COMPARATIVE SURVIVAL STUDY (CSS) of PIT

Transcription

COMPARATIVE SURVIVAL STUDY (CSS)
of PIT-tagged Spring/Summer Chinook and
Summer Steelhead
2010 Annual Report
BPA Contract #19960200
Prepared by
Comparative Survival Study Oversight Committee and Fish Passage Center:
Jack Tuomikoski, Jerry McCann, and Thomas Berggren, Fish Passage Center
Howard Schaller, Paul Wilson, and Steve Haeseker, U.S. Fish and Wildlife Service
Jeff Fryer, Columbia River Intertribal Fish Commission
Charlie Petrosky, Idaho Department of Fish and Game
Eric Tinus and Tim Dalton, Oregon Department of Fish and Wildlife
Robin Ehlke, Washington Department of Fish and Wildlife
Project Leader:
Michele DeHart, Fish Passage Center
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DRAFT 08/31/2010
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Table of Contents
Chapter 1 Introduction ............................................................ 6
Development of the Comparative Survival Study
Data generated in the Comparative Survival Study
Overview of Bootstrapping Estimation Approach
CSS PIT tagging operations
Coordination and pre-assignments during 2010
Snake River hatchery Sockeye
Historic in-river conditions and transportation
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Chapter 2 Annual metrics of juvenile survival, arrival time,
and migration rate .................................................................. 22
Methods
PIT-tagged fish and the annual estimates
Results
Annual summaries of out-migration timing, migration rates, and reach survivals
Annual out-migration timing (Snake River basin groups)
Annual out-migration timing (Snake River and Columbia River basin groups)
Annual out-migration timing (Snake River hatchery sockeye)
Annual fish migration rate (Snake River basin groups)
Annual fish migration rate (Snake River and Columbia River basin Groups)
Annual fish migration rate (Snake River hatchery sockeye)
Annual survival (Snake River basin groups)
Annual survival (Snake River and Columbia River basin groups)
Annual survival (Snake River and hatchery sockeye)
Discussion
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Chapter 3 Effects of the in-river environment on juvenile
travel time, instantaneous mortality rates and survival...... 51
Methods
Study area and definitions
Multiple regression modeling
Fish travel time
Survival
Instantaneous mortality rates
Environmental variables
Variable selection and model building
Survival modeling approach
Results
Discussion
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Chapter 4 Annual SAR by Study Category, TIR, and D for
Snake River Hatchery and Wild Spring/Summer Chinook
Salmon and Steelhead: Patterns and Significance.............. 66
Methods
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Estimation of smolt numbers in study categories
Pre-2006 migration years
Migration years 2006 and later
Estimation of SARs and Ratios of SARs for Study Categories
Estimation of D
Results
Estimates of SAR by Study Category
Wild and hatchery Chinook
Wild and hatchery Steelhead
Estimates of TIR and D
Wild and hatchery steelhead
Discussion
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Chapter 5 Adult passage success rates between dams, D,
and the expression of delayed effects. ................................... 95
Introduction
Methods
Adult passage success by migration year
Modeling success rates vs. smolt outmigration experience and return year conditions
Observations of straying and straying rates
Results
Partitioning D
Discussion
Supporting tables
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Chapter 6 Patterns in Annual Overall SARs .................... 117
Methods
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Estimation of 90% confidence intervals for annual SARs applicable to all mark populations
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Snake River basin populations originating above Lower Granite Dam
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Estimation of overall annual SARs for pre-2006 smolt migration years
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Estimation of overall annual SARs in smolt migration year beginning 2006
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Middle and Upper Columbia River basin populations
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Estimation of overall annual SARs in all smolt migration years
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Results
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Snake River Overall SARs
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Mid Columbia River Overall SARs
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Upper Columbia River Overall SARs
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Comparison of PIT-tag and Run Reconstruction SARs
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First Year Ocean Survival Rate (S.o1)
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Discussion
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Supporting Tables
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Chapter 7 Effects of Bypass Systems on Juvenile Travel
Times and SARs .................................................................... 147
Introduction
Effects of bypass systems on juvenile fish travel time
Methods
Results
Discussion
Effects of bypass systems on post-Bonneville Dam survival
Methods
Results
Discussion
Meta- Analysis comparing SARs of C1 and C0 wild Chinook and steelhead
Methods
Results
Discussion
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References.............................................................................. 167
Appendix A Source of PIT-tagged Fish ............................. 175
PIT-tagged Wild Chinook Aggregate – Composition by Drainage
PIT-tagged Rapid River Hatchery Spring Chinook – Salmon River Drainage
PIT-tagged Dworshak Hatchery Spring Chinook – Clearwater River Drainage
PIT-tagged McCall Hatchery Summer Chinook – Salmon River Drainage
PIT-tagged Imnaha Hatchery Summer Chinook – Imnaha River Drainage
PIT-tagged Catherine Creek AP Spring Chinook – Grande Ronde River Drainage
PIT-tagged Hatchery Chinook Additions to CSS
PIT-tagged Wild Steelhead Aggregate – Composition by Drainage
PIT-tagged Hatchery Steelhead Aggregate – Composition by Drainage
PIT-tagged Hatchery Steelhead by Drainage and Run-type for 2008
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Appendix B Dam-specific Transportation SARs .............. 180
Appendix C Estimate proportion of smolts experiencing TX,
C0, and C1 passage routes..................................................... 184
Methods
Results
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Chapter 1
Introduction
The Comparative Survival Study (CSS; BPA Project 199602000) began in 1996 with the
objective of establishing a long term dataset of the survival rate of annual generations of salmon
from their outmigration as smolts to their return to freshwater as adults to spawn (smolt-to-adult
return rate; SAR). The study was implemented with the express need to address the question of
whether collecting juvenile fish at dams, transporting them downstream of Bonneville Dam
(BON) and then releasing them was compensating for the effect of the Federal Columbia River
Power System (FCRPS) on the survival of Snake Basin spring/summer Chinook salmon which
migrate through the hydrosystem.
The CSS is a long term study within the Northwest Power and Conservation Council’s
Columbia Basin Fish and Wildlife Program (NPCC FWP) and is funded by Bonneville Power
Administration (BPA). Study design and analyses are conducted through a CSS Oversight
Committee with representation from Columbia River Inter-Tribal Fish Commission (CRITFC),
Idaho Department of Fish and Game (IDFG), Oregon Department of Fish and Wildlife (ODFW),
U.S. Fish and Wildlife Service (USFWS), and Washington Department of Fish and Wildlife
(WDFW). The Fish Passage Center (FPC) coordinates the PIT-tagging efforts, data management
and preparation, and CSSOC work. All draft and final written work products are subject to
regional technical and public review and are available electronically on FPC and BPA websites:
FPC: http://www.fpc.org/documents/CSS.html and
BPA: http://www.efw.bpa.gov/searchpublications/index.aspx?projid
The completion of this annual report for the CSS signifies the 14th outmigration year of
hatchery spring/summer Chinook salmon marked with Passive Integrated Transponder (PIT) tags
as part of the CSS. Its’ also the 11th complete brood year return as adults of those PIT-tagged
fish, covering adult returns from 1997-2008 hatchery Chinook juvenile migrations. In addition,
the CSS has provided PIT-tags to on-going tagging operations for wild Chinook since 2002
(report covering adult returns from 1994-2008 wild Chinook juvenile migrations). The CSS
tagged wild steelhead on the lower Clearwater River and utilized wild and hatchery steelhead
from other tagging operations in evaluations of transportation, covering adult returns from 19972006 wild and hatchery steelhead migrations.
The primary purpose of this report is to update the time series of smolt-to-adult survival
rate data and related parameters with additional years of data since the completion of the CSS
10-yr retrospective analysis report (Schaller et al 2007). The 10-yr report provided a synthesis of
the results from this ongoing study, the analytical approaches employed, and the evolving
improvements incorporated into the study as reported in CSS annual progress reports. This
current report specifically addresses the constructive comments of the most recent regional
technical review conducted by the Independent Scientific Advisory Board and Independent
Scientific Review Panel (ISAB and ISRP 2007) and the comments on the CSS study found in
(ISAB 2010). This report completes the 3-salt returns from migration year 2006 for wild and
hatchery Chinook and steelhead (all returns are to Lower Granite Dam). For wild and hatchery
Chinook, this report also provides 3-salt returns from migration year 2007 and 2-salt returns
from migration year 2008 through a cutoff date of 28 May 2010. For wild and hatchery
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steelhead, it provides completed 2-salt returns for wild and hatchery steelhead that outmigrated
in 2007 (any 3-salt returns of PIT-tagged steelhead are few, but will occur after July 1, 2010).
All of the Chinook salmon evaluated in the CSS study exhibit a stream-type life history.
All study fish used in this report were uniquely identifiable based on a PIT-tag implanted in the
body cavity during (or before) the smolt life stage and retained through their return as adults.
These tagged fish can then be detected as juveniles and adults at several locations of the Snake
and Columbia rivers. Reductions in the number of individuals detected as the tagged fish grow
older provide estimates of survival. This allows comparisons of survival over different life
stages between fish with different experiences in the hydrosystem (e.g. transportation vs. in-river
migrants and migration through various numbers of dams) as illustrated in Figure 1.1. The
location of all tagging sites is identified in Figures 1.2 and 1.3.
Freshwater
Hatchery
Smolts/
spawner
Harvest Management
Wild
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Eggs
S/S
Lower Granite
Little Goose
Lower Monumental
SAR
&
TIR
Ice Harbor
McNary
John Day
Direct
survival
through
dams
The Dalles
Bonneville
R/S
Mainstem
Direct
survival
of
transported
fish
Estuary
D
Spawning
/ Rearing
Habitat
Actions
Ocean
Hydrosystem
Actions
Estuary
Habitat
Actions
Figure 1.1. Salmonid life cycle in the Snake River and lower Columbia River basins (Source: Marmorek et
al. 2004).
.

The adults metrics found in this report will be updated in September of 2010 while the draft is being reviewed and
the report will be updated with these metrics in its final version.
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Figure 1.2. CSS PIT tag release locations and PIT-tag detection sites in the Columbia River Basin.
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Figure 1.3. CSS PIT-tag release watersheds and PIT-tag detection sites in the Columbia River Basin.
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Throughout this report we organized groups of stocks primarily according to DPS/ESU
boundaries (e.g., Snake River, Mid Columbia River, Upper Columbia River). However,
we add the caveat that we have presented Snake River stocks only above Lower Granite
Dam; also, Carson National Fish Hatchery is actually located within the Lower Columbia
Chinook ESU but we present it here as a Mid Columbia group. This was for
simplification as this was the only Lower Columbia group presented, but also because its
lineage is from upriver stocks and its location is upstream of Bonneville Dam.
Development of the Comparative Survival Study
Beginning in 1981, collection of fish at lower Snake River dams and
transportation to below Bonneville dam was institutionalized as an operational program
by the U.S. Army Corps of Engineers (USACE). The intention was to mitigate for
mortality impacts associated with the FCRPS, and thus to increase survival of
spring/summer Chinook salmon. However, abundance of Snake River spring/summer
Chinook salmon continued to decline. Fisheries that had been conducted at moderate
levels in the Columbia River main stem during the 1950s and 1960s were all but closed
by the mid 1970s. In 1992, the Snake River spring/summer Chinook salmon
Evolutionarily Significant Unit (ESU) was listed under the federal Endangered Species
Act (ESA). Spawning ground survey results in the mid-1990s indicated virtually
complete brood year failure for some wild populations. For hatchery fish, low abundance
was a concern as the Lower Snake River Compensation Plan (LSRCP) hatcheries began
to collect program brood stock and produce juveniles.
The motivation for the CSS began with the region’s fishery managers expressing
concern that the benefits of transportation were less than anticipated (Olney et al. 1992,
Mundy et al. 1994, and Ward et al. 1997). Experiments conducted by the National
Marine Fisheries Service (NMFS) prior to the mid-1990s sought to assess whether
transportation increased survival beyond that of smolts that migrated in-river through the
dams and impoundments.
Regional opinions concerning the efficacy of transportation ranged from
transportation being the best option to mitigate for the impacts of the FCRPS, to the
survival of transported fish was insufficient to overcome those FCRPS impacts. Although
the survival of fish transported around the FCRPS could be demonstrated to be generally
higher than the survival of juveniles that migrated in the river, evidence on whether
transportation contributed to significant increases in adult abundance of wild populations
was unavailable. If the overall survival rate (egg to spawner) was insufficient for
populations to at least persist, the issue would be moot (Mundy et al. 1994).
The objectives of the CSS design translate these issues about the efficacy of
transportation into key response variables. The CSS uses the following two aspects for
evaluating the efficacy of transportation: 1) empirical SARs compared to those needed
for survival and recovery of the ESU; and 2) SAR comparisons between transport and inriver migration routes. In this broader context, the primary objective is to answer: “Are
the direct and delayed impacts of the configuration and operation of the FCRPS
sufficiently low to ensure that cumulative life-cycle survival is high enough to recover
threatened and endangered populations?” Therefore we measure SARs against the
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regional management goal to maintain SARs between 2-6%, where 2% is a minimum
requirement and an average of 4% is maintained over multiple generations (NPCC 2009).
The secondary objective is to answer: “is the survival of transported fish (SAR) higher
than the survival (SAR) of fish migrating in-river?” Combining these objectives,
effectiveness of transportation is assessed by whether 1) the survival (SAR) of fish
collected at Snake River dams and diverted into barges is higher than the SAR of fish that
migrate through reservoirs and pass these dams via the spillways and turbines; and 2) the
SAR meets the regional objective (2-6%) for the ESU.
The design and implementation of the CSS improved upon shortcomings of the
methods that had previously been used to estimate and compare survival rates for
transported fish and non-transported (in-river migrating) fish. These shortcomings
resulted from the collection and handling protocols, the marking and recovery
technology, the study objectives, the definition and use of a control population, and the
inconsistency and duration of survival studies (Olney et al. 1992, Mundy et al. 1994, and
Ward et al.1997). Transported and in-river fish groups were handled differently in the
first juvenile fish studies. Whereas transported fish were captured at dams, tagged, and
placed in trucks or barges, some in-river control groups of fish were transported back
upstream for release. Thus, unlike the unmarked outmigration run-at-large, these marked
in-river fish were therefore subjected to the same hydrosystem impacts multiple times
whether they were subsequently collected and transported or remained in-river. The early
mark-recapture studies used coded-wire tags (CWT) and freeze brands to mark juveniles
collected at the dams. Therefore, Snake River basin origin of individual fish could not be
identified, and CWT information could be obtained only from sacrificed fish. Evidence
suggested that the process of guiding and collecting fish for either transport or bypass
contributed to juvenile fish mortality and was cumulative when fish were bypassed
multiple times. If such mortality differentially impacted the study fish, and was not
representative of the in-river migrant run-at-large, measures of the efficacy of
transportation would be biased.
All CSS study fish are uniquely identified with a PIT-tag, and the use of this
technology has provided substantial improvements in the evaluation of the efficacy of
transportation. To ensure that all CSS study fish, whether transported or migrating inriver, experience the same effects from handling (thus improving the utility of an in-river
control group relative to transportation), fish are tagged at hatcheries and wild fish are
tagged at subbasin and main stem outmigrant traps upstream of the FCRPS (Figures 1.2
and 1.3). PIT-tagged juveniles are released near their marking station, allowing the
numbers of fish and distribution across subbasins of origin to be predetermined.
Recapture information can be collected without sacrificing each fish, and lower impacts
due to trapping and handling occur where automated detection stations exist.
The Columbia and Snake River mainstem PIT-tag detectors at the dams now
allow passage dates and locations to be recorded for both juvenile and adult PIT-tagged
fish and provide the ability to link that information to the characteristics of each fish at
time and location of release (Figures 1.2 and 1.3). Given sufficient numbers of fish
among release groups and appropriate distribution across subbasins, ESUs, hatchery vs.
wild, and outmigration season, survival rates of subgroups of fish with unique life history
experience, or aggregate groups with common life history experiences, can be estimated
at discrete or combined life-stages throughout their life cycle. The CSS PIT-tagging
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design and application allows the use of the Cormack-Jolly-Seber (CJS; see Chapter 2)
method with multiple mark-recapture information to estimate survival of the total number
of fish estimated to approach the upper most dam (Lower Granite Dam), thus
representing the conditions that the majority of fish migrating through the hydrosystem
experience.
Data generated in the Comparative Survival Study
The Comparative Survival Rate Study (CSS) is a management-oriented, large
scale monitoring study of spring/summer Chinook and steelhead. The CSS was designed
to address several of the basin-wide monitoring needs and to provide demographic and
other data for Snake River and Columbia River wild and hatchery salmon and steelhead
populations. One product of the CSS is annual estimates of SARs for Snake River
hatchery and wild spring/summer Chinook and steelhead. Estimation of the overall,
aggregate SARs of fish that are transported and those that migrate entirely in-river is key
to evaluation of avoidance of jeopardy (i.e., put at risk of extinction) as well as progress
towards recovery goals. Monitoring survival rates over the entire life-cycle can help
identify where survival bottlenecks are occurring, which is critical input for informed
management decisions (Good et al. 2007). The CSS is also examines environmental
factors associated with life-cycle survival rates and evaluates the hypothesized
mechanisms for variations in those rates.
Generally we estimated the survival of various life stages through known release
and detected return numbers of PIT-tagged fish. The PIT-tags in juvenile fish are read as
the fish pass through the coils of detectors installed in the collection/bypass channels at
six Snake and Columbia River dams, including LGR (Lower Granite), LGS (Little
Goose), LMN (Lower Monumental), MCN (McNary), JDA (John Day), and BON
(Bonneville) (Figures 1.2 and 1.3). Upon arrival at LGR, LGS and LMN, smolts can
travel through three different routes of passage: over the spillway via typical spillway or
removable spillway weir (RSW), or into the powerhouse and subsequently through the
turbines, or diversion with screens and pipes into the collection and bypass facility.
Those smolts that pass over the spillway or through the turbines are not detected, but the
bypass facility does detect and record the fish identification number and the time and date
detected. During transportation operations, smolts without PIT-tags that enter the
collection facility are generally put in trucks or barges and transported to below BON.
Prior to 2006, groups of PIT tagged fish were assigned an “action code" that determined
their route in the bypass facility (e.g. in-river or transport). Starting in 2006, researchers
submitted groups of PIT tagged fish that would then follow the same route as un-tagged
fish or, if not submitted, would follow the default return to river route. In addition, PITtag detections are obtained from a special trawling operation (TWX) by NMFS in the
lower Columbia River in the vicinity of Jones Beach. Returning adults with PIT-tags are
detected in the fish ladders at LGR with nearly 100% probability. PIT-tag detection
capability for returning adults has been added at BON, MCN, and IHR in recent years
allowing for additional analyses.
A specific goal of the CSS has been to develop long-term indices of SAR ratios
between transported and in-river fish. A common comparison, termed “Transport: Inriver” ratio, or TIR, is the SAR of transported fish divided by the SAR of in-river fish,
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with SAR being estimated for smolts passing LGR and returning as adults back to the
adult detector at LGR (GRA). Additionally, SARs from LGR to the adult detector at
Bonneville (BOA) are provided. Estimates of TIR address the question of whether
transportation provides an overall benefit to smolt-to-adult survival, compared to leaving
smolts to migrate in-river, under the hydrosystem as currently configured. The overall
value of transportation in avoiding jeopardy and promoting recovery depends on the
extent to which it circumvents direct mortality (i.e., to smolts within the hydrosystem)
and indirect, or “delayed”, mortality (i.e., to smolts after passing BON) caused as a result
of passage through the hydrosystem. However, because TIR compares SARs starting
from collector projects, it does not by itself provide a direct estimate of any delayed
mortality specific to transported fish.
Related to TIR is “D”, the ratio between SARs of transported fish and in-river fish
from downstream of Bonneville Dam (BON) as smolts back to LGR as adults (BON-toGRA SARs). Estimates of D isolates mortality occurring during juvenile salmon passage
between Lower Granite and Bonneville dams from mortality occurring afterwards (during
time in the ocean and upon returning upriver as adults to Lower Granite Dam for
transported smolts). When D is equal to one it indicates that there is no difference in the
survival rate of transported or in-river fish after hydrosystem passage. When D is less
than one (D < 1), it indicates that transported smolts die at a higher rate after passing
BON compared to in-river smolts (which have migrated through the hydrosystem). If D is
greater than one (D > 1), it indicates transported fish have higher survival after passing
BON compared to in-river fish. D has been used extensively in modeling the effects of
the hydrosystem on Snake River Chinook salmon (Kareiva et al. 2000; Peters and
Marmorek 2001; Wilson 2003; Zabel et al. 2008).
Estimation and comparison of annual SARs for hatchery and wild groups of
smolts with different hydrosystem experiences between common start and end points are
made for three categories of fish passage:
1. tagged fish that are detected at Snake River collector dams (LGR, LGS or
LMN) and transported;
2. tagged fish collected at Snake River dams and returned to the river (C1), or
3. tagged fish never collected or transported at the Snake River dams (C0).
The year 2006 marked an important change in fish transportation operations
within the FCRPS. Transportation operations from 1997-2005 began ~ April 1st and
encompassed most of the emigrating groups of CSS marked fish. In 2006, the
transportation operational protocol was altered at the three Snake River collector dams.
The start of transportation was delayed at LGR until April 20 in 2006 and until May 1
from 2007 through 2009. The start of transportation at LGS and LMN was delayed
further to account for smolt travel time between projects, ranging from 4 to 12 days later
than LGR depending on year. This change in operations affects the CSS study because
the transportation protocol now allows a portion of the population to migrate entirely inriver through the hydrosystem before transportation begins.
This 2006 management change coincided with the CSS change in methods that
pre-assigns fish to bypass or transport routes, rather than forming transport and in-river
cohorts at Snake River collector projects as was done through 2005. The new CSS
approach facilitated evaluation of the 2006 change in transportation strategy. Prior to
2006, the electronics at the dams were used to route fish during the out-migration either
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to raceways or back-to-river. The new method pre-assigns the tagged fish to two
different study groups prior to their emigration through the hydrosystem. This is
accomplished through FPC coordination with various marking agencies. By knowing
what PIT tags are used for marking, FPC assigns individual PIT tags to two groups, and
passes this information on to the separation-by-code facilities at each dam. One group
(denoted as Group T in this report) reflects the untagged population, and these tagged fish
are routed in Monitor-Mode in order to go the same direction as the untagged smolts at
each of the collector dams where transportation occurs. The other group (denoted as
Group R in this report) follows the default return-to-river routing at each collector dam
throughout the season. For example, on entering the bypass facilities at the transportation
sites two things can happen. If transportation is taking place, Group T fish are
transported and Group R fish are bypassed. If transportation is not taking place, both
groups are bypassed. Smolts in the two study groups created would experience different
passage routes through the hydrosystem whenever transportation was occurring. In the
future, these two groups will provide the opportunity to compare estimated SARs
between transport and non-transportation management scenarios.
The transport category of fish passage, category 1 above, is termed T0 (i.e. a first
time detected and transported smolt from a collector dam) in years prior to the
transportation delay and TX (i.e. a transported smolt from a collector dam with or without
an upstream detection) in years with a delay. These SARs and the ratios derived from
them in this report are estimated for the entire migration year. For years prior to 2006,
the SARs developed for each of these study categories are weighted by the proportion of
the run-at-large (untagged and tagged fish) represented by these categories to provide
overall annual SARs. A more direct estimation of overall annual SARs is possible
beginning in 2006 with the pre-assignment of PIT-tagged study fish prior to release into a
monitor-mode group (Group T) which passed through the collector dams in the same
manner as untagged smolts. Because no transported smolts and only a small number of
in-river smolts are enumerated at BON, the BON-to-GRA SAR is estimated from the
LGR-to-GRA SAR, adjusted by annual in-river survival rate estimates (through the
hydrosystem) and assumed average direct transport survival rate from empirical studies.
Combining Groups T and R provides a composite group (Group CRT)
comparable to what has been used in the CSS in all migration years through 2005. For
the analyses work in this report, we use Group CRT to estimate CJS reach survival rates
and detection probabilities. These CJS reach survival rate and collection probability
parameter estimates are then used to generate key parameters for both the component
groups T and R. The estimation of TIRs and D will have TX replace T0 smolts in
migration years after 2005, while C0 smolts are estimated the same in all years. The
estimated smolt numbers and adult return data for Group T provides a direct estimation of
the annual overall SARs beginning with the 2006 migrants.
To evaluate different aspects of the effectiveness of transportation relative to
in-river migration, annual SAR ratios between T0 (or TX) and C0 fish are compared, first
from passage at LGR as smolts to their return as adults to LGR (TIR). This represents
the direct effects of transportation versus in-river migration on survival in the freshwater
migration corridor as well as the indirect effects (i.e. delayed effects) in the estuary,
ocean, and during the adult escapement to LGR. The second comparison is with D which
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represents only the delayed differential survival effects in the estuary, ocean, and during
the adult upstream migration between transported and in-river juvenile outmigrants.
Overview of Bootstrapping Estimation Approach
Over the years, we have developed a computer program to estimate the following
quantities with confidence intervals: survival from hatchery release to LGR; reach
survival estimates between each of the dams equipped with PIT-tag detectors; survival
from smolt arrival at LGR dam until return to LGR as adults (LGR-to-GRA SAR);
survival from smolt outbound arrival at BON to LGR as adults (BON-to-GRA SAR); and
the ratio of these SARs for smolts with different hydrosystem passage experience (TIR
and D). Assessment of the variance of estimates of survival rates and ratios is necessary
to describe the precision of these estimates for statistical inference and to help monitor
actions to mitigate effects of the hydrosystem. For a number of the quantities described
above, theoretical estimates of variance are tractable. However, variance components of
other quantities are often unknown or are extremely complicated and thus impracticable
to estimate using theoretical variances. Therefore, we developed a nonparametric
bootstrapping approach (Efron and Tibshirani 1993), where first the point estimates are
calculated from the population, then the data is re-sampled with replacement to create
1000 simulated populations. These 1000 iterations are used to produce a distribution of
values that describe the mean and variance associated with the point estimate. From the
set of 1000 iterations, non-parametric 80%, 90%, and 95% confidence intervals were
computed for each parameter of interest. The 90% confidence intervals were chosen for
reporting in the recent CSS annual reports in an attempt to better balance the making of
Type I (failure to reject a false null hypothesis) and Type II (failure to accept a true
alternative hypothesis) errors in comparisons among study groups of fish for the various
parameters of interest.
CSS PIT tagging operations
Wild and hatchery smolts are marked with glass-encapsulated, passively induced
transponders that are 11-12 mm in length and have a unique code to identify individual
fish. These PIT-tags are normally implanted into the fish’s body cavity using a hand-held
syringe, and they are generally retained and function throughout the life of the fish.
Snake River basin wild and hatchery Chinook and steelhead used in the CSS
analyses were obtained from all available marking efforts above LGR. Wild Chinook
from each tributary (plus fish tagged at the Snake River trap near Lewiston) were
represented in the PIT-tag aggregates for migration years 1994 to 2009. The sample sizes
for each group with tags provided by the CSS from 1994-2009 are presented in Appendix
A. Additionally, during 2010 tagging operations began in cooperation with the
Washington Department of Fish and Wildlife on wild Chinook and steelhead in the
Upper Columbia basin and are ongoing at the time of this report.
Snake River hatchery yearling spring and summer Chinook were PIT-tagged for
the CSS at specific hatcheries within the four drainages above LGR including the
Clearwater, Salmon, Imnaha, and Grande Ronde Rivers. Hatcheries that accounted for a
major portion of Chinook production in their respective drainages were selected. Since
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study inception in 1997, the CSS has PIT-tagged juvenile Chinook at Rapid River,
Dworshak, McCall and Lookingglass hatcheries. Two Chinook stocks are tagged for the
CSS at Lookingglass Hatchery: an Imnaha River stock released into the Imnaha River
and a Catherine Creek stock released in the Grand Ronde River drainage. This latter
stock became available to the CSS in 2001 after the Lookingglass Hatchery complex
changed its operation to rearing only Grande Ronde River basin endemic stocks.
Beginning in 2009, the CSS is also contributing PIT tags to additional LSCRP hatcheries
including spring Chinook from Clearwater Hatchery in the Clearwater River basin and
summer Chinook from Pahsimeroi Hatchery and spring Chinook from Sawtooth
Hatchery in the Salmon River basin.
Wild steelhead smolts from each tributary (plus fish tagged at the Snake River
trap near Lewiston) were represented in the PIT-tag aggregates for migration years 1997
to 2009. Hatchery steelhead from each tributary, plus PIT-tag releases in the mainstem
Snake River at the Lewiston trap and below Hells Canon Dam, were represented in the
PIT-tag aggregates for migration years 1997 to 2007 with more extensive PIT tagging of
hatchery steelhead beginning in 2008. This increased again in 2009 with the addition of
the Niagara Spring Hatchery production. In coming years with the greater coverage of
hatchery steelhead above LGR, separation of metrics into A and B runs and by basin
should be possible.
Based on past estimates of SARs, sufficient numbers of smolts were tagged to
ensure enough returning adults to compute statistically rigorous SAR estimates.
Required samples sizes for SAR estimates are discussed in Appendix B of the CSS 2008
annual report. All attempts were made to ensure that the PIT-tagged fish are
representative of their untagged cohorts. The origins of the wild Chinook, wild steelhead,
and hatchery steelhead in the PIT-tag aggregates appear to be well spread across the
drainages above LGR (Appendix A). At trapping sites, sampling and tagging occur over
the entire migration season. At the hatcheries, fish were obtained across a wide set of
ponds and raceways to most accurately represent production. Pre-release tag loss and
mortality of PIT-tagged fish were monitored, and the tagging files were transferred to the
regional PTAGIS database in Portland, OR. The study requires that prior to preassigning groups, PIT-tagged fish are not necessarily routed or diverted at collector
projects in the proportions that non-tagged fish are; consequently adjustments are made
(described in Chapter 4) in estimation to more closely represent the experience of run-ofthe-river (non-tagged) fish.
Coordination and pre-assignments during 2010
Marked fish utilized in the CSS may be from groups PIT tagged specifically for
this program or may be from marked groups planned for other research studies.
Wherever possible the CSS makes use of mark groups from other research and
coordinates with other marking programs to meet CSS requirements in order to reduce
costs and handling of fish. To that end, the CSS has a history of collaboration and is
currently cooperating with several other agencies in the marking and pre-assignment of
smolts. All of the smolts marked and pre-assigned during the 2010 migration year are
outlined in Tables 1.1-1.3 (these releases will be analyzed in future reports).
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The CSS will continue coordination efforts to affect cost savings and avoid
redundancy as recommended by the ISAB/ISRP reviews (2007 and 2009). Collaboration
on Snake River basin hatchery fish in recent years includes those with the marking
programs of the Lower Snake River Compensation Plan. Specifically this includes Idaho
Fish and Game, Oregon Department of Fish and Wildlife, and Washington Department of
Fish and Wildlife (Table 1.1). Additionally, the CSS has collaborated with Idaho Power
Company (IPC) and the U.S. Fish and Wildlife Service (USFWS).
Table 1.1. Snake River hatchery groups marked during 2010 that have all or part of their PIT tags
provided by the CSS. Many groups have tags cooperatively provided the CSS and other entities.
The hatchery, species, tag funding sources and tag totals are shown for each. Through cooperative
efforts pre-assignments are carried out by either the CSS or the other associated agencies.
9
PIT Tag Funding Source
Hatchery
Rapid River
McCall's
Clearwater
Pahsimeroi
Sawtooth
Magic Valley
Hagerman
Niagara Springs
Clearwater
Lookingglass
(Imnaha AP)
Lookingglass
(Catherine AP)
Species
Chinook
Chinook
Chinook
Chinook
Chinook
Steelhead
Steelhead
Steelhead
Steelhead
20,000
51,000
15,000
24,600
19,000
16,800
ODFW /
WDFW /
CSS
IPC LSRCP USFWS LSRCP Total PIT tags
32,000 20,000
52,000
32,000
52,000
21,800
72,800
6,400 15,000
21,400
6,400
21,400
10,400
35,000
8,100
27,100
22,300 6,000
28,300
7,000
23,800
Chinook
21,000
21,000
Chinook
21,000
21,000
Irrigon
(Grande Ronde, Steelhead
Imnaha)
Dworshak
Chinook
Dworshak
Steelhead
Lyon's Ferry
Steelhead
(Cottonwood AP)
Grand Total
IDFG /
LSRCP
14,000
31,400
52,000
9,000
14,000
19,900
2,000
146,400 265,400 41,000 31,400
52,000
9,000
6,000
19,900
6,000
2,000
452,800
Agencies are Idaho Fish and Game (IDFG), Idaho Power Company (IPC), Oregon Department of Fish and
Wildlife (ODFW), U.S. Fish and Wildlife Service (USFWS), Washington Department of Fish and Wildlife
(WDFW), and Lower Snake River Compensation Plan (LSRCP)
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Coordination and cooperation has been part of the marking efforts on wild fish
throughout the history of the CSS. The CSS has coordinated with the Smolt Monitoring
Project (SMP) over several years of both studies. During the 2010 marking, a new study
group has been added to the CSS through collaboration with Washington Department of
Fish a Wildlife; wild steelhead and Chinook marked in the upper Columbia are now
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included in the study (Table 1.2). Metrics and analyses on these groups will be presented
in future CSS reports.
Table 1.2. Wild fish marked in 2010 that have all or part of their PIT tags provided by the CSS.
Many groups have tags cooperatively provided the CSS and other studies. The location of marking,
species, tag funding sources and tag totals are shown for each. Through cooperative efforts preassignments are carried out by the CSS on these groups except for the Chiwawa Trap and Lower
Wenatchee Trap (i.e. Upper Columbia Basin).
PIT Tag Funding Source
Location
Wild Species SMP CSS IDFG ODFW Total PIT tags
Clearwater/Salmon tributaries
Ch./St.
24,000 40,000
64,000
Snake & Salmon Traps
Ch./St.
23,400 7,000
30,400
Clearwater Trap
Ch./St.
5,200
5,200
Grande Ronde Trap
Ch.
9,000 1,400
10,400
Grande Ronde tributaries
Ch.
2,200
2,500
4,700
Chiwawa Trap, Lower Wenatchee Trap
Ch./St.
30,000
30,000
32,400 69,800 40,000 2,500
Grand Total
144,700
Agencies are Smolt Monitoring Program (SMP), Idaho Fish and Game (IDFG), and Oregon Department of Fish and
Wildlife (ODFW)
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Fish to be utilized in the CSS from groups planned for other research studies during 2010
are shown in table 1.3. Two of the Snake River groups are pre-assigned by the CSS
through coordination with the marking agency – the CTUIR marking in Grande Ronde
basin and the SBT marking in the Salmon River basin. In the future, the CSS will
continue to review on-going and planned programs in the Middle and Upper Columbia
River regions, to establish stock specific or aggregate groups of marks in those regions to
support CSS analysis and develop demographic survival data for those stocks.
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Table 1.3. Groups marked in 2010 that do not include PIT tags provided by the CSS but are
included in the study. The CSS does random pre-assignments for some groups. The location of
marking/hatchery, species, primary marking agency and tag totals are shown for each.
PIT Tag Marking Agency
Location/Hatchery
Wild Groups
Lookingglass Creek
(Grande Ronde basin)
East Fork Salmon,
West Fork Yankee Rivers
(Salmon basin)
Imnaha Trap
(Imnaha basin)
John Day River
Trout Creek
(Deschutes basin)
Hatchery Groups
Snake River
Carson
Cle Elum
Leavenworth
Warm Springs
Species CTUIR SBT
NPT
ODFW
COE
USFWS YINN
SMP
Ch./St. 3,500*
Ch./St.
1,300*
Ch./St.
15,000**
Ch./St.
~9,300
St.
~1,300
63,600●
Sockeye
Chinook
Chinook
Chinook
Chinook
Grand Total
15,000
40,000
15,000
15,000
3,500 1,300 15,000 ~10,600 63,600
30,000 40,000 15,000
* The CSS pre-assigns these groups through cooperative efforts with the primary marking agency
** Pre-assigned by NPT
● Pre-assigned by COE
Agencies are: Confederated Tribes of the Umatilla Indian Reservation (CTUIR), Shoshone-Bannock Tribes (SBT),
Nez Perce Tribe (NPT), Oregon Department of Fish and Wildlife (ODFW), Corps of Engineers (COE), U.S. Fish
and Wildlife Service (USFWS), Yakima Indian Nation (YINN), and Smolt Monitoring Program (SMP)
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Snake River hatchery Sockeye
Included in this year’s report is presentation of the juvenile metrics for the Snake
River hatchery sockeye marked during 2009 at Sawtooth and Oxbow hatcheries (Chapter
3). The 2009 out-migration was the first year with a large enough sample size that would
likely meet the requirements of the analytical frameworks applied in the CSS (for sample
size discussion see Appendix B of the 2008 CSS report). This was in response to a
request by the Shoshone-Bannock tribe to include sockeye in the CSS (Appendix D, CSS
2009 Annual Report) and should meet regional RME needs in regards to Snake River
hatchery sockeye. In future reports analyses including smolt to adult survival rates for
transported and in-river group comparisons should be possible. If these groups continue
to be marked the CSS should be able to provide a consistent time series of smolt to adult
return data and other demographic data towards the research, management and evaluation
of these stocks.
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Historic in-river conditions and transportation
The environmental conditions experienced by out-migrating juvenile yearling
Chinook and steelhead have varied considerably over the historical context of the CSS
(Figure 1.4). The spring spill program has been in place since 1996 though some years
with low flows (2001, 2004, and 2005) had lower spill. During 2007, conditions were
particularly unique with low flows accompanied by high spring spill percentages and low
transportation percentages. The most recent year displayed (2009; Figure 1.4) reflects
relatively high flows with high spill.
Transportation protocol has varied over the years of the study as well. The
transportation program underwent a change in operations during 2006. Transportation
was delayed at LGR until April 20 in 2006 and until May 1 in 2007-2009; these years
included a similar but lagged start date at LGS and LMN. The delayed start date was
combined with an increased spill percentage from 2004 and 2005, and resulted in a lower
proportion of wild smolts being transported. Smolt out-migration timing also would also
affect transportation percentage and these results vary by stock (see Table 4.18 for
details). The percentage of smolts transported in 2001, 2004, and 2005 were three years
with the highest transportation percentages of CSS PIT-tagged wild fish. Conversely,
2007 had one of the lowest transportation percentages in recent years and much lower
than other years with comparable flows. The higher spill percentage and delay of
transportation contributed to a lower percentage of wild smolts transported in 2007 than
other low flow years. The 2008 and 2009 migration years were very similar for wild
smolts and about 40 percent of the PIT tagged Snake River wild stocks were transported.
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Figure 1.4. The top, middle, and bottom panels are summaries of spill percentage, flow, and the
proportion transported over the historical context of the CSS. Spill percentages and flow are shown
for the three primary transportation dams. The proportion transported is shown for the wild Snake
River stocks involved in the CSS as expressed by population proportion of T0 fish in migration years
before 2006 (Table 7.8 and Table 7.12 in the 2009 CSS annual report). The proportion transported
for migration years 2006-2009 is shown in table 4.18 of this report.
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Chapter 2
Annual metrics of juvenile survival, arrival time, and migration rate
The CSS has established a long-term dataset of juvenile survival, arrival timing
and migration rate for PIT tagged spring\summer Chinook, steelhead and sockeye from
the Snake River and Columbia River basins that is in its 14th year for some groups. As a
component of ongoing Research, Monitoring and Evaluation (RM&E) and Data
Management studies, the data in this chapter provide quantitative information across the
in-river juvenile portion of the salmon and steelhead life-cycle. This chapter presents
annual juvenile metrics by hatchery and by the smallest basin possible (e.g., Snake River
wild Chinook and hatchery steelhead). Here we summarize results that have been
obtained to date from the CSS for annual metrics of juvenile survival, arrival time, and
migration rate. The study groups in this chapter encompass three species: Chinook,
steelhead, and new to this annual report, sockeye. These data include smolts from 12
different hatcheries and wild groups from the Snake River, John Day River, and
Deschutes River basins. Where sample size allowed, Snake River wild Chinook and
hatchery steelhead are broken up by basin (Clearwater, Imnaha, Grande Ronde, and
Salmon) and, for hatchery steelhead, by stock (A and B run).
Methods
PIT-tagged fish and the annual estimates
In this chapter, we define the hydrosystem as the overall reach between Lower
Granite (LGR) Dam and Bonneville (BON) Dam. There are six dams between LGR and
BON: Little Goose (LGS), Lower Monumental (LMN), Ice Harbor (IHR), McNary
(MCN), John Day (JDA), and The Dalles (TDA). We divided the hydrosystem into two
reaches for summarizing survival and migration rate: LGR-MCN and MCN-BON. We
used PIT tag detections at LGR and BON to express juvenile out-migration timing (i.e.,
arrival time) for groups of marked smolts in the upper and lower hydrosystem. We
define fish migration rate as the rate at which fish migrate through these reaches,
expressed in kilometers per day. We used Cormack-Jolly-Seber (CJS) methods to
estimate survival rates through the two reaches based on detections at the dams and in a
PIT-tag trawl (TWX) operating below BON (Cormack 1964, Jolly 1965, Seber 1965,
Burnham et al. 1987).
The array of detection sites in the Snake and Columbia Rivers is analogous to
multiple recaptures of tagged individuals, allowing for standard multiple mark-recapture
survival estimates over several reaches of the hydrosystem using the Cormack-JollySeber (CJS) method. This method was used to obtain estimates of survival and
corresponding standard errors for up to six reaches between release site and tailrace of
BON (survival estimates S1 through S6). An overall survival probability from LGR-toBON, referred to as SR is the product of the reach survival estimates. Estimates of
individual reach survival (e.g. LGR-to-LGS) can exceed 100%; however, this is often
associated with an underestimate of survival in preceding or subsequent reaches.
Therefore, when computing an overall multi-reach survival estimate, we allow individual
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reach survival estimates to exceed 100%. However, an estimate of survival rate for a
specific reach was considered unreliable when its coefficient of variation exceeded 25%.
The number of inter-dam reaches for which an annual survival could be estimated
was a function of the number of smolts in the each release and the recovery effort
available. When fewer than six individual reach survival estimates could be made, the
product of the useable estimates was extrapolated to estimate SR. Prior to 1998, there
was limited PIT-tag detection capability at JDA and TWX. Reliable survival estimates in
those years were possible only to the tailrace of LMN or MCN. After 1998, reliable
survival estimates to the tailrace of JDA were possible in most cases. Estimation of SR
with fewer than 6 individual independent estimates was calculated as follows: first, the
product of the survival estimates over the longest reach possible was converted to
survival per mile, then this was expanded to the number of miles between LGR and
BON. However, because survival per mile rates thus generated were generally lower for
the Snake River (LGR to MCN) than for the Columbia River (MCN to BON), direct
estimates of in-river survival over the longest reach possible were preferable
This chapter provides annual information about specific groups of juvenile fish,
organized by management-oriented groups as in previous CSS reports (e.g. Dworshak
hatchery Chinook, John Day River wild Chinook, etc.). We analyzed the following
annual parameters and measurements: out-migration timing, LGR-MCN reach survival
and migration rate, and MCN-BON reach survival and migration rate. For Snake River
wild Chinook all these estimates were reported by four major basins, the Salmon,
Imnaha, Grande Ronde, and Clearwater Rivers; for Snake River hatchery steelhead
groups only arrival timing and migration rate could be be parsed by these basins. Most
years of PIT-tag detection at LGR of CSS analyzed Snake River groups are presented
here (1998-2009; see CSS 2009 annual report for years not shown here). Bonneville
Dam arrival timing, MCN-BON survival, and fish migration rates for Upper and Mid
Columbia River stocks as well as Snake River stocks are shown for the years 2000-2009.
For Snake River groups, LGR-MCN reach survivals are the product of LGR-LGS,
LGS-LMN, and LMN-MCN reach survivals. Individual reach survival rate estimates
may be obtained from the FPC Web site (www.fpc.org; see Chapter 4 for information on
accessing the data). Survival in the MCN-BON reach is then LGR-BON reach survival
(SR) divided by LGR-MCN reach survival. For all groups, we provide nonparametric
bootstrap confidence intervals for the closed form CJS estimators of juvenile reach
survival. When presenting median annual fish migration rates, we followed Conover’s
recommendations for approximating confidence intervals around a quantile to calculate
90% confidence intervals around the estimate (Conover 1999).
Results
Annual summaries of out-migration timing, migration rates, and reach survivals
Annual out-migration timing (Snake River basin groups)
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Figure 2.1 Timing of PIT tag detections at Lower Granite Dam for Snake River Basin wild Chinook
analyzed in the CSS. Each panel represents a major basin within the Snake River. The grey line is
the averaged values for years 1998-2007; migration years 2008 and 2009 are shown separately.
The annual timing of detections of PIT tagged groups from the four major
drainages in the Snake River Basin at LGR (1998-2009) are summarized with density
plots of PIT tag detections at dams within the hydrosystem in Figure 2.1– 2.11. Within a
single migration year and species/rear-type, timing plots showed similar peaks at similar
times across groups implying that different stocks are reacting similarly to the same
environmental variables within a season. Wild Chinook typically arrive at LGR in early
April and finished passing by the end of June (Figure 2.1). The Imnaha River group was
frequently the first to arrive at LGR among the Snake River wild Chinook groups. The
Imnaha was followed by the Salmon and Grand Ronde River groups whereas the
Clearwater River group was typically last and had a more protracted emigration period
that extended into July or August.
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Figure 2.2 Timing of PIT tag detections at Lower Granite Dam for five Snake River Basin hatchery
Chinook groups analyzed in the CSS. Each panel represents a particular hatchery. The grey line is
Yearling Chinook were PIT tagged for the CSS at specific hatcheries within the
four basins above Lower Granite Dam including the Clearwater, Salmon, Imnaha, and
Grande Ronde rivers. Both spring and summer stocks were included. The CSS has PIT
tagged and/or analyzed juvenile Chinook from McCall, Rapid River, Dworshak, and
Imnaha River hatcheries since 1997, and the Catherine Creek hatchery became available
for use in the CSS in 2001. Smolts from both the Imnaha River hatchery (Imnaha stock
Chinook) and the Catherine Creek hatchery (Grande Ronde River stock) are tagged at
Lookingglass hatchery.
The majority of the PIT tagged hatchery Chinook groups emigrating from the
Snake River arrived at LGR within a narrower temporal window than did wild Chinook
(Figure 2.2). Passage at LGR began later in April and few fish were still passing in June
for the five historical CSS hatcheries. Dworshak hatchery fish were often the first to
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arrive at LGR followed by Imnaha and Rapid River groups; Catherine Creek or McCall
hatchery groups were often the last to pass LGR. The Dworshak group also had the most
protracted emigration of the Chinook hatchery groups.
Figure 2.3 Timing of PIT tag detections at Lower Granite Dam for Snake River Basin hatchery
Chinook analyzed in the CSS. Each panel represents a particular hatchery added to the CSS for
migration year 2009.
Outmigration timing in 2009 for the three new hatchery Chinook groups in the CSS are
plotted in Figure 2.3. The Clearwater basin releases of hatchery Chinook from
Clearwater and Dworshak hatcheries (Figure 2.2) had similar lengthy duration of
outmigration as compared to the other six groups. The Pahsimeroi hatchery had the
earliest outmigration in 2009 among all eight groups whereas the Sawtooth release was
more similar to the Imnaha, Rapid River, McCall, and Catherine Creek releases.
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Figure 2.4 Timing of PIT tag detections at Lower Granite Dam for Snake River Basin steelhead
analyzed in the CSS; Salmon River A and B steelhead are plotted as an aggregate here. The top left
panel shows the wild aggregate and the other panels show hatchery steelhead by basin. The grey line
is the averaged aggregate for wild or hatchery steelhead across years 1998-2007 (Snake River), and
the aggregate 10-year average is repeated in each hatchery steelhead panel for reference; 2008 and
2009 are shown separately in each panel.
Hatchery and wild steelhead passed LGR earlier than most Chinook groups
(Figure 2.4) but were somewhat similar in timing to Dworshak or Clearwater hatchery
Chinook. Hatchery steelhead generally passed LGR later than the wild steelhead group.
When separation by basin was possible for the Snake River hatchery steelhead, there
were similar peaks in migrations at similar times but Hell’s Canyon hatchery steelhead
had the longest out-migration period as compared to other basins. The Clearwater
steelhead had an unusual early peak in 2009 as compared to the other basins.
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Annual out-migration timing (Snake River and Columbia River basin groups)
Figure 2.5 Timing of PIT tag detections at Bonneville Dam for Snake River Basin and John Day wild
Chinook analyzed in the CSS. The top four panels each represent a major basin within the Snake
River. The grey line is the averaged values for years 1998-2007 (Snake River) and 2000-2007 (John
Day River), migration years 2008 and 2009 are shown separately for each group.
Displayed in Figure 2.5 are BON detections of PIT tagged wild Chinook
originating from four Snake River basins as well as those from the John Day River. Most
wild Snake River PIT tagged Chinook passed BON at a later date and had a more
protracted emigration than those originating from the John Day River. The Snake River
wild Chinook groups followed a similar order of appearance as at LGR with Imnaha
River fish first, followed by Grand Ronde and Salmon River fish, and Clearwater River
fish arriving last.
28
1
2
3
4
5
6
7
8
9
10
11
12
13
Figure 2.6 Timing of PIT tag detections at Bonneville Dam for five Snake River Basin hatchery
Chinook groups analyzed in the CSS. Each panel represents a particular hatchery. The grey line is
The timing of 8 Snake River Chinook hatcheries, 2 mid Columbia hatcheries (Cle
Elum and Carson) and 1 upper Columbia River hatchery (Leavenworth) are shown in
Figure 2.5 – 2.7. In similar migration years, Carson hatchery was the earliest to emigrate
followed by Pahsimeroi. Timing among different Snake River groups was more similar
than at LGR, and Leavenworth fish were the latest out-migrating group.
29
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
Figure 2.7 Timing of PIT tag detections at Bonneville Dam for Snake River Basin hatchery Chinook
analyzed in the CSS. Each panel represents a particular hatchery added to the CSS for migration
year 2009.
30
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
Figure 2.8 Timing of PIT tag detections at Bonneville Dam for three lower river hatcheries analyzed
in the CSS. Each panel represents a particular hatchery added to the CSS for migration year 2009.
Each panel represents a particular hatchery. The grey line is the averaged values for years 20002007; migration years 2008 and 2009 are shown separately.
31
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
Figure 2.9 Timing of PIT tag detections at Bonneville Dam for Snake River Basin steelhead analyzed
in the CSS. The top left panel shows the wild aggregate and the other panels show the hatchery
steelhead by basin. The grey line is the averaged aggregate for wild or hatchery steelhead across
years 1998-2007 (Snake River), and the aggregate 10-year average is repeated in each hatchery
steelhead panel for reference; 2008 and 2009 are shown separately in each panel.
For steelhead, BON arrival timing was qualitatively similar to the observations at
LGR, with hatchery and wild steelhead passing BON earlier than most Chinook groups
(Figure 2.9). Hatchery steelhead generally passed BON later than wild steelhead. As
with hatchery and wild Chinook, wild steelhead from the Snake River were generally
passing BON later than downriver groups (Figure 2.10).
32
1
2
3
4
5
6
Figure 2.10 Timing of PIT tag detections at Bonneville Dam for wild steelhead analyzed in the CSS.
The panels from top to bottom display Snake River, John Day River, and Trout Creek (Deschutes
basin) wild steelhead timing. The grey line is the average for Snake River wild steelhead across years
1998-2007; 2008 and 2009 migration years are shown separately in each panel.
33
1
2
3
4
5
6
7
8
9
10
11
Annual out-migration timing (Snake River hatchery sockeye)
Figure 2.11 Timing of PIT tag detections at Lower Granite dam for sockeye during 2009 (top two
panels) and BON (bottom two panels). Plots are for Oxbow and Sawtooth hatcheries.
Annual outmigration timing for Snake River sockeye (Figure 2.11) was very compressed
in duration in the latter half of May at LGR, and outmigration was nearly complete at
BON before June. This is in contrast to Snake River hatchery steelhead or Chinook
which had longer emigration periods that occurred as early as April at LGR and extended
into June at BON.
34
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
Annual fish migration rate (Snake River basin groups)
Figure 2.12 Median fish migration rate from LGR to MCN in km/day for Snake River Chinook
from 8 hatcheries (Catherine Creek, Dworshak, Imnaha, McCalls, Rapid River, Clearwater,
Pahsimeroi, and Sawtooth) and wild Chinook from 4 drainages (Clearwater River, Grand Ronde
River, Imnaha River, and Salmon River). Bars are 90% confidence intervals.
Annual fish migration rate expressed in km/day from LGR to MCN for the Snake
River Chinook groups is shown in Figure 2.12. In many years, the hatchery Chinook
groups emigrated at a faster rate than the wild fish. Among the three new Chinook
groups in the CSS, Clearwater hatchery had the second slowest emigration rate in 2009
followed by Dworshak. Sawtooth hatchery had the highest emigration rate through the
upper reach in 2009.
35
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
Figure 2.13 Median fish migration rate from MCN to BON in km/day for Snake River wild Chinook
from four drainages and wild Chinook from the John Day River for the JDA to BON reach. Bars
are 90% confidence intervals.
Annual fish migration rate (Snake River and Columbia River basin Groups)
Fish migration rates in the lower hydrosystem (MCN to BON) for the Snake
River wild and hatchery Chinook are plotted alongside lower river groups (LEAV,
CLEE, CARS, and John Day wild) in Figures 2.13-2.14. Generally, estimates in the
MCN-BON reach are less precise because of lower sample size than for the LGR-MCN
reach. Snake River groups had an increased emigration rate in the lower reach than in the
LGR-MCN reach. In many cases, emigration rates for the Snake River groups were
higher than for lower river groups. As was the case in the upper reach, the faster outmigrating hatchery Chinook groups emigrated faster than wild Chinook groups.
36
1
2
3
4
5
6
7
Figure 2.14 Median fish migration rate from MCN to BON in km/day for Snake River Chinook
from 5 hatcheries and Mid Columbia River Chinook from 2 hatcheries. Bars are 90% confidence
intervals.
37
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
Figure 2.15 Median fish migration rate in km/day for Snake River aggregated hatchery and wild
steelhead; the LGR to MCN and the MCN to BON reaches are plotted in the left and right panels
respectively. Bars are 90% confidence intervals.
Wild steelhead typically emigrated at a faster rate than hatchery steelhead (Figure
2.10-2.11). This trend was opposite that for Chinook, which had higher rates for hatchery
than wild. The migration rate for steelhead was higher in the lower river and similar
across years to other Snake River groups. When sub-basin/stock groups were possible to
estimate for hatchery Steelhead, the Hell’s Canyon group had the slowest emigration rate.
Imnaha basin fish were one of the fastest emigrating groups among hatchery steelhead, as
was the case for Imnaha basin Chinook among wild Snake River Chinook as well.
Figure 2.16 Median fish migration rate for Snake River hatchery steelhead from five basins
(Clearwater, Grande Ronde, Hell’s Canyon, Imnaha and Salmon) for the 2008-2009 migration years;
Salmon River A and B steelhead are plotted as an aggregate here. The left panel displays the LGR to
38
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
MCN reach. The right panel displays the MCN to BON reach. For comparison, estimates for John
Day River basin wild steelhead in the JDA to BON reach are also displayed on the right panel.
Annual fish migration rate (Snake River hatchery sockeye)
Figure 2.17 Median fish migration rate for Snake River hatchery sockeye from two hatcheries
(Oxbow, and Sawtooth) for the 2009 migration year. The left panel displays the migration rate from
LGR to MCN and the right panel displays from MCN to BON; both are expressed in km/day. Bars
are 90% confidence intervals.
Snake River hatchery sockeye emigration rates for 2009 are displayed in Figure
2.17. Historical estimates for the aggregate Snake River sockeye group are shown in
Table 2.1; due to small sample sizes these rates are an aggregate of wild and hatchery
sockeye from all locations in the Snake River basin. In the upper reach, sockeye from the
Oxbow hatchery emigrated at a higher rate than those reported for the aggregate sockeye
group from 1998-2008, whereas those from the Sawtooth hatchery were more similar to
historical estimates (Table 2.1). As with other Snake River groups, both hatchery groups
emigrated faster from MCN to BON than from LGR to MCN. However the rate of
emigration for sockeye was much higher than for most other Snake River groups of
Chinook or steelhead (Figures 2.12 – 2.16).
39
1
Table 2.1 Emigration rate in the LGR to MCN reach for aggregate Snake River sockeye (19982008). Emigration rate was calculated from median fish travel time in the same reach presented in
FPC memo (FPC 26, Jan 2010).
Migr.
Emigration rate
Year
LGR to MCN
(km/day)
1998
23
1999
37
2000
31
2001
19
2002
27
2003
42
2004
35
2005
17
2006
35
2007
28
2008
34
Geomean
29
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
Annual survival (Snake River basin groups)
Estimated in-river survival from LGR tailrace to BON tailrace (termed SR) for PIT
tagged wild Chinook and five groups of CSS PIT tagged hatchery Chinook showed
considerable annual variability, but the SR of both wild populations and hatchery
populations tracked closely across years from 1998 to 2007 (Figure 2.11). In the 16-yr
time series for wild Chinook and the 13-yr time series for hatchery Chinook, a major drop
in in-river survival relative to adjacent years occurred in 2001 (a drought year throughout
the Northwest) and 2004, which were both years with low flows in the Snake River basin
and no spill at the Snake River collector dams. The same pattern of very low LGR-BON
survival (SR) in 2001 and 2004 was also observed for both PIT tagged wild and hatchery
steelhead (Figure 2.12). Across years, steelhead survival from LGR to BON was
generally lower than Chinook survival. For wild and hatchery steelhead in 2001, the
estimated SR was much lower than their Chinook counterparts and included both dead and
holdover steelhead as mortalities. The 2009 survival values from LGR to MCN were
high values for all groups analyzed; for hatchery and wild steelhead these were the
highest values in the time series. The actual values of SR plotted above for both wild and
hatchery Chinook and steelhead are presented in Tables 2.2 to 2.5.
40
1
2
3
4
5
Figure 2.18 Trend in in-river survival (SR) for PIT tagged Snake River wild and hatchery
spring/summer Chinook in migration years 1994 to 2009.
41
1
2
3
4
Figure 2.19 Trend in in-river survival (SR) for PIT tagged Snake River hatchery and wild steelhead
for migration years 1998 to 2009.
42
1
Table 2.2 Estimated in-river survival LGR to BON (SR) of PIT tagged wild Chinook and hatchery
Chinook from Rapid River SFH and Dworshak NFH facilities for migration years beginning 1994
(wild stocks) and 1997 (hatchery stocks) to 2009 (with 90% confidence intervals).
Aggregate
Rapid River SFH
Dwoshak NFH
Mig. Year
Wild Chinook
Hatchery Chinook
Hatchery Chinook
1994
1995
1996
1997
1998
1999
2000
2002
2003
2004
2005
2006 D
2007 D
2008 D
2009 D
Geomean
2001
0.20 A
0.41 B
0.44 A
0.51 A
0.61 C
0.59
0.48
0.61
0.60
0.40
0.48
0.57
0.60
0.46
0.51
0.48
0.23
(0.17 – 0.22)
(0.32 – 0.56)
(0.35 – 0.55)
(0.33 – 0.82)
(0.54 – 0.69 )
(0.53 – 0.68)
(0.41 – 0.58)
(0.52 – 0.76)
(0.52 – 0.69)
(0.33 – 0.51)
(0.39 – 0.61)
(0.43 – 0.79)
(0.57 – 0.63)
(0.36 – 0.60)
(0.43 – 0.61)
(0.20 – 0.27)
0.33 A
0.59 C
0.57
0.58
0.71
0.66
0.35
0.54
0.55 C
0.63
0.56
0.71
0.55
0.33
(0.24 – 0.45)
(0.52 – 0.66)
(0.49 – 0.67)
(0.48 – 0.83)
(0.60 – 0.84)
(0.57 – 0.78)
(0.27 – 0.51)
(0.42 – 0.69)
(0.51 – 0.61)
(0.56 – 0.72)
(0.45 – 0.72)
(0.61 – 0.85)
(0.28 – 0.40)
0.49 A
0.51 C
0.54
0.48
0.62
0.68
0.50
0.51
0.54 C
0.67
0.40
0.44
0.53
0.24
(0.31 – 0.80)
(0.44 – 0.58)
(0.47 – 0.65)
(0.40 – 0.65)
(0.54 – 0.72)
(0.58 – 0.81)
(0.40 – 0.66)
(0.42 – 0.63)
(0.49 – 0.59)
(0.60 – 0.75)
(0.32 – 0.55)
(0.38 – 0.52)
(0.20 – 0.30)
A to C
Footnote shows percent of reach with a constant “per/mile” survival rate applied (A = 77%
expansion LMN to BON; B = 51% expansion MCN to BON; C = 25% expansion JDA to BON).
D
Migration years 2006 and later use reach survival rate estimates of combined T and R groups.
2
3
Table 2.3 Estimated in-river survival LGR to BON (SR) of PIT tagged hatchery Chinook from
Catherine Ck AP, Imnaha R AP, and McCall SFH facilities for migration years 1997 to 2009 (with
90% confidence intervals).
Catherine Ck AP
Imnaha R AP
McCall SFH
Hatchery Chinook
Hatchery Chinook
Hatchery Chinook
Mig. Year
1997
1998
1999
2000
2002
2003
2004
2005
2006 D
2007 D
2008 D
2009 D
Geomean
2001
0.65
0.62 C
0.48 C
0.51 C
0.48 C
0.72
0.48
0.54
0.55
0.25
(0.44 – 1.06)
(0.51 – 0.74)
(0.34 – 0.72)
(0.37 – 0.80)
(0.38 – 0.61)
(0.53 – 1.07)
(0.29 – 1.11)
(0.40 – 0.84)
(0.18 – 0.37)
0.31 A
0.53 C
0.54
0.57
0.50
0.70 C
0.56 C
0.58 C
0.50 C
0.69
0.34
0.67
0.53
0.37
A to C
(0.20 – 0.49)
(0.46 – 0.62)
(0.42 – 0.75)
(0.43 – 0.83)
(0.41 – 0.66)
(0.62 – 0.80)
(0.44 – 0.73)
(0.47 – 0.78)
(0.43 – 0.58)
(0.57 – 0.88)
(0.25 – 0.49)
(0.51 – 0.94)
(0.27 – 0.61)
0.43 A
0.56 C
0.52
0.61
0.58
0.70
0.44
0.53
0.60 C
0.82
0.36
0.57
0.55
0.27
(0.32 – 0.59)
(0.50 – 0.64)
(0.46 – 0.61)
(0.51 – 0.83)
(0.51 – 0.68)
(0.62 – 0.77)
(0.35 – 0.59)
(0.45 – 0.65)
(0.53 – 0.67)
(0.73 – 0.94)
(0.30 – 0.45)
(0.50 – 0.67)
(0.22 – 0.34)
Footnote shows percent of reach with a constant “per/mile” survival rate applied (A = 77%
expansion LMN to BON; B = 51% expansion MCN to BON; C = 25% expansion JDA to BON).
D
43
1
Table 2.4 Estimated in-river survival LGR to BON (SR) of PIT-tagged steelhead for wild stocks from
1997 to 2009 and hatchery stocks from 1997 to 2007 (with 90% confidence intervals).
Aggregate
Aggregate
Mig. Year
Wild Steelhead
Hatchery Steelhead
1997
1998
1999
2000
2002
2003
2004
2005
2006 D
2007 D
2008 D
2009 D
Geomean
2001
0.52 C (0.28 – 1.00)
0.54 C (0.48 – 0.62)
0.45
(0.38 – 0.54)
C
0.30
(0.28 – 0.33)
0.52
(0.41 – 0.69)
0.37
(0.31 – 0.44)
0.18 B (0.13 – 0.26)
0.25 C (0.20 – 0.34)
0.58 C (0.50 – 0.67)
0.38
(0.31 – 0.48)
0.42
(0.35 – 0.52)
0.70 C (0.58 – 0.84)
0.41
0.038 (0.027 – 0.059)
0.40 C (0.26 – 0.71)
0.64
(0.47 – 1.00)
0.45
(0.39 – 0.53)
C
0.22
(0.19 – 0.25)
0.37
(0.29 – 0.49)
0.51
(0.42 – 0.61)
0.17 B
(0.13 – 0.23)
0.36 C
(0.30 – 0.46)
0.62 C
(0.56 – 0.69)
0.49
(0.41 – 0.60)
0.49 (see Table 2.5)
0.67 (see Table 2.5)
0.42
0.038
(0.023 – 0.082)
A to C
Percent of reach with a constant “per mile” survival rate applied (A = 77% expansion LMN to
BON; B = 51% expansion MCN to BON; C = 25% expansion JDA to BON).
D
2
3
Table 2.5 Estimated in-river survival LGR to BON (SR) of PIT tagged steelhead for wild stocks from
1997 to 2009 and hatchery stocks from 1997 to 2007 (with 90% confidence intervals).
Run
Aggregate
Mig. Year1
Drainage
Type
Hatchery Steelhead
1
4
5
6
7
8
9
10
2008
2008
2008
2008
2008
Clearwater R
Grande Ronde R
Imnaha R
Salmon R
Salmon R
2009
2009
2009
2009
2009
2009
Clearwater R
Grande Ronde R
Imnaha R
Salmon R
Salmon R
Mainstem below HCD
B
A (Wallowa)
A
A
B
Geomean
B
A (Wallowa)
A
A
B
A
Geomean
0.39
0.56
0.55
0.40
0.57
0.49
0.61
0.70
0.67
0.70
0.69
0.66
0.67
(0.36 – 0.42)
(0.46 – 0.72)
(0.41 – 0.76)
(0.35 – 0.46)
(0.44 – 0.76)
(0.55 – 0.68)
(0.61 – 0.82)
(0.55 – 0.86)
(0.62 – 0.81)
(0.59 – 0.86)
(0.50 – 0.96)
Further partition of these survival rates into the LGR-MCN reach and MCN-BON
reach are plotted in Figures 2.2 and 2.21. The values of individual in-river survival rates
44
1
2
3
4
5
6
7
8
9
10
11
12
13
14
between each monitored reach from LGR to BON may be obtained from the FPC Web
site (www.fpc.org; see Chapter 4 for information on accessing the data).
Figure 2.20 Annual estimates of reach survivals from LGR to MCN for five Snake River Chinook
hatcheries, wild Chinook, hatchery steelhead and wild steelhead (2000-2007). Estimates were
calculated using the CJS model; confidence intervals are 90% non-parametric bootstrapped
intervals.
Survival estimates from LGR to MCN and MCN to BON are displayed in Figure
2.20 and 2.21 for Snake River originating Chinook groups. In the upper hydrosystem
hatchery Chinook often survived at a higher rate than wild Chinook and Chinook groups
survived at a higher rate than steelhead groups, except for 2009 (Figure 2.23-2.24). In
the lower hydrosystem, there was more variability surrounding the survival estimates but
the patterns were similar for Chinook.
45
1
2
3
4
5
6
7
8
Figure 2.21 Annual estimates of reach survivals from MCN to BON for five Snake River Chinook
hatcheries, wild Chinook, hatchery steelhead and wild steelhead (2000-2007). Estimates were
intervals.
46
1
2
3
4
5
6
7
8
9
10
11
12
13
14
Annual survival (Snake River and Columbia River basin groups)
Figure 2.22 Annual estimates of reach survivals from MCN to JDA for five Snake River Chinook
hatcheries, and two Columbia River Chinook hatcheries (2000-2007). Estimates were calculated
using the CJS model; confidence intervals are 90% non-parametric bootstrapped intervals.
Survival estimates through the entire lower reach (MCN to BON) were not stable
for the Cle Elum (CLEE) and Leavenworth (LEAV) hatchery Chinook groups. However,
we were able to estimate survival in the MCN to JDA reach and, except for 2008 when
CLEE and LEAV survival estimates exceeded one, these are compared with those for
Snake River hatchery Chinook groups within the MCN to JDA reach (Figure 2.22). Point
estimates for Snake River groups were typically higher than for Columbia River groups
within the same year.
47
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
Figure 2.23 Annual estimates of reach survivals from LGR to MCN (left panel) and MCN to BON
(right panel) for Snake River steelhead hatcheries by basin of release (2008-2009). Estimates were
intervals.
(right panel) for Snake River steelhead hatcheries by basin of release (2008-2009). Estimates were
intervals.
For steelhead groups in the LGR to MCN reach, wild steelhead often survived at a
higher rate than hatchery steelhead (Figure 2.23-2.24). One would expect steelhead to
follow a similar pattern of lower survival in the MCN to BON reach. However, estimates
for the MCN to BON reach were imprecise due to smaller sample size than for Chinook
groups, and thus some may be of limited use for a comparative evaluation (Figure 2.23).
For most groups the 2009 survival estimates were the highest in the time series.
48
1
2
3
4
5
6
7
8
9
10
11
12
13
Annual survival (Snake River and hatchery sockeye)
(right panel) for Snake River hatchery sockeye (2009). Estimates were calculated using the CJS
model; confidence intervals are 90% non-parametric bootstrapped intervals.
Snake River hatchery sockeye survival rates for 2009 are displayed in Figure
2.25. Historical estimates for the aggregate Snake River sockeye group are shown in
Table 2.6; due to small sample sizes these rates are an aggregate of wild and hatchery
sockeye from all locations in the Snake River basin. In the upper reach, sockeye from
both Oxbow and Sawtooth hatcheries had a higher point estimate of survival than those
reported for the aggregate sockeye group from 1998-2008 (Table 2.6).
Table 2.6 Juvenile survival for LGR to MCN reach for aggregate Snake River sockeye (1998-2008).
Survival data are from FPC memo (FPC 26, Jan 2010).
Juvenile
Migr.
95% Con. Int.
Survival
Lower Upper
Year
(LGR-MCN)
Limit Limit
1998
1999
2000
2001
2002
2003
2004
2005
2006
2007
2008
Geomean
0.6
0.22
0.98
0.63
0.64
0.26
0.5
0.71
N/A
0.45
0.86
0.62
0.67
0.42
0.37
0.06
0.35
0.5
N/A
0.13
0.47
0.38
0.43
0.84
0.91
0.46
0.66
0.91
N/A
0.77
1.25
0.86
0.9
0.57
49
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
Discussion
In this chapter we provided an extensive synthesis of the patterns of variation in
juvenile yearling Chinook and steelhead passage timing at key dams, emigration rates,
and survival within key reaches of the hydrosystem. These metrics are presented as
annual estimates in management-oriented groups and provide a consistent time-series of
demographic data to inform research, management, and evaluation of these stocks.
Some general statements can be made from these data. Within a single species
but among groups (e.g. 8 hatchery groups of Snake River Chinook in 2009) there were
similar seasonal peaks in arrival timing at across all groups, perhaps suggesting that all
stocks were reacting similarly to environmental influences. In general, wild Chinook
arrived at LGR before hatchery Chinook and wild steelhead before hatchery steelhead. In
2009, Snake River sockeye arrived at LGR after many groups but displayed the most
compressed emigration window and emigrated at a higher rate than most other Snake
River stocks.
Most Snake River stocks emigrated at a higher rate in the lower hydrosystem
(MCN to BON) than the upper hydrosystem (LGR to MCN). Snake River groups often
emigrated more quickly through the lower hydrosystem than the same species originating
from the Columbia River basin.
Survival for the Snake River stocks in the LGR to MCN reach generally showed
an increase over the time series with the highest survival for steelhead occurring in 2009.
These stocks, where discernable, had a higher survival in the upper reach (LGR to MCN)
than the lower reach (MCN to BON) though many lower reach estimates have low
precision and were not statistically different. Point estimates for Snake River groups
were typically higher than for Columbia River groups within the same year. Among the
two sockeye groups in 2009, the reach survival point estimates for the Sawtooth group
were higher than for the Oxbow group.
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Chapter 3
Effects of the in-river environment on juvenile travel time,
instantaneous mortality rates and survival
The CSS is an important component of ongoing Research, Monitoring and
Evaluation (RM&E) and Data Management studies in the Columbia River basin. This
long-term study provides specific information on management actions in the region,
specifically the role of the smolt transportation program, flow augmentation, and spill for
the recovery of listed salmon and steelhead stocks. In addition to providing a time series
of SAR data (see chapter 4 and 6), the CSS provides data on smolt out-migration timing,
juvenile migration rates and travel times, juvenile reach survivals, and evaluates these
parameters for the purpose of informing management and recovery decisions related to
those stocks.
As a long-term study, the CSS has included PIT-tagged smolts from a variety of
basins, locations, species and rear-types in an effort to arrive at, among other goals, a
holistic view of juvenile demographic parameters and their relationships to hydrosystem
management actions in the FCRPS. This chapter summarizes data collected on groups of
juvenile salmonids from the Snake River basin, which consisted of spring/summer
Chinook salmon, steelhead and sockeye salmon.
This chapter updates the multiple regression models of fish travel time,
instantaneous mortality rates and survival rates from Chapter 3 of the 2009 Annual
Report (Tuomikoski et al. 2009). These analyses address an interest of the ISAB/ISRP
for finer scale analyses of the relationships between survival and specific operational
actions or environmental features (ISAB 2006). In this chapter we continue the process
of summarizing and synthesizing the results that have been obtained to date through the
CSS on the responses of juvenile yearling Chinook salmon and steelhead to conditions
experienced within the hydrosystem. These analyses provide an example of how the CSS
PIT-tag results could be used in a predictive fashion to characterize the effects of
management actions on fish travel times and in-river juvenile survival rates, while
directly accounting for measurement uncertainty and environmental variability.
Methods
Study area and definitions
In this chapter, we define the hydrosystem as the overall reach between Lower
Granite Dam (LGR) and Bonneville (BON) Dam. There are six dams between LGR and
BON: Little Goose (LGS), Lower Monumental (LMN), Ice Harbor (IHR), McNary
(MCN), John Day (JDA), and The Dalles (TDA). We divided the hydrosystem into two
reaches for summarizing fish travel time, instantaneous mortality rates and survival:
LGR-MCN and MCN-BON. We define fish travel time (FTT) as the time spent
migrating the LGR-MCN or MCN-BON reach and expressed this in days. We used
Cormack-Jolly-Seber (CJS) methods to estimate survival rates through the two reaches
based on detections at the dams and in a PIT-tag trawl operating below BON (Cormack
1964, Jolly 1965, Seber 1965, Burnham et al. 1987).
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Multiple regression modeling
The goal of the multiple regression models is to evaluate finer-scale analyses of
the relationships between survival and specific operational actions or environmental
features during the juvenile outmigration. Towards this goal, we calculated and
summarized within-year (weekly or multi-weekly) travel time, instantaneous mortality
and survival rate estimates for juvenile yearling Chinook and steelhead across years of
the CSS. We also calculated and summarized seasonal estimates of travel time,
instantaneous mortality rates and survival rates for sockeye. The yearling Chinook,
steelhead and sockeye used in this analysis consisted of fish PIT-tagged both at
hatcheries and fish traps upstream of Lower Granite Dam (LGR) and those tagged and
released at LGR. Due to sufficient numbers of PIT-tagged hatchery and wild yearling
Chinook available, analyses in the LGR-MCN reach were conducted separately for
hatchery and wild yearling Chinook. Due to the limited number of PIT-tagged steelhead
available, hatchery and wild steelhead were combined for analyses in the LGR-MCN
reach. Similarly, hatchery and wild sockeye are combined for analyses in the LGR-MCN
reach. Analyses on the MCN-BON reach included hatchery and wild yearling Chinook
and steelhead from the Snake River, hatchery-marked fish from the Mid-Columbia River,
and fish marked and released at MCN.
Fish travel time
We utilized a cohort-based approach for characterizing fish travel times for
weekly groups of juvenile Chinook salmon and steelhead. Individual fish detected at
LGR with PIT-tags were assigned to a weekly cohort group (i) according to the week of
their detection. Cohorts were identified by the Julian day of the midpoint of the weekly
cohort. For example, the April 1-7 release cohort was identified by Julian day = 94
(April 4). We calculated fish travel time as the number of days between releases at LGR
until detection at MCN for each fish subsequently detected at MCN. For statistical
reasons (described below), we calculated the mean FTTi for each weekly release cohort
instead of the median FTT that was presented in previous reports (Schaller et al. 2007,
Tuomikoski et al. 2009). In preliminary analyses, we used Box-Cox power
transformations to determine whether the FTTi data needed to be transformed in order to
better approximate normality of the residuals in subsequent regressions. These
preliminary analyses indicated that a log-transformation was most appropriate for both
the Chinook and steelhead data. We calculated mean FTTi for each weekly release cohort
of both yearling Chinook and steelhead, in both the LGR-MCN and MCN-BON reaches.
Because the number of PIT-tagged sockeye was low and the juvenile sockeye migration
season is relatively narrow, we calculated a seasonal estimate of LGR-MCN FTT for
sockeye. There were not sufficient numbers of PIT-tagged Snake River sockeye in the
MCN-BON reach to calculate reliable estimates of FTT.
For yearling Chinook, we calculated mean FTTi for eight weekly cohorts from
April 1 through May 26 in the LGR-MCN reach. Separate estimates were developed for
hatchery and wild rearing types of yearling Chinook. In the MCN-BON reach, hatchery
and wild yearling Chinook were combined and we calculated mean FTTi for six weekly
cohorts from April 26 through June 5. For steelhead, we calculated mean FTTi for six
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weekly cohorts from April 17 through May 28 in the LGR-MCN reach. In the MCNBON reach, we calculated mean FTTi for six weekly cohorts of steelhead from April 27
through June 7. Hatchery and wild rearing types of steelhead were combined for both
reaches.
Survival
We estimated the survival rates for each weekly cohort of wild Chinook, hatchery
Chinook and the combined hatchery and wild steelhead in the LGR-MCN reach using
standard CJS methods over migration years 1998-2009. We also estimated seasonal
survival rates for sockeye in the LGR-MCN reach over 1998-2009. Due to lower
numbers of PIT-tagged fish detected and released at MCN, we developed survival
estimates for three, two-week cohorts for yearling Chinook and two, three-week cohorts
for steelhead in the MCN-BON reach over migration years 1999-2009. We calculated
Chi-square adjusted variances (using the ĉ variance inflation factor) for each survival
rate estimate ( Ŝ ) (Burnham et al. 1987:244-246). Using this delineation for the cohorts,
the average coefficient of variation (CV) across the weekly survival rate estimates in the
LGR-MCN reach was 7% for wild yearling Chinook, 7% for hatchery yearling Chinook,
6% for steelhead (combined hatchery and wild) and 22% for sockeye (seasonal estimates,
combined hatchery and wild). In the MCN-BON reach, the average CV across the
survival rate estimates was 14% for yearling Chinook (hatchery and wild combined, twoweek cohorts) and 27% for steelhead (hatchery and wild combined, three-week cohorts).
Each release cohort was identified by the Julian day of the midpoint of the cohort.
Instantaneous mortality rates
In 2003, the ISAB offered the suggestion that “an interpretation of the patterns
observed in the relation between reach survival and travel time or flow requires an
understanding of the relation between reach survival, instantaneous mortality, migration
speed, and flow” (ISAB 2003-1). Consistent with that suggestion, we developed an
approach for estimating instantaneous mortality rates for juvenile salmonids (Schaller et
al. 2007, Tuomikoski et al. 2009). Ricker (1975) provides a numerical characterization
of survival, also known as the exponential law of population decline (Quinn and Deriso
1999):
N
S  t  e  Zt ,
[3.1]
N0
where S is a survival rate, N t is the number of individuals alive at time t, N 0 is the
number of individuals alive at time t = 0, and Z is the instantaneous mortality rate, in
units of t 1 . Eqn. 3.1 is the solution to the differential equation
N
  ZN ,
[3.2]
t
and the instantaneous mortality rate Z is interpreted as the rate of exponential population
decline. Eqn. 3.1 has been called the “first principle” or “first law” of population
dynamics (Turchin 2003), and serves as a foundational basis for most fisheries population
assessment models (Quinn and Deriso 1999).
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The exponential law of population decline provides a useful framework for
understanding the interrelationships between instantaneous mortality rates, time, and
survival. Over a fixed period of time, an increase in Z will result in lower survival over
that time period. Similarly, for a fixed Z, survival will decrease with increasing time. At
time t = 0, survival is 1.0 and survival declines toward zero as t increases. If
instantaneous mortality rates vary over time, Z represents the arithmetic mean mortality
rate over the time period (Keyfitz 1985:18-19). This property of Z may be useful for
capturing mortality rates for smolts in the Columbia Basin, which may experience
different mortality rates over time. For example, if mortality rates experienced through a
reservoir differ from mortality experienced through a dam, then the instantaneous
mortality rate Z represents the arithmetic mean mortality rate over that period of
migration through the reservoir and dam combination. Rearranging Eqn. 3.1, Z can be
estimated as
 log e ( Sˆ )
Zˆ 
.
[3.3]
t
In our application, we calculated instantaneous mortality rates (in units of d-1) for
each survival cohort using Eqn. 3.3. We used the CJS estimates of survival for each
cohort ( Ŝ i ) in the numerator and used the mean FTˆTi in the denominator of Eqn. 3.3. In
previous reports (Schaller et al. 2007, Tuomikoski et al. 2009) we used median FTˆT in
i
the denominator of Eqn. 3.3. However, simulation analyses indicated that using mean
FTˆTi in the denominator of Eqn. 3.3 provides more accurate estimates of the underlying
instantaneous mortality rate than using median FTˆT (Steven Haeseker, USFWS,
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unpublished data). While individuals in each release cohort have variable individual
FTT’s, we used the mean FTˆTi ' s in the denominator of Eqn. 3.3 to characterize the
cohort-level central tendency in the amount of time required to travel a reach.
Combining the cohort-level survival rate estimates ( Ŝ i ) with the cohort-level mean FTˆTi
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estimates, we estimated the cohort-level instantaneous mortality rates ( Ẑ i ) using Eqn.
3.3.
Both  log e ( Sˆ i ) and mean FTˆTi are random variables subject to sampling and
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process error. To calculate the variance of Ẑ i , we used the formula for the variance of
the quotient of two random variables (Mood et al. 1974):
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i
  log(S )    log(S ) 
var(Zî )  var


 FTT   FTT 
2
 var[ log(S )] var[FTT ] 2cor ( log(S ), FTT )  var[ log(S )]  var[FTT ]  ,




  log(S ) 2

 log(S )  FTT
FTT 2


[3.4]
To estimate the variance of –log(S), we used the approximation provided by Blumenfeld
(2001) for log-normally distributed random variables:
[3.5]
var[ log e ( S )]  log e (1  [CV ( S )]2 ) .
Environmental variables
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The environmental variables associated with each cohort were generated based on
fish travel time and conditions at each dam along the reaches. Travel time for each group
between dams was estimated, and we calculated the average spill percentage, temperature
(based on tailwater total dissolved gas monitoring data, downloaded from the COE
website (http://www.nd-wc.usace.army.mil/perl/dataquery.pl) and total water transit time
(WTT) as indicators of conditions each group experienced while passing through the
reach. Water transit time was calculated by dividing the total volume of reservoirs by the
flow rate, and with adjustments in McNary pool to account for Columbia River versus
Snake River flows. Conditions at downstream dams were averaged over a seven-day
window around the median passage date at each dam, and the travel time to the next dam
was used to adjust the start date of the calculations. For example, steelhead travel time
from LGR to LGO for the earliest release cohort in 2005 (detected at LGR from 4/17 to
4/23) was estimated to be 5.0 days based on 378 detections. Average environmental
variables over the time period of April 22 to April 28 at LGO were then calculated. At
each downstream dam, environmental variables were calculated in a similar manner.
Since no PIT-tag detection data were available until 2005 at IHR, travel time to IHR was
estimated as 43% of the total travel time from LMN to MCN (corresponding to the
distance to IHR relative to the distance to MCN). The overall reach environmental
variables were the average of these dam-specific calculated values for spill percentage
and temperature, whereas for water transit time the sub-reach values were summed to
estimate the total reach water transit time. In addition to these environmental predictor
variables, we also used Julian date as a predictor variable to help capture seasonal effects
not reflected in these environmental variables. We use Julian date of release to
characterize effects such as degree of smoltification, photoperiod, predator
abundance/activity, or fish length that may demonstrate a consistent pattern within- and
across-years, but is not already captured by the other environmental variables. The use of
Julian date of release as an attempt to capture seasonal effects is a common modeling
strategy for these data (Berggren and Filardo 1993, Smith et al. 2002, Williams et al.
2005). We also developed a variable that enumerated the number of surface passage
structures (e.g., removable spillway weirs [RSWs] or temporary spillway weirs [TSWs])
in place over the years of observation.
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where  0 ,  1 ,...,  n are estimated parameters used to describe the relationship between
45
environmental variables X1, X2,…, Xn and log(FTT), and  i ~ N (0,  2 ) . In preliminary
Variable selection and model building
We used linear regression techniques to evaluate the associations between the
environmental variables and mean FTT and instantaneous mortality (Z). We used
Akaike’s Information Criterion adjusted for small sample sizes (AICc) for evaluating
model fit and variable selection. As mentioned above, Box-Cox power transformations
indicated that a log-transformation was most appropriate for the FTT data. Therefore we
modeled log(FTT) as the dependent variable in all analyses. The loge transformations
were also implemented to help reduce heteroscedasticity. These regressions were of the
form:
log( FTˆTi )   0   1  X 1,i   2  X 2 ,i  ...   i ,
[3.6]
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analyses we also utilized Box-Cox power transformations to examine whether the Ẑ i
should be transformed. These preliminary analyses indicated that a square-root
transformation was most appropriate, therefore we proceeded to conduct the regressions
using sqrt ( Zˆ i ) as the dependent variable. These regressions were of the form:
sqrt ( Zˆ )      X    X  ...   ,
[3.7]
6
where  0 ,  1 ,...,  n are estimated parameters used to describe the relationship between
7
environmental variables X1, X2,…, Xn and sqrt(Z), and  i ~ N (0,  2 ) . Because there
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i
1
1 ,i
2
i
2 ,i
were large differences in the precision of the Ẑ i , we used inverse-variance weighting in
the fitting process for modeling instantaneous mortality rates. In addition, there was
considerable model selection uncertainty (i.e., multiple models fitting the data similarly
well) in the models for Ẑ i in the cases of sockeye in the LGR-MCN reach and both
Chinook and steelhead in the MCN-BON reach. In these cases, we used model-averaged
predictions for the Ẑ i (Burnham and Anderson 2002) to account for the model selection
uncertainty.
Survival modeling approach
Our approach for modeling survival rates utilized the exponential mortality model
(Eqn. 3.1), allowing the predicted instantaneous mortality rates Zi and the mean FTTi ' s
to vary in response to environmental factors. Using our best-fit models for predicting
Z *i and FTT *i (Eqns. 3.6 and 3.7), predicted survival rates were estimated as:
*
*
S *i  e  Z i FTT i ,
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0
where Z
*
i
is the predicted instantaneous mortality rate, FTT
[3.8]
*
i
is the predicted mean
*
i
24
FTTi, and S is the predicted survival rate for period i, calculated by exponentiating the
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negative product of Z *i and FTT *i .
Results
35
ˆ , Zˆ and Sˆ of cohorts of juvenile yearling Chinook,
Estimates of mean FTT
i
i
i
steelhead and seasonal estimates of sockeye along with predicted values for these
parameters are shown in Figures 3.1, 3.3, and 3.5 (LGR-MCN reach) and Figures 3.2,
ˆ , Zˆ and Sˆ varied considerably over the
3.4, and 3.6 (MCN-BON reach). Mean FTT
i
i
i
period of 1998-2009 in the LGR-MCN each, both within- and across-years (Figures 3.1,
ˆ generally decreased over the
3.3, 3.5). While there were some special cases, mean FTT
i
ˆ
season, S either increased or decreased over the season, and Zˆ increased over the
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season. Within-year estimates of Sî varied by up to 39 percentage points for both wild
Chinook and steelhead, and by up to 32 percentage points for hatchery Chinook. Across
all years and cohorts, estimates of Sî varied by up to 64 percentage points for Chinook
i
i
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and 76 percentage points for steelhead. The large within- and across-year variation in Sî
demonstrates a high degree of contrast in Sˆ over this 1998-2009 timeframe.
i
In the MCN-BON reach, cohorts of yearling Chinook and steelhead demonstrated
ˆ , Zˆ and Sˆ patterns similar to those observed in the LGR-MCN
within-year mean FTT
i
i
i
reach, varying considerably both within- and across-years (Figures 3.2, 3.4, and 3.6). For
ˆ , generally decreased over the migration season. Yearling
both species, mean FTT
i
ˆ , ranging
Chinook in 2001 demonstrated the largest within-year variation in mean FTT
i
from 22 days early in the season to 8 days late in the season (Figure 3.2). Due to
imprecision in the estimates of Sî , general patterns in the estimates of Sî and Zî in the
MCN-BON reach were difficult to discern (Figures 3.4 and 3.6). For both Chinook and
steelhead, Zî generally increased over the season. Steelhead Sî generally decreased over
the season, but no general patterns were evident for Chinook Sˆ .
i
The best fitting models (based on AICc) for mean FTT consistently had model
forms with Julian day, water transit time and spill. The signs of the model coefficients
for these variables indicated that juvenile Chinook, steelhead and sockeye all migrated
faster as water velocity increased (i.e., WTT was reduced) and as spill percentages
increased. Juvenile Chinook and steelhead also migrated faster as the season progressed.
Because we were not able to develop within-season estimates of FTT for sockeye, we
were not able to determine whether sockeye share similar increases in migration speed as
Julian day increases. For steelhead in the LGR-MCN reach and the MCN-BON reach,
we observed a significant effect of the number of surface passage structures in place on
FTT, with the increasing number of surface passage structures at Little Goose, Lower
Monumental, Ice Harbor and John Day dams reducing steelhead FTTs. We also
identified a significant effect (P < 0.001) of the percentage of hatchery steelhead in the
LGR-MCN reach, with hatchery steelhead taking two days longer on average to migrate
through the LGR-MCN reach than wild steelhead. The models that were developed for
all species captured a very high degree of the variation in mean FTT of all species (Table
3.1). The best fitting model (based on AICc) for sockeye FTT contained only spill.
The best fitting models (based on AICc) for Z also had model forms primarily
with Julian day, water transit time and spill. For steelhead in the LGR-MCN reach, the
lowest AICc model contained Julian day, spill and the number of surface passage
structures, with Z predicted to increase with Julian day and Z predicted to decrease as
percent spill increased or the number of surface passage structures increased. For wild
Chinook in the LGR-MCN reach, the lowest AICc model contained Julian day, WTT, an
interaction between Julian day and WTT, and the number of surface passage structures,
with Z predicted to increase with Julian day or with increases in WTT and Z predicted to
decrease as the number of surface passage structures increased. For hatchery Chinook in
the LGR-MCN reach, the lowest AICc model contained Julian day and spill, with Z
predicted to increase with Julian day and Z predicted to decrease as spill increases. The
lowest AICc model for sockeye in the LGR-MCN reach contained only WTT, with Z
predicted to increase as WTT increases. For combined hatchery and wild Chinook in the
MCN-BON reach, the lowest AICc model contained Julian day and WTT, with Z
predicted to increase with Julian day and with increases in WTT. For combined hatchery
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and wild steelhead in the MCN-BON reach, the lowest AICc model contained only
temperature, with Z predicted to increase as water temperatures increase. However, the
survival estimates for steelhead in the MCN-BON reach were the least precise among
those species-reach combinations that we examined, so some caution is warranted in
judging the relative importance of temperature versus other factors for steelhead in this
reach.
Combining the models for predicting mean FTT and Z resulted in generally high
accuracy in predicting reach survival rates for the species-reach combinations that we
examined (Table 3.1). As mentioned above, the models developed for FTT explained a
very high proportion of the observed variation in FTT. Although the models for Z
explained a lower proportion of the variability in Z, when the models for FTT and Z were
combined to make predictions for survival, a relatively high proportion of the variation
was captured. These results show that the models developed by the CSS are effective for
characterizing and understanding sources of variation in the migration rates, mortality
rates and survival rates of Chinook, steelhead and sockeye.
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Figure 3.1 Estimates of mean FTT (in days, blue squares) and predicted mean FTT (yellow circles)
for weekly release groups of wild Chinook (upper panel), hatchery Chinook (second panel),
combined hatchery and wild steelhead (third panel) and seasonal estimates of combined hatchery
and wild sockeye (fourth panel) in the LGR-MCN reach, 1998-2009. Error bars represent the 95%
confidence limits on the mean FTT.
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Figure 3.2 Estimates of mean FTT (in days, blue squares) and predicted mean FTT (yellow circles)
for weekly release groups of combined hatchery and wild Chinook (upper panel) and combined
hatchery and wild steelhead (lower panel) in the MCN-BON reach, 1999-2009. Error bars represent
the 95% confidence limits on the mean FTT.
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Figure 3.3 Estimates of instantaneous mortality rates, Z (d-1, blue squares), and predicted Z (yellow
circles) for weekly release groups of wild Chinook (upper panel), hatchery Chinook (second panel)
combined hatchery and wild steelhead (third panel) and seasonal estimates of combined hatchery
and wild sockeye (fourth panel) in the LGR-MCN reach, 1998-2009. Error bars represent the 95%
confidence limits on Z.
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Figure 3.4 Estimates of instantaneous mortality rates, Z (d-1, blue squares) and predicted Z (yellow
circles) for two-week release groups of combined hatchery and wild Chinook (upper panel) and for
three-week release groups of combined hatchery and wild steelhead (lower panel) in the MCN-BON
reach, 1999-2009. Error bars represent the 95% confidence limits on Z.
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Figure 3.5 Estimates of in-river survival rates(blue squares) and predicted survival rates (yellow
circles) for weekly release groups of wild Chinook (upper panel), hatchery Chinook (second panel)
combined hatchery and wild steelhead (third panel) and seasonal estimates of survival for combined
hatchery and wild sockeye in the LGR-MCN reach, 1998-2009. Error bars represent the 95%
confidence limits on the survival rates.
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Figure 3.6 Estimates of in-river survival rates (blue squares) and predicted survival rates (yellow
circles) for two-week release groups of combined hatchery and wild Chinook (upper panel) and for
three-week release groups of combined hatchery and wild steelhead (lower panel) in the MCN-BON
reach, 1999-2009. Error bars represent the 95% confidence limits on the survival rates.
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Table 3.1 Proportions of variation explained (r2 values) in relationships characterizing Chinook,
steelhead and sockeye mean FTT, instantaneous mortality rates (Z) and in-river survival rates within
the LGR-MCN reach and the MCN-BON reach.
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Reach
LGR-MCN
LGR-MCN
LGR-MCN
LGR-MCN
Species &
Rearing Type
CHN (W)
CHN (H)
STH (H&W)
SOX (H&W)
MCN-BON
MCN-BON
CHN (H&W)
STH (H&W)
mean FTT
0.84
0.83
0.92
0.65
Z
0.43
0.28
0.49
0.35
Survival
0.55
0.41
0.79
0.68
0.96
0.92
0.15
0.55
0.25
0.73
Discussion
In this analysis we provided an extensive synthesis of the patterns of variation in
juvenile yearling Chinook, steelhead and sockeye fish travel time and survival within the
hydrosystem. In addition to these commonly-used metrics of fish travel time and
survival, we also developed and reported estimates of instantaneous mortality rates, along
with estimates of precision for those rates. We observed substantial variation in mean
fish travel time, survival, and instantaneous mortality rates both within- and across-years.
The models that were developed for characterizing the effects of various environmental
and management factors on mean fish travel times, survival rates, and instantaneous
mortality rates capitalized on this variation and demonstrated a high degree of accuracy.
We see these models as powerful tools for continued development, evaluation,
and refinement of alternative hypotheses on the effects of various environmental and
management factors on smolt survival and migration rates. Particularly in the MCNBON reach, we found that estimates of survival have substantial uncertainty. As a result,
estimates of instantaneous mortality rates in this reach also have substantial uncertainty.
Although we were able to develop models that explained a substantial proportion (2573%) of the variation in MCN-BON survival rates, questions remain as to which factors
are primarily important for determining survival in the lower river. We see the only way
to resolve the remaining questions is to invest in more PIT-tagging efforts for reducing
the uncertainty in the lower reach.
We believe that the models developed here provide some useful tools for
predicting the effects of alternative hydrosystem management actions. Some of these
could include changes in water volume, volume shaping/timing, spill levels and timing,
or changes in reservoir elevations. At a minimum, these models provide a basis for
hypothesis development for use in adaptive management experiments on the
hydrosystem.
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Chapter 4
Annual SAR by Study Category, TIR, and D for Snake River Hatchery
and Wild Spring/Summer Chinook Salmon and Steelhead:
Patterns and Significance
This chapter presents smolt-to-adult survival rate (SAR) estimates for the
spring/summer Chinook and summer steelhead PIT-tagged smolts analyzed in the CSS. A
primary focus of comparisons is between the transported and in-river smolt migrants.
Parameters estimated include (i) annual SAR from LGR to GRA (LGR’s adult ladder) by
study category (transported smolts [T0 or TX beginning 2006], in-river migrants not
detected at a Snake River transportation site [C0], and in-river migrants with at least one
detection at a Snake River transportation site [C1]), (ii) TIR (ratio of SAR of transported
to SAR of C0 migrants), and (iii) D (ratio of post-Bonneville transported SAR to SAR of
C0 migrants). Parameters are estimated for PIT-tagged wild Chinook (1994-2008),
hatchery Chinook (1997-2008), and wild and hatchery steelhead (1997-2007).
Three series of tables previously placed in report appendices will be made
available from the FPC Website at www.fpc.org. These appendices have become
voluminous and difficult to use. The data in these tables was placed on the FPC website
so that the data could be easily accessed by users. The data can be downloaded in a
format amenable to analyses by interested users. These tables include (i) the juvenile
migrants reach survival rates, (ii) adult return composition, and (iii) numbers of smolts in
the CSS study categories. Data for (i) to (iii) are accessed as follows:
(i)
On FPC homepage, click on “SURVIVAL DATA => JUVENILES =>
CSS REACH SURVIVAL DATA” to access the individual reach survival
estimates used to expand PIT-tag smolt counts in the three study
categories to LGR equivalents for each migration year (note: 2006 to be
updated and data for 2007 to 2009 added during review period).
(ii)
On FPC homepage, click on “SURVIVAL DATA => SMOLT-TOADULT => CSS RETURNING ADULT AGE COMPOSITION” to
access the number of 1-salt and older returning adults for each PIT-tagged
CSS group (note: 2006 to be updated and returns for smolt migration years
2007 [Chinook and steelhead] and 2008 [Chinook only] to be added
during review period).
(iii)
On FPC homepage, click on “SURVIVAL DATA => SMOLT-TOADULT => NUMBER OF SMOLTS AND RETURNING ADULTS BY
CSS STUDY CATEGORY” to access the estimated number of smolts and
returning adults in each study category (T0 or TX beginning 2006, C0, and
C1), and the estimated population of tagged fish arriving LGR, along with
a bootstrapped 90% confidence interval around each estimate (note: 2006
to be updated and 2007 [Chinook and steelhead] and 2008 [Chinook only]
to be added during review period).
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Methods
Estimation of smolt numbers in study categories
Comparisons between SARs for groups of smolts with different hydrosystem
experiences are made from a common start and end point. Thus, LGR-to-GRA SARs
were estimated for all groups of smolts including those not detected at LGR as juveniles.
The population of PIT-tagged study fish arriving at LGR was partitioned into three
pathways related to the route of subsequent passage through the hydrosystem. Fish were
“destined” to 1) pass in-river through the Snake River collector dams in a non-bypass
channel route (spillways or turbines), 2) pass in-river through the dam’s bypass channel,
or 3) pass in a truck or barge to below BON. These three routes of hydrosystem passage
defined the study categories C0, C1 and T0 (or TX beginning 2006), respectively.
The Snake River basin fish used in SAR estimation were PIT-tagged and released
in tributaries and mainstem locations upstream from LGR reservoir. Other investigators
(Sanford and Smith 2002; Paulsen and Fisher 2005; Budy and Schaller 2007) have used
detection information from smolts released both above LGR and at LGR for their
estimates of SARs. Because all Snake River spring/summer Chinook must pass through
LGR reservoir, we believe that smolts released upstream from LGR most closely reflect
the impacts of the Lower Snake and Columbia River hydrosystem on the untagged runat-large in-river migrating fish. The C0 group may only include smolts released above
LGR, since it is defined as those fish that remained in-river while migrating past the three
Snake River collector dams undetected. Fish collected and marked at LGR do not have a
similar experience. Additionally, the documented bias in SARs (i.e., reduction in
estimated survival rates) for groups marked at LGR is another reason for only using PITtagged fish released upstream of LGR in SAR calculations for this analysis.
Pre-2006 migration years
The PIT-tagged study groups should mimic the experience of the non-tagged fish
that they represent. For migration years prior to 2006, only first-time detected tagged
smolts at a dam are considered for inclusion in the transportation (T0) group since nontagged smolts were nearly always transported when they entered a bypass/collector
facility (where PIT-tag detectors are in operation) at a Snake River dam. Prior to 2006,
smolts that were returned to river at LGR, LGS, and LMN were primarily PIT tagged
study fish. Typically during these years, most of the transported smolts were from LGR
with the remainders be transported from LGS and LMN. Because some smolts died
while migrating in-river from LGR to either LGS or LMN, the numbers transported at
LGS and LMN were divided by their survival from LGR to transportation site.
Therefore, an estimated survival rate was needed to convert actual transport numbers at
LGS and LMN into their LGR equivalents starting number. The PIT-tagged fish destined
for transportation at LGR, LGS, and LMN together formed Category T0. Using the
definitions presented in the following text box, the formula for estimating the number of
fish in Category T0 is:
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T0  X 12 
X 102
X
 1002
S2
S 2  S3
[4.1]
Symbol Definitions:
R1 = number of PIT-tagged fish released
X12 = number of smolts transported at LGR
X102 = number of first-detected smolts transported at LGS
X112 = number of LGR bypassed smolts transported at LGS
X1002 = number of first-detected smolts transported at LMN
X1102 = number of LGR bypassed smolts transported at LMN
X1012 = number of LGS bypassed smolts transported at LMN
X1112 = number of both LGR and LGS bypassed smolts transported at LMN
S1 = estimated survival from hatchery release site to LGR tailrace
S2 = estimated survival from LGR tailrace to LGS tailrace
S3 = estimated survival from LGS tailrace to LMN tailrace
S4 = estimated survival from LMN tailrace to MCN tailrace
S3 = estimated survival from MCN tailrace to JDA tailrace
S3 = estimated survival from JDA tailrace to BON tailrace
P2 = estimated detection probability at LGR
P3 = estimated detection probability at LGS
P4 = estimated detection probability at LMN
P5 = estimated detection probability at MCN
P6 = estimated detection probability at JDA
P7 = estimated detection probability at BON
m12 = number of fish first detected at LGR
m13 = number of fish first detected at LGS
m14 = number of fish first detected at LMN
d2 = number of fish removed at LGR (includes all transported fish, site-specific mortalities,
unknown disposition fish, and fish removed for use by other research studies)
d3 = number of fish removed at LGS (includes all transported fish, site-specific mortalities, and
unknown disposition fish)
d4 = number of fish removed at LMN (includes all transported fish, site-specific mortalities,
unknown disposition fish, and fish removed for use by other research studies)
d0 = site-specific removals at dams below LMN of fish not detected previously at a Snake River
Dam estimated in LGR-equivalents. Pre-2003 uses fixed expansion rate of 50% survival rate for
all removals below LMN. Beginning with migration year 2003, d0 contains site-specific removals
below that have been expanded by their corresponding estimated survival rate from LGR.
d5.0 = removals of C0 type fish at MCN
d6.0 = removals of C0 type fish at JDA
d7.0 = removals of C0 type fish at BON
d1 = site-specific removals at dams below LMN of fish previously detected at a Snake River Dam
estimated in LGR-equivalents. Pre-2003 uses fixed expansion rate of 50% survival rate for all
removals below LMN. Beginning with migration year 2003, d1 contains site-specific removals
below that have been expanded by their corresponding estimated survival rate from LGR.
d5.1 = removals of C1 type fish at MCN
d6.1 = removals of C1 type fish at JDA
d7.1 = removals of C1 type fish at BON
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The PIT-tagged smolts that passed all Snake River dams undetected (C0) were the
group most representative of the non-tagged smolts that migrated in-river during the
years prior to 2006, since the C0 group never entered collection facilities at collector
dams. Detected PIT-tagged smolts were not representative because they do enter these
facilities, and because non-tagged fish that entered a detection/collection facility were
normally removed for transportation. The starting number of C0 fish was also computed
in LGR equivalents, and therefore required estimates of survival. To estimate the number
of smolts that were not detected at any of the collector projects (C0), the number of
smolts first detected (transported and non-transported) at LGR, LGS, and LMN (in LGR
equivalents) was subtracted from the total number of smolts estimated to arrive at LGR.
The number of smolts arriving at LGR was estimated by multiplying the release to LGR
survival rate (S1) and release number (R1) (or equivalently, dividing the number of smolts
detected at LGR [m12] by the CJS estimate of seasonal LGR detection probability p2)
specific for the smolt group of interest.
Smolts detected at MCN, JDA, and BON were not excluded from the C0 group
since fish entering the bypass facilities at these projects, both tagged and untagged, were
generally returned to the river. However, any removal of fish at sites below LMN had to
be taken into account. Using symbols defined in the text box, the formula for estimating
the number of fish in Category C0 is:

m
m14 
C0  R * S1   m12  13 
  d0
S
S
S
*
2
2
3 

where, for migration years 1994-2002,
 (d  d 6.0  d 7.0 ) 
d 0   5.0

0.5


and beginning in 2003,


d5.0
d 6.0
d 7.0
d0  



 S 2 * S3 * S 4 S 2 * S3 * S 4 * S5 S 2 * S3 * S 4 * S 5 * S 6 
[4.2]
.
The last group of interest was comprised of fish that were detected at one or more
Snake River dams and remained in-river below LMN. These PIT-tagged fish formed
Category C1. Prior to 2006, the C1 category existed primarily because a portion of the
PIT-tagged smolts entering the detection/collection facility are returned to the river so
reach survival estimates are possible. Although these fish do not mimic the general
untagged population, they are of interest with regards to possible effects on subsequent
survival of passing through Snake River dam bypass/collection systems (see Chapter 7),
and in investigating non-transport operations. Using symbols defined in the text box, the
formula for estimating the number of fish in Category C1 is:
 (m  d )   (m  d 4 ) 
C1   m12  d 2    13 3    14
  d1
S2

  S 2 * S3 
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[4.3]
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where, for migration years 1994-2002,
 (d  d  d ) 
d1   5.1 6.1 7.1 
0.5


and, beginning in 2003,


d5.1
d 6.1
d 7.1
d1  



 S 2 * S3 * S 4 S 2 * S3 * S 4 * S5 S 2 * S3 * S 4 * S5 * S 6 
.
A combination of exceptionally low in-river survival and no-spill hydrosystem
operations maximized the transportation of smolts in 2001 and resulted in very few
estimated Category C0 migrants. Furthermore, the C0 smolts that did exist passed mostly
through turbines without the opportunity to pass via spill as in prior years. Obtaining a
valid estimate of the number of PIT-tagged wild and hatchery steelhead in Category C0 in
2001 was also problematic due to the apparently large amount of residualism that year
(Berggren et al. 2005a). Most in-river steelhead migrants that returned as adults were
actually detected as smolts in the lower river in 2002 (details in CSS 10-yr Retrospective
Analysis Report). Returning adults of steelhead and Chinook that had no detections were
more likely to have either completed their smolt migration in 2002 or passed undetected
into the raceways during a computer outage in mid-May at LGR than to have traversed
the entire hydrosystem undetected in 2001. Because of the uncertainty in passage route
and the timing of the undetected PIT-tagged migrants in 2001, the C1 group was the only
viable in-river group for estimation purposes. Due to these conditions, C1 data were used
instead of C0 data in the computation of SAR, TIR, and D parameters (described below)
and therefore are presented separately for comparison to other years in the multi-year
geometric averages computed for SR, TIR, and D.
The C0 and C1 groups were combined in two additional migration years. Spills
were lower in migration years 2004 and 2005 than previous years at both LGR and LGS
(excluding 2001), resulting in high collection efficiency at those two dams and a lower
than usual percentage of PIT-tagged smolts estimated to pass the three collector dams on
the Snake River undetected (C0 migrants). In 2004, >6% of the LGR population of wild
and hatchery Chinook PIT-tagged smolts were in Category C0. Only 2.3% of the
hatchery steelhead and 2.6% of the wild steelhead were in Category C0. In 2005, 4.0%
of the wild Chinook LGR population, 4.9 – 7.9% of the five CSS hatchery Chinook
groups, 1.8% of the hatchery steelhead, and 1.4% of the wild steelhead were in the CO
category. When the estimated number of C0 PIT-tagged smolts is extremely low,
attempting to estimate SAR(C0) is problematic since few or no adult returns will result in
unreliable SAR estimates with large confidence intervals. Therefore, we combined the
estimated C0 and C1 smolt numbers for PIT-tagged steelhead in 2004 and both Chinook
and steelhead in 2005 in order to create a larger in-river group for estimating SARs, TIR,
and D.
Migration years 2006 and later
In 2006, the protocol for transportation operations was altered by delaying the
start date of transportation at LGR, LGS, and LMN (see Appendix C for dates). The goal
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of this change in protocol was to improve the overall SARs by allowing more early runat-large migrants to outmigrate entirely in-river when transport SARs have tended to low
(NOAA 2008). Additionally, spill percentages at the Snake River transportation projects
during 2006-2008 were consistently higher than many previous years (see Figure 1.4).
Also in 2006 the CSS began randomly pre-assigning PIT-tagged wild and
hatchery Chinook and wild steelhead smolts into monitor-mode (Group T) and return-toriver mode (Group R) operations. In this chapter, the total release, which is the
combination of T and R groups, is designated as Group CRT. Group T follows the same
fate as the run at large through-out the hydrosystem, while Group R followed a default
return to river action at the transportation dams. With a delayed transportation initiation
during these years, two new smolt experiences are developed. First, in regards to the
transportation study group, the combination of both first-time detected (T0) and priordetected transported smolts obtained from Group T represent the transported fish from
the run at large (referred to as TX). Additionally, the transported fish (TX) only occur
over a particular temporal window of the smolt outmigration. The portion of the run that
this window includes depends on the intersection of the start date of transportation and
timing for the run at large from a particular study group (e.g. Dworshak hatchery
Chinook, or wild Snake River steelhead). Secondly, the C1 group (detected and returned
to river) now represents the portion of the run at large that out-migrates before
transportation started whereas in years before 2006, this group represented a very small
portion of the actual run at large (see discussion of C1 group in previous section). One
advantage of the pre-assignment approach, when calculating an overall SAR, is that these
relationships are automatically encapsulated and proper weighted within Group T since
they “follow the fate” of the run at large. Pre-assignment of the PIT-tagged hatchery
steelhead began in 2008, so methods described in previous section applies to the 2006
and 2007 PIT-tagged hatchery steelhead aggregate. Parameters may have suffixes of “t”,
“r”, or “crt” for groups T, R, and CRT attached whenever necessary to avoid confusion
on which group is being used to create the parameter estimate. The formula for
estimating the number of PIT-tagged smolts in Group T in Category TX is:
TX_t = X12 + X1A2 / S2 + X1AA2 / (S2*S3)
[4.4]
where A = 0 if undetected and 1 if detected at a dam prior to the transportation site.
Since the reach survival rates and collection probabilities are computed using
Group CRT, we may still use Equation 4.2 for estimating number of PIT-tagged smolts in
Category C0. It is not necessary to limit our use to Group T fish when estimating C0,
since the pre-assignment affects only the passage routes of detected smolts. By using
Group CRT, we have access to more PIT-tagged C0 smolts and returning adults for
computing the SAR(C0) estimate.
C0_crt = “see Equation 4.2”
However, when estimating C0 or C1 smolt numbers in either Group T or Group R,
expectation equations should be used. This is because the computation of C0 and C1
smolt numbers with the m-matrix parameters m12, m13, and m14 is sensitive to the
estimated reach survival rates being used. Reach survival rates are estimated using
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Group CRT. Groups T and R are subsets of Group CRT. The magnitudes of m12, m13,
and m14 relative to the release number R1 may vary slightly across groups T and R due to
sampling variability, resulting in shifts in the proportion of C0 and C1 smolts estimated
for each of the two groups. This is not the case when E[C0] and E[C1] equations (shown
below) are used, since the same set of reach survival rates and collection probabilities
generated with Group CRT are passed to groups T and R for use in estimating key study
parameters. Since the random pre-assignment action (bypass or transport) occurs after
collection, the same collection probability should apply to both groups and survival
estimates should be applicable to either group while it is in-river. The reach survival rates
Sj's and collection probabilities Pj's computed with Group CRT are passed to Groups T
and R, while the parameters R1, X12, X1A2, X1AA2, and C1 removals (d1, d2, d3, d4) and C0
removals (d0) are specific to the respective group.
Therefore, when estimating the proportion of Group T smolts by passage
experience as in Appendix C or comparing SARs of C1 smolts bypassed over the entire
season (Group R) with C0 smolts (Group CRT) as in the meta analysis of Chapter 7, we
use the following expectation formulas. For estimating the expected C0 smolt numbers
E[C0]_t and E[C0]_crt, where known removal d0 is a constant, the equation is:
where
E[C0] = R1•S1•(1-P2)•(1-P3)•(1-P4) – d0
[4.5]


d5.0
d 6.0
d 7.0
d0  



 S 2 * S3 * S 4 S 2 * S3 * S 4 * S5 S 2 * S3 * S 4 * S 5 * S 6 
For estimating the expected C1 smolt numbers E(C1)_t and E(C1)_r, where known
removals d1, d2, d3, and d4 are constants, the equation is obtained by re-arranging terms in
Equation 4.3,
where
C1 = [m12 + m13/S2 + m14/(S2•S3)] – [d2 + d3/S2 + d4/(S2•S3) + d1]


d5.1
d 6.1
d 7.1
d1  



 S 2 * S3 * S 4 S 2 * S3 * S 4 * S5 S 2 * S3 * S 4 * S5 * S 6 
and substituting the following expectations for m12, m13, and m14
to yield:
E[m12] = R1•S1•P2
E[m12] = R1•S1•[(1-P2)•S2•P3]
E[m12] = R1•S1•[(1-P2)•S2•(1-P3)•S3•P4]
E[C1] = R1•S1•[P2 + (1-P2)•P3 + (1-P2)•(1-P3)•P4]
– [(d2 + d3/S2 + d4/(S2•S3) + d1]
Estimation of SARs and Ratios of SARs for Study Categories
[4.6]
LGR is the primary upriver evaluation site for most objectives of the CSS. Adults
detected at GRA (LGR’s adult ladder) were assigned to a particular study category based
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on the study category they belonged to as a smolt (fish with no previous detections at any
dam were automatically assigned to Category C0). In the SAR estimation, the adult
steelhead count is the sum of the 1 to 3-ocean returns (mini-jacks returning in the same
year as their smolt outmigration are excluded). The adult Chinook count is the sum of
the 2 to 4-ocean returns. Chinook jacks and mini-jacks (1-ocean or less, precocious
males) are excluded from SARs due to the limited contribution to spawning of these age
classes.
SARs are calculated by study category with the adult tally in the numerator and
estimated smolt numbers in denominator. Prior to 2006 (2008 for hatchery steelhead)
when there was no pre-assignment of CSS study fish to Groups T and R, the formulas
are:
SAR T0  
 ATLGR  ATLGS  ATLMN 
SAR  C0  
SAR  C1  
[4.7]
 AC0 
C0
 AC1
C1
[4.8]
[4.9]
For migration years 2006 and later, the adult counts (i.e. ATLGR, ATLGS, ATLMN)
include both first time detects and previous detected fish. The abbreviated capture
histories for the smolt outmigration experience of adults from the TX group (using a ‘1’
for a single release followed by a 1,0, or 2 to denote bypass, undetected, or transported at
LGR, LGS, or LMN) would be 12, 102, 1002, 12, 102, 112, 1002, 1012, 1102, or 1112.
Using the pre-assigned fish in Group T, the equation for SAR(TX_t) is:
SAR(TX_t) = {ATLGR_t + ATLGS_t + ATLMN_t } / TX_t
[4.10]
Using the total release, the formula for SAR(C0_crt) is:
SAR(C0_crt) = {AC0_crt} / C0_crt
[4.11]
Using the pre-assigned fish in Group T, the equations for SAR[EC1_t] is:
SAR[EC1_t] = {AC1_t} / E[C1_t]
[4.12]
The difference between SAR(T0) (or SAR(TX_t) beginning 2006) and SAR(C0) is
characterized as the ratio of these SARs and denoted as the TIR (transport: in-river ratio):
TIR 
39
T0
SAR T0 
SAR  C0 
73
[4.13]
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
The statistical test of whether SAR(T0) (or SAR(TX_t) beginning 2006) is
significantly different than SAR(C0) is conducted by evaluating whether TIR differs from
one. We use the criteria that the non-parametric 90% confidence interval’s lower limit of
TIR must exceed 1 or its upper limit must be less than 1. This provides a statistical twotailed (α=0.10) test of H0 TIR = 1 versus HA TIR ≠1.
Estimation of D
The parameter used to evaluate the differential delayed effects of transportation in
relation to in-river outmigrants is D. D is the ratio of SARs of transported smolts (T0)
and in-river outmigrants (C0), but unlike TIR, the SAR is estimated from BON instead of
from LGR. If the value of D is around 1, there is little or no differential mortality
occurring between transported and in-river migrating smolts once they are both below
BON. The estimate of D (substituting TX for T0 for migration years 2006 and later) is:
D
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
SARBON  LGR T0 
SARBON  LGR  C0 
[4.14]
The total number of smolts passing BON is not observed directly. However, D
can be estimated by removing the portion of the LGR-to-GRA SAR that contains the
LGR to BON juvenile hydrosystem survival. So, the parameters ST and SR were divided
out of their respective LGR-to-GRA SAR values to estimate the SARBON-LGR for each
study group shown in Equation 4.14. The resulting estimate of D (substituting TX for T0
for migration years 2006 and later) was calculated as:
 SAR T0  


ST


D
 SAR  C0  


SR


[4.15]
where SR is the estimated in-river survival from LGR tailrace to BON tailrace and ST is
the assumed direct transportation survival rate (0.98) adjusted for in-river survival to the
respective transportation sites for those fish transported from LGS or LMN.
In the denominator of D (in-river portion), the quotient is simply SAR(C0)/ SR,
where SR is estimated using CJS estimates (expanded to the entire hydro system if
necessary). Errors in estimates of SR influenced the accuracy of D estimates: recall that
when it was not possible to estimate SR directly, an expansion based on a “per mile”
survival rate obtained from an upstream reach (where survival could be directly
estimated) was instead applied to the remaining downstream reach.
In the numerator of D (transportation portion), the quotient is SAR(T0)/ST, where
ST is a weighted harmonic mean estimate of the in-river survival rate between LGR
tailrace and downstream Snake River transportation sites for the estimated projectspecific proportion of the transported run-at-large at these two downstream transportation
74
1
2
3
4
5
sites. Calculation of ST includes an estimate of survival to each transportation site,
effectively putting ST into LGR equivalents similar to SAR(T0), with a fixed 98%
survival rate for the fish once they were placed into the transportation vehicle (truck or
barge). The ST estimate for years prior to 2006 is:
ST   0.98  *
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
 t 2  t3  t 4 

t3
t4 
 t2  

S 2 S 2 * S3 

[4.16]
where tj is the estimate of the fraction of PIT-tagged fish that would have been
transported at each dam (e.g., t2 = LGR, t3 = LGS, and t4 = LMN) if all PIT-tagged fish
had been routed to transport at the same rate as the run-at-large (i.e., untagged fish).
Beginning in 2006 with pre-assignment to Group T for all PIT-tagged fish groups
except hatchery steelhead, the values for tj were obtained directly using Group T for the
number of PIT-tagged smolts (X) with the following capture histories (shown in
subscript): t2 = X12, t3 = X1A2, and t4 = X1AA2. Since the routing of the PIT-tagged
hatchery steelhead was in the same proportion at each collector dam, the values for tj
were obtained directly with the total release for the above capture histories. Using this
approach for all PIT-tagged groups properly accounted for the effect of the later start of
transportation in years beginning in 2006. The ST estimate for years 2006 and later is:
ST = (0.98)[(X12+X1A2+ X1AA2)/(X12+X1A2/S2+ X1AA2/(S2•S3)]
[4.17]
The estimates of ST have ranged between 0.88 and 0.98 for Chinook and steelhead across
all the years evaluated.
A statistical test of whether D is significantly greater or less than 1 was conducted
in the same manner as was done with TIR. We use the criteria that the non-parametric
90% confidence interval’s lower limit of D must exceed 1 or its upper limit must be less
than 1. This provides a statistical two-tailed (α=0.10) test of H0 D = 1 versus HA D ≠1.
75
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
Results
Estimates of SAR by Study Category
The PIT-tagged wild Chinook aggregate LGR-to-GRA SAR estimates by study
category over the 15-year time span from 1994 to 2008 have exceeded 2% in only 4 years
for C0 fish, 2 years for T0 (or TX beginning 2006) fish, and 1 year for C1 fish (Figure 4.1
and Table 4.1). Therefore, wild Chinook SARs have remained far below those
recommended to maintain a stable population (2%) or to achieve recovery (4%;
Marmorek et al. 1998) over this 15-year period. The estimated SARs were exceptionally
low (< 0.6%) during the two periods 1994 to 1996 and 2003 to 2005 in all three
categories and also in 2001 for in-river migrants. On a positive note, the trend in SARs
since 2005 has been increasing, with the available 2-salt return of the 2008 migrants
approaching the highs not seen since 1999 and 2000.
Figure 4.1 Estimated LGR-to-GRA SAR for PIT-tagged wild Chinook aggregate in transport (T0 or
TX beginning 2006) and in-river (C0 and C1) study categories for migration years 1994 to 2008
(incomplete adult returns for 2008). The transport SAR(TX) after 2005 is a partial year metric
because of the delay in transportation start date (shaded area). For 2001 and 2005, only 1 in-river
SAR was calculated (see methods). Data from Table 4.1.
76
1
Table 4.1 Estimated LGR-to-GRA SAR (%) for PIT-tagged wild Chinook in annual aggregate for
each study category from 1994 to 2008 (with 90% confidence intervals). The transport SAR(TX)
after 2005 is a partial year metric because of the delay in transportation start date.
Mig. Year
1994
1995
1996
1997
1998
1999
2000
2001
2002
2003
2004
2005
Monitormode yrsB
SAR(T0) %
0.45
0.35
0.50
1.74
1.18
2.43
1.43
1.28
0.80
0.34
0.53
0.23
(0.20 – 0.72)
(0.17 – 0.57)
(0.00 – 1.07)
(0.44 – 3.27)
(0.71 – 1.70)
(1.85 – 3.07)
(0.74 – 2.14)
(0.54 – 2.14)
(0.57 – 1.04)
(0.24 – 0.45)
(0.42 – 0.63)
(0.17 – 0.29)
SAR(TX)_t %
SAR(C0) %
0.28 (0.11 – 0.51)
0.37 (0.18 – 0.57)
0.26 (0.10 – 0.48)
2.35 (1.45 – 3.36)
1.36 (1.05 – 1.70)
2.13 (1.78 – 2.50)
2.39 (2.08 – 2.72)
Assume = SAR(C1)
1.22 (0.99 – 1.45)
0.33 (0.23 – 0.43)
0.49 (0.26 – 0.74)
0.11 A
SAR(C0)_crt %
SAR(C1) %
0.07
0.25
0.13
0.93
1.07
1.89
2.33
0.14
0.99
0.17
0.22
(0.07 – 0.15)
(0.02 – 0.14)
(0.18 – 0.32)
(0.06 – 0.23)
(0.60 – 1.32)
(0.91 – 1.22)
(1.76 – 2.04)
(2.12 – 2.52)
(0.10 – 0.18)
(0.84 – 1.14)
(0.12 – 0.23)
(0.16 – 0.29)
SAR(EC1)_t %
2006
0.76 (0.60 – 0.90)
0.97 (0.71 – 1.26)
0.36 (0.18 – 0.56)
2007 C
1.20 (x.xx – x.xx)
0.94 (x.xx – x.xx)
0.88 (x.xx – x.xx)
2008 C
2.17 (x.xx – x.xx)
2.22 (x.xx – x.xx)
2.48 (x.xx – x.xx)
15-yr avg.
1.01 (0.69 – 1.33)
1.03 (0.63 – 1.42)
0. 80 (0.42 – 1.18)
A
In-river SAR is combination of groups C0 and C1
B
Estimated SARs for TX and C1 with Group T, and C0 with combined Group CRT
C
Complete 3-salt for 2007 and 2-salt for 2008 adult returns through July 26, 2010 (bootstrap CI to
be computed after final loading of returning adults in September)
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
Estimated SARs among the hatchery Chinook populations exhibit variation
among years, among hatcheries, and among outmigration categories (Figure 4.2 and
Tables 4.2 to 4.6). However, the inter-annual patterns of variation are generally similar
among hatcheries and between hatchery groups in the aggregate and wild Chinook for
each of the outmigration categories. Within the in-river study categories (C1 and C0), the
wild Chinook often did as well as or better than most hatchery groups (top and middle
panels Figure 4.2). However the wild transported SAR was often below the top of the
hatcheries’ transportation SARs. The exceptions are 2007 and 2008 (when transportation
was delayed until May 1st) where the wild transportation SARs were higher than 4 of the
5 hatcheries’ transportation SARs. These are the only years where this occurred and may
imply a benefit in the changed transportation protocol for wild Chinook. Among the
hatchery groups, the Catherine Creek group displayed a marked increase in transportation
SAR during 2008. The estimated SARs of the PIT-tagged in-river migrants (C0 and C1)
from McCall Hatchery were generally in the same range as their PIT-tagged wild
Chinook counterparts (Figure 4.2 top and middle panel), while the SARs of transported
McCall Hatchery Chinook were generally higher than that of both the wild and remaining
hatchery groups (Figure 4.2 lower panel). Dworshak Hatchery Chinook consistently
exhibited lower SARs for transported smolts than did wild or other hatchery groups. In
general, the two hatchery summer Chinook populations had higher SARs than the
hatchery spring Chinook populations.
77
1
2
3
4
5
6
7
Figure 4.2 Estimated LGR-to-GRA SAR for PIT-tagged wild Chinook aggregate and five CSS
hatchery groups in transport (T0 or TX beginning 2006) and in-river (C0 and C1) study categories for
migration years 1994 to 2008 (incomplete adult returns for 2008). The transport SAR(TX) after 2005
is a partial year metric because of the delay in transportation start date (shaded area). For 2001 and
2005, only 1 in-river SAR was calculated (see methods). Data from Tables 4.2–6.
78
Table 4.2 Estimated LGR-to-GRA SAR (%) for PIT-tagged spring Chinook from Rapid River Hatchery
for each study category from 1997 to 2008 (with 90% confidence intervals). The transport SAR(TX)
Mig. Year
1997
1998
1999
2000
2001
2002
2003
2004
2005
Monitormode yrsB
SAR(T0) %
0.79
2.00
3.04
2.10
1.08
1.01
0.25
0.36
0.27
(0.57 – 1.01)
(1.80 – 2.21)
(2.78 – 3.31)
(1.91 – 2.28)
(0.96 – 1.21)
(0.86 – 1.16)
(0.18 – 0.32)
(0.29 – 0.43)
(0.21 – 0.34)
SAR(TX)_t %
SAR(C0) %
0.45 (0.31 – 0.63)
1.20 (0.95 – 1.48)
2.37 (2.07 – 2.68)
1.59 (1.40 – 1.81)
{Assume =SAR(C1)}
0.67 (0.55 – 0.79)
0.23 (0.17 – 0.29)
0.23 (0.11 – 0.39)
0.12 A
SAR(C0)_crt %
SAR(C1) %
0.53
0.67
1.63
1.33
0.05
0.63
0.15
0.12
(0.07 – 0.16)
(0.39 – 0.68)
(0.56 – 0.79)
(1.46 – 1.79)
(1.07 – 1.58)
(0.02 – 0.08)
(0.53 – 0.74)
(0.08 – 0.24)
(0.07 – 0.16)
SAR(EC1)_t %
2006
0.57 (0.48– 0.66)
0.42 (0.30 – 0.54)
0.19 (0.05 – 0.35)
2007
0.45 (0.33 – 0.56)
0.25 (0.19 – 0.31)
0.38 (0.22 – 0.56)
2008 C
1.39 (x.xx – x.xx)
0.90 (x.xx – x.xx)
1.11 (x.xx – x.xx)
12-yr avg.
1.11 (0.66 – 1.56)
0.71 (0.34 – 1.07)
0.58 (0.30 – 0.85)
A
B
C
Complete 2-salt for 2008 adult returns through July 26, 2010 (bootstrap CI to be computed after
final loading of returning adults in September)
1
Table 4.3 Estimated LGR-to-GRA SAR (%) for PIT-tagged spring Chinook from Dworshak
Hatchery for each study category from 1997 to 2008 (with 90% confidence intervals). The transport
SAR(TX) after 2005 is a partial year metric because of the delay in transportation start date.
Mig. Year
1997
1998
1999
2000
2001
2002
2003
2004
2005
Monitormode yrsB
2
SAR(T0) %
0.83
0.90
1.18
1.00
0.36
0.62
0.26
0.28
0.20
(0.52 – 1.19)
(0.77 – 1.02)
(1.01 – 1.35)
(0.88 – 1.12)
(0.29 – 0.43)
(0.49 – 0.75)
(0.19 – 0.33)
(0.23 – 0.35)
(0.16 – 0.26)
SAR(TX)_t %
SAR(C0) %
SAR(C1) %
0.47 (0.26 – 0.72)
0.36
1.25 (1.08 – 1.42)
0.90
1.19 (1.01 – 1.37)
0.95
1.01 (0.87 – 1.16)
0.81
{Assume =SAR(C1)}
0.04
0.50 (0.42 – 0.58)
0.50
0.21 (0.16 – 0.27)
0.18
0.32 (0.21 – 0.44)
0.18
0.14 A (0.10 – 0.19)
SAR(C0)_crt %
(0.21 – 0.54)
(0.77 – 1.04)
(0.82 – 1.07)
(0.62 – 1.02)
(0.02 – 0.07)
(0.40 – 0.58)
(0.10 – 0.27)
(0.13 – 0.25)
SAR(EC1)_t %
2006
0.36 (0.29 – 0.44)
0.38 (0.30 – 0.47)
0.19 (0.09 – 0.31)
2007
0.59 (0.35 – 0.86)
0.32 (0.27 – 0.38)
0.29 (0.19 – 0.40)
2008 C
0.75 (x.xx – x.xx)
0.47 (x.xx – x.xx)
0.39 (x.xx – x.xx)
12-yr avg.
0. 61 (0.44 – 0.78)
0. 53 (0.32 – 0.73)
0.41 (0.25 – 0.57)
A
B
C
79
1
Table 4.4 Estimated LGR-to-GRA SAR (%) for PIT-tagged spring Chinook from Catherine Creek
AP for each study category from 2001 to 2008 (with 90% confidence intervals). The transport
Mig. Year
2001
2002
2003
2004
2005
Monitormode yrsB
SAR(T0) %
0.23
0.89
0.36
0.38
0.44
(0.12 – 0.35)
(0.59 – 1.20)
(0.20 – 0.56)
(0.21 – 0.57)
(0.24 – 0.65)
SAR(TX)_t %
SAR(C0) %
{Assume =SAR(C1)}
0.49 (0.28 – 0.74)
0.25 (0.10 – 0.41)
0.20 (0.00 – 0.60)
0.18 A
SAR(C0)_crt %
SAR(C1) %
0.04
0.32
0.35
0.32
(0.04 – 0.35)
(0.00 – 0.09)
(0.18 – 0.50)
(0.14 – 0.61)
(0.11 – 0.54)
SAR(EC1)_t %
2006
0.45 (0.24 – 0.67)
0.93 (0.55 – 1.33)
-0- C
2007
0.50 (0.27 – 0.76)
0.37 (0.20 – 0.55)
1.04 (0.25 – 2.40)
2008 D
2.48 (x.xx – x.xx)
1.79 (x.xx – x.xx)
0.85 (x.xx – x.xx)
8-yr avg.
0.78 (0.17 – 1.39)
0.53 (0.15 – 0.92)
0.39 (0.14 – 0.64)
A
B
C
Only 274 PIT-tagged Catherine Creek hatchery Chinook estimated in C1 category with no adult
returns – the 8-yr average includes this zero value.
D
2
3
Table 4.5 Estimated LGR-to-GRA SAR (%) for PIT-tagged summer Chinook from McCall
Hatchery for each study category from 1997 to 2008 (with 90% confidence intervals). The transport
Mig. Year
1997
1998
1999
2000
2001
2002
2003
2004
2005
Monitormode yrsB
SAR(T0) %
1.51
2.69
3.59
3.88
1.24
1.48
0.79
0.40
0.62
(1.26 – 1.77)
(2.44 – 2.96)
(3.29 – 3.87)
(3.60 – 4.18)
(1.10 – 1.38)
(1.27 – 1.70)
(0.68 – 0.92)
(0.34 – 0.48)
(0.54 – 0.71)
SAR(TX)_t %
SAR(C0) %
SAR(C1) %
1.09 (0.88 – 1.34)
1.10
1.38 (1.05 – 1.69)
0.73
2.40 (2.12 – 2.69)
2.03
2.06 (1.84 – 2.29)
2.03
{Assume =SAR(C1)}
0.04
1.03 (0.87 – 1.20)
1.02
0.54 (0.45 – 0.62)
0.34
0.25 (0.09 – 0.44)
0.12
0.20 A (0.16 – 0.26)
SAR(C0)_crt %
(0.92 – 1.29)
(0.62 – 0.87)
(1.82 – 2.26)
(1.68 – 2.38)
(0.01 – 0.07)
(0.89 – 1.18)
(0.24 – 0.46)
(0.07 – 0.16)
SAR(EC1)_t %
2006
1.15 (1.01 – 1.30)
1.04 (0.85 – 1.22)
0.77 (0.42 – 1.20)
2007
1.46 (1.18 – 1.74)
0.71 (0.60 – 0.81)
0.57 (0.31 – 0.86)
2008 C
1.22 (x.xx – x.xx)
0.77 (x.xx – x.xx)
0.80 (x.xx – x.xx)
12-yr avg.
1.67 (1.09 – 2.25)
0. 96 (0.59 – 1.33)
0.81 (0.47 – 1.16)
A
B
C
4
80
1
Table 4.6 Estimated LGR-to-GRA SAR (%) for PIT-tagged summer Chinook from Imnaha River
AP for each study category from 1997 to 2008 (with 90% confidence intervals). The transport SAR
(TX) after 2005 is a partial year metric because of the delay in transportation start date.
Mig. Year
1997
1998
1999
2000
2001
2002
2003
2004
2005
Monitormode yrsB
SAR(T0) %
1.16
0.85
2.69
3.11
0.62
0.79
0.58
0.38
0.28
(0.77 – 1.60)
(0.65 – 1.09)
(2.28 – 3.08)
(2.77 – 3.44)
(0.49 – 0.78)
(0.56 – 1.04)
(0.40 – 0.75)
(0.26 – 0.49)
(0.18 – 0.40)
SAR(TX)_t %
SAR(C0) %
SAR(C1) %
0.86 (0.53 – 1.22)
0.69
0.55 (0.28 – 0.83)
0.30
1.43 (1.08 – 1.82)
1.22
2.41 (2.01 – 2.83)
1.64
{Assume =SAR(C1)}
0.06
0.45 (0.29 – 0.63)
0.55
0.48 (0.34 – 0.62)
0.38
0.23 (0.07 – 0.48)
0.11
0.16 A (0.08 – 0.26)
SAR(C0)_crt %
(0.48 – 0.93)
(0.20 – 0.42)
(0.98 – 1.49)
(1.22 – 2.08)
(0.01 – 0.11)
(0.38 – 0.72)
(0.20 – 0.59)
(0.04 – 0.20)
SAR(EC1)_t %
2006
0.77 (0.58 – 0.97)
1.25 (0.93 – 1.61)
0.40 (0.10 – 0.77)
2007
1.02 (0.69 – 1.37)
0.63 (0.47 – 0.78)
0.52 (0.27 – 0.78)
2008 C
1.75 (x.xx – x.xx)
1.22 (x.xx – x.xx)
1.80 (x.xx – x.xx)
12-yr avg.
1.17 (0.70 – 1.63)
0.81 (0.46 – 1.16)
0.65 (0.35 – 0.96)
A
B
C
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
Wild and hatchery Steelhead
The PIT-tagged steelhead LGR-to-GRA SAR estimates of transported smolts over
the 11-year time span from 1997 to 2007 exceeded 2% in 5 years for the aggregate of
wild stocks and in 4 years for the aggregate of hatchery stocks, but with only one year
(2000) common to both wild and hatchery PIT-tag groups (Figures 4.3 and 4.4 and
Tables 4.7 and 4.8). The SARs for in-river migrants did not exceed 2% in any year for
wild and hatchery PIT-tag groups, but the pattern of inter-annual variability for the inriver SARs was similar for hatchery and wild steelhead (Figures 4.3 and 4.4). The
sample sizes for wild and hatchery steelhead PIT-tag groups have been small, which
results in few adult returns and rather large 90% confidence intervals for the SAR
estimates (Tables 4.7 and 4.8). During the first year with a May 1st transportation start
date, the wild steelhead transported SAR displayed a marked increase as compared to inriver SARs– the highest in the time series (Figure 4.3). However, in the case of hatchery
steelhead, the transportation SAR in 2008 was concurrent with the SAR of in-river
groups.
81
1
2
3
4
5
6
7
8
9
Figure 4.3 Estimated LGR-to-GRA SAR for PIT-tagged wild steelhead aggregate in transport (T0 or
TX beginning 2006) and in-river (C0 and C1) study categories for migration years 1997 to 2007. The
transport SAR(TX) after 2005 is a partial year metric because of the delay in transportation start
date (shaded area). For 2001, 2004, and 2005, only 1 in-river SAR was calculated (see methods).
Data from Table 4.7.
Table 4.7 Estimated LGR-to-GRA SAR (%) for PIT-tagged wild steelhead in annual aggregate for
each study category from 1997 to 2007 (with 90% confidence intervals). The transport SAR(TX)
Mig. Year
1997
1998
1999
2000
2001
2002
2003
2004
2005
Monitormode yrsB
SAR(T0) %
1.45
0.21
3.07
2.79
2.49
2.84
1.99
0.87
0.84
(0.36 – 2.80)
(0.0 – 0.63)
(1.74 – 4.66)
(1.55 – 4.11)
(0.93 – 4.37)
(1.52 – 4.43)
(1.52 – 2.51)
(0.65 – 1.11)
(0.63 – 1.07)
SAR(TX)_t %
SAR(C0) %
SAR(C1) %
0.66 (0.00 – 1.34)
0.23
1.07 (0.51 – 1.73)
0.21
1.35 (0.80 – 1.96)
0.76
1.92 (1.40 – 2.49)
1.81
{Assume =SAR(C1)}
0.07
0.67 (0.46 – 0.90)
0.94
0.45 (0.27 – 0.66)
0.52
0.06 A (0.02 – 0.11)
0.17 A (0.11 – 0.25)
SAR(C0)_crt %
(0.10 – 0.39)
(0.12 – 0.33)
(0.60 – 0.94)
(1.59 – 2.03)
(0.03 – 0.10)
(0.77 – 1.11)
(0.37 – 0.66)
SAR(EC1)_t %
2006
1.31 (1.02 – 1.66)
1.54 (0.72 – 2.44)
0.60 (0.27 – 0.92)
2007 C
4.18 (3.55 – 4.83)
1.42 (1.09 – 1.72)
1.72 (1.20 – 2.36)
11-yr avg.
2.00 (1.36 – 2.65)
0.85 (0.50 – 1.21)
0.64 (0.30 – 0.99)
A
B
C
Incomplete steelhead adult returns until 3-salt returns (if any) occur after 7/1/2010 at GRA.
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3
4
5
6
7
8
9
Figure 4.4 Estimated LGR-to-GRA SAR for PIT-tagged hatchery steelhead aggregate in transport
(T0 or TX beginning 2006) and in-river (C0 and C1) study categories for migration years 1997 to 2007.
The transport SAR(TX) after 2005 is a partial year metric because of the delay in transportation start
date (shaded area). For 2001, 2004, and 2005, only 1 in-river SAR was calculated (see methods).
Data from Table 4.8.
Table 4.8 Estimated LGR-to-GRA SAR (%) for PIT-tagged hatchery steelhead in annual aggregate
for each study category from 1997 to 2007 (with 90% confidence intervals). The transport SAR(TX)
Mig. Year
SAR(T0) %
SAR(C0) %
SAR(C1) %
1997
0.52 (0.24 – 0.81)
0.24 (0.09 – 0.39)
0.17 (0.12 – 0.22)
1998
0.51 (0.22 – 0.84)
0.89 (0.61 – 1.19)
0.22 (0.17 – 0.28)
1999
0.90 (0.51 – 1.33)
1.04 (0.79 – 1.31)
0.59 (0.51 – 0.69)
2000
2.10 (1.22 – 3.07)
0.95 (0.71 – 1.19)
1.05 (0.92 – 1.18)
2001
0.94 (0.24 – 1.78)
{Assume =SAR(C1)}
0.016 (0.005 – 0.03)
2002
1.06 (0.32 – 2.11)
0.70 (0.54 – 0.88)
0.73 (0.61 – 0.85)
2003
1.81 (1.50 – 2.13)
0.68 (0.52 – 0.86)
0.37 (0.26 – 0.47)
2004
2.13 (1.17 – 3.27)
0.21 A (0.15 – 0.26)
2005
2.03 (1.28 – 2.83)
0.24 A (0.18 – 0.30)
B
2006
2.14 (1.49 – 2.84)
1.42 (0.94 – 1.93)
1.23 (1.06 – 1.41)
2007 B C
1.94 (1.51 – 2.38)
1.17 (0.96 – 1.38)
0.92 (0.78 – 1.07)
11-yr avg.
1.46 (1.09 – 1.83)
0.69 (0.44 – 0.94)
0.52 (0.30 – 0.74)
A
B
No pre-assignment for hatchery steelhead, so one group; transport SARs estimated with TX smolts.
C
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3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
Estimates of TIR and D
The TIR is a measure of the relative performance of transported (T0 or Tx
beginning in 2006) and in-river migrating C0 smolts. A TIR > 1.0 indicates that a
transported SAR was greater than an in-river SAR while a TIR < 1.0 indicates that a
transported SAR was less than an in-river SAR. A TIR is statistically different from 1.0
when its 90% confidence interval does not encompass 1.0 (i.e., a lower limit value >1 or
upper limit value <1 of the 90% confidence interval provides a two-tail (α=0.10) test of
H0: TIR = 1 versus HA: TIR ≠1). For wild Chinook, the TIR values were greater than
one in 8 of the 15 years (Table 4.9). However, the wild Chinook TIRs were not
statistically different from 1.0 in most study years.
Estimated TIRs varied substantially among hatcheries and across years. For most
years, estimated TIRs for Rapid River Hatchery spring Chinook and McCall Hatchery
summer Chinook were greater than one with statistical significance (Tables 4.10 and
4.13). Statistical significance in TIRs occurred in very few years for spring Chinook
from Dworshak NFH and Catherine Creek AP facility (Tables 4.11 and 4.12). Results
were more mixed across years for summer Chinook from Imnaha AP facility (Table
4.14).
The pattern of inter-annual variability in TIRs (natural log-transformed) was
similar among the PIT-tagged wild and hatchery groups, but the yearly magnitude of the
wild Chinook TIRs was generally lower than that of most PIT-tagged hatchery groups
(Figure 4.5).
Figure 4.5 Trend in TIR on the natural log scale for PIT-tagged Snake river hatchery and wild
Chinook for migration years 1994 to 2007. The grey reference line denotes a TIR value of 1 (in-river
and transport SARs equal). After 2005, transport operations initiated on a delayed start date
84
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2
compared to previous years. TIR calculation for 2001 and 2005 differs from other years as in-river
SAR component of ratio includes C1 fish (see methods). Data from Tables 4.9–14.
85
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2
3
Table 4.9 Estimated TIR and D of PIT-tagged wild Chinook for migration years 1994 to 2008 (with
90% confidence intervals). Lower limit values >1 are highlighted in yellow and upper limit values <1
are highlighted in blue. After 2005, transport operations initiated on a delayed start date compared
to previous years.
Mig. Year
TIR
D
1994
1.62
(0.62 – 5.05)
0.36
(0.13 – 1.09)
1995
0.95
(0.39 – 2.14)
0.42
(0.17 – 1.09)
1996
1.92
(0.00 – 6.80)
0.92
(0.00 – 3.24)
1997
0.74
(0.17 – 1.58)
0.40
(0.08 – 0.95)
1998
0.87
(0.50 – 1.35)
0.55
(0.31 – 0.87)
1999
1.14
(0.82 – 1.51)
0.72
(0.52 – 0.98)
2000
0.60
(0.32 – 0.92)
0.32
(0.17 – 0.51)
2001D
8.96
(3.61 – 16.8)
2.16
(0.87 – 4.16)
2002
0.65
(0.45 – 0.94)
0.44
(0.29 – 0.68)
2003
1.05
(0.68 – 1.68)
0.68
(0.43 – 1.12)
2004
1.09
(0.68 – 2.19)
0.45
(0.27 – 0.95)
2005 A
2.14
(1.40 – 3.45)
1.07
(0.65 – 1.85)
2006 B
0.78
(0.54 – 1.14)
0.47
(0.31 – 0.75)
2007 B C
1.27
(x.xx – x.xx)
0.80
(x.xx – x.xx)
2008 B C
0.98
(x.xx – x.xx)
0.47
(x.xx – x.xx)
Geomean
1.21
(0.90 – 1.64)
0.59
(0.47 – 0.75)
A
In-river SAR is combination of groups C0 and C1 in derivation of TIR and D.
B
TIR and D use SAR for TX estimated with Group T and C0 with combined Group CRT.
C
Complete 3-salt for 2007 and 2-salt for 2008 adult returns through July 26, 2010 (bootstrap CI to
be computed after final loading of returning adults in September)
D
For migration year 2001, the SAR(C1) value is used in the derivation of TIR and D.
Table 4.10 Estimated TIR and D of PIT-tagged Rapid River Hatchery spring Chinook for 1997 to
2008 (with 90% confidence intervals). Lower limit values >1 are highlighted in yellow and upper
limit values <1 are highlighted in blue. After 2005, transport operations initiated on a delayed start
date compared to previous years.
Mig. Year
4
TIR
D
1997
1.73 (1.08 – 2.85)
0.61 (0.37 – 1.09)
1998
1.66 (1.32 – 2.16)
1.01 (0.80 – 1.36)
1999
1.28 (1.11 – 1.51)
0.79 (0.65 – 0.99)
2000
1.32 (1.13 – 1.55)
0.82 (0.66 – 1.25)
2001D
21.7 (13.3 – 54.1)
7.33 (4.40 – 16.9)
2002
1.51 (1.20 – 1.91)
1.14 (0.87 – 1.52)
2003
1.07 (0.73 – 1.58)
0.75 (0.50 – 1.15)
2004
1.57 (0.88 – 3.67)
0.57 (0.31 – 1.46)
2005 A
2.36 (1.59 – 3.79)
1.31 (0.83 – 2.30)
2006 B
1.35 (0.98 – 1.91)
0.83 (0.60 – 1.19)
2007 B
1.81 (1.26 – 2.53)
1.20 (0.82 – 1.74)
2008 B C
1.54 (x.xx – x.xx)
0.90 (x.xx – x.xx)
Geomean
1.91 (1.27 – 2.88)
1.04 (0.74 – 1.47)
A
B
C
D
86
Table 4.11 Estimated TIR and D of PIT-tagged Dworshak Hatchery spring Chinook for 1997 to 2008
(with 90% confidence intervals). Lower limit values >1 are highlighted in yellow and upper limit
values <1 are highlighted in blue. After 2005, transport operations initiated on a delayed start date
compared to previous years.
Mig. Year
1
2
3
TIR
D
1997
1.75 (0.92 – 3.46)
0.88 (0.40 – 2.01)
1998
0.72 (0.59 – 0.88)
0.37 (0.30 – 0.47)
1999
0.99 (0.81 – 1.24)
0.60 (0.47 – 0.81)
2000
0.99 (0.82 – 1.19)
0.53 (0.42 – 0.75)
2001D
8.76 (5.04 – 20.4)
2.21 (1.23 – 5.30)
2002
1.24 (0.93 – 1.61)
0.84 (0.61 – 1.12)
2003
1.21 (0.81 – 1.75)
0.88 (0.58 – 1.37)
2004
0.89 (0.59 – 1.43)
0.46 (0.28 – 0.77)
2005 A
1.43 (0.97 – 2.17)
0.77 (0.51 – 1.22)
0.95 (0.69 – 1.30)
0.60 (0.43 – 0.83)
2006 B
2007 B
1.84 (1.11 – 2.81)
1.31 (0.78 – 2.02)
2008 B C
1.58 (x.xx – x.xx)
0.70 (x.xx – x.xx)
Geomean
1.40 (1.00 – 1.96)
0.75 (0.59 – 0.96)
A
B
C
D
Table 4.12 Estimated TIR and D of PIT-tagged Catherine Creek AP spring Chinook for 2001 to
2008 (with 90% confidence intervals). Lower limit values >1 are highlighted in yellow and upper
limit values <1 are highlighted in blue. After 2005, transport operations initiated on a delayed start
date compared to previous years.
Mig. Year
4
TIR
D
2001D
5.33 (0.00 – 13.6)
1.38 (0.03 – 3.79)
2002
1.81 (1.02 – 3.43)
1.23 (0.59 – 2.79)
2003
1.45 (0.65 – 3.79)
0.94 (0.41 – 2.53)
2004
1.94 (0.00 – 2.57)
0.95 (0.00 – 1.33)
2005 A
2.48 (1.02 – 10.6)
1.32 (0.50 – 5.90)
2006 B
0.48 (0.25 – 0.88)
0.26 (0.13 – 0.50)
2007 B
1.35 (0.65 – 2.71)
1.02 (0.46 – 2.29)
2008 B C
1.38 (x.xx – x.xx)
0.70 (x.xx – x.xx)
1.67 (1.09 – 2.56)
0.88 (0.63 – 1.24)
Geomean
A
B
C
D
87
1
Table 4.13 Estimated TIR, and D of PIT-tagged McCall Hatchery summer Chinook for 1997 to 2008
Mig. Year
2
3
TIR
D
1997
1.38 (1.06 – 1.80)
0.64 (0.43 – 0.93)
1998
1.96 (1.54 – 2.56)
1.16 (0.89 – 1.54)
1999
1.49 (1.29 – 1.73)
0.87 (0.72 – 1.07)
2000
1.89 (1.67 – 2.15)
1.24 (0.98 – 1.81)
2001D
31.9 (17.9 – 88.4)
8.95 (4.87 – 24.1)
2002
1.44 (1.18 – 1.79)
0.87 (0.68 – 1.14)
2003
1.47 (1.18 – 1.83)
1.09 (0.85 – 1.37)
2004
1.59 (0.87 – 4.37)
0.72 (0.37 – 1.95)
2005 A
3.02 (2.32 – 4.12)
1.66 (1.23 – 2.36)
1.11 (0.90 – 1.38)
0.74 (0.59 – 0.95)
2006 B
2007 B
2.07 (1.57 – 2.63)
1.76 (1.32 – 2.32)
2008 B C
1.59 (x.xx – x.xx)
0.61 (x.xx – x.xx)
Geomean
2.14 (1.35 – 3.39)
1.17 (0.80 – 1.71)
A
B
C
D
Table 4.14 Estimated TIR and D of of PIT-tagged Imnaha AP summer Chinook for 1997 to 2008
Mig. Year
4
5
6
TIR
D
1997
1.36 (0.83 – 2.37)
0.45 (0.24 – 0.92)
1998
1.55 (0.93 – 3.15)
0.87 (0.51 – 1.72)
1999
1.89 (1.40 – 2.51)
1.11 (0.75 – 1.72)
2000
1.29 (1.06 – 1.58)
0.82 (0.56 – 1.25)
2001D
10.8 (4.94 – 39.8)
4.15 (1.83 – 15.3)
2002
1.75 (1.07 – 3.03)
0.95 (0.54 – 1.78)
2003
1.21 (0.80 – 1.86)
0.91 (0.57 – 1.41)
2004
1.64 (0.54 – 5.32)
0.94 (0.27 – 3.14)
2005 A
1.77 (0.91 – 3.93)
1.11 (0.54 – 2.69)
2006 B
0.62 (0.42 – 0.89)
0.36 (0.24 – 0.54)
2007 B
1.63 (1.04 – 2.39)
1.17 (0.71 – 1.82)
2008 B C
1.43 (x.xx – x.xx)
0.51 (x.xx – x.xx)
Geomean
1.68 (1.20 – 2.36)
0.90 (0.66 – 1.24)
A
B
C
D
In the absence of differential delayed mortality below Bonneville Dam of
transported fish compared to in-river migrants, D would be equal to one. When D
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4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
estimates are >1, the post-BON mortality is greater for the in-river migrants and when D
estimates are <1, it is greater for the transported smolts. Statistical significance was
demonstrated for D ≠1 (two-tail test) when either the lower limit of the 90% confidence
interval for D was >1 or the upper limit of the 90% confidence interval for D was <1.
With the exception of 2001, there were few years and hatcheries where a
significant D >1 (post-BON mortality of in-river fish is greater than that of transported
fish) estimates was obtained (Figure 4.6). A significant D >1 estimate was also
demonstrated for McCall Hatchery Chinook in 2005 and 2007 (Table 4.13). On the other
hand, a significant D <1 (post-BON mortality of transported fish is greater than that of inriver fish) was demonstrated for PIT-tagged wild and Dworshak Hatchery Chinook in
nearly half the years (Tables 4.9 and 4.11). Since transport SARs were only significantly
greater than in-river SARs in 2 years for PIT-tagged wild Chinook and Dworshak
Hatchery Chinook smolts, and post-BON mortality of transported fish was not
significantly less than post-BON mortality of in-river fish, it appears that transportation
provides no survival advantage over allowing wild Chinook and Dworshak Hatchery
Chinook to migrate in-river.
Although Snake River wild and hatchery populations demonstrated differences in
estimated magnitude of TIRs and Ds, the historical patterns for these were similar among
wild and hatchery populations. TIRs were higher for hatchery fish than wild fish, but the
TIR pattern for the wild population tracked well with those of the hatchery populations
across years (Figure 4.5). Similarly, hatchery fish had higher D values than wild fish, but
wild and hatchery Ds also tracked well across years (Figure 4.6).
Figure 4.6 Trend in D on the natural log scale for PIT-tagged Snake River hatchery and wild
Chinook in migration years 1994-2007. The grey reference line denotes a D value of 1 (in-river and
transport post-BON survivals are equal). After 2005, transport operations initiated on a delayed
start date compared to previous years. D calculation for 2001 and 2005 differs from other years as
in-river SAR component of ratio includes C1 fish (see methods). Data from Tables 4.9–14.
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4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
Wild and hatchery steelhead
The TIR estimates for the PIT-tagged wild and hatchery steelhead aggregates
exceeded 1 in nine of 11 years, with statistical significance in 7 of the 11 years for wild
stocks and 5 of the 11 years for hatchery stocks (Tables 4.15 and 4.16). The 11-year
geometric means were similar and significantly greater than 1 for the PIT-tagged wild
and hatchery steelhead aggregates (3.00 for wild stocks and 2.91 for hatchery stocks).
Similar to Chinook salmon TIRs, steelhead TIRs were markedly higher in 2001 than
during all other years as seen in the TIR trend across years for both hatchery and wild
steelhead (Figure 4.7).
Despite the marked increase in transport SAR for wild steelhead in 2007 (the
highest in the time-series; Figure 4.3), when compared with in-river outmigrants, the TIR
is the 6th highest in the time-series (Figure 4.7). For hatchery steelhead the time-series of
transport SAR is consistently higher than in-river groups after 2000 (Figure 4.3) though
the TIR value decreases in 2006 and 2007. A variety of operational and environmental
factors that may have influenced the in-river SARs and resultant TIRs in 2006 & 2007
include: allowing early outmigrants to pass via in-river routes, the increased spill
percentage as compared to earlier years, or the increased in-river population produced by
a lower transportation percentage (Figure 1.4). Also, steelhead tend to migrate faster and
have higher in-river survivals in years of better discharge, and the April 15 to June 15
average discharge in 2006 was the highest since the late 1990’s (Figure 1.4).
Figure 4.7 Trend in TIR on the natural log scale for PIT-tagged Snake River hatchery and wild
steelhead in migration years 1997 to 2006. The grey reference line denotes a TIR value of 1 (in-river
and transport SARs equal). After 2005, transport operations initiated on a delayed start date
compared to previous years. TIR calculation for 2001, 2004, and 2005 differs from other years as inriver SAR component of ratio includes C1 fish (see methods). Data from Tables 4.15–16.
90
1
Table 4.15 Estimated TIR and D of PIT-tagged wild steelhead for migration years 1997 to 2007 (with
90% confidence intervals). Lower limit values >1 are highlighted in yellow and upper limit values
<1 are highlighted in blue. After 2005, transport operations initiated on a delayed start date
Mig. Year
1997
1998
1999
2000
2001D
2002
2003
2004 A
2005 A
2006 B
2007 B C
Geomean
2.20
0.20
2.28
1.45
37.0
4.25
4.41
14.3
4.88
0.85
2.95
3.00
TIR
(0.00 – 8.16)
(0.00 – 0.70)
(1.15 – 4.38)
(0.77 – 2.40)
(10.6 – 94.6)
(2.12 – 7.67)
(2.74 – 7.73)
(7.19 – 42.1)
(3.01 – 7.98)
(0.49 – 1.80)
(2.29 – 3.94)
(1.42 – 6.35)
1.18
0.11
1.07
0.50
1.46
2.24
1.75
2.69
1.30
0.52
1.22
0.99
D
(0.00 – 5.74)
(0.00 – 0.41)
(0.53 – 2.09)
(0.27 – 0.82)
(0.40 – 4.40)
(1.09 – 4.25)
(1.04 – 3.16)
(1.29 – 8.78)
(0.76 – 2.30)
(0.29 – 1.11)
(0.90 – 1.77)
(0.61 – 1.61)
A
C
D
B
2
3
Table 4.16 Estimated TIR, and D of PIT-tagged hatchery steelhead for migration years 1997 to 2007
Mig. Year
1997
1998
1999
2000
2001D
2002
2003
2004 A
2005 A
2006 B
2007 B C
Geomean
2.21
0.58
0.87
2.20
59.7
1.51
2.65
10.3
8.44
1.50
1.66
2.91
TIR
(0.99 – 5.66)
(0.23 – 1.05)
(0.48 – 1.41)
(1.22 – 3.58)
(0.00 – 215.6)
(0.38 – 3.33)
(1.93 – 3.71)
(5.43 – 17.9)
(5.04 – 13.4)
(0.93 – 2.42)
(1.22 – 2.16)
(1.42 – 5.97)
0.92
0.39
0.41
0.55
2.40
0.60
1.43
1.85
3.19
1.01
0.92
0.99
D
(0.36 – 2.67)
(0.16 – 0.85)
(0.22 – 0.70)
(0.30 – 0.93)
(0.00 – 10.0)
(0.14 – 1.38)
(0.99 – 2.10)
(0.91 – 3.46)
(1.86 – 5.37)
(0.61 – 1.63)
(0.66 – 1.30)
(0.68 – 1.46)
A
No pre-assignment for hatchery steelhead, so one group; transport SARs estimated with TX smolts.
C
D
B
4
5
6
7
8
The estimate of D was >1 in eight of 11 years for PIT-tagged wild steelhead and
five of 11 years for PIT-tagged hatchery steelhead (Table 4.15 and 4.16). Statistically
significant D >1 (lower limit of 90% CI >1) was demonstrated in only 3 years for wild
stocks and 1 year for hatchery stocks, while statistically significant D <1 (upper limit of
91
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4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
90% CI <1) occurred in 2 years for wild stocks and 3 years for hatchery stocks. The
sample sizes for wild and hatchery steelhead PIT-tag groups have been small, which
results in few adult returns and rather large 90% confidence intervals for both TIR and D
estimates
The natural log D trend across years is presented for both hatchery and wild
steelhead in Figure 4.8. Although differences arise between the estimates for wild and
hatchery steelhead, the TIR and D data suggest that steelhead as a whole respond more
favorably to transportation than do the listed wild Chinook. During 2006 and 2007, there
is no statistical difference between D and one. Most of the D parameter may be
expressed while in the ocean (Figure 6.2, chapter 6) however some delayed effects of
transport on upstream adult success were still evident in these years (see chapter 6 for
adult success comparisons).
Figure 4.8 Trend in D on the natural log scale for PIT-tagged Snake River hatchery and wild
steelhead in migration years 1997-2007. The grey reference line corresponds to a D value of 1 (inriver and transport post-BON survivals are equal). After 2005, transport operations initiated on a
delayed start date compared to previous years. D calculation for 2001, 2004, and 2005 differs from
other years as in-river SAR component of ratio includes C1 fish (see methods). Data from Tables
4.15–16.
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Discussion
The long-term monitoring data provided by the CSS study groups for wild
spring/summer Chinook, hatchery spring Chinook, hatchery summer Chinook, wild
steelhead, and hatchery steelhead have demonstrated considerable variability in SARs
among study groups and between years. Since 2005, the SARs of PIT-tagged wild and
hatchery Chinook and steelhead have been increasing. A variety of operational and
environmental factors during the smolt outmigration that may have influenced the inriver SARs and resultant TIRs in 2006 through 2008 include: allowing early outmigrants
to pass via in-river routes (as a result of the later start of transportation in these years), the
increased spill percentage as compared to earlier years, and the increased total in-river
population produced by a lower transportation percentage (see Figure 1.4 and Appendix
C for the transportation percentages). Additionally, the April 15 to June 15 average
discharge in 2006 was the highest since the late 1990’s (Figure 1.4).
The delayed transport approach with spill, begun in 2006 was consistent with
ISAB recommendations for a multi-species perspective that spread the risk of potential
negative influences from differing routes of hydrosystem passage across several species
at once (ISAB 2008). This includes consideration of stocks not analyzed in this chapter
such as Snake River Sockeye, fall Chinook, or Pacific Lamprey (ISAB 2008). However,
information for Snake River sockeye should be available as adults come back from the
2009 outmigration (see Chapter 1 to 3 for sample sizes, annual juvenile metrics, and
juvenile analyses).
The TIR estimates have been used as the initial indicator of potential benefit for
smolt transportation for each study grouping. The combination of exceptionally low inriver smolt survivals in 2001 and generally average survivals for transported smolts
resulted in exceptionally large TIR values for all CSS groups of PIT-tagged fish for the
2001 migration year. Those TIRs indicated a substantial benefit for smolt transportation
in 2001, under unusual environmental conditions, extreme drought, and hydrosystem
operations which included no spill and maximization of smolt transportation.
For the rest of the CSS evaluation years, TIR estimates indicate the relative smolt
transportation performance for the PIT-tagged spring/summer Chinook has been as
follows: no benefit for the wild spring/summer Chinook and spring Chinook from
Dworshak and Catherine Creek hatcheries, mixed benefit for the summer Chinook from
Imnaha Hatchery, and positive benefit in most years to the spring Chinook from Rapid
River Hatchery and summer Chinook from McCall Hatchery. Overall, Snake River
hatchery Chinook exhibited a generally more positive response to transportation and
relatively lower levels of differential delayed mortality (higher D) than did wild
populations. The annual SARs of Snake River wild and hatchery Chinook were highly
correlated across years.
There appears to be positive benefit of transportation to the PIT-tagged wild and
hatchery steelhead aggregates in most years; however, small sample sizes for steelhead
through 2007 warrant some degree of caution in the degree of confidence on the relative
performance of transportation relative to in-river migration. Also, distribution of PIT-tags
across the drainages that comprise the PIT-tag aggregates varies across years. For
example, PIT-tagged wild steelhead from the Imnaha River drainage comprised 37 % of
the 2007 wild steelhead PIT-tag aggregate, but 69 % of the transported smolts within the
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PIT-tag aggregate due to their later passage timing at the dams coinciding more with the
delayed transportation season. Likewise, PIT-tagged hatchery steelhead released from
Wallowa Hatchery comprised 27 % of the total PIT-tag hatchery steelhead aggregate, but
85 % of the transported smolts within the PIT-tag aggregate since most PIT-tagged
smolts from the other hatcheries in the aggregate followed the default return-to-river
operations at the Snake River transportation sites. With the shift to large-scale PITtagging of hatchery steelhead with a high percentage pre-assigned to Monitor-Mode
operations, which began in 2008 with Dworshak NFH and the Lower Snake River
Compensation hatcheries and expanded in 2009 to include IPC Niagara Springs
Hatchery, there will be an ability in future years to estimate SARs, TIR, and D for a more
representative cross-section of A-run and B-run hatchery steelhead stocks released above
Lower Granite Dam.
Some of the relative transport benefit seen for steelhead may be due to their
poorer in-river survival compared to Chinook. The relation between loge(TIR) and inriver survival rate from LGR to BON (SR) for PIT-tagged wild Chinook and wild
steelhead suggests that transportation is detrimental when SR is above approximately 55%
(Figure 4.10) Whereas SR estimates for the PIT-tagged wild Chinook aggregate have
been above 55% in several recent years, the SR estimates for the PIT-tagged wild
steelhead aggregate has only rarely exceeded 55%.
Figure 4.10 Natural logarithm of Transportation : In-river Ratio (TIR) versus in-river survival rate
(SR) for wild Chinook (open points) for juvenile migration years 1994-2008 and wild steelhead (filled
points) for juvenile migration years 1997-2007. Broken lines represent the 95% prediction intervals
for loge(TIR).
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Chapter 5
Adult passage success rates between dams, D,
and the expression of delayed effects.
Introduction
In the early 1990s, Mundy et al. (1994) concluded that research results to date
were not conclusive regarding the ability of transportation to improve returns to the
spawning grounds (or hatcheries) due to problems associated with experimental design.
Even if transportation provides an apparent survival improvement relative to juvenile
migration through the hydrosystem (as measured by adult return to the dams), the benefit
may not carry through to natal areas if transported fish were more likely to stray or die
before spawning. One of several advantages of the CSS experimental design of tagging
fish at hatcheries or in tributaries before release (rather than at the dams as in previous
studies) is that it allows for partitioning survival rates by treatment of known-origin fish
between locations along their juvenile and adult migrations.
Hatchery Chinook SARs from smolts at LGR to adults at LGR are a primary
focus of CSS and are addressed in detail in Chapter 4. The CSS PIT-tag data allow for
evaluation of the relative upstream passage success of adults between Bonneville (BON)
and Lower Granite dams (LGR) from transport and in-river groups to further partition the
LGR-LGR SARs and assess the extent to which transportation may contribute to straying
or poor upstream passage conversion. The capability of estimating the relative adult
passage success between BON-LGR became possible in 2002 because adult PIT-tag
detection devices were completed in all of the adult ladders at BON.
Given that estimates of TIR and D both rely on smolt-to-adult survival rates
(SARs) based on adult detections at Lower Granite Dam (LGR), these values include
both an ocean mortality component and one occurring during upstream migration (i.e.,
between BON and LGR) in the year of adult return. Partitioning D, which is BONsmolt to
LGRadult differential survival, into two segments can help to describe where any
differences in survival took place. The 2005 and 2006 CSS reports Berggren et al. 2005b
and 2006), contained an analysis/comparison of the inter-dam ‘drop out’ rates of hatchery
and wild Chinook salmon. The 2008 and 2009 CSS reports (Berggren et al. 2008,
Tuomikoski et al. 2009) included adult success rate estimates, the complement of drop
out rates; these estimates were updated for CSS Snake River groups from migration years
2003-2007 and used to partition D into ocean and BONadult to LGRadult differential
survival. Here we updated and extended the analyses from the 2009 report to include
migration years 2000-2008 for all CSS Snake River groups.
This chapter contains summaries of findings from previous annual reports
(Berggren et al. 2003; 2005a; 2005b; 2006; 2008, Schaller et al. 2007) regarding adult
migration (BON-LGR) and success by migration year for both transport and in-river
study categories. We used these estimates to separate D into ocean and adult escapement
partitions. Finally, descriptions of the available information on the observations of
straying fish are provided and a straying rate for in-river and transported outmigrants is
presented.
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Methods
Adult success rates by migration year and ocean survival were estimated for
Snake River CSS groups from migration year 2000-2008. Data on the number of PITtagged adults passing various dams within the FCRPS was used to estimate a success rate
for returning adults from BON to LGR. Using data collected at PIT-tag interrogation
systems on adult fishways, this quantity was directly estimated and compared between
the transport (TX or T0) and in-river (C0 and C1) study categories in the CSS. The
transport group in the 2009 report was composed of only first time detected and
transported fish (T0). In this report, for years with a delayed initiation of transportation
(after 2005) the transport group was expanded to include fish transported with a previous
detection upstream (TX). This is a logical fit with the delayed transport protocol in these
years and follows the CSS study design. Relative ocean survival (e.g., BON as juvenile
to BON as adult) was estimated indirectly by removing the success rate from the
differential delayed mortality estimate (the D estimate; see Chapter 4).
Hatchery and wild Chinook and steelhead marked with PIT tags as juvenile fish in
the Snake River basin were monitored at mainstem dams on their downstream migration;
after spending one to three years in the ocean, the survivors were detected as they passed
upstream as adults through the hydro system. PIT-tag detection systems have been
installed in the fish ladders at BON, MCN, ICH, and LGR and allowed the tracking of
PIT-tagged adults as they passed from lower Columbia River projects to upstream Snake
River projects. The adult fish traverse about 286 river miles and encounter eight dams
from BON to LGR. Once fish negotiate BON, they pass through tribal fisheries (between
BON and MCN) and a sport fishery in both the Columbia and Snake Rivers. The
detections of adults decrease at upriver sites as a result of the combination of straying and
both harvest and passage mortality.
The adult success rate is the proportion of returning PIT-tagged adults that passed
BON and were detected at LGR. This calculation requires an estimate of the number of
PIT-tagged adults (excluding jacks for Chinook) passing BON in the fish ladders.
Beginning with return year 2002 there was the capability to detect nearly all PIT-tagged
adult fish passing the three ladders at BON. However, since a portion of the fish swim
over the weir crests and do not pass through the orifices where the detection equipment is
installed, the detection rate for PIT-tagged adult fish at BON is very high but less than
100%. Upstream adult PIT-tag detections that were not detected at BON (e.g., detected
at MCN, ICH, or LGR but not at BON) were used to estimate the BON detection
efficiency. BON detection efficiency is the number of PIT tag detections at BON divided
by the sum of BON detections and upstream detections not observed at BON. This
parameter was then used to expand the number of BON adult detections in the adult
success rate. The adult success rate was calculated as:
Adult.success.rate 
GRAcount
 BON count  BONefficiency 
which can be re-arranged as:
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Adult.success.rate 
GRAcount
 BON efficiency
BON count
[5.2]
The efficiency was calculated specific to each group of interest. First efficiency
was calculated at BON by aggregating adult detections from the transported and in-river
study groups. Detectability at BON of adults was likely the same regardless of juvenile
history and this approach allowed for use of the maximum number of detections. Then
adult success rates was calculated for adults with in-river and transportation juvenile
histories. Because the C1 and C0 in-river groups had a much smaller sample size than the
TX group, and few adults returned overall, the C0 and C1 were combined into group (CX) .
Finally, the BONefficiency was used to correct the adult success rate for the TX and the CX
subset from a particular migration year, species and release group (e.g. Dworshak
Hatchery Chinook that out-migrated in 2007).
The use of fish detected upstream that were not detected at BON to estimate BON
efficiency was the best available measurement of this parameter. However, this nominal
estimator of efficiency could have been inaccurate if fish passed BON undetected and
through straying/harvest/mortality were never again detected. This problem was
alleviated by comparing these two rates in a fraction (e.g., Success(TX or T0)/SuccessCx).
The assumption here was that the rate for passing BON undetected and never being
detected again was the same for the transported and in-river fish. Since the fish were
from the same species/hatchery the assumption seemed reasonable.
To calculate the differential survival in the ocean, both the juvenile and adult
hydrosystem survival components were removed from the LGRsmolt to LGRadult SARs.
We used D (see Chapter 4) for a particular group and divided by the differential adult
success rate for that same group. The result is an estimate that compares ocean survival
of fish that were transported to ocean survival for fish with an in-river history (shown as
T0 here but the same calculation applies when using the TX group (i.e. after 2005):
 SAR T0  

 Success
ST
T0


Ocean.survival.differential 
Success
 SAR  C0  
Cx


SR


[5.3]
Bootstrapped 90% confidence intervals for the success rates were calculated using a nonparametric percentile bootstrap with 1,000 iterations in program R (R Development Core
Team 2010). Bootstrapped confidence intervals for D are presented in chapter 4 of this
report.
We updated the logistic regression analysis presented in Chapter 6 of the CSS
2009 report with additional years’ data and, follow that approach to further bolster our
sample size, included individuals marked at Lower Granite Dam. The relationships
between upstream adult success and juvenile outmigration experience was evaluated as
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well as riverine conditions during adult upstream migration. For this exercise, adult
success was defined as simply a detection of an adult at LGR that was previously
detected at BON. Individuals were excluded if they were not detected as an adult at
BON. This analysis was performed for hatchery Chinook, wild Chinook, hatchery
steelhead, and wild steelhead separately. CSS-affiliated hatchery marks were relied upon
because there was incomplete coverage of the in-river group across years for hatchery
Chinook and steelhead that were marked at LGR. For the wild groups LGR marking was
incorporated because there was consistent marking of both transported and in-river
migrants across years. For Chinook salmon, only >1-ocean adults (i.e., we excluded
jacks) from migration years (MYs) 2000-2008 were included in the analysis that were
detected as adults by the PIT-tag interrogation sites at BON in return years (RYs) 20012010. For steelhead, individuals from MY’s 2001-2008 which were detected at BON as
adults in RYs 2001-2009 were included; because of the potential for overwintering
behavior to bias the success rate, RY 2010 was excluded for steelhead.
Within the context of the logistic regression-based assessment of transportation
effects, we also wished to account for variation in BON-LGR survival that could be
attributed to in-river migration conditions. Specifically, given the results from the
University of Idaho’s radio telemetry work (Keefer et al. 2004; Naughton et al. 2006),
The influence of discharge, spill, and water temperature on adult passage success was
quantified. These variables were summarized using records from the Fish Passage Center
and USACE’s websites. Discharge and temperature data were summarized for BON (i.e.,
as a proxy for Columbia River conditions) and averaged across 2-week time blocks in
each RY. Similarly, spill was summarized as average Lower Columbia (BON, TDA,
JDA, and MCN, averaged) values for the same time blocks. Environmental variables
were matched with individual fish records based on their BON arrival date. The same
approach was followed as used in the 10-year report and 2009 CSS annual report of
utilizing Lower Columbia in-river variables because the majority of adults (hatchery
Chinook: 2032/2464, or 82%; wild Chinook: 534/675, or 79%, hatchery steelhead:
253/296, or 85%; wild steelhead: 519/651, or 80%) that failed to arrive at LGR dropped
out before MCN, and in-river variables are correlated across sites.
The effects of both transportation history and management/environmental
conditions (i.e., Lower Columbia flow, spill, and temperature) were evaluated on the
upstream migration success of individual fish using logistic regression. We followed the
same model structure used in the 2009 CSS annual report. Thus, for the hatchery groups,
11 a priori models were fitted describing an individual’s survival response (0 =
unsuccessful; 1 = successful) as a function of a combination of transportation and/or
management/environmental predictor variables. Because fish marked at LGR were
included and to control for any possible difference between these and CSS-affiliated
marked fish, a dummy variable (“LGR.marking”) was added for LGR marked wild origin
individual’s in the wild fish model sets. Therefore, the wild fish model sets included 22
total models.
An AIC-based model selection approach was used to determine the level of
support for different models (i.e., hypotheses). To asses the importance of predictor
variables in each model set, the “relative variable importance” was calculated by
summing the Akaike weights across all the models in the set where a particular variable
occurs (Burnham and Anderson 2002; pg 168). Finally, we assessed slope parameter
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sign (+/-) and significance (using a t-test; alpha = 0.05) from our top model(s) in each
model set.
A summary of the data was included for fish detected outside the assumed
migration corridor between BON and LGR. In this effort, we looked at all individuals
from Snake River CSS groups from migration year 2000-2008 that had detections outside
of the FCRPS. Although new observation sites are added to the PTAGIS database every
year, the historical record for these straying fish was limited. For example, while adult
detection capability at PRD has existed since 2003, detection capability has been
available in the Deschutes and John Day rivers only since 2007 and 2008. Nonetheless,
these data were compiled to characterize where presumed straying fish have last been
observed.
We include descriptions of where strays were detected and provide calculated
straying rates for Chinook and steelhead. For the purpose of describing where strays
were last detected, a stray was defined as any adult fish detected outside the FCRPS and
below LGR without a subsequent detection within the FCRPS. A stray rate for Chinook
was calculated both with and without jacks. Most of the Chinook strays were found in
the Mid Columbia River; we pooled data for hatchery Chinook from migration years
2001-2008 to overlap with potential adult detection in this area. Only seven stray wild
Chinook were detected so a rate was not calculated for this group. The majority of the
steelhead strays were found in lower Columbia River subbasins (Deschutes and John Day
rivers); we pooled steelhead data from migration years 2005-2008 to overlap with the
detection of adults in this area. The stray rate was the sum of the strays detected at BOA
divided by the total number of adults detected at BOA for a particular group of interest.
This was calculated for both adults that were transported as juveniles and those that
emigrated in-river. To test for a significant difference between these estimates, we used a
non-parametric bootstrap approach (e.g., resampling with replacement) and calculated a
new test statistic θ where, θ = Straying_ratetransport – Straying_ratebypassed. The 90%
confidence interval around this statistic in relation to the value zero was used to indicate
whether Straying_ratetransport was different than Straying_ratebypassed. At best, any straying
rates would be minimal conservative estimates, because detections are not distributed
across the Columbia Basin for all years, detection efficiencies at some of the newer
detectors have not been established, and there are likely potential straying sites without
PIT-tag detection.
Results
The counts of adults at BON and LGR for the 2000-2008 smolt migration years in
each of the CSS groups are shown in Table 5.1 (see end of chapter). The geometric mean
of the BON detection efficiency for Chinook ranged from 94.6% to 99.1% across
migration year groups. This is similar to those calculated for Chinook in the 2005 annual
report (range: 93.1% to 98.3%; CSS 2005 annual report, Table 58). The adult success
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rates calculated from these counts are shown in Figure 5.2, Figure 5.3, and Table 5.3 (see
end of chapter) along with the success rate differential (i.e., SuccessT0/SuccessCx). The
geometric mean success rate differential across years for hatchery Chinook, wild
Chinook, hatchery steelhead and wild steelhead were 91%, 93%, 92%, and 90%
respectively. The geometric mean of the BON detection efficiency for steelhead was
slightly less than for Chinook and ranged from 80.1% to 99.4% with the lowest rate for
migration year 2000. The 2000 migration year is low because adult steelhead could have
passed BON undetected in the summer/fall of 2001 and subsequently passed LGR with a
detection in the spring of 2002. However, using the efficiency to expand the number of
BON adult detections in the adult success rate allows for the inclusion of the 2000
migration year for steelhead in these analyses. In cases where each of the individual fish
detected at upstream sites was also detected at BON, the efficiency and the adult success
rate are 100%. So, given equation 5.2, the inclusion of the BON detection efficiency in
calculation of the adult success rate adjusted the value of the adult success rate down by
as much as 6.9% but more typically by 5% or less.
The adult passage success rates of fish that were transported (T0 or TX) and fish
that emigrated in-river (Cx) are shown with 90% confidence intervals in Table 5.3. The
success rate differential estimates are shown in with their 90% confidence intervals in
Table 5.3, Figure 5.2 and Figure 5.3. In a few cases, 90% confidence intervals could not
be calculated because too few adults were detected in all, or the number of detections at
BON was the same as the number at LGR. For example, the 2001 in-river Catherine
Creek group had 3 adults which resulted in many bootstrap iterations having a zero in the
denominator of the differential success rate and thereby an upper confidence interval of ∞
(shown as Inf in Table 5.3). All 8 of the adults for the 2005 Imnaha CX hatchery group
that passed BON also passed LGR resulting in no variation when bootstrapping and a
confidence interval from 1-1 (Table 5.3).
As with D, when the value of the adult success rate differential is above or below
one, this indicates that transport was beneficial or detrimental for the group being
measured respectively. The point estimate of the adult success rate differential for
transported to in-river fish was below one on 52 of 69 occasions (Table 5.3, Figure 5.2,
Figure 5.3). The 90% confidence interval around this statistic in relation to the value 1
can be used to indicate whether transport was statistically beneficial or detrimental in
regards to the adult success rate in each case (similar to D in Chapter 4). If the upper
confidence interval was less than one, we conclude that, at alpha level of 10%, the
practice of transportation was detrimental in regards to the adult success rate portion of
the SAR. If the lower confidence interval is more than one, then transportation is found
to be beneficial in regards to adult success. In Table 5.2, the upper confidence interval of
the adult success rate differential was less than one 21 times, more than one three times,
and straddled one 45 times. This is statistically significant evidence indicating that the
transportation of smolts can negatively affect adult success and rarely has a positive
effect on adult success.
Partitioning D
When removing the differential adult success from D, the differential ocean
survival remains. The differential ocean survival is displayed in the bottom panel of
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Figure 5.2. Here, many values are similar in pattern to those for D (top panel; Figure 5.1
and 5.2;) as the ocean survival represents the greatest portion of D temporally. There is a
marked contrast between the differential adult success rates for wild and hatchery
steelhead and the differential ocean survival (middle and lower panel; Figure 5.2). So,
despite some positive effects measured by D for hatchery and wild steelhead, there
remains a measureable negative effect once adults enter the hydrosystem.
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Figure 5.1 The three panels display the log transformed D, differential adult success, and differential
ocean survival in the top middle and bottom panels respectively for CSS hatchery and wild yearling
Chinook. Each differential compares groups that emigrated via transportation (numerator) and inriver (denominator). In each panel, when the log-transformed point estimate is above zero (grey
reference line) transported smolts survived at a higher rate, when below zero, in-river emigrants
survived at a higher rate. Cases where this was significant for the differential adult success (middle
panel) are circled in red.
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Figure 5.2 The three panels display the log transformed D, differential adult success, and differential
ocean survival in the top middle and bottom panels respectively for hatchery steelhead (red triangles)
and wild steelhead (yellow triangles). Each differential compares groups that emigrated via
transportation (numerator) and in-river (denominator). In each panel, when the log-transformed
point estimate is above zero (grey reference line) transported smolts survived at a higher rate, when
below zero, in-river emigrants survived at a higher rate. Cases where this was significant for the
differential adult success (middle panel) are circled in red.
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Consistent with the 10-year report (Schaller 2007; Chapter 6), and the results of
the differential success rate comparisons in this chapter, our AIC-based model-selection
exercise also demonstrates an effect of transportation history on upstream adult migration
success. For wild Chinook, the best model describing individual migration success
included transport and flow effects (Table 5.3). With the additional year’s data, this top
model had higher weight than in the CSS 2009 annual report, although the top four
models had nearly the same AICc score. The relative variable importance across all
models in the set for wild Chinook was 100%, 100%, 47%, 25%, and 24% for transport,
spill, LGR.marking, and temperature, respectively. Because the top four models in this
set were nearly indistinguishable in their AICc scores, we tested for significance of the
coefficients in each model. The transport (-) and flow (+) variables were significant in
each case while the temperature and LGR.marking variables were not significant .
For hatchery Chinook, the best model included transport, flow, and temperature
effects (Table 5.4). With the additional data, the relative variable importance was 100%,
for all four variables. For the top model, transport (-), temperature (+) and flow (+) were
all significantly different from zero.
The best model for wild steelhead included transport, spill and temperature
effects. The relative variable importance was 100%, 100%, 100%, 43%, and 27% for
transport, spill, flow, LGR.marking, and temperature, respectively. Because the top two
models differed from the first by a ∆ AICc of < 2 (Table 5.5), we tested for significance
of the coefficients in each model. In each case, the transport (-), spill (-), and temperature
(+) variables were significant and the LGR.marking variable was not significant.
Similar to the CSS 2009 report, for hatchery steelhead, the best model contained
only the transport variable though each of the top five models differed by a ∆ AICc of ~ 2
(Table 5.6). The relative variable importance was 100%, 53%, 37%, and 33% for
transport, spill, flow, and temperature, respectively. We tested for significance of the
coefficients in each of the top four models. In each case, the transport (-), spill (-), and
flow (+) variables were significant while the temperature variable was not significant
across the top five models.
The adult success rate reflects a combination of fishing and other mortality and
straying between BON and LGR. Here, we summarize data from salmon and steelhead
individuals of Snake River Basin origin marked as part of the CSS for the 2000-2007
migration years that might be categorized as strays. We defined strays as any fish
detected at any site other than BON, MCN, ICH, or LGR during the BON to LGR adult
migration. We present these results to indicate where wild and hatchery steelhead and
Chinook may stray to or overwinter; for this exercise we included strayed jacks for
Chinook. When describing strays by area of last detect we organized these into three
categories: Snake River (above the Snake River-Columbia River Confluence) and the
Columbia River either above or below its confluence with the Snake River.
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30
In the 2009 report, information was available for only 43 adult salmon and
steelhead individuals with “out-of-hydrosystem” detections whereas, with the additional
year’s data, we summarize information for 87 adults. These are summarized by area of
last detection in Figures 5.3-5.4. All but fourteen (84%) of these adults were collected
and transported as juveniles. Of these 87 individual adult salmon, 72 (83%) did not
succeed in their migration to or above LGR. Transported fish from Dworshak hatchery
were detected outside of the FCRPS more commonly than any other group; all of the
Dworshak Hatchery origin Chinook strays were detected within the Columbia upstream
of the Snake River mouth (Figure 5.3). All but one of these fish were never detected
after their mid Columbia River detection. This is in sharp contrast to Rapid River
hatchery, which had a similar number of PIT tagged fish as Dworshak over these years
(Appendix A) but had only 2 detects outside the FCRPS. Also, there was only one adult
that emigrated in-river from Dworshak hatchery that was detected outside the FCRPS.
The geometric mean of the transport percentage for the PIT tagged juveniles from
Dworshak over these years was 50%.
Seven individuals from McCall and Catherine Creek hatcheries had last detects in
the Deschutes and John Day rivers. However, it is important to keep in mind that adult
detection capability has only been available here since 2007. Six of these seven
individuals were transported as juveniles. These stocks were not detected in the Mid
Columbia and represent the only CSS hatchery Chinook groups detected in these lower
Columbia River tributaries (Figure 5.3). Two and five wild Chinook were detected in the
Deschutes/John Day and Mid Columbia rivers.
Steelhead presence outside the presumed migration corridor may be partially due
to the selection of a cold-water holding or overwintering refugia before completing the
adult migration the following spring. Three times as many of these individuals were later
detected passing LGR as compared to Chinook (Figure 5.3-5.4). Most of the individual
steelhead adults detected outside the FCRPS were last seen in the Deschutes or John Day
river systems. This is in contrast with Chinook, which mostly strayed to the Columbia
River system above the confluence with the Snake River. In total, 16 wild or hatchery
steelhead were last detected in the Deschutes or John Day rivers.
31
32
33
34
35
36
37
38
39
It should be noted that several of these PIT tag detector sites were operating only over a
portion of the years aggregated. The John Day river detector (JD1) and the Sherar’s falls
detector (SHERFT) composed several “last detects” of these fish and these two sites have
operated only since 2007; SHERFT operated only over a portion of 2007. This suggests
that many fish that were never seen after their initial BON detection during years prior to
2007 may have been entering these Lower Columbia River tributary rivers. This is in
agreement with the 2003 & 2004 CSS annual report (Berggren et al. 2005a) and the
results in this chapter, where most of the drop-rate (the complement of success rate) for
wild and hatchery Chinook took place between BON and MCN.
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4
5
6
7
8
Figure 5.3 Summary of the last detection area for CSS Chinook originating in the Snake River Basin
with detections other than at BON, MCN, ICH, and LGR dams (2000-2008 migration years). Jacks
are included here. Most of these individuals did not eventually migrate to or above LGR. Grey and
white colors denote transported and in-river outmigrants respectively. Some areas have several PIT
tag detection sites (e.g., Deschutes R. could be Sherars Falls or Warm Springs Hatchery). Detections
below Bonneville are not shown.
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3
4
5
6
7
Figure 5.4 Summary of the last detection area for CSS steelhead originating in the Snake River
Basin with detections other than at BON, MCN, ICH, and LGR dams (2000-2007 migration years).
Most of these individuals did not eventually migrate to or above LGR. Grey and white colors denote
transported and in-river outmigrants respectively. Some areas have several PIT tag detection sites
(e.g., Deschutes R. could be Sherar’s Falls or Warm Springs Hatchery). Detections below Bonneville
are not shown.
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22
Straying rates for adults that were transported as juveniles were significantly
higher than for adults that had emigrated in-river. This relationship was true for Chinook
(with or without jacks) and steelhead. Transported hatchery and wild Chinook strayed 17
and 16 times more often than their in-river counterparts respectively (0.52% vs. 0.03%
and 0.97% vs. 0.06%). Transported hatchery and wild steelhead strayed 8 times more
often than those that emigrated in-river (5.77% vs. 0.69%). All of the comparisons
between transported and in-river outmigrants were statistically significant (Figure 5.3).
The result that transported steelhead strayed about 5% more than their in-river
counterparts is similar to results found with radio-tagging techniques by Keefer et al.
2008 (i.e. hatchery steelhead 5.3% higher and wild steelhead 2.6% higher). The
magnitude of the increased straying rate for transported hatchery Chinook is lower here
than that found by Keefer et al. 2008 (6.9% higher); this may be due to incomplete
coverage of the straying area for PIT-tagged fish.
Figure 5.3 Straying rates for hatchery Chinook (pooled across migration years 2001-2008) both with
and without jacks and wild + hatchery steelhead (pooled across migration years 2005-2007). Each is
shown for adults that were both transported as smolts and those that emigrated in-river. The
bootstrapped 90% confidence interval for each rate is plotted. The confidence interval for the
difference between bootstrapped straying rates (ie. θ) is printed above each pair of estimates. Strays
were defined as adults detected outside the FCRPS without a subsequent detection within the
FCRPS, including at or above LGR.
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40
41
42
43
44
45
Discussion
D represents the differential delayed mortality between transported and in-river
subsets of CSS groups. It appears that most of the positive effects are evident in the
ocean component of the post-Bonneville survival. A lower adult success rate may be due
to higher harvest and/or natural mortality or impaired homing, straying, and the
subsequent greater exposure to harvest. The adult success rate differentials for these
groups are typically below one in these years. The geometric mean of the adult success
rate differential across all Chinook hatcheries and years is 91%. These results indicate
that transportation of hatchery Chinook interferes with the adult success rate. The
consequence is that the benefits of transportation decrease for these groups as adults
move upstream.
In contrast, the adult success rate differential for wild Chinook is nearer to and
above one in years when many hatchery groups are not. The geometric mean of these
adult success rates across all years is 91%. However, the ocean component differential is
below one in all years but 2001. It may be that wild Chinook are more strongly imprinted
at the time they enter the hydrosystem but overall the effects of transportation after
passage of BON on the juvenile migration are negative as compared with in-river
juvenile outmigration.
D is generally higher for wild and hatchery steelhead than for other CSS groups
(see Chapter 4) and this is typically expressed in the ocean differential component. There
is evidence to suggest some overwintering behavior in the Lower and Mid Columbia for
both transported and in-river out-migrants. However, when comparing the success of the
two groups, the success of the returning adults is negatively affected by transportation.
The geometric means of adult success rate differential for hatchery and wild steelhead
across all years were 90% and 86% respectively. In the 2008 CSS annual report
(Berggren et al. 2008), bypassed steelhead were found to have a slightly smaller median
length than in-river steelhead for 2003-2005. If this difference resulted in an ostensibly
less fit transported fish, this would make the transported population more susceptible to
predation, and one would expect the ocean component differential for these groups to be
less than one. However, since the opposite is true, if there is an effect of this size
difference it does not preclude a positive effect of transportation in the ocean component.
The adult success differential measures the relative success in surviving the
straying/harvest/mortality gauntlet during the adult return for fish that out-migrated via
the transportation program and in-river routes. This parameter expresses the combined
difference in natural mortality, straying, and any changes in harvest pressure as a result of
straying. A large majority of point measurements of the adult success rate differential
were less than one (less than zero when log transformed). These results indicate that
during 2000-2007, while transportation can increase or decrease ocean survival, it most
often decreases the fidelity of adults returning to their natal habitat once in the
hydrosystem.
Consistent with these results, our AIC-based model-selection exercise also
demonstrates a negative effect of transportation history on upstream adult migration
success. The transport variable was in the top model(s) within each of four model sets
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17
for wild and hatchery steelhead and wild and hatchery Chinook. This negative effect was
always statistically significant.
Strays were identified in the Lower Columbia and the Middle Columbia rivers
from both Chinook and steelhead stocks. We identified a significant difference in adult
straying rates for fish that were transported as juveniles when compared to those that had
outmigrated in-river. Straying rates during the adult migration were higher for
individuals that were transported as juveniles than those that outmigrated in-river. This
was significant for Snake River hatchery Chinook and Snake River wild and hatchery
steelhead.
Run year survival rates of adults migrating upstream are important to harvest and
hydro managers for comparisons to survival thresholds and performance standards and
are used for run reconstruction and population viability assessments. A ‘return year’
overall adult rate is the success rate that represents all of the individuals in the Snake
River run at large, weighted across their different juvenile in-river and transport route
outmigration experiences. In the future we plan to estimate an overall adult passage
success rate by return year.
110
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Supporting tables
Table 5.1 Counts of adults at LGR and BON for all Snake River CSS groups for the juvenile
outmigration years 2000-2008. Counts are shown for fish with two different routes of passage as
emigrating juveniles (transported [T0 before 2006, TX thereafter] and in-river groups [CX]). The
“adds” column is for any individual adults seen at any upstream facility (MCA, ICH, or LGR) and
not seen at BON; BON efficiency is calculated with these counts.
Rear-type/
species/
Migr Yr
LGR-CX
BONCX
BON-CX
adds
BON
efficiency
(TX + CX)
N/A
5
1
8
12
0
5
3
N/A
176
143
360
246
547
239
228
Geom(ST)
N/A
228
155
400
291
640
218
221
80.1%
N/A
6
2
5
6
11
68
42
Geom (CH)
N/A
97.9%
99.3%
98.7%
97.8%
98.4%
76.3%
84.0%
98.4%
18
96
61
246
265
10
6
8
0
0
0
8
2
0
0
0
2
7
5
9
10
30
5
11
Geom(ST)
3
8
8
10
14
33
7
16
96.4%
0
0
0
0
1
1
1
0
Geom (CH)
100.0%
100.0%
100.0%
97.0%
98.9%
97.7%
92.9%
100.0%
98.9%
24
60
31
131
117
31
3
9
33
80
41
164
132
41
3
11
2
4
0
3
7
1
0
1
22
169
49
232
185
201
145
109
Geom(ST)
21
193
60
281
210
223
167
126
97.6%
2
3
0
6
12
7
6
1
Geom (CH)
93.1%
97.5%
100.0%
98.0%
94.7%
97.1%
96.6%
98.6%
96.7%
9
34
30
111
33
30
83
44
10
44
39
124
52
29
105
53
1
3
0
6
2
2
1
2
13
50
43
137
50
51
81
52
Geom(ST)
14
57
51
154
52
55
99
57
97.3%
1
3
2
6
5
4
3
2
Geom (CH)
92.3%
94.4%
97.8%
95.9%
93.7%
93.3%
98.1%
96.5%
94.6%
LGRTX
BONTX
BON-TX
adds
N/A
183
211
497
349
12
14
13
N/A
295
262
583
491
21
17
15
11
79
48
206
207
7
4
5
2000
HCH-CATH
HCH-DWOR
HCH-IMNA
HCH-MCCA
HCH-RAPH
WCH
HST
WST
2001
HCH-CATH
HCH-DWOR
HCH-IMNA
HCH-MCCA
HCH-RAPH
WCH
HST
WST
2002
HCH-CATH
HCH-DWOR
HCH-IMNA
HCH-MCCA
HCH-RAPH
WCH
HST
WST
2003
HCH-CATH
HCH-DWOR
HCH-IMNA
HCH-MCCA
HCH-RAPH
WCH
HST
WST
2004
111
Rear-type/
species/
Migr Yr
LGRTX
BONTX
BON-TX
adds
HCH-CATH
HCH-DWOR
HCH-IMNA
HCH-MCCA
HCH-RAPH
WCH
HST
WST
11
61
26
84
70
68
10
39
14
121
41
113
88
88
9
60
11
43
17
141
55
38
18
41
LGR-CX
BONCX
BON-CX
adds
BON
efficiency
(TX + CX)
0
3
1
1
2
2
2
1
7
46
8
25
23
48
33
5
Geom(ST)
7
66
12
41
25
59
39
7
97.3%
1
1
0
0
2
2
0
0
Geom (CH)
95.5%
97.9%
98.1%
99.4%
96.6%
97.4%
96.0%
98.5%
97.5%
14
65
23
168
69
49
29
52
1
2
0
2
5
1
1
1
4
30
8
41
20
20
43
17
Geom(ST)
4
35
8
49
23
28
56
17
94.8%
1
1
0
0
1
0
1
5
Geom (CH)
90.0%
97.1%
100.0%
99.1%
93.9%
98.7%
97.7%
92.0%
96.4%
13
57
46
173
107
80
25
48
25
93
62
200
150
92
35
82
0
0
0
3
4
0
0
0
23
80
55
153
69
79
154
32
Geom(ST)
34
131
66
186
102
101
192
46
99.4%
0
1
1
0
3
1
1
1
Geom (CH)
100.0%
99.6%
99.2%
99.2%
97.3%
99.5%
99.6%
99.2%
99.1%
12
16
23
78
41
39
56
134
15
27
27
93
64
47
84
176
0
0
0
1
2
0
0
3
20
127
70
152
71
167
194
138
Geom(ST)
22
172
90
187
95
197
238
175
99.0%
3
3
0
1
5
1
2
2
Geom (CH)
92.5%
98.5%
100.0%
99.3%
95.8%
99.6%
99.4%
98.6%
97.6%
99
65
98
135
237
128
123
113
141
186
346
166
2
0
1
3
5
2
86
124
124
147
225
435
113
209
162
196
303
517
0
0
0
4
6
6
Geom (CH)
99.2%
100.0%
99.7%
98.2%
98.3%
98.8%
99.0%
2005
HCH-CATH
HCH-DWOR
HCH-IMNA
HCH-MCCA
HCH-RAPH
WCH
HST
WST
2006
HCH-CATH
HCH-DWOR
HCH-IMNA
HCH-MCCA
HCH-RAPH
WCH
HST
WST
2007
HCH-CATH
HCH-DWOR
HCH-IMNA
HCH-MCCA
HCH-RAPH
WCH
HST
WST
2008
HCH-CATH
HCH-DWOR
HCH-IMNA
HCH-MCCA
HCH-RAPH
WCH
112
1
Table 5.2 Adult success rates for all CSS groups for the juvenile outmigration years 2000-2008.
Adult success rate for the transported (T0 before 2006, TX thereafter) and in-river groups (CX), and
the success rate differential of those rates are each shown with their 90% confidence interval. Values
were the differential is significant different from one are shown in bold.
Mig.
RearYear type/Species Hatchery Success T0
Success Cx
Success ratio T0/Cx
2000 HCH
CATH
NA
NA
NA
HCH
DWOR
0.608 (0.561 - 0.655) 0.756 (0.707 - 0.801) 0.804 (0.724 - 0.891)
HCH
IMNA
0.8 (0.759 - 0.84)
0.916 (0.877 - 0.954) 0.873 (0.813 - 0.936)
HCH
MCCA
0.841 (0.816 - 0.866) 0.888 (0.862 - 0.916) 0.947 (0.906 - 0.988)
HCH
RAPH
0.695 (0.659 - 0.728) 0.826 (0.787 - 0.863) 0.841 (0.785 - 0.9)
WCH
0.562 (0.379 - 0.745) 0.841 (0.817 - 0.865) 0.669 (0.446 - 0.888)
HST
0.628 (0.416 - 0.927) 0.836 (0.796 - 0.873) 0.751 (0.486 - 1.11)
WST
0.728 (0.513 - 1.013) 0.866 (0.831 - 0.902) 0.84 (0.586 - 1.182)
2001 HCH
CATH
0.611 (0.429 - 0.8)
0.667 (0 - 1)
0.917 (0.5 - Inf)
HCH
DWOR
0.823 (0.76 - 0.885)
0.875 (0.6 - 1)
0.94 (0.782 - 1.331)
HCH
IMNA
0.787 (0.701 - 0.868) 0.625 (0.333 - 1)
1.259 (0.825 - 2.468)
HCH
MCCA
0.812 (0.772 - 0.85)
0.873 (0.683 - 0.98)
0.93 (0.81 - 1.189)
HCH
RAPH
0.773 (0.732 - 0.815) 0.707 (0.495 - 0.904) 1.094 (0.845 - 1.573)
WCH
0.684 (0.432 - 0.917) 0.888 (0.788 - 0.976) 0.77 (0.486 - 1.061)
HST
0.619 (0.286 - 1)
0.663 (0.35 - 1)
0.933 (0.4 - 2)
WST
0.625 (0.333 - 0.9)
0.688 (0.476 - 0.889) 0.909 (0.433 - 1.545)
2002 HCH
CATH
0.677 (0.537 - 0.814) 0.975 (0.864 - 1.091) 0.694 (0.522 - 0.893)
HCH
DWOR
0.731 (0.643 - 0.826) 0.854 (0.812 - 0.892) 0.857 (0.747 - 0.983)
HCH
IMNA
0.756 (0.64 - 0.864)
0.817 (0.735 - 0.896) 0.926 (0.76 - 1.096)
HCH
MCCA
0.783 (0.727 - 0.837) 0.809 (0.767 - 0.85)
0.967 (0.881 - 1.062)
HCH
RAPH
0.84 (0.784 - 0.895)
0.835 (0.791 - 0.876) 1.006 (0.922 - 1.099)
WCH
0.734 (0.615 - 0.845) 0.875 (0.836 - 0.912) 0.839 (0.695 - 0.968)
HST
0.966 (0.943 - NA)
0.839 (0.795 - 0.884) 1.152 (1.087 - NA)
WST
0.806 (0.538 - 1.108) 0.853 (0.799 - 0.905) 0.946 (0.625 - 1.32)
2003 HCH
CATH
0.831 (0.597 - 1.066) 0.857 (0.677 - 1.019) 0.969 (0.636 - 1.425)
HCH
DWOR
0.729 (0.615 - 0.851) 0.828 (0.737 - 0.907) 0.881 (0.719 - 1.075)
HCH
IMNA
0.753 (0.644 - 0.867) 0.825 (0.728 - 0.914) 0.912 (0.756 - 1.109)
HCH
MCCA
0.858 (0.805 - 0.911) 0.853 (0.807 - 0.903) 1.006 (0.92 - 1.095)
HCH
RAPH
0.595 (0.486 - 0.705) 0.901 (0.811 - 0.984) 0.66 (0.522 - 0.825)
WCH
0.966 (0.881 - 1.058) 0.865 (0.784 - 0.944) 1.116 (0.966 - 1.305)
HST
0.775 (0.71 - 0.84)
0.802 (0.73 - 0.869)
0.966 (0.857 - 1.092)
WST
0.801 (0.706 - 0.89)
0.88 (0.8 - 0.952)
0.91 (0.779 - 1.058)
2004 HCH
CATH
0.75 (0.545 - 0.929)
0.955 (0.667 - 1.313) 0.786 (0.476 - 1.227)
HCH
DWOR
0.494 (0.417 - 0.57)
0.682 (0.587 - 0.78)
0.723 (0.584 - 0.894)
HCH
IMNA
0.622 (0.488 - 0.755) 0.654 (0.422 - 0.889) 0.951 (0.643 - 1.514)
HCH
MCCA
0.739 (0.672 - 0.806) 0.606 (0.47 - 0.735)
1.219 (0.986 - 1.593)
HCH
RAPH
0.768 (0.69 - 0.836)
0.889 (0.744 - 1.026) 0.865 (0.716 - 1.059)
WCH
0.752 (0.676 - 0.824) 0.792 (0.702 - 0.884) 0.95 (0.807 - 1.105)
HST
1.067 (0.802 - 1.478) 0.812 (0.713 - 0.904) 1.313 (0.964 - 1.944)
WST
0.64 (0.538 - 0.743)
0.704 (0.4 - 0.986)
0.91 (0.636 - 1.668)
2005 HCH
CATH
0.707 (0.515 - 0.889) 0.9 (0.462 - 1.789)
0.786 (0.327 - 1.857)
HCH
DWOR
0.642 (0.547 - 0.743) 0.832 (0.717 - 0.939) 0.772 (0.626 - 0.959)
HCH
IMNA
0.739 (0.583 - 0.882) 1 (1 - 1)
0.739 (0.583 - 0.885)
113
Mig.
Year
2006
2007
2008
Reartype/Species
HCH
HCH
WCH
HST
WST
HCH
HCH
HCH
HCH
HCH
WCH
HST
WST
HCH
HCH
HCH
HCH
HCH
WCH
HST
WST
HCH
HCH
HCH
HCH
HCH
WCH
Hatchery
MCCA
RAPH
CATH
DWOR
IMNA
MCCA
RAPH
CATH
DWOR
IMNA
MCCA
RAPH
CATH
DWOR
IMNA
MCCA
RAPH
Success T0
0.832 (0.783 - 0.878)
0.748 (0.659 - 0.843)
0.766 (0.657 - 0.86)
0.606 (0.451 - 0.763)
0.725 (0.629 - 0.815)
0.52 (0.333 - 0.694)
0.61 (0.526 - 0.693)
0.736 (0.65 - 0.82)
0.858 (0.812 - 0.9)
0.694 (0.628 - 0.757)
0.865 (0.806 - 0.921)
0.711 (0.59 - 0.833)
0.581 (0.491 - 0.666)
0.74 (0.563 - 0.901)
0.584 (0.426 - 0.743)
0.852 (0.727 - 0.962)
0.833 (0.76 - 0.898)
0.614 (0.513 - 0.716)
0.826 (0.736 - 0.912)
0.663 (0.577 - 0.748)
0.751 (0.693 - 0.805)
0.798 (0.734 - 0.86)
0.575 (0.504 - 0.652)
0.693 (0.627 - 0.756)
0.713 (0.658 - 0.765)
0.674 (0.629 - 0.712)
0.762 (0.705 - 0.823)
1
114
Success Cx
0.829 (0.737 - 0.912)
0.816 (0.676 - 0.96)
0.705 (0.559 - 0.842)
0.75 (0.651 - 0.845)
0.92 (0.731 - 1.143)
0.676 (0.535 - 0.821)
0.608 (0.539 - 0.673)
0.827 (0.747 - 0.908)
0.816 (0.771 - 0.862)
0.658 (0.578 - 0.735)
0.778 (0.707 - 0.845)
0.799 (0.751 - 0.846)
0.69 (0.571 - 0.805)
0.841 (0.684 - 1)
0.727 (0.668 - 0.78)
0.778 (0.707 - 0.851)
0.807 (0.759 - 0.852)
0.716 (0.632 - 0.794)
0.844 (0.801 - 0.887)
0.81 (0.763 - 0.85)
0.777 (0.723 - 0.826)
0.755 (0.689 - 0.82)
0.593 (0.535 - 0.651)
0.763 (0.705 - 0.817)
0.737 (0.684 - 0.791)
0.73 (0.69 - 0.774)
0.832 (0.805 - 0.859)
Success ratio T0/Cx
1.003 (0.89 - 1.14)
0.917 (0.742 - 1.157)
1.086 (0.863 - 1.415)
0.808 (0.583 - 1.067)
0.788 (0.598 - 1.031)
0.769 (0.633 - 0.972)
1.004 (0.906 - 1.131)
0.89 (0.811 - 0.985)
1.052 (0.996 - 1.113)
1.054 (0.944 - 1.201)
1.112 (1.023 - 1.223)
0.891 (0.841 - 0.946)
0.841 (0.722 - 1.016)
0.88 (0.74 - 1.082)
0.803 (0.748 - 0.874)
1.095 (1.001 - 1.204)
1.032 (0.977 - 1.096)
0.857 (0.773 - 0.971)
0.979 (0.932 - 1.032)
0.818 (0.78 - 0.869)
0.965 (0.909 - 1.038)
1.058 (0.974 - 1.159)
0.97 (0.884 - 1.075)
0.908 (0.848 - 0.982)
0.968 (0.901 - 1.042)
0.922 (0.871 - 0.977)
0.916 (0.887 - 0.947)
1
Table 5.3. Wild Chinook logistic regression model-selection results for CSS + LGR marked
individuals. Note, Y = P(Success | X), where X is the variable in question. Models are ordered by
AICc score. The entire set of models is shown. Those with a ΔAIC < 2 can be considered nearly
equivalent. K is the number of estimated parameters (inclusive of variance).
Model
K
AICc
∆ AICc
wi
transport + Qtot_Col
3
3460.1
0.0
53.0%
transport + Qtot_Col + LGR.marking
4
3462.0
2.0
20.0%
transport + Qtot_Col + T_Col
4
3462.1
2.0
20.0%
transport + Qtot_Col + T_Col + LGR.marking
5
3464.0
4.0
7.0%
Qtot_Col + LGR.marking
3
3475.5
15.4
0.0%
Qtot_Col + T_Col + LGR.marking
4
3477.5
17.4
0.0%
Qtot_Col
2
3477.9
17.9
0.0%
transport + Qspill_Col
3
3478.7
18.6
0.0%
transport + T_Col
3
3479.0
19.0
0.0%
Qtot_Col + T_Col
3
3479.9
19.8
0.0%
transport + Qspill_Col + LGR.marking
4
3480.3
20.3
0.0%
transport + Qspill_Col + T_Col
4
3480.5
20.4
0.0%
transport + T_Col + LGR.marking
4
3480.6
20.6
0.0%
transport + Qspill_Col + T_Col + LGR.marking
5
3482.1
22.1
0.0%
Qspill_Col + LGR.marking
3
3492.8
32.7
0.0%
T_Col + LGR.marking
3
3492.8
32.7
0.0%
Qspill_Col + T_Col + LGR.marking
4
3494.6
34.5
0.0%
transport
2
3495.4
35.3
0.0%
transport + LGR.marking
3
3496.7
36.6
0.0%
Qspill_Col
2
3496.7
36.7
0.0%
T_Col
2
3496.8
36.7
0.0%
Qspill_Col + T_Col
3
3498.6
38.5
0.0%
Qtot_Col = Flow at BON. Qspill_Col = spill at BON, JDA, MCN, IHR.
T_Col = Temperature at BON.
Transport is a dummy variables denoting transport at LGR, LGS or LMN.
LGR.marking is a dummy variable denoting whether a smolt was marked at LGR or not.
2
3
4
5
6
Table 5.4. Hatchery Chinook logistic regression model-selection results for CSS marked
Model
K
AICc
∆ AICc
wi
4
11018.7
0.0
98.0%
4
11026.2
7.5
2.0%
transport + T_Col
3
11038.3
19.6
0.0%
Qtot_Col + T_Col
3
11043.3
24.6
0.0%
Qspill_Col + T_Col
3
11053.8
35.1
0.0%
T_Col
2
11063.0
44.3
0.0%
3
11100.1
81.4
0.0%
Qtot_Col
2
11118.6
99.9
0.0%
3
11210.3
191.6
0.0%
Qspill_Col
2
11224.9
206.2
0.0%
transport
2
11227.4
208.7
0.0%
See table 5.3 for variable names7 key.
115
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3
4
5
6
7
8
9
10
11
12
13
Table 5.5. Wild steelhead logistic regression model-selection results for CSS + LGR marked
Model
K
AICc
∆ AICc
wi
4
2809.0
0.0
52.0%
transport + Qspill_Col + T_Col + LGR.marking
5
2809.6
0.6
39.0%
3
2814.7
5.7
3.0%
transport + Qspill_Col + LGR.marking
4
2815.3
6.3
2.0%
4
2816.5
7.6
1.0%
transport + Qtot_Col + T_Col + LGR.marking
5
2816.7
7.8
1.0%
3
2817.6
8.7
1.0%
transport + Qtot_Col + LGR.marking
4
2817.9
8.9
1.0%
transport + T_Col
3
2819.4
10.5
0.0%
transport + T_Col + LGR.marking
4
2819.5
10.5
0.0%
transport
2
2820.9
12.0
0.0%
transport + LGR.marking
3
2821.1
12.2
0.0%
Qspill_Col + T_Col + LGR.marking
4
2823.4
14.5
0.0%
Qspill_Col + LGR.marking
3
2830.0
21.1
0.0%
Qspill_Col + T_Col
3
2831.8
22.8
0.0%
Qtot_Col + T_Col + LGR.marking
4
2833.2
24.2
0.0%
Qtot_Col + LGR.marking
3
2834.6
25.6
0.0%
T_Col + LGR.marking
3
2836.2
27.3
0.0%
Qspill_Col
2
2838.8
29.9
0.0%
Qtot_Col + T_Col
3
2844.6
35.6
0.0%
Qtot_Col
2
2845.9
36.9
0.0%
T_Col
2
2848.1
39.2
0.0%
See table 5.3 for variable names key.
Table 5.6. Hatchery steelhead logistic regression model-selection results for CSS marked
Model
transport
transport + T_Col
Qspill_Col
T_Col
Qspill_Col + T_Col
Qtot_Col
Qtot_Col + T_Col
See table 5.3 for variable names key.
K
2
3
3
4
3
4
2
2
3
2
3
116
AICc
1407.6
1407.7
1408.6
1409.5
1409.6
1410.6
1416.4
1417.9
1418.4
1418.7
1419.9
∆ AICc
0.0
0.1
1.0
1.9
2.0
3.0
8.9
10.3
10.8
11.1
12.3
wi
28.0%
27.0%
17.0%
11.0%
10.0%
6.0%
0.0%
0.0%
0.0%
0.0%
0.0%
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Chapter 6
Patterns in Annual Overall SARs
Success of any hydrosystem mitigation strategy will require achievement of
smolt-to-adult survival rates sufficient to meet recovery and rebuilding objectives, in
combination with a program to maintain or achieve adequate survival in other life stages.
An independent peer review of the transportation program in the early 1990s (Mundy et
al. 1994) concluded: “[u]nless a minimum level of survival is maintained for listed
species sufficient for them to at least persist, the issue of the effect of transportation is
moot.”
The Northwest Power and Conservation Council (NPCC 2009) adopted a goal of
achieving SARs in the 2-6% range (minimum 2%; average 4%) for federal ESA-listed
Snake River and upper Columbia River salmon and steelhead. For the populations in
these listed groups, an overall SAR is the SAR that includes the survival of all
outmigrating smolts weighted across their different in-river and transport route
experiences; it is the SAR of an entire brood of smolts, irrespective of their route of
passage through the hydrosystem. The NPCC (2009) Fish and Wildlife Program
objectives for unlisted populations or listed populations downstream of the Snake River
and Upper Columbia River basins are to “significantly improve the smolt-to-adult return
rates (SARs) for Columbia River Basin salmon and steelhead, resulting in productivity
well into the range of positive population replacement.”
The NPCC (2009) also adopted a strategy to identify the effects of ocean
conditions on anadromous fish survival and use this information to evaluate and adjust
inland actions. The NPCC noted that while we cannot control the ocean, we can monitor
ocean conditions and related salmon survival and take actions to improve the likelihood
that Columbia River salmon can survive varying ocean conditions. A better
understanding of the conditions salmon face in the ocean can suggest which factors will
be most critical to survival, and thus provide insight as to which actions taken inland will
provide the greatest restoration benefit. Analyses in this chapter address the extent to
which wild spring/summer Chinook and steelhead population aggregates may be meeting
the NPCC (2009) biological objectives. Parameters estimated in the CSS allow for
partitioning first year ocean survival, S.o1, from SARs (Wilson 2003; Zabel et al. 2006;
Tuomikoski et al. 2009; Petrosky and Schaller 2010), which can then be used to evaluate
ocean and smolt migration factors that may influence ocean survival as called for in the
Fish and Wildlife Program (NPCC 2009).
The NPCC 2-6% SAR objectives are consistent with analyses conducted by the
Plan for Analyzing and Testing Hypotheses (PATH), in support of the 2000 Biological
Opinion of the Federal Columbia River Power System (FCRPS). Marmorek et al. (1998)
found that median SARs of 4% were necessary to meet the NMFS interim 48-year
recovery standard for Snake River spring/summer Chinook; meeting the 100-year interim
survival standard required a median SAR of at least 2%. The NPCC (2009) SAR
objectives did not specify the points in the life cycle where Chinook smolt and adult
numbers should be estimated. However, the original PATH analysis for Snake River
spring/summer Chinook was based on SARs calculated as adult and jack returns to the
uppermost dam, adjusted for mainstem harvest rates (Marmorek et al. 1998); no
adjustment was made for adult upstream passage loss or straying. PATH analyses also
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did not identify specific SARs necessary for steelhead survival and recovery. However
before completion of the FCRPS, steelhead SARs were somewhat greater than those of
spring/summer Chinook (Marmorek et al. 1998). The Interior Columbia River Technical
Recovery Team (ICTRT 2007) developed biological recovery criteria based on the
Viable Salmonid Population concepts (McElhany et al. 2000). Additional SAR
objectives may be associated with the IC-TRT recovery criteria for abundance and
productivity when adopted or incorporated into a Recovery Plan, as well as with the
objectives identified in Fish and Wildlife Program subbasin plans, and other State and
Tribal fishery management plans. Regardless of specific future SAR objectives, the same
types of data and analytical methods will be required in the future to evaluate the overall
effectiveness of hydrosystem actions in addressing recovery and mitigation goals. To
address these multiple objectives, we present bootstrapped SARs and confidence
intervals based on CSS PIT-tagged adult returns to both Bonneville Dam (BOA) and the
uppermost dam for Snake River fish (e.g., Lower Granite Dam; GRA).
Alternative SAR objectives will likely require enumerating smolts and adults at
different locations, depending on how broadly the objective is defined. That is, different
adult accounting locations would be required if an SAR objective was defined narrowly
for population persistence or more broadly to maintain productive natural populations
with sustainable fisheries. The SAR estimates in this report are based on smolts at the
uppermost dam (Lower Granite, McNary, John Day or Bonneville), and adults at either
Bonneville Dam or the uppermost dam. We have made preliminary comparisons of these
SAR estimates to the NPCC 2-6% SAR objectives, recognizing additional accounting for
harvest, straying and other upstream passage losses may be needed in the future as NPCC
and other SAR objectives are clarified.
To compare historical population productivity in the smolt-to-adult life stage, it is
necessary to account for changes in mainstem harvest rates and upstream passage success
(Petrosky and Schaller 2010). Mainstem Columbia River harvest rates decreased
markedly in the 1970s following construction of the FCRPS and the decline in abundance
and productivity of upriver Columbia and Snake River populations. Therefore, we also
present a time series of SARs for Snake River Chinook and steelhead based on smolts at
the uppermost dam to adult returns to the Columbia River mouth for the 1964-2008 smolt
migration years; this time frame spans completion of the FCRPS, decreases in Columbia
River harvest rates and a period of variable ocean conditions.
The NPCC 2-6% SAR objective for Chinook addresses the total adult return
including jacks (i.e., 1-salt male Chinook). Therefore, in this chapter we present
estimates of overall SAR with jacks included and the CSS standard reporting statistic of
SARs with jacks excluded. Most other Chinook analyses in this and previous reports, are
based strictly on adults (age 2-salt and older). These calculations include the generation
of SARs by study category, TIR, D, and adult upstream migration success rates. By
using only 2-salt and older returning Chinook adults in the estimation of the key CSS
parameters, we are assuring that the results will be more directly reflective of the primary
spawning populations (females and older males) in each Chinook ESU, region or
subbasin. This is consistent with previous population viability (persistence) analyses
(Marmorek et al. 1998; STUFA 2000; Karieva et al. 2000; Deriso et al. 2001; Peters and
Marmorek 2001; Wilson 2003; Zabel et al. 2006; ICTRT 2007).
118
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The primary objective for Snake River wild and hatchery spring/summer Chinook
and steelhead is to update the long-term SAR data series for CSS study fish. Overall
SARs are based on PIT-tagged fish, which experienced the same conditions as untagged
smolts under a given year’s fish passage management scenario. Beginning in migration
year 2006, this “run at large” group was represented by the Group TWS (Chapter 1).
Prior to 2006, we estimated the proportion of run at large represented by each study
group T0, C0 and C1. The CSS 2009 Annual Report (Tuomikoski et al. 2009) compared
overall SARs using the two methods for migration years 2006 and 2007 (through 2-salt
returns). Lastly, the overall SARs with jacks included are presented for all 15 years of
PIT-tagged wild Chinook data and 12 years of PIT-tagged hatchery Chinook data (except
for Catherine Creek hatchery Chinook, which has an 8-year history). The effect of
including jacks in the overall SAR estimates are presented for the wild Snake River
Chinook aggregate and each of the five CSS Snake River hatchery groups. Overall SARs
for Snake River aggregate wild and aggregate hatchery steelhead are presented for 12
years beginning in 1997.
CSS, Lower Snake River Compensation Plan (LSRCP) and Idaho Power
Company (IPC) coordinated efforts to increase the PIT tagging of Snake River hatchery
steelhead beginning in migration year 2008 so key parameters could be estimated at a
finer resolution of run-type and subbasin: for Grande Ronde River A-run (GRN-A),
Imnaha River A-run (IMN-A), Salmon River A-run (SAL-A), Salmon River B-run (SALB), and Clearwater River B-run (CLW-B).
The primary objective for mid Columbia River (BON to PRD) wild and hatchery
spring Chinook and steelhead is to establish and update SAR data series for subbasins in
this region. Overall SARs are presented for 9 years (2000-2008) for John Day River wild
Chinook, Carson Hatchery Chinook, and Cle Elum Hatchery Chinook. Overall SARs are
also presented for one year (2008) for John Day wild steelhead. The CSS is compiling
the data set to estimate SARs for mid Columbia wild steelhead SARs for the John Day
River beginning in 2004, and the Deschutes River beginning in 2006; we expect to begin
reporting these earlier years in the 2011 annual report.
The primary objective for upper Columbia River (above PRD) wild and hatchery
spring Chinook and steelhead is to establish and update SAR data series for subbasins in
this region. Overall SARs are presented for 9 years (2000-2008) for Leavenworth
Hatchery Chinook.
Methods
Estimation of 90% confidence intervals for annual SARs applicable to all mark
populations
For both Snake and Columbia River basin PIT-tag salmonid populations, nonparametric 90% confidence intervals are computed around the estimated annual overall
SARs. The non-parametric bootstrapping approach of Efron and Tibshirani (1993) is
used where first the point estimates are calculated from the population, and then the data
is re-sampled with replacement to create 1000 simulated populations. These 1000
iterations are used to produce a distribution of annual SARs from which the value in the
119
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30
50th ranking is the lower limit and value in the 951st ranking is the upper limit of the
resulting 90% nonparametric confidence interval.
Snake River basin populations originating above Lower Granite Dam
Estimation of overall annual SARs for pre-2006 smolt migration years
Annual estimates of LGR-to-GRA SAR reflective of the run-at-large for wild
steelhead, hatchery steelhead, wild Chinook, and hatchery Chinook that outmigrated in
1997 to 2005 are computed by weighting the SARs computed with PIT-tagged fish for
each respective study category by the proportion of the run-at-large transported and
remaining in-river. The proportions of the run-at-large reflected by each of the CSS
study categories C0, C1 and T0 were estimated as follows. First, the number of PITtagged smolts tj that would have been transported at each of the three Snake River
collector dams (j=2 for LGR, j=3 for LGS, and j=4 for LMN) if these fish had been
routed to transportation in the same proportion as the run-at-large is estimated. This
estimation uses run-at-large collection and transportation data for these dams from the
FPC Smolt Monitoring Program (SMP). The total estimated number transported across
the three Snake River collector dams in LGR equivalents equals T0* = t2+t3/S2+t4/(S2S3).
When a portion of the collected run-at-large fish is being bypassed as occurred in 1997,
then there will be a component of the PIT-tagged fish also in that bypass category
(termed C1* in this discussion). In most years, the C1* is at or near zero. When run-atlarge bypassing occurs, C1* = (T0 + C1) – T0*. The sum of estimated smolts in categories
C0, T0*, and C1* is divided into each respective category’s estimated smolt number to
provide the proportions to be used in the weighted SAR computation.
The proportion of the run-at-large that each category of PIT-tagged fish represents
is then multiplied by its respective study category-specific SAR estimate, i.e., SAR(C0),
SAR(C1), and SAR(T0), and summed to produce an annual overall weighted SARLGR-toLGR for each migration year except 2001 as follows:
SARAnnual  w T0*  * SAR T0 
 w  C0*  * SAR  C0 
31
32
33
 w  C1*  * SAR  C1 
where,

t   t
T0*   t2    3    4 
 S 2   S 2 * S3 
34
35
and,
36
37
38
39
40
reflect the number of PIT-tag smolts in transport and bypass categories, respectively, if
collected PIT-tag smolts were routed to transportation in the same proportion as run-atlarge; and
C1*  T0  C1   T0*
120
1
w T0*  
2
3
4
5
is the transported smolt proportion,
w  C0  
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T0*
T0*  C0  C1* 
C0
T  C0  C1* 
*
0
is the non-detected (LGR, LGS, LMN) smolt proportion, and
w  C1*   1  w T0*   w  C0 
is the bypass (LGR, LGS, LMN) smolt proportion.
Estimation of overall annual SARs in smolt migration year beginning 2006
With the new approach of pre-assigning part of the release into a monitor-mode
group (called Group T) that follows the routing of the untagged population the collector
dams, we now have the opportunity to directly estimate the annual SARs with fewer
parameters required to be estimated during intermediate steps before arriving at the final
overall annual SAR estimate as occurred in pre-2006 years. In these cases, the estimation
of the annual overall SAR is simply the number of returning adults in this group divided
by the estimated number of smolts arriving LGR (both detected and undetected). The
estimated number of PIT-tagged smolts arriving LGR is obtained by multiplying the
release number in Group T by the estimated S1 (survival rate from release to LGR
tailrace) obtained from running the CJS model on the total release. Group T reflects the
untagged fish passage experience under a given year’s fish passage management
scenario.
Middle and Upper Columbia River basin populations
Estimation of overall annual SARs in all smolt migration years
Estimation of overall SARs for Chinook from Carson, Leavenworth, and Cle
Elum hatcheries and wild Chinook and steelhead from the John Day River are based on
estimated PIT-tagged smolts arriving the first PIT-tagged monitored dam and returning
adults indexed at Bonneville Dam. The PIT-tagged smolt numbers are estimated by
multiplying the release number by CJS reach survival rate from (i) release to MCN
tailrace for Leavenworth and Cle Elum Hatchery Chinook (minus PIT-tagged smolts
transported from MCN during the NOAA transportation studies of 2002 to 2005), (ii)
release to JDA tailrace for John Day River wild Chinook and steelhead, and (iii) release
to BON for Carson Hatchery Chinook, plus an overall SAR based on the total PIT-tagged
smolts in the release from the Carson Hatchery facility for years when the estimated
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release-to- BON survival rate exceeded one. Non-parametric 90% confidence intervals
are estimated with the same bootstrapping protocol as used for the Snake River stocks.
The CSS has compiled a historic time series of SARs for Snake River wild
Chinook and steelhead beginning in 1964 prior to completion of the FCRPS. For years
prior to the CSS PIT-tag based estimates, SARs were based on run reconstruction of
smolt numbers at the uppermost Snake River dam and adults returning to the Columbia
River from literature sources (Raymond 1988; Marmorek et al. 1998; Petrosky et al.
2001; Petrosky and Schaller 2010).
As requested in the ISAB/ISRP (2008) review of the CSS Ten-Year Retrospective
Report (Schaller et al. 2007), we continued the comparison of SARs based on PIT tags
and run reconstruction (RR hereafter), 1998-2004, examined SAR methodologies and
developed hypotheses for possible sources of bias in both the PIT tag and RR SARs for
Snake River wild Chinook.
First year ocean survival (S.o1) estimates were back-calculated from the overall
SAR estimates for wild Snake River spring/summer Chinook and steelhead while taking
into account year-to-year variability in hydrosystem survival and age composition of
returning adults to the Columbia River mouth. The method of deconstructing SARs into
first year ocean survival rates used here is described in Petrosky and Schaller (2010)
(Appendix D), and was similar to approaches used in STUFA (2000), Wilson (2003) and
Zabel et al. (2006).. Estimates of S.o1 can then be used to evaluate ocean and smolt
migration factors that may influence ocean survival as called for in the Fish and Wildlife
Program (NPCC 2009).
Results
Snake River Overall SARs
Historic wild Snake River Chinook SARs (upper dam smolts-to-Columbia River
returns, jacks included) decreased nearly five-fold from pre-FCRPS completion in the
1960s to the 1990s and 2000s (Figure 6.1). The geometric mean SAR during 1964-1969
was 5.9% compared to 1.1% during 1992-1999 and 1.3% since 2000.
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Figure 6.1. SARs from smolts at uppermost Snake River dam to Columbia River returns (including
jacks) for Snake River wild Chinook, 1964-2008. SARs based on run reconstruction (1964-1985,
1992-1993, solid line) and CSS PIT tags (1994-2008, dots and solid line). The NPCC (2009) 2-6%
SAR objective for listed wild populations is shown for reference.
SARs (LGR-to-GRA, jacks included) of PIT-tagged Snake River wild Chinook had a
geometric mean of 0.82% and exceeded the NPCC’s minimum SAR objective of 2% in
only a single migration year (1999) during the period 1994-2008 (Table 6.1; Figure 6.2
top left plot). LGR-GRA SARs with jacks included were about 6% higher (geometric
mean of SAR ratios) than SARs with jacks excluded (Table 6.1). SARs based on jack
and adult returns to BOA were about 26% greater (geometric mean of SAR ratios) than
SARs based on returns to GRA (Table 6.2) because of the combined effect of dam
passage loss, straying and Zone 6 harvest (Chapter 5).
The estimated overall SARs for Snake River hatchery spring and summer
Chinook varied by hatchery and year (Figure 6.2; Tables 6.3-6.12). LGR-GRA SARs for
Dworshak hatchery spring Chinook averaged (geometric mean) 0.54% and did not
exceed 2% in any year during 1997-2008 (Table 6.3). LGR-GRA SARs for Rapid River
hatchery spring Chinook averaged 0.85% and exceeded 2% in a single year (1999; Table
6.5). Catherine Creek hatchery Chinook SARs averaged 0.64% and exceeded 2% only
in 2008 (Table 6.7). In general, the two hatchery summer Chinook populations had
higher SARs than the hatchery spring Chinook populations. LGR-GRA SARs for
McCall hatchery summer Chinook averaged (geometric mean) 1.48% and exceeded 2%
in three years (1998-2000; Table 6.9). LGR-GRA SARs for Imnaha hatchery summer
Chinook averaged 1.28% and also exceeded 2% in three years (1999, 2000 and 2008;
Table 6.3). Although some difference in magnitude of SARs between groups was noted,
the overall SARs (LGR-GRA) of wild and hatchery Snake River Chinook groups were
highly correlated (average r = 0.76) during 1997-2008.
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Figure 6.2. Bootstrapped LGR-to-GRA SAR (with jacks included) and upper and lower CI for
Snake River wild Chinook and five Snake River hatchery groups for migration years 1994-2008.
Migration year 2008 is complete through 2-ocean returns only. The NPCC (2009) minimum 2%
SAR for listed wild populations is shown for reference.
Snake River wild steelhead SARs (upper dam smolts-to-Columbia River returns)
decreased nearly four-fold from the 1960s (pre-FCRPS completion) to the 1990s and
2000s (Figure 6.3). The geometric mean SAR during 1964-1969 was 7.2% compared to
1.7% during 1990-1999 and 2.2% during 2000-2007. Snake River wild steelhead and
wild Chinook SARs were highly correlated (0.70) during the 1964-2007 period.
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Figure 6.3. SARs from smolts at uppermost Snake River dam to Columbia River returns for Snake
River wild steelhead, 1964-2007. SARs based on run reconstruction (1964-1996, solid line) and CSS
PIT tags (1997-2007, dots and solid line). The NPCC (2009) 2-6% SAR objective for listed wild
populations is shown for reference.
The geometric mean SAR (LGR-to-GRA) of PIT-tagged Snake River wild
steelhead was 1.41% during the period 1997-2007 (Table 6.13; Figure 6.4 top plot);
SARs exceeded the NPCC’s minimum SAR objective of 2% in five of 11 migration
years. SARs based on adult returns to BOA were about 35% greater (when comparing
geometric mean of SAR ratios) than SARs based on returns to GRA (Table 6.13) because
of the combined effect of adult dam passage loss, straying and Zone 6 harvest (Chapter
5).
The estimated overall SARs (LGR-to-GRA) for Snake River hatchery steelhead
averaged (geometric mean) 1.18% and exceeded 2% only in 2004 (Table 6.14; Figure
6.4, bottom plot). Overall SARs (LGR-to-GRA) of Snake River wild and hatchery
steelhead aggregate groups were not highly correlated (r = -0.003) during 1997-2007.
The first juvenile migration year with sufficient numbers of PIT-tagged smolts to
estimate SARs for basin or run specific (e.g. Imnaha Basin A-run) Snake River hatchery
steelhead stocks is 2008. However, the adult returns are incomplete with only one-salt
returns through the adult run year 2009-2010. Minimum SARs (one-salt adults only)
were in the 3-4% range for A-run hatchery steelhead in 2008 and less than 1% for B-run
hatchery steelhead. Some differences in SARs between A-run and B-run stocks are
expected because of their different ocean maturation and mainstem freshwater harvest
rates.
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Figure 6.4. Bootstrapped LGR-to-GRA SAR and upper and lower CI for wild and hatchery Snake
River steelhead for migration years 1997-2007. The NPCC (2009) minimum 2% SAR for listed wild
populations is shown for reference.
The first juvenile migration year with sufficient numbers of PIT-tagged fish to estimate
SARs for Snake River hatchery sockeye is 2009 (see Chapter 1). CSS plans to begin
reporting the time series of sockeye SARs in the 2011 annual report.
Mid Columbia River Overall SARs
In contrast to Snake River spring/summer Chinook and steelhead, no historic SAR
data sets exist for the mid-Columbia Region extending back to pre-FCRPS completion.
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The Yakama Nation fisheries staff estimated SARs of Yakima River natural origin spring
Chinook based on run reconstruction of smolts at Chandler Dam to adults to the Yakima
River mouth, beginning in smolt migration year 1983. Subbasin-to-subbasin SARs for
Yakima River wild Chinook averaged 3.3%, ranging from 0.6% to 13.4% during 19832001 (Yakima Subbasin Summary; YIN and WDFW 2004). In addition, the Warm
Springs Tribe has operated a smolt trap on the Warm Springs River since the late 1970s,
from which it may be possible to calculate wild spring Chinook SARs using run
reconstruction methods. The CSS will explore incorporating these run reconstruction
SAR estimates into a long-time series for mid-Columbia Chinook in future analyses.
The geometric mean SAR (JDA-to-BOA, without jacks) of PIT-tagged John Day
River wild Chinook was 3.71% during the nine-year period 2000-2008 (Table 6.15;
Figure 6.5 top plot). John Day wild Chinook SARs exceeded the NPCC’s minimum SAR
objective of 2% in all but one migration year (2005; 1.82%). The PIT-tagged John Day
River Chinook group represents an aggregate of three wild populations: the North Fork,
Middle Fork, and upper mainstem John Day rivers. SARs of John Day River wild
Chinook averaged (geometric mean of ratio) more than 5 times those of Snake River wild
Chinook (Tables 6.15 and 6.1), and the wild SARs were highly correlated (r = 0.74)
between regions during the period 2000-2008.
The estimated overall SARs for mid-Columbia River hatchery spring Chinook
varied by hatchery and year (Figure 6.5; Tables 6.16-6.17). REL-BOA SARs and BONto-BOA SARs for Carson hatchery Chinook averaged (geometric mean) 0.73% and
0.94% respectively during 2000-2008 (Table 6.16). MCN-BOA SARs for Cle Elum
hatchery Chinook averaged 1.13% (Table 6.17). The two hatchery populations in the
mid-Columbia region had much lower SARs than the John Day wild population.
Although a difference in magnitude of SARs between groups was noted, the overall
SARs of mid-Columbia wild and hatchery Chinook groups were highly correlated
(average r = 0.84) between populations during 2000-2008.
The CSS is compiling the data set to estimate SARs and confidence intervals for
mid Columbia wild steelhead from the John Day River beginning with migration year
2004, and the Deschutes River beginning with migration year 2006. To date, we have
only the 2008 migration year summarized for wild PIT-tagged John Day River steelhead.
The 2008 one-salt SAR (JDA-to-BOA was 6.68% and exceeded the NPCC’s minimum
SAR objective of 2% (Table 6.18). The PIT tagged John Day River steelhead group
represents an aggregate of five wild populations: the North Fork, Middle Fork, South
Fork upper mainstem and lower mainstem John Day rivers. Fish in the lower mainstem
John Day population from tributaries downstream of the ODFW juvenile seining site are
not trapped and PIT tagged.
No PIT-tag SARs have been compiled for hatchery steelhead populations in the
mid-Columbia region. There may be some potential for run reconstruction SARs for
hatchery steelhead in the Deschutes and Umatilla subbasins.
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Figure 6.5. Bootstrapped SAR (without jacks) and upper and lower CI for wild and hatchery
Chinook from mid-Columbia region for migration years 2000-2008. Smolts are estimated at upper
dam (or release for Carson hatchery); adults are enumerated at BOA. The NPCC (2009) 2-6% SAR
objective or the minimum 2% SAR for listed wild populations is shown for reference.
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Upper Columbia River Overall SARs
Raymond (1988) estimated pre-harvest SARs for upper Columbia River (above
PRD) spring Chinook and steelhead, 1962-1984 smolt migration years. Estimated SARs
for both species were somewhat lower than those in the Snake River during the 1960s.
Raymond’s smolt indices in the upper Columbia were subject to several assumptions,
however, with greater uncertainty in the SAR estimates compared to the Snake River.
The CSS will explore incorporating Raymond’s historic SAR estimates into a long-time
series for upper Columbia Chinook and steelhead in future analyses.
The estimated overall SARs for Upper Columbia River hatchery spring Chinook
were represented by a single hatchery (Leavenworth) during 2000-2008. The geometric
mean MCN-to-BOA SARs (without jacks) for Leavenworth hatchery Chinook was
0.48%; SARs did not exceed 2% in any year during 2000-2008 (Table 6.19; Figure 6.6).
The overall SARs of hatchery Upper Columbia Chinook were highly correlated with wild
and hatchery Chinook SARs from the mid-Columbia (average r = 0.78) and with wild
and hatchery Chinook SARs from the Snake River (average r = 0.80) during 2000-2008.
% SAR MCN to BOA
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Figure 6.6. Bootstrapped SAR (MCN-to-BOA, without jacks) and upper and lower CI for
Leavenworth hatchery Chinook from Upper Columbia region for migration years 2000-2008. The
NPCC (2009) minimum 2% SAR for listed wild populations is shown for reference.
Comparison of PIT-tag and Run Reconstruction SARs
The ISAB/ISRP (2008) review of the CSS Ten-Year Retrospective Report
(Schaller et al. 2007), encouraged the CSS to investigate differences, and reasons for any
differences, between SARs based on PIT tags and those based on run reconstruction
methods. Schaller et al. (2007) found that the NOAA run reconstruction SAR point
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estimates (Williams et al. 2005) were about 19% higher (geometric mean) than those
produced by CSS using PIT tags. It was unclear whether a bias existed in either the run
reconstruction or PIT tag SARs due, in part, to uncertainties and assumptions in the run
reconstruction methods. Knudsen et al. (2009) reported that hatchery Chinook from the
Yakima River that were PIT-tagged and coded-wire-tagged returned at a 25% lower rate
than fish that were only coded-wire-tagged. The Knudsen study illustrated the potential
for PIT tag effects, however, its applicability to other river reaches or populations of fish
is unknown (Tuomikoski et al. 2009; DeHart 2009).
In the CSS 2009 annual report (Tuomikoski et al. 2009), we compared SARs and
estimates of juveniles and associated variance used in the IDFG run reconstruction of
Snake River wild spring/summer Chinook at Lower Granite Dam (Copeland et al. 2008)
with CSS PIT tag estimates. The run reconstruction and CSS SARs were highly
correlated (0.92) during 1996-2004, and both time series indicated SARs were well short
of the NPCC (2009) 2-6% SAR objectives (Figure 6.7; Tuomikoski et al. 2009). The
IDFG run reconstruction SARs were about 35% higher than CSS PIT-tag SARs. The
difference between run reconstruction and PIT tag SARs did not appear to be
predominantly due to differences in juvenile abundance estimation methods. Tuomikoski
et al. (2009) concluded that estimates of juvenile population abundance derived in CSS,
when using the Smolt Monitoring Program (SMP) collection index, were similar to those
reported by Copeland et al. (2008). Tuomikoski et al. (2009) also developed a bootstrap
variance estimator to account for variation in daily detection probability estimates and
collection samples for use with the run reconstruction methods.
Run reconstruction v PIT SARs
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Figure 6.7. IDFG run reconstruction SARs compared to CSS PIT tag SARs and 90% CI, migration
years 1996-2004 (Tuomikoski et al. 2009). NPCC (2009) 2-6% SAR objectives for listed wild
populations are shown for reference.
A key assumption for SARs based on run reconstruction or PIT tag data is that the
sources of the data are representative of the larger population (e.g., tagged juveniles or
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age structures collected). In the following section we examined SAR methodologies and
developed hypotheses for possible sources of bias in both the PIT tag and RR SARs for
Snake River wild Chinook. The potential biases considered below are primarily special
cases of this assumption.
We identified the following factors that could potentially bias PIT-tag SARs: 1)
non-representative tagging; 2) post-tagging mortality; 3) tag loss (shedding, damaged
tags); 4) weighting schemes from different passage routes (C0, C1, T0); and 5) adult
detection efficiency. The CSS Snake River aggregate groups of wild Chinook and
steelhead are not sampled at random locations. The wild Chinook are tagged at locations
widely distributed in the Snake Basin upstream of LGR, but tagging sites tend to be
where densities are highest and compensatory effects (reduced growth and survival rates)
are more likely. CSS wild steelhead tags are less well distributed across the Snake River
subbasins than are wild Chinook tags. The CSS hatchery Chinook groups are generally
representative of the production groups (within hatchery and year), as are the aggregate
hatchery steelhead groups beginning in migration year 2008. Post-tagging mortality is
not typically evaluated beyond 24 hours in most field studies, and mortality effects
associated with tagging small fish may be delayed until emigration and ocean entry. Tag
shedding, damaged tags, and other tag loss have not been thoroughly evaluated in most
field studies. Potential for SAR bias from weighting route-specific SARs does not seem
likely, especially after the CSS began the pre-assignment of tags into the TWS category
in 2006. Finally, adult detection efficiency is high within the FCRPS, however, it can be
an issue for SARs measured to tributary traps sites especially when using hand wand
equipment (Dehart 2009).
We identified the following factors that could potentially bias run reconstruction
SARs: 1) wild smolt indices and wild adult indices may incorporate different proportions
of adipose-intact hatchery fish; 2) window counts used in the RR are not corrected for fall
back or counting period; 3) window counts use length criteria to separate jacks and
adults; and 4) age composition estimation errors tend to inflate SARs.
The IDFG run reconstruction SARs are based on an estimate of the total yield of
natural-origin smolts at LGR (denominator) and an age-structured estimate of total
returns to LGR (numerator) (Copeland et al. 2008; 2009). To estimate wild juvenile
numbers for the run reconstruction, IDFG researchers have multiplied the SMP daily wild
collection indices by the NOAA daily collection efficiency estimates, obtained from the
Northwest Fisheries Science Center (Steve Smith, NOAA). The SMP wild collection
indices include natural-origin smolts and an unknown number of adipose-intact hatchery
smolts, which are not coded-wire-tagged (CWT) and are visually indistinguishable from
wild smolts. These unmarked non-CWT hatchery smolts in the SMP wild collection
indices are primarily fish that had been mis-clipped during mass marking operations at
the hatcheries (typically 1-2% at each hatchery). The mis-clipped fish can inflate the
wild SMP index and the extant of that bias depends on the relative numbers of wild and
hatchery juveniles and the mis-clip rate each year. For example, assume an SMP wild
index of 1,000,000, an SMP hatchery index of 7,000,000 and a mis-clip rate of 1%. In
this case, the actual number of hatchery fish would be 7,070,707 [=(7,000,000)/(0.99)]
and 70,707 mis-clipped hatchery fish would be misclassified as wild. The wild index
(1,000,000) would inflate the actual wild (929,293) population in this case by 7.6%. If
the mis-clip rate were 2% in the above example, then 142,857 mis-clipped hatchery fish
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would be misclassified as wild, for an inflation factor of 16.7%. For a given mis-clip
rate, the inflation factors would increase as the wild smolt index decreased relative to the
hatchery smolt index.
The IDFG has used LGR window counts of adipose intact Chinook for the run
reconstruction SAR estimates since the 1998 run year, which, like the wild smolt indices,
also contain un-clipped hatchery fish (T. Copeland and P. Kennedy, IDFG, personal
communication). If the inflation factor for the wild adult index is the same as for the wild
smolt index, the RR SARs would be unbiased (by this factor). SAR bias could occur if
differential survival between wild and hatchery groups led to a different inflation factor
in the numerator and denominator of SARs, and/or if different criteria were used to
identify wild index smolts and adults. Different proportions of adipose intact hatchery
fish between smolt and adult indices are likely in the pre-2006 RR data sets (T. Copeland
and P. Kennedy personal communication). Since 2006, adult size composition has been
sampled at the Lower Granite trap rather than with video equipment. It may be fruitful in
future analyses to focus on comparisons of CSS and RR SARs for these more recent
years.
A second potential bias in RR SARs is the use of window counts, which are not
corrected for fall back or counting period. Any unaccounted fall back would positively
bias the window count. Not expanding for counting period would negatively bias the
window count. These two errors should tend to counterbalance, but we cannot be sure of
the degree of compensation. Trap data collected since 2006 and PIT tag data might be
used to help identify re-ascensions, but fall backs that go elsewhere will be difficult to
detect in either data set.
RR SARs could also contain bias because window counts have used length
criteria to separate jacks and adults. This could have a discernable effect on RR SARs
for adult sample years computed from U.S. v. Oregon Technical Advisory Committee
(TAC) data (1998-2007) (T. Copeland and P. Kennedy personal communication). In the
future, PIT tag data and trap samples could be analyzed to assess the potential for bias
from use of length criteria in window counts.
Finally, age composition estimation errors may inflate RR SARs. Age
composition errors tend to misclassify some recruits from dominant year classes into
weaker year classes, inflating average SARs (Copeland et al. 2007). The RR used length
data sampled from video or adult trap sampling at LGR and estimated the proportion ageat-length from carcass samples collected opportunistically on the spawning grounds.
Although methods of aging of the sample (fin ray or scale) appear highly accurate,
overall age composition could be biased by non-representative, opportunistic sample
collection, which emphasize certain populations and miss smaller fish (T. Copeland and
P. Kennedy personal communication).
Our preliminary conclusion is that there is potential for bias in both the CSS PIT
tag and IDFG run reconstruction SAR estimates, although both provide useful, highly
correlated estimates. To date a definitive control group has been lacking to quantify the
potential post-marking or tag shedding bias in PIT tag SARs. Similarly, it is not yet
possible to evaluate the extent of bias in RR SARs. We developed several hypotheses in
this report that might help explain the observed differences in SARs between PIT tag and
RR methods. Determining the extent and causes of bias ultimately will be important in
the synthesis and interpretation of the different survival rate data sets.
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42
43
44
45
First Year Ocean Survival Rate (S.o1)
Estimated first year ocean survival, S.o1, for Snake River wild spring/summer
Chinook during 1994-2007 ranged from 0.4% in 2005 to 8.2% in 2000 and the 13-yr
geometric mean was 2.2% (Table 6.20). Estimated S.o1 for wild steelhead during 19972007 ranged from 0.6% in 1998 to 8.2% in 1999 and the 9-yr geometric mean was 2.3%
(Table 6.20). Over the same 8-yr period as shown for wild steelhead, the geometric mean
of S.o1 was 2.5% for Snake River wild spring/summer Chinook, which is nearly 9%
higher than that of wild steelhead. In contrast, the geometric mean of first year ocean
survival during 1964-1969 was estimated to be 13.4% and 19.9% for Snake River
spring/summer Chinook and steelhead, respectively (Petrosky and Schaller 2010).
To date, CSS has estimated S.o1 only for Snake River wild Chinook and
steelhead, but will explore estimating S.o1 for mid-Columbia and upper Columbia wild
Chinook and steelhead in future reports as we develop the relevant time series of SARs
and in-river survival rates. The S.o1 calculations are simplified for these regions without
juvenile fish transportation.
Discussion
In summary, it appears that neither Snake River wild spring/summer Chinook or
wild steelhead wild populations are consistently meeting the NPCC 2-6% SAR objective.
Geometric mean SARs (LGR-to-GRA) were 0.82% and 1.41% for PIT tagged wild
Chinook and steelhead, respectively. Although Snake River hatchery Chinook exhibited
a generally more positive response to transportation and relatively lower levels of
differential delayed mortality (higher D) than wild populations, annual SARs of Snake
River wild and hatchery Chinook were highly correlated across years. In view of this
high correlation, continuing the CSS time series of hatchery SARs will be important to
augment wild Chinook SAR information following future years of low escapements, in
addition to providing valuable management information for the specific hatcheries.
The trend in SARs across years for Snake River hatchery spring/summer Chinook
are similar to those for the aggregate wild Chinook population in smolt migration years
1997-2008 suggesting similar factors influence their survival during the smolt migration
and the estuary and ocean life stages. There were differences among Chinook hatcheries
such as Dworshak NFH, which showed generally poorer SARs within years than Rapid
River, McCall and Imnaha hatcheries; conversely, the McCall and Imnaha hatcheries
typically had among the highest SARs within a year.
Reasons for the observed lack of correlation between Snake River wild and
hatchery steelhead SARs during 1997-2007 are unknown, but may be related to the
opportunistic nature of assembling aggregate hatchery steelhead groups from various
monitoring programs for those years. However, there appears to be a moderate
correlation between wild Chinook and wild steelhead SARs. More representative tagging
for Snake River steelhead hatcheries began in coordination with LSRCP and IPC in
migration year 2008. Future implementation of the CSS study design and analysis for
hatchery steelhead should allow for evaluation of any disparity among groups (e.g.,
133
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among facilities or A-run vs. B-run) to help craft appropriate weightings for aggregate
hatchery steelhead SARs.
The first juvenile migration year with sufficient numbers of PIT-tagged fish to
estimate SARs for Snake River hatchery sockeye is 2009. CSS plans to begin reporting
the time series of sockeye SARs in the 2011 annual report.
Mid-Columbia River wild spring Chinook populations, as represented by the John
Day River aggregate group, have recently experienced SARs relatively close to the range
of the NPCC 2-6% SAR objective. The geometric mean SAR (JDA-to-BOA) for John
Day wild Chinook was 3.7% during 2000-2008 and all but one annual SAR exceeded the
2% minimum. CSS has begun a time series of wild steelhead SARs for the John Day
River, with the one-salt adults from the 2008 migration returning at a rate of 6.7%.
Mid-Columbia River hatchery spring Chinook (Carson and Cle Elum) SARs have
varied by year and hatchery during 2000-2008. SARs for Carson hatchery were less than
those for Cle Elum hatchery; SARs for both hatcheries were consistently less than those
for John Day wild Chinook. Although differing in magnitude, SARs were highly
correlated among wild and hatchery Chinook stocks within the mid-Columbia Region.
The CSS has begun to establish a time series of SARs for Upper Columbia River
wild spring Chinook and steelhead, with PIT tagging in the Wenatchee, Entiat, and
Methow rivers in 2009. Leavenworth hatchery spring Chinook SARs were highly
correlated with wild and hatchery Chinook stocks from both the mid-Columbia and
Snake regions.
PIT tag SARs of Snake River wild spring/summer Chinook were highly
correlated with IDFG run reconstruction SARs, with both time series indicating SARs
were well short of the NPCC 2-6% SAR objective. The run reconstruction SARs were
about 35% higher than PIT-tag SARs. We developed several hypotheses in this report
that might help explain the observed differences in SARs between PIT tag and run
reconstruction methods. Our preliminary conclusion is that there is potential for bias in
both the CSS PIT tag and IDFG run reconstruction SAR estimates, although both provide
useful, highly correlated estimates. The difference in SARs between run reconstruction
and PIT tag SARs did not appear to be primarily due to juvenile abundance estimates. To
date a definitive control group has been lacking to quantify the potential bias from postmarking mortality or tag loss in PIT tag SARs. Determining the extent and causes of bias
ultimately will be important in the synthesis and interpretation of the different survival
rate data sets.
Several studies should yield additional insight into the question of PIT tag effects
on SARs in the near future. The USFWS (in collaboration with the CSS oversight
committee) is working towards implementing a basin-wide independent PIT-tag bias
study in an effort to evaluate and test the repeatability of Knudsen et al. (2009) results.
Double tagging experiments are currently being planned for Carson Hatchery and other
Columbia River hatcheries, Also, as result of the LSRCP and CSS cooperative tagging
and other monitoring, researchers anticipate being able to estimate with relative precision
returns of PIT tagged and untagged McCall hatchery summer Chinook to the South Fork
Salmon River (J. Cassinelli, IDFG, personal communication). The accounting would
include estimates of adult survival from LGR to the South Fork Salmon River, Tribal and
non-Tribal harvest within the subbasin and numbers of hatchery fish that drop out to
spawn below the hatchery weir.
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CSS studies have found that the SAR and first year ocean survival rates for these
populations were strongly related to both ocean conditions and seaward migration
conditions through the FCRPS (Schaller et al. 2007; Petrosky and Schaller 2010).
Parameters estimated in CSS, including in-river survival, transport proportions and D,
allow for partitioning of the SARs to estimate first year ocean survival, S.o1. The NPCC
(2009) highlighted the need for identifying the effects of ocean conditions on anadromous
fish survival so that this information can be used to evaluate and adjust inland actions.
The NPCC recognized that a better understanding of the conditions salmon face in the
ocean can suggest which factors will be most critical to survival, and thus provide data as
to which actions taken inland will provide the greatest benefit in terms of improving the
likelihood that Columbia River Basin salmon can survive varying ocean conditions
(NPCC 2009). The time series of SARs and S.o1 can then be used to evaluate ocean and
smolt migration factors that may influence ocean survival of Snake River and upper
Columbia salmon and steelhead as called for in the Fish and Wildlife Program (NPCC
2009).
Additional CSS related work to date (evaluating PIT tag survival rate information
within season), found positive covariation in mortality rates between the two species: 1)
during freshwater outmigration as smolts through a series of hydropower dams and
reservoirs; 2) during the period of post-hydrosystem, estuarine/marine residence through
adult return; and 3) during the overall life-cycle from smolt outmigration through adult
return, suggesting that shared environmental factors are influencing mortality rates of
both species. In addition, evidence of positive covariation in mortality rates between the
freshwater and subsequent marine-adult life stage for each species, suggests that factors
affecting mortality in freshwater partially affect mortality during the marine-adult life
stage. This work, along with the findings in Schaller et al. (2007) and Petrosky and
Schaller (2010), have illuminated a promising line of inquiry for upcoming CSS study
direction. We plan to explore evaluating the correlation for SARs among the regions. In
addition, we plan to evaluate which environmental and river management variables best
explain the variation in survival rates for the various life stages (eg. SAR , S.o1, and S.r)
and by regional grouping. This study direction is consistent with NPCC direction and past
recommendations from the ISAB.
135
1
Supporting Tables
Table 6.1 Estimated overall LGR-to-GRA SARs for the Snake River basin (above LGR) PIT-tagged
wild spring/summer Chinook aggregate, 1994 to 2008. SARs are calculated with and without jacks.
Juvenile
Migration
year
2
3
4
5
6
Smolts
arriving
LGR A
LGR-to-GRA without Jacks
Non-parametric CI
SAR
Estimate 90% LL 90%UL
LGR-to-GRA with Jacks
Non-parametric CI
SAR
1994
15,260
0.43
0.22
0.66
0.47
0.24
0.70
1995
20,206
0.35
0.20
0.52
0.35
0.19
0.52
1996
7,868
0.42
0.06
0.84
0.43
0.06
0.85
1997
2,898
1.73
0.97
2.68
1.78
0.99
2.73
1998
17,363
1.21
0.82
1.64
1.25
0.84
1.70
1999
33,662
2.39
1.89
2.94
2.55
2.03
3.09
2000
25,053
1.71
1.22
2.24
1.72
1.25
2.20
2001
22,415
1.27
0.54
2.11
1.45
0.70
2.32
2002
23,356
0.92
0.75
1.10
1.04
0.83
1.24
2003
31,093
0.34
0.26
0.41
0.34
0.26
0.42
2004
32,546
0.52
0.43
0.63
0.54
0.44
0.64
2005
35,216
0.22
0.17
0.28
0.24
0.18
0.30
2006
15,274
0.70
0.58
0.81
0.75
0.63
0.87
2007
14,919
0.98
TBD
TBD
1.09
TBD
TBD
2008 B
13,604
2.26
TBD
TBD
2.78
TBD
TBD
0.80
0.86
Geometric Mean
A
Estimated population of tagged study fish alive to LGR tailrace (includes fish detected at the dam and
those estimated to pass undetected) using total tag release through 2005 and TWS tags beginning in 2006.
B
Incomplete with 2-salt returns through July 26, 2010
NOTE: 2007 and 2008 SARs and CI will be re-run in September with final 2010 returns.
Table 6.2 Estimated overall LGR-to-BOA SARs for the Snake River basin (above LGR) PIT-tagged
wild spring/summer Chinook aggregate, 2000 to 2008. SARs are calculated with and without jacks.
Juvenile
Migration
year
7
8
9
10
Smolts
arriving
LGR A
LGR-to-BOA without Jacks
Non-parametric CI
SAR
LGR-to-BOA with Jacks
Non-parametric CI
SAR
2000
25,053
2.60
1.95
3.28
2.69
2.01
3.39
2001
22,415
1.81
0.90
2.89
1.99
1.09
2.99
2002
23,356
1.14
0.94
1.35
1.29
1.07
1.52
2003
31,093
0.34
0.26
0.42
0.34
0.27
0.42
2004
32,546
0.68
0.56
0.80
0.69
0.58
0.80
2005
35,216
0.29
0.23
0.36
0.30
0.23
0.37
2006
15,274
0.84
0.73
0.98
0.90
0.77
1.03
2007
14,919
1.13
0.98
1.27
1.24
1.09
1.39
2008 B
13,604
1.95
1.75
2.15
2.54
2.33
2.78
0.95
1.04
Geometric Mean
A
B
Incomplete with 2-salt returns through May 28, 2010
136
1
Table 6.3 Estimated overall LGR-to-GRA SARs for PIT-tagged Dworshak hatchery spring Chinook,
1997 to 2008. SARs are calculated with and without jacks.
Juvenile
Migration
year
2
3
4
5
6
Smolts
arriving
LGR A
Non-parametric CI
SAR
Non-parametric CI
SAR
1997
8,175
0.62
0.44
0.81
0.63
0.46
0.84
1998
40,218
1.00
0.90
1.11
1.14
1.04
1.25
1999
40,804
1.18
1.05
1.32
1.22
1.08
1.36
2000
39,412
1.00
0.92
1.10
1.01
0.92
1.12
2001
41,251
0.36
0.29
0.43
0.42
0.35
0.49
2002
45,233
0.57
0.48
0.65
0.72
0.63
0.81
2003
38,612
0.24
0.19
0.29
0.25
0.20
0.30
2004
45,505
0.29
0.23
0.34
0.29
0.23
0.34
2005
43,042
0.19
0.15
0.24
0.20
0.16
0.25
2006
29,511
0.35
0.29
0.42
0.46
0.40
0.52
2007
28,511
0.36
0.31
0.42
0.46
0.40
0.53
2008 B
25,643
0.53
TBD
TBD
0.80
TBD
TBD
0.48
0.54
Geometric Mean
A
B
Table 6.4 Estimated overall LGR-to-BOA SARs for PIT-tagged Dworshak hatchery spring Chinook,
Juvenile
Migration
year
7
8
9
10
11
12
13
14
15
16
17
Smolts
arriving
LGR A
Non-parametric CI
SAR
LGR-to-BOA with Jacks C
Non-parametric CI
SAR
2000
39,412
1.58
1.45
1.70
---2001
41,251
0.44
0.37
0.51
---2002
45,233
0.75
0.66
0.85
---2003
38,612
0.31
0.26
0.37
---2004
45,505
0.53
0.46
0.61
---2005
43,042
0.29
0.24
0.35
---2006
29,511
0.56
0.49
0.64
---2007
28,511
0.49
0.42
0.56
---2008 B
25,643
0.89
0.80
0.99
---0.57
Geometric Mean
A
B
C
Will be completed for future reports
137
Table 6.5 Estimated overall LGR-to-GRA SARs for PIT-tagged Rapid River hatchery spring
Chinook, 1997 to 2008. SARs are calculated with and without jacks.
Juvenile
Migration
year
1
2
3
4
5
Smolts
arriving
LGR A
SAR
Non-parametric CI
SAR
Non-parametric CI
1997
15,765
0.65
0.52
0.79
0.65
0.52
0.78
1998
32,148
1.88
1.71
2.07
1.98
1.80
2.18
1999
35,895
2.91
2.69
3.13
3.04
2.82
3.25
2000
35,194
1.94
1.79
2.08
1.96
1.82
2.10
2001
38,026
1.06
0.94
1.18
1.17
1.04
1.29
2002
41,471
0.90
0.79
1.01
1.07
0.95
1.19
2003
37,911
0.24
0.19
0.29
0.31
0.26
0.37
2004
36,178
0.34
0.28
0.41
0.36
0.29
0.42
2005
38,231
0.25
0.20
0.31
0.27
0.22
0.33
2006
26,349
0.50
0.43
0.58
0.60
0.52
0.68
2007
25,798
0.34
0.28
0.40
0.47
0.40
0.54
2008 B
29,071
1.23
TBD
TBD
1.89
TBD
TBD
0.74
0.86
Geometric Mean
A
B
Table 6.6 Estimated overall LGR-to-BOA SARs for PIT-tagged Rapid River hatchery spring
Juvenile
Migration
year
6
7
8
9
10
11
12
13
Smolts
arriving
LGR A
Non-parametric CI
SAR
Non-parametric CI
SAR
2000
35,194
2.71
2.53
2.87
---2001
38,026
1.38
1.24
1.52
---2002
41,471
1.06
0.94
1.18
---2003
37,911
0.34
0.28
0.41
---2004
36,178
0.43
0.36
0.50
---2005
38,231
0.31
0.26
0.37
---2006
26,349
0.74
0.66
0.83
---2007
25,798
0.48
0.41
0.55
---2008 B
29,071
1.71
1.58
1.84
---0.78
Geometric Mean
A
B
C
138
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Table 6.7 Estimated overall LGR-to-GRA SARs for PIT-tagged Catherine Creek hatchery spring
Juvenile
Migration
year
2
3
4
5
6
Smolts
arriving
LGR A
Non-parametric CI
SAR
Non-parametric CI
SAR
2001
10,885
0.22
0.12
0.34
0.26
0.14
0.40
2002
8,435
0.77
0.56
1.00
1.00
0.76
1.28
2003
7,202
0.31
0.20
0.43
0.40
0.25
0.54
2004
5,348
0.36
0.20
0.54
0.40
0.22
0.58
2005
4,848
0.40
0.22
0.60
0.48
0.27
0.68
2006
4,289
0.49
0.32
0.69
0.61
0.41
0.81
2007
4,695
0.43
0.27
0.59
0.83
0.62
1.04
2008 B
6,605
2.04
TBD
TBD
2.87
TBD
TBD
0.49
0.64
Geometric Mean
A
B
Table 6.8 Estimated overall LGR-to-BOA SARs for PIT-tagged Catherine Creek hatchery spring
Juvenile
Migration
year
7
8
9
10
11
12
13
14
15
Smolts
arriving
LGR A
SAR
Non-parametric CI
Estimate
SAR
Non-parametric CI
Estimate
2001
10,885
0.37
0.23
0.51
---2002
8,435
1.11
0.83
1.41
---2003
7,202
0.35
0.22
0.50
---2004
5,348
0.44
0.25
0.64
---2005
4,848
0.50
0.30
0.73
---2006
4,289
0.79
0.58
1.03
---2007
4,695
0.53
0.36
0.71
---2008 B
6,605
2.60
2.28
2.93
---0.66
Geometric Mean
A
B
C
139
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Table 6.9 Estimated overall LGR-to-GRA SARs for PIT-tagged McCall hatchery summer Chinook,
Juvenile
Migration
year
2
3
4
5
6
Smolts
arriving
LGR A
Non-parametric CI
SAR
Non-parametric CI
SAR
1997
22,381
1.31
1.15
1.46
1.41
1.25
1.58
1998
27,812
2.50
2.28
2.73
3.07
2.80
3.32
1999
31,571
3.26
3.02
3.49
3.73
3.48
4.02
2000
31,825
3.12
2.92
3.33
3.63
3.41
3.84
2001
36,784
1.20
1.07
1.34
1.55
1.39
1.71
2002
32,599
1.34
1.19
1.50
1.82
1.64
2.00
2003
43,144
0.68
0.60
0.76
1.00
0.91
1.09
2004
40,150
0.39
0.33
0.46
0.47
0.40
0.55
2005
43,229
0.57
0.50
0.64
0.61
0.54
0.69
2006
21,794
1.06
0.95
1.18
1.27
1.15
1.41
2007
19,082
0.89
0.77
1.01
1.42
1.28
1.56
2008 B
21,044
1.01
TBD
TBD
2.24
TBD
TBD
1.19
1.55
Geometric Mean
A
B
Table 6.10 Estimated overall LGR-to-BOA SARs for PIT-tagged McCall hatchery summer Chinook,
Juvenile
Migration
year
7
8
9
10
11
12
13
14
Smolts
arriving
LGR A
Non-parametric CI
SAR
Non-parametric CI
SAR
2000
31,825
3.76
3.53
3.99
---2001
36,784
1.46
1.30
1.62
---2002
32,599
1.72
1.54
1.91
---2003
43,144
0.81
0.72
0.89
---2004
40,150
0.52
0.44
0.61
---2005
43,229
0.68
0.60
0.77
---2006
21,794
1.29
1.15
1.42
---2007
19,082
1.10
0.97
1.23
---2008 B
21,044
TBD
TBD
TBD
---1.18
Geometric Mean
A
B
Incomplete with 2-salt returns through May 28, 2010 – too early to report
C
140
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Table 6.11 Estimated overall LGR-to-GRA SARs for PIT-tagged Imnaha hatchery summer
Juvenile
Migration
Year
2
3
4
5
6
Smolts
arriving
LGR A
Non-parametric CI
SAR
Non-parametric CI
SAR
1997
8,254
0.98
0.76
1.23
1.35
1.10
1.64
1998
13,577
0.81
0.63
1.00
1.46
1.20
1.73
1999
13,244
2.41
2.09
2.74
3.20
2.82
3.57
2000
14,267
2.89
2.63
3.15
3.99
3.66
4.31
2001
15,650
0.61
0.48
0.77
0.98
0.80
1.17
2002
13,962
0.68
0.52
0.85
1.02
0.83
1.23
2003
14,948
0.53
0.42
0.65
1.26
1.08
1.43
2004
12,867
0.36
0.25
0.46
0.45
0.33
0.58
2005
11,172
0.27
0.17
0.37
0.32
0.23
0.43
2006
8,753
0.80
0.64
0.96
1.12
0.95
1.30
2007
9,596
0.66
0.53
0.80
1.38
1.18
1.59
2008 B
10,148
1.64
TBD
TBD
4.39
TBD
TBD
0.83
1.33
Geometric Mean
A
B
Table 6.12 Estimated overall LGR-to-BOA SARs for PIT-tagged Imnaha hatchery summer
Juvenile
Migration
Year
7
8
9
10
11
12
13
14
15
Smolts
arriving
LGR A
Non-parametric CI
SAR
Non-parametric CI
SAR
2000
14,267
3.61
3.29
3.93
---2001
15,650
0.81
0.66
0.99
---2002
13,962
0.92
0.73
1.13
---2003
14,948
0.71
0.58
0.84
---2004
12,867
0.57
0.43
0.71
---2005
11,172
0.35
0.24
0.46
---2006
8,753
0.99
0.83
1.18
---2007
9,596
0.84
0.69
1.00
---2008 B
10,148
TBD
TBD
TBD
---0.87
Geometric Mean
A
B
Incomplete with 2-salt returns through May 28, 2010 – too early to report
C
141
1
Table 6.13 Estimated overall LGR-to-GRA and LGR-to-BOA SARs for Snake River basin (above
LGR) PIT-tagged wild summer steelhead aggregate, 1997 to 2008.
Juvenile
Migration
year
2
3
4
Smolts
arriving
LGR A
SAR
Estimate
LGR-to-GRA
Non-parametric CI
90% LL 90%UL
SAR
Estimate
LGR-to-BOA
Non-parametric CI
90% LL 90%UL
1997
3,830
1.16
0.37
2.12
---1998
7,109
0.30
0.07
0.66
---1999
8,820
2.84
1.68
4.19
---2000
13,609
2.66
1.62
3.72
2.99
1.88
4.17
2001
12,929
2.47
0.97
4.49
3.98
1.91
6.21
2002
13,378
2.14
1.24
3.21
2.60
1.47
3.82
2003
12,926
1.57
1.22
1.94
1.86
1.47
2.25
2004
13,263
0.85
0.63
1.08
1.31
1.03
1.58
2005
15,124
0.80
0.60
1.01
1.02
0.81
1.26
2006
5,431
1.14
0.91
1.40
1.92
1.59
2.21
2007
7,083
2.56
2.25
2.88
3.29
2.93
3.66
2008 B
5,730
1.40
1.17
1.67
1.87
1.56
2.16
Geometric Mean
1.41
2.17
(through 2007)
A
B
Incomplete with only 1-salt returns available.
Table 6.14 Estimated overall LGR-to-GRA and LGR-to-BOA SARs for Snake River basin (above
LGR) PIT-tagged hatchery summer steelhead aggregates, 1997 to 2008.
Juvenile
Migration
year
5
6
7
8
9
10
11
12
Subbasin
and
run type
Smolts
arriving
LGR A
LGR-to-GRA
Non-parametric CI
SAR
LGR-to-BOA D
90% CI
SAR
Est.
LL
UL
1997
all
24,710
0.39
0.22
0.59
---1998
all
23,507
0.56
0.30
0.85
---1999
all
27,193
0.92
0.59
1.30
---2000
all
24,565
1.89
1.18
2.70
---2001
all
20,877
0.92
0.24
1.74
---2002
all
20,681
0.95
0.40
1.72
---2003
all
21,400
1.46
1.24
1.68
---2004
all
17,082
2.08
1.15
3.19
---2005
all
19,640
1.83
1.17
2.55
---2006
all
13,473
1.96
1.32
2.62
---2007
all
21,828
1.64
1.37
1.92
---2008 B
GRN-A
16,858
3.66
3.40
3.94
---2008 B
IMN-A
12,468
4.01
3.68
4.35
---SAL-A
17,429
4.41
4.15
4.69
---2008 B C
2008 B
SAL-B
18,369
------2008 B
CLW-B
24,718
------1.18
Geometric Mean (through 2007)
A
B
Incomplete with only 1-salt returns – too early to report for B-run stocks without 2-salts next year.
C
Excludes 1,200 PIT-tagged Niagara Springs hatchery steelhead due to their low numbers and exclusive
return-to-river routing at transportation sites.
D
Will be completed for future reports.
142
1
Table 6.15 Estimated overall JDA-to-BOA SARs for PIT-tagged John Day River basin wild spring
Juvenile
Migration
Year
2
3
4
5
6
7
8
Smolts
arriving
JDA A
JDA-to-BOA without Jacks
Non-parametric CI
SAR
JDA-to-BOA with Jacks C
Non-parametric CI
SAR
2000
1,255
11.39
9.58
13.33
---2001
2,721
3.90
3.24
4.50
---2002
2,555
3.72
3.01
4.43
---2003
4,203
2.93
2.46
3.42
---2004
2,755
3.19
2.50
4.01
---2005
3,907
1.82
1.46
2.20
---2006
2,188
2.10
1.56
2.70
---2007
2,606
4.53
3.77
5.30
---2008 B
2,929
5.02
4.22
5.82
---3.71
Geometric Mean
A
Estimated population of tagged study fish alive to JDA tailrace (includes fish detected at the dam and
those estimated to pass undetected).
B
C
Table 6.16 Estimated overall BON-to-BOA and release-to-BOA SARs for PIT-tagged Carson
hatchery spring Chinook, 2000 to 2008. SARs are calculated without jacks D.
Juvenile
Migration
Year
9
10
11
12
13
14
Smolts
arriving
BON A
BON-to-BOA without Jacks
90% CI
SAR
Estimate
LL
UL
Smolts
released
REL-to-BOA without Jacks
90% CI
SAR
Estimate
LL
UL
2000
12,945
3.30
2.71
3.91
14,992
2.85
2.62
2001
12,506
1.78
1.50
2.05
14,978
1.49
1.32
2002
12,349
1.22
0.94
1.54
14,983
1.01
0.88
2003
12,709
0.27
0.19
0.36
14,983
0.23
0.17
2004
NA C
------14,973
0.62
0.51
2005
14,053
0.32
0.23
0.42
14,958
0.30
0.23
2006
10,509
0.60
0.45
0.77
14,971
0.42
0.33
2007
NA C
------14,973
0.56
0.46
2008 B
11,681
1.75
1.48
2.05
14,884
1.37
1.22
0.94
0.73
Geometric Mean
A
Estimated population of tagged study fish alive to BON tailrace (includes fish detected at the dam and
B
C
Not calculated since estimated release-to-BON reach survival rates >1.
D
SARs with jacks will be completed for future reports
143
3.07
1.65
1.14
0.29
0.73
0.37
0.51
0.67
1.53
1
Table 6.17 Estimated overall MCN-to-BOA SARs for PIT-tagged Cle Elm hatchery spring Chinook,
Juvenile
Migration
Year
2
3
4
5
6
7
8
Smolts
arriving
MCN A
MCN-to-BOA without Jacks
Non-parametric CI
SAR
MCN-to-BOA with Jacks C
Non-parametric CI
SAR
2000
13,794
3.81
3.47
4.14
---2001
9,228
0.28
0.19
0.37
---2002
11,728
1.37
1.18
1.56
---2003
11,962
0.59
0.48
0.71
---2004
7,982
1.54
1.31
1.79
---2005
5,784
0.66
0.48
0.83
---2006
10,141
1.25
1.07
1.44
---2007
12,675
1.01
0.87
1.16
---2008 B
11,837
2.75
2.48
3.01
---1.13
Geometric Mean
A
Estimated population of tagged study fish alive to MCN tailrace (includes fish detected at the dam and
B
C
Table 6.18 Estimated overall JDA-to-BOA SARs for PIT-tagged John Day River basin wild summer
steelhead, 2004 to 2008.
Juvenile
Migration
Year
9
10
11
12
13
Smolts
arriving
JDA A
SAR
Estimate
JDA-to-BOA
Non-parametric CI
90% LL
90%UL
2004 B
----2005 B
----2006 B
----2007 B
----2008 C
3,220
6.68
5.74
7.66
3.71
Geometric Mean
A
Estimated population of tagged study fish alive to JDA tailrace (includes fish detected at the dam and
B
PIT-tagged wild steelhead for juvenile migration years 2004 to 2007 will be completed for future reports
C
Incomplete with 1-salt returns only
144
1
Table 6.19 Estimated overall MCN-to-BOA SARs for PIT-tagged Leavenworth hatchery spring
Juvenile
Migration
Year
2
3
4
5
6
Smolts
arriving
MCN A
MCN-to-BOA without Jacks
Non-parametric CI
SAR
MCN-to-BOA with Jacks C
Non-parametric CI
SAR
2000
4,360
1.83
1.48
2.22
---2001
3,808
0.24
0.13
0.38
---2002
178,609
0.36
0.34
0.39
---2003
153,594
0.43
0.40
0.45
---2004
104,754
0.34
0.31
0.37
---2005
7,880
0.09
0.04
0.15
---2006
8,183
0.89
0.72
1.09
---2007
8,882
0.46
0.34
0.59
---2008 B
9,118
1.73
1.49
1.97
---0.48
Geometric Mean
A
Estimated population of tagged study fish alive to MCN tailrace (includes fish detected at the dam and
B
C
145
1
Table 6.20. Estimation of first year ocean survival rates, S.o1, for Snake River wild spring/summer
Chinook 1994-2007, and wild steelhead, 1997-2007 based on CSS parameter estimates for SAR, inriver survival (SR), proportion transported (pT) and D.
Migration
Year
1994
1995
1996
1997
1998
1999
2000
2001
2002
2003
2004
2005
2006
2007
Geometric
Mean
SAR
CSS SAR
lgr to
lgr-lgr
In-river
Prop.
mouth
Survival Transported
System excluding
Columbia
harvest
(SR)
(pT)
D
Survival
PIT-tagged Wild Spring/Summer Chinook Aggregate
S.o1
0.20
0.41
0.44
0.51
0.61
0.59
0.48
0.23
0.61
0.60
0.40
0.48
0.57
TBD
0.863
0.805
0.706
0.572
0.815
0.863
0.709
0.989
0.709
0.694
0.929
0.926
0.667
TBD
0.360
0.420
0.920
0.400
0.550
0.720
0.320
2.160
0.440
0.680
0.450
1.070
0.540
TBD
0.33
0.41
0.77
0.44
0.55
0.69
0.36
2.10
0.48
0.65
0.44
1.01
0.54
TBD
0.004
0.004
0.004
0.017
0.012
0.024
0.017
0.013
0.009
0.003
0.005
0.002
0.008
0.010
0.005
0.004
0.004
0.019
0.014
0.029
0.020
0.015
0.011
0.004
0.006
0.003
0.009
0.013
0.014
0.009
0.006
0.043
0.026
0.042
0.054
0.007
0.024
0.006
0.013
0.003
0.017
TBD
0.448
0.779
0.596
0.588
0.008
0.009
0.022
PIT-tagged Wild Summer Steelhead Aggregate
1997
1998
1999
2000
2001
2002
2003
2004
2005
2006
2007
Geometric
Mean
0.52
0.54
0.45
0.30
0.038
0.52
0.37
0.18
0.27
TBD
TBD
0.715
0.892
0.869
0.846
0.992
0.675
0.723
0.974
0.930
TBD
TBD
1.034
1.034
1.034
1.034
1.034
1.034
1.034
1.034
1.034
TBD
TBD
0.87
0.96
0.94
0.90
1.01
0.85
0.83
0.99
0.96
TBD
TBD
0.012
0.003
0.028
0.027
0.025
0.021
0.016
0.009
0.008
0.011
0.026
0.017
0.005
0.043
0.037
0.034
0.028
0.021
0.012
0.011
0.020
0.034
0.020
0.005
0.045
0.041
0.034
0.033
0.025
0.012
0.011
TBD
TBD
0.288
0.839
1.034
0.923
0.014
0.020
0.023
2
146
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3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
Chapter 7
Effects of Bypass Systems on Juvenile Travel Times and SARs
Introduction
Smolt collection or bypass systems are currently in place at seven of the eight
dams on the lower Snake and Columbia rivers. Although some studies have found that
smolt survival estimates through bypass systems are nearly as high as through spillways
(Muir et al. 2001), there are concerns regarding the effects of bypass systems on
migration delay (Beeman and Maule 2001), delayed mortality (Budy et al. 2002) and
SARs (Tuomikoski et al. 2009). If smolts that migrate through bypass systems express
migration delay or delayed mortality, then the direct survival rates that have been
estimated for smolts utilizing bypass systems (e.g., Muir et al. 2001) or SARs that are
conditioned upon bypass detections may not be providing a comprehensive and accurate
picture of the effects of the various migration routes on migration or survival rates. A
better understanding of the indirect and delayed effects of passage through bypass
systems would assist hydrosystem and fishery managers in developing hydrosystem
operations that could assist in the recovery of ESA-listed stocks.
Toward the objective of improving understanding of the effects of bypass systems
on Chinook salmon and steelhead, we conducted three sets of analyses. In the first set of
analyses, we evaluated the effects of bypass systems on fish travel time from Lower
Granite Dam to Bonneville Dam. This work evaluates whether fish that are detected in
the bypass systems at Little Goose, Lower Monumental, McNary or John Day dams have
shorter or longer travel times relative to fish that are not detected at those dams (i.e.,
passing through spillway or turbine routes).
In the second set of analyses, we evaluated the effects of bypass history on SARs
from Bonneville Dam outmigration as a juvenile until Bonneville Dam return as an adult.
We were interested in evaluating two primary management-oriented questions with these
data. First, we were interested in evaluating whether multiple bypass experiences
negatively affected post-Bonneville Dam SARs. This question addresses one of the key
hypotheses presented in Budy et al. (2002), that previous migration history affects levels
of delayed mortality. Support for the Budy et al. (2002) hypothesis would be indicated
by significant reductions in post-Bonneville Dam SARs as the number of bypass
experiences increased. If so, then hydrosystem management strategies that reduce or
minimize the number of bypass experiences would be expected to increase post-BON
SARs. The second question we were interested in was whether there was evidence that
bypass at particular dams was more harmful than others. If there are indications that a
bypass experience at a particular dam reduces post-BON SARs, then those dams could
targeted for reducing the proportion of fish that experience the bypass system at that dam
through increasing spillway percentages and/or structural modifications to the spillway
(e.g., RSWs or TSWs).
In the third set of analyses, we use techniques developed in Chapter 5 of
Tuomikoski et al. (2009) to explore the hypothesis that cumulative effects of bypassing
smolts at dams results in increased mortality expressed in SARs. We perform random
effects meta-analysis to estimate the summary distributions of the ratio of SAR(C1) to
SAR(C0) from annual estimates of this ratio, for wild Chinook and steelhead.
147
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3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
Effects of bypass systems on juvenile fish travel time
Methods
Data for these analyses consisted of hatchery and wild spring/summer Chinook
salmon and steelhead PIT-tagged and released upriver of Lower Granite Dam (LGR),
along with juveniles that were PIT-tagged and released at LGR during juvenile migration
years 1998-2009. Fish used in this analysis were restricted to those that were detected at
both LGR and Bonneville (BON) dams during the out-migration year, thus all were
known to have survived and their travel time from LGR to BON were estimable given
their detection dates at each location. We then queried and recorded their detection
histories (i.e., whether they were detected or not) at each intermediate dam with a
juvenile bypass detection system, which included Little Goose Dam (LGS), Lower
Monumental Dam (LMN), McNary Dam (MCN) and John Day Dam (JDA). The number
of observations for each migration year, rearing type and species is provided in Table 7.1.
Table 7.1 Number of wild and hatchery Chinook (CHN) and steelhead (STH) detected at both LGR
and BON for use in travel time analysis over migration years 1998-2009.
18
19
20
21
22
23
24
25
26
27
28
29
Year
1998
1999
2000
2001
2002
2003
2004
2005
2006
2007
2008
2009
Total
wild CHN
1,311
2,626
1,051
1,473
2,009
4,414
1,232
1,127
1,267
1,819
1,048
1,933
21,310
hat. CHN
4,409
8,185
1,157
3,788
1,021
1,840
1,729
3,597
10,141
4,593
4,313
7,319
52,092
wild STH
995
1,598
6,755
202
2,618
2,381
140
134
1,005
993
1,258
1,633
19,712
hat. STH
3,196
8,512
2,374
470
1,935
635
305
330
1,321
2,002
4,496
8,604
34,180
Multiple linear regression was used to evaluate whether bypass systems had an
effect on LGR-BON fish travel time (FTT). Previous CSS analyses (e.g., Tuomikoski et
al. 2009) showed that median fish travel times for weekly release cohorts exhibit
substantial within-season variability. To account for this, we fit third-order polynomial
functions of Julian day of release at LGR. To evaluate if bypass systems affected FTT,
indicator variables were added to the model, with 1 denoting bypass detection at a dam
and 0 denoting non-detection at a dam. The initial model took the form
FTT   0  1  D   2  D 2   3  D 3   4  I LGS   5  I LMN   6  I MCN   7  I JDA
(Eqn. 7.1)
where D is the Julian day of release at LGR, and I LGS , I LMN , I MCN , and I JDA are
indicator variables taking the value 1 when a fish is detected in a bypass system at a
148
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3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
particular dam and 0 when a fish is not detected in a bypass system at that same dam.
Consistent with other researchers examining the distribution of data on individual FTT
(Zabel and Anderson 1997), the distributions were positively skewed, often with long
right tails. Thus the untransformed data were not likely to meet the linear regression
model requirement of normally-distributed residuals. Therefore Box-Cox power
transformations were conducted using the model in Equation 7.1 to determine an
appropriate transformation for achieving normally-distributed residuals. The Box-Cox
transformations indicated that an inverse-transformation was appropriate for the majority
of the years (1998-2009), species (Chinook or steelhead) and rearing types (hatchery or
wild) considered. Each year, species and rearing type was analyzed separately using
Equation 7.1, but with the dependent variable being 1/FTT. Estimates of  4 ,  5 ,  6 and
 7 were used to determine the statistical significance (α = 0.05) of the bypass systems on
FTT at LGS, LMN, MCN and JDA, respectively. Estimates of mean delay (or
acceleration) at each dam of bypassed fish relative to undetected fish was computed by
subtracting the back-transformed predictions for FTT of non-detected fish from the backtransformed predictions for FTT of fish detected in the bypass system. Positive values of
mean delay indicated that bypassed fish had longer FTT than fish that were not bypassed,
and negative values of mean delay indicated that bypassed fish had shorter FTT than fish
that were not bypassed.
Results
There were 48 year-dam combinations for each species and rearing type (Table
7.2, Figures 7.1 and 7.2). For wild Chinook, there were 32 year-dam combinations
indicating significant bypass delay (67%), one year-dam combination indicating bypass
acceleration (2%) and the remaining 15 year-dam combinations (31%) indicated no
significant difference between bypassed and non-detected fish. Similarly, for hatchery
Chinook, there were 32 year-dam combinations indicating significant bypass delay
(67%), two year-dam combinations indicating bypass acceleration (4%) and the
remaining 14 year-dam combinations (29%) indicated no significant difference between
bypassed and non-detected fish. For wild steelhead, there were 11 year-dam
combinations indicating significant bypass delay (23%), 8 year-dam combinations
indicating bypass acceleration (17%) and the remaining 29 year-dam combinations (60%)
indicated no significant difference between bypassed and non-detected fish. Similarly,
for hatchery steelhead, there were 16 year-dam combinations indicating significant
bypass delay (33%), 7 year-dam combinations indicating bypass acceleration (15%) and
the remaining 25 year-dam combinations (52%) indicated no significant difference
between bypassed and non-detected fish.
The results indicated similar patterns for hatchery and wild rearing types of yeardam combinations with significant bypass delay or acceleration (Table 7.2). Cases of
significant bypass delay for Chinook ranged from 0.13 d to 5.32 d and averaged 0.69 d.
Cases of significant bypass delay for steelhead ranged from 0.19 d to 2.71 d and averaged
0.73 d. The three cases of significant bypass acceleration for Chinook ranged from 0.20
d to 1.10 d and averaged 0.70 d. The 15 cases of significant bypass relative acceleration
for steelhead ranged from -0.35 d to -7.55 d and averaged -2.38 d.
149
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5
6
7
8
9
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11
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18
19
20
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22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
The year-dam combinations that indicated bypass acceleration compared to nondetected fish occurred more often and generally had a higher magnitude during 2001
(Table 7.2), which was a year when most voluntary spill was eliminated at LGS, LMN,
MCN and JDA. Additional year-dam combinations where voluntary spill was eliminated
included LMN in 2002 for spilling basin repairs and at both LGS and LMN in 2004 and
2005 for maximized transportation operations.
Discussion
The results of this work are consistent with Beeman and Maule (2001), who
measured gatewell and collection channel residence times for radio-tagged juvenile
Chinook and steelhead at McNary Dam. They found that median residence times in the
gatewell and collection channel were 8.9 h and 2.3 minutes for Chinook, and 3.2 h and 28
minutes for steelhead. We found that the amount of delay associated with bypass
systems is approximately 0.7 d, or 16.8 h. Combining our results with those of Beeman
and Maule (2001), indicates that there is some amount of forebay delay occurring for
both species prior to fish entering the gatewells. It is possible that steelhead may resist
the sounding required to enter the gatewells. Plumb et al. (2001) found that steelhead
reduce their migration speeds relative to water velocities as they approached Lower
Granite Dam, with substantial numbers of fish traveling upriver when water velocities
were low or when spill was not provided. Although both species in our analysis
demonstrated more cases of migration delay associated with those fish that were
bypassed, there were fewer cases of significant migration delay for steelhead than
Chinook. If steelhead indeed resist sounding, then one plausible mechanism for this
difference may be that the delay associated with bypassed fish is less than the delay
associated with fish that pass through the turbines, which require deeper sounding than
gatewells. Our results lend some support to this hypothesis. Cases of relative bypass
acceleration compared to non-detected fish mainly occurred in 2001, when involuntary
spill was terminated at most dams. Under these conditions, steelhead that were bypassed
had significantly lower FTTs than steelhead that were not detected in six of the eight
cases for hatchery and wild steelhead. The 2001 results suggest that steelhead passing
through the turbines (the only non-bypass route available) took significantly longer to
migrate than steelhead passing through the bypass systems.
This analysis suggests that caution is warranted when interpreting route-specific
survival rate estimates. The route-specific survival estimates are defined from the upriver
face of a dam to the point of the paired release in the tailrace (Skalski et al. 2002), and
survival is similarly defined in paired hose-release studies into individual passage routes
(e.g., Muir et al. 2001). These two designs do not account for the amount of delay and
mortality that occurs in the forebay. Further, it is not possible to separate the mortality
that occurs for smolts destined for each passage route. Because of these issues, the high
route-specific survival rates that have been estimated for bypass systems (in addition to
the other route-specific estimates) may be providing a misleading picture of the
consequences of total passage survival from the forebay, through the individual passage
routes, and through the tailrace. Our results indicate that there is a significant amount of
migration delay associated with bypass systems, which extends the amount of time
smolts are exposed to predators and therefore may also reduce forebay survival rates.
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4
5
Because of these issues, we believe that caution is warranted when interpreting routespecific survival rate estimates. Other mark-recapture designs that focus on total reach
survival using PIT-tags (Burnham et al. 1987, Skalski et al. 1998) are less likely to suffer
from these design issues and may better reflect true survival rates for smolt populations.
Table 7.2 Estimates of bypass delay (d) for wild and hatchery spring/summer Chinook salmon and
steelhead smolts at Little Goose Dam (LGS), Lower Monumental Dam (LMN), McNary Dam (MCN)
and John Day Dam (JDA) over migration years 1998-2009. Positive values (black shading) indicate
cases where bypassed fish had statistically significant increases in travel time relative to fish not
detected at the dam. Negative values (grey shading) indicate cases where bypassed fish had
statistically significant reductions in travel time relative to fish not detected at the dam. Blank cells
indicate differences that were not statistically significant at the α = 0.05 level.
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
Year
1998
1999
2000
2001
2002
2003
2004
2005
2006
2007
2008
2009
wild Chinook
LGS LMN MCN
0.5 1.0
0.4 0.3 0.8
0.5
0.9
‐1.1
0.6 0.5
0.6 0.5 0.7
0.4 2.1 0.3
0.4
0.4
0.5
0.5
0.5 0.7 0.3
0.6 1.2
0.4 0.7
JDA
0.7
0.4
1.9
0.4
0.4
0.6
hatchery Chinook
LGS LMN MCN JDA
0.7 1.0 ‐0.2 0.9
0.3 0.2 0.4 0.3
0.4
‐0.8 2.2
1.1 0.6
0.6 0.4 0.9
5.3 0.5
0.3 0.7
0.1 0.1 0.3
0.5 0.7 0.4 0.5
0.6 0.7
0.7
0.5 0.5 0.4 0.5
151
wild steelhead
LGS LMN MCN JDA
‐0.4
‐0.4 0.6
0.4 0.2
‐4.6 ‐3.0 ‐7.5
‐0.4
‐0.4
0.4
0.6
1.1
hatchery steelhead
LGS LMN MCN JDA
0.3 0.3
0.4 0.4
‐0.6
‐3.6 ‐4.8 ‐6.1
‐2.1
1.3
2.7
0.7
0.6
0.3
‐0.7
0.8
0.6
‐0.4
0.7
0.6
0.4
0.8
1.3
0.4
0.7
0.7
‐0.7
0.9
1.3
Wild CHN
3.0
2.0
1.0
Bypass delay (d) 0.0
1997
1999
2001
2003
2005
2007
2009
‐1.0
LGS
‐2.0
LMN
MCN
JDA
Hatch. CHN
6
5
4
Bypass delay (d)
3
2
1
0
1997
‐1
1
2
3
4
5
6
7
8
9
10
11
1999
2001
2003
2005
LGS
‐2
2007
LMN
2009
MCN
JDA
Figure 7.1 Estimates of bypass delay for wild (top panel) and hatchery (bottom panel)
spring/summer Chinook salmon smolts at Little Goose Dam (LGS, diamonds), Lower Monumental
Dam (LMN, squares), McNary Dam (MCN, triangles) and John Day Dam (JDA, circles) over
migration years 1998-2009. Positive values indicate cases where bypassed fish had statistically
significant increases in travel time relative to fish not detected at the dam. Negative values indicate
cases where bypassed fish had statistically significant reductions in travel time relative to fish not
detected at the dam.
152
Wild STH
2
Bypass delay (d)
0
1997
1999
2001
2003
2005
2007
2009
‐2
‐4
‐6
LGS
‐8
LMN
MCN
JDA
Hatch. STH
4
2
Bypass delay (d)
0
1997
‐2
1999
2001
2003
2005
2007
2009
‐4
‐6
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
‐8
LGS LMN MCN JDA
Figure 7.2 Estimates of bypass delay for wild (top panel) and hatchery (bottom panel) steelhead
smolts at Little Goose Dam (LGS, diamonds), Lower Monumental Dam (LMN, squares), McNary
Dam (MCN, triangles) and John Day Dam (JDA, circles) over migration years 1998-2009. Positive
values indicate cases where bypassed fish had statistically significant increases in travel time relative
to fish not detected at the dam. Negative values indicate cases where bypassed fish had statistically
significant reductions in travel time relative to fish not detected at the dam.
Effects of bypass systems on post-Bonneville Dam survival
Methods
The data for this analysis consisted of spring/summer Chinook and steelhead of
both hatchery and wild origin that were PIT-tagged and released upriver of Lower
Granite Dam (LGR) during migration years 2000-2008 and subsequently detected at
Bonneville Dam. Detection histories were determined for each smolt at dams with
collection or bypass systems with juvenile PIT-tag detection capabilities, which included
LGR, Little Goose Dam (LGS), Lower Monumental Dam (LMN), McNary Dam (MCN),
John Day Dam (JDA) and Bonneville Dam (BON). At Bonneville Dam, juvenile smolts
could be detected within the juvenile bypass system or within the corner collector (2006 –
present). Within the full dataset, we queried for records of smolts that were detected at
BON, either in the juvenile bypass system or the corner collector. These fish were
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3
4
5
6
7
known to have survived up through detection at BON, and each had an associated bypass
history at upriver dams, with the number of previous bypass experiences ranging from
zero to five. We then determined whether each smolt that was detected at BON returned
to BON as an adult. Thus, these data provide an estimate of the SAR from BON as a
smolt to BON as an adult. The number of smolts and adults used in the analysis for each
year is provided in Table 7.3.
Table 7.3 Number of hatchery and wild Chinook and steelhead detected at Bonneville Dam, the
number of adult returns from those smolts, and the corresponding BON-BON SAR across smolt
migration years 2000-2008.
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
Year
2000
2001
2002
2003
2004
2005
2006
2007
2008
Total
CHN smolts CHN adults
10,437
382
7,120
22
15,388
231
15,657
123
4,187
24
5,238
14
11,058
128
18,141
208
7,041
252
94,267
1,384
SAR
3.66%
0.31%
1.50%
0.79%
0.57%
0.27%
1.16%
1.15%
3.58%
STH smolts
2,957
456
3,339
3,812
280
299
1,199
2,386
12,117
26,845
STH adults
83
3
87
52
8
1
29
73
477
813
SAR
2.81%
0.66%
2.61%
1.36%
2.86%
0.33%
2.42%
3.06%
3.94%
We used logistic regression techniques (Hosmer and Lemeshow 2000) within an
information-theoretic framework (Burnham and Anderson 2002) to address these two
questions for Chinook and steelhead. The dependent variable was the probability of adult
return at BON. We considered five a priori models for characterizing variability in the
probability of adult return. Model 1 consisted of year effects and an additive effect of
hatchery rearing type to examine whether hatchery smolts consistently had lower or
higher post-BON SARs. Model 2 was a year-by-rearing type interaction model, which
allowed for annual differences between post-BON SARs for hatchery and wild smolts.
Models 3, 4 and 5 also included the year-by-rearing type interaction, but differed in the
way bypass effects were modeled. Model 3 included a variable that was the total number
of bypass experiences (“TOT.byp”) at upriver dams. Model 4 included one variable that
was the number of bypass experiences at Snake River dams (LGR, LGS and LMN,
“SNK.byp”) and another variable that was the number of bypass experiences at Columbia
River dams (MCN and JDA, “COL.byp”). Model 4 thus examines whether there is a
difference in the severity of bypass experiences between dams in the two river systems.
Model 5 included indicator variables denoting the location of bypass (“byp.location”) at
upriver dams to determine whether bypass systems at individual dams were more or less
severe than others. Each model was fit for each species and we recorded the Akaike’s
Information Criterion (AIC) for each model, with lower AIC values indicating better
fitting models. We then calculated information-theoretic summary statistics, including
154
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40
 1 
AIC differences, ∆i = AICi – AICmin, the individual model likelihoods = exp   i  ,
 2 
and the model probabilities (Burnham and Anderson 2002):
 1 
exp   i 
2 
.
(Eqn. 7.2)
wi  3 
 1 
exp   i 

 2 
i 1
The best degree of fit was mainly determined by lowest AIC, but the relative probabilities
of each model, given the data and the set of five models considered were also used. The
model probabilities provide the weight of evidence in favor of model i being the best
model for the data, given that one of the five models is the Kullback-Leibler best model
in the set (Burnham and Anderson 2002:75).
Results
For Chinook, Model 1 indicated that post-BON SARs for hatchery smolts averaged 25%
less than wild smolts, and this effect was statistically significant (P < 0.00001). For
steelhead, there was a tendency that post-BON SARs for hatchery smolts were lower than
wild smolts (estimated effect was an 11% reduction for hatchery smolts relative to wild
smolts), but the effect was not statistically significant (P = 0.168). However, for both
Chinook and steelhead, Model 2 with the year-by-rearing type interactions had
substantially lower AIC values than Model 1 (14 points for CHN and 11 points for STH,
Table 7.4), indicating that the relative difference between hatchery and wild smolts varied
across years with wild smolts having higher, lower or equivalent post-BON SARs
compared to hatchery smolts (Table 7.4, Figure 7.3).
Incorporating bypass effects (Models 3, 4 and 5) further reduced AIC values
compared to Model 2 (without bypass effects) for both species (Table 7.4), indicating that
bypass history was important for characterizing variation in post-BON SARs. For
Chinook, Model 3 with the total number of bypass experiences had the lowest AIC value,
followed by Model 4. The Model 3 estimates for Chinook showed a 10% reduction in
post-BON SARs per bypass experience at upriver dams (P = 0.0001, Table 7.5). For
steelhead, Model 4, which differentiated the number of bypasses at Snake River dams
versus the number of bypasses at Columbia River dams, had the lowest AIC value. The
Model 4 estimates for steelhead showed a 6% reduction in post-BON SAR per bypass
experience at Snake River dams (P = 0.21, Table 7.6) and a 22% reduction in post-BON
SAR per bypass experience at Columbia River dams (P = 0.0006, Table 7.6). The Model
5 results, which estimate dam-specific bypass effects, showed similar patterns to the
lowest-AIC models of each species (Table 7.7). For Chinook, estimates of bypass effects
were similar across Snake and Columbia river dams (Table 7.7). For steelhead, estimates
of bypass effects were much more severe at MCN and JDA dams than they were at LGR,
LGS or LMN (Table 7.8).
155
Table 7.4 Information-theoretic summary statistics for the five models considered for Chinook and
steelhead.
Model
species parameters
AIC
∆ AIC
model lik. model prob.
1: year + hatch.
CHN
10
13740.38
26.81
0.00
0.00
2: year*hatch.
CHN
18
13726.53
12.96
0.00
0.00
3: year*hatch. + TOT.byp
CHN
19
13713.57
0.00
1.00
0.70
4: year*hatch. + SNK.byp + COL.byp CHN
20
13715.52
1.95
0.38
0.26
5: year*hatch. + byp.location
CHN
22
13719.74
6.17
0.05
0.03
1
2
3
4
5
6
7
8
9
10
11
12
13
1: year + hatch.
2: year*hatch.
3: year*hatch. + TOT.byp
4: year*hatch. + SNK.byp + COL.byp
5: year*hatch. + byp.location
STH
STH
STH
STH
STH
10
18
19
20
22
7200.41
7189.55
7181.51
7178.72
7182.32
21.69
10.83
2.79
0.00
3.60
0.00
0.00
0.25
1.00
0.17
0.00
0.00
0.17
0.71
0.12
Figure 7.3 Model 3 estimates of post-BON SARs for wild (blue squares) and hatchery (yellow circles)
Chinook salmon smolts with zero bypass experiences at upriver dams (left panel), and Model 4
estimates of post-BON SARs for wild (blue squares) and hatchery (yellow circles) steelhead smolts
with zero bypass experiences at upriver dams (right panel). Error bars represent 95% confidence
intervals on the mean post-BON SAR. Hatchery steelhead in 2001 and wild steelhead in 2005 had
zero adult returns, precluding the estimation of confidence intervals for those cases.
156
1
Table 7.5 Model 3 logistic regression parameter estimates, standard errors, z values and p-values for
Chinook.
2
Variable
Estimate Std. Error z value
TOT.byp
-0.117
0.031
-3.8
2000 wild
-2.756
0.092
-30.1
2000 hatchery
-3.397
0.070
-48.6
2001 wild
-4.818
0.332
-14.5
2001 hatchery
-5.747
0.302
-19.0
2002 wild
-3.637
0.145
-25.0
2002 hatchery
-4.146
0.082
-50.5
2003 wild
-5.087
0.247
-20.6
2003 hatchery
-4.660
0.100
-46.5
2004 wild
-4.468
0.325
-13.7
2004 hatchery
-5.163
0.273
-18.9
2005 wild
-6.736
1.003
-6.7
2005 hatchery
-5.521
0.284
-19.5
2006 wild
-3.987
0.249
-16.0
2006 hatchery
-4.345
0.101
-42.9
2007 wild
-3.896
0.185
-21.0
2007 hatchery
-4.400
0.081
-54.5
2008 wild
-3.198
0.141
-22.7
2008 hatchery
-3.171
0.078
-40.9
157
Pr(> |z| )
1.29E-04
2.00E-16
2.00E-16
2.00E-16
2.00E-16
2.00E-16
2.00E-16
2.00E-16
2.00E-16
2.00E-16
2.00E-16
1.88E-11
2.00E-16
2.00E-16
2.00E-16
2.00E-16
2.00E-16
2.00E-16
2.00E-16
1
Table 7.6 Model 4 logistic regression parameter estimates, standard errors, z values and p-values for
steelhead. The high standard errors for hatchery steelhead in 2001 and wild steelhead in 2005 are
due to the absence of adult returns from those releases.
2
Variable
Estimate Std. Error
SNK.byp
-0.063
0.050
COL.byp
-0.268
0.078
2000 wild
-3.000
0.150
2000 hatchery
-3.985
0.219
2001 wild
-3.793
0.595
2001 hatchery
-17.259 245.684
2002 wild
-3.478
0.170
2002 hatchery
-3.485
0.154
2003 wild
-4.265
0.249
2003 hatchery
-4.113
0.175
2004 wild
-4.460
1.009
2004 hatchery
-3.024
0.395
2005 wild
-17.301 364.979
2005 hatchery
-4.961
1.008
2006 wild
-3.895
0.458
2006 hatchery
-3.359
0.220
2007 wild
-3.135
0.186
2007 hatchery
-3.489
0.160
2008 wild
-3.133
0.162
2008 hatchery
-3.093
0.057
158
z value
-1.3
-3.4
-20.0
-18.2
-6.4
-0.1
-20.4
-22.7
-17.1
-23.5
-4.4
-7.7
0.0
-4.9
-8.5
-15.3
-16.8
-21.7
-19.4
-54.0
Pr(> |z| )
2.07E-01
5.92E-04
2.00E-16
2.00E-16
1.80E-10
9.44E-01
2.00E-16
2.00E-16
2.00E-16
2.00E-16
9.77E-06
1.80E-14
9.62E-01
8.65E-07
2.00E-16
2.00E-16
2.00E-16
2.00E-16
2.00E-16
2.00E-16
1
Table 7.7 Logistic regression parameter estimates, standard errors, z values and p-values for bypass
effects of Models 3, 4 and 5 for Chinook.
2
3
Model 3
Variable Estimate Std. Error
TOT.byp
-0.117
0.031
z value Pr(> |z| )
-3.8
0.0001
Model 4
SNK.byp
-0.111
0.041
COL.byp
-0.126
0.048
z value Pr(> |z| )
-2.7
0.0062
-2.6
0.0087
Model 5
LGR.byp
-0.088
0.073
LGS.byp
-0.185
0.072
LMN.byp
-0.055
0.073
MCN.byp
-0.114
0.061
JDA.byp
-0.143
0.078
z value Pr(> |z| )
-1.2
0.2285
-2.6
0.0101
-0.8
0.4528
-1.9
0.0626
-1.8
0.0650
Table 7.8 Logistic regression parameter estimates, standard errors, z values and p-values for bypass
effects of Models 3, 4 and 5 for steelhead.
4
5
6
7
8
9
Model 3
TOT.byp
-0.127
0.041
z value Pr(> |z| )
-3.1
0.0018
Model 4
SNK.byp
-0.063
0.050
COL.byp
-0.268
0.078
z value Pr(> |z| )
-1.3
0.2074
-3.4
0.0006
Model 5
LGR.byp
-0.101
0.089
LGS.byp
-0.116
0.079
LMN.byp
0.061
0.094
MCN.byp
-0.249
0.110
JDA.byp
-0.291
0.116
z value Pr(> |z| )
-1.1
0.2549
-1.5
0.1445
0.7
0.5148
-2.3
0.0233
-2.5
0.0116
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46
Discussion
The results of this analysis lends support to the Budy et al. (2002) hypothesis that
the cumulative effects of migration conditions through the hydrosystem affect levels of
delayed mortality expressed in post-BON SARs of both Chinook and steelhead. This
support comes from Models 3-5, which contained variables measuring the location and
number of previous bypass experiences at upriver dams, being the best fitting models
based on AIC values among the five models considered for Chinook and steelhead. For
both species, there was evidence that as the number of bypass experiences increased,
post-BON SARs decreased. As for location of bypass, we found little evidence that postBON SARs of Chinook depended on their location of bypass. However, we found
evidence that bypass location affected post-BON SARs of steelhead, with McNary and
John Day dam bypass histories having a stronger detrimental effect than bypass at LGR,
LGS or LMN.
The results from this analysis indicate that SARs conditioned upon bypass
detections should be viewed with some caution. Our results showed that post-BON
SARs for bypassed smolts are lower than post-BON SARs for non-detected smolts.
Therefore analyses that utilize detected smolts as the starting population for calculating
SARs are likely to be biased low relative to smolts that are not detected at that same dam.
Furthermore, we have provided evidence that subsequent downstream bypass experiences
may further influence the resulting SARs, with smolts that pass undetected through the
dams expected to have higher SARs than those smolts that are bypassed one or more
times.
The life-cycle modeling conducted by Kareiva et al. (2000) and Wilson (2003)
indicated that improving survival in the estuary and ocean was critical for achieving
recovery objectives of ESA-listed Snake River spring/summer Chinook. The results for
our work indicate that bypass experiences upriver may be one factor that is lowering
post-BON SARs of Chinook and steelhead. Therefore management strategies that reduce
the number of bypass experiences through increasing spill proportions or structural
modifications to spillways (e.g., RSWs or TSWs), especially at McNary and John Day
dams (in the case of steelhead), could assist in increasing post-BON survival rates.
Additionally, researchers have found that Chinook and steelhead smolts arriving at BON
earlier in the season tend to have higher SARs than smolts that arrive later in the season
(Scheuerell et al. 2009). Given the results in the first section of this chapter, increased
spillway passage and reduced bypass passage is expected to reduce migration delay,
which would allow for Chinook and steelhead smolts to arrive at the estuary faster and in
better condition than under a management strategy that maintains higher levels of passage
through bypass systems.
Meta- Analysis comparing SARs of C1 and C0 wild Chinook and steelhead
In this section, techniques developed in Chapter 5 of Tuomikoski et al. (2009) are
used to explore the hypothesis that cumulative effects of bypass at dams can result in
mortality expressed in SARs. A random effects meta-analysis is performed to estimate
summary distributions of the ratio of SAR(C1) to SAR(C0) from annual estimates of this
ratio, for wild Chinook and steelhead.
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7
8
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11
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13
14
15
16
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19
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22
23
24
25
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37
The C0 group is the estimated number of fish that passed LGR, LGS, and LMN
undetected; the C1 group is made up of fish that were detected at least once at any of
LGR, LGS, or LMN, and not transported. Fish in either group may or may not be
detected at some later facility (i.e. MCN, JDA, BON, TWX). If the SARs of the two
groups are equal, we should expect estimates of SAR(C1)/SAR(C0) to center around 1; if
SAR(C1) is generally higher, the ratio should on average be > 1; and if SAR(C1) is
generally lower, we the ratio should on average be < 1.
Methods
Annual estimates of SARs for Chinook from 1994-2006 migration years, and for
steelhead from 1997 -2006, were used in the analysis. The SAR(C0) and SAR(C1) were
estimated using E[C0] and E[C1] estimated smolt numbers (below) and returning adults
(without Jacks for Chinook) for each category, and expressed as a differential for
comparison (i.e., SAR(C1)/SAR(C0)). Data from migration year 2007 were not used, due
to the delayed start of smolt transportation in that and subsequent years, and the desire to
avoid non-stationarity. Migration year 2006 is included here because although
transportation was delayed, the delay was shorter than in subsequent years, and the
portion of the run transported was similar to preceding years, as shown in the following
table:
Year
Lower Granite
Dam (LGR)
Little Goose Dam
(LGS)
Lower Monumental
Dam (LMN)
19942005
2006
2007
March 25
April 1
April 1
April 20
May 1
April 24
May 8
April 28
May 11
The equations for estimating the expected number of PIT-tagged smolts in C0 and C1
categories are as follows with known numbers removed (dj) at each dam (j) expressed in
LGR-equivalents (j = 2 for LGR, 3 for LGS, 4 for LMN, 5 for MCN, 6 for JDA, and 7 for
BON):
where
E[C0] = R1•S1•(1-P2)•(1-P3)•(1-P4) – d0
[7.1]


d5.0
d 6.0
d 7.0


d0  

 S 2 * S3 * S 4 S 2 * S3 * S 4 * S5 S 2 * S3 * S 4 * S 5 * S 6 
where
E[C1] = R1•S1•[P2 + (1-P2)•P3 + (1-P2)•(1-P3)•P4]
– [(d2 + d3 /S2 + d4 /(S2•S3) + d1]


d5.1
d 6.1
d 7.1


d1  

 S 2 * S3 * S 4 S 2 * S3 * S 4 * S5 S 2 * S3 * S 4 * S5 * S 6 
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In years prior to 2006, PIT-tagged smolts were being bypassed at a relative
similar rate across the full season, since transportation occurred across the full season.
But beginning in 2006, the start of transportation was delayed, causing a higher portion of
C1 fish to migrate earlier in the season, when conditions are favorable (and hence survival
on average would be expected to be greater than over the whole season). Also beginning
in 2006, the CSS began to pre-assign PIT-tagged smolts into two groups (Groups T and
R) as described in Chapter 4. Prior to that year a single aggregate of PIT-tagged wild
Chinook and another aggregate of wild steelhead were created for each migration year.
The 2006 pre-assigned smolts in Group R follow the return-to-river operations at each of
the collector dams over the entire migration season, and therefore provide a more
consistent comparison with the years prior to 2006. Therefore, for migration year 2006, a
combination of Groups T and R, comparable to the single release group of past years was
used for the C0 estimate, while Group R fish was used for C1 estimate (i.e., E[C1] for
Group R). This allows the comparison between C1 and C0 smolts to reflect just the
impacts of how these smolts passed the Snake River collector dams, since any underlying
but unmeasured seasonal trend for in-river survival, if it occurs in 2006, would then apply
equally to the C0 and C1 groups.
Formulas used to estimate heterogeneity (between-year) variance, summary
means, confidence intervals of the mean, and prediction intervals are provided in
Tuomikoski et al. (2009). Except as noted below, sample variances used for each year
were derived from bootstrap outputs. For wild steelhead, there were no C0 adults
detected returning from juvenile migration year 2004. Since the point estimate and
sampling variance of SAR(C1)/SAR(C0) are therefore undefined, that year was omitted
from the analysis. Data from migration year 2001 were also omitted from the analysis,
even though three steelhead adults without juvenile detections at the transport projects
were later detected as adults. This was because there was substantial residualism of
steelhead that year and these “C0” fish may have passed raceways undetected during a
computer outage in mid-May at LGR (Berggren et al. 2005a). The resultant point
estimate of SAR(C1)/SAR(C0) was anomalously low (one fifth of the next lowest annual
point estimate), and the data from 2001 would have been highly influential in the
summary distribution. For wild Chinook, only one C0 adult each was detected returning
from juvenile migration years 2001 and 2005. Consequently, for those years the
theoretical variance of the natural logarithm of the ratio of two survival rates was used as
the estimate of sampling variance, as described in Tuomikoski et al. (2009). Due to the
computer outage, the one “C0” Chinook adult return from the 2001 migration may
actually have been transported. However, the point estimate was neither the lowest nor
the highest of the series, and due to the large sampling variance and consequently tiny
weight it receives in estimating the summary effect (Figure 1) it has little influence, and
so was retained in the estimation.
Results
Forest plots are commonly used in meta-analysis to present resulting summary
mean distributions and show the influence of estimates from each study on the summary.
Figures 7.1 and 7.2 are forest plots showing the summary mean distribution of
SAR(C1)/SAR(C0), along with contribution and precision of each annual estimate, for
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wild Chinook and wild steelhead, respectively. Figure 7.3 shows the 90% confidence
interval of the summary mean and the 90% prediction interval for both Chinook and
steelhead in box and whisker format.
The confidence intervals of the means of SAR(C1)/SAR(C0) for both species are
entirely below one, indicating a significant mortality effect, at 5% α level, from bypass at
one or more collector facilities. Although the mean of the Chinook summary
distribution is higher than the mean for steelhead, the confidence interval of the Chinook
mean is much smaller, indicating greater confidence in the conclusion of a bypass
mortality effect. The wider steelhead confidence interval results from fewer PIT-tagged
smolts per year and fewer years of data.
Figure 7.1 Forest plot of SAR(C1)/SAR(C0) for wild Chinook. Squares are centered on the point
estimate for each year; horizontal lines display the 90% confidence interval for each estimate. X-axis
is logarithmic, with vertical line at SAR(C1)/SAR(C0) = 1. The area of each box is proportional to
the weight it receives in estimating the summary effect. The diamond is the summary estimate and
has its vertical points lined up with the summary mean estimate; the width of the diamond shows the
90% confidence interval of the mean.
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Figure 7.2 Forest plot of SAR(C1)/SAR(C0) for wild steelhead. Squares are centered on the point
estimate for each year; horizontal lines display the 90% confidence interval for each estimate. X-axis
is logarithmic, with vertical line at SAR(C1)/SAR(C0) = 1. The area of each box is proportional to
the weight it receives in estimating the summary effect. The diamond is the summary estimate and
has its vertical points lined up with the summary mean estimate; the width of the diamond shows the
90% confidence interval of the mean.
10.0
1.0
C1/C0
0.1
9
10
11
12
Chinook
Steelhead
Figure 7.3 Summary mean SAR(C1)/SAR(C0) (center lines), 90% CIs of summary mean (boxes), and
90% prediction limits of summary (whiskers).
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Discussion
The summary distributions here show the limitations of relying on SARs of C1
fish as surrogates for the pre-2006 untagged in-river migrating population, for purposes
of estimating TIR and D. Due either to limited numbers of C0 adult returns or
indeterminate passage history of returnees, or both, on occasion annual TIRs and Ds
intended to reflect the experience of untagged fish are estimated for some years using
either a mix of C1 and C0 fish or only C1 fish. In addition, estimates of within-season
blocks of TIR and D based on passage timing at LGR or another dam are made to
examine trends in these quantities over the migration season. These SAR ratios are
necessarily calculated using only C1 fish, since a dam passage date is available only for
fish which are detected (or released) at that dam. Whatever the reason for the
substitution, it seems that TIRs and Ds using C1 fish will tend to substantially
overestimate the true values that would be obtained using C0 fish. This caveat should be
clearly stated anytime this substitution is employed by investigators.
Results presented here should be interpreted with some cautions in mind. A basic
assumption of meta-analysis is that the individual studies summarized are statistically
independent from each other. Since adjacent year classes of Chinook or steelhead overlap
during their ocean residence, and fish from two or more year classes can make the
upstream adult migration in the same year, a particular year’s environmental conditions
can influence the survival of multiple cohorts. Conversely, given the general strong
dependence of marine survival on conditions during the first critical months at sea (e.g.,
Pearcy 1992), adjacent year classes should experience somewhat different environmental
conditions (temporally and spatially). The degree of dependence between adjacent year
classes of SARs is difficult to estimate. However, only the ratios of SARs are analyzed
here; lack of independence in the absolute SARs does not necessarily imply similar
dependence in the ratios of SARs. To the extent that lack of independence is a problem
in this analysis, the confidence intervals shown here will be too narrow, with increased
probability of a Type 1 error [see Discussion in Tuomikoski et al. (2009), Chapter 5].
The underestimation of the confidence interval of the mean would have to be very large
to affect the conclusion of a bypass mortality effect for Chinook. However, given the
proximity of the upper confidence limit of the steelhead mean to 1, the potential
underestimation of the interval suggests the finding of bypass mortality for steelhead
should be considered provisional.
The above analysis looked at PIT-tagged wild Chinook and wild steelhead;
however, there is further evidence that of a reduced SAR of bypassed fish across the PITtagged hatchery Chinook and steelhead groups analyzed in Chapter 4. For the migration
years with uniquely estimated SAR(C0) between 1997 and 2007 (excluding 2001 and
2005 for Chinook and 2001, 2004, and 2005 for steelhead because an estimate for C0 fish
was not possible without including C1 fish), the average SAR(C1) was less than the
average SAR(C0). This implies that the process of being “collected” to the point
necessary for PIT-tag detection and subsequently migrating in-river compromised smoltto-adult survival (Figure 7.4).
This reduction in smolt viability is potentially due to the stress, injury, and/or
disease factors associated with the “collection” process (Budy et al. 2002; Marmorek et
al. 2004). Improving SARs for bypassed and transported salmonid smolts would appear
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to require a reduction in the detrimental effects of the “collection” process. Alternatively,
operations could be implemented which reduced the proportion of in-river migrating fish
that experience the collection process, such as increasing spill and/or flow levels, thereby
increasing the SARs of in-river migrants through reducing the number of collection and
bypass experiences of smolts.
Figure 7.4 Comparison of average SAR(C0) and SAR(C1) for the PIT-tagged PIT-tagged hatchery
steelhead aggregate [HST] and the four CSS PIT-tagged hatchery Chinook groups with longest time
series (Rapid River [RAPH], Dworshak [DWOR], McCall [MCCA] and Imnaha [IMNA]) for years
noted in text. Years 2006 and 2007 use SAR(C1) values of Group R fish to eliminate the effect of
starting transportation later in those two years compared to the earlier years being averaged.
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15
Appendix A
Source of PIT-tagged Fish
PIT-tagged Wild Chinook Aggregate – Composition by Drainage
Table A.1 Number of PIT-tagged wild Chinook parr/smolts from tributaries above Lower Granite
Dam (plus Snake River trap) used in the CSS analyses for migration years 1994 to 2009.
Clearwater Snake
Grande
Salmon
Imnaha
River
River trapA Ronde River
River
River
Migr
Total
Year
PIT tags
(Rkm 224)
(Rkm 225)
(Rkm 271)
(Rkm 303)
(Rkm 308)
1994
49,657
8,292
1,423
8,828
27,725
3,391
1995
74,639
17,605
1,948
12,330
40,609
2,148
1996
21,523
2,246
913
7,079
7,016
4,269
1997
9,781
671
None
3,870
3,543
1,697
1998
33,836
4,681
921
8,644
11,179
8,411
1999
81,493
13,695
3,051
11,240
43,323
10,184
2000
67,841
9,921
1,526
7,706
39,609
9,079
2001
47,775
3,745
29
6,354
23,107
14,540
2002
67,286
14,060
1,077
9,715
36,051
6,428
2003
103,012
15,106
381
14,057
60,261
13,165
2004
99,743
17,214
541
12,104
56,153
13,731
2005
111,152
23,897
318
9,243
67,829
9,865
2006
52,978
8,663
2,639
10,457
30,094
1,125
2007
52,496
3,041
373
9,267
28,561
11,254
2008
47,899
4,477
0
8,316
24,266
10,840
2009
47,880
5,111
0
7,848
26,140
8,781
Average percent
of total
15.7%
1.6%
15.2%
54.2%
13.3%
A
Snake River trap at Lewiston, ID, collects fish originating in Salmon, Imnaha, and Grande Ronde rivers.
PIT-tagged Rapid River Hatchery Spring Chinook – Salmon River Drainage
Table A.2 Rapid River Hatchery spring Chinook (RAPH) PIT-tagged and released in Salmon River
basin specifically for CSS (long time series), 1997 to 2009.
Migration
Hatchery
Fish# /
Median Length at PIT Tags
PIT Tag
Year
Release
lb
Tagging (mm)
Released
Proportion
1997
85,838
20.5
100 A
40,451
0.4712
1998
896,170
20.3
117
48,336
0.0539
1999
2,847,283
17.9
120
47,812
0.0168
2000
2,462,354
19.2
119
47,747
0.0194
2001
736,601
18.8
118
55,085
0.0748
2002
2,669,476
19.8
122
54,908
0.0206
2003
2,330,557
18.8
119
54,763
0.0235
2004
2,762,058
24.5
(none taken)
51,969
0.0188
2005
2,761,430
19.1
124
51,975
0.0188
2006
2,530,528
19.3
129
51,874
0.0205
2007
2,498,246
20
117
51,759
0.0207
2008
2,493,719
16.7
125
51,689
0.0207
2009
2,503,711
20.0
(none taken)
51,725
0.0207
A
Tagged in fall 5 months before release; otherwise tagged in winter/spring 1-3 months before release.
175
1
2
3
4
5
6
7
8
9
10
11
12
13
14
PIT-tagged Dworshak Hatchery Spring Chinook – Clearwater River Drainage
Table A.3 Dworshak Hatchery spring Chinook (DWOR) PIT-tagged and released in Clearwater
River basin specifically for CSS (long time series), 1997 to 2009.
Migration
Hatchery
Fish# /
PIT Tag
Year
Release
lb
Tagging A (mm)
Released
Proportion
1997
53,078
12.7
118
14,080
0.2653
1998
973,400
20.9
121
47,703
0.049
1999
1,044,511
21
116
47,845
0.0458
2000
1,017,873
24
112
47,743
0.0469
2001
333,120
19.7
121
55,139
0.1655
2002
1,000,561
20.1
119
54,725
0.0547
2003
1,033,982
21.4
120
54,708
0.0529
2004
1,078,923
20.2
113
51,616
0.0478
2005
1,072,359
19.2
112
51,819
0.0483
2006
1,007,738
20
108
51,900
0.0515
2007
963,211
17.7
114
51,649
0.0536
2008
939,000
23.5
105
49,384
0.0526
2009
1,014,748
21.2
113
50,829
0.0501
A
Tagged in winter/spring 1-3 months before release.
PIT-tagged McCall Hatchery Summer Chinook – Salmon River Drainage
Table A.4 McCall Hatchery summer Chinook (MCCA) PIT-tagged and released in Salmon River
Migration
Hatchery
Fish# /
PIT Tag
Year
Release
lb
Tagging A (mm)
Released
Proportion
1997
238,647
17.1
128
52,652
0.2206
1998
393,872
17.5
126
47,340
0.1202
1999
1,143,083
23.9
117
47,985
0.042
2000
1,039,930
23.3
117
47,705
0.0459
2001
1,076,846
19.4
129
55,124
0.0512
2002
1,022,550
23
122
54,734
0.0535
2003
1,053,660
21.1
121
74,317
0.0705
2004
1,088,810
20.9
(none taken)
71,363
0.0655
2005
1,047,530
20.9
121
71,725
0.0685
2006
1,096,130
18.1
126
51,895
0.0473
2007
1,087,170
19.1
122
51,726
0.0476
2008
1,060,540
19.5
129
51,678
0.0487
2009
1,106,700
21.3
(none taken)
51,495
0.0465
A
Tagged in winter/spring 1-3 months before release.
176
1
2
PIT-tagged Imnaha Hatchery Summer Chinook – Imnaha River Drainage
3
4
Table A.5 Imnaha Hatchery summer Chinook (IMNA) PIT-tagged and released in Imnaha River
Migration
Hatchery
Fish# /
PIT Tag
Year
Release
lb
Tagging (mm)
Released
Proportion
1997
50,911
17
122A
13,378
0.2628
1998
93,108
21.1
122A
19,825
0.2129
1999
184,725
18.5
117
19,939
0.1079
2000
179,797
19.1
113
20,819
0.1158
2001
123,014
16
121
20,922
0.1701
2002
303,737
14.1
121
20,920
0.0689
2003
268,426
16.3
123
20,904
0.0779
2004
398,469
26.1
98
20,910
0.0525
2005
435,186
24.5
105
20,917
0.0481
2006
320,752
27.1
105
20,623
0.0643
2007
432,530
21.6
107
20,885
0.0483
2008
348,910
20.3
116
20,760
0.0595
2009
234,963
20.0
110
20,863
0.0888
A
Tagged in winter/spring 1-3 months before release; otherwise tagged in fall 5-7 months before release.
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
PIT-tagged Catherine Creek AP Spring Chinook – Grande Ronde River Drainage
Table A.6 Catherine Creek Hatchery spring Chinook (CATH) PIT-tagged and released in Grande
Ronde River basin specifically for CSS (long time series), 2001 to 2009.
Migration
Hatchery
Fish# /
PIT Tag
Year
Release
lb
Tagging A (mm)
Released
Proportion
2001
136,833
19.7
117
20,915
0.1529
2002
180,343
18.6
115
20,796
0.1153
2003
105,292
12.8
123
20,628
0.1959
2004
162,614
23.2
109
20,994
0.1291
2005
189,580
25.1
106
20,839
0.1099
2006
68,820
22.7
102
20,958
0.3045
2007
71,268
26.9
102
20,817
0.2921
2008
116,882
17.9
112
20,717
0.1772
2009
138,843
22.7
107
20,840
0.1501
A
Tagged in fall 5-7 months before release.
PIT-tagged Hatchery Chinook Additions to CSS
Table A.7 Additional hatchery spring and summer Chinook PIT-tagged A and released in Grande
Ronde River basin with participation with the CSS beginning in 2009.
Hatchery
Fish# /
PIT Tags
PIT Tag
Release
lb
Released
Proportion
Hatchery
Stock
Clearwater H (CLWH)
spring
2,214,144
16.8
68,649
0.0310
Sawtooth H (SAWT)
spring
274,644
14.0
18,671
0.0680
Pahsimeroi H (PAHP)
summer
870,842
11.3
18,749
0.0215
A
No lengths taken at time of tagging
177
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
PIT-tagged Wild Steelhead Aggregate – Composition by Drainage
Table A.8 Number of PIT-tagged wild steelhead smolts from tributaries above Lower Granite Dam
(plus Snake River trap) used in the CSS analyses for migration years 1997 to 2009.
Clearwater Snake
Grande
Salmon
Imnaha
River
River trapA Ronde River
River
River
Migr
Total
Year
PIT tags
(Rkm 224)
(Rkm 225)
(Rkm 271)
(Rkm 303)
(Rkm 308)
1997
7,703
5,518
68
248
1,158
711
1998
10,512
4,131
1,032
887
1,683
2,779
1999
15,763
5,095
886
1,628
5,569
2,585
2000
24,254
8,688
1,211
3,618
6,245
4,492
2001
24,487
8,845
867
3,370
7,844
3,561
2002
25,183
10,206
2,368
3,353
6,136
3,120
2003
24,284
5,885
1,197
4,261
6,969
5,972
2004
25,156
7,642
1,922
2,977
7,102
5,513
2005
25,000
8,391
2,749 B
3,771
5,652
4,437
2006
16,579
8,301
4
1,950
4,090
2,234
2007
17,857
5,001
1
2,170
4,112
6,573
2008
16,229
7,249
11
1,048
5,649
2,272
2009
16,628
4,067
4
1,494
5,953
5,110
Average % of total
35.7%
4.9%
12.3%
27.3%
19.8%
A
Snake River trap at Lewiston, ID, collects fish originating in Grande Ronde, Salmon, and Imnaha rivers;
wild steelhead at this trap are not part of pre-assigned smolts in 2006 to 2009 – the few tags shown on wild
steelhead were originally planned for use on wild Chinook tagging.
B
Includes 1,400 PIT-tagged wild steelhead released in Asotin Creek (Rkm 234).
PIT-tagged Hatchery Steelhead Aggregate – Composition by Drainage
Table A.9 Number of PIT-tagged hatchery steelhead smolts from tributaries above Lower Granite
Dam (plus Snake River trap) used in the CSS analyses for migration years 1997 to 2007.
Clearwater Snake
Grande
Salmon
Imnaha
River
River trapB Ronde River
River
River
Migr
Total
Year
PIT tagsA (Rkm 224)
(Rkm 225)
(Rkm 271)
(Rkm 303)
(Rkm 308)
1997
35,705
12,872
725
6,039
9,394
6,379
1998
30,913
8,451
4,209
4,904
8,457
4,604
1999
36,968
11,486
3,925
5,316
9,132
6,808
2000
32,000
8,488
3,290
5,348
8,173
6,436
2001
29,099
9,155
3,126
4,677
7,859
3,995
2002
26,573
7,819
4,722
3,888
7,011
2,839
2003
26,379
4,912
4,171
3,113
7,764
6,123
2004
19,879
3,400
4,841
2,263
4,072
5,098
2005
23,520
7,228
3,354
2,395
3,684
6,802
2006
16,068
4,545
2,146
4,397
3,208
1,667
2007
26,608
3,893
2,545
8,979
8,820
2,086
Average % of total
27.1%
12.2%
16.9%
25.5%
17.4%
A
Total includes PIT-tagged hatchery steelhead released below HCD ranging between 57 and 301tags per
year, and averaging 0.9% of total across the 11 years.
B
Snake River trap at Lewiston, ID, collects fish released in Grande Ronde, Salmon, and Imnaha rivers, and
below Hells Canyon Dam.
178
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
Dam used in the CSS analyses for migration year 2008.
Median
Length at
PIT Tags
Tributary / run
Tag
PIT Tag
Hatchery Fish# /
lb
Tagging (mm) Released
SiteA
Proportion
Release
Clearwater – B
CLWH
819,264
4.6
(none taken)
20,018
0.0244
DWOR 2,025,453
5.8
175
27,276
0.0135
IRRI
803,847
4.4
134
16,465
0.0205
LYFE
175,961
4.6
(none taken)
4,000
0.0227
Grande Ronde – A
Imnaha – A
IRRI
274,865
4.8
136
14,877
0.0541
Salmon – A
MAVA
713,194
4.6
(none taken)
10,030
0.0141
A-run
HAGE 1,208,489
4.1
(none taken)
18,116
0.0150
Salmon – B
MAVA
907,723
4.7
(none taken)
24,442
0.0269
B-run
HAGE
179,034
4.7
(none taken)
11,330
0.0633
A
Hatchery at which steelhead were PIT-tagged: CLWH – Clearwater H; DWOR – Dworshak NFH;
Irrigon H – IRRI; Magic Valley H – MAVA; and Hagerman NFH – HAGE. Niagara Springs H (NISP)
is not included this year since its release of 1200 PIT-tagged smolts (none in monitor-mode) is not on scale
with the magnitude of PIT-tagging at the other hatcheries being analyzed.
B
Tagged in fall 5-7 months before release; otherwise tagged in winter/spring 1-4 months before release.
Dam used in the CSS analyses for migration year 2009.
Median
Length at
PIT Tags
Tributary / run
Tag
PIT Tag
Hatchery Fish# /
lb
Tagging (mm) Released
SiteA
Proportion
Release
Clearwater – B
CLWH
748,928
4.7
(none taken)
21,193
0.0270
DWOR 1,297,545
6.5
185
28,307
0.0218
Grande Ronde – A
IRRI
652,424
3.8
187
22,239
0.0341
LYFE
170,232
4.7
(none taken)
5,991
0.0352
Imnaha – A
IRRI
187,401
4.5
179
20,848
0.1112
MAVA
812,563
4.8
(none taken)
15,486
0.0191
Salmon – A
HAGE 1,249,216
4.4
(none taken)
16,576
0.0133
NISP 1,248,101
3.9
(none taken)
17,064
0.0137
Salmon – B
MAVA
839,634
4.8
(none taken)
21,911
0.0261
HAGE
171,094
4.6
(none taken)
8,344
0.0488
Below HCD – A
NISP
526,743
4.6
(none taken)
7,398
0.0140
A
Hatchery at which steelhead were PIT-tagged: CLWH – Clearwater H; DWOR – Dworshak NFH;
Irrigon H – IRRI; Magic Valley H – MAVA; Hagerman NFH – HAGE; and Niagara Springs H – NISP.
B
Tagged in fall 5-7 months before release; otherwise tagged in winter/spring 1-4 months before release.
179
1
2
Appendix B
Dam-specific Transportation SARs
Table B.1 Estimated dam-specific transportation SARs (%) of the PIT-tagged wild Chinook
aggregate for juvenile migration years 1994 to 2008 (with 90% confidence intervals). Transported
smolts from total PIT-tag release in years through 2005 and from Group TWS in years beginning
2006.
Migr
SAR(TLGR)
Adult
SAR(TLGS) A
SAR(TLMN) A
Adult
Year
%
(CI%)
#
%
(CI%)
%
(CI%)
#
Adult #
1994
0.67 (0.28 – 1.12)
7
0.52 (0.00 – 1.11)
2
NA
None
1995
0.41 (0.18 – 0.68)
7
0.28 (0.00 – 0.84)
1
NA
None
1996
0.37 (0.00 – 1.10)
1
1.18 (0.00 – 3.41)
1
NA
None
1997
1.08 (0.00 – 2.37)
2
6.67 (0.00 – 14.8)
2
NA
None
1998
1.34 (0.72 – 2.01)
11
0.84 (0.00 – 1.66)
3
1.27 (0.00 – 3.53)
1
1999
2.53 (1.82 – 3.28)
28
2.82 (1.49 – 4.47)
9
2.09 (0.72 – 3.58)
6
2000
1.22 (0.31 – 2.27)
4
2.46 (0.87 – 4.29)
6
1.07 (0.00 – 2.38)
2
2001
1.33 (0.46 – 2.23)
6
1.39 (0.00 – 4.11)
1
NA
None
2002
0.61 (0.30 – 0.95)
10
1.08 (0.70 – 1.53)
20
0.60 (0.00 – 1.79)
1
2003
0.31 (0.19 – 0.45)
16
0.51 (0.28 – 0.75)
13
0.17 (0.00 – 0.50)
1
2004
0.55 (0.42 – 0.67)
49
0.46 (0.25 – 0.68)
13
0.72 (0.25 – 1.24)
6
2005
0.22 (0.16 – 0.29)
27
0.31 (0.16 – 0.48)
10
NA
None
2006
0.72 (0.49 – 0.96)
28
0.72 (0.51 – 0.93)
31
1.24 (0.78 – 1.77)
17
2007
1.23 (x.xx – 0.xx)
26
1.44 (x.xx – x.xx)
9
0.89 (x.xx – x.xx)
3
2008 B
2.68 (x.xx – 0.xx)
94
1.63 (x.xx – x.xx)
28
0.92 (x.xx – x.xx)
4
A
Transported smolt include first-time detected fish only from total release in years through 2005 and
first-time and prior-detected fish from Group TWS in years beginning 2006.
A
Migration year 2008 is incomplete until 3-salt returns at GRA.
3
4
Table B.2 Estimated dam-specific transportation SAR percentages of PIT-tagged Rapid River
hatchery spring Chinook for juvenile migration years 1997 to 2008 (with 90% confidence intervals).
Transported smolts from total PIT-tag release in years through 2005 and from Group TWS in years
beginning 2006.
Migr
SAR(TLGR)
Adult
SAR(TLGS) A
SAR(TLMN) A
Adult
Year
%
(CI%)
#
%
(CI%)
%
(CI%)
#
Adult #
1997
0.80 (0.58 – 1.02)
33
NA
None
2.63 (0.00 – 7.89)
1
1998
2.12 (1.89 – 2.35)
239
1.18 (0.75 – 1.72)
16
1.02 (0.00 – 2.29)
2
1999
3.20 (2.89 – 3.52)
236
3.22 (2.79 – 3.64)
152
1.03 (0.31 – 2.13)
3
2000
2.34 (2.10 – 2.58)
243
1.89 (1.52 – 2.30)
79
2.23 (1.43 – 3.06)
27
2001
1.18 (1.04 – 1.33)
182
0.74 (0.49 – 1.00)
21
0.69 (0.17 – 1.29)
4
2002
1.14 (0.91 – 1.39)
61
0.94 (0.72 – 1.17)
50
1.05 (0.37 – 1.74)
6
2003
0.32 (0.23 – 0.43)
27
0.13 (0.05 – 0.23)
5
0.17 (0.00 – 0.53)
1
2004
0.39 (0.31 – 0.48)
53
0.30 (0.17 – 0.42)
16
0.18 (0.00 – 0.54)
1
2005
0.26 (0.19 – 0.33)
41
0.35 (0.22 – 0.51)
14
NA
None
2006
0.67 (0.53 – 0.83)
53
0.54 (0.39 – 0.70)
34
0.63 (0.38 – 0.89)
17
2007
0.58 (0.42 – 0.75)
35
0.20 (0.00 – 0.41)
3
0.17 (0.00 – 0.42)
2
2008 B
1.49 (x.xx –x.xx)
161
1.33 (x.xx – x.xx)
69
0.98 (x.xx – x.xx)
7
A
A
5
180
Table B.3 Estimated dam-specific transportation SAR percentages of PIT-tagged Dworshak
beginning 2006.
Migr
SAR(TLGR)
Adult
SAR(TLGS) A
SAR(TLMN) A
Adult
Year
%
(CI%)
#
%
(CI%)
Adult #
%
(CI%)
#
1997
0.86 (0.54 – 1.23)
16
NA
None
NA
None
1998
0.99 (0.85 – 1.14)
110
0.62 (0.41 – 0.85)
22
NA
None
1999
1.26 (1.01 – 1.53)
62
1.29 (0.99 – 1.59)
49
0.83 (0.21 – 1.62)
4
2000
1.18 (1.01 – 1.37)
116
1.08 (0.83 – 1.32)
53
0.69 (0.40 – 1.03)
14
2001
0.36 (0.29 – 0.44)
60
0.44 (0.27 – 0.60)
18
0.16 (0.00 – 0.47)
1
2002
0.64 (0.44 – 0.83)
26
0.74 (0.54 – 0.96)
32
0.27 (0.00 – 0.60)
2
2003
0.28 (0.18 – 0.39)
20
0.28 (0.16 –0.41)
12
0.18 (0.00 – 0.38)
2
2004
0.17 (0.12 – 0.24)
22
0.45 (0.34 – 0.58)
37
0.36 (0.00 – 0.81)
2
2005
0.21 (0.16 – 0.29)
32
0.20 (0.11 – 0.31)
11
NA
None
2006
0.39 (0.24 – 0.56)
16
0.41 (0.28 – 0.56)
25
0.52 (0.31 – 0.75)
15
2007
0.63 (0.32 – 0.99)
9
0.66 (0.21 – 1.33)
3
0.51 (0.00 – 1.20)
2
2008 B
0.48 (x.xx – x.xx)
17
0.93 (x.xx – x.xx)
35
1.84 (x.xx – x.xx)
13
A
A
1
2
Table B.4 Estimated dam-specific transportation SAR percentages of PIT-tagged Catherine Creek
beginning 2006.
Migr
SAR(TLGR)
Adult
SAR(TLGS) A
SAR(TLMN) A
Adult
Year
%
(CI%)
#
%
(CI%)
Adult #
%
(CI%)
#
2001
0.33 (0.18 – 0.50)
11
NA
None
NA
None
2002
1.09 (0.66 – 1.53)
16
0.72 (0.29 – 1.18)
8
NA
None
2003
0.32 (0.12 – 0.57)
5
0.57 (0.14 – 1.06)
4
NA
None
2004
0.29 (0.10 – 0.48)
6
0.57 (0.14 – 1.04)
4
1.37 (0.00 – 4.17)
1
2005
0.32 (0.11 – 0.53)
6
0.95 (0.36 – 1.72)
5
NA
None
2006
0.26 (0.08 – 0.53)
3
0.54 (0.19 – 0.95)
6
0.89 (0.22 – 1.69)
4
2007
0.51 (0.22 – 0.84)
7
0.20 (0.00 – 0.61)
1
1.08 (0.00 – 2.22)
3
2008 B
2.47 (x.xx – x.xx)
47
2.87 (x.xx – x.xx)
44
2.03 (x.xx – x.xx)
7
A
A
181
1
Table B.5 Estimated dam-specific transportation SAR percentages of PIT-tagged McCall hatchery
summer Chinook for juvenile migration years 1997 to 2008 (with 90% confidence intervals).
beginning 2006.
Migr
SAR(TLGR)
Adult
SAR(TLGS) A
SAR(TLMN) A
Adult
Year
%
(CI%)
#
%
(CI%)
Adult #
%
(CI%)
#
1997
1.49 (1.21 – 1.76)
87
2.86 (0.85 – 5.83)
3
3.23 (0.00 – 9.52)
1
1998
2.93 (2.65 – 3.22)
263
1.00 (0.46 – 1.62)
9
0.64 (0.00 – 1.88)
1
1999
4.36 (3.88 – 4.83)
206
3.23 (2.82 – 3.65)
161
4.93 (2.26 – 7.58)
10
2000
4.54 (4.18 –4.94)
386
3.26 (2.69 – 3.83)
92
2.45 (1.61 – 3.36)
19
2001
1.41 (1.23 – 1.58)
184
0.76 (0.49 – 1.05)
20
0.40 (0.00 – 0.91)
2
2002
1.63 (1.31 – 1.95)
70
1.43 (1.14 – 1.74)
59
1.00 (0.00 – 2.21)
2
2003
0.82 (0.66 – 0.98)
68
0.85 (0.62 – 1.10)
36
0.81 (0.34 – 1.31)
7
2004
0.43 (0.35 – 0.51)
70
0.36 (0.21 – 0.53)
14
NA
None
2005
0.67 (0.59 – 0.77)
116
0.53 (0.36 – 0.72)
24
0.02 (0.00 – 0.07)
1
2006
1.35 (1.12 – 1.59)
80
0.98 (0.75 – 1.23)
46
1.60 (1.14 – 2.03)
37
2007
1.55 (1.21 – 1.90)
54
1.35 (0.77 – 2.05)
12
1.30 (0.65 – 1.98)
10
2008 B
1.24 (x.xx – x.xx)
69
1.24 (x.xx – x.xx)
49
1.91 (x.xx – x.xx)
15
A
A
2
3
Table B.6 Estimated dam-specific transportation SAR percentages of PIT-tagged Imnaha hatchery
summer Chinook for juvenile migration years 1997 to 2008 (with 90% confidence intervals).
beginning 2006.
Migr
SAR(TLGR)
Adult
SAR(TLGS) A
SAR(TLMN) A
Adult
Year
%
(CI%)
#
%
(CI%)
Adult #
%
(CI%)
#
1997
1.21 (0.84 – 1.66)
25
NA
None
NA
None
1998
0.92 (0.69 – 1.18)
37
0.66 (0.17 – 1.22)
4
NA
None
1999
3.43 (2.82 – 4.08)
74
2.31 (1.80 – 2.86)
53
2.63 (0.00 – 5.31)
3
2000
3.99 (3.50 – 4.48)
154
2.48 (1.91 – 3.09)
45
2.26 (1.18 – 3.36)
12
2001
0.73 (0.56 – 0.92)
42
0.37 (0.13 – 0.64)
6
NA
None
2002
0.74 (0.38 – 1.12)
12
0.82 (0.51 – 1.19)
16
1.55 (0.00 – 2.97)
3
2003
0.58 (0.36 – 0.81)
18
0.64 (0.32 – 0.99)
10
0.67 (0.00 – 1.58)
2
2004
0.34 (0.21 – 0.48)
16
0.42 (0.20 – 0.68)
8
1.23 (0.00 – 2.91)
2
2005
0.34 (0.20 – 0.48)
15
0.15 (0.00 – 0.36)
2
NA
None
2006
0.83 (0.47 – 1.22)
16
0.81 (0.54 – 1.11)
19
1.22 (0.61 – 1.90)
10
2007
1.26 (0.82 – 1.70)
21
0.39 (0.00 – 1.12)
1
NA
None
2008 B
1.51 (x.xx – x.xx)
50
2.44 (x.xx – x.xx)
42
1.37 (x.xx – x.xx)
4
A
B
182
1
Table B.7 Estimated dam-specific transportation SAR percentages of PIT-tagged wild steelhead in
the annual aggregate groups for 1997 to 2007 (with 90% confidence intervals). Transported smolts
from total PIT-tag release in years through 2005 and from Group TWS in years beginning 2006.
Migr
SAR(TLGR)
Adult
SAR(TLGS) A
Adult
SAR(TLMN) A
Adults
Year
%
CI %
#
%
(CI%)
#
%
(CI%)
#
1997
1.87 (0.47 – 3.59)
4
NA
None
NA
None
1998
0.34 (0.00 – 1.00)
1
NA
None
NA
None
1999
2.69 (0.98 – 4.65)
6
4.44 (1.12 – 8.43)
4
2.99 (0.00 – 7.04)
2
2000
3.50 (1.51 – 5.64)
7
3.37 (0.00 – 6.86)
3
2.73 (0.74 – 5.36)
3
2001
3.09 (1.16 – 5.59)
5
NA
None
NA
None
2002
3.91 (1.55 – 6.82)
5
1.61 (0.00 – 4.92)
1
2.22 (0.65 – 4.41)
3
2003
1.73 (1.15 – 2.40)
21
2.75 (1.71 – 3.85)
18
2.20 (0.84 – 4.07)
5
2004
0.91 (0.66 – 1.19)
31
0.87 (0.37 – 1.40)
7
0.63 (0.00 – 1.90)
1
2005
0.97 (0.71 – 1.25)
34
0.62 (0.27 – 1.01)
7
NA
None
2006
1.23 (0.82 – 1.75)
19
1.56 (1.03 – 2.13)
22
1.16 (0.45 – 2.08)
5
2007 B
4.25 (3.40 – 5.10)
70
4.85 (3.61 – 6.28)
35
4.66 (2.69 – 6.94)
13
A
B
Migration year 2007 is incomplete until 3-salt returns (if any) occur at GRA after 7/1/2010.
2
3
Table B.8 Estimated dam-specific transportation SAR percentages of PIT-tagged hatchery
steelhead in the annual aggregate groups for 1997 to 2007 (with 90% confidence intervals).
Transported smolts from total PIT-tag release in years through 2007 since pre-assignment of
hatchery steelhead smolts to Group TWS begins in 2008.
Migr
SAR(TLGR)
Adult
SAR(TLGS) A
SAR(TLMN) A
Adult
Year
%
CI %
#
%
(CI%)
Adult #
%
(CI%)
#
1997
0.59 (0.27 – 0.96)
9
NA
None
NA
None
1998
0.63 (0.24 – 1.13)
5
0.28 (0.00 – 0.84)
1
0.64 (0.00 – 1.91)
1
1999
1.03 (0.50 – 1.69)
8
1.37 (0.34 – 2.57)
4
NA
None
2000
3.01 (1.74 – 4.56)
14
1.37 (0.00 – 3.90)
1
1.09 (0.00 – 3.09)
1
2001
1.21 (0.30 – 2.32)
4
NA
None
NA
None
2002
2.42 (0.70 – 4.93)
3
NA
None
NA
None
2003
1.98 (1.49 – 2.49)
41
2.12 (1.51 – 2.76)
32
1.21 (0.59 – 1.86)
10
2004
1.70 (0.58 – 2.83)
6
4.60 (1.28 – 8.54)
4
NA
None
2005
2.37 (1.43 – 3.43)
15
1.03 (0.00 – 2.29)
2
2.86 (0.00 – 8.82)
1
2006
1.65 (0.63 – 3.02)
5
2.58 (1.51 – 3.82)
13
2.37 (1.02 – 4.07)
7
2007 B
1.88 (1.22 – 2.59)
19
2.63 (1.78 – 3.51)
25
1.97 (1.13 – 3.02)
12
A
first-time and prior-detected fish from total release in years beginning 2006.
B
Migration year 2007 is incomplete until 3-salt returns (if any) occur at GRA after 7/1/2010.
183
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
Appendix C
Estimate proportion of smolts experiencing
TX, C0, and C1 passage routes
The random pre-assignment of part of a release of PIT-tagged fish to monitormode (Group T) allows direct estimation of the proportion of smolts experiencing TX, C0,
and C1 passage routes for the CSS PIT-tag groups in recent years. Pre-assigning of the
CSS PIT-tag wild and hatchery Chinook and wild steelhead groups began with the 2006
smolt migration season. Pre-assignments do not begin until 2008 for PIT-tagged
hatchery steelhead. Group T reflects the untagged fish passage experience under a given
year’s fish passage management scenario.
Methods
In years prior to 2006, when marks were not pre-assigned to passage groups, the
estimated number of smolts in each study category was adjusted to a projection of what
that number could be if the proportion of smolts in each study category was the same as
the run-at-large. This was done by utilizing the COE transportation and bypass numbers
at LGR, LGS, and LMN, which are collected at the level of species and rearing type (the
latter to a lesser degree of accuracy). These seasonal proportions were applied to the
PIT-tagged smolts transported for a given group of interest at each dam and summed in
LGR-equivalents to provide a projection of T0* smolts transported for that particular
group. The projection of C1* bypassed was simply the remainder of (T0 + C0 –T0*)
smolts. These projections are presented in Chapter 7 (Tables 7.7, 7.8, 7.13, and 7.14 for
PIT-tagged wild Chinook, hatchery Chinook by individual hatchery, wild steelhead, and
hatchery steelhead, respectively) of the CSS 2009 Annual Report (Tuomikoski 2009).
In years 2006 and later, the proportion of TX, C0, and C1 smolts are computed
directly from Group T for each corresponding CSS PIT-tag group. The reach survival
rates Sj and collection probabilities Pj are computed with the total release (combined
Group T smolts and the return-to-river Group R smolts) and passed to Group T, while the
parameters R1, X12, X1A2, X1AA2, and C1 removals (d1, d2, d3, d4) and C0 removals (d0) are
specific to Group T. As described in Chapter 4, equation 4.4 is used for estimating the
TX smolt numbers, and the expectation equations 4.5 and 4.6, respectively, are used for
estimating the C0 and C1 smolt numbers in Group T. In order for the proportion of Group
T smolts being routed to TX, C0, and C1 to reflect those in-river migrants estimated alive
to the tailrace of LMN expanded to LGR-equivalents, any removals below LMN need to
be added back into the C0 and C1 estimates. The following equations are therefore used
to estimate the number of PIT-tagged smolts in Group T for each of the three passage
history experience categories:
TX = X12 + X1A2 / S2 + X1AA2 / (S2•S3)
[C.1]
C0* = E(C0) + d0 = R1•S1•(1-P2)•(1-P3)•(1-P4)
[C.2]
C1* = E(C1) + d1 = R1•S1•[P2 + (1-P2)•P3 + (1-P2)•(1-P3)•P4]
– [(d2 + d3/S2 + d4/(S2•S3)]
[C.3]
184
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
and
P[TX] = TX / (TX + C0* + C1*)
[C.4]
P[C0*] = C0* / (TX + C0* + C1*)
[C.5]
P[C1*] = C1* / (TX + C0* + C1*)
[C.6]
Results
Beginning in 2006 there was a major shift in the transportation operations within
the FCRPS. The start of transportation was delayed at the three Snake River collector
dams due to research findings suggesting that fish transported too early in the migration
season survival less than if the fish were allowed to migrate in-river. In years prior to
2006, transportation commenced as soon as the Snake River collection facilities became
operational each year, which was around March 25 at LGR and April 1 at LGS and LMN.
For years 2006 to 2009, the start of collecting fish for transportation has been delayed to:
Year
Lower Granite
Dam (LGR)
Little Goose Dam
(LGS)
Lower Monumental
Dam (LMN)
2006
2007
2008
2009
April 20
May 1
May 1
May 1
April 24
May 8
May 9
May 5
April 28
May 11
May 12
May 8
In years prior to 2006, the start time of transportation encompassed most of the
emigrating groups of CSS marked fish. With the change to a later start of transportation
beginning in 2006, there is now a portion of the population that migrates entirely in-river
through the hydrosystem before transportation begins. This reduces the proportion of the
smolt population being transported in a given year as seen in Table C.1 particularly in
2007 through 2009 with the later start of transportation compared to 2006. The
outmigration of PIT-tagged Dworshak NFH spring Chinook tends to commence earlier
than the other four CSS PIT-tag hatchery Chinook group and has consistently had the
lowest proportion transported in all four years (range 8.3% - 52.2%). The other four CSS
hatchery groups had fairly similar proportions transported within any given year, with the
highest proportions occurring in 2006 (range 65.3 – 70.5%) and lowest proportions in
2007 (range 22.5 – 47.3%). The PIT-tagged wild Chinook aggregate also had the highest
proportion transported in 2006 (66.4%) and lowest in 2007 (21.3%). The PIT-tagged
wild steelhead aggregate likewise had the highest proportion transported in 2006
(64.9%), while both years 2007 and 2008 had the lowest proportion transport at 40.1%
and 40.5%, respectively. With the later start of transportation in 2007 to 2009 (the first
half of May), the goal of reaching a 50% spread-the-risk transport versus in-river
migration appears to be more attainable now than was possible in earlier years for both
wild Chinook and wild steelhead stocks.
185
1
2
3
4
Table C.1 Estimated proportion of PIT-tagged smolts in CSS wild and hatchery Chinook and wild
steelhead groups experiencing passage through transportation, bypass, or without detection at the
Snake River transportation sites (based on PIT-tagged fish in the monitor-mode (TWS) group).
(Non-parametric 90% confidence intervals are shown.)
Fish
source1
Transportation
LL
Passage w/o detection
Bypass passage
Pr(C0)
LL
UL
Pr(C1)
LL
UL
Smolt Migration Year 2006
RAPH
0.705
0.697
0.713
0.213
0.209
0.218
0.082
0.074
0.090
DWOR
0.522
0.515
0.530
0.319
0.314
0.325
0.158
0.151
0.166
CATH
0.680
0.654
0.706
0.256
0.241
0.269
0.064
0.040
0.090
MCCA
0.653
0.643
0.663
0.275
0.269
0.281
0.072
0.062
0.081
IMNA
0.669
0.654
0.685
0.215
0.206
0.223
0.116
0.101
0.131
WCh
0.664
0.652
0.676
0.151
0.147
0.156
0.184
0.173
0.197
WSt
0.649
0.631
0.667
0.072
0.067
0.077
0.280
0.262
0.298
RAPH
0.347
0.341
0.354
0.519
0.513
0.525
0.134
0.126
0.141
DWOR
0.083
0.081
0.086
0.687
0.682
0.692
0.230
0.225
0.235
CATH
0.473
0.452
0.494
0.465
0.451
0.479
0.062
0.042
0.081
MCCA
0.274
0.267
0.281
0.616
0.610
0.623
0.110
0.102
0.117
IMNA
0.225
0.216
0.234
0.552
0.543
0.561
0.223
0.212
0.234
WCh
0.213
0.207
0.220
0.490
0.483
0.496
0.297
0.289
0.306
WSt
0.401
0.385
0.416
0.385
0.373
0.399
0.214
0.198
0.229
RAPH
0.585
0.578
0.593
0.281
0.275
0.286
0.134
0.127
0.141
DWOR
0.338
0.331
0.345
0.470
0.463
0.478
0.192
0.184
0.199
CATH
0.600
0.579
0.619
0.293
0.281
0.306
0.107
0.088
0.125
MCCA
0.521
0.511
0.531
0.361
0.353
0.368
0.118
0.109
0.127
IMNA
0.541
0.528
0.552
0.283
0.275
0.292
0.176
0.164
0.188
WCh
0.428
0.417
0.437
0.299
0.293
0.306
0.273
0.263
0.284
WSt
0.405
0.390
0.420
0.317
0.305
0.329
0.278
0.261
0.293
RAPH
0.437
0.430
0.443
0.404
0.398
0.410
0.159
0.152
0.167
DWOR
0.341
0.334
0.347
0.478
0.472
0.485
0.181
0.173
0.189
CATH
0.562
0.543
0.582
0.353
0.341
0.366
0.085
0.066
0.103
MCCA
0.404
0.395
0.412
0.468
0.460
0.475
0.128
0.120
0.137
IMNA
0.504
0.491
0.517
0.373
0.364
0.383
0.123
0.110
0.135
WCh
0.426
0.417
0.435
0.225
0.221
0.230
0.349
0.339
0.359
WSt
0.453
0.439
0.467
0.190
0.183
0.198
0.357
0.343
0.372
1
Hatchery Chinoook: DWOR =Dworshak H; IMNA=Imnaha AP; MCCA=McCall H; RAPH=Rapid
River H; and CATH=Catherine Creek AP. Wild Chinook aggregate is WCh and wild steelhead
aggregate is WSt.
5
6
7
8
9
10
11
12
13
14
15
16
Pr(TX)
UL
There are several benefits of having Group T for estimating these three passage
experience proportions. The previous constraint of limiting transportation to first-time
detects has been eliminated in creating the TX group, and so fish bypassed at an upstream
dam are now included if transported at a downstream dam. Delaying the start of
transportation does not add any complication to the estimation process. Since Group T
follows the monitor-mode operations at the transportation sites, it best reflects the
untagged population of transported and bypassed smolts at those sites. Therefore, there is
no need to adjust the PIT-tag data using proportions of collected run-at-large smolts
transported and bypassed at the dams, which is available only at the species and rearing
type level, to individual PIT-tagged hatchery groups that may have different passage
timing history.
186

COMPARATIVE SURVIVAL STUDY (CSS) of PIT

Transcription

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