Schematic of the mark-recapture model used to estimate survival (ø) and detection probabilities (p) of

juvenile salmonids passing through McNary Dam for releases during 2004–09. 

 
15

To assess how well the covariates or environmental variables explained model parameters, Akaike’s 

Information Criterion (AIC) (Akaike, 1973; Burnham and Anderson, 1998) was used for comparing 

models. AIC allowed us to measure how well the model fit relative to the number of parameters used in 

the model:

AIC = -2L + 2N, (3)

where N is the number of parameters and L is the log-likelihood. Although our sample sizes were large, 

we used AICc

AICc = -2L + 2N + (2N (N + 1)/(n – N – 1)) , (4)

which is a modification for small sample sizes in relation to the number of parameters in a model where 

n is sample size. When sample sizes are large in relation to the number of parameters in a model, AICc is 

equivalent to AIC, thus AICc provides more flexibility when sample size varies over a large range.

Further, AICc can be used to compare nested and non-nested models, as opposed to strictly using a 

Likelihood Ratio Test, which is restricted to nested models.

We interpreted ΔAICc values based on the recommendations of Burnham and Anderson (1998), 

where ΔAICc < 2 between two models suggests no evidence that one of the models is best; 2 < ΔAICc < 

10 suggests some evidence; and ΔAICc > 10 suggests strong evidence that the model with the smaller 

AICc is the best model. Many of our model runs resulted in nested models having a ΔAICc < 2. In these 

cases, candidate models were determined by examining the deviance or likelihood. If nested models 

differed by only one parameter and the deviance was nearly equal between models, then this suggested 

the additional parameter did not improve model fit. Therefore, we eliminated the model with the 

additional parameter from the candidate set. Model selection tables shown in the results of this report

contain only models with ΔAICc<10; however, appendixes A and B contain all candidate models for 

survival of fish passing through the spillway and bypass outfall, respectively, regardless of ΔAICc value.

We took a hierarchical approach to model selection by evaluating detection parameters and 

determining the best model using AICc similar to the strategy of Lebreton and others (1992). The best 

model for detection probabilities was used for all other analyses when examining survival. We began 

our model selection at the farthest downstream parameter, λ, and worked our way upriver (starting with 

λ and then p). We tested and incorporated the possibility that λ could be related to fish weight or tag 

burden into the detection probability model where the model fit was improved and then assessed 

survival of juvenile salmonids as a function of covariates. Various combinations of variables were 

created for each model to represent potential drivers, or previous hypotheses, as to which factors

influence survival of juvenile salmonids as they migrate past McNary Dam. Although hypotheses were 

developed previously, selection procedures were used conceptually so that important hypotheses were 

not left out of the model set, which could occur without a systematic approach to hypotheses 

development (Collett, 2003). The effect of “study year” was then added to the best models to assess 

additional variation not explained by covariates. Variables that were highly correlated (for example, fish 

weight and tag burden, total discharge and spill discharge) were substituted into the best models with 

their correlate to assess which variable was more important or had more influence regarding model fit, 

but were not kept within the same model if they were highly correlated. 
16

There are assumptions that are made when using mark-recapture models. For CJS models, these 

assumptions relate to inferences to the population of interest, error in interpreting acoustic signals, and 

statistical fit of the data to the structure of the model. The assumptions are:

1. Tagged individuals are representative of the population of interest. 

2. Survival probabilities of tagged fish are the same as those of untagged fish. For example, the tagging 

procedures or detection of fish at downstream telemetry arrays should not influence survival or 

detection probabilities. If the tag negatively affected survival, then estimates of survival rates will be 

biased accordingly. In this study, tag burden was examined as a covariate.

3. All sampling events are instantaneous. That is, sampling should take place over a short distance 

relative to the distance between telemetry arrays so that the chance of mortality at a telemetry array 

is minimized. This assumption is necessary to attribute mortality correctly to a specific river reach. 

This assumption usually is satisfied by the location of telemetry arrays.

4. The fate of each tagged fish is independent of the fate of other tagged fish. Therefore, survival or 

mortality of one fish has no effect on the survival or mortality of the other fish.

5. The prior detection history of a tagged fish has no effect on its subsequent survival. This assumption 

could be violated if parts of the river are not monitored for tagged fish. For acoustic telemetry, this 

assumption usually is satisfied by the passive nature of detecting acoustic tags, by monitoring all 

routes of passage at a dam, and by monitoring the entire cross section of the river channel.

6. All tagged fish alive at a sampling location have the same detection probability. This assumption 

also could be violated as described in assumption 5, but usually is satisfied with acoustic telemetry 

by monitoring the entire cross section of the river channel.

7. All tags are identified correctly and the status of tagged fish (that is, alive or dead) is known without 

error. This assumes that fish do not lose their tags and that the tag is functioning when the fish is in 

the study area. Additionally, the assumption is that all detections are of live fish and that dead fish 

are not detected and interpreted as live (that is, false-positive detections). This assumption is 

addressed by releasing tagged, dead fish and seeing if the fish are detected at the detection arrays 

used to assess survival of juvenile salmonids. Tag life studies are performed in conjunction with 

field studies.

There are formal ways proposed by Burnham and others (1987) to test some of these assumptions, such 

as the independence of fate of individuals, fish in a group having equal survival and detection 

probabilities, and prior recapture history not influencing survival and detection probabilities 

downstream. However, these tests require three downstream detection sites that we did not have during

all study years. Nonetheless, others have found that survival estimates generated using CJS models are 

robust to many violations of these assumptions (Skalski and others, 1998). Tag life studies and the 

release of tagged, dead fish were conducted during field studies (Adams and others, 1998, 2008; Adams 

and Counihan, 2009; Adams and Liedtke, 2009, 2010; Perry and others, 2006, 2007; Timko and others, 

2007, 2008, 2010; Steig and others, 2007, 2008, 2009, 2010; and Sullivan and others, 2009).
17

Results

Yearling Chinook Salmon

Survival Analysis

The best supported spillway and bypass models for p and λ for yearling Chinook salmon

included a year effect for both parameters (table 7). These models of p and λ were used for all other 

spillway and bypass survival analyses.

Table 7. Model selection results based on varying λ and p with respect to year for yearling Chinook salmon, 2004–

09.

[The best-fit models are indicated in bold. The Phi (ø) portion of the model was held constant for all models of λ and p. The 

best-fit model for λ was determined first and then used to assess the best-fit model for p. ø, the probability of survival from 

dam passage through a route to the first downstream detection array; p, the probability of being detected at the first 

downstream detection array given the individual survived; λ, the joint probability of surviving and being detected from the 

first downstream array to the next downstream array; g, all combinations of the photoperiod, passage location, bay type, spill 

pattern, and year group covariates; y, year; AICc, Akaike’s Information Criterion]

No. Model Number of

parameters AICc ΔAICc Deviance

Spillway

1 ø(g) p(y) λ(y) 117 8,312.50 0.00 8,074.82

2 ø(g) p(y) λ 112 8,709.94 397.45 8,482.58

3 ø(g) p λ(y) 112 9,047.15 734.65 8,819.78

Bypass

1 ø(g) p(y) λ(y) 48 5,593.62 0.00 5,496.64

2 ø(g) p(y) λ 43 5,727.26 133.64 5,640.47

3 ø(g) p λ(y) 43 6,168.51 574.88 6,081.71
18

Spillway survival of yearling Chinook salmon was best explained by the model that included tag 

burden, spill bay discharge, bay type, temperature, and the interaction between spill bay discharge and 

bay type (table 8). Tag burden and bay type were both negatively related to spillway survival, and the 

remaining covariates were positively related to spillway survival (table 9). The model that included tag 

burden, spill bay discharge, bay type, and temperature (but not the interaction between spill bay 

discharge and bay type) also was well supported with an AICc within 1.38 of the model that included the 

interaction, indicating no difference between the two models (table 8). Fifteen other models, all of 

which included tag burden, had AICc values within 10 units of the best model and, therefore, provide 

some explanation of spillway survival for yearling Chinook salmon (table 8). We found that spillway 

survival increased as spill bay discharge increased for both bay types, and that survival was higher for 

fish passing through conventional spill bays compared to TSW bays (fig. 7). Similarly, spillway survival 

increased as total discharge increased for all spill patterns. Survival was highest (94 percent or higher) 

for spill patterns that discharged the most spill through the north or south portions of the spillway

(patterns 1 and 5), and least for spill patterns that discharged water more uniformly through all portions 

of the spillway (fig. 8).

The best-fit model for survival of fish passing through the juvenile bypass outfall included only 

the group covariate for photoperiod and was only slightly better (1.12 ΔAICc) than the intercept model 

(table 10). Bypass survival was lower during the day than at night (table 9). The only covariate 

associated with spill operations that we modeled that provided any support to bypass survival was spill 

pattern (table 10). The model that included photoperiod and spill pattern had an AICc value 5.51 units 

lower than the model with photoperiod alone, and the model that included only spill pattern had an AICc

value 6.21 units lower than the best model. Based on these AICc values, spill pattern provided little 

explanation of variation in bypass survival for yearling Chinook salmon.
19

Table 8. Model selection for fish that passed through the spillway at McNary Dam relating survival (ø) as a function of individual and group 

covariates using the fixed structure of the best model for p and λ parameters for yearling Chinook salmon, 2004–09.

[The best-fit models are indicated in bold. Q, discharge]

Model Number of

parameters AICc ΔAICc Deviance

Tag burden + Spill bay Q + Bay type + Temperature + Spill bay Q*Bay type 18 8,199.62 0.00 8,163.53

Tag burden + Spill bay Q + Bay type + Temperature 17 8,201.00 1.38 8,166.92

Tag burden + Spill bay Q + Bay type 16 8,201.81 2.18 8,169.73

Tag burden + Total Q + Temperature 16 8,202.53 2.90 8,170.46

Tag burden + Spill bay Q + Temperature 16 8,202.70 3.08 8,170.63

Tag burden + Total Q + Temperature + Passage location 18 8,203.22 3.60 8,,167.13

Tag burden + Temperature 15 8,203.45 3.82 8,173.38

Tag burden + Total Q 15 8,203.86 4.24 8,173.80

Tag burden + Total Q + Passage location 17 8,203.99 4.37 8,169.91

Tag burden + Temperature + Passage location 17 8,204.42 4.80 8,170.34

Tag burden + Total Q + Spill pattern 19 8,205.03 5.40 8,166.93

Tag burden + Spill Q 15 8,206.33 6.71 8,176.27

Tag burden + Spill Q + Passage location 17 8,206.71 7.09 8,172.63

Tag burden + Spill pattern + Temperature 19 8,207.03 7.41 8,168.93

Tag burden + Spill pattern 18 8,207.95 8.32 8,171.86

Tag burden + Spill bay Q 15 8,208.43 8.81 8,178.37

Tag burden + Spill bay Q + Passage location 17 8,209.43 9.81 8,175.35
20

Table 9. Slope (Beta) coefficients, standard error, and 95-percent confidence limits of model parameters for 

yearling Chinook salmon passing McNary Dam, 2004–09.

[CL, confidence limit]

Variable Beta Standard 

error Lower CL Upper CL

Spillway

Intercept 2.338 0.677 1.011 3.666

Tag burden -0.324 0.084 -0.488 -0.161

Spill bay discharge 0.114 0.049 0.019 0.210

Bay type -0.992 0.305 -1.590 -0.394

Temperature 0.111 0.059 -0.004 0.227

Bay type*spill bay discharge 0.074 0.038 -0.001 0.149

Bypass

Intercept 3.009 0.227 2.563 3.455

Photoperiod (light) -0.413 0.247 -0.898 0.072
21

0.91

0.92

0.93

0.94

0.95

0.96

0.97

0.98

0.99

1.00

0 2 4 6 8 10 12 14 16

Survival

Spill bay discharge (kcfs)

Standard Bay TSW

Figure 7. Survival of yearling Chinook salmon that passed through conventional spill bays (black plot) and the 

TSWs (gray plot) at McNary Dam in relation to spill bay discharge, 2004–09. Other covariates in the model were 

held constant at their mean value to examine the relationship to the variable of interest. 
22

Figure 8. Spillway survival of yearling Chinook salmon in relation to total discharge for each spill pattern at McNary 

Dam, 2004–09. Other covariates in the model were held constant at their mean value to examine the relationship to 

the variable of interest. Legend text identifies the spill pattern number followed by the associated percentage of spill 

discharge through the south, middle, and north portions of the spillway, respectively.

0.86

0.88

0.90

0.92

0.94

0.96

0.98

1.00

0 50 100 150 200 250 300 350 400 450

Spillway survival

Total discharge (kcfs)

1_50_42_8

2_43_34_23

3_36_32_32

4_30_39_31

5_15_43_42
23

Table 10. Model selection for fish that passed through the juvenile bypass system outfall at McNary Dam relating 

survival (ø) as a function of individual and group covariates using the fixed structure of the best model for p and λ

parameters for yearling Chinook salmon, 2004–09.

[The best-fit models are indicated in bold]

Model Number of 

parameters AICc ΔAICc Deviance

Photoperiod 14 5,553.48 0.00 5,525.39

Intercept 13 5,554.60 1.12 5,528.52

Photoperiod + Spill pattern 19 5,558.99 5.51 5,520.84

Spill pattern 18 5,559.69 6.21 5,523.55

Juvenile Steelhead

Survival Analysis

The best supported models for p and λ for juvenile steelhead included a year effect for both 

parameters. The fit of the λ models was further improved by the addition of the tag burden covariate for 

fish that passed through the spillway and the fish weight covariate for fish that passed through the 

juvenile bypass system (table 11).

The best-fit model for fish passing through the spillway included temperature, spillway 

discharge, and fish weight (table 12). Survival was negatively related to temperature, but positively 

related to spillway discharge and fish weight (table 13, fig. 9). The model that replaced spillway 

discharge with total discharge and spill pattern also was well supported (1.81 ΔAICc, table 12). Spillway 

survival increased as total discharge increased for all spill patterns, and spill patterns one and four

provided the highest spillway survival (fig. 10). Four other models, all of which included temperature 

and fish weight, and three that included at least one covariate related to spillway operations, were within 

4.5 AICc units, and therefore provided some support to variation in spillway survival. The addition of a 

year factor to five of the top six models improved the models substantially, decreasing ΔAICc by 5.45, 

6.88, 7.62, 5.64, and 4.40, respectively (table 12).

The model that best explained survival of juvenile steelhead passing McNary Dam through the 

juvenile bypass system outfall included temperature and total discharge (table 14). Bypass survival was 

negatively related to increasing water temperature, but positively related to increasing total discharge 

(table 13). The second best model included temperature and spill discharge and was within 1.21 AICc of 

the best model (table 14).
24

Table 11. Model selection results based on varying λ and p with respect to year for juvenile steelhead at McNary 

Dam, 2004–09.

[The best-fit models are indicated in bold. The Phi (ø) portion of the model was held constant for all models of λ and p. The 

best-fit model for λ was determined first and then used to assess the best-fit model for p. ø, the probability of survival from 

dam passage through a route to the first downstream detection array; p, the probability of being detected at the first 

downstream detection array given the individual survived; λ, the joint probability of surviving and being detected from the 

first downstream array to the next downstream array; g, all combinations of the photoperiod, passage location, bay type, spill 

pattern, and year group covariates; y, year]

Model Number of 

parameters AICc ΔAICc Deviance

Spillway

1 ø(g*t) p(y) λ(y + tag burden) 114 6,579.59 0.00 6,347.36

2 ø(g*t) p(y) λ(y) 113 6,605.77 26.18 6,375.61

3 ø(g*t) p(y) λ 108 6,659.25 79.66 6,439.46

4 ø(g*t) p λ(y) 108 7,486.42 906.83 7,266.63

Bypass

1 ø(g) p(y) λ(y + fish weight) 49 2,609.71 0.00 2,509.61

3 ø(g) p(y) λ 42 2,663.70 53.99 2,578.16

2 ø(g) p(y) λ(y) 47 2,694.79 85.08 2,512.35

4 ø(g) p λ(y) 42 2,865.14 255.43 2,779.60
25

Table 12. Model selection for fish that passed through the spillway at McNary Dam relating survival (ø) as a function of individual and group 

covariates using the fixed structure of the best model for p and λ parameters for juvenile steelhead, 2004–09.

[The best-fit models are indicated in bold]

Model Number of 

parameters AICc ΔAICc Deviance

Temperature + Spill discharge + Fish weight1 17 6,464.37 0.00 6,430.27

Temperature + Total discharge + Spill pattern + Fish weight2 21 6,466.18 1.81 6,424.04

Temperature + Total discharge + Percent spill + Fish weight3 18 6,466.72 2.35 6,430.61

Temperature + Total discharge + Spill pattern + Total discharge*Spill pattern + Fish weight4 25 6,467.26 2.89 6,417.05

Temperature + Spill discharge + Spill pattern + Fish weight 21 6,468.25 3.88 6,426.10

Temperature + Total discharge + Fish weight5 17 6,468.82 4.45 6,434.73

Temperature + Spill bay discharge + Spill pattern + Fish weight 21 6,471.93 7.56 6,429.79

Temperature + Spill pattern + Fish weight 20 6,473.18 8.81 6,433.05

Temperature + Spill discharge 16 6,473.82 9.45 6,441.73

1

Addition of year to this model decreased AICc by 5.45.

2

Addition of year to this model decreased AICc by 6.88.

3

Addition of year to this model decreased AICc by 7.62.

4

Addition of year to this model decreased AICc by 5.64.

5

Addition of year to this model decreased AICc by 4.40.
26

Table 13. Slope (Beta) coefficients, standard error, and 95-percent confidence limits of model parameters for 

juvenile steelhead passing McNary Dam, 2004–09.

[CL, confidence limit. The addition of year improved model fit for spillway survival]

Variable Beta Standard 

error

Lower CL Upper CL

Spillway

Intercept 4.605 0.651 3.329 5.881

Temperature -0.313 0.053 -0.417 -0.209

Fish weight 0.010 0.003 0.004 0.016

Spill discharge 0.009 0.002 0.004 0.013

Bypass

Intercept 4.877 1.113 2.696 7.059

Temperature -0.292 0.092 -0.472 -0.112

Total discharge 0.006 0.002 0.002 0.010
27

Figure 9. Spillway survival of juvenile steelhead in relation to spillway discharge at McNary Dam, 2004–09. Other 

covariates in the model were held constant at their mean value to examine the relationship to the variable of 

interest.

0.89

0.90

0.91

0.92

0.93

0.94

0.95

0.96

0.97

0.98

0.99

1.00

0 50 100 150 200 250 300

Spillway survival

Spillway discharge (kcfs)
28

Figure 10. Spillway survival of juvenile steelhead in relation to total discharge for each spill pattern at McNary Dam,

2004–09. Other covariates in the model were held constant at their mean value to examine the relationship to the 

variable of interest. Legend text identifies the spill pattern number followed by the associated percentage of spill 

discharge through the south, middle, and north portions of the spillway, respectively.

0.86

0.88

0.90

0.92

0.94

0.96

0.98

1.00

0 50 100 150 200 250 300 350 400 450

Spillway survival

Total discharge (kcfs)

1_50_42_8

2_43_34_23

3_36_32_32

4_30_39_31

5_15_43_42
29

Table 14. Model selection for fish that passed through the juvenile bypass system outfall at McNary Dam relating survival (ø) as a function of 

individual and group covariates using the fixed structure of the best model for p and λ parameters for juvenile steelhead, 2004–09.

[The best-fit models are indicated in bold]

Model Number of 

parameters AICc ΔAICc Deviance

Temperature + Total discharge 16 2,570.27 0.00 2,538.04

Temperature + Spill discharge 16 2,571.48 1.21 2,539.25

Temperature + Spill pattern + Total discharge 21 2,573.29 3.02 2,530.90

Temperature + Spill pattern 20 2,575.11 4.84 2,534.75

Temperature + Percent spill 16 2,576.55 6.28 2,544.32

Temperature 15 2,577.33 7.06 2,547.13

Spill discharge 15 2,577.35 7.08 2,547.15

Spill pattern 19 2,578.16 7.89 2,539.84

Spill pattern + Total discharge 20 2,578.49 8.22 2,538.14

Total discharge 15 2,578.69 8.42 2,548.49

Percent spill 15 2,580.22 9.95 2,550.02

Tag burden 15 2,581.26 10.99 2,551.05

Intercept 14 2,581.33 11.06 2,553.16
30

Subyearling Chinook Salmon

Survival Analysis

The best-supported spillway and bypass models for p and λ for subyearling Chinook salmon 

included a year effect for both parameters (table 15). These models of p and λ were used for all other 

spillway and bypass survival analyses.

The best model for describing survival of subyearling Chinook salmon passing through the

spillway included spill pattern, tag burden, temperature, spill bay discharge, spillway discharge, and 

percentage of spill (table 16). Spillway survival was positively related to spill pattern 4 and spillway 

discharge, but negatively related to all other covariates (table 17). Replacing spillway discharge and 

percentage of spill in the top model with total discharge resulted in essentially equal support (0.33

ΔAICc, table 16). Likewise, replacing tag burden with fish weight or spill bay Q with bay type provided 

models that fit the data well (1.52 ΔAICc and 0.68 ΔAICc, respectively, table 16). Spillway survival was 

highest for spill patterns 4 and 5, which distributed spill relatively uniformly among the three portions 

of the spillway, and lowest for spill patterns that discharged more water through the southern spill bays 

(figs. 11, 12, and 13). Spillway survival decreased for all spill patterns as percentage of spill and spill 

bay discharge increased (figs. 11 and 13). Conversely, spillway survival increased for all spill patterns 

as total discharge increased (fig. 12).

Bypass survival of subyearling Chinook salmon was explained best by the model that included 

temperature, spill pattern, fish weight, total discharge, and the interaction between spill pattern and total 

discharge (table 18). Bypass survival was negatively related to temperature, and spill patterns 1, 2, and 

5, but was positively related to fish weight, total discharge, and spill patterns 3 and 4 (table 17, figs. 14 

and 15). The addition of year to the best model decreased AICc by 2.39 units. Bypass survival decreased 

as total discharge increased for the interaction between spill pattern and total discharge for patterns 3 

and 4, increased for patterns 1, 2 and 5, and was constant during no-spill conditions (fig. 14). Bypass 

survival decreased for all spill patterns as temperature increased, and survival was highest for spill 

patterns 2 and 4 (fig. 15).
31

Table 15. Model selection results based on varying λ and p with respect to year for subyearling Chinook salmon, 

2004–09.

[The best-fit models are indicated in bold. The Phi (ø) portion of the model was held constant for all models of λ and p. The 

best-fit model for λ was determined first and then used to assess the best-fit model for p. ø, the probability of survival from 

dam passage through a route to the first downstream detection array; p, the probability of being detected at the first 

downstream detection array given the individual survived; λ, the joint probability of surviving and being detected from the 

first downstream array to the next downstream array; g, all combinations of the photoperiod, passage location, bay type, spill 

pattern, and year group covariates; y, year]

Model Number of

parameters AICc ΔAICc Deviance

Spillway

1 ø(g) p(y) λ(y) 123 8,544.86 0.00 8,294.55

2 ø(g) p(y) λ 120 8,621.33 76.46 8,377.23

3 ø(g) p λ(y) 120 9,274.83 729.97 9,030.73

Bypass

1 ø(g) p(y) λ(y) 57 4,124.33 0.00 4,008.13

2 ø(g) p(y) λ 52 4,192.13 67.80 4,086.30

3 ø(g) p λ(y) 52 4,391.08 266.75 4,285.25
32

Table 16. Model selection for fish that passed through the spillway at McNary Dam relating survival (ø) as a function of individual and group 

covariates using the fixed structure of the best model for p and λ parameters for subyearling Chinook salmon, 2004–09.

[The best-fit models are indicated in bold. Q, discharge; PassLoc, passage location; Temp, temperature]

Model Number of

parameters AICc ΔAICc Deviance

Spill pattern + Tag burden + Temp + Spill bay Q + Spill Q + Percent spill 20 8,406.22 0.00 8,366.10

Spill pattern + Tag burden + Temp + Spill bay Q + Total Q 19 8,406.55 0.33 8,368.45

Spill pattern + Tag burden + Temp + Spill bay Q + Spill Q + Percent spill + PassLoc 22 8,406.59 0.37 8,362.45

Spill pattern + Tag burden + Temp + Bay type + Total Q 19 8,406.90 0.68 8,368.80

Spill pattern + Fish weight + Temp + Spill bay Q + Total Q 19 8,407.74 1.52 8,369.64

Spill pattern + Tag burden + Temp + Spill bay Q + Total Q + Spill pattern*Total Q 23 8,408.18 1.97 8,362.03

Spill pattern + Tag burden + Temp + Total Q 18 8,408.57 2.35 8,372.47

Spill pattern + Tag burden + Temp + Bay type + Total Q + Total Q*spill pattern 23 8,408.65 2.44 8,362.50

Tag burden + Temp + Bay type + Total Q 15 8,410.22 4.00 8,380.15

Spill pattern + Temp + Spill bay Q + Total Q 18 8,410.46 4.25 8,374.37

Spill pattern + Temp + Spill bay Q + Total Q + PassLoc 20 8,410.51 4.29 8,370.39

Spill pattern + Temp + Bay type + Total Q 18 8,410.64 4.42 8,374.54

Spill pattern + Temp + Spill bay Q + Spill Q + Percent spill 19 8,410.67 4.45 8,372.56

Spill pattern + Tag burden + Temp + Spill bay Q + Total Q + Spill pattern*Spill bay Q 23 8,411.15 4.93 8,365.00
33

Table 16. Model selection for fish that passed through the spillway at McNary Dam relating survival (ø) as a function of individual and group covariates 

using the fixed structure of the best model for p and λ parameters for subyearling Chinook salmon, 2004–09.—Continued

[Q, discharge; PassLoc, passage location; Temp, temperature]

Model Number of

parameters AICc ΔAICc Deviance

Tag burden + Temp + Spill bay Q + Spill Q + Percent spill 16 8,411.27 5.05 8,379.19

Spill pattern + Temp + Bay type + Total Q + PassLoc 20 8,411.31 5.10 8,371.20

PassLoc + Temp + Spill bay Q + Spill Q + Percent spill + Tag burden 18 8,411.64 5.42 8,375.54

Tag burden + Temp + Spill Q + Total Q + PassLoc + PassLoc*Spill Q 19 8,411.67 5.45 8,373.56

Tag burden + Temp + Spill Q + Total Q 15 8,411.74 5.53 8,381.68

Tag burden + Temp + Spill Q + Total Q + PassLoc 17 8,412.35 6.13 8,378.27

Spill pattern + Temp + Total Q 17 8,412.42 6.21 8,378.34

Tag burden + Temp + Spill bay Q + Spill Q + Percent spill + PassLoc + PassLoc*Spill bay Q 20 8,412.64 6.43 8,372.53

Temp + Bay type + Total Q 14 8,414.26 8.04 8,386.20

Temp + Spill bay Q + Spill Q + Percent spill 15 8,415.37 9.15 8,385.30

Temp + Bay type + Total Q + PassLoc 16 8,415.58 9.36 8,383.50

Temp + Spill Q + Total Q + PassLoc + PassLoc*Spill Q 18 8,415.63 9.41 8,379.53

Temp + Spill bay Q + Spill Q + Percent spill + PassLoc 17 8,415.65 9.43 8,381.56
34

Table 17. Slope (β) coefficients, standard error, and 95-percent confidence limits of model parameters for 

subyearling Chinook salmon passing McNary Dam, 2004–09.

[CL, confidence limit. The addition of year improved model fit for bypass survival]

Variable β Standard 

Error Lower CL Upper CL

Spillway

Intercept (spill pattern 2) 8.054 1.212 5.679 10.429

Spill pattern 4 0.313 0.173 -0.026 0.651

Spill pattern 5 -0.372 0.172 -0.710 -0.035

Spill pattern 1 -0.480 0.220 -0.912 -0.048

Spill pattern 3 -1.212 0.592 -2.372 -0.052

Temperature -0.235 0.055 -0.343 -0.128

Spill discharge 0.013 0.004 0.006 0.021

Spill bay discharge -0.048 0.024 -0.095 0.000

Percent spill -0.033 0.009 -0.050 -0.016

Tag burden -0.170 0.068 -0.303 -0.038

Bypass

Intercept 9.271 1.901 5.545 12.997

Temperature -0.434 0.082 -0.595 -0.274

Fish weight 0.025 0.016 -0.007 0.057

Total discharge 0.001 0.004 -0.008 0.009

Spill pattern 1 -0.842 1.758 -4.288 2.604

Spill pattern 2 -1.368 1.178 -3.676 0.941

Spill pattern 3 6.118 7.192 -7.979 20.214

Spill pattern 4 2.807 0.996 0.854 4.759

Spill pattern 5 -0.956 1.227 -3.361 1.450

Spill pattern 1*total discharge 0.003 0.011 -0.018 0.024

Spill pattern 2*total discharge 0.009 0.007 -0.005 0.022

Spill pattern 3*total discharge -0.038 0.039 -0.113 0.038

Spill pattern 4*total discharge -0.011 0.005 -0.021 -0.001

Spill pattern 5*total discharge 0.006 0.007 -0.009 0.020
35

Figure 11. Spillway survival of subyearling Chinook salmon in relation to percent spill for each spill pattern at 

McNary Dam, 2004–09. Other covariates in the model were held constant at their mean value to examine the 

relationship to the variable of interest. Legend text identifies the spill pattern number followed by the associated 

percentage of spill discharge through the south, middle, and north portions of the spillway, respectively.

0.80

0.82

0.84

0.86

0.88

0.90

0.92

0.94

0.96

0.98

1.00

0 10 20 30 40 50 60 70 80 90

Spillway survival

Percent spill

1_78_22_0

2_55_41_4

3_47_36_17

4_39_34_27

5_27_40_33
36

Figure 12. Spillway survival of subyearling Chinook salmon in relation to total discharge for each spill pattern at 

McNary Dam, 2004–09. Other covariates in the model were held constant at their mean value to examine the 

relationship to the variable of interest. Legend text identifies the spill pattern number followed by the associated 

percentage of spill discharge through the south, middle, and north portions of the spillway, respectively.

0.60

0.65

0.70

0.75

0.80

0.85

0.90

0.95

1.00

0 50 100 150 200 250 300 350 400 450

Spillway survival

Total discharge (kcfs)

1_78_22_0

2_55_41_4

3_47_36_17

4_39_34_27

5_27_40_33
37

Figure 13. Spillway survival of subyearling Chinook salmon in relation to total discharge for each spill pattern at 

McNary Dam, 2004–09. Other covariates in the model were held constant at their mean value to examine the 

relationship to the variable of interest. Legend text identifies the spill pattern number followed by the associated 

percentage of spill discharge through the south, middle, and north portions of the spillway, respectively.

0.74

0.76

0.78

0.80

0.82

0.84

0.86

0.88

0.90

0.92

0.94

0.96

0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15

Spillway survival

Spill bay discharge (kcfs)

1_78_22_0

2_55_41_4

3_47_36_17

4_39_34_27

5_27_40_33
38

Table 18. Model selection for fish that passed through the juvenile bypass system outfall at McNary Dam relating survival (ø) as a function of 

individual and group covariates using the fixed structure of the best model for p and λ parameters for subyearling Chinook salmon, 2004–09.

[The best-fit models are indicated in bold. Q, discharge]

Model Number of

parameters AICc ΔAICc Deviance

Temperature + Spill pattern + Fish weight + Total Q + Spill pattern*Total Q1 26 4,062.74 0.00 4,010.28

Temperature + Spill pattern + Total Q + Spill pattern*Total Q 25 4,063.24 0.50 4,012.81

Temperature + Spill pattern + Fish weight 20 4,065.41 2.67 4,025.13

Temperature + Spill pattern 19 4,066.09 3.35 4,027.84

Temperature + Fish weight 15 4,067.41 4.67 4,037.25

Temperature 14 4,067.56 4.82 4,039.43

1

Addition of year to this model decreased AICc by 2.39.
39

Figure 14. Bypass survival of subyearling Chinook salmon in relation to total discharge, with an interaction 

between spill pattern and total discharge, for each spill pattern at McNary Dam, 2004–09. Other covariates in the 

model were held constant at their mean value to examine the relationship to the variable of interest. Legend text 

identifies the spill pattern number followed by the associated percentage of spill discharge through the south, 

middle, and north portions of the spillway, respectively.

0.60

0.65

0.70

0.75

0.80

0.85

0.90

0.95

1.00

0 50 100 150 200 250 300 350 400

Bypass survival

Total discharge (kcfs)

1_55_41_4

2_39_34_27

3_78_22_0

4_27_40_33

5_47_36_17

No spill
40

Figure 15. Bypass survival of subyearling Chinook salmon in relation to water temperature at McNary Dam, 2004–

09. Other covariates in the model were held constant at their mean value to examine the relationship to the variable 

of interest. Legend text identifies the spill pattern number followed by the associated percentage of spill discharge 

through the south, middle, and north portions of the spillway, respectively.

0.50

0.55

0.60

0.65

0.70

0.75

0.80

0.85

0.90

0.95

1.00

15 16 17 18 19 20 21 22 23

Bypass survival

Temperature (oC)

1_55_41_4

2_39_34_27

3_78_22_0

4_27_40_33

5_47_36_17

No spill
41

Sockeye Salmon

Survival Analysis

Initial analyses of λ and p models for sockeye salmon passing through the spillway indicated that 

λ was best fit with year and tag burden covariate effects and p was best fit with a year effect (table 19).

However, because of low downstream detection probabilities for sockeye salmon in most years, survival 

probabilities for many models, including spill pattern, using this p model were not estimable. In order to 

analyze the effect of spill pattern on survival, we chose to use a model of λ and p with only the spill 

pattern effect for the analyses. 

The best model for describing survival of sockeye salmon passing through the spillway included 

passage location, spill discharge, temperature, and tag burden (table 20). Spillway survival was 

positively related to passage location and temperature, but negatively related to spill discharge and tag 

burden (table 21). The model that replaced spill discharge with total discharge and percentage of spill 

also was well supported (1.83 ΔAICc, table 20). The addition of year to the top model improved the 

model substantially, decreasing ΔAICc by 109.61 (table 20). Regardless of spill passage location, 

spillway survival decreased as spillway discharge or total discharge increased, and survival was highest 

for fish passing through north spill bays and lowest for fish passing through the middle portion of the 

spillway (figs. 16 and 17). Spillway survival was more than 98 percent for all spill passage locations at 

75 kcfs spillway discharge and decreased to between 81 and 92 percent, depending on spill-passage 

location (fig. 16). Spillway survival was 96 percent or more for all spill passage locations at about 200 

kcfs total discharge, but steadily decreased to between 86 and 94 percent at 425 kcfs (fig. 17).

Table 19. Model selection results for sockeye salmon passing through the spillway based on varying λ and p with

respect to year, 2004–09.

[The best-fit models are indicated in bold. The Phi (ø) portion of the model was held constant for all models of λ and p. The 

best-fit model for λ was determined first and then used to assess the best-fit model for p. ø, the probability of survival from 

dam passage through a route to the first downstream detection array; p, the probability of being detected at the first 

downstream detection array given the individual survived; λ, the joint probability of surviving and being detected from the 

first downstream array to the next downstream array; g, all combinations of the photoperiod, passage location, bay type, spill 

pattern, and year group covariates; y, year]

Model Number of

parameters AICc ΔAICc Deviance

1 ø(g) p(y) λ(y + tag burden) 54 3,945.89 0.00 3,836.57

2 ø(g) p(y) λ(y) 53 3,949.13 3.25 3,841.87

3 ø(g) p(y) λ 50 4,015.40 69.52 3,914.28

4 ø(g) p λ(y) 50 5,721.43 1,775.54 5,620.30
42

Table 20. Model selection for fish that passed through the spillway at McNary Dam relating survival (ø) as a function of individual and group 

covariates using the fixed structure of the best model for p and λ parameters for sockeye salmon, 2004–09.

[The best-fit models are indicated in bold]

Model Number of

parameters AICc ΔAICc Deviance

Passage location + Spill discharge + Temperature + Tag burden1 13 5,171.48 0.00 5,145.40

Passage location + Total discharge + Temperature + Percent spill + Tag burden 14 5,173.31 1.83 5,145.22

Passage location + Total discharge + Temperature + Tag burden 13 5,174.16 2.68 5,148.08

Passage location + Percent spill + Temperature + Tag burden 14 5,175.61 4.13 5,147.52

Passage location + Spill discharge + Tag burden 12 5,178.99 7.51 5,154.92

Spill discharge + Temperature + Tag burden 11 5,179.32 7.84 5,157.26

Total discharge + Temperature + Percent spill + Tag burden 12 5,181.19 9.71 5,157.12

1

Addition of year to this model decreased AICc by 109.606.
43

Table 21. Slope (β) coefficients, standard error, and 95-percent confidence limits of model parameters for sockeye

salmon passing through the spillway at McNary Dam, 2004–09.

[CL, confidence limit]

Variable β Standard 

error

Lower CL Upper CL

Intercept (middle passage location) 1.517 1.861 -2.130 5.164

North passage location 0.755 0.303 0.162 1.349

South passage location 0.448 0.164 0.127 0.769

Spill discharge -0.014 0.003 -0.019 -0.008

Temperature 0.379 0.123 0.137 0.621

Tag burden -0.439 0.082 -0.601 -0.278
44

Figure 16. Spillway survival of sockeye salmon in relation to spillway discharge for each spillway passage location 

at McNary Dam, 2004–09. Other covariates in the model were held constant at their mean value to examine the 

relationship to the variable of interest.

0.80

0.82

0.84

0.86

0.88

0.90

0.92

0.94

0.96

0.98

1.00

0 25 50 75 100 125 150 175 200 225 250 275

Spillway survival

Spillway discharge (kcfs)

South

Middle

North
45

Figure 17. Spillway survival of sockeye salmon in relation to total discharge for each spillway passage location at 

McNary Dam, 2004–09. Other covariates in the model were held constant at their mean value to examine the 

relationship to the variable of interest.

0.84

0.86

0.88

0.90

0.92

0.94

0.96

0.98

1.00

75 100 125 150 175 200 225 250 275 300 325 350 375 400 425 450

Spillway survival

Total discharge (kcfs)

South

Middle

North
46

Discussion

Spillway Survival

This analysis provided many models that explained variation in spillway survival of juvenile

salmonids passing McNary Dam. Models supported by the data included spillway-related variables, as 

well as other variables. Predominant variables unrelated to spill bay operations that influenced spillway 

survival were water temperature, tag burden, and total discharge. Water temperature was a factor in 

nearly all supported models for all species with survival being inversely related to increasing 

temperatures. Tag burden also was a factor in nearly all supported models for all species except juvenile 

steelhead, and also was negatively related to survival. Although tag burden was not a supported factor in 

models for steelhead, fish weight was supported in most models for steelhead. Total discharge was not a 

factor in the best models for spillway survival for yearling Chinook salmon, but was a factor in many 

supportive models for juvenile steelhead, subyearling Chinook salmon, and sockeye salmon.

Predominant variables related to spill bay operations that influenced spillway survival were spill 

pattern, spillway discharge, spill bay discharge, bay type, and spill passage location. The combination of 

these factors in the models, and the extent to which they influenced survival, varied by species. Both 

spill bay discharge and bay type were factors in the best three models for yearling Chinook salmon.

Spillway survival was positively related to an increase in spill bay discharge. Survival was higher for 

yearling Chinook salmon passing through conventional spill bays, compared to TSW bays, for all spill 

bay discharge levels. Although spill pattern was not a factor in models for yearling Chinook salmon, we 

analyzed spillway survival by spill pattern for comparison with other species and found that spill pattern 

1 (predominantly south spill) provided the highest survival, similar to steelhead. The addition of a year 

factor did not improve any models for yearling Chinook salmon, suggesting that the covariates included 

in the models adequately captured the factors that cause year-to-year variation in survival. 

The best model for steelhead included spillway discharge that was positively related to spillway 

survival. The next best model (within 1.81 AICc) replaced spillway discharge with spill pattern and total 

discharge. Similar to yearling Chinook salmon, spillway survival increased as total discharge increased,

and survival was highest for spill pattern 1, which discharged spill predominantly through the south 

portion of the spillway. The addition of a year factor improved the top three models for steelhead, 

indicating there are some other variables not included in our analysis that might be influencing year-toyear variation in survival for steelhead (for example, fish condition or disease).

Spill pattern was the most predominant factor related to spill bay operations in supportive 

models for subyearling Chinook salmon spillway survival, followed by spill bay discharge, spill 

discharge, and percentage of spill. We found that spillway survival decreased for subyearling Chinook 

salmon as percentage of spill or spill bay discharge increased. Conversely, spillway survival increased 

as total discharge increased. Uniform spill patterns (patterns 4 and 5) provided higher survival than spill 

patterns that discharged most water through southern spill bays (patterns 1–3), and pattern 5 provided

the highest survival. This result for summer migrating subyearling Chinook salmon was the opposite of

what we found for spring migrants, which had higher survival for southern spill patterns. The addition 

of a year factor to the best models did not explain any further variability in spillway survival for 

subyearling Chinook salmon.

The variables related to spill bay operations that were in the best models for sockeye salmon 

included spillway passage location and spillway discharge. Spillway survival was negatively related to 

an increase in both spillway discharge and total discharge. Spillway survival was highest for sockeye 

salmon passing through the north portion of the spillway, followed by the middle and south locations.

The addition of a year factor improved the best model for sockeye salmon, indicating there are some 
47

other variables not included in our analysis that might be influencing year-to-year variation in spillway 

survival. Because sockeye salmon, unlike the other species, were released 167–358 km upstream of 

McNary Dam, tag life may have been an issue with this species. Obviously, maximum travel times of 

tagged study fish should be shorter than the minimum tag life of tags used in the study. We found that 

maximum travel times of fish detected at the first site downstream of McNary Dam did not exceed the 

expected tag life for tags used in 2008 and 2009 (17 and 22 days, respectively). However, maximum 

travel times did exceed tag life for tags used in 2006 and 2007 (14 days). This suggests the likelihood 

that there were some tagged fish for which tags expired prematurely, indicating the potential for bias in 

survival estimates for sockeye salmon. It also provides a possible explanation for why year improved 

the best model for spillway survival. 

Bypass Survival

Compared to models for spillway survival, fewer models were identified by this analysis that 

explain variation in survival of juvenile salmonids passing through the juvenile bypass system outfall at 

McNary Dam. Further, few models contained covariates related to spill bay operations. Photoperiod was 

the only factor in the best and only model that had support for bypass survival of yearling Chinook 

salmon. No other models were within 2 AICc units except for the intercept model (1.12 ΔAICc). Bypass 

survival of yearling Chinook salmon was lower during the day, compared to night, which is consistent 

with results reported by Adams and others (2011). Temperature was a predominant variable in all 

models describing bypass survival for both juvenile steelhead and subyearling Chinook salmon, similar 

to models for spillway survival. Spillway discharge and spill pattern were the only covariates related to 

spill bay operations that were present in supportive models for bypass survival of juvenile steelhead and 

subyearling Chinook salmon, respectively. Spillway discharge was found only in the second-best model 

for juvenile steelhead, and spill pattern was a predominant factor for subyearling Chinook salmon 

bypass survival in the top four models.
48

Spillway and Bypass Survival

The results of these analyses, while they were not designed to yield predictive models, can be 

used to help develop dam-operation strategies that optimize juvenile salmonid survival. For example, 

increasing total discharge typically had a positive effect on both spillway and bypass survival for all 

species except sockeye salmon. Likewise, an increase in spill bay discharge improved spillway survival 

for yearling Chinook salmon, and an increase in spillway discharge positively affected spillway survival 

for juvenile steelhead. The strong positive relation between spill and survival indicates that increasing 

the amount of water through the spillway is one strategy that could be used to improve spillway survival 

for yearling Chinook salmon and juvenile steelhead. However, increased spill did not improve spillway 

survival for subyearling Chinook salmon and sockeye salmon. Our results indicate that a uniform spill 

pattern would provide the highest spillway survival and bypass survival for subyearling Chinook 

salmon. Conversely, a predominantly south spill pattern provided the highest spillway survival for 

yearling Chinook salmon and juvenile steelhead. Although spill pattern was not a factor for spillway 

survival of sockeye salmon, spill bay operations that optimize passage through the north and south spill 

bays maximized spillway survival for this species. Bypass survival of yearling Chinook salmon could be 

improved by optimizing conditions to facilitate bypass passage at night, but the method to do so is not 

apparent from this analysis because photoperiod was the only factor affecting bypass survival based on 

the best and only supported model. Bypass survival of juvenile steelhead would benefit from lower 

water temperatures and increased total and spillway discharge. Likewise, subyearling Chinook salmon 

bypass survival would improve with lower water temperature and increased total discharge with a 

uniform spill pattern. When total discharge is high (greater than 200 kcfs), there may be a benefit to 

having more of the flow in the spillway discharged in the bays closest to the powerhouse (south spill).

This spill pattern may inhibit the potential for an eddy that could cause fish passing through the bypass 

pipe to be pulled back upstream into the tailrace of the powerhouse. When total discharge is low (less 

than 200 kcfs) and the amount of water passing through the powerhouse is proportionally higher than 

water passing the spillway, survival may be improved by having a uniform spill pattern compared to a 

pattern that passed more water through the southern spill bays. Having more water passing through the 

southern spill bays when the predominant flow is being discharged through the powerhouse may cause 

eddies in the north portion of the spillway and could cause a decrease in survival. 

These analyses provided a unique opportunity to examine data from multiple years of research to 

investigate factors influencing spillway and bypass survival at McNary Dam. By first using statistical 

models to select among variables hypothesized to influence survival, and then quantifying the 

magnitude of the effects, we were able to examine how changes to dam operations might positively or

negatively influence survival. This is critical information that managers need to develop long-term 

operational plans. Although development of predictive models was beyond the scope of our analysis, the 

relations we identified could be used to develop simulation models to gauge the effect of management 

actions on dam survival.
49

References Cited

Adams, N.S., and Counihan, T.D., eds., 2009, Survival and migration behavior of juvenile salmonids at 

McNary Dam, 2007: U.S. Geological Survey Report to the U.S. Army Corps of Engineers, Walla 

Walla District, Washington, Contract W68SBV70178419.

Adams, N.S., and Evans, S.D., eds., 2011, Summary of juvenile salmonid passage and survival at 

McNary Dam—Acoustic survival studies 2006–09: U.S. Geological Survey Open-File Report 2011–

1179, 144 p.

Adams, N.S., and Liedtke, T.L., eds., 2009, Juvenile salmonid survival, passage, and egress at McNary 

Dam during tests of temporary spillway weirs, 2008: U.S. Geological Survey Report to the U. S. 

Army Corps of Engineers, Walla Walla District, Washington, Contract W68SBV80448890.

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52

Appendix A: All Candidate Models Examined for Spillway Survival

Table A1. Model selection for fish that passed through the spillway at McNary Dam relating survival (ø) as a function of individual and group covariates 

using the fixed structure of the best model for p and λ parameters for yearling Chinook salmon, 2004–09. 

[The best-fit models are indicated in bold. Q, discharge]

Model Number of 

parameters AICc ΔAICc Deviance

Tag burden + Spill bay Q + Bay type + Temperature + Spill bay Q*Bay type 18 8,199.62 0.00 8,163.53

Tag burden + Spill bay Q + Bay type + Temperature 17 8,201.00 1.38 8,166.92

Tag burden + Spill bay Q + Bay type 16 8,201.81 2.18 8,169.73

Tag burden + Total Q + Temperature 16 8,202.53 2.90 8,170.46

Tag burden + Spill bay Q + Temperature 16 8,202.70 3.08 8,170.63

Tag burden + Spill bay Q + Bay type + Temperature + Spill bay Q*Bay type + Year 23 8,203.17 3.54 8,157.02

Tag burden + Total Q + Temperature + Passage location 18 8,203.22 3.60 8,167.13

Tag burden + Temperature 15 8,203.45 3.82 8,173.38

Tag burden + Total Q 15 8,203.86 4.24 8,173.80

Tag burden + Total Q + Passage location 17 8,203.99 4.37 8,169.91

Tag burden + Spill bay Q + Bay type + Temperature + Year 22 8,204.20 4.58 8,160.07

Tag burden + Temperature + Passage location 17 8,204.42 4.80 8,170.34

Tag burden + Total Q + Spill pattern 19 8,205.03 5.40 8,166.93

Tag burden + Spill Q 15 8,206.33 6.71 8,176.27

Tag burden + Spill Q + Passage location 17 8,206.71 7.09 8,172.63

Tag burden + Total Q + Temperature + Year 21 8,206.87 7.24 8,164.74

Tag burden + Spill pattern + Temperature 19 8,207.03 7.41 8,168.93

Tag burden + Spill pattern 18 8,207.95 8.32 8,171.86
53

Table A1. Model selection for fish that passed through the spillway at McNary Dam relating survival (ø) as a function of individual and group covariates 

using the fixed structure of the best model for p and λ parameters for yearling Chinook salmon, 2004–09.—Continued

[Q, discharge]

Model Number of

parameters AICc ΔAICc Deviance

Tag burden + Spill bay Q 15 8,208.43 8.81 8,178.37

Tag burden + Spill bay Q + Passage location 17 8,209.43 9.81 8,175.35

Spill pattern + Fish weight 18 8,209.85 10.23 8,173.76

Tag burden + Bay type 15 8,211.71 12.09 8,181.65

Tag burden 14 8,212.33 12.71 8,184.28

Tag burden + Passage location 16 8,212.50 12.88 8,180.43

Temperature 14 8,214.55 14.93 8,186.50

Spill bay Q + Bay type 15 8,215.15 15.52 8,185.09

Passage location + Temperature 16 8,215.37 15.74 8,183.30

Bay type + Fish weight 15 8,215.97 16.35 8,185.91

Spill pattern 17 8,216.99 17.36 8,182.91

Fish weight 14 8,217.27 17.64 8,189.21

Total Q 14 8,218.38 18.75 8,190.32

Total Q + Passage location 16 8,218.60 18.98 8,186.53

Spill bay Q 14 8,218.90 19.27 8,190.84

Spill Q 14 8,219.86 20.24 8,191.81

Spill Q + Passage location 16 8,220.08 20.46 8,188.01

Spill bay Q + Passage location 16 8,220.38 20.76 8,188.31

Intercept only 13 8,220.45 20.83 8,194.41

Bay type 14 8,220.58 20.95 8,192.52

Passage location 15 8,220.89 21.26 8,190.82
54

Table A2. Model selection for fish that passed through the spillway at McNary Dam relating survival (ø) as a function of individual and group covariates 

using the fixed structure of the best model for p and λ parameters for juvenile steelhead, 2004–09.

[The best-fit models are indicated in bold]

Model Number of

parameters AICc ΔAICc Deviance

Temperature + Spill discharge + Fish weight1 17 6,464.37 0.00 6,430.27

Temperature + Total discharge + Spill pattern + Fish weight2 21 6,466.18 1.81 6,424.04

Temperature + Total discharge + Percent spill + Fish weight3 18 6,466.72 2.35 6,430.61

Temperature + Total discharge + Spill pattern + Total discharge*Spill pattern + Fish weight4 25 6,467.26 2.89 6,417.05

Temperature + Spill discharge + Spill pattern + Fish weight 21 6,468.25 3.88 6,426.10

Temperature + Total discharge + Fish weight5 17 6,468.82 4.45 6,434.73

Temperature + Spill bay discharge + Spill pattern + Fish weight 21 6,471.93 7.56 6,429.79

Temperature + Spill pattern + Fish weight 20 6,473.18 8.81 6,433.05

Temperature + Spill discharge 16 6,473.82 9.45 6,441.73

Temperature + Spill bay discharge + Bay type + Fish weight 18 6,475.74 11.37 6,439.63

Temperature + Percent spill + Fish weight 17 6,476.07 11.70 6,441.97

Temperature + Spill bay discharge + Fish weight 17 6,476.29 11.92 6,442.19

Temperature + Fish weight 16 6,477.54 13.17 6,445.45

Temperature + Total discharge 16 6,479.48 15.11 6,447.40

Temperature + Spill pattern 19 6,480.42 16.05 6,442.30

Temperature + Tag burden 16 6,481.75 17.38 6,449.66

Temperature + Percent spill 16 6,482.71 18.34 6,450.63

Temperature + Spill bay discharge 16 6,483.19 18.82 6,451.10

Temperature 15 6,484.47 20.10 6,454.39
55

Table A2. Model selection for fish that passed through the spillway at McNary Dam relating survival (ø) as a function of individual and group covariates 

using the fixed structure of the best model for p and λ parameters for juvenile steelhead, 2004–09.—Continued

Model Number of

parameters AICc ΔAICc Deviance

Fish weight 15 6,490.43 26.06 6,460.36

Tag burden 15 6,492.39 28.02 6,462.31

Spill pattern + Fish weight 19 6,494.81 30.44 6,456.69

Spill pattern + Tag burden 19 6,495.65 31.28 6,457.53

Intercept only 14 6,496.47 32.10 6,468.40

Spill pattern 18 6,500.63 36.26 6,464.52

1

Addition of year to this model decreased AICc by 5.45. 

2

Addition of year to this model decreased AICc by 6.88. 

3

Addition of year to this model decreased AICc by 7.62. 

4

Addition of year to this model decreased AICc by 5.64.

5

Addition of year to this model decreased AICc by 4.40.
56

Table A3. Model selection for fish that passed through the spillway at McNary Dam relating survival (ø) as a function of individual and group covariates 

using the fixed structure of the best model for p and λ parameters for subyearling Chinook salmon, 2004–09.

[The best-fit models are indicated in bold. Temp, temperature; Q, discharge; Passloc, Passage location]

Model Number of

parameters AICc ΔAICc Deviance

Spill pattern + Tag burden + Temp + Spill bay Q + Spill Q + Percent spill 20 8,406.22 0.00 8,366.10

Spill pattern + Tag burden + Temp + Spill bay Q + Total Q 19 8,406.55 0.33 8,368.45

Spill pattern + Tag burden + Temp + Spill bay Q + Spill Q + Percent spill + Passloc 22 8,406.59 0.37 8,362.45

Spill pattern + Tag burden + Temp + Bay type + Total Q 19 8,406.90 0.68 8,368.80

Spill pattern + Fish weight + Temp + Spill bay Q + Total Q 19 8,407.74 1.52 8,369.64

Spill pattern + Tag burden + Temp + Spill bay Q + Total Q + Spill pattern*Total Q 23 8,408.18 1.97 8,362.03

Spill pattern + Tag burden + Temp + Total Q 18 8,408.57 2.35 8,372.47

Spill pattern + Tag burden + Temp + Bay type + Total Q + Total Q*Spill pattern 23 8,408.65 2.44 8,362.50

Tag burden + Temp + Bay type + Total Q 15 8,410.22 4.00 8,380.15

Spill pattern + Temp + Spill bay Q + Total Q 18 8,410.46 4.25 8,374.37

Spill pattern +Temp + Spill bay Q + Total Q + Passloc 20 8,410.51 4.29 8,370.39

Spill pattern + Temp + Bay type + Total Q 18 8,410.64 4.42 8,374.54

Spill pattern + Temp + Spill bay Q + Spill Q + Percent spill 19 8,410.67 4.45 8,372.56

Spill pattern + Tag burden + Temp + Spill bay Q + Total Q + Spill pattern*Spill bay Q 23 8,411.15 4.93 8,365.00

Percent spill + Tag burden + Temp + Spill bay Q + Spill Q 16 8,411.27 5.05 8,379.19

Spill pattern + Temp + Bay type + Total Q + Passloc 20 8,411.31 5.10 8,371.20

Percent spill + Tag burden + Temp + Spill bay Q + Spill Q + Passloc 18 8,411.64 5.42 8,375.54

Tag burden + Temp + Spill bay Q + Total Q + Passloc + Passloc*Spill bay Q 19 8,411.67 5.45 8,373.56

Tag burden + Temp + Spill bay Q + Total Q 15 8,411.74 5.53 8,381.68

Tag burden + Temp + Spill bay Q + Total Q + Passloc 17 8,412.35 6.13 8,378.27

Spill pattern + Temp + Total Q 17 8,412.42 6.21 8,378.34

Percent spill + Tag burden + Temp + Spill bay Q + Spill Q + Passloc + Passloc*Spill bay Q 20 8,412.64 6.43 8,372.53
57

Table A3. Model selection for fish that passed through the spillway at McNary Dam relating survival (ø) as a function of individual and group 

covariates using the fixed structure of the best model for p and λ parameters for subyearling Chinook salmon, 2004–09.—Continued

[Temp, temperature; Q, discharge; Passloc, Passage location]

Model Number of

parameters AICc ΔAICc Deviance

Temp + Bay type + Total Q 14 8,414.26 8.04 8,386.20

Temp + Spill bay Q + Spill Q + Percent spill 15 8,415.37 9.15 8,385.30

Temp + Bay type + Total Q + Passloc 16 8,415.58 9.36 8,383.50

Temp + Spill bay Q + Total Q + Passloc + Passloc*Spill bay Q 18 8,415.63 9.41 8,379.53

Temp + Spill bay Q + Spill Q + Percent spill + Passloc 17 8,415.65 9.43 8,381.56

Temp + Spill bay Q + Total Q 14 8,416.54 10.32 8,388.48

Temp + Spill bay Q + Total Q + Passloc 16 8,417.06 10.84 8,384.98

Total Q + Temp + Tag burden 14 8,417.66 11.44 8,389.60

Spill pattern + Tag burden + Temp 17 8,420.34 14.12 8,386.25

Tag burden + Temp + Spill bay Q + Spill Q + Passloc + Passloc*Spill bay Q 19 8,421.54 15.33 8,383.44

Spill pattern + Temp + Percent spill 17 8,421.60 15.38 8,387.51

Spill pattern + Temp + Spill bay Q + Spill Q 18 8,421.96 15.74 8,385.87

Temp + Spill Q + Percent spill 14 8,422.11 15.89 8,394.05

Temp + Spill Q + Total Q 14 8,422.17 15.96 8,394.11

Temp + Total Q 13 8,422.35 16.13 8,396.30

Spill pattern + Temp + Spill bay Q 17 8,423.03 16.81 8,388.94

Temp + Total Q + Passloc 15 8,423.56 17.34 8,393.49

Spill pattern + Temp 16 8,423.82 17.60 8,391.75

Bay type + Temp + Spill Q 14 8,423.93 17.71 8,395.87

Spill pattern + Spill bay Q + Total Q 17 8,424.25 18.03 8,390.16

Temp + Spill bay Q + Spill Q + Passloc 16 8,424.29 18.07 8,392.22

Temp + Spill bay Q + Spill Q 14 8,424.32 18.10 8,396.26
58

Table A3. Model selection for fish that passed through the spillway at McNary Dam relating survival (ø) as a function of individual and group 

covariates using the fixed structure of the best model for p and λ parameters for subyearling Chinook salmon, 2004–09.—Continued

[Temp, temperature; Q, discharge; Passloc, Passage location]

Model Number of

parameters AICc ΔAICc Deviance

Spill pattern + Total Q 16 8,426.60 20.38 8,394.52

Bay type + Total Q 13 8,428.61 22.40 8,402.56

Spill bay Q + Spill Q + Percent spill + Passloc 16 8,429.64 23.42 8,397.56

Tag burden + Spill bay Q + Total Q 14 8,429.80 23.59 8,401.74

Spill bay Q + Spill Q + Percent spill 14 8,430.01 23.79 8,401.95

Spill bay Q + Total Q 13 8,430.09 23.87 8,404.04

Temp + Spill Q 13 8,431.26 25.04 8,405.21

Temp + Spill Q + Passloc 15 8,432.95 26.74 8,402.89

Spill pattern + Total Q + Spill pattern*Total Q 18 8,432.99 26.77 8,396.89

Tag burden + Total Q 13 8,435.97 29.75 8,409.92

Total Q 12 8,436.17 29.96 8,412.13

Total Q + Passloc 14 8,436.69 30.47 8,408.63

Spill Q + Percent spill 13 8,437.43 31.21 8,411.38

Spill Q + Percent spill + Passloc 15 8,438.13 31.92 8,408.07

Temp + Spill bay Q + Spill Q + Percent spill + Passloc + Passloc*Spill bay Q 19 8,438.92 32.70 8,400.81

Temp + Bay type + Spill bay Q 14 8,440.66 34.45 8,412.61

Temp + Bay type 13 8,441.03 34.82 8,414.98

Tag burden + Temp + Spill bay Q 14 8,446.16 39.94 8,418.10

Temp + Spill bay Q + Percent spill 14 8,449.43 43.21 8,421.37

Temp + Spill bay Q + Percent spill + Passloc 16 8,450.24 44.03 8,418.17

Temp + Spill bay Q 13 8,450.76 44.54 8,424.71

Tag burden + Temp 13 8,450.85 44.64 8,424.80
59

Table A3. Model selection for fish that passed through the spillway at McNary Dam relating survival (ø) as a function of individual and group 

covariates using the fixed structure of the best model for p and λ parameters for subyearling Chinook salmon, 2004–09.—Continued

[Temp, temperature; Q, discharge; Passloc, Passage location]

Model No. 

parameters AICc ΔAICc Deviance

Temp + Spill bay Q + Passloc 15 8,451.26 45.04 8,421.20

Photoperiod + Temp + Percent spill 14 8,452.83 46.61 8,424.77

Photoperiod + Temp 13 8,453.80 47.58 8,427.75

Temp + Percent spill 13 8,454.55 48.33 8,428.50

Temp 12 8,455.36 49.15 8,431.32

Temp + Passloc 14 8,455.49 49.27 8,427.43

Spill pattern + Spill bay Q + Spill Q 17 8,456.18 49.96 8,422.09

Spill pattern + Percent spill 16 8,456.58 50.36 8,424.50

Spill pattern + Spill Q + Spill pattern * Spill Q 20 8,458.25 52.04 8,418.14

Spill bay Q + Spill Q + Passloc 15 8,458.80 52.59 8,428.74

Spill pattern + Spill Q 16 8,458.82 52.60 8,426.75

Bay type + Spill Q 13 8,459.42 53.21 8,433.37

Spill bay Q + Spill Q 13 8,459.75 53.53 8,433.70

Spill pattern + Percent spill + Spill pattern*Percent spill 20 8,459.80 53.58 8,419.68

Photoperiod + Spill Q 13 8,466.25 60.03 8,440.20

Spill Q 12 8,467.98 61.77 8,443.94

Spill Q + Passloc 14 8,468.87 62.65 8,440.81

Spill Q + Passloc + Passloc*Spill Q 16 8,469.13 62.92 8,437.06

Spill pattern 15 8,470.29 64.07 8,440.22

Bay type + Spill bay Q + Bay type*Spill bay Q 14 8,495.62 89.40 8,467.56

Bay type + Spill bay Q 13 8,504.48 98.27 8,478.43

Spill bay Q + Passloc + Passloc*Spill bay Q 16 8,506.11 99.89 8,474.03
60

Table A3. Model selection for fish that passed through the spillway at McNary Dam relating survival (ø) as a function of individual and group 

covariates using the fixed structure of the best model for p and λ parameters for subyearling Chinook salmon, 2004–09.—Continued

[Q, discharge; Passloc, Passage location]

Model Number of

parameters AICc ΔAICc Deviance

Year 15 8,512.36 106.14 8,482.29

Bay type 12 8,515.97 109.75 8,491.93

Photoperiod + Spill bay Q + Photoperiod*Spill bay Q 14 8,519.69 113.47 8,491.63

Photoperiod + Spill bay Q 13 8,529.93 123.71 8,503.87

Photoperiod 12 8,530.45 124.24 8,506.41

Passloc 13 8,534.75 128.53 8,508.70

Passloc + Percent spill 14 8,536.71 130.50 8,508.66

Spill bay Q 12 8,537.19 130.98 8,513.15

Passloc + Percent spill + Passloc*Percent spill 16 8,537.77 131.55 8,505.70

Intercept 11 8,538.06 131.85 8,516.03
61

Table A4. Model selection for fish that passed through the spillway at McNary Dam relating survival (ø) as a function of individual and group 

covariates using the fixed structure of the best model for p and λ parameters for sockeye salmon, 2004–09.

[The best-fit models are indicated in bold]

Model Number of

parameters AICc ΔAICc Deviance

Passage location + Spill discharge + Temperature + Tag burden 13 5,171.48 0.00 5,145.40

Passage location + Total discharge + Temperature + Percent spill + Tag burden 14 5,173.31 1.83 5,145.22

Passage location + Total discharge + Temperature + Tag burden 13 5,174.16 2.68 5,148.08

Passage location + Percent spill + Temperature + Tag burden 14 5,175.61 4.13 5,147.52

Passage location + Spill discharge + Tag burden 12 5,178.99 7.51 5,154.92

Spill discharge + Temperature + Tag burden 11 5,179.32 7.84 5,157.26

Total discharge + Temperature + Percent spill + Tag burden 12 5,181.19 9.71 5,157.12

Passage location + Total discharge + Percent spill + Tag burden 13 5,181.59 10.11 5,155.51

Percent spill + Temperature + Tag burden 11 5,181.61 10.13 5,159.55

Total discharge + Temperature + Tag burden 11 5,,181.85 10.37 5,159.79

Passage location + Percent spill + Tag burden 12 5,182.51 11.03 5,158.44

Passage location + Total discharge + Tag burden 12 5,183.01 11.53 5,158.94

Passage location + Temperature + Spill bay discharge + Tag burden 13 5,184.03 12.56 5,157.95

Spill discharge + Tag burden 10 5,185.95 14.48 5,165.91

Total discharge + Percent spill + Tag burden 11 5,188.68 17.20 5,166.62

Percent spill + Tag burden 10 5,189.62 18.14 5,169.57

Total discharge + Tag burden 10 5,189.70 18.22 5,169.65

Spill pattern + Passage location + Temperature + Tag burden 14 5,191.75 20.28 5,163.66
62

Table A4. Model selection for fish that passed through the spillway at McNary Dam relating survival (ø) as a function of individual and group covariates 

using the fixed structure of the best model for p and λ parameters for sockeye salmon, 2004–09.—Continued

Model Number of

parameters AICc ΔAICc Deviance

Passage location + Spill bay discharge + Tag burden 12 5,193.14 21.66 5,169.07

Spill pattern + Passage location + Spill bay discharge + Tag burden 14 5,194.81 23.33 5,166.72

Spill pattern + + Spill bay discharge + Tag burden 13 5,195.62 24.14 5,169.54

Passage location + Spill discharge + Temperature 12 5,196.39 24.91 5,172.32

Passage location + Total discharge + Temperature 12 5,199.21 27.73 5,175.14

Bay type + Temperature + Spill bay discharge + Tag burden 12 5,201.12 29.64 5,177.05

Spill pattern + Temperature + Tag burden 12 5,201.23 29.75 5,177.16

Temperature + Spill bay discharge + Tag burden 11 5,201.78 30.30 5,179.72

Passage location + Temperature + Tag burden 12 5,202.73 31.26 5,178.67

Passage location + Percent spill + Temperature 12 5,204.49 33.01 5,180.42

Spill discharge + Fish weight 10 5,206.26 34.78 5,186.21

Passage location + Spill discharge 11 5,206.26 34.78 5,184.20

Spill discharge + Temperature 10 5,207.53 36.05 5,187.48

Passage location + Total discharge + Percent spill 12 5,207.76 36.28 5,183.69

Spill pattern + Spill discharge + Temperature 12 5,208.94 37.46 5,184.87

Total discharge + Temperature 10 5,209.46 37.99 5,189.42

Total discharge + Fish weight 10 5,209.64 38.16 5,189.59

Spill pattern + Spill bay discharge + Tag burden 12 5,210.97 39.50 5,186.91
63

Table A4. Model selection for fish that passed through the spillway at McNary Dam relating survival (ø) as a function of individual and group covariates 

using the fixed structure of the best model for p and λ parameters for sockeye salmon, 2004–09.—Continued

Model Number of

parameters AICc ΔAICc Deviance

Passage location + Total discharge 11 5,211.67 40.19 5,189.61

Spill bay discharge + Tag burden 10 5,212.26 40.78 5,192.21

Temperature + Tag burden 10 5,213.08 41.61 5,193.04

Spill pattern + Passage location + Tag burden 13 5,213.84 42.36 5,187.76

Spill pattern + Passage location + Total discharge 13 5,215.50 44.02 5,189.42

Spill pattern + Passage location + Spill bay discharge + Temperature 13 5,216.44 44.97 5,190.36

Spill discharge + Spill bay discharge 10 5,216.70 45.22 5,196.65

Passage location + Percent spill 11 5,216.78 45.30 5,194.72

Percent spill + Temperature 10 5,216.83 45.35 5,196.78

Spill discharge 9 5,217.61 46.13 5,199.57

Passage location + Tag burden 11 5,218.02 46.55 5,195.97

Total discharge + Percent spill 10 5,219.02 47.54 5,198.97

Spill pattern + Tag burden 11 5,221.93 50.45 5,199.87

Total discharge 9 5,222.02 50.55 5,203.99

Tag burden 9 5,227.31 55.84 5,209.27

Percent spill 9 5,229.32 57.84 5,211.28

Spill pattern + Passage location + Temperature 13 5,240.28 68.80 5,214.20

Spill pattern + Passage location + Spill bay discharge 13 5,244.10 72.62 5,218.02
64

Table A4. Model selection for fish that passed through the spillway at McNary Dam relating survival (ø) as a function of individual and group covariates 

using the fixed structure of the best model for p and λ parameters for sockeye salmon, 2004–09.—Continued

Model Number of

parameters AICc ΔAICc Deviance

Passage location + Spill bay discharge 11 5,245.67 74.19 5,223.61

Spill pattern + Temperature 11 5,253.62 82.14 5,231.56

Bay type + Temperature + Spill bay discharge 11 5,258.57 87.09 5,236.51

Temperature + Spill bay discharge 10 5,261.55 90.08 5,241.51

Passage location + Temperature 11 5,268.44 96.96 5,246.38

Spill pattern + Bay type + Spill bay discharge 12 5,278.35 106.87 5,254.28

Fish weight 9 5,278.43 106.95 5,260.39

Spill pattern + Spill bay discharge 11 5,280.20 108.73 5,258.15

Bay type + Spill bay discharge 10 5,284.39 112.91 5,264.34

Bay type + Temperature 10 5,288.46 116.98 5,268.41

Temperature 9 5,288.62 117.14 5,270.58

Spill bay discharge 9 5,289.73 118.25 5,271.69

Spill pattern + Passage location 12 5,292.11 120.63 5,268.04

Passage location 10 5,306.96 135.48 5,286.91

Spill pattern 10 5,310.94 139.46 5,290.89

Bay type 9 5,328.93 157.46 5,310.89

Intercept 8 5,329.44 157.96 5,313.41
65

Appendix B: All Candidate Models Examined for Bypass Survival

Table B1. Model selection for fish that passed through the juvenile bypass system outfall at McNary Dam relating survival (ø) as a function of individual 

and group covariates using the fixed structure of the best model for p and λ parameters for yearling Chinook salmon, 2004–09.

[The best-fit models are indicated in bold]

Model Number of

parameters AICc ΔAICc Deviance

Photoperiod 14 5,553.48 0.00 5,525.39

Intercept 13 5,554.60 1.12 5,528.52

Photoperiod + Spill pattern 19 5,558.99 5.51 5,520.84

Spill pattern 18 5,559.69 6.21 5,523.55
66

Table B2. Model selection for fish that passed through the juvenile bypass system outfall at McNary Dam relating survival (ø) as a function of individual 

and group covariates using the fixed structure of the best model for p and λ parameters for juvenile steelhead, 2004–09.

[The best-fit models are indicated in bold]

Model Number of

parameters AICc ΔAICc Deviance

Temperature + Total discharge 16 2,570.27 0.00 2,538.04

Temperature + Spill discharge 16 2,571.48 1.21 2,539.25

Temperature + Spill pattern + Total discharge 21 2,573.29 3.02 2,530.90

Temperature + Spill pattern 20 2,575.11 4.84 2,534.75

Temperature + Percent spill 16 2,576.55 6.28 2,544.32

Temperature 15 2,577.33 7.06 2,547.13

Spill discharge 15 2,577.35 7.08 2,547.15

Spill pattern 19 2,578.16 7.89 2,539.84

Spill pattern + Total discharge 20 2,578.49 8.22 2,538.14

Total discharge 15 2,578.69 8.42 2,548.49

Percent spill 15 2,580.22 9.95 2,550.02

Tag burden 15 2,581.26 10.99 2,551.05

Intercept 14 2,581.33 11.06 2,553.16
67

Table B3. Model selection for fish that passed through the juvenile bypass system outfall at McNary Dam relating survival (ø) as a function of individual 

and group covariates using the fixed structure of the best model for p and λ parameters for subyearling Chinook salmon, 2004–09. 

[The best-fit models are indicated in bold. Q, discharge]

Model Number of

parameters AICc ΔAICc Deviance

Temperature + Spill pattern + Fish weight + Total Q + Spill pattern*Total Q1 26 4,062.74 0.00 4,010.28

Temperature + Spill pattern + Total Q + Spill pattern*Total Q 25 4,063.24 0.50 4,012.81

Temperature + Spill pattern + Fish weight 20 4,065.41 2.67 4,025.13

Temperature + Spill pattern 19 4,066.09 3.35 4,027.84

Temperature + Fish weight 15 4,067.41 4.67 4,037.25

Temperature 14 4,067.56 4.82 4,039.43

Total Q 14 4,087.62 24.88 4,059.48

Spill pattern + Total Q + Spill pattern*Total Q 24 4,090.14 27.40 4,041.75

Spill Pattern + Total Q 19 4,091.10 28.36 4,052.85

Spill pattern 18 4,097.98 35.24 4,061.76

Percent spill 14 4,105.97 43.23 4,077.83

Turbine discharge 14 4,118.08 55.34 4,089.94

Intercept 13 4,119.27 56.53 4,093.15

1

Addition of year to this model decreased AICc by 2.39.
68

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http://wfrc.usgs.gov/
Adams and others—A Multi-Year Analysis of Spillway Survival for Juvenile Salmonids as a Function of Spill Bay Operations at McNary Dam, Washington and Oregon, 2004–09—Open-File Report 2012-1125