U.S. DEPARTMENT OF COMMERCE

National Oceanic and Atmospheric Administration

National Marine Fisheries Service

NOAA Technical Memorandum NMFS-NWFSC-63

Effects of the Federal

Columbia River Power System

on Salmonid Populations

February 2005
NOAA Technical Memorandum

NMFS Series

The Northwest Fisheries Science Center of the National

Marine Fisheries Service, NOAA, uses the NOAA

Technical Memorandum NMFS series to issue informal scientific and technical publications when complete formal review and editorial processing are not

appropriate or feasible due to time constraints. Documents published in this series may be referenced in the

scientific and technical literature.

The NMFS-NWFSC Technical Memorandum series of

the Northwest Fisheries Science Center continues the

NMFS-F/NWC series established in 1970 by the

Northwest & Alaska Fisheries Science Center, which

has since been split into the Northwest Fisheries

Science Center and the Alaska Fisheries Science

Center. The NMFS-AFSC Technical Memorandum

series is now being used by the Alaska Fisheries

Science Center.

Reference throughout this document to trade names

does not imply endorsement by the National Marine

Fisheries Service, NOAA.

This document should be cited as follows:

Williams, J.G., S.G. Smith, R.W. Zabel, W.D. Muir,

M.D. Scheuerell, B.P. Sandford, D.M. Marsh, R.A.

McNatt, and S. Achord. 2005. Effects of the federal

Columbia River power system on salmonid populations. U.S. Dept. Commer., NOAA Tech. Memo.

NMFS-NWFSC-63, 150 p.
NOAA Technical Memorandum NMFS-NWFSC-63

Effects of the Federal

Columbia River Power System

on Salmonid Populations

John G. Williams, Steven G. Smith, Richard W. Zabel,

William D. Muir, Mark D. Scheuerell, Benjamin P. Sandford,

Douglas M. Marsh, Regan A. McNatt, and Stephen Achord

Northwest Fisheries Science Center

Fish Ecology Division

2725 Montlake Boulevard East

Seattle, Washington 98112

February 2005

U.S. DEPARTMENT OF COMMERCE

Carlos M. Gutierrez, Secretary

National Oceanic and Atmospheric Administration

Vice Admiral Conrad C. Lautenbacher, Jr. USN (Ret), Administrator

National Marine Fisheries Service

William T. Hogarth, Assistant Administrator for Fisheries
Most NOAA Technical Memorandums NMFS-NWFSC

are available online at the Northwest Fisheries Science

Center web site (http://www.nwfsc.noaa.gov)

Copies are also available from:

National Technical Information Service

5285 Port Royal Road

Springfield, VA 22161

phone orders (1-800-553-6847)

e-mail orders (orders@ntis.fedworld.gov)

ii
Table of Contents 

List of Figures...............................................................................................................................................v 

List of Tables ...............................................................................................................................................ix 

Abbreviations and Acronyms ....................................................................................................................xiii 

Executive Summary ....................................................................................................................................xv 

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

Historical Background............................................................................................................................1 

Impacts from Dams ................................................................................................................................3

The PATH Process.................................................................................................................................4 

Stock Evaluations Subsequent to PATH................................................................................................5 

General Analytical Approach.................................................................................................................6 

Adult Return Rate .........................................................................................................................................8 

Rates Based on Nontagged Fish.............................................................................................................8 

Methods ...........................................................................................................................................8 

Results............................................................................................................................................10 

Discussion......................................................................................................................................12 

Rates Based on PIT-Tagged Fish .........................................................................................................14 

Methods .........................................................................................................................................14 

Results............................................................................................................................................16 

Discussion......................................................................................................................................18 

Transportation Evaluations.........................................................................................................................21 

Methods................................................................................................................................................21 

Estimating D (PATH Method).......................................................................................................23 

Estimating D (Non-PATH Method)...............................................................................................24 

Results..................................................................................................................................................25 

Snake River Spring-Summer Chinook Salmon .............................................................................25 

Snake River Fall Chinook Salmon.................................................................................................33 

Upper Columbia River Subyearling Migrants...............................................................................33 

Snake River Steelhead ...................................................................................................................37 

Discussion ............................................................................................................................................42 

Juvenile Migrant Survival...........................................................................................................................46 

Methods................................................................................................................................................46 

Reach Survival Estimates ..............................................................................................................46 

Probability of Detecting PIT-Tagged Fish Versus Length at Tagging ..........................................49 

Results..................................................................................................................................................51 

Snake River Yearling Chinook Salmon Survival ..........................................................................51 

Upper Columbia River Yearling Migrant Survival........................................................................56 

iii
Snake River Subyearling Fall Chinook Salmon Survival..............................................................56 

Upper Columbia River Subyearling Migrant Survival ..................................................................62 

Snake River Steelhead Survival.....................................................................................................62 

Probability of Detecting PIT-Tagged Fish Versus Length at Tagging ..........................................67 

Discussion ............................................................................................................................................69 

Probability of Detecting PIT-Tagged Fish Versus Length at Tagging ..........................................69 

Avian Predation .............................................................................................................................70

Juvenile Survival, Travel Time, and River Environment ...........................................................................72 

Methods................................................................................................................................................72 

Snake River Spring Migrants.........................................................................................................72 

Run-of-River Subyearling Chinook Salmon from McNary Dam..................................................76 

Results..................................................................................................................................................77 

Snake River Yearling Chinook Salmon.........................................................................................77 

Snake River Steelhead ...................................................................................................................86 

Run-of-River Subyearling Chinook Salmon from McNary Dam..................................................93 

Discussion ..........................................................................................................................................100 

Snake River Spring Migrants.......................................................................................................101 

Run-of-River Subyearling Chinook Salmon from McNary Dam................................................104 

Latent Mortality Associated with the FCRPS...........................................................................................106 

Definitions..........................................................................................................................................106 

Efforts to Quantify the Magnitude of FCRPS Latent Mortality........................................................108 

Upstream/Downstream Comparisons...........................................................................................109 

Multiply Bypassed Fish ...............................................................................................................111 

Disrupted Timing.........................................................................................................................115 

Latent Mortality of Transported Fish...........................................................................................115 

Discussion ..........................................................................................................................................117 

Selective Mortality....................................................................................................................................119 

Discussion.................................................................................................................................................123 

Large-Scale Processes........................................................................................................................123 

Diversity .............................................................................................................................................125 

Hydropower System and Harvest.......................................................................................................126 

Summary and Conclusions .......................................................................................................................128 

References.................................................................................................................................................131 

Appendix A...............................................................................................................................................143 

Submission by Idaho Department of Fish and Game on Upstream/Downstream Comparisons........143 

NOAA Fisheries Service’s Comment on IDFG’s Upstream/Downstream Comparison ....................146 

Appendix B...............................................................................................................................................149 

Time-Series Model for Forecasting SARs from Coastal Ocean Upwelling.......................................149 

Ocean-Climate Data ...........................................................................................................................150 

iv
List of Figures 

Figure 1. The Columbia River basin, with major hydroelectric generating dams and, in bold, 

PIT-tag detection sites at traps, dams, and the PIT-trawl. .....................................................................2 

Figure 2. Estimated SAR for wild Snake River spring-summer Chinook salmon.....................................10 

Figure 3. Ratio of the median adult fish count (2001–2003) for wild steelhead at Bonneville Dam and 

hatchery and wild spring Chinook salmon at Priest Rapids Dam divided by the median count 

at each respective dam for steelhead (1993–1000) and Chinook salmon (1991–2000). .....................11 

Figure 4. Estimated SAR of wild Snake River steelhead. .........................................................................12 

Figure 5. The ln(BYN/BYN–1) for the composite wild spring-summer Chinook salmon population 

in the Snake River basin above the upper Snake River dams..............................................................14 

Figure 6. Estimated SAR for wild and hatchery Snake River spring-summer Chinook salmon, based 

on analyses of adult returns from the general untagged population and from SAR for PIT-tagged 

fish weighted by the estimated migration distribution of the untagged juvenile population. .............16 

Figure 7. Estimated SAR for wild and hatchery Snake River steelhead based on analyses of fish 

PIT tagged as juveniles or the overall unmarked population...............................................................17 

Figure 8. Three pathways that juvenile salmon travel on their way downstream through the mainstem Snake 

and Columbia rivers.............................................................................................................................22 

Figure 9. Temporal change in SAR of wild Snake River spring-summer Chinook salmon 

PIT tagged at Lower Granite Dam, 1995 and 1998. ..........................................................................29 

Figure 10. Temporal change in SAR of wild Snake River spring-summer Chinook salmon 

PIT tagged at Lower Granite Dam, 1999 and 2000.............................................................................30 

Figure 11. Temporal change in SAR of hatchery Snake River spring-summer Chinook salmon 

PIT tagged at Lower Granite Dam, 1995 and 1998.............................................................................31 

Figure 12. Temporal change in SAR of hatchery Snake River spring-summer Chinook salmon 

PIT tagged at Lower Granite Dam, 1999.............................................................................................32 

Figure 13. SAR of PIT-tagged, hatchery Snake River fall Chinook salmon released above 

Lower Granite Dam and bypassed or transported from Lower Granite, Little Goose, 

Lower Monumental, or McNary dams prior to 1 September 1995–2000, with ratios of 

transported:bypassed fish and 95% confidence bounds. .....................................................................34 

Figure 14. SAR of PIT-tagged, hatchery Snake River fall Chinook salmon released above 

Lower Granite Dam and bypassed or transported from Lower Granite, Little Goose, 

Lower Monumental, or McNary dams on 1 September or later, 1995–2000, with ratios of 

transported:bypassed fish and 95% confidence bounds. .....................................................................34 

Figure 15. Relative recovery rates of coded-wire-tagged adult summer-fall Chinook salmon recovered 

from fisheries or at hatcheries from subyearling fish tagged as juveniles in 1995 at McNary Dam

and either transported to below Bonneville Dam or released into the tailrace of McNary Dam.........35 

v
Figure 16. Relative recovery rates of coded-wire-tagged adult summer-fall Chinook salmon recovered 

in fisheries or at hatcheries from subyearling fish tagged as juveniles at McNary Dam in 1996 

and either transported to below Bonneville Dam or released into the tailrace of McNary Dam.........35 

Figure 17. Relative recovery rates based on SAR for combined weekly releases of transported 

and in-river subyearling Chinook salmon PIT tagged and released at McNary Dam in 2001, 

plotted with weekly average water temperature and flow. ..................................................................36 

Figure 18. Relative recovery rates based on SAR for combined weekly releases of transported 

and in-river subyearling Chinook salmon PIT tagged and released at McNary Dam in 2002, 

plotted with the weekly average water temperature and flow. ............................................................36 

Figure 19. Temporal change in SAR of hatchery Snake River steelhead PIT tagged at 

Lower Granite Dam. ............................................................................................................................40 

Figure 20. Temporal change in SAR of wild Snake River steelhead PIT tagged at Lower Granite Dam, 1999 

and 2000. .............................................................................................................................................41 

Figure 21. Estimated survival, with standard errors, from release at Snake River basin hatcheries 

to Lower Granite Dam tailrace, 1993–2003, versus distance to Lower Granite Dam.........................53 

Figure 22. Median travel times and migration rates for PIT-tagged hatchery fall 

Chinook salmon, 1995–2001...............................................................................................................59 

Figure 23. Estimated survival probabilities from point of release in the Snake River to the tailrace 

of Lower Granite Dam for PIT-tagged hatchery subyearling fall Chinook salmon, 1995–2001. .......60 

Figure 24. Estimated survival probabilities to the tailrace of Lower Monumental Dam for PIT-tagged 

hatchery subyearling fall Chinook salmon leaving Lower Granite Dam, by week, 1995–2001.........61 

Figure 25. Relationships between detection probability and fish length for Snake River spring-summer 

Chinook salmon released at Lower Granite Dam................................................................................68 

Figure 26. Relationships between detection probability and fish length for Snake River steelhead 

released at Lower Granite Dam. ..........................................................................................................69 

Figure 27. Comparison of survival estimates derived assuming mean detection probabilities and those 

using length-related detection probabilities.........................................................................................70 

Figure 28. Estimated annual average travel times for yearling Chinook salmon through the section 

of the lower Snake and Columbia rivers now inundated by mainstem hydropower dams..................78 

Figure 29. Median travel time and flow exposure index for PIT-tagged Snake River yearling 

Chinook salmon groups, 1995–2003. ...................................................................................................80 

Figure 30. Median travel time and water travel time for PIT-tagged Snake River yearling 

Chinook salmon groups, 1995–2003. ...................................................................................................81 

Figure 31. Partial fits for generalized additive model of median travel time from 

Lower Granite Dam to McNary Dam, with pointwise 95% confidence intervals, 

yearling Chinook salmon, 1995–2003.................................................................................................82 

Figure 32. Estimated survival from Lower Granite Dam to McNary Dam for PIT-tagged 

Snake River yearling Chinook salmon, plotted against water travel time index, 1995–2003.............82 

Figure 33. Estimated survival from Lower Granite Dam to McNary Dam versus 

water travel time for PIT-tagged yearling Snake River Chinook salmon, 1995–2003. ......................83 

Figure 34. Estimated mortality per day versus water travel time index for PIT-tagged 

yearling Snake River Chinook salmon, 1995–2003. ...........................................................................83 

vi
Figure 35. Best-fit sigmoid curve and piecewise linear regression model for estimated survival 

from Lower Granite Dam to McNary Dam for PIT-tagged, yearling Snake River 

Chinook salmon versus flow exposure index, 1995–2003..................................................................84 

Figure 36. Partial fits for generalized additive model for estimated survival from Lower Granite Dam 

to McNary Dam, with pointwise 95% confidence limits, yearling Chinook salmon, 1995–2003. .....85 

Figure 37. Partial fits for generalized additive model for estimated survival from Lower Granite Dam

to McNary Dam, with pointwise 95% confidence intervals, yearling Chinook salmon, 1995–2003..86 

Figure 38. Observed survival estimates for Snake River yearling Chinook salmon between 

Lower Granite Dam and McNary Dam in 2001 plotted against fitted values from selected 

multiple-regression model including functions for water travel time and temperature.......................87 

Figure 39. Median travel time and water travel time index for groups of PIT-tagged 

Snake River steelhead, 1995–2003......................................................................................................88 

Figure 40. Partial fits for generalized additive model of steelhead median travel time from 

Lower Granite to McNary dams, with pointwise 95% confidence intervals, 1995–2003...................89 

Figure 41. Estimated survival from Lower Granite Dam to McNary Dam for PIT-tagged 

Snake River steelhead, plotted against water travel time index, 1995–2003.......................................90 

Figure 42. Estimated survival from Lower Granite Dam to McNary Dam versus water travel time 

for PIT-tagged Snake River steelhead, 1995–2003. ............................................................................90 

Figure 43. Estimated mortality per day versus water travel time for PIT-tagged 

Snake River steelhead, 1995–2003......................................................................................................91 

Figure 44. Best-fit sigmoid curve and piecewise linear regression model for estimated survival from 

Lower Granite Dam to McNary Dam for PIT-tagged Snake river yearling Chinook salmon 

versus flow exposure index, 1995–2003. ............................................................................................92 

Figure 45. Partial fits for generalized additive model for estimated steelhead survival from 

Lower Granite Dam to McNary Dam, with pointwise 95% confidence limits, 1995–2003l. .............92 

Figure 46. River conditions at McNary Dam, 19 June–31 August, 1999–2002........................................94 

Figure 47. River conditions at John Day Dam, 19 June–31 August 1999–2002.......................................95 

Figure 48. Median travel time between McNary and John Day dams plotted against 

various river condition indices for run-of-river subyearling Chinook salmon released 

in the McNary Dam tailrace, 1999–2002. ...........................................................................................99 

Figure 49. Estimated survival between McNary Dam tailrace and John Day Dam tailrace plotted 

against various river condition indices for run-of-river subyearling Chinook salmon 

released in tailrace of McNary Dam, 1999, 2001, and 2002. ............................................................100 

Figure 50. Estimated survival from Lower Granite Dam to McNary Dam for PIT-tagged 

Snake River yearling Chinook salmon, 2001, plotted with flow exposure, 

water travel time index, and temperature exposure against data at Lower Granite Dam. .................102 

Figure 51. Survival and mortality affecting Snake River anadromous salmonids migrating 

in-river at various life stages. ............................................................................................................107 

Figure 52. Five-day running average of the number of smolts arriving at Bonneville Dam 

in 2000 for fish from the John Day River migrating in-river, and for two fish groups 

transported from Lower Granite Dam. ..............................................................................................110 

vii
Figure 53. Relative adult return rates of hatchery and wild spring-summer Chinook salmon 

marked above Lower Granite Dam and detected between 0 and 4 times during their 

migration through Lower Granite, Little Goose, Lower Monumental, and McNary dams. .............112 

Figure 54. Relative return rates of hatchery and wild steelhead marked above Lower Granite Dam

 and detected between 0 and 4 times during their migration through Lower Granite, 

Little Goose, Lower Monumental, and McNary dams. .....................................................................113 

Figure 55. Relative adult return rates of hatchery and wild spring-summer Chinook salmon 

marked above Lower Granite Dam and detected only at Lower Granite, Little Goose, 

Lower Monumental, or McNary dams. .............................................................................................114 

Figure 56. Relative adult return rates of hatchery and wild steelhead marked above 

0Lower Granite Dam and detected only at Lower Granite, Little Goose, 

Lower Monumental, or McNary dams. ............................................................................................116 

Figure 57. Relative return rates of multiply bypassed fish compared to nondetected fish under a 

range of values for the slope parameter of the length-selective guidance relationship 

and the length-based selection coefficient.........................................................................................117 

Figure 58. Selection coefficients by year for length at release and release date......................................120 

Figure 59. Time series of the observed SAR survival for wild Snake River spring-summer 

Chinook salmon from 1965–2002 compared to the forecasts from a time series model 

based on the coastal ocean upwelling index at 45°N 125°W. ...........................................................124 

Figure 60. Normalized time series of the Pacific Decadal Oscillation and Columbia River flow at 

The Dalles Dam. ................................................................................................................................124 

Figure 61. Estimated SAR of spring-summer Chinook salmon to the upper dam on the Snake River 

and estimated annual harvest rate. ....................................................................................................127 

Figure A-1. Comparison of Snake and Yakima rivers wild/natural stream type 

Chinook salmon SAR. .......................................................................................................................144 

viii
List of Tables 

Table 1. Annual numbers of fish PIT tagged and released in different areas of the Columbia River basin.7 

Table 2. Annual SAR for spring-summer Chinook salmon PIT tagged above Lower Granite Dam 

with detection histories of groups that represented the unmarked population.....................................17 

Table 3. Bootstrapped confidence intervals around annual SAR for Chinook salmon PIT tagged above 

Lower Granite Dam with detection histories of groups that represented the unmarked population....18 

Table 4. Annual SAR for steelhead PIT tagged above Lower Granite Dam with detection histories of 

groups that represented the unmarked population. ..............................................................................19 

Table 5. Bootstrap confidence intervals around annual SAR for steelhead PIT tagged above 

Lower Granite Dam with detection histories of groups that represented the unmarked population....19 

Table 6. Estimated combined annual percentage of the nontagged yearling Chinook salmon population 

transported from Lower Granite, Little Goose, Lower Monumental, and McNary dams. ..................25 

Table 7. Annual SAR for spring-summer Chinook salmon PIT tagged at Lower Granite Dam for 

transportation studies between 1995 and 2000, compared to annual SAR of fish not detected 

downstream after release at Lower Granite Dam. ...............................................................................26 

Table 8. Confidence intervals around annual SAR for spring-summer Chinook salmon PIT tagged 

at Lower Granite Dam for transportation studies between 1995 and 2000, compared 

to intervals around annual SAR of nondetected fish. ..........................................................................26 

Table 9. Annual estimates of differential post-Bonneville Dam survival for wild Snake River 

spring-summer Chinook salmon transported from various dams 

and for weighted average from all sites...............................................................................................28 

Table 10. Annual estimates of differential post-Bonneville Dam survival for hatchery Snake River 

spring-summer Chinook salmon transported from various dams

and for weighted average from all sites...............................................................................................28 

Table 11. Conversion rates for adult wild spring-summer Chinook salmon PIT tagged as juveniles 

at Lower Granite Dam in 2000 and 2001 and either returned to the river or transported. ..................32 

Table 12. Estimated combined annual percentage of the nontagged steelhead population 

transported from Lower Granite, Little Goose, Lower Monumental, and McNary dams. ..................37 

Table 13. Annual SAR for steelhead PIT tagged at Lower Granite Dam for transportation studies 

between 1998 and 2000, compared to annual SAR of fish not detected downstream 

after release at Lower Granite Dam. ...................................................................................................38 

Table 14. Confidence intervals around annual SAR for steelhead PIT tagged at Lower Granite Dam 

for transportation studies between 1998 and 2000, compared to intervals around 

annual SAR of nondetected fish. .........................................................................................................38 

Table 15. Annual estimates of differential post-Bonneville Dam survival for Snake River 

wild steelhead transported from various dams and for weighted average from all sites .....................39 

ix
Table 16. Annual estimates of differential post-Bonneville survival for Snake River hatchery 

steelhead transported from various dams and for weighted average from all sites. ...........................39 

Table 17. Conversion rates for wild adult steelhead PIT tagged as juveniles at Lower Granite Dam 

in 2000 and 2001 and either returned to the river or transported. .......................................................42 

Table 18. Estimated survival for yearling Chinook salmon from Snake River basin hatcheries 

to the tailrace of Lower Granite Dam, 1993–2003. .............................................................................52 

Table 19. Estimated survival for yearling Chinook salmon from the Salmon River trap 

to Lower Granite Dam tailrace, 1993–2003.. ......................................................................................54 

Table 20. Estimated survival for yearling Chinook salmon from the Snake River trap 

to Lower Granite Dam tailrace, 1995–2003. .......................................................................................54 

Table 21. Estimated survival from Lower Granite Dam tailrace to McNary Dam tailrace 

and from McNary Dam tailrace to Bonneville Dam tailrace for hatchery 

and wild yearling Chinook salmon, 1998–2003..................................................................................55 

Table 22. Hydropower system survival estimates derived by combining empirical survival estimates 

from various reaches for Snake River yearling Chinook salmon, 1997–2003. ...................................55 

Table 23. Survival estimates for upper Columbia River yearling Chinook salmon.. ................................57 

Table 24. Survival estimates for PIT-tagged yearling Yakima River Chinook salmon.............................58 

Table 25. Survival estimates for PIT-tagged upper Columbia River subyearling Chinook salmon 

and percentage recovery of PIT-tagged fish on bird islands. ..............................................................63 

Table 26. Survival estimates for PIT-tagged Yakima River fall Chinook salmon and percentage 

recovery of PIT-tagged fish on bird islands.. ......................................................................................63 

Table 27. Estimated survival for hatchery and wild steelhead from the Salmon River trap 

to Lower Granite Dam tailrace, 1993–2003. ......................................................................................64 

Table 28. Estimated survival for hatchery and wild steelhead from the Snake River trap 

to Lower Granite Dam tailrace, 1995–2003. .......................................................................................64 

Table 29. Estimated survival from Lower Granite Dam tailrace to McNary Dam tailrace and from 

McNary Dam tailrace to Bonneville Dam tailrace for hatchery and wild steelhead, 1998–2003. ......65 

Table 30. Hydropower system survival estimates derived by combining empirical survival estimates 

from various reaches for Snake River steelhead, 1997–2003..............................................................66 

Table 31. Survival estimates for upper Columbia and Yakima rivers steelhead. ......................................66 

Table 32. Survival estimates for sockeye salmon smolts PIT tagged and released upstream 

from Lower Granite Dam.. ..................................................................................................................67 

Table 33. Recovery percentages of PIT-tagged steelhead recovered from McNary pool bird colonies....71 

Table 34. Numbers of run-of-river subyearling Chinook salmon collected and tagged at 

McNary Dam and released in the McNary Dam tailrace, 1999–2002.................................................76 

Table 35. Median travel time of PIT-tagged yearling Chinook salmon between 

Lower Granite Dam and Bonneville Dam, 1995–2003. ......................................................................78 

Table 36. Summary of multiple-regression model for estimated survival of yearling 

Chinook salmon between tailraces of Lower Granite and McNary dams, 1995–2003. ......................87 

Table 37. Median travel time of PIT-tagged steelhead between Lower Granite Dam and 

Bonneville Dam, 1995–2003...............................................................................................................87 

x
Table 38. Summary of multiple-regression model for estimated survival of steelhead 

between tailraces of Lower Granite and McNary dams, 1995–2003...................................................93 

Table 39. Survival estimates and median travel times from McNary Dam to John Day Dam, 

and river condition indices for weekly groups of run-of-river subyearling 

Chinook salmon released in the tailrace of McNary Dam...................................................................96 

Table 40. Product-moment correlation coefficients among independent variables 

for groups of subyearling Chinook salmon released in McNary Dam tailrace, 1999–2002................97 

Table 41. Product-moment correlations between river environment exposure indices 

and median travel time and estimated survival between McNary Dam tailrace 

and John Day Dam tailrace for run-of-river subyearling Chinook salmon, 1999–2002. ....................98 

Table 42. Sample size and mean length at tagging for the total tagged population 

and returning adults of Snake River spring-summer Chinook salmon and 

steelhead passive PIT taggedat Lower Granite Dam, 1995–2000. ....................................................121 

Table 43. Sample size, mean release day of the year for the total tagged population 

and returning adults of Snake River spring-summer Chinook salmon 

and steelhead PIT tagged at Lower Granite Dam. .............................................................................122

xi
xii
Abbreviations and Acronyms 

BPA Bonneville Power Administration 

CJS Cormack-Jolly-Seber 

COE [U.S. Army] Corps of Engineers 

CSS [Multi-State] Comparative Survival Study 

CWT coded-wire tag 

DART data access in real time 

ESA [U.S.] Endangered Species Act 

ESU evolutionarily significant unit 

FCRPS Federal Columbia River Power System

gam generalized additive model 

IDFG Idaho Department of Fish and Game

kcfs thousand cubic feet per second 

LRT likelihood ratio test 

PATH Plan for Analyzing and Testing Hypotheses 

PIT passive integrated transponder 

RKm river kilometer 

SAR smolt-to-adult return rate 

SIMPAS simulated passage model 

SR single-release [model] 

SURPH survival with proportional hazards 

WTT water travel time 

xiii
xiv
Executive Summary 

This technical memorandum summarizes past efforts to determine direct and indirect 

effects of the Federal Columbia River Power System (FCRPS) on Columbia River salmon stocks. 

 We based analyses and derived results from juvenile and adult studies through the end of 2003 

that address five major areas: 

1) adult return rates, 

2) transportation evaluations, 

3) juvenile migrant survival, 

4) links between juvenile survival, travel time, and the river environment, and 

5) latent mortality associated with the FCRPS. 

(For most past and present methods used to develop linkages between the FCRPS and salmon 

survival, this report refers readers to references containing the details.) 

Our ability to discern FCRPS-related effects relates directly to the quality of available data, 

which is quite variable. We can precisely estimate survival of downstream migrants from release 

points to the uppermost dams and through the hydropower system, and we have begun to develop 

similar capabilities for upstream migrants. For several evolutionarily significant units (ESUs), we 

have developed a measure of the relative performance of transported fish compared to in-river 

migrants, but we have limited precision of sample sizes of adult returns. Unfortunately, we have 

limited ability to quantify the magnitude of hydropower system–related latent mortality. However, 

we believe a major component of latent mortality is the disruption of timing of transported fish and 

in-river migrants, and we are beginning to discern some migrational timing effects. 

Areas of additional or continued study that would help resolve some uncertainties about 

effects of the FCRPS include: 

• migrational timing and its effect on smolt-to-adult return rate (SAR) for both transported 

and in-river migrants, 

• selectivity of bypass systems, for fish size as well as fish health, and 

• mechanisms leading toward latent mortality. 

Some of the data limitations noted above arise from the fact that adult return rates provide 

the best indicator of population performance, but this measure reflects the effects of several 

confounding factors, of which the FCRPS is but one. Clearly, ocean conditions have the dominant 

influence on adult return rates, overriding variability associated with the hydropower system. 

Return rates have increased by an order of magnitude since the upturn in ocean conditions that 

began in 1999, while survival through the hydropower system has remained relatively constant. 

Improvements in SAR, however, do not preclude the existence of hydropower system-related 

latent mortality or an interaction between latent mortality and ocean condition. 

xv
Transportation is not a panacea for negative effects of dams on fish stocks. When 

comparing annual indices of transported, wild, yearling Snake River spring-summer Chinook 

salmon (Oncorhynchus tshawytscha) and hatchery fall Chinook salmon versus in-river fish, in 

many cases transportation appeared to confer little benefit or harm. However, under certain times 

of the year and under low-flow conditions (particularly in 2001), transportation appeared to 

increase return rates of some segments of the yearling migrant populations. Further, the benefits 

of transportation decreased at transportation sites closer to Bonneville Dam. Thus future 

operations should focus on optimizing adult return rates, independent of the transportation process 

currently in operation. Strategies such as “spread the risk” and promotion of diversity suggest we 

should allow more fish to migrate in the river whenever it appears migration might lead to 

reasonable return rates compared to the alternatives. At times transportation may provide the best 

alternative. We note that transportation apparently has not provided any benefit to Snake River 

sockeye salmon. 

Under most conditions, we have estimated relatively high direct (within the hydropower 

system) survival of yearling juvenile migrants, and substantial improvements in downstream

survival appear unlikely, particularly improvements related to passage through dams. Summer 

subyearling migrants suffer greater mortality in reservoirs than do spring migrants, and 

improvements in river conditions may confer considerably improved survival. In 2001 the low 

survival experienced by spring migrants and generally lower survival of summer migrants likely 

resulted from conditions in the reservoirs, potentially low flow, and possibly a lack of spill. 

Therefore, we may face diminishing returns in terms of improving survival via technological fixes 

to dams. Efforts to reduce mortality in the reservoirs, understand how to reduce latent or indirect 

mortality (mortality expressed downstream of the hydropower system that results from

hydropower system passage), and maintain diversity by improving habitat conditions in estuary 

and freshwater spawning and rearing habitats will likely have the strongest influence on overall 

stock viability. 

For Snake River spring-summer Chinook salmon, we found that increased flow had a 

benefit to juvenile migrant survival, although the effect was small relative to the detriment that 

occurs when water temperatures become too high. For steelhead, the benefit of increased flow was 

apparently greater. However, in our multiple-regression model the benefit is offset somewhat by 

a countering trend of decreased steelhead survival as the season progresses, possibly related to 

their increased propensity to residualize as water temperature increased. For yearling Chinook 

salmon, temperatures above 13°C, typically reached in late May, appeared detrimental to survival. 

 For both species, we consistently observed a strong relationship between flow and travel time. 

Thus increased flow may benefit spring migrants by moving them out of the lower Snake River 

before temperatures become too high. 

Flow clearly can affect the timing of smolt migration to the estuary, which appears to 

greatly influence their SAR. Delayed migration, which reduces available energy reserves in 

smolts, could affect survival. Low-flow years exacerbate the problem, both within the 

hydro-power system and in freshwater areas upstream that fish negotiate before arriving at the first 

dam.

xvi
Introduction 

The construction and operation of the 31 Federal Columbia River Power System (FCRPS) 

dams have contributed to the decline of anadromous salmon populations in the Columbia River 

basin and continue to affect them. (See Figure 1 for major dams in the Columbia River basin—not 

all are FCRPS dams.) While the dams provide about 60% of the Pacific Northwest region’s 

hydroelectric generating capacity, supply irrigation water to more than a million acres of land, and 

store water to enhance flood control, they also block access to historical salmon spawning areas or 

alter their migratory corridor, increasing mortality both directly and indirectly. In addition to the 

FCRPS, human impacts from construction of hundreds of other dams, agriculture, commercial 

fishing, mining, and dredging all have affected various Columbia River basin anadromous salmon 

populations. Thus ascribing effects of the FCRPS is complicated. 

Since completion of the FCRPS dams, many physical and operational changes occurred in 

an attempt to minimize impacts on anadromous salmon populations. Research shows that direct 

survival of salmonid migrants increased as the result of these changes. Thus the majority of 

deleterious effects to salmon from having passed through the FCRPS dams are expressed 

indirectly, but to an unknown degree, downstream of the hydropower system. Determining the 

extent to which direct and indirect effects of the hydropower system negatively affect salmon 

populations, in the context of all other factors, is critical to defining additional measures needed 

within the FCRPS to ensure salmon survival. Although we can measure annually direct survival 

and travel time of fish, inferences regarding delayed mortality often rely on long-term trends in 

adult fish return rates, data which are inherently variable. Thus estimating the extent to which the 

FCRPS and all other human activities affect salmon populations requires understanding direct and 

indirect effects in concert with natural variability in salmon populations. Our knowledge of 

natural salmon variability through time is lacking, but the historical record provides some

indication of its magnitude. 

Historical Background 

The abundance of all animal populations fluctuates over time. For salmon, we most 

often tend to associate changes in populations to human activities; in many cases, rightly so. 

However, we generally lack knowledge of natural population fluctuations independent of human 

interactions. Despite a long Native American oral history in the Pacific Northwest, little hard 

information exists about the size and extent of historical salmon population fluctuations. 

Chapman (1986) estimated that peak adult salmon returns to the Columbia River basin in the 

1800s ranged from 7.4 million to 8.8 million fish. Of these, Chapman estimated that spring and 

summer Chinook salmon (Oncorhynchus tshawytscha) numbered 500,000–590,000 and 

2 million–2.5 million, respectively. However, at the end of the last ice age (approximately 

15,000 years before present), glaciers covered most of the upper Columbia River basin and much

1 
Figure 1. The Columbia River basin, with major hydroelectric generating dams and, in bold, PIT-tag 

detection sites at traps, dams, and the PIT-trawl. 

of the Salmon River drainage (McPhail and Lindsey 1986). Thus these salmon populations are 

fairly recent in origin. Chatters et al. (1995) concluded that over the past 7,000 years, salmon 

production in the Columbia Basin varied tremendously with changes in climate. They speculated 

that average salmon populations were much lower approximately 3,500 years ago compared to 

recent centuries, but higher 1,200 years ago. These speculations comport with recent findings of 

Finney et al. (2002), which showed that Alaska sockeye salmon populations also varied greatly 

over the past 2,000 years. 

Anecdotal evidence indicates that natural variations in Columbia River salmon abundance 

also occurred over shorter time spans. Chance (1973) quotes from a number of early diaries, 

which reported that in 1811 and again in the late 1820s salmon populations from the middle 

Columbia River (between the confluence of the Snake River and Kettle Falls) were so low that 

settlers and Native Americans relied on horse flesh for survival. Although Snake River basin 

salmon populations were probably also low at these times, based on catch records for the 

Columbia River basin as a whole, all stocks rebounded to high levels near the end of the century. 

At that time, Columbia River salmon populations began to decline dramatically as a result of 

overfishing. Beginning in the early twentieth century, the declines were exacerbated by 

2 
environmental degradation due to mining, grazing, logging, water withdrawals for irrigation, and 

dams constructed on major tributaries for power production and water storage. Although stocks 

decreased, a sign of run size variability still existed. The upriver run (above Bonneville Dam) of 

spring Chinook salmon averaged 119,000 fish from 1940 to 1949, with an average harvest rate of 

60%; increased to 208,000 fish from 1950 to 1959, with an average harvest rate of 60%; and 

decreased to 171,000 from 1960 to 1969, with an average harvest rate of 39% (WDFW and ODFW

2002). 

Impacts from Dams 

Concerns about the potential impacts of the FCRPS on anadromous fish were raised prior 

to the construction of Bonneville Dam (Griffin 1935). In fact, coincident with the dam’s 

completion, studies began in 1939 to estimate survival of juvenile salmon passing through turbines 

and spill to determine the dam’s effect on juvenile salmon (Holmes unpubl. report). Results from

these studies and those by Schoeneman et al. (1961) at McNary Dam in the mid-1950s led to 

concern about the probable impact of dams on juveniles. As five additional dams were scheduled 

for construction on the mainstem Columbia and Snake rivers, a Fish Passage Program within the 

Bureau of Commercial Fisheries (now NOAA Fisheries Service) began to study the adaptability 

of salmon to new environments created by dams, effects of impoundments on fish migration, 

effects of dam passage on migrants, and ways to mitigate these effects. 

Raymond (1979) provided the initial summary of changes in survival and travel time for 

yearling migrants that occurred during and after dam completion. In short, the 1966–1968 

average annual survival of wild yearling Chinook salmon outmigrants from a trap on the Salmon 

River to Ice Harbor Dam averaged approximately 89% (Lower Monumental, Little Goose, and 

Lower Granite dams were not yet completed). Prior to the completion of John Day Dam, the 1966 

and 1967 survival from Ice Harbor to The Dalles Dam averaged 64%. Combining these two 

estimates with an estimated survival between The Dalles and Bonneville dams provided overall 

juvenile Chinook salmon and steelhead survival estimates ranging between approxi-mately 40% 

and 55% through the stretch of river from the conjunction of the Clearwater and Snake rivers to 

below Bonneville Dam but with only four dams in place (Williams et al. 2001). After completion 

of the system (with eight dams in place), survival estimates for yearling Chinook salmon and 

steelhead decreased to mean values of approximately 16% and 11% (1975–1980), respectively 

(but near 0 for both in the very low-flow year of 1977) (Williams et al. 2001). 

Reservoirs behind dams increased travel time for juvenile migrants. Annual travel time 

estimates for fish were 10 days (high flow) to 20 days (low flow) to migrate through the 

hydropower system with four mainstem dams in place (expansion of data from Raymond 1979), 

but after completion of all eight dams, annual travel time estimates ranged from 15 days (high flow) 

to 40 days (low flow). 

Concurrent with research documenting direct effects of the dams on fish, other researchers 

worked on means to mitigate them. This research led the U.S. Army Corps of Engineers (COE) to 

construct juvenile bypass systems at dams, modify spillways, and implement a transportation 

program to collect fish at upstream dams and barge them to a release site below Bonneville Dam.

Despite these efforts, by the early to mid-1990s, stocks had not recovered. As a consequence, 12 

3
of 16 Columbia River basin evolutionarily significant units (ESU) (Waples 1991) were listed as 

threatened or endangered under the Endangered Species Act (ESA) (NMFS 1992).

The PATH Process 

To provide information needed to write biological opinions (BiOp) associated with the 

stock listings and to develop estimates of FCRPS impacts, in 1995 the National Marine Fisheries 

Service (NMFS or NOAA Fisheries Service) created the Plan for Analyzing and Testing 

Hypotheses (PATH). A summary of the PATH process, based on a paper by Marmorek and Peters 

(2001), follows. 

A group of approximately 30 scientists worked for nearly 5 years to develop analyses to 

explain the impact of the FCRPS on anadromous fish stocks above Bonneville Dam. PATH 

scientists identified two key uncertainties deemed to most strongly affect survival and recovery 

potentials of Snake River spring-summer and fall Chinook salmon: extra mortality of in-river 

migrants and the relative post–Bonneville Dam survival of transported fish compared to 

post–Bonneville Dam survival of in-river migrants (designated as D). 

Extra mortality was a construct of the models used by PATH, a parameter used to account 

for any mortality occurring outside the juvenile migration corridor not accounted for by the other 

terms used in the PATH life cycle models such as productivity and carrying capacity, mortality in 

reservoirs and at dams, and estuarine and ocean mortality affecting all salmonid populations. The 

existence of extra mortality required the presumption that changes in ocean conditions had no 

systematic differences between impacts on upstream and downstream Columbia River stocks. 

No direct measurements of extra mortality were possible; it was only inferred from other measured 

quantities. Because the observed historical patterns in extra mortality were linked with several 

possible causes, PATH formulated three alternative hypotheses concerning extra mortality and the 

possibility of FCRPS actions to decrease it: 

1. Dam removal—extra mortality resulted from adverse effects to smolts from migrating 

through the eight mainstem FCRPS dams. Removal of dams in the Snake River would 

eliminate extra mortality. 

2. Ocean regime shift—extra mortality followed a 60-year cycle related to long-term cycles 

in ocean conditions. No FCRPS actions will directly reduce extra mortality, but extra 

mortality will eventually dissipate when ocean conditions improve. 

3. Stock viability—extra mortality resulted from processes not affected by any FCRPS action 

or ocean regime shift. Stocks will remain low due to interactions with hatchery fish, the 

presence of diseases such as bacterial kidney disease (BKD), or reduction in nutrients 

associated with historical declines in spawning stock. 

In the PATH models, D represents an annual value of the differential survival downstream

of Bonneville Dam for transported fish compared to in-river migrants. Low values of D indicate 

that transported fish incurred greater mortality downstream of Bonneville Dam than in-river 

migrants. Further, a low enough D value would explain historical stock productivity patterns 

without requiring extra mortality to explain changes in productivity. 

4
Many PATH participants believed that extra mortality existed; however, the group never 

reached consensus about whether it existed and, if so, what causes it. Schaller et al. (1999 and 

2000), Deriso et al. (2001), Petrosky et al. (2001), and Budy et al. (2002) argued that extra 

mortality existed and is linked to the FCRPS. Zabel and Williams (2000) suggested that 

differences in productivity could have occurred as a result of differences in underlying stock 

responses to changing ocean conditions. Subsequent to PATH, Levin and Tolimieri (2001) and 

Levin (2003) found that Chinook salmon populations used in the PATH life cycle models for the 

Snake, upper Columbia, and middle Columbia rivers had different productivity and that 

productivity varied between different time periods but not consistently with changes in ocean 

conditions. The degree to which the hydropower system affects survival of fish that successfully 

migrated as far as below Bonneville Dam remains contentious. We provide more details about this 

mortality in the “Latent Mortality” section (page 106). 

Stock Evaluations Subsequent to PATH 

Due to the perceived complexity of PATH products by some Northwest Fisheries Science 

Center (NWFSC) scientists not involved with PATH, a matrix model was developed in 1999 to 

evaluate the status of listed Snake River spring-summer Chinook salmon stocks. The model 

results indicated that little room existed to increase stock productivity within the migration 

corridor of the FCRPS because of improvements made at dams between the mid-1970s and late 

1980s. Results indicated that factors currently driving productivity occurred in the freshwater 

spawning and rearing areas and in estuary/early ocean residence (Kareiva et al. 2000). The matrix 

model set a value for D at 0.7 and used a range of values for delayed mortality. 

Concurrent with matrix-modeling efforts, other NWFSC staff developed draft white papers 

to summarize knowledge about how the FCRPS affected stocks. After considering comments 

based on regional review, final versions of the white papers were posted on the NWFSC website 

(http://www.nwfsc.noaa.gov/publications/whitepapers/index.cfm). They covered the following: 

• Passage of juvenile and adult salmonids past Columbia and Snake River dams. 

• Predation on salmonids relative to the FCRPS. 

• Salmonid travel time and survival related to flow in the Columbia River basin. 

• Summary of research related to transportation of juvenile anadromous salmonids around 

Snake and Columbia River dams. 

In developing the NMFS 2000 FCRPS BiOp (NMFS 2000), the Biological Effects Team

reviewed and analyzed fish passage assumptions NMFS used in earlier fish passage modeling 

exercises, those developed in the PATH process, fish passage information contained in the four 

white papers, and the most recent empirical data to determine the fish passage parameters for input 

into the simulated passage (SIMPAS) model. To update the 2000 BiOp or develop a new one to 

replace it, NOAA Fisheries Service needs an update on effects of the FCRPS on ESA-listed 

salmonids in the Columbia River basin. In this technical memorandum we update information 

about hydropower system survival for listed juvenile and adult salmon through the mainstem

Snake and Columbia River dams (to the extent data are available), results from transportation 

studies, flow effects on survival and travel time, and overall effects of FCRPS operations on adult 

returns. We focus primarily on Snake River spring-summer Chinook salmon, because they 

5
migrate through the entire FCRPS mainstem dam complex and they have the most empirical 

information. Fewer data exist for all other stocks, so we either provide incomplete information or 

make inferences where we deem reasonable. 

Returns of many listed Columbia River salmon stocks in the last several years have far 

exceeded numbers seen in recent decades. Thus we also discuss associations between direct 

survival through the FCRPS and changes in adult returns. Again, we do this most effectively for 

Snake River spring-summer Chinook salmon, because we know the most about fluctuation over 

time. For other stocks, we mostly rely on changes in combined wild and hatchery adult returns to 

dams, because reliable estimates of wild adult returns and smolts do not exist. 

The sections that follow provide summaries of methods and results from work described in 

recent annual reports to the COE and the Bonneville Power Administration (BPA) or in 

peer-reviewed literature. We direct readers who want additional information to those sources. In 

a few cases, some of this work is not readily available, because it is in press or in unpublished 

manuscripts under journal review. The authors will provide additional details of this information 

on request. 

General Analytical Approach 

The rapid decline of salmon stocks coincident with the completion of the Snake River 

dams in the early 1970s resulted in a singular paradigm that largely implicated the FCRPS as the 

primary reason for decreased salmon abundance. Although efforts have been under way since the 

early 1980s to mitigate FCRPS effects, the perspective and analytical framework to empirically 

define them—and solutions for them—concentrated on analyses and conclusions that implicate 

the FCRPS as the major influence on stocks. Scientific inquiry, however, relies on the acquisition 

of data from varied sources and from analyses and interpretation of data that explain relationships 

from an empirically based perspective. We cannot treat any one description as the most likely 

model or hypothesis a priori; instead, we must carefully weigh the available evidence against 

alternative hypotheses to explain probable FCRPS impacts on Columbia River basin salmon 

populations. Our analytical approach to assessing the effects of dams on salmon populations 

consisted of considering multiple working hypotheses. We used a variety of descriptions, models, 

and data sources to look for consistency in factors that could explain variable stock productivity 

over time. The results described in this report include smolt-to-adult returns (SAR) for untagged 

and passive integrated transponder (PIT)–tagged yearling and subyearling Chinook salmon 

populations, and SARs of transported and in-river migrating yearling and subyearling Chinook 

salmon from the upper Columbia River basin. We also used juvenile salmon migrant survival and 

migratory history studies that address the underlying mechanisms for reduced SARs such as reach 

survival, travel time, and latent mortality for yearling and subyearling Chinook salmon 

populations. Further, we discuss potential mechanistic causes for overall returns based on 

empirical data gathered from temporal timing of stocks moving through the FCRPS. These studies 

relied mainly on analyses of PIT-tagged fish. PIT tagging of juvenile salmonids began on a small 

scale in 1987 and has expanded tremendously since then, although not homogeneously throughout 

the Columbia River basin (Table 1). 

6
This technical memorandum contains results from our widely varied analyses. We fully 

respect the approach of previous individual analyses, but we thought that we needed to consider all 

lines of evidence simultaneously, instead of relying on various studies in isolation. As detailed 

below, we believe our analyses indicate that the FCRPS has affected and still affects migrant fish. 

 While we conclude that some level of hydropower system–related latent mortality exists, it does 

not override the strong returns resulting from good ocean conditions. We caution that ocean 

conditions will not remain favorable forever; therefore, we must continue to monitor FCRPS 

effects in concert with all other negative anthropogenic effects on salmon in order to avoid the 

losses incurred during the 1980s and 1990s. 

Table 1. Annual numbers of fish PIT tagged and released in different areas of the Columbia River basin. 

Outmigration 

year 

Upper 

Columbia 

Rivera

Snake 

River 

Middle lower 

Columbia 

Riverb

Columbia 

Riverc

Willamette 

River 

1987 7,673 2,619 – – –

1988 – 19,728 25,088 – –

1989 4,998 92,254 22,894 – –

1990 7,857 66,804 22,099 1,700 –

1991 6,644 70,462 32,613 724 –

1992 11,021 66,144 30,645 1,002 –

1993 24,326 132,409 29,693 733 –

1994 33,916 335,845 1,853 721 1,775

1995 34,982 514,551 – – –

1996 46,213 373,356 3,044 2,980 –

1997 40,153 458,881 107,685 10,708 –

1998 147,133 589,815 200,595 12,666 –

1999 168,593 763,014 477,897 18,336 3,429

2001 214,688 561,453 178,734 33,025 7,791

2002 613,296 858,240 223,181 59,511 9,597

2003 1,023,730 907,460 121,805 124,748 3,927

Total 2,385,223 5,813,035 1,477,826 266,854 26,519 a

 Drainage above the confluence with the Yakima River (above RKm 539). 

b

 Drainage between the confluence with the Wind and Yakima rivers (between RKm 252 and 539). c

 Drainage from the Wind River to the ocean (below RKm 252).

7
Adult Return Rate 

Rates Based on Nontagged Fish 

Methods 

SAR provides a measure of survival that encompasses smolt migration, estuary/ocean 

residence, and adult return stages. Where possible we calculated SAR by dividing returning adults 

from a single broodyear by the broodyear’s smolts. Changes in SAR over a number of years 

provide an index of temporal variability in stock productivity. For Snake River spring-summer 

Chinook salmon, we estimated recent (1997 to 2001 outmigration) SAR from Lower Granite Dam,

adjusted for annual downstream harvest, and compared them to earlier years’ estimates of SAR 

(catch plus escapement) to the upper Snake River dam. In brief, from Petrosky et al. (2001) we 

used estimated wild adult (3-, 4-, and 5-year-old fish that spend 1, 2, or 3 years in the ocean) 

1964–1999 returns (we adjusted 1993 to 1996 1-ocean fish for estimated additional returns to 

Oregon) and 1964–1999 harvest rates. We used Raymond (1988) for estimates of smolt 

abundance between 1964 and 1984. We derived estimates for wild smolts from 1993 to 2003 by 

expanding the daily collection of wild fish at Lower Granite Dam (FPC 2003a) by the daily 

estimates of detection efficiency (derived with methodology used in Sandford and Smith 2002) of 

wild smolts at the dam for each year. For smolt years 1995 to 2003, we adjusted smolt estimates 

by an estimated percentage of nonclipped hatchery fish arriving at the dam that were not identified 

as hatchery origin. This adjustment decreased numbers of wild smolts by 6%, 1%, 0%, 2%, 4%, 

3%, 1%, 4%, and 4% for smolt years 1995 through 2003, respectively. We estimated smolt 

abundance from 1985 to 1993 based on a Beverton-Holt curve generated from estimated numbers 

of smolts from 1964 to 1984 and 1994 to 2003 (R ≅ 0.80) and the estimated number of wild fish 

passing the upper Snake River dam1

 2 years earlier. We estimated wild adult returns to Lower 

Granite Dam from 1997 through 2003 from annual fish counts of spring-summer Chinook salmon 

reported to have passed the dam. Fish counters at the dam enumerated fish as they passed through 

the counting window and assigned them to either a group with adipose fins (ostensibly wild fish) 

or a group without adipose fins (known hatchery fish with fins clipped as juveniles). We adjusted 

the clipped (missing adipose fin) hatchery fish returns by the estimated proportion of nonclipped 

(fish with an adipose fin, but possibly with other clipped fins) hatchery fish in the return. We used 

estimates of 89.6%, 87.7%, 86.5%, 96.0%, 92.3%, 89.6%, and 88.9% for identifiable adult (2- and 

3-ocean fish) hatchery fish in return years from 1997 through 2003, respectively. We then 

subtracted the corrected hatchery count from the total adult return to derive the wild fish estimate.

To separate adult returns into the respective 2- and 3-ocean component, we used two 

methods. For the 1997 return year, we used PIT-tag data to estimate the percentage of 3-ocean fish 

 1

 Beginning in the late 1960s (Raymond 1988), the uppermost dam on the Snake River changed as follows: through 

1968, Ice Harbor Dam; in 1969, Lower Monumental Dam; from 1970 to 1974, Little Goose Dam; and from 1975 to 

present, Lower Granite dam.

8
that returned from the 1994 outmigration. We expanded the estimated number of jacks (1-ocean 

fish) plus 2-ocean fish from the 1994 outmigration (data from Petrosky et al. 2001) to derive the 

number of 3-ocean fish to meet the estimated percentage in the return. We then subtracted this 

estimate from that of wild 1997 adults to derive the number of 2-ocean fish. For returns from 1998 

through 2003, we used age-class data collected by Idaho Department of Fish and Game (IDFG) 

(1998–2001 data from Kiefer et al. [2002]; 2002–2003 data from IDFG2

). We then estimated the 

total adult return for outmigration years from 1995 through 2001 (only through 2-ocean returns for 

the last year) by combining the estimated number of wild jacks with the 2- and 3-ocean returns for 

each year. To account for harvest rates in the Columbia River that varied between 0% and 40% 

over the time period, we expanded adult returns to the uppermost Snake River dam for the period 

between 1964 and 1999 based on estimated Columbia River harvest rates in Petrosky et al. (2001). 

 We expanded adult returns for 2000 to 2003 based on unpublished harvest rates.3

For Snake River yearling Chinook salmon, in addition to SAR based on Petrosky et al. 

(2001), we plotted SAR for the period from 1964 to 1984 from Raymond (1988). For Snake River 

steelhead, we used Raymond’s (1988) SAR estimates for the period from 1964 to 1984. We used 

Petrosky’s (IDFG) updated steelhead SAR from 1985 to 1994, submitted as part of the PATH 

process (Marmorek et al. 1998). Petrosky4

 used the same methods used in the PATH report to 

develop preliminary 1995–2000 SAR estimates for subbasin planning. He cautioned that these 

estimates were preliminary, updated, wild adult and smolt numbers, which had not yet been 

reviewed by the Snake River Technical Recovery Team. Adult wild A-run and B-run estimates 

were also from the Technical Advisory Committee. Updated adult-age structure information was 

from Lower Granite Dam scale sampling for the 1995–2001 run years (cooperators were NMFS 

and IDFG, data collection and archiving; USFWS and Utah State University, scale reading). 

For wild stocks where we lacked direct juvenile and adult information, we compared the 

median count of adult fish from the 2001–2003 return years to the median adult count from the 

1992–2000 return years. We obtained counts of adult fish at dams for the composite wild and 

hatchery stocks from the Columbia River Data Access in Real Time (DART) website (CBR UW

2004) For natural-origin Snake River fall-run Chinook salmon, we used updated (unpublished) 

adult escapements for return years 2000–2002 over Lower Granite Dam developed by NOAA 

Fisheries Service (NMFS 2003) and adult returns from 1991 to 1999 from unpublished data 

submitted to the Biological Review Team for Chinook salmon.5

 We then compared the difference 

in median returns for adult fish between the two periods to the difference in median SARs for 

Snake River spring-summer Chinook salmon for the same periods. 

 2 R. Kiefer, IDFG, Boise, ID 83707. Pers. commun., March 2004. 3 P. Dygert, NOAA Fisheries Service, Seattle, WA. Pers. commun., December 2003. 4 C. Petrosky, IDFG, Boise, ID. Pers. commun., March 2004. 5 T. Cooney, NOAA Fisheries Service, Seattle, WA. Pers. commun., January 2003. 

9
Results 

Snake River spring-summer Chinook salmon 

Estimated SAR (catch + escapement) of wild Snake River spring-summer Chinook salmon 

from the 1999 and 2000 outmigrations increased to levels only observed prior to construction of 

the final mainstem FCRPS dams (Figure 2). The median SAR of 3.0% (range 1.6–3.8%) from the 

1998–2000 outmigrations was similar to the median SAR of 3.1% (range 1.9–4.6%) from the 

1964–1970 outmigrations based on data from Petrosky et al. (2001), and 81% of the median 3.7% 

SAR (range 3.3–6.1%) for the same years based on Raymond’s (1988) analyses. The median SAR 

of 3.0% from the 1998–2000 outmigrations was 5 times as high as the median SAR of 0.6% (range 

0.20–1.9%) from the previous 10 years (1988–1997 out-migrations). From the low-flow 2001 

outmigration, the SAR presently stands at approximately 1.6%, with 3-ocean fish still returning in 

spring and summer 2004. This return rate already exceeds total SARs for all wild Snake River 

spring-summer Chinook salmon outmigrations between 1976 and 1997. However, given the low 

number of smolts in the outmigrations because of earlier poorer returns, the absolute wild adult 

return did not reach the levels that occurred in the 1960s. 

Snake River fall Chinook salmon 

The median estimated SAR for natural-origin fall-run Chinook salmon between 2000 and 

2002 was 3.4 times higher than the median adult return for the period 1991–1999 (Figure 3). SA

R (%) 

1960 1970 1980 1990 2000

0.0

0.5

1.0

1.5

2.0

2.5

3.0

3.5

4.0

4.5

5.0

5.5

6.0

6.5

2-ocean

only

Raymond

Petrosky et al.

New estimates

Outmigration year

Figure 2. Estimated SAR for wild Snake River spring-summer Chinook salmon. Initial estimates from

1964 to 1984 are from Raymond (1988). Petrosky et al. (2001) used Raymond’s smolt estimates, 

but they used a new algorithm to develop an alternative SAR for the 1964–1984 period. They also 

estimated SAR for outmigration years 1992–1996.

10
0.0

0.5

1.0

1.5

2.0

2.5

3.0

3.5

4.0

4.5

5.0

5.5

6.0

6.5

7.0

7.5

8.0

8.5

Wild

steelhead

above

Bonneville

Dam

Wild and

hatchery

spring

Chinook

salmon

above

Priest

Rapids

Dam

Wild and

hatchery

fall

Chinook

salmon

above

Lower

Granite

Dam

Ratio of

SARs for

wild

Snake

River

springsummer

Chinook

salmon

Stocks

Ratio of median adult returns

Figure 3. Ratio of the median adult fish count (2001–2003, from CBR UW 2004) for wild steelhead at 

Bonneville Dam and hatchery and wild spring Chinook salmon at Priest Rapids Dam divided by the 

median count at each respective dam for steelhead (1993–1000) and Chinook salmon (1991–2000). 

 Data for fall Chinook salmon were derived from information supplied to the Chinook Salmon 

Biological Review Team and Technical Advisory Committee. 

Upper Columbia River spring Chinook salmon 

As with historical data, the response of spring Chinook salmon stocks in the upper 

Columbia River increased, but to a greater degree than wild Snake River spring-summer Chinook 

salmon. The median estimated adult return was nearly 8 times higher (Figure 3). 

Wild steelhead above Bonneville Dam 

Median counts of wild, upper-river summer steelhead at Bonneville Dam were 4.3 times 

higher, from 33,000 (range 24,000–58,000) to 143,000 (range 112,000–149,000) (Figure 3). We

have no information on counts of wild steelhead into the upper Columbia River. 

Wild Snake River steelhead 

A plot of the trend over time indicates that SARs for Snake River steelhead increased 

considerably in 2002 and 2003 compared to the previous 10 years (Figure 4) and reached levels 

not observed since the early 1970s and middle 1980s. 

11
1960 1970 1980 1990 2000

0

1

2

3

4

5

6

7

Raymond

Petrosky

Outmigration year

SAR (

%)

Figure 4. Estimated SAR of wild Snake River steelhead. Early data are from Raymond (1988). Data from

1985 to 2000 (1985–1994) are from Petrosky (submitted to PATH; see Marmorek and Peters 1998). 

 Data from 1995 to 2000 are from C. Petrosky.

6

Snake River sockeye salmon 

We have little specific information about Snake River sockeye salmon. Between 1990 and 

2001, 478 PIT-tagged sockeye salmon arriving at lower Snake River dams were transported, while 

3,925 migrated in-river. Of these, two transported fish (0.4% SAR) and one in-river fish returned 

(0.03% SAR). Adult returns of sockeye salmon to Lower Granite Dam between 1990 and 2003 

ranged from 3 to 282 fish (annual median was 13 fish). Snake River sockeye salmon have not 

demonstrated increased SARs in the last several years, similar to what occurred for Snake River 

Chinook salmon and steelhead. 

Discussion 

By any measure, Snake River spring-summer Chinook salmon abundance increased 

dramatically in the last few years. This increase apparently largely resulted from a shift in 

ocean conditions, and the changing ocean conditions, along with changes in climatic conditions 

that interacted with habitat, abundances of hatchery fish, and changes in flow within the 

hydropower system, led to the greater survival. However, the relative role of the hydropower 

system in overall stock performance is still uncertain. We do believe that improvements made to 

the hydropower system from the 1970s through the 1990s were crucial to preventing even more 

drastic declines during the recent period of poor ocean conditions and that possible negative 

effects of the hydropower system are more likely to influence stocks during periods of poor 

ocean conditions. Unfortunately, we cannot reliably predict future ocean conditions, and thus we 

 6

 C. Petrosky, IDFG, Boise, ID. Pers. commun., March 2004. 

12
cannot rely on the persistence of good ocean conditions. With predictions of increased global 

warming in the near future, global climate change may actually lead to ocean conditions that are 

worse than any we have yet experienced. For these reasons, we must continue to assess the effects 

of the hydropower system in the context of all impacts, including those occurring in both seawater 

and freshwater habitats. 

The high SAR estimates for the unmarked population do not surprise us. As outlined in the 

introduction, historically they varied (although for Snake River fish we only have empirical 

estimates since 1964). Williams and Matthews (1995) found that conditions in the hydropower 

system improved tremendously from those that initially caused large losses of juvenile migrants 

(Raymond 1979). Williams et al.(2001) also found that survival of yearling Snake River Chinook 

salmon through the present eight dams of the mainstem FCRPS recently matched or exceeded 

those estimated to have occurred when the mainstem FCRPS had only four dams. Without actual 

measures of survival, but under the presumption of success from transportation, Raymond (1988) 

and Williams (1989) predicted that large returns of Snake River spring-summer Chinook salmon 

could once again occur if ocean conditions improved. Using new modeling tools that predict adult 

returns based on ocean conditions that juveniles encounter during their first several months at sea, 

recent analyses by Scheuerell and Williams (in press) found that ocean conditions have a high 

correlation (R2

 = 0.71) with SARS of wild Snake River spring-summer Chinook salmon (see the 

“Large Scale Processes” subsection, page 123, for details). Recent research by Peterson and 

Schwing (2003) demonstrated that ocean conditions improved dramatically in 1999. We do not 

know how long these improved conditions will last, but at the time of these analyses we predicted 

good adult returns from juvenile outmigrations through 2003 (with adults returning through 2006) 

(Scheuerell and Williams in press). Based on 1990s returns, the comparative escapement to 

spawning when comparing one broodyear to the next one it produced 

[ln(escapementBY/escapementBY – 1)] already exceeded 1.0 for 4 consecutive years, the longest 

stretch since such records began in the 1960s (Figure 5). 

As with yearling Chinook salmon, estimated adult returns of natural-origin fall Chinook 

salmon to above Lower Granite Dam were nearly 3.5 times higher than outmigration levels in the 

early to mid-1990s. Total numbers of fall-run Chinook salmon over Lower Granite Dam also 

increased tremendously, but much of this increase resulted from large releases of Lyons Ferry 

Hatchery fish above the dam. Total numbers of natural-origin fish above Lower Granite Dam in 

recent years exceeded all levels observed since 1975, when the dam was completed. The two 

periods are not directly comparable, however, because harvest rates on fall Chinook salmon 

changed substantially after ESA listing of Snake River fall-run Chinook in 1992, and releases of 

unmarked hatchery fall Chinook salmon above Lower Granite Dam increased. 

Steelhead SAR did not follow the same patterns as yearling Chinook salmon SAR. Ocean 

conditions appear to affect steelhead differently, although they do have an effect. British 

Columbia stocks also experienced a very steep decline in steelhead SAR in the early 1990s, which 

was attributed to changed ocean conditions (Welch et al. 2000). In the 1990s, low spawning 

populations (some the lowest in the last 35 years) produced comparatively low numbers of wild 

smolts compared to the 1960s. Thus even with recent large increases in adult returns, total adult 

returns of wild steelhead remain at nearly one-half the level of the 1960s. 

13
60 65 70 75 80 85 90 95 00

-2.5

-2.0

-1.5

-1.0

-0.5

0.0

0.5

1.0

1.5

2.0

2.5

Broodyear

ln (

B

YN/B

YN-1))

Figure 5. The ln(BYN/BYN–1) for the composite wild spring-summer Chinook salmon population in the 

Snake River basin above the upper Snake River dams (Ice Harbor Dam in 1962, Lower 

Monumental Dam in 1969, Little Goose Dam in 1970, and Lower Granite Dam in 1975). BYN = 

escapement over the upper Snake River dam for the current brood. BYN–1 = escapement over the 

upper Snake River Dam for the brood that produced offspring for the current brood. 

Rates Based on PIT-Tagged Fish 

Methods 

We estimated annual SAR for PIT-tagged Snake River fish based on a Lower Granite Dam

equivalent for smolts and adult returns to Lower Granite Dam by following the methods of 

Sandford and Smith (2002). We estimated how many fish passed the dam on each day of the 

migration season and totaled the daily estimates. To get each day’s estimate, we used the 

following process: 

1. For fish detected on a given day at Little Goose Dam that were previously detected at 

Lower Granite Dam, tabulate according to their detection (passage) day at Lower Granite 

Dam.

2. For fish detected on the same day at Little Goose Dam that were not previously detected at 

Lower Granite Dam, assign them an estimated “nondetection passage day” at Lower 

Granite Dam, assuming that their distribution over days at Lower Granite Dam was 

proportionate to that of fish detected at Lower Granite Dam.

3. Repeat this process for all days of detection at Little Goose Dam.

4. Sum all these detected and nondetected fish for a given day at Lower Granite Dam.

14
5. Estimate that day’s detection probability by calculating the proportion of detected fish to 

the total of detected and nondetected fish (after making an adjustment for fish transported 

at Lower Granite Dam). 

6. Divide the total detected number at Lower Granite Dam on that day (bypassed and 

transported) by the estimated detection probability to get an estimated daily total. 

Formally, this process is referred to as the Schaefer method (Schaefer 1951). We modified 

the method slightly for estimates in the very early and late periods of the passage distribution 

where the above process was not applicable (i.e., for days when no detections occurred at Little 

Goose Dam of fish previously detected at Lower Granite Dam). 

We then estimated SAR for various “detection-history categories,” in particular for fish 

transported from Lower Granite, Little Goose, Lower Monumental, or McNary dams; for fish 

bypassed back to the river one or more times at these dams; and for fish never detected at these 

dams. (Results and discussion of SAR for multiply bypassed fish is contained in the “Latent 

Mortality” section, page 106.) To do this, we developed daily passage estimates at Lower Granite 

Dam using the following process: 

1. For each daily Lower Granite passage group, we estimated detection probabilities at Little 

Goose, Lower Monumental, and McNary dams using the Cormack-Jolly-Seber survival 

model (Cormack 1964, Jolly 1965, Seber 1965). 

2. We multiplied the estimated daily Lower Granite Dam total by the appropriate detection 

and transport probabilities. For example, the detection-history category “not detected at 

Little Goose Dam and then transported from Lower Monumental Dam” is equivalent to 

multiplying the Lower Granite Dam daily estimate by (1 – probability of Little Goose Dam

detection) × (probability of Lower Monumental detection) × (probability of transportation 

from Lower Monumental Dam for fish detected there). 

3. We summed the estimates for all daily groups to get total smolts in each detection-history 

category. 

Next we calculated SAR. For a given detection-history category, this is the ratio of 

observed number of adults to estimated number of smolts. We also estimated the precision for the 

estimated SAR using bootstrap methods where the individual fish information (i.e., detection 

history, detection dates, and adult return record) and the entire estimation process were 

boot-strapped 1,000 times. Confidence limits were generated from the bootstrapped estimates. If 

no adult salmon returned, we used the “rule of 3,” based on the estimated number of juveniles, to 

construct an approximate 95% confidence interval (Hanley and Lippman-Hand 1983). 

Finally we weighted SAR of PIT-tagged fish by the estimated percentage for the detection 

history of the untagged population. Because the untagged fish population passing through the 

Lower Granite, Little Goose, and Lower Monumental dams bypass systems were transported, we 

used the estimated percentage of first-time detections of PIT-tagged fish at those dams to weight 

the SAR for transported fish at those dams. We combined these SAR with the estimated SAR for 

fish not detected at collector dams (including McNary Dam) plus the SAR of fish bypassed at 

McNary Dam to derive a weighted SAR for the total population based on SAR of PIT-tagged fish. 

15
Results 

Snake River spring-summer Chinook salmon 

The overall estimated SAR for wild and hatchery spring-summer Chinook salmon (Lower 

Granite Dam to Lower Granite Dam, not adjusted for harvest) was based on weighting SAR of 

PIT-tagged fish by migration histories of the untagged population. It ranged from 0.1% to 2.3% 

(Figure 6). 

1994 1995 1996 1997 1998 1999 2000

0.0

0.5

1.0

1.5

2.0

2.5

3.0

3.5

PIT-tagged wild

Unmarked wild

PIT-tagged hatchery

Unmarked hatchery

Outmigration year

SA

R (

%)

Figure 6. Estimated SAR for wild and hatchery Snake River spring-summer Chinook salmon, based on 

analyses of adult returns from the general untagged population and from SAR for PIT-tagged fish 

weighted by the estimated migration distribution of the untagged juvenile population. Total returns 

of PIT-tagged wild fish equaled 26, 60, 16, 40, 211, 720, and 594 from outmigration years 

1994–2000, respectively. For the same years, total hatchery adult returns equaled 22, 14, 154, 87, 

682, 1,690, 3,110, and 2,878, respectively.

Estimated annual SAR for PIT-tagged Chinook salmon marked above Lower Granite Dam

with different detection histories as juveniles varied widely between years and dams for the 

1993–2000 outmigrations (Table 2). Most estimates had wide 95% confidence bounds (Table 3). 

When confidence bounds between two different groups did not overlap, it indicated a significant 

difference in SAR between the two groups. Thus no significant differences existed for any 

comparison groups of wild spring-summer Chinook salmon. For hatchery spring-summer 

Chinook salmon, the annual SAR for fish transported from Lower Granite Dam was significantly 

higher than for in-river migrants (nondetected category) from migration years 1997–2000. 

Snake River steelhead 

The overall estimated SAR for wild and hatchery steelhead (Lower Granite Dam to Lower 

Granite Dam, not adjusted for harvest) based on weighting SAR of PIT-tagged fish by juvenile 

migration histories of the untagged population ranged from 0.3% to 3.1% (Figure 7). 

16
1994 1995 1996 1997 1998 1999 2000 2001

0

1

2

3

4

5

PIT-tagged wild

Unmarked wild

PIT-tagged hatchery

Outmigration year

SAR (

%)

Figure 7. Estimated SAR for wild and hatchery

Snake River steelhead based on analyses 

of fish PIT tagged as juveniles or the 

overall unmarked population (wild only). 

All analyses are based on juveniles and 

adults at Lower Granite Dam. Total 

returns of adult PIT-tagged wild fish 

from the 1994 through 2001 

out-migrations equaled 21, 8, 15, 13, 25, 

101, 283, 11, respectively. Total adult 

returns for hatchery fish from the same 

outmigration years equaled 51, 104, 69, 

49, 76, 186, 267, and 9, respectively. 

Table 2. Annual SAR (total adult returns/estimated juveniles) for spring-summer Chinook salmon PIT 

tagged above Lower Granite Dam with detection histories of groups that represented the unmarked 

population. 

Transported from (first time detected) 

Year 

Rearing 

typea

Lower Granite 

Dam Little Goose Dam

Lower 

Monumental 

Dam 

McNary 

Dam Nondetected

1993 W 0.10 (2/2088) 

0.34 (1) 

 0.34 (1/295) – (0/853) – (0/605) – (0/1056) 

H 0.09 (4/4643) – (0/765) – (0/2448) – (0/1992) 0.06 (2/3161) 

1994 W 0.71 (8/1128) 0.91 (4/441) 0.15 (1/648) – (0/2670c 0.27 (6/2245) 

H 0.11 (2/1894) 0.12 (1/867) 0.11 (1/947) 0.02 (2/12368)c 0.09 (7/7707) 

1995 W 0.39 (7/1781) 0.29 (1/345) – (0/195) NA 0.47 (9/1920) 

H 0.59 (14/2381) 0.79 (5/630) 0.39 (1/255) NA 0.45 (27/6049) 

1996 W 0.35 (1/284) 1.17 (1/86) – (0/43) NA 0.20 (4/2015) 

H 0.30 (6/2007) – (0/510) – (0/366) NA 0.17 (29/17016)

1997 W 0.99 (2/202) 5.22 (2/38) – (0/14) NA 1.65 (14/847) 

H 0.89 (226/25523)b 0.70 (5/718) 0.69 (2/291) NA 0.67 (162/24277)

1998 W 1.30 (11/848) 0.89 (3/336) 0.97 (1/104) NA 1.43 (31/2169) 

H 1.74 (812/46772)b 0.84 (66/7853)c 0.57 (7/1238)c NA 1.26 (260/20566)

1999 W 2.59 (32/1237) 2.15 (9/418) 1.75 (7/400) NA 2.08 (73/3505) 

H 2.75 (698/25340)b 2.91 (481/16551)b 1.24 (25/2018) NA 1.83 (567/30932)

2000 W 1.07 (4/374) 1.94 (6/309) 1.00 (2/201) NA 2.17 (124/5718)

H 3.08 (1029/33398)b 2.18 (310/14200)b 1.76 (86/4898) NA 1.66 (755/45393) a W = wild; H = hatchery. 

b

 Groups significantly higher than nondetected fish. 

c

 Groups significantly lower than nondetected groups. 

17
Table 3. Bootstrapped confidence intervals (95%) around annual SAR (see Table 2) for Chinook salmon 

PIT tagged above Lower Granite Dam with detection histories of groups that represented the 

unmarked population. 

Transported from (first time detected) 

Year 

Rearing 

typea

Lower 

Granite Dam 

Little Goose 

Dam 

Lower 

Monumental Dam

McNary 

Dam Nondetected

1993 W 0.00–0.19 0.00–1.01 0–0.35b 0.00–0.50b 0.00–0.28b

H 0.02–0.17 0.00–0.39b 0–0.12b 0.00–0.15b 0.00–0.17 

1994 W 0.19–1.16 0.18–2.35 0.00–0.35 0.00–0.11 b 0.13–0.48 

H 0.00–0.27 0.00–0.34 0.00–0.23 0.00–0.03 0.04–0.18

1995 W 0.22–0.62 0.00–0.61 0–1.54b NA 0.28–0.60

H 0.30–0.83 0.33–1.38 0.00–0.86 NA 0.30–0.59

1996 W 0.00–1.43 0.00–3.72 0–6.98b NA 0.00–0.46

H 0.20–0.44 0.00–0.59b 0–0.82b NA 0.12–0.21

1997 W 0.00–2.22 0.00–24.2 0–21.4b NA 0.81–2.64

H 0.80–0.96 0.31–1.12 0.00–1.35 NA 0.60–0.74

1998 W 0.72–2.31 0.28–1.58 0.00–3.13 NA 1.08–1.75

H 1.66–1.81 0.70–0.97 0.32–0.81 NA 1.16–1.36

1999 W 1.66–3.27 0.71–3.38 0.93–2.80 NA 1.73–2.36

H 2.58–2.97 2.62–3.09 0.91–1.83 NA 1.63–1.94

2000 W 0.25–1.91 0.81–3.41 0.00–1.81 NA 1.80–2.48

H 2.93–3.27 1.86–2.42 1.32–2.34 NA 1.40–1.75 a W = wild; H = hatchery. 

b Based on “rule of 3” where 0 adults returned. 

Estimated annual SAR for PIT-tagged steelhead marked above Lower Granite Dam with detection 

histories as juveniles equivalent to the unmarked population varied widely between years and 

dams for the 1993–2000 outmigrations (Table 4). Most estimates had wide 95% confidence 

bounds (Table 5). 

Discussion 

For spring-summer Chinook salmon, few treatments of PIT-tagged fish from any year 

attained a SAR that met the 2% to 6% SAR range identified in PATH as a goal necessary for 

recovery of the listed stocks while allowing for historical harvest rates (Table 2). In contrast, our 

estimated SAR for the wild population based on total wild returns to Lower Granite Dam, divided 

by the estimated number of wild juveniles producing the adult returns for the same years, exceeded 

2.5% in 1999 and 2000 (Figure 6). Estimated differences in SAR based on PIT-tagged versus 

untagged fish showed no clear trend in the early years, but this lack of trend may have resulted 

from estimating SAR from small numbers of adult returns. For wild fish, when total adult returns 

increased to over 200 fish, beginning in 1998, the estimated SAR based on PIT-tagged fish was 

clearly lower than the untagged estimate. We observed the same trends for wild steelhead. In all 

years, the estimated return rate for the untagged population exceeded the return rate of PIT-tagged 

fish (Figure 7). 

18
Table 4. Annual SAR (total adult returns/estimated juveniles) for steelhead PIT tagged above Lower 

Granite Dam with detection histories of groups that represented the unmarked population. 

Transported from (first time detected) 

Year 

Rearing 

type 

Lower 

Granite Dam 

Little Goose 

Dam 

Lower 

Monumental 

Dam McNary Dam Nondetected

1993 W 0.24 (2/845) – (0/76) – (0/193) 1.85 (1/54) – (0/358) 

H 0.05 (1/2036) 0.59 (1/170) 0.59 (2/340) – (0/91) 0.35 (2/576) 

1994 W 1.70 (6/352) 0.46 (1/218) 0.52 (1/194) – (0/250) 0.93 (6/644) 

H 1.08 (21/1941)b – (0/1007) 0.41 (2/489) 0.07 (1/1513) 0.10 (7/6910)

1995 W – (0/287) – (0/66) 4.17 (1/24) NA 0.35 (1/285) 

H 0.70 (14/1993) 1.60 (5/312) – (0/88) NA 0.90 (11/1216)

1996 W 0.99 (1/101) – (0/33) – (0/11) NA 0.52 (3/574) 

H 0.36 (4/1104) – (0/353) – (0/94) NA 0.36 (14/3875)

1997 W 1.32 (3/227) – (0/44) – (0/23) NA 0.43 (2/462) 

H 0.60 (10/676) – (0/158) – (0/119) NA 0.17 (7/4129)

1998 W 0.33 (1/304) – (0/93) – (0/93) NA 1.20 (9/747) 

H 0.63 (5/791) 0.24 (1/419) 0.52 (1/192) NA 0.93 (24/2590)

1999 W 2.49 (6/241) 4.22 (4/95) 2.54 (2/79) NA 2.79 (25/897)

H 0.95 (8/838) 1.20 (4/333) – (0/250) NA 1.43 (37/2594)

2000 W 2.81 (7/249) 3.08 (4/130) 2.12 (3/141) NA 1.82 (37/2017)

H 3.04 (14/461)b 0.98 (1/102) 0.61 (1/163) NA 0.97 (39/4040) a W = wild; H = hatchery. 

b

 Groups significantly higher than nondetected fish. 

Table 5. Bootstrap confidence intervals (95%) around annual SAR (see Table 4) for steelhead PIT tagged 

above Lower Granite Dam with detection histories of groups that represented the unmarked 

population. 

Transported from (first time detected) 

Year 

Rearing 

type 

Lower 

Granite Dam 

Little Goose 

Dam 

Lower 

Monumental Dam

McNary 

Dam Nondetected 

1993 W 0.00–0.63 0.00–3.95b 0.00–1.55b 0.00–8.21 0–0.84b 0.34 (1) 0.42

H 0.00–0.15 0.00–1.84 0.00–1.72 0.00–3.30b 0.00–0.99 

1994 W 0.29–2.91 0.00–1.69 0.00–1.26 0.00–1.20b 0.28–1.95 

H 0.68–1.52 0.00–0.30b 0.00–0.89 0.00–0.14 0.04–0.15

1995 W 0.00–1.05b 0.00–4.55b 0.00–11.7 NA 0.00–1.05

H 0.39–1.25 0.62–3.15 0.00–3.41b NA 0.50–1.23

1996 W 0.00–3.96 0.00–9.09b 0.00–27.3b NA 0.00–1.04

H 0.17–0.57 0.00–0.85b 0.00–3.19b NA 0.17–0.53

1997 W 0.00–2.59 0.00–6.82b 0.00–13.0b NA 0.00–1.10

H 0.23–1.08 0.00–1.90b 0.00–2.52b NA 0.07–0.28

1998 W 0.00–1.02 0.00–3.23b 0.00–3.23b NA 0.55–1.92

H 0.14–1.25 0.00–0.70 0.00–1.64 NA 0.65–1.22

1999 W 0.80–4.46 1.07–9.09 0.00–8.10 NA 2.06–3.57

H 0.49–1.64 0.59–2.00 0.00–1.20b NA 1.08–1.86

2000 W 0.46–5.88 0.79–4.61 0.00–4.93 NA 1.30–2.31

H 1.54–4.61 0.00–2.76 0.00–2.59 NA 0.60–1.34 a W = wild; H = hatchery. 

b

 Based on “rule of 3” where 0 adults returned. 

19
The results of our analyses suggest that SAR for PIT-tagged wild fish do not represent the 

total SAR for the unmarked population. Thus we conclude that although PIT-tagged wild Chinook 

salmon and steelhead provide useful data when assessing the difference in return rates of different 

treatment groups, they did not apparently represent SAR for the wild populations. On the other 

hand, we saw no evidence that estimating PIT-tagged hatchery Chinook salmon systematically 

resulted in underestimated SAR of untagged hatchery Chinook salmon. We have no SAR 

estimates for unmarked hatchery steelhead to compare to PIT-tagged steelhead. We urge caution, 

however, when using absolute return rates of hatchery PIT-tagged fish to make inferences about 

the total untagged population, because hatchery fish in the Snake River basin are not PIT tagged in 

proportion to the total hatchery population. Thus a bias will likely exist in PIT-tagged-derived 

SAR based on hatchery fish. We also note that these results came from data for studies conducted 

prior to the 2002 outmigration. Beginning in 2002, rather than return all detected wild PIT-tagged 

fish to the river at the upper Snake River dams, a proportion are now bypassed to the tailrace. 

Returns from these outmigrations should indicate whether lower rates of return from PIT-tagged 

fish, compared to estimates for the nontagged population, still exist. 

20
Transportation Evaluations 

Methods 

We evaluated the efficacy of transportation two ways. First, we compared the return rate 

of transported fish to the return rate of control fish that migrated volitionally through the 

hydro-power system. This provided a ratio of return rates of transported (T) fish and in-river 

migrants (I), hereafter T:I. We also evaluated D, which is defined as the ratio of post-Bonneville 

Dam survival for transported fish to that of in-river migrants. Details of the methodology are 

provided below. 

We based our evaluation of transportation on comparisons of SAR from fish PIT tagged as 

juveniles that migrated through the hydropower system (in-river fish) versus SAR of fish collected 

and transported (Figure 8). We based most of our evaluations on fish from two general sources: 

fish PIT tagged for the Multi-State Comparative Survival Study (CSS 2003) above Lower Granite 

Dam that passed through sort-by-code systems installed in bypass systems at collector dams

(Lower Granite, Little Goose, and Lower Monumental dams on the Snake River and McNary Dam

on the Columbia River), and those that were specifically released to evaluate transportation. Of 

the fish collected, some were automatically diverted to raceways for transportation, while others 

were returned to the river to allow estimation of survival for the downstream migrants. We also 

PIT-tagged juvenile fish collected at Lower Granite Dam, some of which we released into 

raceways for subsequent transportation and others we released to the dam’s tailrace. Finally, 

because slide gates are not 100% effective at diverting PIT-tagged fish back to the river, some

nondesignated fish PIT tagged above Lower Granite Dam get transported. We evaluated these fish 

where possible, but sample sizes were quite small, SAR for these groups have large confidence 

bounds. 

Groups of fish PIT tagged above and at Lower Granite Dam each present advantages and 

disadvantages for evaluating transportation. For fish PIT tagged above the dam, those collected at 

Lower Granite Dam presumably represent the untagged population collected at the dam, while 

those not collected (therefore not detected) represent the unmarked population of fish that passed 

the dam through turbines and spill. However, for fish tagged above the dam, we do not have a 

direct measure of how many nondetected fish pass the dam, but we can estimate this number. 

Moreover, when an adult that was not detected as a juvenile returns, we do not know when it 

passed the dam as a juvenile. For these fish groups, we can only estimate annual transport to 

in-river ratios (T:I) and annual values of D. For fish PIT tagged at Lower Granite Dam, no “true” 

controls exist because all fish for studies are first collected from the dam’s juvenile bypass 

facilities. Thus no sample exists that represents untagged, uncollected fish. However, tagging at 

dams has some advantages. After release, we know the number of downstream migrants that 

subsequently represent the untagged population. Further we can estimate temporal SAR trends for 

transported and in-river migrants. From this we can estimate temporal D trends. 

21
Lower Granite Dam

Bonneville Dam

Little Goose Dam

Lower Monumental Dam

Ice Harbor Dam

The Dalles Dam

John Day Dam

McNary Dam

2

3

3

3

3

3

3 2

2

2

1

1

1

1

3

1 = Transported 

2 = Bypassed 

3 = Nondetected

Figure 8. Three pathways that juvenile salmon travel on their way downstream through the mainstem Snake 

and Columbia rivers. 

Studies specifically designed to evaluate transportation of Snake River fall Chinook 

salmon began only in 2001. However, since PIT-tag systems do not effectively bypass 100% of 

PIT-tagged fish back to the river, each year a relatively small number of PIT-tagged fish arriving 

at Lower Granite, Little Goose, Lower Monumental, and McNary dams are transported. In 1995, 

we began PIT tagging and releasing Lyons Ferry Hatchery fall Chinook salmon in the Clearwater 

and free-flowing Snake River above Lewiston to evaluate survival. We estimated SAR for the 

combined fish group transported from any collector dam and compared them to SAR of the 

combined fish bypassed only once at each dam. We also conducted separate analyses for fish 

detected prior to 1 September and fish detected on 1 September or later. We further developed 

ratios of combined transported fish:combined bypassed fish for each year, and we developed 95% 

confidence bounds for the ratios. 

22
We used two data sets to evaluate transportation for upper Columbia River subyearling 

Chinook salmon at McNary Dam. For the first set, we used data from studies in 1995 and 1996 to 

evaluate the efficacy of transportation at McNary Dam (after construction of the new juvenile 

bypass/collection facilities in 1994). In those 2 years, approximately 110,000 and 120,000 

juvenile subyearling Chinook salmon, respectively, were collected in the juvenile bypass facility 

at the dam and coded-wire tagged (CWT). Fish were tagged 5 days per week in proportion to the 

daily collection. Each day approximately 60% of the fish were released to the dam’s tailrace 

through the bypass facility pipe; the other 40% were transferred into barges and released 

downstream of Bonneville Dam. Evaluations of transported fish returns, compared to those 

released to the McNary Dam tailrace, were based on CWT recoveries from commercial and 

recreational fisheries and hatcheries. For the second data set, we used subyearling Chinook 

salmon PIT tagged at McNary Dam in 2001 and 2002 to provide additional transportation 

evaluations to determine whether results from the 1995 and 1996 studies applied under the 

apparently improved ocean conditions that began in 1999. 

Estimating D (PATH Method) 

The PATH definition of D (see Figure 4.2-1 caption in Marmorek and Peters 1998) 

involves terms for “direct survival” of in-river migrants and “direct survival” of transported 

juvenile fish. This requires estimating the number of fish in each group (transported or in-river 

migrants) that were alive in the river below Bonneville Dam. To estimate post–Bonneville Dam

survival, the number of adult returns to Lower Granite Dam counted in each group is divided by 

the estimated number of juveniles counted below Bonneville Dam. The estimate of D is calculated 

as the ratio of transported group post-Bonneville Dam survival to in-river migrant group 

post-Bonneville Dam survival. 

For a given dam, the expected return rates (SAR) for transported and in-river migrants each 

have two components: the expected survival probability from the dam to below Bonneville Dam

and the expected survival probability from below Bonneville Dam to adult return. The SAR can 

be described by the following equations: 

SAR S T T = ⋅λT (1) 

and 

SAR S I I = ⋅λI (2) 

where the subscripts T and I refer to transported and in-river migrants, respectively; S is the 

downstream survival component; and λ is the post-Bonneville Dam component. The ratio of the 

SAR is the familiar T:I ratio: 

T I SAR

SAR

S

S

S

S

D T

I

T

I

T

I

T

I

: = = ⋅ = ⋅ λ

λ

 (3) 

This equation decomposes the T:I ratio into downstream and post-Bonneville Dam

components and introduces the parameter D, which is the ratio of post-Bonneville Dam survival 

23
for transported fish to that for in-river migrants. If transported fish and in-river migrants have the 

same survival probability from the transport release site to return as adults, then D = 1.0. If 

transported fish incur greater mortality after release from the barge, then D < 1.0. 

Transportation benefits fish stocks from a particular location only if the expected SAR for 

transported fish exceeds that for in-river migrants (i.e., if T:I > 1.0). Because ST (survival in the 

barge from the collection dam to below Bonneville Dam) is near 1.0, the decision reduces to 

comparing survival to below Bonneville for fish left in the river versus differential 

post-Bonneville Dam survival. In terms of the equations, transportation benefits fish only if D > 

SI. 

One consequence of this relationship is that if D is the same for each transportation site, 

then the benefit of transportation is greater for collection sites farther upstream. This is because 

SI increases for sites farther downstream. In other words, fish transported from Lower Granite 

Dam avoid the higher direct mortality incurred by fish prior to their collection and transportation 

from McNary Dam. The value of D may depend on the collection site; thus we apply a separate 

value for each collection site. We did not estimate survival from above Lower Granite Dam to the 

tailrace, because both in-river migrants and transported juveniles transited the same area in 

common; thus any value cancels calculations, with no effect on estimated D. 

The estimated number of in-river migrants (control group) alive below Bonneville Dam is 

derived by multiplying the annual estimate of the number of “control” fish arriving at Lower 

Granite Dam by the estimated annual average survival between Lower Granite and Bonneville 

Dam tailrace. With the PATH definition, it is impossible to calculate date-specific differential 

survival between transported fish and the “true” control group within a single migration season. 

While we can estimate the number of juveniles in the “never-detected” category that passed Lower 

Granite Dam on any particular day, we have no way of knowing what day a returning adult in that 

category passed Lower Granite Dam as a juvenile. Thus we cannot calculate the SAR for the 

never-detected group for a specific date. 

Estimating D (Non-PATH Method) 

We also determined how differential post-Bonneville survival between transported and 

in-river migrants might change within a single migration season. As identified above, we used fish 

marked at Lower Granite Dam and compared transported fish to those released into the tailrace 

that subsequently had the same detection history as the untagged fish population. We used 6-day 

blocks for fish marked and released at Lower Granite Dam and compared SAR for those 

transported within each block to those released to the dam tailrace that subsequently had the same

detection history as unmarked fish in the population. For studies in 2000, the transport groups 

were developed from fish collected at Little Goose Dam. We used the same methods to determine 

temporal D values that we used to determine average D over the season. 

24
Results 

Snake River Spring-Summer Chinook Salmon 

Annual estimates of SAR for transported and in-river migrants 

Based on Sandford and Smith’s (2002) methodologies, which were applied to fish PIT 

tagged above Lower Granite Dam from 1993 through 2003, we estimated that the combined 

annual percentage of the nontagged Chinook salmon population transported from Lower Granite, 

Little Goose, Lower Monumental, and McNary dams ranged from approximately 62% to nearly 

100% (Table 6). Clearly, the status of the yearling Chinook salmon in the Snake River basin 

depends to a large degree on the efficacy of transportation. 

Estimated annual SAR for PIT-tagged and transported Chinook salmon marked above 

Lower Granite Dam during outmigration years 1993–2000 varied widely between years and dams

(Table 2), as did the 95% confidence bounds (Table 3). For hatchery spring-summer Chinook 

salmon, the annual SAR for fish transported from Lower Granite Dam was significantly higher 

than for in-river migrants (nondetected category) from migration years 1997–2000 and from Little 

Goose Dam in 1999 and 2000. On the other hand, nondetected fish returned at higher rates than 

hatchery and wild fish transported from McNary Dam in 1994 and hatchery fish transported from

Little Goose and Lower Monumental dams in 1998. 

Annual SAR for PIT-tagged, juvenile spring-summer Chinook salmon marked at Lower 

Granite Dam during outmigration years 1995–2000 varied widely between years and at sites 

(Table 7). The fish included in these results were first-time detections at the respective dam. For 

fish marked at Lower Granite Dam, first-time detection was defined as after release from Lower 

Granite Dam (nondetected fish represented the route of passage of the nontagged population 

downstream of Lower Granite Dam). Annual adult returns for wild spring-summer Chinook 

salmon collected and marked at Lower Granite Dam indicated significantly higher annual SAR for 

transported fish in 1995 and 1999, but not in 1996, 1998, and 2000 (Table 8). Nondetected 

hatchery (1999) and wild (2000) fish returned at significantly higher rates than fish transported 

from Lower Monumental Dam.

Table 6. Estimated combined annual percentage of the nontagged yearling Chinook salmon population 

transported from Lower Granite, Little Goose, Lower Monumental, and McNary dams. 

Year Wild Hatchery

1993 88.5 88.1 

1994 87.7 84.0 

1995 86.4 79.6 

1996 71.0 68.7 

1997 71.1 71.5 

1998 82.5 81.4 

1999 85.9 77.3

2000 70.4 61.9 

2001 99.0 97.3

2002 72.1 64.2

2003 70.4 61.5

25
Table 7. Annual SAR (total adult returns/estimated number of juveniles) for spring-summer Chinook 

salmon PIT tagged at Lower Granite Dam for transportation studies between 1995 and 2000, 

compared to annual SAR of fish not detected downstream after release at Lower Granite Dam (fish 

that represented the migration history for the nontagged population). 

Transported from

Year 

Rearing 

typea

Lower 

Granite Dam 

Little Goose 

Damb

Lower 

Monumental Damb

McNary 

Dam Nondetected 

1995 W 0.38 (91/24066)c 0.39 (9/2318) 0.31 (3/968) NA 0.23 (26/11495)

H 0.54 (448/83063)c 0.37 (17/4562) 0.37 (4/1086) NA 0.32 (123/38543)

1996 W 0.11 (9/7949) – (0/350) –(0/140) NA 0.08 (4/5223) 

H 0.13 (47/35632) 0.10 (1/1001) –(0/523) NA 0.11 (27/25060)

1997 – No studies – 1998 W 0.60 (34/5689) – (0/2350) –(0/70) NA 0.95 (28/2932) 

H 0.62 (245/39596) 0.32 (6/1864) 0.16 (1/610) NA 0.57 (134/23552)

1999 W 2.10 (176/8384)c 0.70 (1/143) 0.86 (2/234)d NA 1.35 (26/1920)

H 1.97 (833/42273)c 2.09 (12/574) 0.87 (13/1486)d NA 1.45 (242/16664)

2000e W NA 1.47 (255/17371) 0.81 (7/869) NA 1.46 (384/26329)

H NA NA NA NA NA a W = wild; H = hatchery. 

b Fish transported from Little Goose and Lower Monumental dams include only first-time detections downstream of 

Lower Granite Dam. c Groups significantly higher than nondetected fish. 

d

 Groups significantly lower than nondetected groups. 

e

 Fish were tagged at Lower Granite Dam, released into the tailrace, and collected and transported from Little Goose 

Dam.

Table 8. Confidence intervals (95%) around annual SAR (see Table 7) for spring-summer Chinook salmon 

PIT tagged at Lower Granite Dam for transportation studies between 1995 and 2000, compared to 

intervals around annual SAR of nondetected fish (fish that represent the migration history for the 

nontagged population). 

Transported from

Year 

Rearing 

typea

Lower Granite 

Dam 

Little Goose 

Dam 

Lower 

Monumental Dam

McNary 

Dam Nondetected

1995 W 0.29–0.45 0.17–0.59 0.10–0.54 NA 0.17–0.27

H 0.51–0.57 0.26–0.48 0.18–0.57 NA 0.28–0.36

1996 W 0.05–0.18 0.00–0.86b 0.00–2.14b NA 0.02–0.15

H 0.10–0.17 0.00–0.21 0.00–0.57b NA 0.07–0.14

1997 No studies

1998 W 0.46–0.76 0.00–1.28b 0.00–4.29b NA 0.61–1.28

H 0.58–0.67 0.16–0.54 0.00–0.50 NA 0.48–0.65

1999 W 1.82–2.45 0.00–2.92 0.00–1.82 NA 0.94–1.79

H 1.90–2.06 1.04–3.31 0.53–1.27 NA 1.32–1.59

2000c W NA 1.36–1.61 0.55–1.17 NA 1.36–1.55

H NA NA NA NA NA a W = wild; H = hatchery. 

b Used “rule of 3” where 0 adults returned. c Fish were tagged at Lower Granite Dam, released into the tailrace, and collected and transported from Little 

Goose Dam.

26
Transport location-specific and overall annual estimates of differential 

post-Bonneville Dam survival (D) 

Annual estimates provide a general illustration of differences in return rates between 

transported and in-river migrants and differences between transport locations. 

Large adult returns in recent years generally improved our ability to estimate the ratio of 

post-Bonneville Dam survival for transported fish to that of in-river migrants separately for each 

transportation dam and greatly improved precision of the overall estimate. In all comparisons of 

hatchery and wild Snake River spring-summer Chinook salmon, the greatest number of returning 

PIT-tagged adults came from the 1999 and 2000 outmigrations (Tables 9 and 10). 

Results were not consistent. To summarize them, we offer the following observations: 

1. For wild and hatchery fish, the geometric mean annual D from migration years 1994 

through 2000 ranged between 0.55 and 0.61. That is, averaged over years and across 

migration seasons, survival for fish transported from below Bonneville Dam as a juvenile 

to return as an adult has averaged less than two-thirds that of in-river migrants that arrived 

below Bonneville Dam. 

2. Wild and hatchery spring-run Chinook salmon transported from Lower Monumental Dam

have had the lowest average post-Bonneville Dam survival. Average in-river survival 

from Lower Monumental Dam to Bonneville Dam has exceeded this average D, indicating 

that fish not transported from Lower Monumental Dam had higher average annual SAR 

than fish transported from the site. 

3. For wild spring-summer Chinook salmon, average differential post-Bonneville Dam

survival for fish transported from Lower Granite Dam roughly equaled the average 

survival of in-river migrants that migrated between Lower Granite and Bonneville dams. 

Wild Chinook salmon transported from Lower Granite Dam in 2000 had particularly low 

annual post-Bonneville Dam survival. Thus on an average annual basis, transportation 

provided no benefit. In some years transported fish had higher average annual returns than 

in-river fish, but in some years it was lower. 

4. For hatchery spring-summer Chinook salmon, average differential post-Bonneville Dam

survival for fish transported from Lower Granite Dam has considerably exceeded the 

average estimated survival for the in-river migrants between Lower Granite and 

Bonneville dams. Thus on an average annual basis, transportation led to increased returns 

when compared to in-river fish. 

5. Small sample sizes resulted in imprecise annual D estimates. For example, even with more 

than 2,000 returns of hatchery Chinook salmon in 2000, the 95% confidence interval was 

still wide (Table 10). The number of juvenile fish from the outmigration, however, 

provided the ability to make a relatively precise estimate for survival of in-river migrants 

between Lower Granite and Bonneville dams. 

27
Table 9. Annual estimates of differential post-Bonneville Dam survival (D) for wild Snake River 

spring-summer Chinook salmon transported from various dams and for weighted average from all 

sites. Total adult returns are provided in parentheses (when adults in a category = 0, the number of 

juveniles is given as well). All fish were tagged upstream from Lower Granite Dam. Approximate 

95% confidence intervals for weighted averages are in brackets. 

Transported from

Year 

 Nontransported* All sites 

Lower 

Granite Dam 

Little Goose 

Dam 

Lower 

Monumental Dam

1994 6 0.683 (13) [0.254, 1.844] 0.770 (8) 1.187 (4) 0.239 (1) 

1995 10 0.457 (8) [0.177, 1.184] 0.559 (7) 0.467 (1) (0/195) 

1996 5 1.081 (2) [0.202, 5.783] 0.688 (1) 2.453 (1) (0/43) 

1997 17 0.498 (4) [0.162, 1.539] 0.224 (2) 1.262 (2) (0/14) 

1998 48 0.430 (15) [0.238, 0.783] 0.480 (11) 0.334 (3) 0.421 (1) 

1999 104 0.656 (48) [0.460, 0.934] 0.730 (32) 0.641 (9) 0.563 (7) 

2000 174 0.336 (12) [0.184, 0.613] 0.245 (4) 0.474 (6) 0.274 (2) 

Geometric mean: 0.553 0.478 0.779 0.353 

* Nontransported fish are PIT-tagged fish with passage histories most representative of nontagged fish that migrated to 

Bonneville Dam in-river. 

Table 10. Annual estimates of differential post-Bonneville Dam survival (D) for hatchery Snake River 

spring-summer Chinook salmon transported from various dams and for weighted average from all 

sites. Total adult returns are in parentheses (when adults in category = 0, the number of juveniles 

is given as well). All fish were tagged upstream from Lower Granite Dam. Approximate 95%

confidence intervals for weighted averages are given in brackets. 

Transported from

Year 

 Nontransporteda All sites 

Lower 

Granite Dam

Little 

Goose Dam 

Lower 

Monumental Dam

1994b 7 0.316 (6) [0.104, 0.963] 0.314 (2) 0.445 (1) 0.468 (1) 

1995 32 0.886 (20) [0.501, 1.572] 0.808 (14) 1.238 (5) 0.661 (1) 

1996 32 0.409 (6) [0.168, 0.995] 0.780 (6) (0/510) (0/366) 

1997 185 0.523 (233) [0.430, 0.639] 0.561 (226) 0.469 (5) 0.517 (2) 

1998 336 0.638 (885) [0.561, 0.727] 0.829 (812) 0.405 (66) 0.319 (7) 

1999 736 0.903 (1203) [0.821, 0.993] 0.930 (697) 1.036 (481) 0.477 (25) 

2000 915 0.870 (1426) [0.798, 0.948] 0.961 (1030) 0.726 (310) 0.658 (86) 

Geometric mean: 0.606 0.700 0.654 0.502 a Nontransported fish are PIT-tagged fish with passage histories most representative of nontagged fish that migrated to 

Bonneville Dam in-river. 

b Two fish transported from McNary Dam returned as adults. Estimated differential post-Bonneville Dam survival for 

McNary transport = 0.098. 

28
Within-season variability in transportation and D

For fish PIT tagged at Lower Granite Dam, we have known timing for transported and 

subsequently nondetected fish. From these fish we determined that not only did SAR vary over the 

course of the outmigration, but the variation in timing changed between years. Transported 

Chinook salmon had greater temporal changes in SAR than in-river migrants (Figures 9, 10, 11, 

and 12). For wild fish, due to higher variability about SAR estimates, we detected only one 

1995

15-20 Apr21-26 Apr

27 Apr-2 May

3-8 May

9-14 May

0.00

0.25

0.50

0.75

20 16

11

15 9

2

11

9

2

1

Transported

Not detected

SAR (

%)

1998

7-12 Apr

13-18 Apr19-24 Apr25-30 Apr

1-6 May

7-12 May

0.0

0.5

1.0

1.5

2.0

2.5

**

12

16

9

14

8

1

4

1

2

2

Date at dam as juveniles

SAR (%)

Figure 9. Temporal change in SAR of wild Snake River spring-summer Chinook salmon PIT tagged at 

Lower Granite Dam, 1995 and 1998. No significant differences in return rates were detected 

between treatment group pairs. Numbers above the bars indicate total SAR for each group.

29
1999

31 Mar-5 Apr

6-11 Apr

12-17 Apr18-23 Apr24-29 Apr

30 Apr-5 May

6-11 May

12-17 May18-23 May24-29 May

0

1

2

3

4

4

1

1

2

3

5

2

80

8 8

45

21

3

4

4

4

Transported

Not detected

SA

R (

%)

2000

6-11 Apr

12-17 Apr18-23 Apr24-29 Apr

30 Apr-5 May

6-11 May

12-17 May18-23 May24-29 May

30 May-4 Jun

5-10 Jun

0.0

0.5

1.0

1.5

2.0

2.5

3.0

3.5

4.0

4.5

5.0

5.5

6.0

6.5

*

3

2

74

70

42

42 4348 3180

29

70

16

43 3

6

9

11

4 5 1 1

Date at dam as juveniles

SAR (

%)

Figure 10. Temporal change in SAR of wild Snake River spring-summer Chinook salmon PIT tagged at 

Lower Granite Dam, 1999 and 2000. In 2000, in one treatment pair, transported fish returned at 

significantly higher rates. Numbers above the bars indicate the total adult returns for each group. 

30
15-20 Apr

21-26 Apr

27 Apr-2 May

3-8 May

9-14 May

15-20 May

0.00

0.25

0.50

0.75

1.00

*

*

*

Transported

Not detected

40

18 41 22

104

32

175

40

49

9

28

1

1995

SAR (

%)

1998

7-12 Apr

13-18 Apr19-24 Apr25-30 Apr

1-6 May

7-12 May

13-18 May19-24 May

0.00

0.25

0.50

0.75

1.00

1.25 **

* *

6

25

46

50

20 18

9

1

16

24

11

42

4

10

1

1

2

Date at dam as juveniles

SAR (

%)

Figure 11. Temporal change in SAR of hatchery Snake River spring-summer Chinook salmon PIT tagged 

at Lower Granite Dam, 1995 and 1998. * = significantly higher return rates of transported fish 

occurred for several treatment pairs in both years; ** = a significantly higher return rate of 

nondetected fish occurred for one treatment pair in 1998. Numbers above the bars indicate total 

adult returns for each group. 

31
1999

18-23 Apr24-29 Apr

30 Apr-5 May

6-11 May

12-17 May18-23 May24-29 May

0.0

0.5

1.0

1.5

2.0

2.5

3.0

3.5

4.0

4.5

**

* *

*

Transported

Not detected

9

8

161 51

240

67

226

52

89

22

72

13

35

8

Date at dam as juveniles

SAR (

%)

Figure 12. Temporal change in SAR of hatchery Snake River spring-summer Chinook salmon PIT tagged 

at Lower Granite Dam, 1999. * = significantly higher return rates occurred for transported fish in 

several treatment pairs. A significantly higher rate for nondetected fish occurred in one treatment 

pair. Numbers above the bars indicate total adult returns for each group. 

significantly higher SAR in one treatment pair (the transported fish in the 12–18 May 2000 period 

returned at higher rates). The SAR of hatchery fish had tighter confidence bounds, and thus we 

detected more significant differences in treatment pairs. In 1998 and 1999, the earliest 

nondetected in-river fish migrating below Bonneville Dam returned at significantly higher rates 

than transported fish, whereas in all years transported fish returned at significantly higher rates for 

several group pairs during the mid to late outmigration. 

Adult upstream conversion rates 

In 2002 and 2003, based on PIT-tag detections at Bonneville and Lower Granite dams of 

wild 2- and 3-ocean spring-summer Chinook salmon adults returning from the 2000 and 2001 

outmigrations, transported and in-river fish had nearly the same high adult conversion rates (Table 

11). These conversion rates (the percentage of adult fish at Bonneville Dam estimated to 

Table 11. Conversion rates (number of adult fish detected at Lower Granite Dam/number of adult fish 

detected at Bonneville Dam) for adult wild spring-summer Chinook salmon PIT tagged as juveniles 

at Lower Granite Dam in 2000 and 2001 and either returned to the river or transported. 

Year of outmigration Year of adult return In-river Transported 

2000 2002 0.86 (196/228) 0.87 (97/111) 

2003 0.82 (324/394) 0.84 (117/140) 

2001 2003 NA 0.92 (91/99)

32
33

have migrated successfully to the upper dam) were not adjusted for harvest between Bonneville 

and McNary dams (zone 6). They far exceed the average values ascribed to the hydropower 

system used in recent PATH analyses (Marmorek et al. 1998). As adult fish passage facilities and 

upstream conditions have changed comparatively little in the past several decades, analyses based 

on old conversation rates likely contain considerable error. 

Snake River Fall Chinook Salmon 

For juvenile fish detected prior to 1 September, in 4 out of 6 years the SAR of the combined 

bypassed group exceeded the SAR of the combined transported group (Figure 13). For juvenile 

fish detected in the late period, transported and bypassed fish each had 2 years when they returned 

at higher rates than the other (Figure 14). However, the confidence bounds about the ratios for 

groups extended from 0 (or nearly so) to higher than 1 (and mostly considerably higher than 1). 

Thus no empirical evidence exists to suggest that transportation either harms or helps fall Chinook 

salmon. This does not, however, constitute evidence that T:I = 1. Based on variability in results, 

we suggest that the average T:I likely falls somewhere between 0.67:1 and 1:50:1. (This range is 

symmetric around 1.0 on the multiplicative scale [1:3 to 3:2], not on the additive scale.) Given the 

relationships among in-river survival, T:I, and D, this implies that D lies in the range determined 

by multiplying an estimate of in-river survival by the likely range in T:I; i.e., (0.67)*(in-river 

survival) to (1.50)*(in-river survival). No evidence exists to suggest that changes in juvenile 

in-river survival between Lower Granite and Bonneville dams would have any effect on the 

survival of either transported or in-river migrants after they pass Bonneville Dam. Thus because 

D pertains only to post-Bonneville Dam survival of transported fish relative to that of in-river fish, 

without further information we expect the range of likely values for D suggested above will hold 

even under changes in juvenile survival. 

Upper Columbia River Subyearling Migrants 

In 1995 and 1996, subyearling Chinook salmon transported from McNary Dam generally 

had higher return rates than in-river migrants when flows at the dam exceeded approximately 

6,500 m3

/second (approximately 225,000 cubic feet per second) and water temperatures remained 

below 18°C (Figures 15 and 16). Counter to studies in the early 1980s conducted at the old 

juvenile facility at McNary Dam, where transported fish returned at 2 to 4 times the rate of fish 

released to the dam tailrace, these results suggested that transporting subyearling Chinook salmon 

under conditions of higher water temperatures and lower flows decreased adult return rates 

compared to returning fish to the river. The preliminary returns from fish PIT tagged in 2001 and 

2002 (a total of 62 1-ocean and 2-ocean returns from marking in 2001 and 143 1-ocean returns 

from marking in 2002) did not apparently decrease as the season progressed, as had occurred in the 

earlier years (Figures 17 and 18, compared to Figures 15 and 16).
Chinook salmon detected

3.53.02.52.01.51.00.50.0

4

2

0

11

26

3

1

6

SAR transportedSAR bypassed

SAR (%)

1997 

95% confidence interva

1995 1996 1998

Release year

8 7 6 5 4 3 2 1 0

Ratio of

trans

ported:bypassed fish

Chinook salmon detected

0.00.51.01.52.02.53.03.5 SAR transported

3

1 2

17 9

10 2 20

12

59

4

6

SAR bypassed

SAR (%)

1995 1996 1997 1998 1999 2000

012345678 95% confidence intervals

Release year

Ratio of

 transported:bypassed fish

Figure 13. SAR of PIT-tagged, hatchery Snake River fall Chinook 

salmon released above Lower Granite Dam and bypassed or transported from Lower Granite, Little Goose, Lower Monumental, or McNary dams (not adjusted to Lower Granite Dam equivalents) prior to 1 September 1995–2000, with ratios of transported:bypassed fish and 95% confidence bounds. Numbers above the bars indicate total adult returns for each group. 

Figure 14. SAR of PIT-tagged, hatchery Snake 

salmon released above Lower Granite Dtransported from Lower Granite, Little Monumental, or McNary dams (not adjuDam equivalents) on 1 September or latratios of transported:bypassed fish and 9Numbers above the bars indicate total agroup. 

34
Figure 15. Relative recovery rates of coded-wire-tagged adult 

summer-fall Chinook salmon recovered from fisheries or at hatcheries from subyearling fish tagged as juveniles in 1995 at McNary Dam and either transported (T) to below Bonneville Dam or released into the tailrace of McNary Dam(I = in-river). 

Figure 16. Relative recovery rates of summer-fall Chinook salmon recoverhatcheries from subyearling fish taggMcNary Dam in 1996 and either tranBonneville Dam or released into the t(I = in-river). 

Ratio of T:I fish Ratio of T:I fish

0.00.51.01.52.02.5

Flow

0

6/19

6/23

6/27

7/1

7/2

7/4

7/8

7/13

7/16

0.00.51.01.52.02.5

Watertemperatu

Release date

0.00.51.01.52.02.5

100150200250300

Flow

Flow (kcfs)

0

6/19

6/23

6/27

7/1

7/2

7/4

7/8

7/13

7/16

7/18

8/3

0.00.51.01.52.02.5

161718192021222324

Watertemperature

Release date

Water temperature

o

Rati

C

o of T:I fish Ratio of T:I fish

35
36

Figure 18. Relative recovery rates based on SAR f

releases of transported (T) and in-river (I) salmon PIT tagged and released at McNary with the weekly average water temperature total 1-ocean fish have returned to date. 

012

Flow

Ratio of T:I fish

6/26

7/3

7/10

7/17

7/24

7/31

012

Watertemperature

Release date

Ratio ofT:I fish

Figure 17. Relative recovery rates based on SAR for combined 

weekly releases of transported (T) and in-river (I) subyearling Chinook salmon PIT tagged and released at McNary Dam in 2001, plotted with weekly average water temperature and flow. Data include only 62 total 1-ocean and 2-ocean fish that returned: * indicates no transported fish returned. 

0123

708090100110120130

*

Flow

Ratio of T:I fish

Flow (kcfs)

6/26

7/3

7/10

7/17

7/24

7/31

8/7

8/14

0123

1718192021

*

Watertemperature

Release date

Ratio of T:I fish

Water temperature

o

C
Snake River Steelhead 

Annual estimates of SAR for transported and in-river migrants 

Based on Sandford and Smith (2002) methodologies applied to fish PIT tagged above 

Lower Granite Dam from 1993 through 2003, we estimated that the combined annual percentage 

of the nontagged steelhead (Oncorhynchus mykiss) population transported from Lower Granite, 

Little Goose, Lower Monumental, and McNary dams ranged from approximately 68% to nearly 

100% (Table 12). As with yearling Chinook salmon, because of the high proportion of steelhead 

transported, the status of Snake River basin steelhead depends to a large degree on the efficacy of 

transportation. 

Table 12. Estimated combined annual percentage of the nontagged steelhead population transported from

Lower Granite, Little Goose, Lower Monumental, and McNary dams. 

Year Wild Hatchery

1993 93.2 94.7

1994 91.3 82.2

1995 91.8 94.3

1996 79.8 82.9

1997 87.5 84.5

1998 88.2 87.3

1999 87.6 88.5

2000 83.9 81.5

2001 99.3 96.7

2002 75.2 70.4

2003 72.9 68.4

Estimated annual SAR for steelhead PIT tagged above Lower Granite Dam and transported 

during outmigration years 1993 to 2000 varied widely between years and dams (Table 4), as did 

the 95% confidence bounds (Table 5). At any one dam the number of wild steelhead juveniles 

generally was 300 fish or less, and adult returns of wild steelhead in most years at any one dam

rarely exceeded five fish. For hatchery steelhead in migration years 1994 and 2000, the annual 

SAR for fish transported from Lower Granite Dam was significantly higher than for in-river 

migrants (nondetected category). 

Annual SAR for PIT-tagged juvenile steelhead marked at Lower Granite Dam during 

outmigration years 1998 to 2000 varied widely between years, treatments, and sites (Table 13). 

The fish included in these results were first-time detections at the respective dam. For fish marked 

at Lower Granite Dam, first-time detection was defined as after release from Lower Granite Dam

(nondetected fish represented the route of passage of the nontagged population downstream of 

dam). The annual SAR of transported wild and hatchery steelhead were significantly higher for 

transported fish than in-river migrants from both the 1999 and 2000 outmigrations (Table 14). Too 

few fish returned from the 1998 marking to determine differences in return rates. 

37
Table 13. Annual SAR (total adult returns/estimated number of juveniles) for steelhead PIT tagged at 

Lower Granite Dam for transportation studies between 1998 and 2000, compared to annual SAR 

of fish not detected downstream after release at Lower Granite Dam (fish that represented the 

migration history for the nontagged population). Fish transported from Little Goose Dam and 

Lower Monumental Dam include only first-time detections downstream of Lower Granite Dam. 

Transported from

Year 

Rearing 

typea

Lower Granite 

Dam Little Goose Dam

Lower 

Monumental Dam

McNary 

Dam Nondetected 

1998 W NA 0.35 (1/287) – (0/231) NA 0.37 (7/1878) 

H NA 0.71 (7/990) 0.43 (2/462) NA 0.41 (24/5835) 

1999 W 1.42 (86/6052)c 0.80 (1/125) 3.14 (5/159) NA 0.54 (8/1471) 

H 1.07 (441/41057)c 1.43 (15/1048)c 0.46 (4/870) NA 0.79 (82/10442)

2000b W NA 3.96 (979/24738)c 4.75 (88/1854)c NA 1.85 (435/23506)

H NA 1.99 (11/553) 1.39 (5/360) NA 0.85 (79/9276) a W = wild; H = hatchery. 

b Fish were tagged at Lower Granite Dam, released into the tailrace, collected, and transported from Little Goose Dam. c

 Returns are significantly higher than nondetected fish. 

Table 14. Confidence intervals (95%) around annual SAR (see Table 13) for steelhead PIT tagged at Lower 

Granite Dam for transportation studies between 1998 and 2000, compared to intervals around 

annual SAR of nondetected fish (fish that represent the migration history for the nontagged 

population). 

Transported from

Year 

Rearing 

typea

Lower Granite 

Dam 

Little Goose 

Dam 

Lower 

Monumental Dam

McNary 

Dam Nondetected

1998 W NA 0.00–1.05 0.00–1.30c NA 0.16–0.62

H NA 0.10–1.39 0.00–1.25 NA 0.27–0.56

1999 W 1.18–1.69 0.00–2.48 0.60–6.84 NA 0.27–0.90

H 1.02–1.14 1.01–1.81 0.23–0.70 NA 0.63–0.92

2000b W NA 3.78–4.13 3.87–5.79 NA 1.71–1.99

H NA 0.98–3.39 0.27–2.79 NA 0.70–1.07 a W = wild; H = hatchery. 

b

 Fish were tagged at Lower Granite Dam, released into tailrace, collected, and transported from Little Goose Dam. c

 “Rule of 3” was used. 

Transport location-specific and overall annual estimates of differential 

post-Bonneville Dam survival 

In this section we summarize data on annual estimates of D for steelhead. Large adult 

returns in recent years generally improved our ability to estimate differential post-Bonneville Dam

survival separately for each transportation dam and greatly increased the precision of the overall 

estimate. For hatchery and wild Snake River steelhead, the greatest number of returning 

PIT-tagged adults occurred in 1999 and 2000 (Tables 15 and 16). 

38
Table 15. Annual estimates of differential post-Bonneville Dam survival (D) for Snake River wild 

steelhead transported from various dams and for weighted average from all sites. Total adult 

returns are provided in parentheses (when adults in a category = 0, the number of juveniles is given 

as well). All fish were tagged upstream from Lower Granite Dam. Approximate 95% confidence 

intervals for weighted average are in brackets. 

Transported from

Year 

 Nontransported* All sites 

Lower Granite 

Dam 

Little Goose 

Dam 

Lower 

Monumental Dam 

1994 6 0.531 (8) [0.178, 1.581] 0.663 (6) 0.211 (1) 0.266 (1) 

1995 1 0.981 (1) [0.058, 16.710] (0/287) (0/66) 10.023 (1) 

1996 5 0.978 (2) [0.181, 5.279] 0.678 (1) 2.214 (1) (0/11) 

1997 4 0.536 (3) [0.115, 2.492] 0.844 (3) (0/44) (0/23) 

1998 9 0.118 (1) [0.014, 0.976] 0.165 (1) (0/93) (0/93) 

1999 18 1.013 (12) [0.475, 2.163] 0.735 (6) 1.343 (4) 0.882 (2) 

2000 41 0.691 (14) [0.368, 1.296] 0.660 (7) 0.801 (4) 0.613 (3 

Geometric mean: 0.582 0.550 0.842 1.757 

* Nontransported fish are PIT-tagged fish with passage histories most representative of nontagged fish that migrated to 

Bonneville Dam in-river. 

Table 16. Annual estimates of differential post-Bonneville survival (D) for Snake River hatchery steelhead 

transported from various dams and for weighted average from all sites. Total adult returns are 

provided in parentheses (when adults in a category = 0, the number of juveniles is given as well). 

All fish were tagged upstream from Lower Granite Dam. Approximate 95% confidence interval for 

weighted average given in brackets. 

Transported from

Year 

 Nontransporteda All sitesb

Lower 

Granite Dam 

Little Goose 

Dam 

Lower 

Monumental Dam 

1994 7 2.707 (23) [1.140, 6.429] 3.684 (20) (0/1007) 1.943 (2) 

1995 14 0.435 (19) [0.214, 0.884] 0.392 (14) 0.996 (5) (0/88) 

1996 17 0.294 (4) [0.097, 0.896] 0.446 (4) (0/353) (0/94) 

1997 8 0.968 (10) [0.374, 2.505] 1.615 (10) (0/158) (0/119) 

1998 26 0.326 (7) [0.139, 0.767] 0.374 (5) 0.152 (1) 0.373 (1) 

1999 41 0.332 (12) [0.171, 0.642] 0.336 (8) 0.457 (4) (0/250) 

2000 41 1.051 (14) [0.562, 1.967] 1.291 (13) (0/102) 0.345 (1) 

Geometric mean: 0.627 0.776 0.411 0.630 a Nontransported fish are PIT-tagged fish with passage histories most representative of nontagged fish that migrated to 

Bonneville Dam in-river. 

b

 In 1994, one fish transported from McNary Dam returned as an adult. Estimated differential post-Bonneville Dam

survival for McNary Dam transport = 0.417. 

39
Nonetheless, as with yearling Chinook salmon, results were not consistent. To summarize 

results, we offer the following observations: 

• For hatchery and wild steelhead, the geometric mean annual estimated D from migration 

years 1994 through 2000 ranges widely (Tables 15 and 16). Sometimes survival for 

transported fish from below Bonneville Dam as a juvenile to return as an adult is lower 

than the in-river migrants; other times it is higher. 

• For hatchery steelhead, average differential post-Bonneville Dam survival for fish 

transported from Lower Granite Dam considerably exceeded the average estimated 

survival for the in-river migrants that migrated between Lower Granite and Bonneville 

dams. (Data are not sufficient to judge for wild steelhead.) 

• It is very difficult to estimate annual D values precisely. The number of juvenile fish from

the outmigration, however, provided the ability to make a relatively precise estimate of 

survival for in-river migrants between Lower Granite and Bonneville dams. 

Within-season variability in transportation and D

For steelhead PIT tagged at Lower Granite Dam, we have known timing for transported 

and, subsequently, nondetected fish. From these fish we determined that not only did SAR vary 

over the course of the outmigration, but the variation in timing changed between years (Figures 19 

and 20). No consistent pattern appeared. The majority of treatment pairs did not have significant 

differences in adult returns. As with wild spring-summer Chinook salmon, it appeared that SAR 

were generally slightly higher for the first fish groups in a season. Likewise, transported fish 

tended to have higher SAR during the middle of the migration. 18-23 Apr 24-29 Apr

30 Apr-5 May

6-11 May

12-17 May18-23 May24-29 May

0.0

0.5

1.0

1.5

2.0

2.5 **

*

Transported

Not detected

16

6

39

12

106

11

80

20

62

18

91

7

36

5

Date at dam as juveniles

SAR (

%)

Figure 19. Temporal change in SAR of 

hatchery Snake River steelhead PIT 

tagged at Lower Granite Dam. In 

one treatment pair, significantly

more nondetected fish returned.(**) 

In another pair, significantly more 

transported fish returned.(*) 

Numbers above bars indicate total 

adult returns for each group. 

40
1999

31 Mar-5 Apr

6-11 Apr

12-17 Apr18-23 Apr24-29 Apr

30 Apr-5 May

6-11 May

12-17 May18-23 May24-29 May

0.0

0.5

1.0

1.5

2.0

2.5

3.0

3.5

7

1

19

1

9

2

7

1

11

2

20

9

1

Transported

Not detected

Date at dam as Juveniles

SAR (

%)

2000

31 Mar-5 Apr

6-11 Apr

12-17 Apr18-23 Apr24-29 Apr

30 Apr-5 May

6-11 May

12-17 May18-23 May24-29 May

0.0

0.5

1.0

1.5

2.0

2.5

3.0

3.5

4.0

4.5

5.0

5.5

*

*

*

*

17

2

37

25

192

67

293

199

227

47

166

59

46

27

2

5

2

2

1 1

Date at dam as Juveniles

SA

R (

%)

Figure 20. Temporal change in SAR of wild Snake River steelhead PIT tagged at Lower Granite Dam, 1999 

and 2000. For four treatment pairs, significantly more transported fish returned (*) than 

nondetected fish. Numbers above bars indicate total adult returns for each group. 

41
Adult upstream conversion rates 

Between 2001 and 2003, based on PIT-tag detections at Bonneville and Lower Granite 

dams of wild 1- and 2-ocean steelhead adults returning from the 2000 outmigrations, transported 

fish had lower conversion rates to Lower Granite Dam than in-river fish (Table 17). We know that 

steelhead transported as juveniles return to the river generally later than in-river migrant juveniles, 

thus some conversion rate differences may relate to differences in harvest directed at steelhead or 

incidental to fall Chinook salmon harvest. We have not yet had the opportunity to evaluate this 

possibility. Another possibility for the difference could relate to higher stray rates for transported 

fish compared to in-river fish. Again we have no data at this time to determine the reason for this 

difference. 

Table 17. Conversion rates (number of adult fish detected at Lower Granite dam/number of adult fish 

detected at Bonneville Dam) for wild adult steelhead PIT tagged as juveniles at Lower Granite Dam

in 2000 and 2001 and either returned to the river or transported. 

Year of outmigration Year of adult return In-river Transported 

2000 2001 0.83 (347/418) 0.70 (316/451) 

2002 0.78 (286/366) 0.71 (320/450) 

2001 2002 NA 0.65 (194/298)

2003 NA 0.96 (136/142)

Discussion 

Results of all transportation studies clearly indicate that transported fish survive at lower 

rates downstream of Bonneville Dam than fish that migrate through the hydropower system. 

Nonetheless, for wild yearling Chinook salmon and steelhead, in almost all cases fish transported 

after 1 May returned at similar or higher rates than fish that migrated through the FCRPS 

reservoirs and dams. In some years, fish transported as early as 15–20 April returned at higher 

rates than in-river fish, but not consistently. For subyearling migrants, it did not appear that 

transportation consistently provided higher returns. In fact, in many comparisons, the fish that 

migrated through reservoirs and dams had higher return rates than those transported (because of 

very low sample sizes, differences were not statistically significant). The higher returns occurred 

even though the presumed—but not directly measured—survival of in-river migrants was 

generally quite low. 

Yearling Chinook salmon transported by barge from Snake River dams arrived to their 

release point below Bonneville Dam typically in about 1.5 days, while those that migrated through 

the seven remaining dams took from 3 to 4 weeks early in the migration season, to less than 2 

weeks by the end of May (Smith et al. 2000a and 2000b, Zabel et al. 2001). Thus smolts marked 

on the same day, but either transported or returned to the river, most likely encountered different 

physical and biological conditions within the estuary and nearshore ocean upon their arrival. The 

Columbia River estuary and nearby ocean are very dynamic environments. Coastal winds, 

upwelling, sea surface temperatures, and other physical conditions can change very quickly 

(Garcia Berdeal et al. 2002). Large changes in biological conditions (such as forage fish 

42
abundance and predatory fish abundance) in the Columbia River plume (Emmet and Brodeur 2000, 

Emmett et al. 2001) and the estuary7

 have been observed between and within years. Growth and 

survival of salmonids in their first months at sea appear critical to determining overall salmonid 

year-class strength. This is based on the relationship between returns of jack salmon with numbers 

of adults returning from the same broodyear class in later years, and between ocean purse seine 

catches of juvenile salmonids in June and subsequent jack and adult returns (Pearcy 1992). 

Much of the observed seasonal, average delayed mortality for transported fish could 

simply result from varying ocean conditions at the time they enter the ocean. This comports with 

estimates of D observed in fish we marked at dams and results reported in the CSS, where D was 

lowest for the earliest migrating stocks (Lookingglass and Dworshak Hatcheries) and highest for 

the later migrants from McCall and Imnaha River acclimation ponds (CSS 2003). 

Our analyses of seasonal trends in post-Bonneville Dam survival suggests that 

within-season variation could have important implications for management decisions that a single 

seasonal estimate of D would mask. If the efficacy of transportation is largely determined by time 

of ocean entry, then for early migrating stocks delay of arrival below Bonneville Dam should 

increase survival. Alternatively, for early migrating hatchery stocks, later hatchery release dates 

might lead toward a later arrival date at transport dams. Unfortunately, at this time we have no 

way to predict conditions that will exist when smolts first arrive in the estuary or ocean. 

The smoltification process in salmonids causes morphological, behavioral, and 

physiological changes that affect downstream migration as well as the ability to survive in the 

marine environment. This process is regulated by developmental stage, photoperiod, and water 

temperature cues that enable salmonids to migrate when environmental conditions are most 

favorable for downstream passage and survival in the sea (Folmar and Dickhoff 1980, Wedemeyer 

et al. 1980). The act of migration further stimulates smolt development (Zaugg et al. 1985, Muir 

et al. 1994). Spring-summer Chinook salmon and steelhead migrations in the Snake and Columbia 

rivers show similar seasonal patterns each year, beginning in early April and tailing off near the 

end of May. Zaugg and Wagner (1973) found that gill Na + –K + ATPase (an indicator of 

migratory readiness) and migratory urge declined at water temperatures of 13°C and higher. 

Steelhead that migrate too late in the season, when water temperatures are above this threshold, 

may have a tendency to residualize. Although this same behavior has not been demonstrated in 

spring-summer Chinook salmon, exposure to water temperatures above 13°C has been shown to 

retard gill Na + –K + ATPase activity (Muir et al. 1994). Furthermore, Congleton et al. (2004) 

found that hatchery spring-summer Chinook salmon arriving at the collector dams had depleted 

the majority of their energy reserves; for those fish left in-river to migrate (not transported), energy 

reserves became depleted as they progressed downstream. Energy depletion was greater for 

smolts arriving at the dams later in the migration season and during the prolonged migration, as 

observed during the 2001 low-flow year. Construction of the FCRPS altered smolt migration 

timing. Regardless of when fish arrive at Lower Granite Dam, the nontransported fish certainly 

take longer to migrate through the entire FCRPS, and they arrive later at the ocean and likely in 

different condition than they did historically. Further, transported fish cover the distance more 

quickly and arrive at the ocean sooner than they would have in an unregulated system.

 7 R. Emmett, NOAA Fisheries Service, Newport, OR. Pers. commun., December 2003. 

43
The hypotheses that transportation-induced stress or disease transmission (Budy et al. 

2002) cause lower adult returns are not supported by the temporal variability in measured values 

of D and SAR. If these hypotheses held true, we would not expect to see the much higher SAR and 

D values later in the season. It appears more likely that early transported fish arrive too soon to the 

estuary. 

Although D values below 1.0 indicate a differential mortality between transported and 

in-river migrants, we expect that some transported fish would die due to natural selection if they 

continued their downstream migration through the hydropower system. Very low values of D, 

however, indicated a substantial differential mortality after release from transportation barges 

compared to the fish that survived to below Bonneville Dam after migrating through the FCRPS 

reservoirs and dams. Aside from a differential mortality between fish transported from upper 

Snake River dams (2% mortality in barges assumed) and fish that migrated in-river to below 

Bonneville Dam (approximately 50% mortality), the two groups marked on the same day have 

substantially different timing to the ocean (20–25 days for the earliest fish, and 15 days or less for 

the latest fish). We presume that the late migrants leaving Lower Granite Dam may miss the 

window of opportunity for best survival conditions by arriving too late below Bonneville Dam. 

The declining lipid reserves for late migrants observed by Congleton et al. (2004) may also 

decrease their survival. 

Nonetheless, on average when the annual weighted D is combined with the average 

survival through the hydropower system, it yielded for wild spring-summer Chinook salmon and 

steelhead an overall survival estimate for the entire stock of approximately 50%. This value is as 

high or higher than the estimated survival of juvenile fish migrating through the FCRPS when only 

four dams and reservoirs existed during the 1960s (Williams et al. 2001). 

With the low number of adult returns of PIT-tagged fish to date, especially for wild fish, 

definitive conclusions are not possible. We tentatively conclude that D values for fish transported 

from Lower Monumental and McNary dams are lower than for dams farther upstream. Combined 

with the higher survival to Bonneville Dam for fish left in the river at McNary Dam, a spring 

transportation program at McNary Dam likely provides only marginal benefits at best to Snake 

River stocks. There is no evidence that D values for Chinook salmon transported from Little 

Goose Dam are lower than for fish transported from Lower Granite Dam. 

Although annual SAR for fish PIT tagged above Lower Granite Dam generally exceeded 

those of fish PIT tagged at the dam, ratios of return rates of transported to nondetected fish (which 

migrate past dams through turbines and spill) were similar. Thus results from studies with fish PIT 

tagged at Lower Granite Dam provide information on the relative differences in return rates of 

transported and in-river migrant fish in the population. The numbers of wild fish tagged above 

Lower Granite Dam estimated to have arrived at the dam were very small. The vast majority of 

these fish were bypassed back to the river; therefore, the SAR of transported and nondetected wild 

fish tagged above Lower Granite Dam had large errors. This made statistical power very low to 

show differences in return rates among fish with different juvenile migration histories. 

If D varies from location to location, a combination of strategies at different locations 

might maximize survival of in-river migrants. For instance, if D is high for fish transported from

Lower Granite Dam, but low for fish transported from dams farther downstream, it might make 

44
sense to choose configurations and operations to maximize collection and transportation of smolts 

at Lower Granite Dam, but not to collect and transport fish at downstream dams. This strategy 

would involve eliminating or reducing spill at Lower Granite Dam and spilling to the gas cap (a 

maximum level of supersaturated atmospheric gases set for the forebays and tailraces of dams) and 

full bypass operations at all other dams. Options to change collection strategies at dams to 

potentially benefit spring Chinook salmon, of course, may have no effect or negative effect for 

other species. 

For subyearling Chinook salmon, a severe lack of data on transported fish hindered our 

ability to provide good comparisons between transported and in-river fish. Solving this problem

will require directing more collected and detected PIT-tagged fish toward transportation (and that 

will require sufficient PIT-tagged fish for evaluation purposes). Preliminarily, our analyses 

suggest that transportation appeared to neither greatly harm nor help the fish. Thus a combination 

of transportation and good conditions for fish not collected and transported is consistent with a 

“spread the risk” strategy until more is known. 

45
Juvenile Migrant Survival 

Methods 

Reach Survival Estimates 

All mainstem dams on the lower Snake and Columbia rivers except The Dalles Dam have 

juvenile fish bypass facilities (Figure 1) (Matthews et al. 1977). These systems use screens to 

divert migrant smolts away from turbine intakes and into gatewells. Fish pass out of gatewells 

through orifices into a collection channel, where they pass directly to a pipe that discharges them

to the tailrace, or they pass through a dewatering section leading to sampling or collection facilities. 

Except for Ice Harbor Dam, all bypassed fish pass through detectors that identify nearly 100% of 

PIT-tagged fish. PIT-tagged fish detected in facilities at Lower Granite, Little Goose, Lower 

Monumental, and McNary dams (collector dams, also called transport dams) are routed to 

raceways for loading into trucks or barges for subsequent transportation to below Bonneville Dam

or routed back to the river via a slide gate (Marsh et al. 1999). The most downstream site for 

detecting PIT-tagged juvenile fish is in the Columbia River estuary between RKm 65 and 84, 

where a two-boat trawl tows a PIT-tag detector (Ledgerwood et al. 2000). 

We estimated survival probabilities for juvenile migrant fish from PIT-tag detection 

histories. The estimated survival probability for a particular segment of the migration corridor 

provided a group-level statistic, interpreted as an estimate of the proportion of the group that 

survived the segment. PIT-tagged fish were defined as a “group” for survival estimation in three 

primary ways: 

1. Fish tagged at the same time and released as a batch at a single point (typical for studies 

that address a specific research question and for daily samples of fish collected at a smolt 

trap). 

2. Tagged fish held together in a holding facility for a period of time and then released from

the same point over a short period of time (typical for volitional releases from hatcheries). 

3. Tagged fish released at various sites upstream from a particular dam, then grouped 

according to the date when they were detected at the dam and returned to the tailrace 

(typical for attempts to gather a time series of survival estimates throughout the migration 

season). 

For estimates and analyses in this report, groups sometimes contain both hatchery and wild fish, 

or we treat the two rearing types separately. In all cases, a fish group includes only one species. 

No matter how the group was defined, survival probabilities were estimated using the 

detection records (detection histories) for every individual fish in the group. Because each PIT tag 

is uniquely coded, and because returning a portion of detected fish to the river allows detection at 

multiple dams, we analyzed the detection history data using a multiple-recapture model for 

46
single-release groups. We used a model originally presented and investigated by Cormack (1964), 

Jolly (1965), and Seber, known as the Cormack-Jolly-Seber (CJS) model or single-release (SR) 

model. Use of this model for survival estimation using PIT-tagged fish was first described in 

detail by Skalski (1998). 

For survival estimation using the SR model, we needed at a minimum the release of a 

PIT-tagged fish group at the beginning of the river segment of interest, one detection site where at 

least some of the detected fish were returned to the river for subsequent detection opportunities, 

and at least one detection site farther downstream. If there were only one detection site 

downstream from the release site, or if all detected fish at the first site were removed from the river, 

then we could not distinguish failure to detect a passing (surviving) fish from mortality before 

arrival at the detection site (i.e., we could not estimate survival probabilities separately from

detection probabilities). Fish detected downstream from the first detection site constitute a sample 

of the fish that were alive at the first site; they were used to estimate the proportion of fish passing 

the first site that were detected (detection probability). Having obtained the estimate of the 

detection probability, we then estimated the survival probability. When there was a series of

detection sites with return-to-river capabilities, we estimated survival from release to the first site, 

then between each pair of consecutive sites, except that the inability to distinguish mortality from

the failure to detect a surviving fish always precluded estimation between the last two sites. 

In 1993 when a study specifically designed to estimate migrant smolt survival began, 

PIT-tag detectors were operational only at Lower Granite, Little Goose, Lower Monumental, and 

McNary dams. Only Lower Granite and Little Goose dams were equipped with slide gates to 

divert PIT-tagged fish from the bypass system back to the river. Under this configuration, we 

could only estimate survival for groups of fish from the point of release above Lower Granite Dam

to the Lower Granite Dam tailrace and from Lower Granite Dam tailrace to Little Goose Dam

tailrace. PIT-tag detectors and slide gates were added gradually to other dams after 1993 (in a 

downstream direction). Under present conditions, provided the estuarine trawl detected sufficient 

fish from the group, we could estimate survival for any group of PIT-tagged fish from any release 

point upstream from Bonneville Dam to its tailrace. 

In this section, we present all survival estimates from point of release (or the tailrace of a 

dam) to the tailrace of a dam downstream. All survival and detection probability estimates were 

computed using a statistical computer program for analyzing release-recapture data called survival 

with proportional hazards (SURPH), developed at the University of Washington (Skalski et al. 

1993, Smith et al. 1994). 

Assumptions of single-release model 

Using the SR model, the passage of a single PIT-tagged salmonid through the hydropower 

system is modeled as a sequence of events. Examples of such events are survival from the Lower 

Granite Dam tailrace to Little Goose Dam tailrace and detection at Little Goose Dam. Each event 

has an associated probability of occurrence. The detection history is the record of the event 

outcomes. (As previously noted, the detection history is an imperfect record of outcomes. If the 

history ends with one or more zeroes, we cannot distinguish mortality from survival without 

detection). The SR model represents detection history data for a group of tagged fish as a 

multinomial distribution: each multinomial cell probability (detection history probability) is a 

47
function of the underlying survival and detection event probabilities. Estimates of survival 

probabilities under the SR model are random variables, subject to sampling variability. When true 

survival probabilities are close to 1.0 or when sampling variability is high, it is possible for 

estimates of survival probabilities to exceed 1.0. For practical purposes, estimates should be 

considered equal to 1.0 in these cases. 

Three key assumptions led to the multinomial cell probabilities used in the SR model: 

1. Fish in a single group of tagged fish have common event probabilities (each conditional 

detection or survival probability is common to all fish in the group). 

2. Event probabilities for each individual fish are independent from those for all other fish. 

3. Each event probability is conditionally independent from all other probabilities. 

For a broader description of these assumptions and how they may be tested, see Burnham et al. 

(1987) and Zabel et al. (2002). 

To varying degrees, the three assumptions were inevitably violated for any particular 

group of migrating salmonids. Reasons why the assumptions might not have strictly held related 

to variation in fitness among fish in a group; for example, variation in migration rate means that 

individuals from the same group may have passed a dam under different conditions, and inherent 

traits or behavioral preferences might make detection of some fish more likely at all dams. 

Violations of model assumptions can cause bias in resulting parameter estimates. 

However, known causes and degrees of SR model violations for migrating juvenile salmonids 

have been investigated and shown to cause minimal bias (Skalski 1998). Studies were planned 

and analyses designed to minimize the potential of significant bias due to violation of model 

assumptions. 

Data sources and limitations 

Information for juvenile salmonids PIT tagged and released in the Columbia River basin 

was obtained from the regional Pacific States Marine Fisheries Commission PIT-tag information 

system (PTAGIS) database (PSMFC 2004). We grouped fish by migration year, species, run, 

rearing type, release site, and in some cases by date or time period. 

Sometimes, due to small or zero sample sizes at the most downstream observation sites, 

caused by very poor survival to those sites or low detection rates at those sites, survival for some

cohorts for the McNary to John Day Dam or John Day to Bonneville Dam reaches was not 

estimated or alternative survival estimates were calculated using the pooled estimate for a 

particular species, run, or rearing type. In particular, estimates to Bonneville Dam were not 

calculated for mid-Columbia and Yakima River groups until 2001 and 2002, respectively. 

Our estimates were calculated using only information available from PTAGIS (PSMFC 

2004). We were not aware of all experimental caveats and details involved in the studies for which 

many of the fish were tagged. Thus although we used available PIT-tagged fish for survival 

estimates, we recognize that not all fish were released for the sole purpose of estimating 

48
downstream reach survival. Therefore some survival estimates, even if mathematically correct, 

may not reflect or represent true survival among the untagged population. 

Annual average survival estimates from Lower Granite and McNary dams 

Between 1993 and 2003, hatchery and wild yearling Chinook salmon and steelhead were 

tagged in varying numbers at various locations upstream from Lower Granite Dam. Studies were 

conducted involving fish collected and tagged at Lower Granite Dam and then released into the 

tailrace. To estimate survival for each year, we created daily release groups from Lower Granite 

Dam by combining fish tagged at the dam and released into the tailrace with previously tagged fish 

that were detected at the dam and returned to the tailrace the same day. For each daily group, 

detection data downstream from Lower Granite Dam were usually sufficient to calculate SR model 

survival estimates between Lower Granite and Little Goose dams, between Little Goose and 

Lower Monumental dams, and between Lower Monumental and McNary dams. If data for a daily 

group were not sufficient, we pooled adjacent days until estimates to McNary Dam were possible. 

To obtain survival estimates downstream of McNary Dam, we regrouped fish into daily 

groups at McNary Dam, using the same methods described above for Lower Granite Dam. 

Detection data downstream from McNary Dam were usually not sufficient for each daily group. 

Therefore, we pooled the daily groups into weekly groups. For weekly groups leaving McNary 

Dam, we estimated survival between McNary and John Day dams and between John Day and 

Bonneville dams. 

Using these methods, we obtained estimates for particular river sections from multiple 

groups of PIT-tagged fish throughout each migration season. Annual average estimates for these 

river sections were obtained using a mean weighted by relative variability of the estimate. This 

method resulted in survival estimates with little or no bias (Muir et al. 2001). 

Annual average survival estimates through the entire hydropower system 

For Snake River yearling Chinook salmon and steelhead, we estimated the annual mean 

survival probability from the head of Lower Granite Dam reservoir to Bonneville Dam tailrace. 

We calculated this estimate by multiplying three components: 1) the estimate of survival from the 

Snake River trap (near the head of the reservoir) to Lower Granite Dam (hatchery and wild fish 

pooled), 2) the weighted mean survival estimate for daily groups from Lower Granite Dam tailrace 

to McNary Dam tailrace, and 3) the weighted mean estimate for weekly groups from McNary Dam

tailrace to Bonneville Dam tailrace. 

Probability of Detecting PIT-Tagged Fish Versus Length at Tagging 

Zabel et al. (2004) estimated the relationship between detection probability (at Little 

Goose, Lower Monumental, and McNary dams) versus length at tagging for spring-summer 

Chinook salmon and steelhead (hatchery and wild) PIT tagged and released at Lower Granite Dam

during the years 1998 through 2002. We present the methods and results of this analysis in the 

subsections that follow. 

49
Data 

Study fish were yearling Chinook salmon and steelhead of both wild and hatchery origin. 

The fish were captured, PIT tagged, and released at Lower Granite Dam as part of transportation 

studies (Harmon et al. 2000, Marsh et al. 2001). We analyzed control fish that were released to the 

tailrace. Our analysis comprised all release groups by species and origin from 1998 to 2002 that 

contained at least 10,000 fish released in a year. Because survival and detection probabilities may 

vary over a season, we divided each yearly release group into six weekly release groups over the 

period 10 April to 21 May. The tagged fish were potentially detected in the bypass systems at 

Little Goose, Lower Monumental, McNary, John Day, and Bonneville dams (Figure 1). We

combined detections at the last two sites to increase the sample size so that an individual fish had 

four opportunities for detection. 

Survival and detection probability estimation 

First, we introduce three terms (based on terminology from Lebreton et al. 1992) for the 

site-specific survival and detection probabilities: 

1. φnw is the probability of fish released in week w (w = 1,2,...,6) surviving through the nth 

river segment (n = 1,2,3). 

2. pnw is the probability of detecting an individual from the wth release group at the nth 

detection site, given the individual was alive at that site. 

3. βw is the combined probability for fish released in week w of surviving the last river 

segment and being detected at the last site, since the data cannot distinguish between these 

two probabilities. 

To incorporate length of fish into the analysis, we modified the CJS model (for details see Zabel 

and Achord 2004) by expressing survival and detection probabilities as functions of fish length. 

We used a logit link to ensure that survival and detection probabilities ranged from 0 to 1. For 

example, the relationship for fish released in week w between detection probability at site n and 

length was 

1 exp( )

exp( ) ( )

0, ,

0, ,

l

l

p l

nw l n

nw l n

nw + + ⋅

+ ⋅ = α αα α (4) 

where l is fish length (standardized to have 0 mean) and a is the coefficient. Note that we allowed 

overall survival and detection probabilities (i.e., the intercept terms) to vary by weekly release 

group, but we kept site-specific length effects constant across a season to keep the analysis 

tractable. If length was not included in the probability, the above equation reduced to 

p exp( )/1 exp( ) nw = α0,nw + α0,nw (5) 

which is a constant. When all survival and detection probabilities were related to length, we 

referred to the model as φ1(l) φ2(l) φ3(l)p1(l)p2(l)p3(l). As an aside, if fish residualize, it is 

considered a mortality in the modeling. Thus size-selective residualism (or male precocity) is 

incorporated in the survival term and does not bias the estimation of size-selective detection 

probabilities. 

50
Model parameters were estimated using maximum likelihood (Mood et al. 1974). The 

likelihood function was numerically optimized with respect to the parameters. Standard errors 

were estimated based on numerical approximations of the Hessian matrix (Burnham et al. 1987). 

We used the readily available software MARK (White and Burnham 1999) and SURPH 

(Lady et al. 2001) to conduct all analyses. 

We constructed alternative models by either including or not including length relationships 

in each survival and detection probability. To compare alternative models, we used likelihood 

ratio tests (LRTs) (Mood et al. 1974). The LRTs were designed so that they compared a null 

model to a more complex alternative model. We implemented a top-down approach to the model 

selection process. In other words, we began with a full model, 

φ1(l)φ2(l)φ3(l)p1(l)p2(l)p3(l), (6)

where all survival and detection probabilities were related to length. Then we determined if we 

could remove individual length relationships (in either a survival or detection probability) based 

on an LRT. At each step we chose the candidate length relationship for testing whose length 

coefficient (αl) had the lowest coefficient of variation (CV, mean/standard error). If the null 

hypothesis of the LRT was not rejected (there was no support for including the length term in the 

model), then the length term was removed. We then designated this simpler model as the 

alternative model and attempted to remove an additional length term. We repeated the process 

until we rejected a null hypothesis and thus accepted the more complex alternative model. 

Once we completed our model selection analyses, we focused on an additional question: 

How does the existence of length-related recapture probabilities affect our ability to estimate 

population-wide survival? In particular, does the commonly used CJS model, which ignores 

variability in recapture probabilities among individuals, produce biased results? To address this 

question, we estimated population survival using two methods: 

• Method 1: Ignore length relations in detection and survival probabilities and use the CJS 

model, φ1φ2φ3p1p2p3. The weekly survival estimates were combined into a seasonal mean, 

with each weekly estimate weighted by the number of fish released per week. 

• Method 2: Include length-related detection probabilities where appropriate, but ignore 

length effects on survival. In other words, use model φ1φ2φ3p1(*)p2(*)p3(*), where * means 

include the length relationship or not depending on results from the model selection 

process. Again, weekly survival estimates were combined into a weighted mean for the 

season. 

Results 

Snake River Yearling Chinook Salmon Survival 

Hatchery release groups 

Seven hatcheries in the Snake River basin released PIT-tagged yearling spring and summer 

Chinook salmon each year between 1993 and 2003: Dworshak, Kooskia, Lookingglass, Rapid 

River, McCall, Pahsimeroi, and Sawtooth. For each hatchery each year we identified the 

51
PIT-tagged fish group that was most representative of the hatchery’s production release. For these 

groups of yearling Chinook salmon, we calculated estimates of survival from release to the Lower 

Granite Dam tailrace. Many of the groups were released as a batch on a single occasion; others 

were released volitionally over a period of days from hatchery ponds or raceways. 

Mean estimated survival from Snake River basin hatcheries to the tailrace of Lower 

Granite Dam (average for hatcheries combined) has ranged from a low of 0.494 in 1997 to 0.697 

in 2000. For all hatcheries, average survival has been higher since 1998 than it was in 1993 

through 1997 (Table 18). 

A strong inverse relationship exists between survival and migration distance (r2

 = 0.941, 

p < 0.001) (Figure 21), with mean survival highest (0.765) from Dworshak National Fish Hatchery 

(116 km from Lower Granite Dam), and lowest (0.403) from Sawtooth National Fish Hatchery 

(747 km from Lower Granite Dam). However, survival from Sawtooth and Pahsimeroi hatcheries 

improved in recent years, likely due to better control of BKD, weakening the relationship between 

distance and survival to Lower Granite Dam.

Table 18. Estimated survival for yearling Chinook salmon from Snake River basin hatcheries to the tailrace 

of Lower Granite Dam, 1993–2003. Distance (km) from each hatchery to Lower Granite Dam in 

parentheses in header. Standard errors are in parentheses following each survival estimate. 

Year 

Dworshak 

(116) 

Kooskia 

(176) 

Imnaha 

River weir 

(209) 

Rapid 

River (283)

McCall 

(457) 

Pahsimeroi

(630) 

Sawtooth 

(747) Mean

1993 0.647

(0.028) 

0.689 

(0.047) 

0.660 

(0.025) 

0.670 

(0.017) 

0.498 

(0.017) 

0.456 

(0.032) 

0.255 

(0.023) 

0.554 

(0.060) 

1994 0.778

(0.020) 

0.752 

(0.053) 

0.685 

(0.021) 

0.526 

(0.024) 

0.554 

(0.022) 

0.324 

(0.028) 

0.209 

(0.014) 

0.547 

(0.081) 

1995 0.838

(0.034) 

0.786 

(0.024) 

0.617 

(0.015) 

0.726 

(0.017) 

0.522 

(0.011) 

0.316 

(0.033) 

0.230 

(0.015) 

0.576 

(0.088) 

1996 0.776

(0.017) 

0.744 

(0.010) 

0.567 

(0.014) 

0.588 

(0.007) 

0.531 

(0.007) 

— 0.121

(0.017) 

0.555 

(0.096) 

1997 0.576

(0.017) 

0.449 

(0.034) 

0.616 

(0.017) 

0.382 

(0.008) 

0.424 

(0.008) 

0.500 

(0.008) 

0.508 

(0.037) 

0.494 

(0.031) 

1998 0.836

(0.006) 

0.652 

(0.024) 

0.682 

(0.006) 

0.660 

(0.004) 

0.585 

(0.004) 

0.428 

(0.021) 

0.601 

(0.033) 

0.635 

(0.046) 

1999 0.834

(0.011) 

0.653 

(0.031) 

0.668 

(0.009) 

0.746 

(0.006) 

0.649 

(0.008) 

0.584 

(0.035) 

0.452 

(0.019) 

0.655 

(0.045) 

2000 0.841

(0.009) 

0.734 

(0.027) 

0.688 

(0.011) 

0.748 

(0.007) 

0.689 

(0.010) 

0.631 

(0.062) 

0.546 

(0.030) 

0.697 

(0.035) 

2001 0.747

(0.002) 

0.577 

(0.019) 

0.747 

(0.003) 

0.689 

(0.002) 

0.666 

(0.002) 

0.621 

(0.016) 

0.524 

(0.023) 

0.653 

(0.032) 

2002 0.819

(0.011) 

0.787 

(0.036) 

0.667 

(0.012) 

0.755 

(0.003) 

0.592 

(0.006) 

0.678 

(0.053) 

0.387 

(0.025) 

0.669 

(0.055) 

2003 0.720

(0.008) 

0.560 

(0.043) 

0.715 

(0.012) 

0.691 

(0.007) 

0.573 

(0.006) 

0.721 

(0.230) 

0.595 

(0.149) 

0.654 

(0.028) 

Mean 0.765

(0.026) 

0.671 

(0.032) 

0.665 

(0.015) 

0.653 

(0.034) 

0.571 

(0.024) 

0.526 

(0.045) 

0.403 

(0.052) 

— 

52
0 200 400 600 800

0.25

0.50

0.75

1.00

Kooskia

Imnaha River weir

Rapid River

McCall

Pahsimeroi

Sawtooth

Dworshak

r

2 = 0.941, p < 0.001

Distance (km)

% surviv

al

Figure 21. Estimated survival, with standard errors, from release at Snake River basin hatcheries to Lower 

Granite Dam tailrace, 1993–2003, versus distance (km) to Lower Granite Dam. The correlation 

between survival and migration distance is also shown. 

Salmon and Snake River trap release groups 

We estimated survival from release to Lower Granite Dam for wild and hatchery 

PIT-tagged yearling Chinook salmon and steelhead from the Salmon River (White Bird) and 

Snake River smolt traps. While fish were tagged and released nearly daily from these traps, daily 

groups rarely had sufficient data to calculate reliable survival estimates. For traps, we pooled all 

fish tagged and released between the beginning of operations in the spring and 31 May. Estimated 

survival between 1993 and 2003 to the tailrace of Lower Granite Dam for yearling Chinook 

salmon PIT-tagged at the Salmon River trap (233 km upstream from Lower Granite Dam)

averaged 0.777 for hatchery fish and 0.862 for wild fish (Table 19). 

Estimated survival from the Snake River trap, at the head of Lower Granite Reservoir (52 

km upstream from Lower Granite Dam), to the tailrace of Lower Granite Dam averaged 0.929 for 

hatchery yearling Chinook salmon and 0.935 for wild yearling Chinook salmon between 1993 and 

2003 (Table 20). 

Annual average survival estimates from Lower Granite and McNary dams 

Except for the low-flow year, 2001, mean estimated survival from Lower Granite Dam

tailrace to McNary Dam tailrace between 1998 and 2003 was consistent from year to year, ranging 

from a low of 0.729 for wild Chinook salmon in 2003 to a high of 0.791 for both hatchery and wild 

fish in 1999 (Table 21). In 2001, mean estimated survival was only about 55%. Over the 5 years 

(excluding the low-flow year, 2001), average estimated survival was nearly identical for hatchery 

(0.766) and wild (0.767) Chinook salmon. 

53
Table 19. Estimated survival for yearling Chinook salmon from the Salmon River (Whitebird) trap to 

Lower Granite Dam tailrace (233 km), 1993–2003. Standard errors are in parentheses. Simple 

arithmetic means across all years are given. 

Year Hatchery Wild

1993 0.782 (0.019) 0.832 (0.014) 

1994 0.761 (0.024) 0.817 (0.017) 

1995 0.802 (0.012) 0.863 (0.011) 

1996 0.735 (0.026) 0.822 (0.029) 

1997 NA NA

1998 0.740 (0.012) 0.926 (0.016) 

1999 0.800 (0.013) 0.909 (0.012) 

2000 0.806 (0.015) 0.920 (0.021) 

2001 0.819 (0.007) 0.878 (0.009) 

2002 0.792 (0.016) 0.844 (0.016) 

2003 0.728 (0.016) 0.807 (0.011) 

Mean 0.777 (0.010) 0.862 (0.014) 

Table 20. Estimated survival for yearling Chinook salmon from the Snake River trap (near head of Lower 

Granite Reservoir) to Lower Granite Dam tailrace (52 km), 1995–2003. Standard errors are in 

parentheses. Simple arithmetic means across all years are given. 

Year Hatchery Wild

1993 0.823 (0.016) 0.847 (0.024) 

1994 0.951 (0.029) 0.913 (0.036) 

1995 0.886 (0.013) 0.944 (0.015) 

1996 0.974 (0.032) 0.984 (0.039) 

1997 NA NA

1998 0.928 (0.013) 0.915 (0.019) 

1999 0.930 (0.013) 0.950 (0.011) 

2000 0.911 (0.018) 0.951 (0.023) 

2001 0.956 (0.015) 0.921 (0.058) 

2002 0.925 (0.027) 0.985 (0.038) 

2003 1.001 (0.030) 0.943 (0.033) 

Mean 0.929 (0.016) 0.935 (0.013) 

Data were not sufficient to estimate survival from McNary Dam tailrace to Bonneville 

Dam tailrace for any Snake River yearling Chinook salmon until 1999. From 1999 to 2003, data 

were sufficient to estimate survival for pooled hatchery and wild groups, but not for the rearing 

types separately. Annual average estimates ranged from 0.501 in 2001 to 0.763 in 2002, and 

averaged 0.667 for the 5 years 1999–2003 (Table 21). 

Annual average survival estimates through the FCRPS 

For yearling Chinook salmon (hatchery and wild combined), estimated survival through 

the hydropower system, from the Snake River trap at the head of Lower Granite Reservoir to the 

54
Bonneville Dam tailrace, through eight mainstem dams and reservoirs, ranged from 0.266 in the 

low-flow year of 2001 to 0.551 in 2002 (Table 22). 

Comparison of wild and hatchery yearling Chinook salmon 

Wild yearling Chinook salmon had nearly equal to slightly higher survival than 

hatchery-reared fish between the Salmon and Snake River traps and Lower Granite Dam tailrace 

(Tables 19 and 20). Hatchery and wild yearling Chinook salmon had similar average estimated 

survival from the Lower Granite Dam tailrace to the McNary Dam tailrace, through four dams and 

reservoirs (Table 21). Annually, estimated survival has been similar for hatchery and wild 

yearling Chinook salmon, with neither stock having consistently higher survival. In estimating 

juvenile downstream migrant survival for these stocks the similarity in survival between 

Table 21. Estimated survival from Lower Granite Dam tailrace to McNary Dam tailrace and from McNary

Dam tailrace to Bonneville Dam tailrace for hatchery and wild yearling Chinook salmon, 

1998–2003. Standard errors are in parentheses. Simple arithmetic means across all years are given. 

Lower Granite to McNary Dam McNary to Bonneville Dam

Year Hatchery Wild Hatchery + wild 

1998 0.773 (0.012) 0.771 (0.015) NA 

1999 0.791 (0.007) 0.791 (0.014) 0.704 (0.058) 

2000 0.763 (0.026) 0.775 (0.014) 0.640 (0.122) 

2001 0.556 (0.019) 0.541 (0.027) 0.501 (0.027) 

2002 0.759 (0.008) 0.768 (0.026) 0.763 (0.079 

2003 0.746 (0.019) 0.729 (0.020) 0.728 (0.030) 

Mean

All years 0.731 (0.036) 0.729 (0.039) 0.667 (0.046) 

Excluding 2001 0.766 (0.008) 0.767 (0.010) 0.709 (0.026) 

Table 22. Hydropower system survival estimates derived by combining empirical survival estimates from

various reaches for Snake River yearling Chinook salmon (hatchery and wild combined), 

1997–2003. Standard errors are in parentheses. 

Year 

Snake River trap

to Lower Granite Dam 

Lower Granite Dam

to Bonneville Dam 

Snake River trap to 

Bonneville Dam 

1997 NA NA NA

1998 0.925 (0.009) NA NA

1999 0.940 (0.009) 0.557 (0.046) 0.524 (0.043) 

2000 0.929 (0.014) 0.486 (0.093) 0.452 (0.087) 

2001 0.954 (0.015) 0.279 (0.016) 0.266 (0.015) 

2002 0.953 (0.022) 0.578 (0.060) 0.551 (0.057) 

2003 0.993 (0.023) 0.532 (0.023) 0.528 (0.023) 

Mean

All years 0.949 (0.010) 0.486 (0.054) 0.464 (0.052) 

Excluding 2001 0.948 (0.012) 0.538 (0.020) 0.514 (0.021) 

55
56

PIT-tagged hatchery and wild fish through this reach and from the Snake River trap to the Lower 

Granite Dam tailrace (about 50% of the hydropower system) supports the use of hatchery fish as 

surrogates for wild fish. 

Upper Columbia River Yearling Migrant Survival 

Fewer years of PIT-tag data exist for fish stocks from the upper Columbia River basin 

compared to those in the Snake River basin. Nonetheless, the data indicate that juveniles 

migrating from the two basins under normal flow conditions had similar survival (Tables 23 and 

24 compared to Table 22). This was not the case in the 2001 low-flow year. Fish from the upper 

Columbia River had higher estimated survival to the McNary Dam tailrace (hatchery releases), 

and sometimes from the Bonneville Dam tailrace (dam releases), than fish from the Snake River. 

A spill program existed at upper Columbia River dams in 2001, but not at Snake River dams, thus 

possibly explaining some of the difference in survival. For fish released at dams, a stock effect 

may also have played a part. Yearling summer-fall Chinook salmon released at upper Columbia 

River dams also had higher survival from McNary Dam to Bonneville Dam, whereas spring 

Chinook salmon from the Yakima River did not. Yakima River spring Chinook salmon had 

survival similar to Snake River spring Chinook in the lower river. 

Snake River Subyearling Fall Chinook Salmon Survival 

Summer-migrating subyearling fall Chinook salmon have a much more complex migration 

pattern than spring-migrating salmonids. Thus results from PIT-tag studies did not fall into neat, 

discrete parts. Most data on fall Chinook salmon survival came from studies using fish released 

upstream from Lower Granite Dam. Since 1992, Connor et al. (2003a) have beach seined, PIT 

tagged, and released wild fall Chinook salmon in their rearing areas. Since 1995, NOAA Fisheries 

Service has also PIT-tagged subyearling fall Chinook at Lyons Ferry Hatchery, trucked them 

upstream above Lower Granite Dam, and released them at a time and size to match wild 

subyearling fall Chinook salmon in their rearing areas (Smith et al. 2003). Since travel time to the 

Lower Granite Dam typically averaged 1 month or more from time of release after tagging, 

survival estimates to Lower Granite Dam represented survival during both rearing and migration 

(Connor et al. 2003a, 2003b, Smith et al. 2003). Subyearling fall Chinook salmon rear and 

develop physiologically as they migrate, and their migration rate increased with migration 

distance and increased size. Unlike yearling smolts, which generally all migrated quickly to 

Lower Granite Dam, some fall Chinook salmon did not begin migrating for months. Thus for 

yearling smolts, standard techniques to measure travel times or survival did not work as well. 

From 1995 to 2000, we released nearly 200,000 PIT-tagged smolts above Lower Granite Dam. 

Subsequently we detected only about 68,700. Of these, approximately 13% were not detected at 

a Snake River dam until after 1 September of the year, some not until the following spring. The 

early fish had SAR of about 0.32%, while the late fish had SAR of about 1.55%. For the “active” 

migrants (early fish), those that passed the Snake River dams in June, July, and August in the year 

of release for the hatchery fish, the median pooled travel time for all years from release to 

detection at Lower Granite Dam averaged 43.5 days (Smith et al. 2003). Within each 
Table 23. Survival estimates for upper Columbia River yearling Chinook salmon. Standard errors are in parentheses. 

Year Release sitea

No. of 

fish 

Release site to 

Rocky Reach 

Dam 

Rocky Reach 

to McNary Dam

Release site to 

McNary Dam 

McNary to John 

Day Dam

John Day 

Bonneville D

Hatchery spring Chinook salmon 

1999 Above RIS 14,894 0.782 (0.030) 0.727b (0.053) 0.570c (0.015) 0.890c (0.018) – 

2000 Above RIS 14,877 0.705 (0.028) 0.692b (0.088) 0.543c (0.051) 0.892c (0.064) – 2001 Above RIS 15,014 0.756 (0.014) 0.565 (0.015) 0.461 (0.036) 0.812 (0.051) 0.788 (0.2002 Above RIS 404,138 0.799 (0.074) 0.642 (0.032) 0.522 (0.017) 0.856 (0.012) 0.867 (0.2003 Above RIS 355,321 – – – – 0.559 (0.025) 0.892 (0.006) 0.796 (0.

Hatchery summer Chinook salmon 1999 Wells Hatchery 5,998 – – – – 0.390c (0.050) 1.258c (0.520) 0.995 (0.2000 Wells Hatchery 5,997 – – – – 0.208c (0.020) 0.582 (0.081) 0.695 (0.

Above RIS 45,981 – – – – 0.962 (0.011) 0.738 (0.012) 0.695 (0.

2001 Wells Hatchery 6,000 0.443 (0.031) 0.483 (0.061) 0.214c (0.020) 0.407c (0.100) – 

Above RIS 90,118 – – – – 0.723 (0.026) 0.863 (0.018) 0.787 (0.

Below RIS 113,333 – – – – 0.817 (0.031) 0.922 (0.009) 0.788 (0.

2002 Wells Hatchery 5,992 0.591 (0.034) 0.759 (0.063) 0.450c (0.030) 0.792c (0.160) 1.202 (0.

Above RIS 90,125 – – – – 0.771 (0.024) 0.866 (0.013) 1.202 (0.

2003 Wells Hatchery 5,996 – – – – 0.449 (0.025) 1.158 (0.456) – 

Above RIS 103,907 – – – – 0.787 (0.034) 0.856 (0.035) 0.846 (0.

Below RIS 117,149 – – – – 0.767 (0.024) 0.942 (0.022) 0.667 (0.

Wild spring Chinook salmon 2003 Above RIS 6,402 – – – – 0.324 (0.021) 1.072 (0.033) 0.740 (0.

a Above RIS = hatchery and wild fish released upstream of Rock Island Dam. Below RIS = hatchery fish released downstream of Roc

Chinook salmon released from Wells Hatchery are a separate category. 

b Includes data from Bickford et al. 2001. c Includes data from Columbia Basin Research, online at www.cbr.washington.edu/pitSurv/ [accessed March 2004].

57
58

Year Release site

No. of 

fish 

Release site to 

Prosser Dam 

Prosser to 

McNary Dam

Release site to 

McNary Dam 

McNary to John 

Day Dam

John Day 

Bonneville 

Hatchery spring Chinook salmon1999 Above Roza Dam 39,702 0.517 (0.025) 0.909 – 0.472 (0.023) 0.929 (0.024) – 2000 Above Roza Dam 40,417 0.474 (0.016) 0.712 (0.027) 0.339 (0.019) 0.683 (0.041) – 

Below Roza Dam 7,929 – – – – 0.749 (0.025) 0.683 (0.041) – 

2001 Above Roza Dam 41,234 0.313 (0.037) 0.638 (0.006) 0.201 (0.021) 0.757 (0.040) – 

Below Roza Dam 895 – – – – 0.496 (0.022) 0.812 (0.105) – 

2002 Above Roza Dam 40,701 0.395 (0.021) 0.732 (0.009) 0.289 (0.016) 0.938 (0.036) 1.150 (0.

Below Roza Dam 1,261 – – – – 0.520 (0.030) 0.938 (0.036) 0.356 (0.

2003 Above Roza Dam 41,671 0.378 (0.029) 0.660 (0.035) 0.253 (0.030) 1.041 (0.071) 0.914 (0.

Below Roza Dam 4,308 – – – – 0.510 (0.022) 0.877 (0.079) 0.914 (0.

Wild spring Chinook salmon 1999 Above Roza Dam 312 0.581 (0.089) 0.923 (0.192) 0.538 (0.084) 0.866 (0.056) – 

Below Roza Dam 3,040 – – – – 0.774 (0.022) 0.866 (0.056) – 

2000 Above Roza Dam 6,209 0.678 (0.065) 0.600 (0.027) 0.414 (0.044) 0.814 (0.055) – 

Below Roza Dam 5,727 – – – – 0.819 (0.036) 0.795 (0.048) – 

2001 Above Roza Dam 2,179 0.312 (0.010) 0.759 (0.027) 0.237 (0.011) 0.631 (0.070) – 

Below Roza Dam 1,606 – – – – 0.688 (0.019) 0.658 (0.055) – 

2002 Above Roza Dam 8,717 0.397 (0.021) 0.658 (0.044) 0.254 (0.026) 0.870 (0.054) 0.921 (0.

Below Roza Dam 3,022 – – – – 0.643 (0.010) 0.870 (0.054) 0.626 (0.

2003 Above Roza Dam 7,803 0.377 (0.016) 0.728 (0.024) 0.274 (0.015) 0.883 (0.113) 0.782 (0.

Below Roza Dam 9,333 – – – – 0.637 (0.008) 0.768 (0.045) 1.156 (0.

Table 24. Survival estimates for PIT-tagged yearling Yakima River Chinook salmon. Standard errors are in parentheses. 
migration year, the median migration rate between each pair of dams was substantially greater 

between Lower Monumental and McNary dams and between McNary and Bonneville dams than 

between pairs of dams upstream from Lower Monumental Dam (Figure 22). 

Survival of both wild and hatchery fish to Lower Granite Dam varied widely among years 

and within years, with survival declining as the migration season progressed, flows decreased, and 

water clarity and temperature increased (Connor et al. 2003a, Smith et al. 2003). Certainly a need 

exists for an estimated average survival through the Lower Granite Dam reservoir. However, with 

data collected to date we could not partition the mortality that occurred within 

10 20 30 40

0

5

10

15

20

25

LGR -

LGO

(60 km)

LGO -

LMO

(46 km)

LMO -

MCN

(119 km)

MCN -

BON

(236 km)

Travel time

2001

2000

1999

1998

1997

1996

1995

Days

0 10 20 30 40

0

10

20

30

40

50

60

REL -

LGR

LGR -

LGO

LGO -

LMO

LMO -

MCN

MCN -

BON

Migration rate

K

m/day

Figure 22. Median travel times and migration rates (with 20th and 80th percentiles) for PIT-tagged hatchery

fall Chinook salmon, 1995–2001. Rel = release site in the Snake River, LGR = Lower Granite Dam,

LGO = Little Goose Dam; LMO = Lower Monumental Dam, MCN = McNary Dam, and BON = 

Bonneville Dam. The lengths of the reaches are in parentheses in the upper panel. 

59
the hydropower system, because measures of survival (and travel time) represented both rearing 

and migration. 

Connor et al. (2003a) divided wild subyearling fall Chinook salmon into four equally sized 

cohorts for each year (1998–2000). They estimated 57% to 88% survival to Lower Granite Dam

tailrace for the earliest migrating cohort, PIT tagged in early to mid-May, to 36% for fish tagged 

in mid-June. For hatchery subyearling Chinook salmon, estimated survival was 35% to 55% for 

early June releases, 16% to 49% for mid-June releases, and 2% to 24% for the last releases in early 

July for fish released at Billy Creek near Asotin, Washington, during those years (Figure 23) 

(Smith et al. 2002b, 2003). 

0.00

0.25

0.50

0.75

24 May 31 May 7 Jun 14 Jun 21 Jun 28 Jun 4 Jul

Billy Creek

2001

2000

1999

1997

1996

1995

1998

0.00

0.25

0.50

0.75

24 May 31 May 7 Jun 14 Jun 21 Jun 28 Jun 4 Jul 11 Jul

Pittsburg Landing

Release date

% survival probability

Figure 23. Estimated survival probabilities (with standard errors) from point of release in the Snake River 

(Billy Creek or Pittsburg Landing) to the tailrace of Lower Granite Dam for PIT-tagged hatchery

subyearling fall Chinook salmon, 1995–2001. 

60
Estimating survival for subyearling Chinook salmon below Lower Granite Dam was also 

difficult. Because of lower detection efficiencies (due to lower fish guidance efficiencies for fall 

Chinook), fewer PIT-tagged fish, poor survival to Lower Granite Dam, and fish dispersed over a 

wide time period, survival for Snake River fall Chinook was only estimated as far as the Lower 

Monumental Dam tailrace through 2001, and only for hatchery-origin fish (Smith et al. 2002a, 

2003). Survival between the Lower Granite and Lower Monumental Dam tailraces has been 

highly variable, with a general decline in mid to late August, and has been much lower overall than 

for migrating yearling spring Chinook salmon (Figure 24). We did not estimate survival over this 

reach for 2002. Due to larger releases of fish in 2003, we estimated survival between the Lower 

Granite and McNary Dam tailraces. Survival ranged from 75% for fish leaving Lower Granite 

Dam the second week in June to 22% for fish leaving the second week in July. 

We have no survival estimates for juvenile fish that migrated in September and October, 

nor for undetected fish. But, based on adult returns of PIT-tagged fish, these groups accounted for 

14% and 36% of the total adult return of the in-river PIT-tagged fish released from 1995 through 

2000. Nonetheless, the PIT-tagged fish did not represent the untagged population because all 

untagged fish collected at dams were transported. Thus we had expected that nearly all adult 

returns to Lower Granite Dam would come from untagged fish transported from collector dams as 

juveniles. Recently however, results from reading scales of adult fall Chinook salmon passing 

Lower Granite Dam indicated that 40% to 50% of the adult return came from fish that entered the 

ocean as yearlings (Connor et al. in press). This suggests that many transported fish overwintered 

in the estuary, juveniles migrated during the winter (outside of the juvenile bypass system

operation window) and were not collected or transported, or juveniles collected and transported in 

the fall decreased growth sufficiently to show an apparent overwinter, freshwater check on the 

scale. In any case, this indicates a substantial change from hypothesized historical migration 

patterns for the fish. 

0.00

0.25

0.50

0.75

1995

1996

1997

1998

11 Jun 25 Jun 9 Jul 23 Jul 6 Aug 20 Aug

1999

2000

2001

Date at Lower Granite Dam

% survival probability

Figure 24. Estimated survival probabilities (with standard errors) to the tailrace of Lower Monumental 

Dam for PIT-tagged hatchery subyearling fall Chinook salmon leaving Lower Granite Dam, by

week, 1995–2001. 

61
62

Juvenile fall Chinook salmon historically moved out of the upper Snake River spawning 

and rearing areas in late March and early April. The peak of the run passed Ice Harbor Dam by 

mid-June. The construction of the Hells Canyon dams substantially altered conditions for migrant 

fish. Thus little in the migration of juvenile fall Chinook salmon under present conditions matches 

historical run timing. 

Upper Columbia River Subyearling Migrant Survival 

Fewer years of PIT-tag data exist for fish stocks from the upper Columbia River basin 

compared to the Snake River basin. Depending on year and release site, survival values ranged 

widely (Tables 25 and 26). 

Snake River Steelhead Survival 

Hatchery release groups 

Two hatcheries in the Snake River basin, Dworshak and Clearwater, released PIT-tagged 

fish most years between 1993 and 2003. Although we estimated survival for release groups, 

because the hatcheries released fish at numerous sites within the Clearwater basin, we did not 

tabulate survival from the hatcheries to Lower Granite Dam, as we did for yearling Chinook 

salmon. 

Salmon and Snake River trap release groups 

From 1993 to 2003, estimated survival to the Lower Granite Dam tailrace for steelhead PIT 

tagged at the Salmon River trap (223 km above Lower Granite Dam) averaged 0.854 for hatchery 

fish and 0.869 for wild fish (Table 27). 

From 1993 to 2003, estimated survival from the Snake River trap, at the head of Lower 

Granite Reservoir (52 km above Lower Granite Dam), to the Lower Granite Dam tailrace averaged 

0.927 for hatchery steelhead and 0.935 for wild steelhead (Table 28). 

Annual average survival estimates from Lower Granite and McNary dams 

Except for the low-flow year (2001), mean estimated survival from Lower Granite Dam 

tailrace to McNary Dam tailrace from 1997 to 2003 ranged from a low of 0.533 for hatchery 

steelhead in 2002 to a high of 0.746 for wild fish in 1999 (Table 29). In 2001, mean estimated 

survival was very low: 0.170 for hatchery steelhead and 0.168 for wild. Over the 5 years 

(excluding 2001), average estimated survival was 0.606 for hatchery and 0.670 for wild steelhead. 

Data were not sufficient to estimate survival from McNary Dam to Bonneville Dam for any 

Snake River steelhead until 1997. From 1997 to 2003, data were sufficient to estimate survival 

from McNary Dam tailrace to Bonneville Dam tailrace for pooled hatchery and wild groups, but 

not for the rearing types separately. Annual average estimates ranged from 0.250 in 
63

Year Release site

No. of 

fish 

PIT-tag recovery

on bird islands

Release site to McNary 

Dam 

McNary Dam to John 

Day Dam

John Day Dam 

Bonneville Dam

Hatchery fall Chinook1999 Below Roza Dam* 7,324 0.0104 0.588 (0.108) 0.669 (0.053) – – 2000 Below Roza Dam* 4,051 0.0222 0.645 (0.119) 0.573 (0.137) – – 2001 Below Roza Dam* 3,979 0.0206 0.330 (0.037) 0.696 (0.113) – – 2002 Below Roza Dam* 4,001 0.0165 0.223 (0.011) 0.867 (0.132) 0.723 (0.232003 Below Roza Dam* 3,987 0.0025 0.183 (0.083) 0.783 (0.071) 0.716 (0.00Wild fall Chinook1999 Below Roza Dam* 876 0.0011 0.790 (0.021) 0.720 (0.188) – – 2000 Below Roza Dam* 1,979 0.0344 0.272 (0.025) – – – – 

Year Release sitea No. of fish 

PIT-tag recovery

on bird islands

Release site to 

McNary Dam 

McNary Dam to 

John Day Dam

John Day Dam 

Bonneville Dam

Hatchery fall Chinook 1999 Below RIS 6,778 0.0081 0.800b (0.037) 0.720b (0.017) – – 

2000 Below RIS 6,091 0.0144 0.624b (0.068) 0.483b (0.069) – – 2001 Below RIS 35,762 0.0063 0.667b (0.050) 0.683b (0.062) – – 2002 Below RIS 66,554 0.0051 0.716b (0.019) 0.778b (0.030) 0.788 (0.112003 Below RIS 81,253 0.0028 0.558 (0.034) 0.820 (0.042) – – Wild fall Chinook 1999 Above Yakima 5,042 0.0113 0.398 (0.024) 0.833 (0.119) – – 2000 Above Yakima 10,967 0.0098 0.432 (0.035) – – – – 2001 Above Yakima 9,481 0.0127 0.366 (0.025) 0.563 (0.029) – – 2002 Above Yakima 414 0.0048 0.402 (0.058) 0.696 (0.290) – – 2003 Above Yakima 2,975 0.0084 0.315 (0.020) 0.600 (0.122) – – 

Table 25. Survival estimates for PIT-tagged upper Columbia River subyearling Chinook salmon and percentage recovery o

islands. Standard errors are in parentheses. 

Table 26. Survival estimates for PIT-tagged Yakima River fall Chinook salmon and percentage recovery of PIT-tagged fish 

errors are in parentheses. 

a Below RIS = hatchery and wild fish released downstream of Rock Island Dam. Above Yakima = wild fish released above confluence 

rivers. 

b Includes data from Columbia Basin Research, online at www.cbr.washington.edu/pitSurv/. * Fish released downstream of Roza Dam.
Table 27. Estimated survival for hatchery and wild steelhead from the Salmon River (Whitebird) trap to 

Lower Granite Dam tailrace (233 km), 1993–2003. Standard errors are in parentheses. Simple 

arithmetic means across all years are given. 

Year Hatchery Wild

1993 0.875 (0.011) 0.832 (0.019) 

1994 NA NA

1995 0.882 (0.013) 0.892 (0.025) 

1996 0.851 (0.022) 0.956 (0.060) 

1997 0.872 (0.017) 0.876 (0.062) 

1998 0.879 (0.016) 0.892 (0.070) 

1999 0.825 (0.014) 0.816 (0.039) 

2000 0.870 (0.019) 0.815 (0.041) 

2001 0.786 (0.009) 0.878 (0.019) 

2002 0.814 (0.041) 0.780 (0.050) 

2003 0.885 (0.028) 0.952 (0.092) 

Mean 0.854 (0.011) 0.869 (0.018) 

Table 28. Estimated survival for hatchery and wild steelhead from the Snake River trap (near head of 

Lower Granite Reservoir) to Lower Granite Dam tailrace (52 km), 1995–2003. Standard errors are 

in parentheses. Simple arithmetic means across all years are given. 

Year Hatchery Wild

1993 0.917 (0.008) 0.898 (0.009) 

1994 NA NA

1995 0.936 (0.011) 0.955 (0.013) 

1996 0.941 (0.020) 0.973 (0.022) 

1997 0.963 (0.016) 0.968 (0.051) 

1998 0.926 (0.010) 0.919 (0.017) 

1999 0.908 (0.012) 0.910 (0.024) 

2000 0.947 (0.014) 0.977 (0.027) 

2001 0.893 (0.008) 0.958 (0.010) 

2002 0.893 (0.019) 0.899 (0.023) 

2003 0.946 (0.018) 0.893 (0.026) 

Mean 0.927 (0.008) 0.935 (0.011) 

2001 to 0.770 in 1998, and averaged 0.540 for the 7 years (Table 29). Estimated survival between 

McNary Dam tailrace and Bonneville Dam tailrace was lower in all 3 years from 2001 to 2003 

than in any year between 1997 and 2000. 

Annual average survival estimates from Lower Granite and McNary dams 

Except for the low-flow year 2001, from 1997 to 2003 mean estimated survival from

Lower Granite Dam tailrace to McNary Dam tailrace ranged from a low of 0.533 for hatchery 

steelhead in 2002 to a high of 0.746 for wild fish in 1999 (Table 29). In 2001, mean estimated 

survival was very low: 0.170 for hatchery steelhead and 0.168 for wild. Over the 5 years 

(excluding 2001), average estimated survival was 0.606 for hatchery and 0.670 for wild steelhead. 

64
Table 29. Estimated survival from Lower Granite Dam tailrace to McNary Dam tailrace and from McNary

Dam tailrace to Bonneville Dam tailrace for hatchery and wild steelhead, 1998–2003. Standard 

errors are in parentheses. Simple arithmetic means across all years are given. 

Lower Granite to McNary McNary to Bonneville 

Year Hatchery Wild Hatchery + wild pooled 

1997 0.728 (0.053)* 0.651 (0.082) 

1998 0.644 (0.015) 0.698 (0.030) 0.770 (0.081) 

1999 0.673 (0.019) 0.746 (0.019) 0.640 (0.024) 

2000 0.574 (0.038) 0.714 (0.028) 0.580 (0.047) 

2001 0.170 (0.013) 0.168 (0.010) 0.250 (0.016) 

2002 0.533 (0.045) 0.593 (0.039) 0.488 (0.090) 

2003 0.606 (0.028) 0.597 (0.022) 0.510 (0.015) 

Mean

All years 0.533 (0.075) 0.586 (0.087) 0.540 (0.071) 

Excluding 1997 and 2001 0.606 (0.025) 0.670 (0.031) 0.598 (0.051) 

* Hatchery and wild pooled; data insufficient to estimate separately. 

Data were not sufficient to estimate survival from McNary Dam to Bonneville Dam for any 

Snake River steelhead until 1997. From 1997 to 2003 data were sufficient to estimate survival 

from McNary Dam tailrace to Bonneville Dam tailrace for pooled hatchery and wild groups, but 

not for the rearing types separately. Annual average estimates ranged from 0.250 in 2001 to 0.770 

in 1998 and averaged 0.540 for the 7 years (Table 29). Estimated survival between McNary Dam

tailrace and Bonneville Dam tailrace was lower in all 3 years from 2001 to 2003 than in any year 

from 1997 to 2000. 

Annual average survival estimates 

For steelhead (hatchery and wild combined), estimated survival through the hydropower 

system, from the Snake River trap at the head of Lower Granite Reservoir to the Bonneville Dam

tailrace through eight mainstem dams and reservoirs, ranged from a low of 0.038 in the 2001 

low-flow conditions of to 0.462 in 1998 (Table 30). 

Comparison of wild and hatchery steelhead 

Wild steelhead had slightly higher survival than hatchery-reared fish between the Lower 

Granite Dam tailrace and the McNary Dam tailrace, through four dams and reservoirs (Table 29). 

For steelhead, estimated survival through this reach averaged about 5% higher for wild fish 

compared to hatchery origin, with wild steelhead survival higher in 4 of the 6 years (Table 29). 

Upper Columbia River steelhead survival 

Fewer years of PIT-tag data exist for fish stocks from the upper Columbia River basin than 

for those in the Snake River basin. Nonetheless, the data indicate that juveniles migrating from the 

two basins under normal flow conditions have similar survival (Table 31 compared to Tables 29 

and 30). This was not the case in the 2001 low-flow year. Fish from the upper Columbia River 

had higher estimated survival to the McNary Dam tailrace (hatchery releases) and sometimes 

65
Bonneville Dam tailrace (dam releases) than did fish from the Snake River. A spill program

existed at upper Columbia River dams in 2001, but not at Snake River dams, possibly explaining 

some of the difference in survival. For fish released at dams, a stock effect may also have played 

a part. 

Table 30. Hydropower system survival estimates derived by combining empirical survival estimates from

various reaches for Snake River steelhead (hatchery and wild combined), 1997–2003. Standard 

errors are in parentheses. 

Year 

Snake River trap to 

Lower Granite Dam

Lower Granite Dam

to Bonneville Dam 

Snake River trap to 

Bonneville Dam 

1997 0.964 (0.015) 0.474 (0.069) 0.457 (0.067) 

1998 0.924 (0.009) 0.500 (0.054) 0.462 (0.050) 

1999 0.908 (0.011) 0.440 (0.018) 0.400 (0.016) 

2000 0.964 (0.013) 0.393 (0.034) 0.379 (0.032) 

2001 0.911 (0.007) 0.042 (0.003) 0.038 (0.003) 

2002 0.895 (0.015) 0.262 (0.050) 0.234 (0.045) 

2003 0.932 (0.015) 0.309 (0.011) 0.288 (0.011) 

Mean

All years 0.928 (0.010) 0.346 (0.060) 0.323 (0.057) 

Excluding 2001 0.931 (0.012) 0.396 (0.038) 0.370 (0.038) 

Table 31. Survival estimates for upper Columbia and Yakima rivers steelhead. 

Year Release sitea No. of fish

Release site to 

McNary Dam 

McNary Dam to 

John Day Dam

McNary Dam to 

Bonneville Dam

Hatchery summer steelhead 

1999 Above Rock Island Dam 134,251 0.616 (0.013) 1.016 (0.013) – – 

2000 Above Rock Island Dam 63,227 0.607 (0.009) 0.861b (0.059) – –

2001 Above Rock Island Dam 4,029 0.203 (0.029) 0.535 (0.146) 0.178 (0.078)

2002 Above Rock Island Dam 3,623 0.529 (0.107) 1.119 (0.168) 0.856 (0.349)

2003 Above Rock Island Dam 39,1203 0.447 (0.014) 1.027 (0.025) 0.800 (0.042)

Wild summer steelhead

1999 Rock Island Dam 1,156 0.635 (0.055) 1.103 (0.148) – – 

2000 Rock Island Dam 1,200 0.679 (0.102) 0.873 (0.224) – – 

2001 Rock Island Dam 1,174 0.211 (0.022) 0.304 (0.082) – – 

2002 Rock Island Dam 1,200 0.623 (0.063) 0.680 (0.125) – – 

Wild spring-summer steelhead (Yakima) 

1999 Lower Yakima 1,241 0.798 (0.033) 0.967 (0.099) – –

2002 Lower Yakima 1,335 0.314 (0.054) 0.924 (0.302) 0.560 (0.585)

2003 Lower Yakima 575 0.394 (0.099) 0.860 (0.359) – – a In the upper Columbia River, hatchery fish were released upstream of Rock Island Dam (designated “Above Rock 

Island Dam”), and wild fish were released at Rock Island Dam. In the Yakima River, fish released downstream of 

Roza Dam are designated “Lower Yakima.” 

b

 Includes data from Bickford et al. (2001). 

66
Snake River sockeye salmon survival 

We have much less information about Snake River sockeye salmon (Oncorhynchus nerka) 

than for Snake River Chinook salmon and steelhead. Although the sample sizes were small, and 

consequently survival estimates were imprecise, by pooling all PIT-tagged sockeye salmon smolts 

detected and returned to the Lower Granite Dam tailrace each year, we could estimate survival 

between Lower Granite and McNary dams from 2000 to 2003 (Table 32). In 2003, estimated 

survival for sockeye smolts was similar to that for yearling Chinook salmon, but in the other 3 

years estimated sockeye salmon survival was considerably lower (see Table 21). 

The experience of PIT-tagged fish does not represent that of the untagged population, 

however. As with Chinook salmon, most untagged sockeye salmon smolts were collected and 

transported to below Bonneville Dam. Nonetheless, few adult sockeye salmon returned to Lower 

Granite Dam from 1990 to 2003. The median annual return was 13 (range 3 to 282). Low 

numbers of returning adults suggest that transportation provides little if any benefit to Snake River 

sockeye salmon. Moreover, based on PIT-tag data, the alternative of in-river migration looks 

poor. 

Table 32. Survival estimates for sockeye salmon smolts PIT tagged and released upstream from Lower 

Granite Dam. All smolts detected and returned to the Lower Granite Dam tailrace in each year were 

pooled into one group. Standard errors are in parentheses. 

Year 

No. of 

smolts 

Lower Granite 

Dam to 

Little Goose Dam

Lower Granite Dam

to Lower 

Monumental Dam

Lower Monumental 

Dam to 

McNary Dam 

Lower Granite 

Dam to McNary 

Dam 

2000 496 0.902 (0.131) 0.703 (0.138) 0.884 (0.251) 0.560 (0.142) 

2001 610 0.760 (0.053) 0.504 (0.087) 0.623 (0.275) 0.239 (0.099) 

2002 262 0.819 (0.100) 0.832 (0.144) 0.584 (0.142) 0.397 (0.085) 

2003 679 0.838 (0.039) 1.044 (0.116) 0.829 (0.164) 0.725 (0.122) 

Probability of Detecting PIT-Tagged Fish Versus Length at Tagging 

We analyzed data from over 340,000 PIT-tagged fish in nine release groups. Detection 

probability was clearly related to fish length for all release groups. The model selection process 

chose length relationships in 21 out of 24 year/site combinations (Figures 25 and 26). In 20 out of 

21 cases where a length relationship was selected, the length coefficient αl was negative, 

indicating that smaller fish had a higher probability of detection. 

When we compared the two methods for estimating population survival, we found a high 

level of correlation and little evidence for bias (Figure 27). Comparing method 1 to method 2, the 

survival estimates produced by the two methods were very highly correlated (r = 0.999) and 

method 1 produced survival estimates that averaged 0.02% lower than method 2. 

67
Length at tagging (mm)

% d

ete

ction prob

a

bility

Wild

Little Goose Dam Lower Monumental Dam McNary Dam

1999 

2000 

2002 

1998 

1999

Hatchery

68

Figure 25. Relationships between detection probability (solid line) and fish length (mm) for Snake River 

spring-summer Chinook salmon released at Lower Granite Dam. Dashed lines represent 

approximate 95% confidence intervals. Nonsignificant relationships do not have confidence 

intervals plotted. Dotted lines are the scaled distribution of lengths in 5-mm increments. 
Figure 26. Relationships between detection (solid line) probability and fish length (mm) for Snake River 

steelhead released at Lower Granite Dam. Dashed lines represent approximate 95% confidence 

intervals. Nonsignificant relationships do not have confidence intervals plotted. Dotted lines are 

the scaled distribution of lengths in 5-mm increments.

Discussion 

Probability of Detecting PIT-Tagged Fish Versus Length at Tagging 

This analysis clearly demonstrated a negative relationship between detection probability 

and fish length for juvenile Snake River spring-summer Chinook salmon and Snake River 

steelhead. Thus bypassed fish did not represent a random sample of the migrant population. 

Fortunately, this relationship did not appear to bias CJS model survival estimates. However, the 

results do call into question the conclusion of Budy et al. (2002) that passage through bypass 

systems results in delayed mortality (this is discussed in greater detail in the “Latent Mortality” 

subsection, page 106). Also, the results have implications for transportation studies. Transported 

and in-river control fish (nondetected fish) may represent different population segments, which 

might partially explain the relatively poor performance of transported fish. Detailed analyses of 

detection probability by tagging length is needed in the future. 

Length at tagging (mm)

% detection probability

Wild

Little Goose Dam Lower Monumental Dam McNary Dam

2000

2002

1999

Hatchery

69
Survival estimates derived

with length-related detection probabilities

1.0 

.09

0.8 

0.7

Survival estimates derived with 

mean detection probabilities

 0.7 0.8 0.9 1.0

70

Figure 27. Comparison of survival estimates derived assuming mean detection probabilities 

(Cormack-Jolly-Seber method) and those using length-related detection probabilities. Wild and 

hatchery spring-summer Chinook salmon and steelhead were tagged and released at Lower Granite 

Dam (1998–2002), and survival was estimated from Lower Granite to Little Goose Dam, Little 

Goose to Lower Monumental Dam, and Lower Monumental to McNary Dam. The dashed line is 

the one-to-one line. 

Avian Predation 

All PIT-tagged fish from the Snake River that survived to the McNary pool were subject to 

predation by piscivorous birds residing on various islands, including Caspian terns, double-crested 

cormorants, gulls, and pelicans. The bird colony locations included but were not limited to 

Richland Island, Island 18, Foundation Island, Badger Island, and Crescent Island. All of these 

islands are located in the McNary Dam reservoir, mostly above the confluence with the Snake

River. Predation also occurred from birds residing in various locations below McNary Dam to the 

mouth of the Columbia River and much of this information is contained in Fresh et al. (in press). 

Beginning in 1998, NOAA Fisheries Service researchers began visiting bird colonies after 

the end of the nesting season and scanning for PIT tags. The recovery data are available from the 

PTAGIS database (PSMFC 2004). To investigate avian predation from bird colonies in the 

McNary Dam pool, the most valuable information is an estimate of the proportion of fish entering 

the pool that were taken by piscivorous birds. However, we have no PIT-tag estimates of survival 

to the head of McNary Dam pool. Instead, for Snake River fish we calculated the proportion of 

PIT-tagged fish that were detected as they passed Lower Monumental Dam whose tags were later 

detected on a bird colony. For fish from the upper Columbia River, we calculated the proportion 

of entire hatchery releases recovered on bird colonies. We also obtained records from PIT-tagged 

smolts if the tag was deposited on a colony and in such a way that it was detectable. Thus these 
proportions constitute minimum estimates of mortality from bird predation. When compared 

across fish cohorts or years, the proportions represent a relative impact index. 

Between 1998 and 2003, the greatest avian predation apparently occurred in the low-flow 

year 2001 (Table 33), a year in which over 10% of PIT-tagged steelhead released in the upper 

Columbia River and more than 20% of PIT-tagged steelhead detected at Lower Monumental Dam

were later recovered on bird colonies. However, PIT-tagged fish made up a much larger portion 

of all Snake River fish that remained in the river below Lower Monumental Dam; without spill, a 

higher percentage of nontagged fish were transported. Thus the total number of salmonid smolts 

taken by avian predators in 2001 was probably not as elevated as suggested by these proportions. 

 Nonetheless, as the survival estimates presented in the “Results” subsection (page 51) are based 

on these PIT-tagged fish, increased avian predation on PIT-tagged fish is a partial explanation of 

the low estimates we obtained in 2001. 

Snake River steelhead were taken by birds in much larger proportions than Snake River 

yearling Chinook salmon. Recovery proportions for upper Columbia River stocks were lower than 

for Snake River stocks, but this is partly because the release group numbers do not take into 

account mortality from the release site to the head of the McNary Dam reservoir (wide range in 

values of survival from release site to McNary Dam). If mortality averaged 50% to McNary Dam,

doubling these recovery proportions, then avian predators had similar effects on upper Columbia 

River fish. 

Table 33. Recovery percentages of PIT-tagged steelhead recovered from McNary pool bird colonies. 

Percentages are based on the number of fish detected at Lower Monumental Dam for Snake River 

fish and numbers released for upper Columbia River fish. 

Year 

Snake River yearling 

Chinook salmon 

Snake River 

steelhead 

Upper Columbia 

River steelhead 

1998 0.49 4.20 NA 

1999 0.84 4.51 1.92 

2000 0.98 3.66 2.36 

2001 5.59 21.06 11.49 

2002 1.19 10.09 3.81 

2003* 1.06 3.71 1.34 

* Crescent Island Caspian tern colony was the only site sampled. 

71
Juvenile Survival, Travel Time, 

and River Environment 

Methods 

Snake River Spring Migrants 

Smith et al. (2002b) investigated relationships among survival, travel time, and river 

conditions for migrant yearling Chinook salmon and steelhead in the lower Snake River. They 

analyzed data from PIT-tagged juveniles migrating through the river segment between the Lower 

Granite and McNary Dam tailraces in the 1995 through 1999 migration seasons. Other researchers 

have conducted similar analyses to evaluate effects of these variables on salmonid survival and 

commented on the approaches (see NPPC 2003 and USFWS 2003). 

The following is not intended as a comprehensive update of the findings of Smith et al. 

(2002b), nor as a comprehensive response to the documents noted above, which were submitted to 

the Northwest Power Planning Council, Portland, Oregon. Instead, we address selected issues 

concerning the relations of survival and travel time with river conditions that arose after the 1999 

migration season. In particular, incorporating observations from the low-flow year 2001 sheds 

light on how salmonids respond to conditions not observed before PIT-tag data became available. 

In the discussion that follows, we note when additional years of data did not alter previous 

conclusions and we describe instances when new information suggests new hypotheses to explain 

patterns. 

As described in earlier sections, we used fish PIT tagged above and at Lower Granite Dam

for migration years 1999 to 2003. We developed survival estimates as described in the “Juvenile 

Migrant Survival” section (page 46). 

Median travel time 

Travel times were calculated for yearling Chinook salmon and steelhead for the following 

reaches: 

1) Lower Granite Dam to Little Goose Dam (60 km), 

2) Little Goose Dam to Lower Monumental Dam (46 km), 

3) Lower Monumental Dam to McNary Dam (199 km), 

4) Lower Granite Dam to McNary Dam (225 km), 

5) Lower Granite Dam to Bonneville Dam (461 km), 

6) McNary Dam to John Day Dam (123 km), 

7) John Day Dam to Bonneville Dam (113 km), and 

8) McNary Dam to Bonneville Dam (236 km). 

72
Travel time between any two dams was calculated for each fish detected at both dams as the 

number of days between last detection at the upstream dam (generally at a PIT-tag detector close 

enough to the outfall site that fish arrived in the tailrace within minutes after detection) and first 

detection at the downstream dam. Travel time included the time required to move through the 

reservoir to the forebay of the downstream dam and any delay associated with residence in the 

forebay, gatewells, or collection channel prior to detection in the juvenile bypass system. 

Migration rate through a river section was calculated as the length of the section (km)

divided by the travel time (days), which included any delay at dams as noted above. 

For each group, we determined the 20th percentile, median, and 80th percentile travel 

times and migration rates. The true, complete set of travel times for a release group includes travel 

times of both detected and nondetected fish. However, using PIT tags, travel times cannot be 

determined for a fish that traverses a river section but is not detected at both ends of the section. 

Travel time statistics are computed only from travel times for detected fish, which represent a 

sample of the complete set. Nondetected fish pass dams via turbines and spill; thus their time to 

pass a dam is typically minutes to hours shorter than fish detected passing to the tailrace via the 

juvenile bypass system. 

River environment variables 

We used the methods of Smith et al. (2002b) to calculate indices of exposure to various 

river conditions, including river discharge (flow in thousands of cubic feet per second [kcfs]), 

percentage of flow that passes over spillways, and water temperature (°C). Indices were 

calculated at Little Goose, Lower Monumental, and McNary dams for each release group, based 

on its detection distribution at each dam. 

In analyses of relations between survival and travel time and indices of exposure for data 

from 1995 through 1999, Smith et al. (2002b) used only the indices calculated for Lower 

Monumental Dam, after confirming that spill, temperature, and flow levels were very similar 

between Little Goose and Lower Monumental dams. Levels of these variables remained similar 

for data collected from 2000 through 2003, with the exception of spill percentage in 2002. The 

analyses reported here continue the use of Lower Monumental Dam indices for temperature and 

flow (but see next paragraph). In all years from 1995 through 2003 except 2002, spill percentages 

at Lower Monumental and Little Goose dams were sufficiently similar that the index for one dam

served to represent conditions at both. This was not true in 2002 because spill continued at 

customary levels at Little Goose Dam, but there was little spill at Lower Monumental Dam in 

April and May. For spill percentage in the analyses reported here, we used the mean of the indices 

calculated for the two dams. Though a more refined index is possible, we felt that the mean, which 

tended to be about half the spill percentage index in most other years, was a reasonable 

representation of migration through the system, which provided spill at only one of the two dams

in 2002. 

The Fish Passage Center analyzed flow travel time for juvenile migrants and concluded 

that exposure to water velocity was likely more important to an individual migrant’s response than 

exposure to flow volume (DeHart et al. 2003). Accordingly, in addition to the indices used in 

Smith et al. (2002b), the analyses in this section include a variable to reflect water travel time 

73
74

(WTT). We derived our approximate WTT variable from the flow exposure indices at Lower 

Monumental and McNary dams and from Figures 1 and 2 of the Fish Passage Center’s 2002 

annual report (FPC 2003b, DeHart et al. 2003). For each daily release group from Lower Granite 

Dam, we calculated WTT days from Lower Granite Dam to Ice Harbor Dam using the exponential 

decay equation (Figure 1 from DeHart et al. 2003) 

 (7) 

where f1 is the flow exposure index (kcfs) at Lower Monumental Dam, and from Ice Harbor Dam

to McNary Dam using the equation (Figure 2 from DeHart et al. 2003) 

 (8) 

where f2 is the flow exposure index (kcfs) at McNary Dam. The total WTT for each group was the 

sum of these two components. 

Mortality per day versus water travel time 

To investigate interactions among the relations of travel time, survival, and WTT, we 

calculated the following quantity for each release group from Lower Granite Dam:

 (9) 

and examined its relationship to WTT (Ŝ and TT are the group’s estimated survival probability and 

median travel time from Lower Granite Dam to McNary Dam, respectively). For example, if fish 

travel time was positively related to WTT, but reach survival was not, then the mortality per day 

must decrease as WTT and fish travel time increase. Conversely, if mortality per day is constant, 

then a positive relationship between WTT and fish travel time would result in a positive 

relationship between reach survival and WTT, independent of any other flow-related effects on 

survival. 

Threshold models for survival versus flow

As Smith et al. (2002b) observed, survival estimates varied little within seasons when the 

flow level was moderate to high. After accounting for differences in annual means, Smith et al. 

(2002b) found no relation between 1995–1999 survival estimates and flow exposure for yearling 

Chinook salmon, and only a weak relation for steelhead. 

With additional years of data, the lowest survival estimates were observed in the lowest 

flow year, 2001. Along with the recognition that zero survival would likely result if flow were 

zero, and with the observation of little or no relation between flow and survival at moderate to high 

flow levels, the 2001 data suggest that a “threshold effect” may exist. That is, there may be a flow 

level above which survival has little variability, but below which survival decreases with 

decreasing flow. 

We have no hypothesized mechanism to suggest a theoretical basis for the exact “shape” 

of such a threshold relation (although we recognize that WTT might relate to such a mechanism). 

28 97 3 160 0 02148 1 . . . e − f +

12 12 1 232 0 008776 2 . . . e − f +

Mort. per Day = −1 $( / 1 ) S TT
Y Bottom Top Bottom

e V X Slope = + −

+ −

( )

( ) 1 50

However, we explored two mathematical forms that might describe the relationship: a sigmoid 

curve and a piecewise linear regression line. 

The sigmoid curve had the following equation form (Boltzmann sigmoid): 

 (10) 

where X and Y were the independent (flow exposure index) and dependent (estimated survival) 

variables, respectively, and Top, Bottom, V50, and Slope were parameters we estimated. A 

sigmoid curve is S shaped: assuming positive Slope, the curve rises from low to high values of X 

and Y, with relatively shallow slope at low and high ends of the range of X values, and steeper 

slope in the intermediate range. The Bottom and Top parameters are the minimum and maximum

Y values on the curve, respectively. The V50 parameter is the X value for which Y is halfway 

between Bottom and Top, and Slope describes the steepness of the curve, with larger values 

denoting a shallower curve. We used this form for estimated survival only. In these models, the 

Bottom parameter was always set equal to 0.0. 

The selected piecewise linear regression model was the one that minimized sum of squared 

error among models with the following properties: linear relationship between flow exposure and 

estimated survival when the exposure was below the threshold and no relationship when the 

exposure was above the threshold (survival constant, equal to the fitted value of the linear 

regression line at the threshold flow value). Selection of the threshold, or break point, was part of 

the least-squares optimization. 

Both the sigmoid curve and the piecewise linear-regression model were fitted using 

unweighted least squares. For the piecewise linear fit, we used bootstrap methods to characterize 

uncertainty in estimation of maximum survival, slope below the threshold, and most importantly, 

the threshold. 

Generalized additive and multiple-regression models 

We explored multiple-regression (analysis of covariance) models that included 

year-effects variables and two or more quantitative environmental variables. Because the 

independent variables were correlated with each other, and because some relations had notable 

nonlinearity, we checked multiple-regression models using the generalized additive model (gam) 

function of S-Plus (MathSoft 2000), a nonparametric multiple-regression technique. The 

nonparametric splines calculated in the gam function were used to suggest parametric curve 

functions (polynomials) to use in parametric multiple-regression models. Resulting 

multiple-regression models were rejected if graphic inspection of residuals revealed remaining 

nonlinearity or notable lack of normality. Partial fits of predictor variables from the generalized 

additive models were plotted without vertical axis labels. All variables in a gam model, and 

therefore the vertical axis in partial fit plots, are transformed and scaled, making direct 

interpretation of units impossible. Relative influence of individual predictor variables can be 

gauged by the relative range of the partial fit functions, and the shape of the nonlinear relation 

between predictor and dependent variable can be seen. 

75
All gam and multiple-regression models for survival estimates were weighted by 

respective inverse relative variances (inverse of coefficient of variation squared) of the survival 

estimates. Multiple-regression models for travel time were unweighted. 

Run-of-River Subyearling Chinook Salmon from McNary Dam 

Study groups of PIT-tagged migrants 

In 1999 through 2002, we collected run-of-river subyearling Chinook salmon (mostly wild 

fish from the Hanford Reach) at McNary Dam, PIT tagged them, and released them. Study designs 

and release sites varied from year to year, but we included a series of releases into the McNary 

Dam tailrace each year. For this analysis, we combined individual (daily) release groups of 

subyearling Chinook salmon into McNary Dam tailrace into weekly groups for 1999 to 2002 

(Table 34). 

Table 34. Numbers of run-of-river subyearling Chinook salmon (mostly wild fish from the Hanford Reach) 

collected and tagged at McNary Dam and released in the McNary Dam tailrace, 1999–2002. 

Release dates 1999 2000 2001 2002 

19–25 June 3,704 5,102 6,089 4,156 

26 June–02 July 8,146 5,045 7,511 5,468 

03–09 July 6,267 5,138 3,814 5,655 

10–16 July 9,195 5,038 6,935 3,703 

17–23 July 5,692 3,100 5,703 9,710 

24–30 July – – 8,494 10,675 

31 July–06 August – – – 5,328 

07–13 August – – – 8,001 

14–20 August – – – 3,664 

Travel time and survival estimates 

For all fish detected at John Day Dam, we calculated the time (days) from release at 

McNary Dam to first detection at John Day Dam. Then for each weekly group we calculated the 

median travel time (days). We constructed detection histories for each weekly pooled group and 

used the SR model to calculate survival estimates from release to John Day Dam. Detection 

histories were only two digits long, indicating detection at and below John Day Dam (Bonneville 

Dam in all years and estuary trawl in 2002). 

River environment variables 

We calculated indices of exposure to the following river condition variables: river 

discharge (flow in kcfs); amount of flow over spillways (kcfs); percentage of flow that passed over 

spillways; water temperature (°C); and water clarity (Secchi disk reading). We obtained daily 

values for each of these variables from the DART web site (CBR UW 2004). In a few cases, we 

interpolated data for days when it was missing or obviously incorrect (e.g., Secchi disk reading of 

0 between 2 days that each had readings of 5 m). We calculated indices of exposure at McNary 

Dam for each weekly group as the averages of the respective daily values at McNary Dam during 

76
the week of release. For John Day Dam, exposure indices were based on the group’s distribution 

of detections at the dam. For each weekly release group we tabulated John Day detections by day, 

then determined the days on which the 25th and 75th percentiles of passage occurred. The John Day 

Dam exposure indices were the averages of the respective daily values at John Day Dam between 

the dates of the 25th and 75th percentiles (inclusive). 

We used various graphical methods, pairwise product-moment correlations, and simple 

and multiple linear regression modeling to explore relations among indices of exposure to selected 

environmental factors and survival and travel time. Because of concomitant temporal trends in 

river conditions, exposure indices for release groups of PIT-tagged fish were generally highly 

correlated with each other and with release dates. Correlation of such magnitude among predictor 

variables generally makes it very difficult for multivariate statistical methods to distinguish the 

relative importance of the predictors’ influence on the response variable. Nonetheless, we 

explored bivariate patterns and used multivariate methods to shed light on relations. Samples were 

of sufficient size that correlations with relatively little explanatory power (e.g., r

2

 = 0.16) were 

statistically significant (P < 0.05). One response to this is to lower the level required to declare a 

correlation significant. Our approach, however, was simply to focus on the amount of variability 

in the response variable that is “explained” by variability in the predictor (i.e., the r

2

 value). 

In some regression models of data from multiple years, we used variables for “year effects” 

to account for differences in annual mean survival and travel time potentially not captured by the 

environmental variables. We also calculated “adjusted” predictor and response variables by 

subtracting the respective overall means from each unadjusted variable. Correlation between 

adjusted predictor and adjusted response would indicate a within-season relationship between the 

variables beyond differences in annual means. However, lack of correlation between adjusted 

variables could occur if there was no within-season relationship, or if differences in annual means 

of travel time or survival (annual effects) were due to year-to-year differences in the predictor 

variable and the within-year ranges of the predictor variable did not overlap sufficiently. 

Results 

Snake River Yearling Chinook Salmon 

Travel time versus flow and water travel time 

Except for the low flow year of 2001, the annual median travel time (days) for all 

PIT-tagged Snake River spring-summer Chinook salmon passing between Lower Granite and 

Bonneville dams from 1 April to 31 May each year varied by only a few days (Table 35). Based 

on earlier data derived from Raymond (1979), these times were approximately 40–50% longer 

than when no dams existed in the mainstem Snake and Columbia rivers (Figure 28). 

77
78

Table 35. Median travel time (days) of PIT-tagged yearling Chinook salmon between Lower Granite Dam

and Bonneville Dam, 1995–2003. 

Year 

Median travel time

(days) 

1995 18.4 

1996 16.2 

1997 14.1 

1998 19.0 

1999 16.1 

2000 16.4 

2001 31.0 

2002 16.9 

2003 14.4 

Figure 28. Estimated annual average travel times for yearling Chinook salmon through the section of the 

lower Snake and Columbia rivers now inundated by mainstem hydropower dams (approximately

from Lewiston, Idaho, to Bonneville Dam tailrace). Estimates for the 0- and 4-dam scenarios are 

derived after data in Raymond (1979). Data for 8 dams were derived from PIT-tagged fish between 

1997 and 2003. 

0

10

20

30

40 0 dams

4 dams

8 dams

Low flow Moderate flow High flow

 Columbia River

Snake River (35-53 kcfs) (71-106 kcfs) (106-177 kcfs)

(141-177 kcfs) (212-318 kcfs) (353-494 kcfs)

Days
79

Within individual years, median travel time for groups of PIT-tagged yearling Chinook 

salmon has generally decreased throughout the migration season as flows have generally increased 

(Figure 29) and as WTT has decreased (Figure 30). However, water velocity is clearly not the only 

driver of travel time in all years: in 1998, and especially in 2002 and 2003, the early part of the 

migration season featured relatively long periods of nearly constant flow. In these years, 

nonetheless, median travel times for yearling Chinook salmon decreased throughout the period, 

even without change in flow. This result suggests that physiological characteristics of juvenile 

fish (possibly degree of smoltification) or physiological responses to day length or moon phase 

might have influenced migration rates more than flow. 

As in Smith et al. (2002b), this observation is supported by the partial fits for a generalized 

additive model of travel time that included year effects and nonparametric splines for date and 

flow (Figure 31). This model indicated that flow had a nearly linear effect on travel time 

throughout the range of observed flow exposures, but that release date had more influence early in 

the season, until about the end of April. A generalized additive model using the WTT index gave 

essentially the same information. 

Survival and mortality versus water travel time 

Smith et al. (2002b) found that the relationship between flow exposure and survival of 

yearling Chinook salmon within seasons was generally weak and inconsistent. Translating the 

flow exposure measures into a WTT index resulted in qualitatively similar results (Figure 32). 

Significant (α = 0.05) negative slopes (increased WTT related to decreased survival) occurred for 

data within the 1998, 2000, and 2003 seasons; the R2

 was 35% in 2003 and 11% in the other 

2 years. Results in 2001 depended on whether the analysis was weighted according the relative 

precision of the estimates. 

Including all years in an unweighted analysis resulted in a significant regression 

(Figure 33). Data from 2001 were highly influential in this result; excluding 2001 data resulted in 

a slightly negative but not significant slope and no predictive value (see subsections below on 

threshold models, multiple regression, and discussion of 2001, pages 84–88). 

For years other than 2001, estimated mortality per day tended to decrease with increasing 

WTT (bottom panel, Figure 34). Data from 2001 stood apart from data from other years (top panel, 

Figure 34) and appeared to indicate two distinct sets of release groups. See the “Snake River 

Spring Migrants” subsection (page 101), for discussion of this pattern.
7

89

101112131415161718

50100150200

1995 250

10 Apr 20 Apr 30 Apr 10 May 20 May

05

101520

50100150200

1996 250

10 Apr 20 Apr 30 Apr 10 May 20 May

05

101520

1997 

10 Apr 20 Apr 30 Apr 

05

10152025

50100150200

1998 250

10 Apr 20 Apr 30 Apr 10 May 20 May

05

101520

50100150200

1999 250

10 Apr 20 Apr 30 Apr 10 May 20 May

05

101520

2000

10 Apr 20 Apr 30 Ap

0

10203040

050100150200250 2001

10 Apr 20 Apr 30 Apr 10 May 20 May

0

10203040

050100150200

2002 250

10 Apr 20 Apr 30 Apr 10 May 20 May

0

102030

2003 

10 Apr 20 Apr 30 Apr 

Date at Lower G ranite Dam

Median traveltime (days)

Figure 29. Median travel time (solid line) and flow exposure index (dotted line) for PIT-tagged Snake River yearling Chinook 

80
7

89

101112131415161718

510152025 1995

10 Apr 20 Apr 30 Apr 10 May 20 May

05

101520

510152025 1996

10 Apr 20 Apr 30 Apr 10 May 20 May

05

101520

199

10 Apr 20 Apr 30 

05

10152025

510152025 1998

10 Apr 20 Apr 30 Apr 10 May 20 May

05

101520

510152025 1999

10 Apr 20 Apr 30 Apr 10 May 20 May

05

101520

2000

10 Apr 20 Apr 30 

0

10203040

5101520

2001 25

10 Apr 20 Apr 30 Apr 10 May 20 May

0

10203040

510152025 2002

10 Apr 20 Apr 30 Apr 10 May 20 May

0

102030

10 Apr 20 Apr 3

20

Date at Lower Granite Dam

Median travel time (days)

81

Figure 30. Median travel time (solid line) and water travel time (dotted line) for PIT-tagged Snake River yearling Chinook sal
82 

Figure 31. Partial fits for generalized additive model of median travel time from Lower Granite Dam to 

McNary Dam (days), with pointwise 95% confidence intervals, yearling Chinook salmon, 

1995–2003. Predictor variables were release dates from Lower Granite Dam, flow exposure index 

(kcfs), and year effects. Because all variables were transformed, Y-axis units are not meaningful. 

Relative influence on travel time is judged by relative ranges of transformed predictor variables, 

which are all plotted with the same Y-axis scale. Shape of the relationship is judged by the spline. 

Figure 32. Estimated survival from Lower Granite Dam to McNary Dam for PIT-tagged Snake River 

yearling Chinook salmon, plotted against water travel time index, 1995–2003. 

0.0

0.3

0.6

0.9

1.2

1.5

1995

0.0

0.3

0.6

0.9

1.2

1.5

1998

5 10 15 20 25 0.0

0.2

0.4

0.6

0.8

1.0

2001

Weighted

Unweighted

1996

1999

5 10 15 20 25 0.0

0.3

0.6

0.9

1.2

1.5

2002

1997

2000

5 10 15 20 25

2003

Estimated survival

Water travel time index (days)

 90 100 110 120 130 140 150 0 50 100 150 200 250 

 Day of year at Lower Granite Dam Flow exposure (kcfs)
5 15 25

0.0

0.3

0.6

0.9

1.2

1.5

All years except 2001

R2= 0.3% P = 0.31

All years

R2= 7.5% P < 0.001

Water travel time index (days)

Estimated survival

83

Figure 33. Estimated survival from Lower Granite Dam to McNary Dam versus water travel time for 

PIT-tagged yearling Snake River Chinook salmon, 1995–2003. ○ = data from 2003: + = data 

from all other years. 

Figure 34. Estimated mortality per day versus water travel time index for PIT-tagged yearling Snake River 

Chinook salmon, 1995–2003. Top panel includes 2001 data (○); bottom panel excludes 2001. 

Lowess smooth (black line) in bottom panel indicates that mortality per day tended to increase with 

decreased water travel time. 

5 15 25

0.00

0.05

0.10

0.15

0.20

0.25

5.0 7.5 10.0 12.5 15.0

0.00

0.05

0.10

0.15

0.20

0.25

Estimated mortality per day

Water travel time index (days)
SURV e F = + −

0 7854

1 48 13 9 72

.

( . ) .

SURV =−0. . 2954 +0 0147F .

Threshold models for survival versus flow

The equation for the best-fit Boltzmann curve (Figure 35) was 

 (11) 

with R2

 = 10.5%. The best-fit piecewise linear regression model was almost identical to the 

Boltzmann curve (Figure 35). The threshold flow exposure value was 73.0 kcfs; maximum

survival was 0.777, and the linear equation for survival below the threshold was 

Bootstrap 95% confidence intervals on the estimated parameters are as follows: maximum

survival (0.752,0.835); slope (0.0053,0.0181); and threshold (70.1, 99.4). 

 

 (12) 

Importantly, we note that without the low-flow, low-survival points from 2001, we could 

not fit the threshold models. The 2001 points “pulled down” the curve or line in the low-flow 

range. Further, the individual points from 2001 do not fit the curves very well. Taken as a whole, 

the points from 2001 effectively acted as a single “center of gravity” or almost as a single point 

that obscured the within-season dynamics. 

Figure 35. Best-fit sigmoid curve (dashed line) and piecewise linear regression model (solid line) for 

estimated survival from Lower Granite Dam to McNary Dam for PIT-tagged, yearling Snake River 

Chinook salmon versus flow exposure index, 1995–2003. ○ = data from 2001; + = all other years. 

Point of “break,” or threshold, is not precisely estimated. 

50 100 150 200

0.0

0.3

0.6

0.9

1.2

1.5

73.0 kcfs

Flow exposure index (kcfs)

Estimated survival

84 
85

Generalized additive and multiple-regression models for survival 

Exploratory analysis using generalized additive models (gam) suggested a regression 

model for survival that used functions of the indices of WTT, percent spill, and water temperature 

exposure. Partial fits from the gam indicated temperature had little effect on survival when water 

temperature was low to moderate, but that the strongest relationship to survival estimates was that 

of temperature when it was high (Figure 36). The influence of WTT and percentage spill was 

small relative to the dramatic decrease in survival that occurred at high temperatures. The spline 

When temperatures were in this lower range, as they were for 65% of the release groups, the WTT 

index had the strongest association with estimated survival (Figure 37). From the smallest WTT 

(4.8 days) to about 14.0 days, the decline in survival was nearly linear. Beyond 14.0 days, there 

was little association. For the spill percentage index (spill %), there was a peak in survival at about 

20.6% spill; survival was lower on either side of 20.6%. 

Data were sparse at WTT greater than 14.0 days (10% of groups) or spill % less than 10% 

(57 groups with 0% spill, all from 2001; only 9 groups with spill percentage exposure between 0% 

and 10%). The highest survival values for the spill percentage spline were at 0% spill. All these 

points were from 2001, and the peak survival at 0% spill in the partial fit from the multiple 

regression was due to confounding with the year effect for 2001. 

Figure 36. Partial fits (transformed nonparametric splines) for generalized additive model for estimated 

survival from Lower Granite Dam to McNary Dam, with pointwise 95% confidence limits, yearling 

Chinook salmon, 1995–2003. Predictor variables were year effects, water travel time index (days), 

spill percentage index, and temperature index (°C). Because all variables were transformed, Y-axis 

units are not meaningful. Relative influence on survival is judged by relative ranges of transformed 

predictor variables, which are all plotted on the same Y-axis scale. Shape of the relationship is 

judged by the spline itself. All data are illustrated; that is, full range of temperature exposures. 

5 15 25

Water travel time index (days)

0 25 50

Spill % exposure index

7.5 10.0 12.5 15.0 17.5

Temperature exposure index ( oC)

indicated that a small decline in survival began at a temperature exposure of 11.85°C, decline 

became steeper between 12.0 and 13.0°C, and above 13.0°C the decline was sharp and nearly 

linear. Of the 458 release groups in the data set, 159 (35%) had temperature exposure indices 

greater than 11.85°C, and 70 (15%) were greater than 13.0°C (27 groups in 2001 had a 

temperature index greater than 13.0°C). Indices of 11.85°C or above were reached for at least a 

few groups in every year of the study; 13.0°C was reached in all years but 1996 and 2002 (for only 

one group in 2003). 

At temperature exposures below 11.85°C, differences in temperature exposure had little 

influence on survival (spline for temperature in Figures 36 and 37 is nearly flat in that range). 
86

Figure 37. Partial fits (transformed nonparametric splines) for generalized additive model for estimated 

survival from Lower Granite Dam to McNary Dam, with pointwise 95% confidence intervals, 

yearling Chinook salmon, 1995–2003. Predictor variables were year effects, water travel time 

index (days), spill percentage index, and temperature index (°C). Because all variables were 

transformed, Y-axis units are not meaningful. Relative influence on survival is judged by relative 

ranges of transformed predictor variables, which are all plotted on the same Y-axis scale. Shape of 

the relationship is judged by the spline itself. Fits were based on all data; only release groups with 

temperature exposure less than 11.85°C are illustrated (i.e., a subset of Figure 36; range of Y axes 

is about 35% of those in Figure 36). 

Based on the generalized additive model results, we fit a multiple-regression model (Table 

36) that included year effects, a function of WTT that was linear between the minimum 4.8-day 

WTT and 14.0 days and flat above 14.0 days, a function of temperature that was flat up to 13.0°C 

and linear above it, a function of spill percentage that was flat below 10% and a second-order 

polynomial above that level. 

Data from 2001 clearly did not fit a model of survival as strictly a function of flow or WTT 

(e.g., Figures 32 through 34). The multiple-regression model that included strong effects at high 

temperatures provided a much better fit for 2001 data (Figure 38). 

Snake River Steelhead 

Travel time versus flow and water travel time 

With the exception of the low-flow year of 2001, the annual median travel time (days) for 

all Snake River steelhead passing between Lower Granite and Bonneville dams from 1 April to 31 

May each year varied by only a few days (Table 37). 

Within seasons, median travel time for groups of PIT-tagged steelhead has consistently 

tracked the WTT index (Figure 39). Results from a generalized additive model (including year 

effects and nonparametric splines for date and flow exposure index) indicated that date also 

influenced travel time for steelhead (Figure 40), but not as much as flow. Unlike the result for 

yearling Chinook salmon, flow appeared to have more influence than date on steelhead travel time 

throughout the migration season. A generalized additive model using the WTT index gave 

essentially the same information. 

5 10 15 20 25

Water travel time index (days)

0 10 20 30 40 50

Spill % exposure index

8 9 10 11 12

Temperature exposure index ( oC)
87

Table 36. Summary of multiple-regression model for estimated survival of yearling Chinook salmon 

between tailraces of Lower Granite and McNary dams, 1995–2003. R2 for this model is 78.1%. 

Parameter Estimate 

Standard 

error t statistic P value 

Intercept 0.6610 0.0376 17.58 0.000 

Year effects 

 1996 –0.0891 0.0464 –1.92 0.056 

 1997 –0.1039 0.1142 –0.91 0.364 

 1998 0.0469 0.0337 1.39 0.164 

 1999 0.0644 0.0330 1.95 0.052 

 2000 0.0466 0.0358 1.30 0.194 

 2001 –0.0875 0.0377 –2.32 0.021 

 2002 0.0678 0.0349 1.94 0.053 

 2003 0.0448 0.0359 1.25 0.213 

Slope for WTT < 14 days

a 0.0104 0.0026 –3.99 <0.001 

Slope for TEMP > 13°Cb –0.1378 0.0112 –12.29 <0.001 

% spillc < 10: linear 0.00283 0.00179 1.58 0.115 

% spill < 10: quadratic –0.0000942 0.0000416 –2.26 0.024 

F statistic for % spill < 10 polynomial F2,445 = 3.25 0.040 a WTT = water travel time index. To calculate fitted value: if WTT > 14 contribution is 0; if WTT < 14 use 

0.0104*(14 – WTT). 

b TEMP = temperature exposure index. To calculate fitted value: if TEMP < 13 contribution is 0; if TEMP > 13 

use –0.1378*(TEMP – 13). 

c

 % spill = percentage spill index. To calculate fitted value, if % spill < 10 contribution is 0; if % spill > 10 use 

0.00283*(% spill – 10) – 0.0000942*(% spill – 10)2. 

Table 37. Median travel time (days) of PIT-tagged 

steelhead between Lower Granite Dam and 

Bonneville Dam, 1995–2003. 

Figure 38. Observed survival estimates for Snake 

River yearling Chinook salmon between 

Lower Granite Dam and McNary Dam in 

2001 plotted against fitted values from

selected multiple-regression model 

including functions for water travel time 

and temperature (and spill percentage, 

which was 9 for all 2001 groups). 

Multiple fitted values of 0.574 were for 

early season groups migrating in low 

flows and low water temperatures. 

Year 

Median Lower Granite 

Dam–Bonneville Dam 

travel time (days) 

1995 20.2 

1996 15.3 

1997 12.2 

1998 14.4 

1999 15.4 

2000 13.6 

2001 29.8 

2002 18.4 

2003 15.4 

0.1 0.2 0.3 0.4 0.5 0.6

0.10

0.35

0.60

Fitted value from regression model

Estimated survival
7.5

8.08.59.09.5

10.010.511.011.512.012.513.013.514.014.5

5101520 1995

10 Apr 20 Apr 30 Apr 10 May 20 May

05

101520

51015

1996 20

10 Apr 20 Apr 30 Apr 10 May 20 May

05

101520

1997 

10 Apr 20 Apr 30 A

05

10152025

51015

1998 20

10 Apr 20 Apr 30 Apr 10 May 20 May

05

101520

5101520 1999

10 Apr 20 Apr 30 Apr 10 May 20 May

05

101520

2000

10 Apr 20 Apr 30 A

0

10203040

5101520 2001

10 Apr 20 Apr 30 Apr 10 May 20 May

05

101520

5101520 2002

10 Apr 20 Apr 30 Apr 10 May 20 May

0.02.55.07.5

10.012.515.017.5

2003

10 Apr 20 Apr 30 A

Date at Lower G ranite Dam

Median travel time (days)

88 

Figure 39. Median travel time (solid line) and water travel time index (dotted line) for groups of PIT-tagged Snake River s
90 100 110 120 130 140 150

Day of year at Lower Granite Dam

0 50 100 150 200 250

Flow exposure index (kcfs)

89

Figure 40. Partial fits for generalized additive model of steelhead median travel time from Lower Granite 

to McNary dams (days), with pointwise 95% confidence intervals, 1995–2003. Predictor variables 

were release date from Lower Granite Dam, flow exposure index (kcfs), and year effects. Because 

all variables were transformed, Y-axis units are not meaningful. Relative influence on travel time 

is judged by relative ranges of transformed predictor variables, which are all plotted with the same 

Y-axis scale. Shape of the relationship is judged by the spine itself. 

Survival and mortality versus water travel time 

Smith et al. (2002b) found that the relationship between flow exposure and survival of 

steelhead within seasons was generally weak and inconsistent. Translating the flow exposure 

measures into a WTT index resulted in qualitatively similar results (Figure 41). Significant (α = 

0.05) negative slopes (increased WTT related to decreased survival) occurred for data within the 

1995, 1999, and 2000 seasons. The R2

 values were 16%, 21%, and 51%, respectively. Only 2000 

had an R2

 value that appeared mildly predictive. 

Including all years in an unweighted analysis resulted in a significant simple linear 

regression (Figure 42). As with yearling Chinook salmon, data from 2001 were highly influential 

in this result, and the 2001 data do not fit the line well at all (there are substantial problems with 

residuals). Excluding 2001 data there is a slight and significant negative slope, but little predictive 

value (see following subsections on “Threshold models for survival versus flow,” page 91, and 

“Snake River Spring Migrants,” page 101). For years other than 2001, estimated mortality per day 

was fairly constant, regardless of WTT (bottom panel, Figure 43). This indicates that the observed 

relationship between WTT and steelhead travel time induces a relationship between WTT and 

steelhead survival. Data from 2001 clearly stand apart from data from other years (top panel, 

Figure 43). The “baseline” mortality per day appeared to be higher, and, contrary to the more 

constant pattern for other years, the estimated mortality per day decreased with increasing WTT. 
0.0

0.3

0.6

0.9

1.2

1.5

1995

0.0

0.3

0.6

0.9

1.2

1.5

1998

5 10 15 20

0.0

0.2

0.4

0.6

0.8

1.0

2001

1996

1999

5 10 15 20

0.0

0.3

0.6

0.9

1.2

1.5

2002

1997

2000

5 10 15 20

2003

Estim

ated survival

Water travel time index (days)

90

Figure 41. Estimated survival from Lower Granite Dam to McNary Dam for PIT-tagged Snake River 

steelhead, plotted against water travel time index, 1995–2003. 

Figure 42. Estimated survival from Lower 

Granite Dam to McNary Dam versus 

water travel time for PIT-tagged 

 5 10 15 20

0.0

0.3

0.6

0.9

1.2

1.5

All years except 2001

R2= 2.9%, P = 0.001

All years

R2= 13.5%,

P < 0.001

Water travel time (days)

Estimated survival

Snake River steelhead, 1995–2003. 

○ = data from 2001; + denotes 

data from all other years. 
5 10 15 20

0.00

0.05

0.10

0.15

0.20

0.25

0.30

5.0 7.5 10.0 12.5 15.0

0.00

0.05

0.10

0.15

0.20

0.25

0.30

Water travel time index (days)

Estimated mortality per day

91

SURV = + 0. . 0316 0 0065F .

SURV

e F = + −

0 7728

1 59 48 18 64

.

( . ) .

Figure 43. Estimated mortality per day versus water travel time for PIT-tagged Snake River steelhead, 

1995–2003. Top panel includes 2001 data (○); bottom panel excludes 2001. Lowess smooth (black 

line) in bottom panel indicates that mortality per day was fairly constant at different water travel 

times, consistent with existence of both fish travel time/water travel time and survival/water travel 

time relationship. 

Threshold models for survival versus flow

The equation for the best-fit Boltzmann curve (Figure 44) was as follows: 

 (13) 

with R2

 = 10.2%. In the best-fit piecewise linear regression model (Figure 44), the threshold flow 

exposure value was 115.4 kcfs, maximum survival was 0.779, and the linear equation for survival 

below the threshold was 

 (14) 
92

Figure 44. Best-fit sigmoid curve (dashed line) and 

piecewise linear regression model (solid line) for 

estimated survival from Lower Granite Dam to 

McNary Dam for PIT-tagged Snake river yearling 

Chinook salmon versus flow exposure index, 

1995–2003. ○ = data from 2001; + = data from 

all other years. Point of “break” or threshold is 

estimated extremely imprecisely.

Bootstrap 95% confidence intervals on the estimated parameters are maximum survival (0.693, 

0.849), slope (0.0046, 0.0202), and threshold (78.9, 132.6). 

As with yearling Chinook salmon without the low-flow, low-survival points from 2001, we 

could not fit the threshold models. The 2001 points “pulled down” the curve or line in the 

low-flow range. Further, the individual points from 2001 do not fit the curves very well. Taken 

as a whole, the points from 2001 effectively acted as a single “center of gravity,” or almost as a 

single point that obscured the true within-season dynamics. 

Generalized additive and multiple-regression models for survival 

Two different multiple-regression models were suggested by exploratory analysis using 

gams. Both models included functions of indices of WTT and % spill. Each model had a third 

variable: temperature index in one case and release date in the other. Although the R2

 value for the 

regression model with date was slightly higher (70.9%) than with temperature (68.3%), we 

illustrate the model that includes water temperature (Figure 45). 

Figure 45. Partial fits (transformed nonparametric splines) for generalized additive model for estimated 

steelhead survival from Lower Granite Dam to McNary Dam, with pointwise 95% confidence 

limits, 1995–2003l. Predictor variables were year effects, water travel time index (days), spill 

percentage index, and temperature index (°C). Because all variables were transformed, Y-axis 

units are not meaningful. Relative influence on survival is judged by relative ranges of transformed 

predictor variables, which are all plotted on the same Y-axis scale. Shape of the relationship is 

judged by the spline itself. 

5 15

Water travel time (days)

0 25 50

% spill exposure

7.5 10.0 12.5 15.0 17.5

Temperature exposure (oC)

50 100 150 200

0.0

0.3

0.6

0.9

1.2

1.5

115.4 kcfs

Flow exposure index (kcfs)

Estim

ated survival
Based on the gam results (Figure 45), we fit a multiple-regression model (Table 38) that 

included year effects, a function of WTT that was linear for WTT less than 11.3 days and flat for 

longer travel times, a function of % spill that was linear for the 0%–30.4% range and flat above it, 

and a function of water temperature that was linear throughout the observed range. 

Table 38. Summary of multiple-regression model for estimated survival of steelhead between tailraces of 

Lower Granite and McNary dams, 1995–2003. R2

 for this model is 68.3%. 

Parameter Estimate Standard error t statistic P value 

Intercept 0.9905 0.0915 10.83 <0.001 

Year effects 

 1996 –0.1127 0.0804 –1.40 0.162 

 1997 –0.1465 0.0809 –1.81 0.071 

 1998 –0.0873 0.0661 –1.32 0.188 

 1999 –0.0433 0.0642 –0.67 0.501 

 2000 –0.0725 0.0657 –1.10 0.271 

 2001 –0.3668 0.0754 –4.86 <0.001 

 2002 –0.1253 0.0687 –1.82 0.069 

 2003 –0.1297 0.0662 –1.96 0.051 

Slope for WTT index < 11.34a 0.0310 0.0044 7.05 <0.001 

Slope for % spill < 30.4b –0.0036 0.0013 –2.72 0.007 

Slope for temp.

c –0.0276 0.0062 –4.42 <0.001 a WTT = water travel time index. To calculate fitted value: if WTT > 11.34, contribution is 0; if WTT < 11.34, use 

0.0310*(11.34 – WTT). 

b

 % spill = percentage spill index. To calculate fitted value: if % spill > 30.4, contribution is 0; if % spill < 30.4, 

use –0.0036*(30.4 – % spill). 

c Temp. = temperature exposure index. 

Run-of-River Subyearling Chinook Salmon from McNary Dam 

River conditions for 1999–2002 

The study period included 1 year with relatively high flow, especially in late summer 

(1999), 1 year with very low flow (2001), and 2 intermediate years (2000 and 2002) (Figures 46 

and 47). Water temperature was strongly correlated with flow: water was warmest in 2001, 

coolest in 1999, and intermediate the other 2 years. Flow and water temperature at McNary and 

John Day dams were very highly correlated (Figures 46 and 47), but spill and water clarity differed 

between the two dams. At McNary Dam there were large differences from year to year in 

percentage of flow that was spilled (Figure 46). Spill usually did not occur when flow was below 

175 kcfs (no spill occurred at all in 2001 after 19 June and at McNary Dam on 44 days between 19 

June and 31 August 2000 and on 29 days in 2002, mostly in August). When flow was above 175 

kcfs, the rate and percentage of spill were highly correlated with flow. Because the study fish were 

collected in the bypass system at McNary Dam and released in the tailrace, it is very unlikely that 

spill at McNary Dam influenced their travel time or survival to John Day Dam. Therefore, beyond 

the description above, we made no further use of the variable. 

93
Flow

0

100

200

300

400

1 Jul 16 Jul 1 Aug 16 Aug 1 Sep

Kcfs

Temperature

15

16

17

18

19

20

21

22

23

1 Jul 16 Jul 1 Aug 16 Aug 1 Sep

°C

Spill

0

50

100

150

200

1 Jul 16 Jul 1 Aug 16 Aug 1 Sep

Kcfs

% spill

0

10

20

30

40

50

60

1 Jul 16 Jul 1 Aug 16 Aug 1 Sep

%

Water clarity

0

1

2

3

4

5

6

7

1 Jul 16 Jul 1 Aug 16 Aug 1 Sep

1999

2000

2001

2002

S

ecchi disk

94

Figure 46. River conditions at McNary Dam, 19 June–31 August, 1999–2002.

Spill occurred at John Day Dam on all days between 19 June and 31 August 1999, 2000, 

and 2002 and on no days in 2001 (Figure 47). The percentage of total flow spilled was fairly 

constant in 1999, and averaged 26.6% between 19 June and 31 August. In 2000 spill alternated 

between blocks of days with average of a little less than 30% and blocks a little more than 40%. 

The average for 2000 was 34.7%. The average percentage spilled in 2002 was 29.2%. The 

relatively constant spill percentage in years at John Day Dam (in 2001 spill was constant at 0%) 

resulted in a lack of correlation between flow and percentage of flow spilled, but also resulted in 

a lack of contrast in spill percentage among the years 1999, 2000, and 2002. 
Flow

0

100

200

300

400

1 Jul 16 Jul 1 Aug 16 Aug 1 Sep

K

cfs

Temperature

15

16

17

18

19

20

21

22

23

1 Jul 16 Jul 1 Aug 16 Aug 1 Sep

°C

Spill

0

50

100

150

200

1 Jul 16 Jul 1 Aug 16 Aug 1 Sep

Kcfs

% spill

0

10

20

30

40

50

60

1 Jul 16 Jul 1 Aug 16 Aug 1 Sep

%

Water clarity

0

1

2

3

4

5

6

7

1 Jul 16 Jul 1 Aug 16 Aug 1 Sep

1999

2000

2001

2002

S

ecchi disk

95

Figure 47. River conditions at John Day Dam, 19 June–31 August 1999–2002. 

At McNary Dam, water clarity was correlated with flow and temperature on an annual 

basis: water was clearest in 2001, most turbid in 1999, and intermediate in 2000 and 2002 (Figure 

46). A similar pattern in annual average clarity occurred at John Day Dam (Figure 47), though 

with less difference among years (2001 was not nearly as different from 2000 and 2002 as it was 

at McNary Dam), and with more variability in the reported data within years. 
Travel time, survival estimates, and river environment indices 

We calculated survival estimates, median travel times, and river condition indices for 

groups for 5 weeks in the years 1999–2000, 6 weeks in 2001, and 9 weeks in 2002 (Table 39). 

Exposure indices were generally highly correlated with each other (Table 40). For example, the 

Table 39. Survival estimates and median travel times from McNary Dam to John Day Dam, and river 

condition indices for weekly groups of run-of-river subyearling Chinook salmon released in the 

tailrace of McNary Dam.

McNary Dam indices John Day Dam indices 

Year 

Dates 

at 

McNary 

Dam 

Estimated 

survival to 

John Day Dam

(standard 

error) 

Median 

travel 

time 

(days)

Flow 

(kcfs)

Temp.

(C°)

Clarity 

(Secchi)

Flow 

(kcfs)

Spill 

(kcfs) 

Spill 

(%) 

Temp.

(C°)

Clarity 

(Secchi)

1999 6/19–25 0.788 (0.042) 4.3 333.4 16.0 2.5 302.8 33.5 11.1 16.0 2.6 

1999 6/26–

7/02

0.746 (0.032) 3.8 305.1 15.7 2.5 287.7 56.6 19.4 16.4 2.3 

1999 7/03–09 0.765 (0.059) 5.5 255.3 16.3 3.1 265.4 83.4 31.5 18.0 3.1 

1999 7/10–16 0.770 (0.053) 5.2 267.6 18.0 3.1 242.8 63.5 26.2 18.9 3.2 

1999 7/17–23 1.026 (0.162) 6.4 238.6 18.2 3.2 230.4 61.0 26.5 19.2 3.4 

 

2000 6/19–25 0.593 (0.195) 4.4 197.6 17.2 4.1 198.0 66.3 34.1 19.1 4.8 

2000 7/26–

7/02

0.547 (0.228) 5.3 188.8 18.1 4.0 170.7 61.0 35.6 18.5 4.2 

2000 7/03–09 0.675 (0.256) 6.5 173.6 18.2 4.2 173.1 56.5 33.2 19.4 4.7 

2000 7/10–16 1.974 (1.108) 11.2 172.5 19.1 3.9 162.3 56.0 34.3 20.4 4.8 

2000 7/17–23 0.616 (0.233) 8.8 162.6 19.9 3.8 160.4 49.9 31.1 20.9 4.6 

 

2001 6/19–25 0.572 (0.026) 13.8 125.0 16.9 4.9 89.0 0.0 0.0 19.3 4.2 

2001 6/26–

7/02

0.560 (0.036) 27.6 117.3 17.6 5.7 79.7 0.0 0.0 20.6 4.3 

2001 7/03–09 0.520 (0.077) 26.9 92.1 19.2 5.8 84.9 0.0 0.0 21.1 4.4 

2001 7/10–16 0.655 (0.054) 16.6 80.8 20.5 6.0 79.1 0.0 0.0 20.7 4.2 

2001 7/17–23 0.586 (0.048) 13.7 82.2 20.4 6.0 84.1 0.0 0.0 21.0 4.1 

2001 7/24–30 0.597 (0.049) 13.3 81.5 21.4 6.0 90.5 0.0 0.0 21.5 4.7 

 

2002 6/19–25 0.888 (0.079) 3.8 325.9 15.7 4.5 308.7 100.7 32.3 16.9 4.3 

2002 6/26–

7/02

0.964 (0.086) 4.6 322.1 17.0 4.5 271.2 90.9 32.9 17.6 4.2 

2002 7/03–09 0.679 (0.033) 5.2 262.4 16.8 4.2 252.3 69.8 27.6 18.2 4.0 

2002 7/10–16 0.814 (0.078) 5.0 239.8 18.7 4.2 225.5 60.9 26.9 19.0 4.7 

2002 7/17–23 0.598 (0.069) 4.8 228.7 19.7 4.8 185.6 50.5 27.5 20.7 4.5 

2002 7/24–30 0.655 (0.076) 7.7 173.0 20.1 4.6 160.5 46.9 29.3 20.7 4.6 

2002 7/31–

8/06

0.811 (0.231) 8.7 159.3 20.2 4.6 152.9 40.6 26.4 21.3 5.3 

2002 8/07–13 0.448 (0.078) 5.6 156.5 20.1 4.6 145.8 40.5 27.7 21.1 5.0 

2002 8/14–20 0.571 (0.131) 4.9 144.3 20.9 5.3 149.9 43.4 29.0 20.9 5.0 

96
Table 40. Product-moment correlation coefficients (r) among independent variables for groups of 

subyearling Chinook salmon released in McNary Dam tailrace, 1999–2002. Each variable was 

adjusted by subtracting respective annual mean. 

McNary Dam indices John Day Dam indices 

Flow Temp. (C°) Clarity Flow Spill % spill Temp. (C°)

Flow 

Temp. (C°) –0.84a 

McNary Dam 

indices 

Clarity –0.53 0.61 

Flow 0.94a –0.79b –0.43 

Spill 0.64b –0.60 –0.04 0.72b 

% spill –0.05 –0.06 0.39 0.01 0.70b 

Temp. (C°) –0.90a 0.88a 0.56 –0.90a –0.55 0.10 

John Day Dam

indices 

Clarity –0.73b 0.63b 0.48 –0.69b –0.35 0.19 0.78b

a r2 > 0.65 

b 0.40 < r2

 < 0.65 

product-moment correlation coefficients (r) between flow and temperature exposure were –0.84 

and –0.90 for McNary Dam and John Day Dam indices, respectively. Flow indices at the two 

dams were very highly correlated (r = 0.94), as were the two temperature indices (r = 0.88). For 

analyses of relationships with survival and travel time, it was clearly not necessary to use indices 

of flow and temperature for both dams; they gave essentially the same information. We chose to 

use the flow and temperature indices from John Day Dam. Similarly, the spill volume index was 

too highly correlated with either the flow index or the spill percentage index (or both), to provide 

unique information, so we did not use the spill volume index. Correlations between indices of

water clarity at the two dams were not as strong. It is possible that the two separate indices could 

give independent information as predictor variables in travel time and survival models. 

Unadjusted for annual means, pairwise correlations were highly significant (P < 0.01) 

between median travel time and all variables except the John Day clarity index (Figure 48 and 

Table 41). Adjusted for annual means, none of the adjusted variables was significantly correlated 

with adjusted median travel time (P > 0.05) (Table 41). 

The difference between results for adjusted and unadjusted data for travel time is caused 

almost exclusively by the “separation” of 2001 data from that of other years and by the narrow 

range of indices within 2001. Particularly for the John Day flow index, it is not possible to 

determine from the data whether the points from 2001 belong on the same line as those from other 

years, or whether there are generalized year effects that affect both the flow index and travel time, 

but without a causal link. Assuming that the points are appropriately fit to a single flow/travel time 

function, it appears the relationship is curved (Figure 48); for a fixed difference (kcfs) in flow 

volume, the reduction in travel time (slope of the curve) was greater at lower flow levels than at 

higher flow. Because water velocity is related to flow volume, a plausible explanation for the 

shape of the curve is a direct link between water velocity and migration rate for subyearling 

Chinook salmon. 

97
Table 41. Product-moment correlations between river environment exposure indices and median travel 

time and estimated survival between McNary Dam tailrace and John Day Dam tailrace for 

run-of-river subyearling Chinook salmon, 1999–2002. Correlations (r) and corresponding P values 

are given for unadjusted variables and for variables adjusted for annual means. P values are for 

two-sided test of null hypothesis of zero correlation. 

Median travel time (1999–2002) Estimated survival (excludes 2000)

Unadjusted Adjusted Unadjusted Adjusted 

Index r P value r P value r P value r P value

Flow at John Day Dam –0.747 <0.001 –0.256 0.250 0.714 <0.001 0.506 0.032

Temp. (C°) at John Day

Dam

 0.518 0.008 0.297 0.179 –0.610 0.004 –0.384 0.116

% spill at John Day Dam –0.756 <0.001 0.011 0.962 0.501 0.024 0.260 0.297

Clarity at McNary Dam 0.651 <0.001 0.040 0.861 –0.584 0.007 –0.118 0.641

Clarity at John Day Dam 0.188 0.367 0.225 0.314 –0.381 0.097 –0.107 0.674

For analyses of relations between river indices and estimated survival, we omitted data 

from 2000 because the estimates were not sufficiently precise (i.e., standard errors were too large, 

see Table 39). Unadjusted for annual means, pairwise correlations were highly significant (P < 

0.01) between estimated survival and all variables except the John Day clarity index (Figure 49 

and Table 41). Adjusted for annual means, the correlations between estimated survival and the 

temperature index, the clarity indices, and the % spill index at John Day Dam were not significant. 

 However, there was a significant correlation between adjusted estimated survival and adjusted 

John Day flow index (Table 41). 

In 1999 and 2001, the within season (i.e., using data from 1 year at a time) correlation 

between John Day flow index and estimated survival was negative (greater flow related to lower 

survival) but not significant. In 2000 when the range of the flow index was greater, the correlation 

was positive and significant. There is no indication of a curved relationship between flow and 

survival over the range of observed flow index (Figure 49). In the multiyear analysis, the 

regression line slopes for adjusted and unadjusted flow were nearly the same and indicated that, on 

average, each 10 kcfs increase in the flow index was associated with a 1.3%–1.5% increase in 

survival. 

The temperature index at John Day Dam was also sufficiently correlated with the flow 

index to make independent assessment of these two variables impossible. Certainly the two 

predictors are too correlated for multiple-regression methods to separate effects of the two 

variables (when both are included, the flow variable is statistically significant and the 

temperature variable is not). However, the pairwise relationship of estimated survival with 

temperature deserves a closer look, because a causal mechanism is plausible. 

Careful examination of the observed temperature index data indicates there was a gap 

in the range of temperature data: while points are fairly evenly distributed over the rest of the 

range, there were no data between 19.3°C and 20.6°C (Figure 49). It is noteworthy that for the 

data with a temperature index less than 19.3°C (10 data points from 1999 and 2002) the slope 

98
100 200 300

0

10

20

30

R2 = 77.5%

 P= 0.014

John Day flow (kcfs)

15 16 17 18 19 20 21

0

10

20

30

John Day temperature (°C)

0 10 20 30 40

0

10

20

30

John Day % spill

2 3 4 5 6

0

10

20

30

1999

2000

2001

2002

McNary clarity (Secchi disk)

2 3 4 5 6

0

10

20

30

John Day clarity (Secchi disk)

Median travel time McNary Dam-John Day Dam

99

Figure 48. Median travel time between McNary and John Day dams plotted against various river condition 

indices for run-of-river subyearling Chinook salmon released in the McNary Dam tailrace, 

1999–2002. Flow index panel illustrates exponential-decay curve fit to data. 

between survival and temperature was nearly zero. Similarly, for data with an index greater than 

20.6°C (10 points from 2001 and 2002) the slope was nearly zero (Figure 49). The mean estimated 

survival was 0.801 for groups that migrated in cooler water and 0.600 for groups that migrated in 

warmer water, suggesting there may be a threshold temperature around 20°C, above which 

survival decreases markedly. 
100 200 300

0.4

0.5

0.6

0.7

0.8

0.9

1.0

R2 = 50.9%

P < 0.001

John Day flow (kcfs)

15 16 17 18 19 20 21

0.4

0.5

0.6

0.7

0.8

0.9

1.0

R2 =

45.7%

 P = 0.001

John Day temperature (°C)

0 10 20 30 40

0.4

0.5

0.6

0.7

0.8

0.9

1.0

John Day % spill

2 3 4 5 6

0.4

0.5

0.6

0.7

0.8

0.9

1.0 1999

2001

2002

McNary clarity (Secchi disk)

2 3 4 5 6

0.4

0.5

0.6

0.7

0.8

0.9

1.0

John Day clarity (Secchi disk)

Estimated survival McNary Dam-John Day Da

m

100

Figure 49. Estimated survival between McNary Dam tailrace and John Day Dam tailrace plotted against 

various river condition indices for run-of-river subyearling Chinook salmon released in tailrace of 

McNary Dam, 1999, 2001, and 2002. Flow index panel illustrates simple linear regression line 

without year effects. Temperature index panel illustrates constant mean survival above and below 

20o

C. 

Discussion 

As a consequence of FCRPS dam construction on the main stem of the lower Snake and 

Columbia rivers, the average travel time of yearling Chinook salmon and steelhead migrating 

between the confluence of the Clearwater and Snake rivers to the lower river below Bonneville 

Dam has increased substantially. As a result, for smolts left in-river to migrate, timing of arrival 

to the estuary and nearshore ocean is delayed on average by several weeks. As discussed in the 

“Transportation Evaluations” section (page 21), timing of ocean entry can greatly affect SAR. 

Coupled with the declining lipid reserves in migrating yearling Chinook salmon observed by 
Congleton et al. (2004), fish arrived to the estuary later and likely with lower energy reserves than 

they did prior to completion of the FCRPS, and even more so in low-flow years. It seems 

reasonable that flow can affect survival below the hydropower system. The data also suggest the 

possibility of an ocean × FCRPS interaction that causes fish in poor condition to do even worse in 

years with poor ocean conditions. We have no direct measurements to confirm this speculation. 

Furthermore, as a consequence of the FCRPS construction, springtime flows and turbidity have 

been greatly reduced, which likely has led to increased vulnerability of smolts to predators on 

ocean entry. 

Snake River Spring Migrants 

For spring migrants from the Snake River (steelhead and yearling Chinook salmon), 

conclusions regarding the influence of the river environment on travel time and survival depended 

in very large part on the interpretation of information from the low-flow year 2001. Data from that 

year were highly influential (or outliers) in univariate analyses of the influence of flow (cf., 

Figures 33–35 and 42–44). Threshold models for survival versus flow exposure cannot even be 

estimated without including the low-flow data along with the more moderate- to high-flow data 

from other years. The 2001 data are crucial to fitting models of flow and survival to data points 

from 1995 through 2003. This is especially true for the specific threshold models included here, 

but would be equally true, for example, in data sets that use different groupings (say weekly) at 

Lower Granite Dam. The 2001 data tends to function much like a single point in such multiyear 

analyses, particularly the “anchor points” of low survival late in 2001. 

Because it is tempting to interpret the threshold models as a prescription for a certain 

amount of flow, it is crucial to note the extreme imprecision in the breakpoint estimates. The 

estimated breakpoint for yearling Snake River Chinook salmon was 73.0 kcfs, but bootstrap 

methods were used to calculate a 95% confidence interval of 70.1 to 99.4. For Snake River 

steelhead, the situation was even worse: the breakpoint estimate was 115.4 kcfs, but we reach 95% 

confidence in our interval only if it is as wide as somewhere between 78.9 and 132.6 kcfs. We

know that salmonid survival will approach zero if flow is zero, and we know that survival was 

lower in low-flow 2001 than the more constant survival levels we have seen with moderate to high 

flow. But the current data give almost no information for establishing an exact threshold above 

which survival is as high as it can get and below which survival drops off more or less steeply. 

The cases where within-year data from 2001 do not fit the multiyear trends (e.g., positive 

slope between WTT and estimated survival for steelhead within 2001; apparent occurrence of 

two distinct sets of release groups of yearling Chinook salmon) should lead to closer examination 

of mortality patterns in 2001. The greatest WTTs (lowest flow volumes) in the entire data set 

occurred at the beginning and end of 2001 (middle and bottom panels, Figure 50). Both the 

highest and lowest yearling Chinook salmon survival of 2001 occurred during these periods, 

which caused the two distinct sets of points (Figure 50). Survival during the peak flows of 2001 

was no higher than in the low flows at the beginning of the season. The “missing variable” is 

water temperature (top panel, Figure 50). In the entire data set of 458 yearling Chinook salmon 

release groups, only 13 experienced temperature exposures greater than 15°C. Of these, 12 

101
0.00

0.25

0.50

0.75

0

10

20

30

40

50

60

70

80

90 Survival

Flow

exposure

Flo

w (kcfs)

75 100 125 150 175

0.00

0.25

0.50

0.75

10

15

20

25

Survival

Water

travel time

Date at Lower Granite Dam

W

ater travel tim

e (days)

0.00

0.25

0.50

0.75

9

10

11

12

13

14

15

16

17

Survival

Temperature

exposure

T

e

mperature (°C)

Estimated survival

102

Figure 50. Estimated survival from Lower Granite Dam to McNary Dam for PIT-tagged Snake River 

yearling Chinook salmon, 2001, plotted with flow exposure, water travel time index, and 

temperature exposure against data at Lower Granite Dam.

occurred at the end of the 2001 season. The low flows in 2001 extremely influenced past modeled 

relationships between WTT and survival, particularly because they generally did not consider the 

unique water temperature pattern that year. Some recent analyses showed that the within-season 

data from 2001 were better modeled using temperature rather than flow, and Anderson and Van 

Holmes (2004) concluded that “the relationship [between WTT and survival] is spurious... 

temperature, not flow, produced the correlation.” 

The new multivariate analyses in this technical memorandum corroborate the conclusion 

that exposure to very warm water was likely the most influential environmental condition 

affecting juvenile salmonid survival in the mainstem Snake River in 2001. However, though the 
effects are small relative to that of elevated temperature, our results also suggest that at lower 

temperatures WTT and spill levels also influence survival. Other researchers have also included 

temperature, WTT, and % spill in multiple linear models to analyze the impact of these factors on 

juvenile survival (State Managers et al. 2003). The generalized additive and nonlinear 

multiple-regression models used here advance understanding by providing a more refined model 

of the nature of the relationships between these variables and juvenile salmonid survival. 

For yearling Chinook salmon, when temperatures were below 13°C, our generalized 

additive and multiple-regression models indicated that variation in survival is relatively small, but 

that variation was related to WTT and spill. The multiple-regression model for yearling Chinook 

salmon featured a WTT threshold at 14 days, which was consistent with flow at Lower 

Monumental Dam of about 70 kcfs. However, having adjusted for temperature, the “flat” part of 

the fitted model occurred when WTT is greater than 14 days, in which range flows are low, while 

in the univariate threshold flow model there was a slope in this range. This occurred because of 

the other variables in the model and because WTT is essentially the inverse of flow. Inversion is 

a strong transformation, and the resulting models emphasized different parts of the range. In the 

multivariate model, there was relatively little change in survival over large changes in flow: WTT 

of 5 days was consistent with 196 kcfs flow at Lower Monumental Dam, and WTT of 10 days 

occurred with average Lower Monumental Dam flow exposure of 93 kcfs. Predicted survival for 

these two WTT values differed by only 0.05, equal to the difference in predicted survival for only 

a 0.4°C difference in temperature when temperature was above 13°C. These results should serve 

as a further caveat against simple application of the univariate flow threshold model. For 

steelhead, the multiple-regression model for survival had a linear decrease throughout the entire 

WTT range, perhaps consistent with the extremely imprecise estimate of a threshold in the 

univariate flow model. 

Multivariate models of survival for both species included functions for % spill. For 

steelhead, survival increased linearly as % spill increased from 0% to 29.4%, at which predicted 

survival reached a maximum. Above 29.4%, survival did not increase further (but did not 

decrease). For models of yearling Chinook salmon, predicted survival reached its maximum at 

about 20.6% (generalized additive model) or 25.0% (multiple-regression model). In all cases, the 

point of maximum survival is not precisely estimated; these estimates may be a rough guideline. 

In the case of yearling Chinook salmon, there was some suggestion that % spill above the 

maximum could result in decreased survival, particularly when water temperatures were high. 

Multivariate models indicated that the condition that had strongest effect on survival of 

yearling Chinook salmon was high water temperatures. The date on which temperature at Lower 

Monumental Dam reached 13°C varied from year to year, ranging from 7 May in 1998 to 11 June 

in 1997. The average date on which this apparent threshold temperature was reached was 25 May. 

 In addition, as noted in the section on juvenile reach survival, Zaugg and Wagner (1973) found 

that gill Na + –K + ATPase (an indicator of migratory readiness) and migratory urge declined at 

water temperatures of 13°C and higher. Steelhead that migrate too late in the season, when water 

temperatures are above this threshold, may have a tendency to residualize. Residualization leads 

to lower estimates of survival, because mortality and cessation of migration cannot be 

distinguished using PIT-tag data. 

103
For both species, we observed a strong and consistent relationship between flow and travel 

time. This suggests that one effect of springtime flow in the Snake River is to help juvenile 

salmonid migrants move out of the river before temperatures get too high. This might be 

especially important in low-flow years such as 2001. In this sense, it may be justifiable to interpret 

the temperature effects on survival we observed, at least to some degree, as indirect flow effects, 

mediated through smolt travel time. 

The strong effects on survival of elevated temperatures, the average late-May date of 

occurrence of such temperatures, and the relatively minor effects of % spill and WTT are all 

consistent with previous informal observations that survival for Snake River spring migrants tends 

to be fairly constant for the first several weeks of the season, beginning in early April and 

extending to mid to late May, when survival decreases in many years. 

However, as reflected in the year-effect coefficients in the multiple-regression models, the 

level of the nearly constant early to mid-season survival can vary considerably from year to year. 

This suggests that large-scale processes, most probably related to climate, affect the average 

quality (vitality) of fish arriving in the FCRPS each year. The magnitude of the estimated year 

effects, relative to those for the FCRPS-related variables of WTT, water temperature, and % spill 

suggests that events that occur in the juvenile fish life cyle above the FCRPS partially determine 

survival through it. 

Our results indicate that survival of juvenile migrants through the highly modified FCRPS 

migration corridor is relatively good at moderate- to high-flow levels, but poor at low-flow levels, 

particularly for steelhead. At low-flow levels, the FCRPS causes the river to function more like a 

series of impoundments and less like a river. Prior to dam construction, variations in migration 

conditions likely had less effect on juvenile survival because the slope of the natural channel 

gradient provided a lower limit for juvenile migration travel times. With the dams in place and 

reservoir elevations held constant, at low-flow levels WTT is reduced more than it would be in a 

free-flowing river with fluctuating levels. At some threshold level, migrants likely lose the cues 

necessary to migrate successfully. 

Run-of-River Subyearling Chinook Salmon from McNary Dam 

Based on the data available from run-of-river subyearling Chinook salmon from 1999 

through 2002, we have insufficient information to make definitive statements regarding 

potentially complex dynamics among travel time, survival, and environmental (river) conditions 

between McNary Dam and John Day Dam. For example, strong correlations among river 

conditions (flow, spill, temperature) made it impossible to determine which variable had the 

strongest influence on response variables. Further, because within most years there was a 

relatively narrow range in river condition values, and with little overlap between years in some

cases, it was not possible to separate processes and relations that occur within migration seasons 

from potential annual differences due to generalized “year effects.” 

We provide the following conclusions for run-of-river subyearling Chinook salmon from

McNary Dam (tempered with the above caveats): 

104
1. Travel time (migration rate) between McNary and John Day dams likely depended on 

water velocity. Increasing flow had more effect on reducing travel time when flow was 

low than when it was high. 

2. Before adjusting for differences in annual means, estimated survival was significantly 

correlated with flow, temperature, and % spill at John Day Dam. After adjusting for annual 

means, only the correlation with flow remained significant. This result apparently 

occurred because there was not sufficient within-year variation in temperature or % spill 

indices to distinguish between generalized year effects and direct influence of temperature 

or % spill. (For example, lower mean survival in 2001 may have been due to the lack of 

spill at John Day Dam or due to some other difference between years. Lacking periods of 

0% spill in the other years, we cannot determine which is the case). 

3. Travel time may have affected survival, because faster travel meant less exposure to 

predators in John Day reservoir. 

4. Average survival was nearly constant for water temperature below 19.3°C, and nearly 

constant, but considerably lower for water temperature above 20.6°C. There may be a 

threshold temperature, above which increased mortality occurs in this reach. 

The relationships identified among flow, temperature, travel time, and survival of 

subyearling fall Chinook salmon between McNary and John Day dams are consistent with those 

found for subyearling Chinook salmon in the Snake River (Connor et al. 2003a and 2003b, Smith 

et al. 2003). In both locations, the effects of flow and temperature were confounded, making it 

difficult to confidently predict the effect of either variable independently. In laboratory studies, 

Marine et al. (2004) found that exposure of Sacramento River fall Chinook salmon fry to water 

temperatures above 20°C resulted in decreased growth, increased osmoregulatory impairment, and 

increased vulnerability to predation. That temperature value was near the same temperature 

threshold found to affect survival for fall Chinook salmon migrants in the McNary to John Day 

Dam reach. 

105
Latent Mortality Associated 

with the FCRPS 

Comparing SAR with estimates of survival through the FCRPS (for both juveniles 

migrating downstream and adults migrating upstream) clearly indicates that the majority of 

mortality suffered by both transported and in-river migrants during the smolt-to-adult life stage 

occurs outside the hydropower system. Current survival within the hydropower system is 

typically as high or higher than it was during the 1960s, when the FCRPS consisted of only four 

mainstem dams, and survival for transported fish is even higher. Yet overall adult return rates of

Snake River spring migrants have rarely approached estimated return rates from the 1950s and 

1960s. Thus considerable effort has gone into studies and analyses to determine why the adult 

return rates were depressed, particularly for outmigration years 1977–1996. Explanations for the 

differences in adult return rates range from changes in ocean conditions to “delayed” effects on 

juveniles as a result of their passage through the hydropower system. Other factors, such as the 

number of hatchery fish released into the system, may also play a role. We believe all these factors 

may have contributed to decreased adult returns during at least some part of the last 25 years. 

While we can identify a number of possible mechanisms to account for differences in stock 

productivity over time, the debate is fueled by a lack of quantifiable empirical evidence to support 

or refute competing hypotheses. In the sections that follow, we first define “latent mortality” and 

attempt to eliminate some of the confusion associated with this definition. Then we discuss efforts 

to quantify latent mortality, including the use of downstream stocks as controls for upstream

stocks. 

Definitions 

We define latent mortality associated with the FCRPS (for Snake River fish) as any 

mortality that occurs after fish pass Bonneville Dam as juveniles that would not occur if the 

FCRPS dams did not exist. Latent mortality associated with the FCRPS might result from changes 

in migration timing; injuries or stress incurred during migration through juvenile bypass systems, 

turbines, or spill at dams that does not cause direct mortality; disease transmission or stress 

resulting from the artificial concentration of fish in bypass systems or barges (Williams 2001, 

Budy et al. 2002); depletion of energy reserves from prolonged migration (Congleton et al. 2004); 

altered conditions in the estuary and plume as a result of FCRPS construction or operation; or 

disrupted homing mechanisms. 

To standardize the discussion, we introduce the following notation (Figure 51). First, we 

designate survival terms using S and mortality terms using μ = 1 – S. Terms for in-river migrants 

are denoted by the subscript I and terms for transported fish by the subscript T. We partition 

survival and mortality into the following life stages: downstream migration through the 

hydropower system (subscript ds), estuary/ocean (subscript e/o), and upstream migration through 

the hydropower system (subscript us). We further partition the estuary/ocean stage to reflect 

106
Lower Granite Dam

Bonneville Dam

Estuary/Ocean

SI,ds

SI,e/o = Se/o·(1-μI,δ)

SI,us

107

= ⋅ ⋅ − μ ⋅

= ⋅ ⋅ − μ ⋅

Figure 51. Survival (S) and mortality (μ) affecting Snake River anadromous salmonids migrating in-river 

(denoted by subscript I) at various life stages. The life stages are: downstream migration through 

the hydropower system (ds), estuary/ocean (e/o), and upstream migration through the hydropower 

system (I). The estuary/ocean survival is partitioned into survival that would occur in the absence 

of the hydropower system (se/o) and latent mortality associated with the passage through the 

hydropower system (μΙ,α). Transported fish (denoted by subscript T) are affected by the same 

survival and mortality processes and are represented by changing the subscript I to T. 

mortality that would occur in the absence of the hydropower system (Se/o) and hydropower 

system-related latent mortality (subscript δ), which applies to both transported fish and in-river 

migrants. This partitioning of estuary/ocean survival reflects an assumption that for in-river fish, 

latent mortality is essentially entirely expressed in the estuary/ocean stage. Thus SAR of in-river 

and transported fish are expressed as 

 (15) 

 (16) 

Note that we use the same natural seawater survival (Se/o) for both in-river and transported 

fish. This is the survival that fish would experience in the absence of dams. Also, we use different 

upstream survival terms for in-river and transported fish. Differential upstream survival for the 

two groups could result from latent mortality for transported fish related to impaired homing, for 

example. Based on the equations above, we express D as: 

SAR T S T ,ds S e / o T , S T ,us (1 ) δ

SAR I S I ,ds S e / o I , S I ,us (1 ) δ
I I us

T T us

S

S

D

, ,

, ,

(1 )

(1 )

− μ ⋅

− μ ⋅ =

δ

δ 

Note that any difference in upstream survival between transported and in-river juvenile migrants 

is also expressed in D. 

The term “latent mortality associated with the FCRPS” encompasses several definitions 

used in the past: delayed mortality, extra mortality, and D, all of which have specific definitions 

but have often been used loosely and almost interchangeably. Extra mortality is a term that arose 

in the PATH process. Marmorek and Peters (2001) defined extra mortality as 

 . . . any mortality occurring outside of the juvenile migration corridor that is not 

accounted for by either: 1) productivity parameters in spawner-recruit relationships; 

2) estimates of direct mortality within the migratory corridor (from passage 

models); or 3) for the delta model only, common year effects affecting both Snake 

River and Columbia River stocks. Extra mortality can in theory occur either before 

or after the hydropower migration corridor. 

Thus extra mortality is purely a modeling construct. Further, hydropower effects were just one of 

several hypotheses that were proposed in PATH to explain extra mortality. Thus “extra mortality” 

is not synonymous with “latent mortality related to the hydropower system.” For this reason, we 

do not use the term extra mortality (a modeling construct) to describe hydropower system-related 

latent mortality. 

Another source of confusion arises from the relationship between D and “delayed” 

mortality associated with in-river migrants. D refers to the ratio of smolt:adult survival (measured 

from below Bonneville Dam to Lower Granite Dam) of transported fish relative to that of in-river 

migrants. Because D is typically below 1.0 for Snake River spring-summer Chinook salmon and 

steelhead, it provides one measure of latent mortality for transported fish, but not an absolute 

measure; it is only relative to in-river fish. This latent mortality may result from stress experienced 

on the barge, disruption of timing to the estuary, or increased straying or fallback of adult migrants. 

 While we cannot identify specific mechanisms that lead to D < 1.0, we can directly estimate D, 

because it relates to the juvenile survival and SAR for in-river migrants. Of course, the SAR for 

in-river migrants includes any hydropower-related latent mortality, so the magnitude of D depends 

on the magnitude of latent mortality of in-river migrants. Thus D is not an absolute measure of the 

latent mortality of transported fish, because the amount of latent mortality expressed in D varies 

with hypothesized (not measured) levels of hydropower-related latent mortality of in-river 

migrants.

Efforts to Quantify the Magnitude 

of FCRPS Latent Mortality 

Quantifying the magnitude of latent mortality (for either transported or in-river migrants) 

is extremely difficult. This is primarily because no suitable control exists. Several methods have 

been explored to overcome this shortcoming, and in this section we discuss several of them. 

 (17) 

108
Upstream/Downstream Comparisons 

In attempting to evaluate FCRPS impacts on upper Columbia and Snake River basin stocks, 

several groups of people (Marmorek et al. 1998 and 2004, Schaller et al. 1999, Deriso et al. 2001) 

have conducted analyses using downstream stocks (e.g., spring Chinook salmon from the John 

Day River basin) as controls for upstream stocks (e.g., spring-summer Chinook salmon from the 

Snake River basin), while Zabel and Williams (2000) pointed out potential problems with these 

analyses.8

 Schaller et al. (1999) observed differential temporal responses in productivity between 

upstream and downstream stocks after completion of the final four hydropower dams on the lower 

Snake and Columbia rivers. They attributed these changes to the hydropower system, but they did 

not estimate latent mortality per se. Deriso et al. (2001) estimated differential mortality between 

upstream and downstream stocks. When considering a variety of assumptions about potential 

direct mortality incurred passing through the mainstem dams on the Snake and Columbia rivers, 

they observed that upstream stocks consistently suffered more mortality than could be attributed to 

changes from historical productivity patterns. Certainly the initial completion of dams in the 

Snake River caused drastic changes in Snake River stock productivity, and thus their initial 

decreased productivity compared to downstream stocks was not surprising. However, given the 

large changes in FCRPS dams and operations that juvenile migrants presently encounter compared 

to the initial years following completion of the dams (Williams and Matthews 1995) and the 

substantial increase in juvenile migrant survival compared to earlier years (Williams et al. 2001), 

latent mortality mechanisms would likely need to have changed over the last 25 years to explain 

continued differences in productivity patterns between upstream and downstream stocks. So 

while analyses of the covariability of populations are inherently interesting, we also think it is 

extremely difficult to ascribe differences in variability among stocks to particular factors, 

particularly those that represent a relatively small proportion of the entire life cycle (such as 

migration through the hydropower system). Below we provide several lines of reasoning. 

Salmon biology 

Salmon populations are notorious for their local adaptation (Richer 1972, Taylor 1991, 

Unwin and Glova 1997, Hendry et al. 2000), which has led to extreme biodiversity among 

populations (Hilborn et al. 2003). Even within salmon populations, a diversity of life history 

strategies are supported, and differential growth opportunities between freshwater and seawater 

habitats, along with cost of migration, are presumed factors that contribute to the selection of life 

history traits (Gross 1987, Randall et al. 1987, Gross et al. 1988, Taylor 1990a). Further, 

upstream/downstream comparisons of past modeling efforts assumed that the major source of 

environmentally induced variability in salmon productivity arose from ocean conditions, and that 

the two stock groupings would show high levels of covariability under the assumption that they 

shared a common ocean habitat. However, Bradford (1995) concluded that, across all of the 

salmon species he analyzed, the freshwater environment contributed considerably to the 

variability in egg-to-adult survival. Further, Myers et al. (1997) found no correlation between 

freshwater survival rates among salmon populations more than a few hundred kilometers apart. As 

just one example of differences between John Day River spring Chinook salmon stocks and the 

wild stocks from the Snake River basin, the former have a relatively narrow migration window, 

 8

 For further discussion of analyses using downstream stocks, see Appendix A. 

109
110

based on PIT-tag detections at Bonneville Dam, while the latter, representing the untagged 

population, have a very extended migration (Figure 52) based on estimated timing of transported 

PIT-tagged fish to below Bonneville Dam. Furthermore, hatchery fish from McCall, which have 

demonstrated the highest SAR for hatchery fish in the Snake River, also showed a narrow 

migration window similar to those wild fish from the John Day River. As noted earlier, migratory 

timing can have a large influence on adult returns. Thus we believe it is likely that poor correlation 

in freshwater survival could exist between upstream and downstream stocks. Not surprisingly 

then, salmon populations from distinct Columbia River basin regions responded differently to 

large-scale climate patterns (Levin 2003), and poor correlation existed between productivity 

patterns of upstream and downstream Columbia River stocks (Botsford and Paulsen 2000). 

Figure 52. Five-day running average of the number of smolts arriving at Bonneville Dam in 2000 for fish 

from the John Day River migrating in-river, and for two fish groups transported from Lower 

Granite Dam (wild fish from the Snake River and McCall Hatchery fish). The relatively early and 

protracted arrival timing of the wild Snake River fish is evident in the cumulative frequency plot. 

Potential problems with models 

All the analyses listed above relied on models, yet using models with potentially 

mis-specified parameters has added another element of uncertainty. All the analyses assumed 

without testing that the Ricker model appropriately described the population dynamics of the 

analyzed populations. In fact, the Ricker model is often rejected when compared to simpler 

models of Snake River stocks (Zabel and Levin 2002). Further, the use of spawner and 

reconstructed recruit data constitutes a model that requires several assumptions. The potential 

multiplication of errors associated with the stock reconstructions could have potentially led to 

2000 Arrival timing at (or below) Bonneville

0

5

10

15

20

25

30

4/1 4/16 5/1 5/16 5/31 6/15 6/30 7/15 7/30 8/14

Wild S/S & John Day

0

100

200

300

400

500

600

Mc

Call

wild S/S

John Day

McCall

0.0

0.5

1.0

Cumulative

frequency

2000 Arrival timing at (or below) Bonneville

0

5

10

15

20

25

30

4/1 4/16 5/1 5/16 5/31 6/15 6/30 7/15 7/30 8/14

Wild S/S & John Day

0

100

200

300

400

500

600

Mc

Call

wild S/S

John Day

McCall

0.0

0.5

1.0

Cumulative

frequency
unidentified bias. One assumption in particular might have accounted for many temporal 

differences between upstream and downstream stocks identified in the analyses. In the run 

reconstructions for PATH, values used for adult survival generally ranged from 40% to 60% 

through eight dams (Marmorek et al. 1998). Recent data from PIT tags suggest that adult upstream

survival exceeds 85% for yearling Chinook salmon (see Table 11). Thus, when models used 

conditions with eight dams in place and compared them to what might occur with four dams

removed, the high upstream adult mortality used in the models resulted in an inflation of the 

upstream/downstream differences attributed to latent mortality. Further, the models used in the 

analyses generally ignored differential environmental effects that occurred in several distinct life 

stages, particularly those associated with freshwater spawning and rearing. 

Potential problems with data used 

Data quality problems exacerbated the problems with models. Past spawner counts were 

notoriously noisy because of the high degree of sampling error (Holmes 2001), which led to 

limited power to detect effects with these data (Hinrichsen 2001). Thus using these data to 

measure the magnitude of latent mortality is problematic. Further, data quality was unequal 

among populations. The John Day populations in particular lacked age composition data in early 

years. Zabel and Levin (2002) demonstrated that the practice of applying mean-age com-positions 

to returning adults in run reconstruction led to severe biases in estimated stock-recruit model 

parameters. When we considered all these sources of uncertainty, we concluded that the 

uncertainty of any estimate of FCRPS-related latent mortality using upstream/downstream

comparisons was large enough to render the estimates misleading and essentially useless. 

Multiply Bypassed Fish 

The comparison of SAR from in-river migrants with different juvenile migration histories 

showed that, for some stocks in some years, multiply bypassed fish returned at significantly 

(one-sided tests) lower rates than fish that were never detected in a bypass system (Sandford and 

Smith 2002). Most data from the 1995 through 1998 outmigrations indicated that multiply 

bypassed spring-summer Chinook salmon and hatchery steelhead had lower SAR than those not 

detected at collector dams (Figures 53 and 54). Budy et al. (2002) interpreted this as direct 

evidence that fish passing through bypass systems suffered “delayed” mortality. However, in 

more recent data, SAR did not differ for wild steelhead (2000 outmigration) or wild Chinook 

salmon (1999 and 2000 outmigrations) (Figures 53 and 54). 

In this subsection we present an alternative hypothesis for the observation that multiply 

detected fish sometimes returned at lower rates than nondetected fish. We hypothesize that 

because bypass systems select for smaller fish (see discussions related to Figures 25 and 26) and 

that smaller fish typically have returned at lower rates (see the “Selective Mortality” section, page 

119), multiply bypassed fish would also return at comparatively lower rates. 

To test this hypothesis, we examined whether the combination of observed patterns in 

size-selective guidance and size-selective mortality could lead to lower return rates of multiply 

111
0.0

0.5

1.0

1.5

1

2

3

4

Number of detections

27

48

33

15

29

30

13

7

162

190

63

17

315

260

169

19

567

702

422

118

10

753

474

122

13

Nondetected * P < 0.05

*

*

* *

*

* *

*

*

*

*

*

1

3

1

1

*

*

0/350

*

*

*

1995 1996 1997 1998 1999 2000

0.0

0.5

1.0

1.5

9

19

13

7

14

10

8

3177

62

17

73 227

225

98

20

113

225

165

56 Nondetected

8

* * * *

* P < 0.05

*

2*

4

5

4 1

0/5330/46

0/10

Year of outmigration

Relative return rate

112

Figure 53. Relative adult return rates of hatchery (top chart) and wild (bottom chart) spring-summer 

Chinook salmon marked above Lower Granite Dam and detected between 0 and 4 times during 

their migration through Lower Granite, Little Goose, Lower Monumental, and McNary dams. 

Nondetected fish had a relative return rate of 1.0. Numbers above the line and bars indicate total 

adult returns. Lack of a bar indicates no adults returned (0 adults/estimated number of juveniles). 

bypassed fish. We did not attempt to predict return rates for specific years and stocks, rather 

we examined general behavior based on data from wild spring Chinook salmon and steelhead. 

First we allowed the slope parameter of the size-selective guidance relationship to vary across 

observed values. We then used these relationships to estimate size distributions of nondetected 

fish and fish detected three times (out of four opportunities). We then assumed that sizeselective mortality varied linearly with fish length, and we estimated the slope of this relationship 

for various values in the range of observed selection coefficients. Based on this estimate, we 
0.0

0.5

1.0

1.5

1

2

3

4

Number of detections

11 14 7

11

24 37

26

31

31

14

15

8

6

16 15 8

59

39

29

39

106 71

17

Nondetected

*

*

*

*

* * *

* *

*

* P<0.05

*

1

2

1

3

2

4

2

*

*

*

1995 1996 1997 1998 1999 2000

0.0

0.5

1.0

1.5

9

7

16

28

21

36 89 77

34

6

Nondetected * P < 0.05, one-sided

3 2

10

1

1

4

5

2

1 1

3

6

*

*

*

*

*

*

*

1

1

3

3

0/166

0/67

0/53

0/118

Year of outmigration

R

elativ

e r

eturn rate

113

Figure 54. Relative return rates of hatchery (top chart) and wild (bottom chart) steelhead marked above 

Lower Granite Dam and detected between 0 and 4 times during their migration through Lower 

Granite, Little Goose, Lower Monumental, and McNary dams. Nondetected fish had a relative 

return rate of 1.0. Numbers above the line and bars indicate total adult returns. Lack of a bar 

indicated no adults returned (0 adults/estimated numbers of juveniles). 
0.0

0.5

1.0

1.5

Lower Granite Dam only

Little Goose Dam only

Lower Monumental Dam

only

McNary Dam only

27 29 162 260 567 755

19

13

11

5

14

6

7

14

80

73

23

61

74

104 76

56

246

234 169

177

97 4

1

160

Nondetected

*

*

* *

* * *

*

*

* P< 0.05

*

3*

1995 1996 1997 1998 1999 2000

0.0

0.5

1.0

1.5

9 31 73 124 8

7

35

14 11

17

18

99

79

31

73

66

37 50

* *

* P<0.05

**Sig. > 1.0

**

**

3

1

1

2

0/948

4 2 14

1

3

3 3

(ratio=2.0)

Nondetected

* *

Year of outmigration

R

elative return r

ate

114

Figure 55. Relative adult return rates of hatchery (top chart) and wild (bottom chart) spring-summer 

Chinook salmon marked above Lower Granite Dam and detected only at Lower Granite, Little 

Goose, Lower Monumental, or McNary dams. Nondetected fish had a relative return rate of 1.0. 

Numbers above the lines indicated total adult returns. Lack of a bar indicated no adults returned (0 

adults/estimated number of juveniles). 

then compared return rates of multiply detected to nondetected fish (Figure 55). From this 

analysis, we concluded that the combination of size-selective guidance and size-selective 

mortality can lead to substantially depressed return rates of multiply detected fish. Further, and 

potentially independent of size, differential collection may occur because of the physiological 

condition of fish. In 1987 and 1989 at Lower Granite Dam, Elliot and Pascho (1991) found 
consistently higher levels of BKD in fish guided into gatewells (equivalent to detected PIT-tagged 

fish) than for fish collected in fyke nets (equivalent to undetected PIT-tagged fish passing through 

turbines). Thus multiply bypassed fish could presumably die at higher rates than nondetected fish. 

Differential guidance of less fit fish may also explain why transported fish returned at lower rates 

than nondetected fish. 

A further complication is that return rates vary by specific detection sites (Figures 56 and 

57). In particular, fish only detected at Lower Granite Dam tend to return at higher rates than 

nondetected fish, while fish detected at the lower dams tend to return at lower rates. This could 

result either from different selection regimes (for size or other traits such as disease level) exist-ing 

at the bypass systems, or from different bypass configurations, or some combination of both. For 

example, the Lower Granite Dam bypass system does not contain fish separation by size capability; 

therefore fish do not encounter the same amount of dewatering structures and flumes as do fish at 

the lower three dams. The complexity of the issue certainly merits continued study. 

Given the propensity for bypassed fish to return at lower rates, we emphasize that it is 

important to take care when identifying control fish. We note that in all our evaluations, 

transportation effectiveness and estimates of D relied on nondetected fish to represent in-river 

migrants, yet these fish that did not enter bypass systems at collector dams represented less than 

30% of the population. Thus in the future, if we consider alternative operational scenarios that 

include less transportation than presently occurs, we will need to reconsider the population of 

control fish to accurately represent potential in-river migrants. 

Disrupted Timing 

The construction of the FCRPS has resulted in the extension of travel times of downstream

migrants. Zabel and Williams (2002) observed that for 1 out of 2 years they analyzed, in-river 

migrants that migrated earlier in the season returned at higher rates than later migrants. This 

pattern also occurred in 2 of the 3 years analyzed since then (see “Selective Mortality” section, 

page 119). Thus, delayed entry into the estuary may have led to lower return rates, which is a form

of latent mortality associated with passage through the hydropower system. More detailed 

analyses with more years of data hold promise to estimate the magnitude of this effect. Similarly, 

fish transported as juveniles, particularly early in the season, arrived below Bonneville Dam

earlier than they would have had they migrated through a free-flowing river. We believe this has 

also contributed to poorer than expected return rates, which again is a form of latent mortality. 

Latent Mortality of Transported Fish 

We believe the strongest evidence for some form of latent mortality is that estimates of D

are consistently well below 1.0 for all Snake River ESUs. Since transported fish return from

below Bonneville Dam at substantially lower rates than in-river migrants, they must suffer from

some form of latent mortality. Regardless of the cause—timing issues, greater susceptibility to 

predation, disease or stress due to crowding, or problems with homing—transported fish incurred 

mortality as a result of transportation that was not expressed until after the fish were released from

the barges. 

115
0.0

0.5

1.0

1.5

11 14 7 24 37 39

24

5

5

6

20

15

23

16

67

18

18

8 5

Nondetected Lower Granite Dam only

Little Goose Dam only

* *

*

*

* P < 0.05

1

3

3

3

3

3

1

(ratio = 1.7)

1

2

4 3

Lower Monumental Dam

only

McNary Dam only

* *

*

*

*

1995 1996 1997 1998 1999 2000

0.0

0.5

1.0

1.5

2.0

16

8

11

7

37

40

32

13

4

0/137

2 1 1

9

1 1

1

2

2

(ratio = 7.0)

2

2

1

1

3

(ratio = 2.2)

1

3

0/1250/3520/242

2

Nondetected

* * *

*

*

Year of outmigration

Relative return rate

116

Figure 56. Relative adult return rates of hatchery (top chart) and wild (bottom chart) steelhead marked 

above Lower Granite Dam and detected only at Lower Granite, Little Goose, Lower Monumental, 

or McNary dams. Nondetected fish had a relative return rate of 1.0. Numbers above the lines 

indicated total adult returns. Lack of a bar indicated no adults returned (0 adults/estimated number 

of juveniles). 
δ = 0.7

δ = 0.6

δ = 0.4 δ = 0.5

δ = 0.4

δ = 0.2

δ = 0.6

δ = 0.8

Wild steelhead

-0.025 -0.020 -0.015 -0.010 -0.005

Detection slope parameter

Wild Chinook salmon

-0.014 -0.012 -0.010 -0.008 -0.006 

1.0

0.9

0.8

0.7

0.6

Relative return rate of multiply detected fish c

ompared to nondetected fish

0.9

0.8

0.7

0.6

0.5

117

Figure 57. Relative return rates of multiply bypassed fish compared to nondetected fish under a range of 

values for the slope parameter of the length-selective guidance relationship and the length-based 

selection coefficient. 

Discussion 

Based on the evidence presented above, clearly some level of latent mortality exists. 

However, we have very limited capability to precisely estimate the overall magnitude of

hydropower system-related latent mortality for either transported fish or nondetected in-river 

migrants. Certainly we have much stronger evidence for substantial latent mortality of transported 

fish (see values of D in the “Transportation Evaluations” section, page 21). For in-river migrants, 

and based on the likely disruption of historical migration-timing patterns, an assumption that some
level of latent mortality exists appeared reasonable. However, recent return rates of wild fish, and 

modeling efforts that suggest the ability to predict them (see the “Large-Scale Processes” 

subsection, page 123), imply that hydropower system-related latent mortality under the ocean 

conditions that juveniles encountered in 1999 and 2000, in and of itself, would not prevent stocks 

from returning to abundances observed before the hydropower system was completed. We do not 

argue that recent return rates could not have been even higher—we have no evidence for this one 

way or another. We also recognize the possibility that much higher latent mortality may have 

existed when smolts experienced poor ocean conditions. Our observation that length-related, 

selective mortality appeared related to ocean conditions does support a hypothesis that latent 

mortality might increase under poor ocean conditions. However, little other evidence supports or 

refutes this hypothesis. So we are left with the rather unsatisfying conclusion that for in-river 

migrants, hydropower system-related latent mortality ranges somewhere from very weak to 

potentially strong. Further, we have little data at present to discern among this broad range of 

alternatives. 

118
δ = x x R T −

varT

X

Selective Mortality 

As indicated in the previous section, numerous factors affect SAR. Some recent efforts by 

Zabel and Williams (2002) determined that size and migration timing of fish within popula-tions 

influenced SAR. In this section we expand on results from Zabel and Williams (2002). 

The first step in the analysis involved calculating the directional selection coefficient 

(Endler 1986), which for trait x is defined as 

 (18) 

where is the mean value of the trait in the entire tagged population (T) and in returning adults 

(R). Note that the returning adults represented a subpopulation of the entire tagged population, 

and we refer to their traits at the time of tagging. If the trait is length, for instance, then a positive 

value of δ means that larger fish returned at a higher rate than smaller ones. We performed a 

Monte Carlo test to determine whether the selection coefficient was significantly different from

zero (for details, see Zabel and Williams 2002). 

In the top plot of Figure 58, points above the horizontal dashed line (i.e., greater than 0) 

indicate that larger fish returned at greater rates than smaller ones. In the bottom plot, points 

below the line (i.e., less than 0) indicate that earlier migrants returned at greater rates than later 

migrants, and the opposite held true for points above the line. 

When we updated the results from Zabel and Williams (2002) by adding more years (1998 

through 2000 for Snake River spring-summer Chinook salmon and Snake River steelhead for 1999 

and 2000), the main conclusions still held: the size of individuals and the timing of their 

outmigration strongly influenced return rates. Selective mortality based on fish length was 

generally not as strong in 1998 through 2000 as it was in 1995 and 1996 for spring-summer 

Chinook salmon (perhaps due to better ocean conditions), although the level of length-based 

selective mortality was similar across years for transported wild fish (Figure 58 and Table 42). For 

the 2 years of data on steelhead return rates, we observed strong length-based selective mortality, 

with steelhead in all groups incurring greater selective mortality than Chinook salmon (Figure 58 

and Table 42). In-river spring-summer Chinook salmon migrants early in the season typically 

returned at higher rates, as demonstrated by negative selection coefficients (P < 0.05 for 4 out of 

5 years for wild fish and 3 out of 5 years for hatchery fish) (Table 43). While the magnitude of 

timing-based selection varied yearly for in-river migrants, the pattern of variability was consistent 

among hatchery and wild Chinook salmon and steelhead, with strong selection in 1995, 1998, and 

2000 and weaker selection in 1995 and 1999 (Figure 58, bottom plot). Timing-based selection was 

variable for transported fish, with fish transported early in the season returning at higher rates in 

some years, and fish transported later returning at higher rates in other years. Also, there was little 

consistency between wild and hatchery Chinook salmon. 

119
Selection for release date

-0.800

-0.600

-0.400

-0.200

0.000

0.200

0.400

0.600

199519961997199819992000

Year

Selection coefficient

Selection for length

-0.100

0.000

0.100

0.200

0.300

0.400

0.500

0.600

0.700

0.800

0.900

199519961997199819992000

Year

Selection coefficient

Chinook in-river wild

Chinook in-river

hatchery

Chinook transported

wild

Chinook transported

hatchery

Steelhead in-river wild

Steelhead in-river

hatchery

Steelhead transported

wild

Steelhead transported

hatchery

120

Figure 58. Selection coefficients by year for length at release (top) and release date (bottom). 
Table 42. Sample size (N) and mean length (mm) at tagging (standard errors are in parentheses) for the total 

tagged population and returning adults of Snake River spring-summer Chinook salmon and 

steelhead PIT tagged at Lower Granite Dam, 1995–2000. 

Total population Returning adults 

Release group N Mean length N Mean length

% 

return δa P valueb

Snake River spring-summer Chinook salmon 

1995 

In-river wild 5,331 107.37 (0.11) 5 113.80 (3.44) 0.094 0.790 0.039

In-river hatchery 21,596 136.55 (0.12) 62 143.95 (2.20) 0.287 0.422 0.001

Transport wild 3,369 106.84 (0.14) 12 110.17 (2.87) 0.356 0.409 0.079

Transport hatchery 15,583 136.17 (0.14) 93 141.62 (1.30) 0.597 0.315 0.002

1996 

In-river wild 1,392 109.31 (0.07) 7 115.00 (1.83) 0.050 0.741 0.023

In-river hatchery 53,420 139.45 (0.06) 53 146.59 (2.31) 0.099 0.479 0.001

Transport wild 8,656 110.49 (0.08) 10 113.00 (1.50) 0.116 0.351 0.139

Transport hatchery 36,867 139.62 (0.07) 53 146.30 (2.14) 0.144 0.477 0.001

1998 

In-river wild 8,676 113.01 (0.07) 53 113.75 (0.82) 0.611 0.115 0.208

In-river hatchery 61,541 135.72 (0.05) 229 135.43 (0.75) 0.372 -0.025 0.643

Transport wild 5476 111.97 (0.09) 33 114.09 (1.13) 0.603 0.306 0.036

Transport hatchery 38,773 135.95 (0.06) 243 136.73 (0.67) 0.627 0.062 0.169

1999 

In-river wild 11,827 109.38 (0.08) 152 110.20 (0.58) 1.285 0.099 0.106

In-river hatchery 61,491 137.82 (0.05) 891 139.29 (0.43) 1.449 0.114 0.001

Transport wild 8,113 109.43 (0.09) 172 111.05 (0.56) 2.120 0.196 0.004

Transport hatchery 43,169 138.16 (0.06) 866 138.71 (0.37) 2.006 0.042 0.110

2000 

In-river wild 42,899 110.38 (0.03) 605 111.37 (0.27) 1.410 0.139 0.000

Transport wild 15,414 109.77 (0.06) 261 111.41 (0.43) 1.693 0.228 0.000

Snake River steelhead 

1999 

In-river wild 8,338 186.36 (0.30) 64 200.80 (3.68) 0.768 0.528 < 0.001 

In-river hatchery 59,487 218.78 (0.10) 380 224.81 (1.25) 0.639 0.253 < 0.001 

Transport wild 5853 186.56 (0.35) 82 204.66 (3.06) 1.401 0.672 < 0.001 

Transport hatchery 40,525 219.61 (0.12) 439 227.60 (1.11) 1.083 0.333 < 0.001 

2000 

In-river wild 47,998 184.69 (0.13) 936 201.72 (1.11) 1.950 0.602 < 0.001 

Transport wild 22,212 183.77 (0.18) 959 192.70 (0.95) 4.317 0.331 < 0.001 a δ is the selection coefficient (see eq. 17). 

b P value is based on a Monte Carlo test to determine if it is greater than 0. If P < 0.05, then δ is significantly greater 

than 0 at the α = 0.05 level. 

121
Table 43. Sample size (N), mean release day of the year (standard error is in parentheses) for the total 

tagged population and returning adults of Snake River spring-summer Chinook salmon and 

steelhead PIT tagged at Lower Granite Dam.

Total population Returning adults 

Release group N Mean rls date N Mean rls date

% 

return δa

P valueb

(2 tailed)

Snake River spring-summer Chinook salmon 

1995 

In-river wild 31,766 119.81 (0.10) 63 114.81 (1.94) 0.198 –0.290 0.007 

In-river hatchery 104,279 121.06 (0.03) 321 118.42 (0.43) 0.308 –0.268 0.000 

Transport wild 21,359 119.84 (0.10) 78 125.77 (2.07) 0.365 0.410 0.000 

Transport hatchery 81,780 120.95 (0.03) 455 122.29 (0.40) 0.556 0.143 0.001 

1996 

In-river wild 14,078 117.62 (0.09) 7 116.43 (4.27) 0.050 –0.112 0.427 

In-river hatchery 53,976 126.52 (0.04) 53 126.23 (1.97) 0.098 –0.030 0.416 

Transport wild 8699 117.80 (0.11) 10 114.5 (2.62) 0.115 –0.314 0.167 

Transport hatchery 37,027 126.09 (0.05) 53 125.68 (1.41) 0.143 –0.042 0.382 

1998 

In-river wild 8,714 111.93 (0.13) 53 103.79 (1.14) 0.608 –0.687 < 0.001

In-river hatchery 61,853 114.55 (0.04) 230 109.17 (0.61) 0.372 –0.481 < 0.001

Transport wild 5,496 111.83 (0.16) 34 106.09 (1.44) 0.619 –0.499 < 0.001

Transport hatchery 39,032 114.96 (0.06) 245 116.86 (0.68) 0.628 0.174 0.004 

1999 

In-river wild 11,853 118.79 (0.13) 152 116.65 (0.73) 1.282 –0.148 0.029 

In-river hatchery 61,742 121.88 (0.04) 892 121.67 (0.29) 1.445 –0.023 0.242 

Transport wild 8128 119.88 (0.14) 172 121.11 (0.75) 2.116 0.098 0.101 

Transport hatchery 43,305 122.74 (0.04) 867 125.37 (0.27) 2.002 0.296 < 0.001 

2000 

In-river wild 43,241 124.55 (0.08) 610 119.29 (0.51) 1.411 –0.331 < 0.001 

Transport wild 15,535 120.37 (0.13) 261 118.97 (0.89) 1.680 –0.087 0.078 

Snake River steelhead 

1999 

In-river wild 8361 124.41 (0.16) 64 124.08 (1.73) 0.765 –0.022 0.431 

In-river hatchery 59,759 128.26 (0.05) 381 125.16 (0.56) 0.638 –0.234 < 0.001

Transport wild 5872 126.40 (0.19) 83 127.40 (1.31) 1.413 0.069 0.263 

Transport hatchery 40,771 128.29 (0.06) 442 130.00 (0.53) 1.084 0.134 0.003 

2000 

In-river wild 48,357 117.22 (0.05) 941 112.02 (0.24) 1.946 –0.467 < 0.001

Transport wild 22,360 113.00 (0.06) 964 113.45 (0.26) 4.311 0.049 0.059 a δ is the selection coefficient (see eq. 17). 

b P value is based on a Monte Carlo test to determine if it is greater than or less than 0. If P < 0.05, then δ is 

significantly greater or less than 0 at the α = 0.05 level. 

122
Discussion 

In this section, we consider important issues that do not fit into the major topics presented 

in the preceding sections. We also discuss issues that tie together conclusions from several 

sections. 

Large-Scale Processes 

Increasing evidence points to dramatic changes in the marine ecosystem of the North 

Pacific Ocean over the past 2000 years resulting from shifts in climate (Finney et al. 2002, Moore 

et al. 2002). Throughout this region, variations in zooplankton, benthic invertebrates, seabirds, 

and fish all have been connected to changes in ocean-climate conditions (McGowan et al. 1998). 

In particular, analyses of data from the last 100 years demonstrated a strong influence of ocean 

conditions on catches and the production of Pacific salmon (Oncorhynchus spp.) across a range of 

spatial and temporal scales (Mantua et al. 1997, Beamish et al. 1999). The varied response of 

salmon to past environmental changes likely reflects their complex life history strategies and the 

wide diversity of freshwater and marine habitats that they occupy (Hilborn et al. 2003). 

Recent analyses suggest that Chinook salmon from the Columbia River basin also respond 

to cyclic changes in ocean-climate conditions. Modeling exercises directed at explaining the 

negative effects of various anthropogenic activities on the productivity of Snake River 

spring-summer Chinook salmon identified the estuary and ocean environments as important 

sources of unexplained variation in stock performance (Kareiva et al. 2000, Wilson 2003). Using 

catch records from commercial fisheries, Botsford and Lawrence (2002) found reasonable 

correlations between the inferred survival of Columbia River Chinook salmon and physical 

attributes of the ocean, such as sea-surface temperature and coastal upwelling. Building upon 

these previous studies, Scheuerell and Williams (in press) (see Appendix B) found that by 

beginning with the first SAR estimate in 1964, they could actually forecast the subsequent 

observed changes in the smolt-to-adult survival of Snake River spring-summer Chinook salmon 

through 2000 from variation in coastal ocean upwelling, including the rapid decline between the 

1960s and 1970s and the increase in the late 1990s (Figure 59). Furthermore, their model predicts 

a SAR of 2.5, 2.9, and 3.0 for 2001–2003 outmigrations, respectively. All these analyses highlight 

the important effects of the ocean in determining smolt-to-adult survival, and they support 

Pearcy’s (1992) assertion that the primary influence of the ocean on salmon survival occurs early 

within the first year that juveniles occupy coastal waters. 

The climate processes that affect the ocean’s physical environment, and thereby influence 

salmon growth and survival, also affect climate patterns in rainfall and temperature on the 

continental land masses (Rodionov and Assel 2003, Coulibaly and Burn 2004). For instance, 

during time periods of relatively poor ocean conditions for Columbia River salmon, such as those 

indicated by a positive phase of the Pacific Decadal Oscillation (PDO) (Mantua et al. 1997), we 

123
0

4

3

2

1

5

6

R2 = 0.71

1960 1970 1980 1990 2000

Year of ocean entry

Observed

Model

0

4

3

2

1

5

6

R2 = 0.71

1960 1970 1980 1990 2000

Year of ocean entry

Observed

Model S

AR (%) 

124

Figure 59. Time series of the observed SAR survival for wild Snake River spring-summer Chinook salmon 

(●) from 1965–2002 compared to the forecasts (▲) from a time series model based on the coastal 

ocean upwelling index at 45°N 125°W. Dotted lines represent the 90% credible limits around the 

forecasts. Note that the SAR estimates for the 2001 and 2002 outmigrations (○) are preliminary in 

that they are based on age-3 (jack) returns in 2002 and age-3 plus age-4 returns in 2003. The 

forecast for the SAR for the 2003 outmigration is also shown. 

Figure 60. Normalized time series of the Pacific Decadal Oscillation (PDO, top) and Columbia River flow 

at The Dalles Dam (bottom). The mean of each series over the various regime intervals as defined 

by Mantua et al. (1997) is superimposed to illustrate the ocean-land teleconnections evident in 

many climate processes. Note that when the PDO index is predominantly positive (e.g., 

1977–1998), ocean conditions are deemed poor for Columbia River salmon. During these same 

time periods, river flows are also below the long-term mean. 

-3

-2

-1

0

1

2

3

PDO

1880 1900 1920 1940 1960 1980 2000

100

150

200

250

300

350

Flow (kcfs)

Year
also observe below-average river flows in the Columbia River basin (Figure 60), suggesting 

additional negative effects on salmon populations (reviewed by Budy et al. 2002). We note also 

that the highest salmon catches in the Columbia River occurred during the 1880s, coinciding with 

the period of the highest normalized Columbia River flows in the last 120 years. Several lines of 

evidence suggest the Northeast Pacific underwent another ocean regime shift in 1998 

(Peterson and Schwing 2003). Already we have witnessed improved smolt-to-adult survival and 

subsequent adult returns in recent years, suggesting a positive switch in the environmental 

conditions that favor salmon growth and survival. Assuming these patterns in ocean and 

continental climate hold, salmon populations in the Pacific Northwest should continue to respond 

favorably until conditions switch again. Concentrating more effort on forecasting changes in 

salmon responses to future climate change and negative anthropogenic activities should help us to 

better manage Columbia River salmon and avoid the massive losses incurred during the last period 

of poor climate conditions. 

Diversity 

Dams have become major selective forces on migratory salmonid populations. They 

dramatically change environmental conditions in the migratory corridor, including reducing river 

velocities, blocking spawning areas, and fostering altered biotic communities. The history of

Snake River fall Chinook salmon provides an extreme example of this. Historically, most Snake 

River fall Chinook spawned above the Hells Canyon Dam complex; now the entire ESU spawns 

below Hells Canyon in a much altered temperature regime (Ebel 1968, Connor et al. 2003a). 

Further, it is likely that in the pre-impoundment era, most ocean-type Chinook salmon fry in the 

Columbia River basin were swept by spring flows to the estuary (Mains and Smith 1964, Park 

1969) where most of their juvenile rearing occurred. In the current river configuration, ocean-type 

Chinook salmon originating from the Snake River, Hanford Reach, or upper Columbia River 

encounter slack water in impounded reservoirs and hold up to rear to a larger size before 

continuing to migrate volitionally. 

The fact that salmon populations have the capability to evolve rapidly (Hendry et al. 2000) 

and that we have demonstrated strong selective forces on some stocks (see “Selective Mortality” 

section, page 119) suggests Columbia River salmonids will evolve in response to selective 

pressures created by dams. We do not know the long-term consequences of these selective 

pressures because they have only acted on populations for 10–15 generations. Thus while almost 

all management is focused on actions that will take effect within a generation, we believe it is 

important to also consider the impacts of management actions on evolutionary time scales. In 

particular, how will dams and their associated mitigation actions affect the diversity of salmonid 

populations?

NOAA Fisheries Service defines a viable salmonid population as “an independent 

population of any Pacific salmonid (genus Oncorhynchus) that has a negligible risk of extinction 

due to threats from demographic variation, local environmental variation, and genetic diversity 

changes over a 100-year time frame” (McElhany et al. 2000). Genetic diversity is important 

because it protects a species by allowing a wider use of environments, protects against short-term

spatial and temporal environmental changes, and provides the raw material for surviving 

long-term environmental change (McElhany et al. 2000). Indeed, Hilborn et al. (2003) concluded 

125
that the entire Bristol Bay sockeye salmon population has remained at a high level specifically due 

to diversity of populations. Thus efforts to ensure diversity in listed Columbia River stocks is 

warranted. To this end, NOAA Fisheries Service suggests it is necessary to “limit or remove 

human-caused selection or straying that weakens the adaptive fit between a salmonid population 

and its environment or limits a population’s ability to respond to natural selection” (McElhany et 

al. 2000). 

Similarly, the Independent Scientific Group recommended that “because the full 

assemblage of salmonids in the Columbia River basin probably used many migration strategies, a 

diversity of management schemes should be used to assist migration. Without diversity of 

management, there is likely to be further stock selection” (ISG 1996). Fish bypass systems, 

spill-ways, the use of transportation, flow augmentation, and other management strategies may 

select for particular stocks or life histories and could therefore reduce diversity if used exclusively. 

 Therefore, in their review of transportation, the Independent Scientific Advisory Board 

con-cluded that “spreading the risk of negative outcomes among alternative routes of hydroelectric 

passage is advisable to prevent a recovery action designed for one listed species from becoming a 

factor in the decline of another species,” and “in the face of uncertainties associated with potential 

negative effects of transportation on genetic and life history diversity” (ISAB 1998). 

We concur. In light of these conclusions and the material presented in this report, we 

believe particular attention needs to focus on: 

• exploration of alternative transportation strategies, including allowing more fish to migrate 

volitionally, adopting seasonally varying transportation schemes, and considering ways to 

delay the delivery of early transported migrants to the estuary; 

• the ability of augmentation and spill to speed downstream migration; 

• consideration of population structure in mitigation actions to determine whether actions 

equally benefit all segments within and between populations; and 

• how anthropogenic changes potentially create selection pressures on fish stocks, e.g., 

whether the unprecedentedly large avian predator populations select against larger fish. 

Hydropower System and Harvest 

The estimated SAR of spring-summer Chinook salmon to the upper dam on the Snake 

River provides an index of escapement over time. The estimated SAR to Lower Granite Dam for 

the last several broodyears actually exceeded most of those in the 1960s (Figure 61). As depicted 

in Figure 52, to some degree this return rate resulted from reduced mainstem harvest on the 

upstream stocks. The data suggest that if the ocean conditions that produced the present higher 

rates of return continue for a few years into the future, and if harvest rates continue at the current 

levels, absolute adult escapement over Lower Granite Dam could possibly exceed levels observed 

in the 1960s. We infer from these data that a decreased harvest rate on adult salmon has potentially 

offset the loss of juveniles that results from mortalities caused by passage through the hydropower 

system, and that under good ocean conditions, this change might allow for the maintenance of 

stock viability. 

126
1960 1970 1980 1990 2000

0

1

2

3

4

2-ocean

only

0.00

0.05

0.10

0.15

0.20

0.25

0.30

0.35

0.40

0.45

0.50

0.55

Harvest rate

SAR (escapement)

over upper dam

Outmigration year

SA

R (

%)

Harvest rate

127

Figure 61. Estimated (escapement-based) SAR of spring-summer Chinook salmon to the upper dam on the 

Snake River (solid line) and estimated annual harvest rate (dashed line). 
Summary and Conclusions 

Our ability to discern FCRPS-related effects is directly related to the quality of available 

data, which is quite variable. We can precisely estimate survival of downstream migrants from

release points to the uppermost dams and through the hydropower system, and we are developing 

similar capabilities for upstream migrants. For several ESUs, we are developing a general sense 

of the relative performance of transported fish compared to in-river migrants, but we are somewhat 

limited by sample sizes of adult returns. Unfortunately, we have limited ability to quantify the 

magnitude of hydropower system-related, latent mortality. However, we believe a major 

component of latent mortality is the disruption of migration timing of transported fish and in-river 

migrants, and we are beginning to discern some migrational timing effects. 

Areas where additional or continued study would help resolve some uncertainties about 

effects of the FCRPS include 

• migrational timing and its effect on SAR for both transported and in-river migrants, 

• selectivity of bypass systems, for fish size as well as fish health, and 

• mechanisms leading toward latent mortality. 

Some of the data limitations discussed above arise from the fact that probably the best 

indicator of population performance is adult return rate, but this measure reflects the effects of 

several confounding factors, of which the FCRPS is but one. Given the existence of the 

hydropower system, it is clear, though, that ocean conditions are the dominating factor in 

determining return rates, overriding variability associated with the hydropower system. Return 

rates have increased by an order of magnitude since the recent upturn in ocean conditions, while 

survival through the hydropower system has remained relatively constant. Improvements in SAR, 

however, do not preclude the existence of FCRPS-related latent mortality or a latent 

mortality/ocean condition interaction. 

Transportation is not a panacea. When comparing annual indices of transported wild 

yearling Snake River spring-summer Chinook salmon and hatchery fall Chinook salmon versus 

in-river fish, in many cases, transportation appeared to confer little benefit or harm. However, 

under certain times of the year and low-flow conditions (particularly in 2001), transportation 

appeared to increase return rates of some segments of the yearling migrant populations. Further, 

the benefits of transportation decreased at sites closer to Bonneville Dam. Thus future operations 

should focus on optimizing adult return rates independent of the transportation process currently 

in operation. Strategies such as “spread the risk” and promotion of diversity suggest we should 

allow more fish to migrate in the river whenever it appears in-river migration might lead to 

reasonable rates of return compared to alternatives. At times, transportation may provide the best 

alternative. We do note that transportation apparently has not provided any benefit to Snake River 

sockeye salmon. 

128
Direct juvenile survival under most conditions for yearling migrants is relatively high, and 

substantial improvements in downstream survival appear unlikely, particularly improve-ments 

related to passage through dams. Summer migrants suffer greater mortality in reservoirs than do 

spring migrants, and improvements in river conditions may confer considerable survival 

improvements. The low survival experienced by spring migrants in 2001 and generally lower 

survival of summer migrants likely resulted from conditions in the reservoirs, potentially low flow, 

and possibly a lack of spill. Therefore, we believe that we may face diminishing returns in terms 

of improving survival via technological fixes to dams. Efforts to reduce mortality in the reservoirs, 

obtaining an understanding about to how to reduce latent mortality, and maintaining diversity by 

improving habitat conditions in the estuary and in freshwater spawning and rearing habitats will 

likely have the most influence on overall stock viability. 

For spring-summer Chinook salmon from the Snake River, we found that increased flow 

had a benefit to juvenile migrant survival, though the effect was small relative to the detriment that 

occurs when water temperatures become too high. For steelhead, the benefit of increased flow was 

apparently greater. However, in our multiple-regression model the benefit is offset somewhat by 

a countering trend of decreased steelhead survival as the season progresses, possibly related to 

increased propensity to residualize as water temperature increases. For yearling Chinook salmon, 

temperatures above 13°C appeared detrimental to survival; these temperatures are typically 

reached in late May. For both species, we have consistently observed a strong relationship 

between flow and travel time. Thus one benefit of flow may be to move spring migrants out of the 

lower Snake River before temperatures become detrimental. 

Flow clearly can affect smolt migration timing to the estuary, and arrival timing appeared 

to greatly influence their SAR. Delayed migration reduces available energy reserves in smolts, 

and it could have affected survival, a condition exacerbated in low-flow years, both within the 

hydropower system and in the freshwater areas upstream that fish negotiate prior to arriving at the 

first dam. 

129
130
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142
Appendix A 

Submission by Idaho Department of Fish and Game 

on Upstream/Downstream Comparisons9

Upstream/downstream differences in smolt-to-adult return rates (SARs) should be used as 

one method to empirically estimate hydrosystem caused latent mortality of upstream stocks. The 

best available scientific information indicates that similar stocks of anadromous fish (e.g., stream

type chinook salmon), that enter the ocean through the same (or nearby) estuary at similar times, 

have similar SARs (Adkison and Finney 2003, Beamish et al. 1997, Coronado and Hilborn 1998, 

Hilborn and Coronado 1997, Peterman et al. 1998, and Weitkamp et al. 1997). The best available 

scientific data indicate that stream type Chinook salmon from the Yakima and Snake rivers have 

the same general pattern of SARs during recent periods of both poor and good ocean productivity, 

but the Yakima River fish consistently return at a higher rate (Figure A-1). Considerable evidence 

suggests that the consistently lower SARs for Snake River chinook salmon is a result of 

hydrosystem induced delayed (latent) mortality (e.g., Budy et al. 2002). Therefore, the difference 

in these SARs would be an empirical estimate of the differential mortality between Snake River 

and downriver chinook salmon. An alternative hypothesis proposed by NOAAF is that the 

differences in SARs are a result of the genetic differences in intrinsic productivity between these 

two populations. 

Researchers in the region are currently generating information that could be used to 

evaluate the question whether upstream/downstream SAR differences should be used to estimate 

latent mortality empirically. The number of streams and anadromous populations in the Columbia 

Basin that are being PIT-tagged in sufficient numbers to estimate SARs has been increasing 

recently, and will likely continue to increase. As increasing numbers of SAR estimates become

available for wild/natural populations, they should fit into one of two basic patterns depending on 

which of the two competing hypothesis is correct. If latent hydrosystem mortality is largely 

responsible for the SAR differences, the downstream populations should have consistently higher 

SARs. If the NOAAF hypothesis is correct, the result will be more variable; with some of the 

downstream wild/natural populations having lower and other downstream populations having 

higher SARs. 

 9

 This submission subsection of Appendix A is reprinted verbatim from an attachment (titled “Technical Comments on 

BiOp Remand collaboration process”) to a memo to Robert Lohn, NOAA Fisheries Service Regional Administrator, 

from Sharon W. Kiefer, Anadromous Fish Manager, IDF&G, dated 16 June 2004. (Available from NOAA Fisheries 

Service, Northwest Regional Office, 7600 Sand Point Way NE, Seattle, WA 98115.) 

143
0.00%

2.00%

4.00%

6.00%

8.00%

10.00%

12.00%

14.00%

16.00%

1982 1984 1986 1988 1990 1992 1994 1996 1998 2000 2002

Smolt Migration Year

S

A

R

%

Yakima SARs Snake SARs

144

Figure A-1. Comparison of Snake and Yakima rivers wild/natural stream type chinook salmon 

smolt-to-adult return rates (SARs). Yakima River SARs from Bill Bosch, Yakima Nation fisheries 

(personnel communication), and Snake River SARs from NOAAF May 6, 2004 draft technical 

memorandum “Effects of the Federal Columbia River Power System on Salmon Populations.” 

Potential exists to evaluate this question as a result of tribal efforts to re-establish coho 

salmon into the Yakima and Snake rivers. The Nez Perce Tribe has been releasing lower 

Columbia River origin coho smolts into the Clearwater River since 1998 for reintroduction. 

Lower Columbia River coho have also been used by the Yakama Nation to re-establish coho in the 

Yakima River. Because similar hatchery stock was used for both of these reintroduction efforts, 

intrinsic productivity differences should be minimized and SAR comparison should 

be possible. 

There may be the opportunity to consider concepts for actual directed research to evaluate 

these two competing hypotheses, such as exchanging yearling hatchery releases of stream type 

chinook between upriver and downriver areas. Clearly, releases would have to be into locations 
where returning adults would be intercepted prior to spawning in order to eliminate or greatly 

minimize effects of undesirable stock interactions or straying. Comparisons of SARs between the 

test releases and normal inbasin releases could provide additional insights into whether the 

observed differences observed between Snake and Yakima rivers SARs are primarily a result of 

intrinsic productivity differences between stocks or latent mortality. 

Literature Cited 

Adkison, Milo D. and Bruce P. Finney. 2003. The Long-Term Outlook for Salmon Returns 

to Alaska. Alaska Fishery Research Bulletin 10(2):83–94. 

Beamish, Richard J., Chrys-Ellen M. Neville, and Alan J. Cass. 1997. Production of Fraser 

River sockeye salmon (Oncorhynchus nerka) in relation to decadal-scale changes in the climate 

and the ocean. Can. J. Fish. Aquat. Sci. Vol. 54:543–554. 

Budy, P., G. P. Thiede, N. Bouwes, C. E. Petrosky, and H. Schaller. 2002. Evidence 

linking delayed mortality of Snake River salmon to their earlier hydrosystem experience. NAJFM 

22(1):35–51. 

Coronado, Claribel and Ray Hilborn. 1998. Spatial and temporal factors affecting survival 

in coho salmon (Oncorhynchus kisutch) in the Pacific Northwest. Can. J. Fish. Aquat. Sci. Vol. 

55:2067–2077. 

Hilborn, Ray and Claribel Coronado. 1997. Changes in ocean survival of coho and 

Chinook salmon in the Pacific Northwest. In, Emmett, R.L., and M.H. Schiewe (editors). 1997. 

Estuarine and ocean survival of Northeastern Pacific salmon: Proceedings of the workshop. U.S. 

Dep. Commerce, NOAA Tech. Memo. NMFS-NWFSC-29, 313 p. 

Peterman, Randall M., Brian J. Pyper, Michael F. Lapointe, Milo D. Adkison, and Carl J. 

Walters. 1998. Patterns of covariation in survival rates of British Columbian and Alaskan 

sockeye salmon (Oncorhynchus nerka) stocks. Can. J. Fish. Aquat. Sci. Vol. 55:2503–2517. 

Weitkamp, Laurie, Peggy Busby, and Kathleen Neely. 1997. Geographical variation in life 

histories of salmonids. In, Emmett, R.L., and M.H. Schiewe (editors). 1997. Estuarine and ocean 

survival of Northeastern Pacific salmon: Proceedings of the workshop. U.S. Dep. Commerce, 

NOAA Tech. Memo. NMFS-NWFSC-29, 313 p. 

145
NOAA Fisheries Service’s Comment 

on IDFG’s Upstream/Downstream Comparison 

The IDFG submission suggests that one approach for approximating the magnitude of 

latent (delayed) mortality caused by the hydropower system would involve comparing the SARs 

of populations that vary in the number of dams that they must pass during their migrations to and 

from the ocean. Unfortunately, testing for this so-called “upstream/downstream comparison” 

relies on a statistical model that simply includes one term to account for the number of dams

without any specific allowance for other intrinsic and extrinsic factors. We know that a suite of 

endogenous and exogenous factors affect the survival of salmon throughout their life. Genetic 

diversity among populations leads to differences in their sex ratio, size and age at maturity, 

fecundity, egg size, and spawning behavior, all of which contribute to variation in the intrinsic 

productivity of salmon populations (Gross 1985, Peterman et al. 1986, Ward and Slaney 1988, 

Taylor 1990b, Gross 1991, Quinn and Unwin 1993, Roni and Quinn 1995, Unwin and Glova 1997, 

Hutchings and Jones 1998, Beckman et al. 2003, Hill et al. 2003). Similarly, spatial and temporal 

disparities in survival arise from variation in the amount of spawning and rearing habitat, the 

density of predators, the density of conspecific and other competitors, prey availability, the 

presence of exotic species, pathogens, temperature, flow, and water quality (Groot and Margolis 

1991, Lichatowich et al. 1995, Mobrand et al. 1997, Beamer and Pess 1999, Yamomoto et al. 1999, 

Levin et al. 2002, Regetz 2003, Greene and Beechie 2004, Vollestad et al. 2004, Zabel and Achord 

2004). Even with no dams in place, we would expect that all these important features would vary 

for populations across the Columbia River basin. Thus, although freshwater productivity of some

stocks might appear similar during some time periods, we would not expect to observe similar 

patterns in the time series of freshwater productivity for the various stocks over a long time. 

The accompanying text by IDFG claims that the “best available scientific information 

indicates that similar stocks of anadromous fish (e.g., stream type chinook salmon), that enter the 

ocean through the same (or nearby) estuary at similar times, have similar SARs (Beamish et al. 

1997, Hilborn and Coronado 1997, Weitkamp et al. 1997, Coronado and Hilborn 1998, Peterman 

et al. 1998, Adkison and Finney 2003).” However, none of the cited references actually supports 

this argument. Adkison and Finney (2003) never mention SARs per se; instead they argue that the 

overall stock productivity tends to follow cyclic changes in the ocean environment and that 

regional differences exist in the response of salmon stocks to climate. Beamish et al. (1997) only 

presented SAR data for one population (Chilko Lake sockeye salmon) and indicated that overall 

patterns in the combined spawner-recruit data from a variety of Fraser River stocks may mask 

important stock-specific freshwater and marine effects. Similarly, Peterman et al. (1998) 

demonstrated that high mortality in the ocean synchronized the otherwise highly variable 

freshwater survival indices among Bristol Bay sockeye salmon, but none of their data indicated 

similar marine survival rates for neighboring stocks over time—only that they tended to rise and 

fall together. Hilborn and Coronado (1997) and Coronado and Hilborn (1998) tested whether the 

marine survival rates of hatchery coho salmon would co-vary by geographic region. They found 

that fish from the lower Columbia River clustered with those from the Oregon coast, but this was 

not surprising due to the similarities in freshwater life stages among hatchery fish that are spawned, 

fed, and reared independent of environmental variability. Again relying on hatchery coho salmon, 

Weitkamp et al. (1997) found that the recovery of CWTs could be grouped only by very broad 

regions, such that the Washington coast differed from the Oregon and California coasts. 

146
As an example of the potential for upstream/downstream comparisons, IDFG presents 

SAR data for Chinook from the Snake River (data from NOAA Fisheries Service) and Yakima

River (data from Yakama Nation Fisheries based on estimates from the Chandler Facility) (Figure 

A-1). Not presented is the caveat Bill Bosch10 provided to NOAA Fisheries Service in early 2004 

regarding the data from Chandler, which stated “Smolt accounting at Prosser is based on statistical 

expansion of Chandler smolt trap sampling data using available flow data and estimated Chandler 

entrainment rates. Chandler smolt passage estimates are prepared primarily for the purpose of 

comparing relative wild versus Cle Elum Supplementation and Research Facility passage 

estimates and not for making survival comparisons. While these Chandler smolt passage estimates 

represent the best available data, there is likely a relatively high degree of error associated with 

these estimates due to inherent complexities, assumptions, and uncertainties in the statistical 

expansion process. Therefore, these estimates are subject to revision.” Data from PIT-tagged wild 

fish suggest a high bias in SARs based on estimates of fish at the Chandler facility. Wild Yakima

River fish PIT tagged in 2000 and released below Roza Dam had a juvenile survival to McNary 

Dam of 81.9% (Table 24 of this technical memorandum). The preliminary SAR based on adult 

returns back to Bonneville Dam is 3.2% (Bosch 2004), which suggests that the SARs for wild 

Yakima River spring Chinook salmon from the 2000 outmigration were much lower than 

estim-ates based on the Chandler facility and closer to the estimated SARs for wild Snake River 

fish. 

We agree that testing for FCRPS-induced latent mortality is worthwhile, but at present we 

see no effective reference system for comparing such mortality with that of Snake River 

spring-summer Chinook salmon. As suggested by IDFG, increased PIT tagging across 

populations within the Columbia River basin should allow for more comparisons of 

population-specific SARs in the future. If SARs across populations show no identifiable patterns 

coincident with the number of dams, the cause of the variation among populations would remain 

a mystery. If, however, we consistently find that SARs are lower for populations that pass more 

dams during their migrations, the cause would still remain unclear due to the enormous number of

uncontrolled variables and inherent differences in stock productivity owing to genetic and 

environmental drivers. 

 10 W. Bosch, Yakama Nation Fisheries, Toppenish, WA 98948, pers. commun.. March 2004. 

147
148
Appendix B

Time-Series Model for Forecasting SARs 

from Coastal Ocean Upwelling 

We modeled the effect of ocean-climate conditions on salmon survival using a class of 

Bayesian time series models known as dynamic linear models (DLMs), a form of the more general 

Kalman filter (Pole et al. 1994). This technique has been applied effectively to ecological data, 

and the methodology has been described in detail elsewhere (Cottingham and Carpenter 1998, 

Lamon et al. 1998, Scheuerell et al. 2002), so we describe it briefly here. At each time step t the 

observed response variable (Yt, a scalar) is sequentially fitted to the 1 × m vector of predictor 

variables (Xt) with the m × 1 regression parameter vector (θt) plus an error term (t, a scalar) 

according to the observation equation 

 Yt = Xtθt + υt υt ~ N[0,Vt] (19) 

The observation errors υt have a variance Vt that is time-dependent and is usually not 

known well enough to approximate it with a fixed value. Therefore, as the analysis proceeds 

through time, Vt is estimated from all of the prior data. The discounting scheme described below 

also applies to Vt. 

The DLM makes use of changes in the parameter set over time through a system equation. 

 Using prior information from Bayesian learning, the m × 1 vector of regression parameters (t) 

evolves through time according to the first-order Markov process 

θt = Gθt -1 + ωt ωt ~ N[0,Wt] (20) 

The m × m system evolution matrix G dictates how the parameters change systematically 

through time while the m × 1variance vector ωt describes the stochastic change in each of the 

parameter estimates (θt) over time. The system variance matrix (Wt) has the variance in ωt along 

the diagonal and zeros elsewhere. Wt is determined by the component discount factors applied to 

the posterior covariance matrix of the previous time step (Pole et al. 1994). In our case, there are 

no within-season effects, and therefore the evolution matrix G collapses to the identity matrix I, 

and therefore the change in the parameter set θt is governed entirely by the variance vector ωt. 

One-year forecasts are generated at each time step, and the parameters are updated as new 

information is incorporated into the model. Through the use of discounting, prior data are given 

weights that determine how influential the prior data are when updating the parameter estimates. 

These discounts represent the rate of exponential decay of useful information, such that when the 

discount is 1 (its maximum value), all of the prior information is retained. A discount value 

approaching 0, on the other hand, means no prior information is used at all. In general, the lower 

the discount value, the faster a parameter can change through time, but at the cost of decreased 

149
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precision of the estimate. Therefore, in ecological applications, we typically select discounts 

greater than 0.8 because we wish to maximize the precision of our model forecasts. In this case, 

we selected the discounts by varying them systematically and then minimizing the negative 

log-likelihood of the overall model. Our final discounts were 0.9, 0.95, and 0.9 for the trend, 

regression, and variance blocks, respectively. 

Ocean-Climate Data 

We chose the Pacific Coastal Upwelling Index (CUI), otherwise known as the Bakun Index, 

as our measure of ocean-climate conditions. Coastal upwelling is thought to influence salmon 

during their ocean residence through bottom-up forcing of the marine food web (Nickelson 1986, 

Gargett 1997). Other researchers have used coastal upwelling as an ocean environment factor in 

comparing catches of Pacific salmon and Dungeness crab in this region (Botsford and Lawrence 

2002). We obtained the CUI from the National Marine Fisheries Service Pacific Fisheries 

Environmental Laboratory (PFEL, online at http://www.pfeg.noaa.gov). PFEL generates monthly 

indices of intensity of large-scale, wind-induced coastal upwelling at 15 standard locations along 

the west coast of North America (each 3 degrees of latitude from 21°N to 60°N). Following 

Botsford and Lawrence (2002), we chose the CUI for 45°N lat. 125°W long. to compare with 

ocean survival of Chinook salmon from the Columbia River basin. This area of the North Pacific 

represents a region that salmon from the Columbia River move into after reaching the ocean 

(Miller et al. 1983). Previous studies suggest that the primary influence of the ocean on salmon 

survival occurs within the first year that juveniles occupy coastal waters (Pearcy 1992). Through 

the use of Bayes Factors, we identified the April, September, and October upwelling indices as the 

best predictor variables; therefore the model results presented in this technical memorandum are 

based on those metrics. 
Most NOAA Technical Memorandums NMFS-NWFSC are available online at the

Northwest Fisheries Science Center web site (http://www.nwfsc.noaa.gov).

Recent NOAA Technical Memorandums NMFS

published by the

Northwest Fisheries Science Center

NOAA Tech. Memo.

NMFS-NWFSC62 Krahn, M.M., M.J. Ford, W.F. Perrin, P.R. Wade, R.P. Angliss, M.B. Hanson, B.L. Taylor,

G.M. Ylitalo, M.E. Dahlheim, J.E. Stein, and R.S. Waples. 2004. 2004 Status review of Southern

Resident killer whales (Orcinus orca) under the Endangered Species Act. U.S. Dept. Commer., NOAA

Tech. Memo. NMFS-NWFSC-62, 73 p. NTIS number pending.

61 Berejikian, B.A., and M.J. Ford. 2004. Review of relative fitness of hatchery and natural salmon. U.S.

Dept. Commer., NOAA Tech. Memo. NMFS-NWFSC-61, 28 p. NTIS number pending.

60 Ford, M.J., T.A. Lundrigan, and P.C. Moran. 2004. Population genetics of Entiat River spring Chinook

salmon. U.S. Dept. Commer., NOAA Tech. Memo. NMFS-NWFSC-60, 45 p. NTIS PB2004-107039.

59 Sloan, C.A., D.W. Brown, R.W. Pearce, R.H. Boyer, J.L. Bolton, D.G. Burrows, D.P. Herman, and

M.M. Krahn. 2004. Extraction, cleanup, and gas chromatography/mass spectrometry analysis of

sediments and tissues for organic contaminants. U.S. Dept. Commer., NOAA Tech. Memo. NMFSNWFSC-59, 47 p. NTIS PB2004-105739.

58 Beechie, T.J., E.A. Steel, P. Roni, and E. Quimby (editors). 2003. Ecosystem recovery planning for

listed salmon: an integrated assessment approach for salmon habitat. U.S. Dept. Commer., NOAA Tech.

Memo. NMFS-NWFSC-58, 183 p. NTIS PB2004-105734.

57 Rogers, J.B. 2003. Species allocation of Sebastes and Sebastolobus sp. caught by foreign

countries from 1965 through 1976 off Washington, Oregon, and California, USA. U.S. Dept. Commer.,

NOAA Tech. Memo. NMFS-NWFSC-57, 117 p. NTIS PB2004-105737.

56 MacCall, A.D., and T.C. Wainwright (editors). 2003. Assessing extinction risk for West Coast salmon.

U.S. Dept. Commer., NOAA Tech. Memo. NMFS-NWFSC-56, 198 p. NTIS PB2003-104642.

55 Builder Ramsey, T., et al. 2002. The 1999 Northwest Fisheries Science Center Pacific West Coast upper

continental slope trawl survey of groundfish resources off Washington, Oregon, and California. U.S. Dept.

Commer., NOAA Tech. Memo. NMFS-NWFSC-55, 143 p. NTIS PB2003-104641.

54 Krahn, M.M., et al. 2002. Status review of Southern Resident killer whales (Orcinus orca) under the

Endangered Species Act. U.S. Dept. Commer., NOAA Tech. Memo. NMFS-NWFSC-54, 133 p. NTIS

PB2003-104520.

53 Waknitz, F.W., T.J. Tynan, C.E. Nash, R.N. Iwamoto, and L.G. Rutter. 2002. Review of potential

impacts of Atlantic salmon culture on Puget Sound chinook salmon and Hood Canal summer-run chum

salmon evolutionarily significant units. U.S. Dept. Commer., NOAA Tech. Memo. NMFS-NWFSC-53,

83 p. NTIS PB2002-108143.