Independent Scientific

Advisory Board

for the Northwest Power and Conservation Council,

Columbia River Basin Indian Tribes,
and National Marine Fisheries Service
851 SW 6th Avenue, Suite 1100
Portland, Oregon 97204

Review of the Comparative

Survival Studys Draft 2013
Annual Report

Richard Alldredge
Kurt Fausch
Colin Levings
Katherine Myers
Robert Naiman
Bruce Rieman
Greg Ruggerone
Laurel Saito
Dennis Scarnecchia
Carl Schwarz
Chris Wood
ISAB 2013-4
October 14, 2013

ISAB Review of the Draft 2013 CSS Annual

Report
Contents
I. Background...................................................................................................1
II. Summary.....................................................................................................1
III. Suggested Topics for Further CSS Review...................................................3
IV. Comments on the draft CSS 2013 Annual Report by Chapter.....................7
Chapter 1. Introduction.................................................................................7
Chapter 2. Life cycle modeling approach to estimating in-river and early
ocean survival..............................................................................................8
Chapter 3. Effects of the in-river environment on juvenile travel time,
instantaneous mortality rates and survival................................................13
Chapter 4. Patterns in Annual Overall SARs...............................................15
Chapter 5. Estimation of SARS, TIRS and D for Snake River Subyearling Fall
Chinook.......................................................................................................18
Appendix A: (SR), SAR, TIR, and D for Snake River Hatchery and Wild
Spring/Summer Chinook Salmon, Steelhead, and Sockeye........................20
V. Editorial Suggestions.................................................................................22
Chapter 1....................................................................................................22
Chapter 2....................................................................................................22
Chapter 3....................................................................................................24
Chapter 4....................................................................................................25
Chapter 5....................................................................................................26
Appendix A.................................................................................................26
References.....................................................................................................27

ISAB Review of the Draft 2013 CSS Annual

Report
I. Background
The Northwest Power and Conservation Councils 2009 amendments to the
Columbia River Basin Fish and Wildlife Program call for a regular system of
independent and timely science reviews of the Fish Passage Centers (FPC)
analytical products. These reviews include evaluations of the Comparative
Survival Studys (CSS) draft annual reports. This ISAB review of the draft
2013 CSS Annual Report is the ISABs fourth review of CSS annual reports in
response to the Councils 2009 Program. These ISAB reviews began three
years ago with the evaluation of the CSSs draft 2010 Annual Report (ISAB
2010-5), followed by reviews of the 2011 and 2012 draft annual reports (ISAB
2011-5 and ISAB 2012-7).

II. Summary
This ISAB review begins by suggesting topics for further CSS review, then
provides general and specific comments on each chapter of the report, and
ends with specific editorial suggestions.
The ISAB suggests five topics for further CSS review:
1. hypotheses on mechanisms regulating smolt-to-adult survivals (SARs)
2. life-cycle modeling questions and Fish and Wildlife Program SAR
objectives
3. data gaps
4. rationalization of CSS's Passive Integrated Transponder (PIT)-tagging,
and
5. publication of a synthesis and critical review of CSS results
The CSS is a large-system study that has collected a substantial amount of
PIT-tag data from multiple species and stocks over a 17-year period, but to
date identification of hypotheses on the causal mechanisms regulating SARs
has been limited. The ISAB suggests a comparative approach to identifying
hypotheses that may lead to a greater understanding of causal mechanisms.
The CSS posed important questions related to stream productivity and
hydrosystem survival that were not addressed by the life-cycle model in this
report and need to be addressed by the next version of the model.
1

A detailed reevaluation of SAR objectives (2-6%) is warranted. These

objectives should be reevaluated for each species and Evolutionarily
Significant Unit (ESU) of salmon and steelhead based on realistic values
needed to support robust viable populations. Discrepancies in SARs between
PIT-tagged and non-PIT-tagged fish reported in other publications raise two
important issues that could be addressed now: (1) what are the implications
of correcting biased SAR estimates from PIT tags with respect to
performance against recovery and Fish and Wildlife Program objectives, and
(2) what proportion of US Endangered Species Act (ESA)-listed populations
are being PIT-tagged and what are the implications for imposing this
additional mortality? Further work is needed to analyze the relationship
between the ratio of transport/in-river SARs and in-river survival. With many
years of experience now, the CSS needs to identify critical data gaps. What
crucial pieces of information are not addressed by the CSS, and what
improvements can be made to provide them? Some examples provided by
the ISAB include the lack of habitat-specific estimates of smolt survival in the
estuary, information on how age at maturation affects SARs, the contribution
of mini-jacks to SARs, and the relationship between SARs and biomass of
adult returns of hatchery and wild salmon.
The ISAB recommends a new focus on rationalization of the PIT-tagging
program given the very large detection infrastructure already in place and
the overlapping objectives of the different tagging studies (see IEAB
document 2013-1 and ISAB 2013-3). It may be possible to reduce the
numbers of populations and fish that are PIT tagged without significant loss
of information, leading to greater program efficiencies at lower cost. The
ISAB also recommends that the CSS prepare and submit a manuscript for
peer-reviewed publication that synthesizes and critically reviews the results
of the CSS study.
Most of the information in the CSS's 2013 report is an annual update of
information in previous year's reports. Our summary, therefore, focuses on
new information presented in Chapter 2, which develops and describes a
simple life-cycle model. In this model, information from multiple populations
is used to estimate parameters common to the different populations (ocean
survival) while allowing each population to have a different spawner/recruit
relationship. The key advantage of this approach is the reduction in the total
number of parameters used to describe dynamics of the populations because
of the assumption of common ocean survival. Additionally, estimates can be
obtained for certain life states for populations that lack direct data. The
conceptual basis of the model appears to be sound, although evidence
2

supporting the primary assumption of common ocean survival was not

provided in the report. Three versions of the model with different levels of
complexity were evaluated. While the ISAB understands that model
development is at the initial stage, there are numerous difficulties in the
models description that make it uncertain if the three versions of the model
have been implemented correctly. Model equations do not match the flow
diagram. No estimates of precision from the models were presented. Only a
small amount of model assessment was done. Comparison of models using
the Akaike information criterion (AIC) should be included.
An alternate but similar approach would be through the use of state-space
models in a Bayesian context. This would allow the incorporation of natural
variation in the transition between life stages that is currently ignored in this
approach and the ability to incorporate prior information on some
parameters in a more natural way rather than, for example, assuming the
second year of ocean survival is exactly 0.6. Applying a hierarchical
approach to the spawning parameters across the populations would also
allow some sharing of information across population when data are sparse.
Finally, it would also provide probabilistic forecasts of future population
trajectories.

III. Suggested Topics for Further CSS Review

(1) Hypotheses on mechanisms regulating SARS. The CSS is a largesystem study with substantial PIT-tag data collected from multiple species
over a 17-year period. However, to date, identification and evaluation of
hypotheses on the causal mechanisms regulating smolt-to-adult survival
(SAR) have been limited. In general, each species/year combination is
treated in isolation. Many figures in the 2013 CSS Annual Report show
related stocks tracking each other over time, often quite strongly. This of
course is not surprising. But has the CSS looked at the opposite side? That is,
are there stocks that should be tracking each other but are not? Perhaps this
would help to identify hypotheses on causal mechanisms. For example, the
2013 historic return of fall Chinook (1.2 million) to the Columbia River does
not track adult returns of spring/summer Chinook and steelhead. The historic
2013 returns of fall Chinook have been attributed by the Columbia River
Inter-Tribal Fisheries Commission (CRITFC) and the Northwest Power and
Conservation Council (NPCC) to various factors, including "high spring river
flows when the fish migrated to the ocean as juveniles two to five years ago,
spill of juvenile fish over dams, good ocean conditions, ongoing projects to

improve fish passage at dams and the habitat where fish spawn, and
improved survival of fish produced in hatcheries" (Columbia Basin Bulletin
9/27/2013). Can CSS data be used to provide a more scientific explanation
for the cause(s) of historic returns of fall Chinook salmon in 2013? If PIT tag
data are sufficient, they might be used to evaluate why the Hanford Reach
Fall Chinook stock (and perhaps some other stocks) have persisted so well
over the years versus those trending in a different direction. The Hanford
Reach Fall Chinook stock is one of the most robust populations in the Basin.
The fish go through many mainstem dams, and the adults support a
somewhat robust fishery. What is the survival for this stock through the
hydrosystem and in the ocean? What is spawner to smolt survival?
Partitioning survival might provide clues as to why this stock is doing
relatively well compared to other species and stocks.
Discrepancies in SARs of adult salmon and steelhead as they migrate
upstream through the FCRPS should be evaluated. For example, the size of
the discrepancies in SARs measured for LGR-BOA (Lower Granite Dam to
Bonneville Dam adult fish ladder) versus LGR-Lower Granite Dam adult fish
ladder (GRA) seem large enough to have significant implications for
population recovery. Differences in geometric means for wild Snake River
spring/summer Chinook (25%) and steelhead (36%) suggest average losses
during upstream migration from BOA to GRA of 20% and 26%, respectively.
An even greater discrepancy (average losses of 43% - 64%) is evident for fall
Chinook, although that comparison is not raised explicitly, and it is difficult to
evaluate quickly in this report (our numbers based on a partial summary for
2006 to 2009 in Table 5.17). How much of these differences might be
attributed to fishing activity or other sources of mortality that could be
mitigated? Which dams cause more adult mortality? For Chinook, the
estimates of percentage loss seem similar with and without jacks and
perhaps that similarity gives us a clue about the likely mechanisms. In any
case, it seems that the LGR-BOA SAR data could be used more effectively to
explore patterns in upstream survival.
Understanding when, where, and why survivals of hatchery and wild salmon
differ is key to achieving Fish and Wildlife Program SAR objectives. Is it
reasonable to conclude based on statistical analysis that SAR values are
typically higher for wild than hatchery Chinook, whereas juvenile in-river
survival (SR ) values are typically the same for wild and hatchery Chinook or
perhaps slightly higher in hatchery Chinook (based on SR values for Snake
River Chinook in Figures A.2A and Tables A.1 A.3 vs. corresponding SAR
values for the group of in-river control PIT-tagged smolts, termed C0, Figures
4

A.7 and A.8)? This conclusion, if supported by the data, would indicate that
wild Chinook typically survive better than hatchery fish below Bonneville and
should be reported by CSS. Further investigation seems warranted to find the
mechanism(s) that could explain the difference.
(2) Life-cycle modeling questions and SAR objectives. Chapter 2 (lifecycle modeling) poses two questions:
(1)"What changes in stream productivity [salmonid productivity in rearing
streams] would be required to achieve population recovery if
hydrosystem survival were to remain at the status quo?"
(2) "What changes in hydrosystem survival would be required to achieve
a 20% increase in population abundance by a particular time in the
future?"
These are important questions, yet they are not addressed in this report. The
ISAB encourages the CSS to address these questions using the next version
of the life-cycle model.
The ISAB appreciates the discussion of the 2-6% SAR objective in the
Introduction of Chapter 4, and we agree that a more detailed look at SAR
objectives is warranted. Ideally, SAR objectives should be established for
each species and ESU of salmon based on realistic values needed to support
robust viable populations. The values should consider differences in SARs for
yearling versus subyearling life histories. The life-cycle model presented in
Chapter 2 appears to be poised to address this issue, at least for Grande
Ronde spring Chinook. It would be worthwhile for CSS to utilize the SAR data
in hand to help develop SAR objectives for each species and ESU.
An issue that continues to be unresolved is related to mortality caused by
PIT-tagging. Knudsen et al. (2009) found that returns of upper Yakima
hatchery spring Chinook salmon marked with PIT tags, as well as control tags
(CWT+elastomer tag+adipose fin clip), were 25% lower than control fish
without PIT tags. This implies that the non-PIT-tagged group enjoyed a 33%
higher survival rate, which is sufficient to explain why SAR estimates from
run reconstruction are 19% (Schaller et al. 2007) to 35% (Kennedy et al.
2011) higher than SAR estimates from PIT-tag data. The ISAB is aware of the
4-yr USFWS study to address these concerns with respect to Snake River
spring/summer Chinook, but there are issues that could be addressed now by
CSS: (1) what are the implications of correcting biased SAR estimates from
PIT tags with respect to performance against recovery and Fish and Wildlife
Program targets; and (2) what proportion of ESA-listed populations are being
5

PIT-tagged, and what are the implications for imposing this additional
mortality, i.e., ~25%, unless the discrepancy is due to tag shedding rather
than mortality? After correcting for tag loss, which occurred primarily after
release and before adult return, Knudsen et al. (2009) found that SARs of PITtagged fish were still 10% lower than those of control fish without PIT tags.
As a final suggestion, further work by CSS is needed to analyze the
relationship between the ratio of transport/in-river SARs (TIR) and in-river
survival (SR) (see comments on Appendix A, p. 44-45).
(3) Data gaps. Based on many years of experience, the CSS needs to
identify critical data gaps. What crucial pieces of information need to be
produced by the CSS or others in the region and what improvements can be
made to provide them?
For example, the ISAB has already identified the lack of habitat-specific
estimates of smolt survival in the estuary as an important regional data gap
(ISAB 2012-7). What data and what approaches to collecting data are
needed to address this issue?
Another example is data on age at maturation of Chinook salmon and
steelhead, which are often overlooked in the Columbia River Basin, even
though it is a highly important trait that affects salmonid productivity and
viability. Important future questions might include: how does age at
maturation (years spent at sea) affect SAR? Can extensive SAR data be used
to better estimate annual mortality at sea, so that we have a better idea
about the cost salmon and steelhead incur when spending an additional year
in the ocean?
Another gap is data on mini-jacks, which contribute many fish to SARs
among fall hatchery Chinook salmon when included in the calculation, such
that ~62% of the mature population is represented by jacks and mini-jacks
versus larger, older Chinook salmon (Larson et al. 2013). What percentage of
mature hatchery spring Chinook salmon are mini-jacks, and how would
inclusion of mini-jacks affect estimates of SARs?
A final example is the lack of information on the biomass of adult returns to
the Columbia River Basin in relation to survival. For example, periods of high
SARs might be correlated with decreased adult body size, reflecting densitydependent growth of salmon in the ocean. This has important implications
for the impacts of hatchery releases on wild salmon survival and recovery in
the Columbia River Basin. Is it possible for the CSS to develop a time series

of estimates of the annual biomass of adult hatchery and wild salmon returns
to the Columbia River Basin?
(4) Rationalization of CSS PIT-tagging. The IEAB Fish Tagging (FT) model
is a non-linear mathematical programming model that estimates how many
(juvenile) fish should be tagged with what type of tags (CWT, PIT, genetic) to
satisfy a set of required outcomes, such as a minimum number of tags of
each type detected/recovered at certain locations or indicators (IEAB
document 2013-1). At present, the model can be used to evaluate tradeoffs
in using different tag types and to search for cost efficiencies in the numbers
and geographic locations where fish are tagged. In its recent review of the FT
model (ISAB 2013-3), the ISAB recommended: Focus on rationalization of
the PIT-tagging program given the very large detection infrastructure already
in place and the overlapping objectives of the different tagging studies (e.g.,
estimating in-river and transport survival, evaluating effectiveness of habitat
improvements, measuring straying rates, and so forth). This evaluation
should also consider tradeoffs between adding more fixed costs to improve
detection rates by modification of infrastructure vs. ongoing costs and
handling effects of tagging more fish. For example, results presented in the
2013 CSS Annual Report indicate similar patterns in SARs for Major
Population Groups (MPGs) from the same region of the Columbia River Basin.
Thus, the FT model might be used to investigate whether it is possible to
reduce the numbers of populations and fish that need to be PIT tagged
without significant loss of information. Such an evaluation might result in
greater program efficiencies and cost reductions. The CSS/FPC staff could
also assist with further improvements to the FT model in developing stockspecific estimates of smolt survival and to validate, modify, and improve
assumptions in the FT model about juvenile and adult mortality rates by river
reach and dam passage and species- and stock-specific ocean mortality
rates, as recommended by ISAB (see IEAB document 2013-1 and ISAB 20133).
(5) Publication of a synthesis and critical review of CSS results.
Although the CSS investigators have published a number of articles on
components of the CSS study, the ISAB recommends that the CSS prepare
and submit a manuscript for peer-reviewed publication that synthesizes and
critically reviews the results of the overall CSS study (as suggested in
ISAB/ISRP 2007-6). The ISAB considers it vitally important to the Fish and
Wildlife Program for CSS to summarize and evaluate the current state of
understanding on questions addressed by CSS and to make this information
available to the scientific community at large, as well as to the general
7

public. A balanced and well-reasoned review article, for example, might

help to resolve the current debate over the validity and interpretations of
survival estimates in published and unpublished BPA-funded studies (e.g.,
http://www.nwcouncil.org/media/6877226/1.pdf). The ISAB suggests a
retrospective approach to the review that focuses on the original question
that the CSS was designed to address, that is, can transportation of fish to
below Bonneville Dam compensate for the effect of the hydro system on
juvenile survival rates of the Snake River spring and summer Chinook
salmon during their downstream migration? and related hypotheses drawn
from the most significant conclusions in the CSS (2007) Ten-year
Retrospective Summary Report and other CSS reports and publications. The
review should carefully consider the weight of evidence both opposing and
supporting the CSS hypotheses, results, and conclusions, using information
from the scientific literature and assessing the importance and reliability of
the evidence reviewed.

IV. Comments on the draft CSS 2013 Annual Report

by Chapter
Chapter 1. Introduction
The introduction to the 2013 CSS Annual Report is identical to the
introduction in the 2012 report with the exception of a few updates. While
this section is generally well written, the ISAB reiterates its 2012 suggestion
for addition of a table with an historical timeline of key objectives and results
from past years of CSS work. There is no mention of whether the CSS
Oversight Committee explored adding this table, although this action was
suggested in the CSS's response to the 2012 ISAB review. The table could
also include citations to past reports and publications for more detailed
information on past results, which would be useful to those not familiar with
the CSS's past work.
Specific Comments and Questions
Page 2, l. 4-6. How is PIT tag loss considered in the analyses? Is it possible
that there is a different proportion of PIT tag loss for transported and in-river
fish, or could PIT tag loss occur in different proportion for these two groups in
the estuary/ocean phase of life? How is this considered in the analysis and
the interpretation of results?

P. 2, Figure 1.1. The ISAB continues to have the same problems with this
figure (ISAB 2012-7, p. 16). In response to our review, the CSS Oversight
Committee said they would consider revising the figure, but apparently
decided not to. For readers unfamiliar with salmon life history, the Federal
Columbia River Power System (FCRPS) and the factors/actions affecting
survival of Columbia River Basin salmon, the figure is too cryptic. For
example, why do the arrows have different colors? Can the significance of
the boxes be explained?
P. 3, Figure 1.2. An explanation in the report about why all dams are not
outfitted with both juvenile and adult PIT tag detectors would be useful. A
few issues are confusing in the legend. What are CSS Release Sites Basins?
Does marking also occur at the two John Day rotary screw trap sites?
Page 7, l. 35-36. PIT-tag detection probability is given as nearly 100% for
returning adults, but no indication of detection probability is given for smolts.
The ISAB suggested in its 2012 review that a typical range in detection
probabilities for juveniles be included for each monitored dam, but the CSS
response was that detection probabilities are highly variable and depend on
many factors, so that indicating values would be complicated and likely
confusing. However, it seems important to help readers gauge the degree of
uncertainty by giving them some idea about the typical value and range of
detection probabilities for smolts. Surely a typical range of values could be
included briefly here. Much later (Table 5.1) a detection probability of 0.32 is
listed for Bonneville; this value seems low enough to justify our request for
more information.
Page 8, l. 7-11. It seems that the less fit fish will have been eliminated from
the in-river cohort but not the transported fish so there is potential bias in D
(the estuary and ocean survival rate of Snake River transported fish relative
to fish that migrate in-river through the Federal Columbia River Power
System) because the transported cohort is arguably different than the inriver cohort. How is this considered in the analysis and in the interpretation
of results?
Page 9, l. 10-14. It is not clear how the uncertainty in the Cormack-JollySeber (CJS) reach survival rates and detection probability parameter
estimates for the composite group (Group CRT) is used in the interpretation
of key parameters for the component groups T and R.

Page 12, l. 16-20. The ISAB appreciates that including new groups when
possible is a valuable endeavor.

Chapter 2. Life cycle modeling approach to estimating inriver and early ocean survival
The CSS's objective in this chapter is to develop a multiple-stock model that
links freshwater spawning and rearing (FSR) production and survival to
mainstem passage survival and ocean survival. The ultimate goal is to use
the model to assess important management scenarios to recover spring
Chinook salmon. Three different versions of the model (BH, LC, and LCX) with
different levels of complexity were evaluated using data for the Grande
Ronde Major Population Group (GRMPG) of spring/summer Chinook salmon.
The investigation uses a long time series of SAR data and smolt per spawner
data for up to six populations within the GRMPG. The analytical approach is
characterized as a first step, indicating the investigators plan additional work
with the model. The ISAB encourages the investigators to continue with
model development and to explore ideas presented in the report.
Nevertheless, there are numerous difficulties in the description of the model
that make it uncertain if the three model versions have been implemented
correctly in this initial step. Below, the ISAB provides a number of detailed
comments on the analysis.
The ISAB advises that an alternate but similar approach would be through
the use of state-space models in a Bayesian context. This would allow the
incorporation of natural variation in the transition between life stages that is
currently ignored in the CSS's approach and the ability to incorporate prior
information on some parameters in a more natural way rather than, for
example, assuming the second year of ocean survival is exactly 0.6. Applying
a hierarchical approach to the spawning parameters across the populations
would also allow some sharing of information across population when data
are sparse. Finally, it would also provide probabilistic forecasts of future
population trajectories.
The Introduction and other sections of Chapter 2 pose two questions:
(1)"What changes in stream productivity [salmonid productivity in rearing
streams] would be required to achieve population recovery if
hydrosystem survival were to remain at the status quo?"

10

(2) "What changes in hydrosystem survival would be required to achieve

a 20% increase in population abundance by a particular time in the
future?"
These are important questions yet they are not addressed in this report. The
ISAB encourages the CSS to address these questions using the next version
of the model.
The three models used by CSS provide a sensitivity analysis in that the initial
model (BH) is a simple Beverton-Holt model and subsequent models increase
complexity, including variables that would enable the model to address
management scenarios. Graphs are used to show the fit of the models to
data, but a more formal statistical evaluation of model fit would be
worthwhile in addition to graphs. For example, comparison of the smolts per
spawner model fits using the BH and LCX models did not visually seem very
different, but it may be very different when looking at residuals.
The key utility of the LCX model is the inclusion of the survival function that
involves the PDO, upwelling index, and Powerhouse passage. A form of the
relationship was developed in Petrosky and Schaller (2010). It would be
worthwhile to show a plot of Chinook survival in relation to these three
variables and to describe the amount of survival variability explained by
them. Given that the Powerhouse variable is key to management scenarios,
are there changes in the hydrosystem over time that are not accounted for
by this variable, other than spill which is part of the index? The discussion
suggests that the Powerhouse variable (NPH) is the key variable in the
survival function, yet no data were presented to show this, including B3
which is discussed but not shown.
The modeling approach assumes survival at sea is essentially the same
among the populations. It would be worthwhile to provide a correlation
matrix describing the extent to which population survivals are correlated.
How are missing survival values handled when developing a pooled survival
estimate in Equation 9?
There is no evidence provided in the report supporting the primary
assumptions in the model related to ocean survival, i.e., (1) that GRMPG
populations share a common ocean survival, (2) that ocean survival is not
density-dependent (capacity parameter set to infinity), (3) that survival in
the 1st ocean year is a function of PDO, UPW, and NPH, and (4) that survival
in subsequent ocean years is a constant (2nd ocean year = 0.6, 3rd ocean
11

year = 0.7). For example, does evidence from tagging (PIT tags, CWT tags,
genetics) support the assumption for a common ocean survival among
GRMPG populations? Positive and significant relationships between ocean
growth and adult abundance of Columbia River Chinook and coho salmon
and steelhead (e.g., Jacobson et al. 2012 and other references cited in their
report) are a reflection of limits to ocean carrying capacity of salmon. There
is also evidence for density-dependent (feeding competition) effects on
growth and survival at both juvenile (1st ocean year) and later ocean stages.
An accumulating body of scientific evidence supports the hypothesis that
1st-year ocean growth and survival and, thus, brood-year strength is
determined in two stages, called the "Critical Size and Critical Period"
hypothesis (Beamish and Mahnken 2001; Farley et al. 2007; Jacobson et al.
2012). The modeling approach described in this chapter addresses only the
earliest (ocean entrance) stage, when predation is the primary cause of
mortality, versus later stages during the first summer, fall, and winter at sea
when mortality is physiologically based. The use of environmental variables
that reflect physiological and bioenergetic constraints on growth (e.g.,
availability of nutrients regulating food supply; ambient water temperatures
in ocean regions where juvenile Columbia River Basin salmon are distributed
during summer, fall, and winter) might improve model fits and predictive
capabilities. Biological indices directly reflecting growth after ocean entry
also have a strong relationship to abundance of adult returns (Jacobson et al.
2012).
The ISAB is aware of at least two other life-cycle models under development
by NMFS scientists that use Grande Ronde spring Chinook data. Buhle et al.
(2013; draft in review by ISAB) incorporate Grande Ronde data into a
statistical model that estimates the effect of hatchery supplementation on
wild salmon productivity and capacity parameters. Cooney et al. (2013; draft
in review by ISAB) are developing a model specific to Grande Ronde spring
Chinook while targeting the freshwater phase. It would be worthwhile for CSS
to communicate with these other investigators.
The discussion notes the large model residuals for Upper Grande Ronde and
Catherine Creek populations during the early period when smolt survival
data were not available. As a consequence, model results for these
populations relied on pooled survival data. The interpretation for the large
residuals was that actual survival in these streams must have been much
higher during this early period, which then declined when monitoring began.
The investigators should consult (or continue to consult) with people familiar
12

with the Grande Ronde Basin, such as Rich Carmichael and Tom Cooney, to
see if there is evidence for a somewhat rapid decline in spawner to smolt
productivity during this early time period. What known changes might have
caused this decline?
Tables 2.3 and 2.4 show the modeled productivity and capacity estimates for
the six populations and three models. The ISAB understands that the habitat
condition of these six watersheds varies considerably from disturbed to
somewhat pristine. How well do the productivity and capacity estimates
correlate with known condition of the habitats? If these estimates do not
match expectations, does this mean that the pooling approach has forced all
variability onto the spawner to smolt stage, leading to unreasonable
estimates? What are the units in these tables? If the units are smolts per
spawner at low spawner density and total smolts, how do they compare with
observed values?
Two of the models include age structure of Chinook. Is fecundity allowed to
vary with age, as it should? We encourage the investigators to further
develop models that incorporate age at maturation as this tends to be an
important life history characteristic in the Columbia Basin that does not
receive the attention that it deserves. Growth is a key factor affecting age at
maturation. Variable age at maturation helps reduce risk associated with
catastrophic events.
The models and data provide evidence for strong density dependence at the
spawner-to-smolt stage. When comparing this relationship among the
populations, what does it tell us about the need for habitat restoration? Is the
decline in productivity steeper for degraded versus undisturbed habitats, or
does the overall relationship shift with respect to habitat condition?
Specific Comments and Questions
P. 21, l. 15-25. The data used in the model fitting are described, but no data
are shown in the report. It would be helpful to actually see the brood table
for the adults, the covariates (NPH, PDO, UPW), and the juvenile data used in
the model fitting. The brood data are assumed to be known exactly, but as
indicated on p. 21, data include reconstructions from fishery catches, which
are not known exactly. Hence there is some additional error in the brood
table that may not be captured by the model, that is, does the process error

variance (the Rp,a of equation 10) capture all of the uncertainty in the
observed data?
13

P 23. Figure 2.1 indicates that smolts are subject to two survival rates (s0
and s1), but equation (2) only uses s1. This needs to be clarified. The ISAB
does not understand the figure. Why are there three spawner boxes with the
first two for populations 1 and 2? What are populations 1 and 2, and why are
they special?
P. 24. A life cycle model is created starting on page 24 that predicts the
expected number of fish in the next stage given the number at the previous
stage. No variability is introduced in the number of fish moving to the next
stage, e.g., equation (2) indicates that the number of ocean fish is exactly
equal to the number of smolts multiplied by the survival rate rather than this
being a binomial process. A flow diagram of the model is presented in Figure
2.1, but the diagram does not use the notation from equations (1), (2), etc. It
would be helpful to add the defined variables from the equations to the flow
diagram.
P. 25, l. 17. Equation (8) needs clarification. It is true that the total number of
spawners from a brood year is defined this way, but not all spawners from
the brood year are on the spawning grounds in the same year. Consequently,
using Sp,t for the number of spawners back in equation (1) mixes spawners
from different calendar years into the same year of spawning. Should not the
number of spawners in year t be a combination of 3 year-olds from this brood
year + 4 year-olds from the previous brood year, + 5 year-olds from two
years previous? This is shown at the bottom of Figure 2.1 where recruits are
merged from several brood years (the notation is a bit odd as Run3(p, t+3)
becomes Recruits (t). The t-index jumps here invisibly. Better notation is
needed.
Sp, t

P. 26, l. 21-31. The ISAB does not understand the likelihood equations (10),
(11), and (12). In equation (10), the product is taken over the index t, yet t
appears on the left term. It should be function of (p,a). Similarly in equation
(11), the left term should be a function of (p) only. How are equations (10)
and (11) then combined over all (p,a)? Presumably by a direct product, but
this is never explicitly stated. Equation (11) is in terms of Jp,t but this is never
defined in Table 2.1, nor in the model equations (1) to (8). How are these
J p,t

2
values determined? Similarly in equation (12), neither Rt nor R is ever defined
in the table of notation nor in the model equations. How was the variance
estimated? Were the MLE equations solved explicitly?

14

No model assessment is reported, e.g. evaluating plots of observed vs.

expected results for lack of fit or any substantial outliers, assessing whether
an over-dispersion to determine if any adjustment is needed, etc.
Because all of these models are likelihood fits, a table of AIC values should
be presented to show the relative support of the three models to the data.
The use of the fitted model to investigate scenarios is a nice way to
investigate what type of future average population trajectory can be
expected. The report does not present any results arising from this feature of
the models.
P. 28, l. 17-20. The ISAB is concerned that in Table 2.4 the smolt capacity
terms go to infinity in some models. Also it appears that the smolt
productivity (Table 2.3) and capacity are highly negatively correlated so that
if estimated capacity declined the estimate productivity increases almost
directly. Perhaps a re-parameterization of the model may be more
numerically stable. What is the sampling correlation of the two parameters?
P. 28, l. 19-20. How do predictions of capacity in Table 2.4 agree with levels
of smolt production in streams, i.e. are the estimated capacities much higher
than observed levels of production, etc.? Standard errors should be
presented for all estimates to assess how well they have been determined.
P. 30, 33. It is also odd, in Figure 2.3 and 2.6, that the fitted values for
recruits in the CC population do not match the large upward trend seen in
the 1970s. A similar situation is evident in the GR population. The other
populations seem to match the observed data much better. Why is this so?
There is some explanation in the Discussion (page 38, l. 7-16), but the ISAB
had difficulty following the logic. Perhaps it is a model fitting error where the
model converges to a local minimum without changing the initial parameters
for the LC and GR populations?

Chapter 3. Effects of the in-river environment on juvenile

travel time, instantaneous mortality rates and survival
Regression models were used to investigate the influence of environmental
and operational covariates on the estimates of instantaneous mortality and
fish travel time. A statistics-on-statistics approach was used rather than
embedding the covariates directly into the CJS mark-recapture models. The
ISAB also commented on this issue in our 2012 review, to which the authors

15

responded that perhaps they would include a paragraph in future reports

about this topic. AIC was used to investigate the different models, but only
the top model in the model set was used for inference rather than the usual
model-averaging approach.
Specific Comments and Questions
P. 41, l. 12-19. The ISAB suggests also including fall Chinook salmon in this
chapter in the future.
P. 41-42, Study area and definitions. The written description of the three
reaches, the species and cohorts used would be easier to digest if a diagram
was presented showing the general reach structure (a Y pattern with LGR>MC< and RIS->MCN joining before MCN->BON) and which species and
cohort structure used for each reach.
P. 44, l. 13-23. The discussion of the meaning of Z is a bit long and
superfluous. The instantaneous mortality rate parameter is well known in the
fisheries literature. Simply cite any one of a number of standard reference
books.
P. 44, l. 24. Equation 3.3 needs some care. The estimated value of Z applies
to all fish that start passage at the start of a reach, including those that do
not survive to the end of the reach. However, the mean FTT is based only
those fish that survive the entire reach. Consequently, the mean FTT is based
on fish that tend to swim faster (because they did survive) and so will
underestimate the exposure time of the entire cohort of fish. It should be
possible to modify the CJS model to incorporate both the travel time and Z
directly in the estimation process, or perhaps small simulation in an appendix
will show that equation (3) works well enough that any bias is negligible.
[Again, the responses to the 2012 report dealt with this issue; perhaps
adding a paragraph to future reports is justified.] The modified CJS model
would also give the SE of Z directly.
P. 45, l. 1-3: Would it also make sense to estimate the variance using
bootstrapping?
P. 45-46, Multi-model inference. The use of informationtheoretic techniques
for model selection is a standard method for this class of problems. However,
this method typically presents the AIC model weights for the top models and
does not just pick the best model. The appendix needs to be improved to
show the model weights for the top models. In the response to the 2012
report, the CSS indicated that all models were more than 3 AIC points lower
16

than the top model. Is this still the case? As well, it is quite common to
present the total model weight of models that contain each variable to see
the relative importance of each variable (as in the 2012 report). Model
averaging should be used for the predictions from the model set. The
appendices also dont present any standard errors for the coefficients.
P. 46, l. 29, equation 3.7: Consider specifying log(Z) or sqrt(Z) as the
dependent variable.
P. 48, l. 23-25: This interpretation seems reasonable, but the data are not
sufficient to rule out other explanations. The ISAB encourages the CSS team
to consider other explanations in addition to spill.
P. 48, l. 26-29: Interpretations of the results in Appendix 3.1 are questionable.
WTT has 5 positive and 3 negative coefficients while surface passage has 3
negative out of 10 scenarios, and the interaction of Day and WTT means the
interpretation of WTT effect depends on Day.
P. 48, lines 41 to 43: Interpretation of results appears questionable based on
Appendix 3.2. WTT has 2 positive and 2 negative coefficients, Spill has 4
positive and 4 negative coefficients, Temp has 7 positive and 1 negative
coefficients, and Surf Pass has 1 positive and 2 negative coefficients.
P. 50-51, Figs. 3.1-3.2. Each estimate is treated as an independent
observation, even though several of the response values are from the same
calendar year. Is a random effect of year needed to address any correlation
in the estimates within a year? It is difficult to tell from Figure 3.1 3.2 if this
could be a problem. Some assessment of this potential problem is needed.
P. 53. Table 3.3 (incorrectly labeled as Table 2.3) shows that the R2 for
predicting Z are generally low, so it is not clear if the best models in
Appendix 3.2 actually have any predictive power.
P. 53, l. 22-24: See previous comments regarding interpretation of results.
P. 54, l. 4-17: 3.2): See previous comments regarding interpretation of results
based on the material presented.

Chapter 4. Patterns in Annual Overall SARs

This Chapter updates the CSS time series of smolt-to-adult return rate (SAR)
estimates of previous reports with an additional year of data (final 2010
estimates for steelhead and new 2011 estimates for Chinook salmon). The
17

same methods are used as in previous years. The ISAB advises that annual
updating and reporting of the SAR values is important and should continue.
In addition, the ISAB appreciates the new reporting in this chapter of SARs
for Snake River Basin wild spring/summer Chinook and steelhead at finer
geographic and major-population-group (MPG) scales.
As in last year's report, SAR estimates are compared to the NPCC (2009) 2%6% SAR objectives, and the conclusions are identical to those in last year's
report. The ISAB appreciates the discussion of the SAR objective in the
Introduction, and we agree that a more detailed consideration of SAR
objectives is warranted. Ideally, SAR objectives should be estimated for each
species and ESU of salmon based on realistic values needed to support
robust viable populations. The values should consider differences in SAR for
yearling versus subyearling life histories. The life cycle model presented in
Chapter 2 appears to be poised to address this issue, at least for Grande
Ronde spring Chinook. It would be worthwhile for CSS to utilize the SAR data
in hand to help develop SAR objectives for each species and ESU.
The report notes the potential to expand some analyses. Some work is being
planned to investigate the systematic differences in SARs between run
reconstruction (RR) and PIT-tag methods, but no results are reported here.
The ISAB encourages this expansion when data allow. The SAR data form the
basis for many additional analyses that are needed to inform management of
the hydrosystem.
Specific Comments and Questions
P. 60. More discussion or equations are needed to explain the difference
between T0*and T0 and to define ti. T0* appears (on page 60) to be calculated
identically to T0 in Equation A.1, but perhaps that is because the ti are not
equivalent to the Xi in Appendix A (i.e., it is not clear).
P. 61, L. 41-43, P. 62, L. 1-17. The investigators back-calculate survival during
the first year at sea, while assuming a constant 80% annual survival of subadults. As noted in the report, this approach assigns all ocean survival rate
variability of the S.o1 life stage. We interpret this to mean that year-to-year
variability in survival after the first year is transferred to S.o1. If so, it is not
clear why the metric S.o1 is needed given that it does not necessarily
capture the true variability in survival that occurs during the first year at sea.
For example, the plot below shows the tight correlation of S.o1 with S.oa
(Columbia mouth) based on data in Table 4.52. The problem is that readers
less familiar with the methods may think S.o1 does capture variability only
18

associated with this life stage while removing variability during subsequent
stages at sea. On page 85, the investigators note that S.o1 and S.oa are
perfectly correlated, so why include S.o1?

P. 63, l. 7-11. The influence of jack salmon on SAR values is noted. To what
extend has the relative abundance of jack salmon changed over time and
therefore influenced the variability in SAR values? To what extent do jacks
affect SAR values for hatchery versus wild salmon, given that jacks are more
common among hatchery salmon? Larson et al. (2013) found that mini-jacks
contribute many fish to SARs among fall hatchery Chinook salmon when
included in the calculations. What fraction of total SARs does mini-jacks
represent if included?
P. 63, l. 15-18. The SAR of the reintroduced Clearwater Chinook stock is
strikingly low compared with that of other stocks. Can you reference any
projects that are looking at this low SAR value?
Investigators in the Snake River Basin have reported somewhat low and
variable survival of smolts from release locations to the uppermost detection
dam. Is there any correlation in upstream survival with survival through the
hydrosystem and beyond?
P. 67, l. 10-11. Why is it not possible to calculate a SAR when very few
sockeye are transported?

19

P. 67, l. 15-39. SARs for John Day and Yakima Chinook are clearly much
greater than SARs of Snake River Chinook. How do the SAR values compare
after standardizing for passage through dams?
P. 71, l. 14-15. It is not clear why calculation of the Snake River sockeye SAR
from LGR-to-GRA in 2010 is not possible, given that it was calculated for LGRto-BOA (shown in Table 4.33).
P. 79, l. 14-17. Fig. 4.11 does not show in-river survival as described in the
text it is Fig. 4.13 that contains these data. But the authors make a good
point about the high mortality in the RIS-MCN reach. Survival in the upper
Columbia needs to be monitored. The effect of this high mortality on
Wenatchee steelhead is noted in the text, but the effect seems to be even
greater for Leavenworth Chinook where MCN-BOA SAR is often 1% or less
(Fig. 4.11).
P. 83, l. 10. It would be worth indicating that Knudsen et al.s (2009) result
that CWT/elastomer/ad clip-marked fish with PIT tags returned at a 25%
lower rate than those without PIT tags implies that the survival rate for fish
without PIT tags was 33% higher than for those with PIT tags. Stating the
ratio in this way facilitates direct comparison with the 19% (line 5) and 35%
(line 15) higher SAR estimates from run reconstruction relative to PIT tags.
P. 85, l. 7-9. Would not the high degree of correlation between S.oa and S.o1
be expected because of the assumption that survival is constant (80%) for
each subsequent year at sea? It seems that variability could only come from
annual variation in age at maturity. If this is true, then this paragraph seems
misleading or uninformative and should be revised or deleted (see above
comments related to P. 61, L. 41-43, P. 62, L. 1-17).
P. 86, l. 26-34. The lack of correlation of wild and hatchery steelhead SARs
may be related to large differences in life history characteristics. Wild smolts
are older (2 or more winters in freshwater) than hatchery smolts (1 winter in
freshwater). The apparently lower SAR of B-run steelhead (Clearwater) might
be related to more years spent at sea or differences between A- and B-run
types in ocean distribution and migration patterns.
P. 87, l. 36-45. The ISAB agrees that more work needs to be done on
potential biases associated with PIT tag shedding and mortality, and the
authors provide a good discussion of this issue.
P. 88, l. 6-46. As noted above, the usefulness of the S.o1 calculation is
questioned because it is perfectly correlated with S.oa and the suggestion
20

that you have an independent estimate of S.o1 may be somewhat

misleading. This does not mean that research conducted with S.o1 is not
valid, rather the investigators could have simplified the analysis and simply
used S.oa.
P. 89, 15-16. Is there benefit in investing in juvenile PIT-detection equipment
in some of the dams to address the issue in the 4th bullet point of the
conclusions?

Chapter 5. Estimation of SARS, TIRS and D for Snake River

Subyearling Fall Chinook
The ISAB acknowledges that the inclusion of estimates of SARs, TIRs, and D
for fall Chinook salmon in the CSS is a work in progress. This chapter first
estimates the amount of bias in SARs that could be introduced by holdover
juveniles. It then estimates SARs, TIRs, and Ds for subyearling fall Chinook
based only on release groups that are thought to have small numbers of
holdovers.
Unless one is familiar with how the CSS estimates the SARs, it is not clear
how holdovers cause problems. It would be helpful to give an explanation of
how holdovers cause problems in the CSS methodology by looking at several
scenarios. For example, suppose holdovers did not migrate through the
hydrosystem and died before reaching LGR. Then the CJS estimates of
survival are unaffected and S1 captures the death rate from release to LGR.
Estimates of SAR are unbiased. Then suppose holdovers migrated through
the hydrosystem and were not detected (e.g., migrated when the PIT-tag
detectors were offline). Then the holdovers are indistinguishable from the
previous scenario. Estimates of survival though the hydrosystem are
unaffected except for S1, which now is a combination of survival from the
release site to LGR + holdover proportion. Estimates of the number of smolts
alive at LGR are biased downwards (holdovers are thought to have died).
Consequently, when an adult fish returns from the holdover group, it inflates
the SAR because the denominator does not include the holdovers. If only
some holdovers are detected (e.g., those that stay in the hydrosystem until
the next year), then explain the impacts on the various parts of the estimate
of SAR. A diagram would be helpful. This comment was also made in the
ISAB's 2012 review perhaps some clarification is needed to prevent it being
made in future drafts.

21

The simulation was generally well described but only in writing. Many
readers would find a model description with equations or a figure describing
the parts of the model easier to follow. This is especially true for the equation
for Nbias (p. 119), where it is unclear how HOu is computed and why it enters
into the equation for Nbias in the way it does. It should be noted that the
simulation is actually completely deterministic and that all ranges for the
extent of the bias simply reflect three different survival rates when
backcasting the holdover detections at Bonneville to LGR.
The report indicates that there is a model that gives some indication of which
release groups have low holdover proportions. For the groups where the
holdover proportions are high, is it possible to model some of the movement
and thereby estimate the size of bias?
Specific Comments and Questions
P.116, l.35. fish passing during the winter shutdown are not represented
in estimates of survival and detection This needs to be clarified. These
fish look like deaths after release prior to LGR and only affect S1. Other
estimates of survival and detection are unaffected. The ISAB agrees that
returning fish will contribute to the numerator of the SAR and cause bias.
P.117, l.2. However, using the predictions to isolate and remove individual
marked fish proved unsuccessful. The ISAB is not sure how this differs
from removing entire groups of fish that are thought to have high holdover
rates? More details are needed.
P.117, l.34. The presence of winter migrants and survival estimates in the
CSS method. The ISAB did not understand the last phrase starting with and
survival estimates. If the holdovers were not detected, only S1 is affected
(along with C0).
P. 117, l. 34-36: The authors state, Since holdover fish could not be easily
removed from release groups for SAR estimation using predicted holdover
probability, it was important to evaluate the total bias that could occur in
SAR estimates if any holdover fish were present in the release groups used.
It would be useful to have additional explanation for why this is the case. If
the explanation is available elsewhere in the report, refer to the location of
those details here.
P.117, l.38. CJS derived SAR estimates. The CJS model is used only to
estimate the C0 value, and so it is not correct to say that the SAR is derived
from this model.
22

P.117, l.37. Does the 21 December date refer to the Bonneville shutdown
date, and does the 5 December date refer to the LGR shutdown date? This
needs clarification.
P. 119, l. 11-14. The ISAB agrees that this conservative approach is a good
idea.
P. 119, l. 22-23. Adding a (winter passage) proportion to the (estimated
spring passage) population does not make sense. Is the first value a number
(i.e., a population rather than a proportion)? Unfortunately, it is impossible to
tell from the imprecise definition of HOu in the equation that follows. This
section remains very unclear (despite ISAB comments about the issue in
reviewing the draft 2012 report). The ISAB does not understand the
calculation of NBias, although we presume it is done correctly, and just not
explained accurately.
P.120, l.13. Why is the % bias expressed as a fraction of the (incorrect) CSS
SAR and not the correct simulated SAR?
p.120, l.20. Those fish would have been part of the Co Here the authors
need to be careful about the actual Co and the estimated Co (which is used
in the SAR). If the holdovers were undetected, then yes they are part of the
actual Co, but they would have been treated as deaths after release and
prior to LGR and would NOT be included in estimated Co and not in the
denominator of the SAR.
P.125, l.16. low holdover detection probability. Perhaps this should read
low holdover detection rates. A release group could have a 0 holdover
detection probability (migrates during shutdown) but still have substantial
bias in the SAR.
P. 140, l. 17-19. The confidence intervals on the wild mark groups tended to
be much wider than those of the hatchery groups due largely to relatively
low numbers of wild fish marked each year relative to hatchery releases. It
would be useful to mention other reasons for the wider confidence intervals.
P. 143, Table 5.26. It seems worth noting that all TIR are greater than 1 and
three D values are significantly less than 1.
P.146, l.8. Wont there be bias even if the holdovers were NOT detected in
the hydrosystem? Please clarify.

23

Appendix A: (SR), SAR, TIR, and D for Snake River

Hatchery and Wild Spring/Summer Chinook Salmon,
Steelhead, and Sockeye
This Appendix presents the methodology for the computation of the SR, SAR,
TIR, and D parameters along with extensive tables of results. This chapter is
an update of similar material from previous years.
In order to understand the equations, a flow diagram would be helpful
showing where the various statistics and parameter lie. This was also
commented on in the ISAB's 2012 review.
The model fitting of the relationship between log(TIR) and SR needs
additional thought because the TIR implicitly includes SR. The ISAB suggests
that plotting log(TIR) - log(SR) against time or by itself would be more
informative. This should provide some information about possible differential
ocean survival.
Specific Comments and Questions
P. 2, l. 33-41. The sentence on lines 38-39 indicates that if point estimates of
reach survival exceed 100%, they are considered unreliable and deleted for
the plots. Were these points retained for computing the SR values and
confidence intervals that are presented in the tables? Selectively omitting
survival estimates that exceed 100% will bias the distribution of the
remaining estimates, and consequently, the median or average of this
distribution will tend to underestimate SR.
The notation d0 and d1 in which the subscripts refer to C0 and C1 fish is
confusing because it seems incongruous with the notation d2, d3 and d4 in
which the subscripts refer to dams.
P. 9, l. 34. This is not really an expected value since it depends on the
random variables d5,0, etc.
P. 10, l. 30-32. It is not clear why for 2010, equation A3 is considered to be
better than equation A6 because of remarkably low detection probabilities
at LMN that were probably a result of the noted bias. A short explanation
would be helpful.
P. 11. In Equation A.10, SAR(Tx_t) is shown to be calculated by summing
adult counts at three dams (ATLGR_t + ATLGS_t + ATLMN_t). However the ATi are not

24

defined anywhere; is there a procedure to obtain a cumulative count over the

dams that prevents counting the same adult fish more than once?
Is it statistically reasonable to conclude from SR values for Snake River
Chinook in figures A.2 - A.3 (i.e., data in tables A.1 - A.3) versus
corresponding SAR values for C0 fish in figures A.7 and A.8 that SAR values
are typically higher for wild than hatchery Chinook whereas SR values are
typically the same for wild and hatchery Chinook (or perhaps slightly higher
in hatchery Chinook)? This conclusion (if supported by the data) would
indicate that wild Chinook typically survive better than hatchery fish below
Bonneville and would be worth reporting here.
P.44-45. Characterizing the relationship between loge(TIR) and in-river
survival (SR): The sentence on lines 36-37 states that the effectiveness of
transportation as measured with TIR should be partly dependent on in-river
survival. More generally, TIR must depend on the trade-off between (i.e.,
the relative magnitudes of) SR and D. For Figure A.18, it might be more
informative to include a reference line that corresponds to the expected
relationship between loge(TIR) and logeSR when D=0. The plot would then
show the amount of variation in TIR that could be attributed to the null
hypothesis (SR) alone and how much remained to be attributed to D (that
statistic could also be calculated). A key point, suggested in the text but not
the existing figure, is that a linear relationship between loge(TIR) and logeSR
(not SR) is expected by definition, and need not be estimated empirically by
regression. From equation A.15 (i.e., by definition), TIR = D ST/SR, so log(TIR)
= logD + logST logSR where the logST might reasonably be assumed to be
constant at log(0.98). Note that the expected linear relationship requires
taking the log of SR (which is not done in Figure A.18).

V. Editorial Suggestions
Glossary
The ISAB recommends that all acronyms and abbreviations used in the report
be included in the glossary. It is very helpful to be able to look at the glossary
to be reminded of the definitions. The use of ESU was mentioned in the last
review, but was not changed in this edition. The authors did explain their age
designation methodology (1 salt, 2 salt, and so on) in last year's response to
the ISAB review, and the ISAB requests inclusion of these descriptions in the
glossary. A number of dam acronyms are missing (e.g., RIS, with no
explanation at its first appearance in Table 1.3). This comment was made in
25

last years review. The response indicated that these acronyms would be
(had been?) added to the final report for 2012.

Missing Section
For future reviews of the CSS Annual Report, the ISAB recommends the
inclusion of the draft executive summary. The ISAB understands that this
might be modified after the CSS response to our review, but a draft executive
summary would provide a useful overview of the report's new contents,
major results, and conclusions for ISAB reviewers.

Chapter 1
P. 1, l. 22. Is 17th year correct? Last year's report states, "15th year"

Chapter 2
p.19, l.30. How are empirical abundances used to evaluate spatial and
temporal variation in salmon survival? Is some rewording needed here?
p.20, l.14. The authors need to clarify what is meant by intermediate
number of populations and why the number of populations causes problems.
Some rewording here?
p.20, l.41. What is the power-house contact rate (NPH)? This does not appear
in the glossary, and is never explicitly defined anywhere. Is this simply the
number of powerhouses on the outward migration path? Why is it a rate?
p.21. l.22. Why are data only from years that overlapped all populations
used? Data from years where some of the populations are measured are also
informative and should be included.
p.22, l.14. The capacity parameter is set to infinity for the ocean. But infinity
is poorly represented in most computer packages, and so was some large
value used? Need to be more specific here.
p.24, equation (1) and following equations. The left side of the equation is
the expected number of smolts (or other stages of the population) and
should be indicated as so.
p.26, equation (9). It would clarify the text if the beta-terms were indexed by
PDO, UPW or NPH rather than 1, 2, and 3.
P. 25, l. 11. Should be third year in ocean; not second year.

26

p.26, l. 22. Why is there is an additional a1 parameter when ap parameters

have already been defined?
p.28, l. 24 within the range of variability of the empirical data Which
data? How were empirical data on the ocean survival rates obtained?
Perhaps it is meant in the range of the estimates from the other models?
p.28, l. 27. Report the SE for the estimate of the beta-coefficients. What is
meant by the NPH effect is stronger in this analysis? There are 4 beta
parameters, but only 3 estimates are reported.
P. 30. Figure 2.3. Plot the Y axis (here and other plots) on the log-scale to
uncompress the scales.
P. 31. Figure 2.4. Make these plots on the log-log scale.
p.32, l. 6. Refers to the BH model, but figures are for the LC model.
p.39, l. 6. How does the logit transform make the effect of NPH stronger?
p.39,l. 12. This paragraph is difficult to follow and needs to be rewritten. It is
not clear what the authors are trying to say here.
p.39, l. 41. The authors claim that there are only 13 parameters for the LC
model. But there are 6x2=12 parameters alone for the recruit/spawner
relationship, plus the ocean survival, maturation, and variance parameters
for more than 13 parameters. Please explain how this count was obtained.

Chapter 3
Given that this chapter of the report is updated each year, it is important to
be clear about what years are covered in the text, tables, and figures (e.g., if
statistical values, or goodness-of-fit values are shown, the year(s) over which
these values were calculated should be indicated). Some specific locations
where clarification is needed are noted below.
p.43, l.10. survival rate implies survival per unit time. The CJS model
simply gives you a survival probability for that reach.
p. 43, lines 12, 13, 17: Should these years be 1998-2012? The values in Table
3.1 are slightly different than they were in the 2012 report, which is likely
because one more year of data is included in obtaining these values. If true,
this means these lines should indicate that one more year of data was used.

27

p.43, l.19. It would be preferable to use the median c-hat procedure used in
MARK and developed by White (2013) to estimate the c-hat value because
the methods from Burnham et al. (1987) have been shown to perform poorly.
p. 43, l. 24: Should this be 41% rather than 43% to correspond with Table
3.1?
p. 43, Table 3.1: Here is a case where it might be helpful in the caption to
indicate the years over which the CV was calculated. The inclusion of the
number of cohorts is appreciated.
p.44, Equation 3.3: An extra minus sign is present in the equation.
p. 46, l.12-13: It appears from the way this paragraph was written that only
six environmental factors were evaluated this year as compared to seven
last year (see lines 4-7 on this page). However, on lines 12 and 13, the
authors still refer to seven variables and 128 possible model combinations.
Should these numbers be changed to reflect the different number of
variables mentioned earlier in the paragraph?
p. 46, l. 18-22: It is not clear whether the authors did two log transformations
(e.g., log10 and ln). The latter could be written as loge which the authors do
state was something they looked at, but once they mentioned this it
becomes ambiguous when they use log without a base indicated. Typically,
log implies log10. This is not the same transformation as loge so it is
important to be clear which is being referred to in Equation 3.6.
p.46, l.19. dependent variable is an old-fashioned terminology. Use
response variable instead.
p.46, l.27. The authors indicate that a log-transform is needed for Z, but then
equation 3.7 does not show any transform? Was a transformation used?
p.53, l.1. Table should be numbered 3.3 rather than 2.3. r2 should be R2 . It is
not clear how the R2 is computed for survival as it never was used in a
regression model directly but is derived using equation 3.8.
p.54, l.34. It is not clear why improvements in the precision of the estimated
survival rates are needed. There may be enough residual variation in the
regression models that improving precision of estimates of survival has no
impact. A small simulation should be done to see if this is a worthwhile
activity.

28

p. 54, last paragraph. Rather than precision the authors likely mean
accuracy. Precision refers to the number of decimal places with which one
can make an estimate, and how repeatable an estimate is (i.e., getting the
same value over and over again). Accuracy refers to how close one is to the
true value. We suggest replacing the word precision throughout this
paragraph with accuracy.
p.55, l.12. Model with Day2 but lacking Day in the predictor set should not be
fit as they are not sensible. Such models assume a very strict functional form
for the effect of Day that is centered around the value of 0 which is simply
not sensible. The all subsets model selection procedure will need some
guidance to not fit these models. Similarly, models with the Day*WTT
interaction but lacking the main effect of Day and WTT should also not be fit.
Missing tables. In the CSS response to the 2012 ISAB review, the authors
state in several responses that they have provided Tables 3.4-3.7. Why were
these tables not included in the 2013 report?

Chapter 4
P. 57, l. 45 and other places throughout the text. The ISAB appreciates (in
response to our comment last year) that confusion about fish age has been
eliminated by explicitly defining the CSS convention of using salt years,
which is now used consistently throughout the annual report. As noted above
in our editorial suggestions for the glossary, however, the ISAB requests
inclusion of an explanation of this age designation terminology in the
glossary.
P. 63, Figure 4.1 The caption should indicate that RR data for Chinook only
extend to 1984 (not 1993 as indicatedthis point was raised in last years
review too). Also the data point for 2011 seems to be missing (its expected
from reading the caption).
P. 67, l. 14-39. The "Mid-Columbia River Overall SARs" section was
mistakenly inserted (same section is repeated on p. 72, l. 3-38).
P. 69, Figure 4.5 - the caption and text on page 69, line 9 refers to 14
migration years (1997-2010) but only 13 points are indicated in the figure
(2010 seems to be missing).
p. 66. Fig. 4.7 is out of order (precedes Figs. 4.4, 4.5, and 4.6) in the draft.
This figure is repeated on p. 71 (more appropriate place).

29

Tables 4.30 and 4.31 are missing and need to be completed.

P. 76-77, The bottom paragraphs (l. 33-43) and next page (l. 1-6) are same as
those at top of page 76, l. 3-19.

Chapter 5
p. 140, l. 4-5 "SAR estimates by study category for wild subyearling fall
Chinook were only available 4 for three of three years and only for the Snake
River release groups (Table 5.24)." The sentence does not make sense.
p. 145, l. 20 mentioned (not mention)
p. 147, l. 13 add in to groups IN 2008

Appendix A
P. 8. Figure A.1 is very helpful, and it might be useful to include it in Chapter
4 as well.
p. 9, l.13. with the m-matrix parameters. The values of m12 etc. are
statistics and not parameters.
p. 10, l. 28. than instead of that
p. 25. Figure A.8: Update the caption to indicate four (not three CSS hatchery
summer Chinook groups).
p. 44. Table A.37: Add bold font for TIR estimate for 2011 (upper CI
significantly below 1).

30

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33