Salmonid Gap Analysis
1.0
INTRODUCTION AND BACKGROUND
1.1
GAP ANALYSIS
1.1.1
Draft
Purpose
This report provides an assessment of technical information regarding juvenile salmonid
survival in the Sacramento-San Joaquin River Delta (Delta) linked to State Water Project
(SWP) and Central Valley Project (CVP) operations in the Delta. The report provides a
review of available information, identifies gaps in existing knowledge, highlights areas of
scientific agreement and disagreement, and provides recommendations for future actions.
The report also addresses eight specific management questions identified by the
Collaborative Adaptive Management Team (CAMT).
Information provided in this report is intended to inform policy and management decisions,
including future biological opinions related to water project operations in the south Delta.
The report is also intended to provide CAMT and others with a technical basis for
prioritizing future investigations of salmonid behavior and survival in the Delta.
1.1.2
Scope of Analyses
This gap analysis report reflects the scope identified in the work plan adopted by the CAMT:
The scope of the CAMT Salmonid Scoping Team (SST) is to review existing
information and develop new information on salmonid survival as affected by
factors linked to State Water Project and Central Valley Project-linked
operations, including San Joaquin River inflow, delta exports, and south delta
hydrodynamics. The primary focus of this work is the Sacramento-San
Joaquin Delta south of the San Joaquin River (including Old and Middle River,
the State and Federal Export Facilities, and the Head of Old River Barrier).
The geographic scope also includes those pathways and export-related facilities
that provide access for Sacramento River salmonids into the central and south
Delta, such as the Delta Cross Channel (DCC). The water project-linked
effects considered within this scope may include entrainment, hydrodynamics,
barriers, predator-prey interactions, food supply, aquatic macrophytes, habitat
suitability, and water quality as part of the “driver-linkage-outcome” cascade.
The results are intended to contribute information relevant to the ESA
consultation on the Long Term Operation of the CVP and SWP.
The management questions given to the SST in January caused the group to refocus on those
issues for many months, and add-to and restructure the already compiled material contained
in the November draft of the Gap Analysis Report. In particular, the management questions
Introduction and Background
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highlighted the following specific management actions and infrastructure elements related to
operations of the SWP and CVP which were, as time allowed, considered at various levels of
detail in the gap analysis:
1. Temporary, operable, and non-physical barriers including the Delta Cross Channel,
Head of Old River Barrier (HORB) and others
2. Clifton Court Forebay gates
3. SWP and CVP exports
4. Old and Middle river flow
5. Vernalis inflow:export ratio
6. San Joaquin River inflow
A detailed description of the above water project operations is provided in Appendix A.
The gap analysis describes and addresses some of the potential biological and physical
relationships between SWP and CVP water project operations and salmonid survival, but
does not attempt to address all the potential factors that may affect salmonid survival in the
Delta.
1.1.3
Project and Non-project Related Effects
A large number of factors determine the survival rates and population dynamics of Central
Valley Chinook salmon and steelhead populations. These factors include, but are not limited
to:
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Migration barriers and impediments;
The quality and availability of suitable spawning gravels;
The physical condition (e.g., size and health) of juvenile salmon and steelhead at the
time of ocean entry, relative to ocean conditions;
River flows and fluctuations in flows (including seasonal timing and magnitude of
river flows within the upstream tributary areas where spawning and some rearing
occurs);
Water temperatures;
Predation by fish, birds, and marine mammals;
Food availability in both freshwater and coastal marine habitats;
Hatchery operations;
Water quality and pollutants;
Operation of upstream reservoirs;
Commercial and recreational harvest; and
The abundance and geographic distribution of non-native aquatic species (e.g., Egeria
densa, the overbite clam Potamocorbula spp. and warm water Midwestern fish
species).
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Most of these factors are outside of the limited scope of this gap analysis and are not
addressed herein. The omission of these factors from the analysis does not mean that they
are not important to salmonid survival, spatial distribution, productivity or abundance. Nor
should this omission be interpreted to mean that the effect of these factors on survival may
not be influenced by water project operations. These factors may or may not influence
whether and how water project operations effect juvenile salmonid survival and should be
considered in the context of a broader assessment of factors that may affect survival.
For example, it has been hypothesized that a substantial proportion of the juvenile mortality
in the Delta is the result of predation, especially inside and near the water project facilities,
but mechanistic linkages between water project operations and conditions supporting high
predation in other areas of the Delta is largely unknown. In addition, there are potential
linkages between water project operations (e.g. barrier installations) and outcomes such as
habitat quality, growth, and life history diversity. Similarly, effect of factors such as upstream
flows, habitat quality and habitat availability on the size, timing, distribution and physical
condition of juvenile salmon and steelhead entering the Delta has the potential to influence
the likelihood of outcomes related to potential effects of water project operation related
drivers on migration behavior or survival. Certain water project operations could affect
habitat conditions in the Delta resulting in increased mortality in some migration pathways
and/or reduced growth. Reduced growth could result in reduced survival of juvenile salmon
at ocean entry.
The potential effects of water project operations in the Delta on sublethal effects such as
reduced growth or altered migration timing that influence subsequent survival of juveniles
(e.g. in the ocean) and overall population life history diversity have not been evaluated.
Water project operations, along with uses of water, potentially could affect seasonal diversity
in migration timing, geographic diversity in rearing strategies and habitat use in the
tributaries influenced by SWP and CVP operations such as the Feather, American,
Sacramento, and Stanislaus rivers and Delta. Operations have the potential to constrain life
history diversity as a result of altering instream flows, export operations, and other habitat
conditions by favoring one type of life history attribute over others. Over time, this can
represent a selective pressure that reduces diversity within a population. The cumulative
effect of water project operations on the juvenile salmonid mortality in and beyond the
Delta, in relation to other stressors, is a major gap in our knowledge.
1.1.4
Management Questions
The CAMT identified thirteen key management questions regarding salmonid survival in the
Delta. Eight of the questions are explicitly addressed in Section 5 of this report. The
remaining five questions are beyond the scope of this report.
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The following eight management questions are addressed in this report:
1. To what extent do SWP and CVP export operations affect water velocity and flow
direction at selected locations in the Delta? To what extent do those specific
hydrodynamic changes influence salmonid migration rate or route selection, and
salmonid survival?
Export operations of concern include export rates and
installation/operation of gates and barriers, including the Clifton Court Forebay radial
gates, the Head of Old River barrier, and south Delta agricultural barriers.
2. To what extent do either: (1) water exports; (2) inflows; or (3) the ratio of San Joaquin
River inflow to water exports during April and May affect the survival of Chinook
salmon or steelhead out-migrating down the San Joaquin River, particularly given very
low ambient rates of survival and associated issues of detection?
3. To what extent does the January 1 onset of OMR flow management improve the survival
of the target salmonid species?
4. To what extent do salvage-density-based export restrictions improve survival of targeted
populations of Chinook salmon and/or steelhead?
5. In considering the effectiveness of flow metrics as a management tool, are there
alternative or additional metrics (e.g., OMR flows, export volumes, monthly export
limits, etc.) that could be used to manage south Delta water operations, and improve
survival of migrating salmonids in the south Delta?
6. Are there biological response metrics that would be useful for assessing the effectiveness
of RPA actions (for example, as suggested in Anderson et al. 2014, pages 5, 42)?
7. Do DSM2 Hydro and/or other available hydrodynamic models provide outputs that are
appropriate and useful for assessing how exports from the south Delta, river inflows, and
tides may influence the magnitude, duration, and direction of water velocities within
selected channels and channel junctions in the Delta? What are the strengths and
limitations of various simulation models and their application to assessing the
relationship between water project operations and salmonid migration and survival?
8. What information is needed to address concerns that the results of tests using hatcheryreared fall-run Chinook salmon may not be representative of results of other runs of
natural-origin salmonids? Could a correction factor be developed to allow for application
of such test results?
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The following additional management questions deal with broader effects of project
operations on salmonid survival and are beyond the scope of this report but may be
addressed in a later phase of the CAMT salmon efforts.
1. To what extent do project-related hydrodynamic effects and project driven water
movements and reservoir practices influence predation, and what information is needed
to inform management of any project-related predation effects?
2. What are the indirect ecological effects of water export and project driven water
movements, temperatures and reservoir practices; and are there management actions that
would minimize indirect project effects that influence salmonid survival?
3. What are the most likely tools to invest in, either in terms of monitoring or modeling, to
improve our ability to assess the real-time distribution of juvenile salmonids and juvenile
losses in the Delta and in the Sacramento River system?
4. Are there experimental modifications of the 6-year steelhead study that would enhance
the understanding of the effect of inflow/export conditions on south Delta survival of
steelhead?
5. How well do current hydrodynamic simulation models with behavior algorithms predict
actual migration rate and route selection of juvenile salmonid within the Delta and the
Sacramento River system and, how well do the current passage/survival and lifecycle
models predict survival observed in CWT and acoustic tag survival studies?
1.1.5
Report Organization
The following briefly outlines the organizational structure and content of the Gap Analysis
Report, in the context of the scope and questions described above.
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Section 1.2 of this introduction presents general background information on Central
Valley salmonid populations, the Delta, water project operations, and the gap analysis
approach.
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Section 2 addresses the application of various hydrodynamic simulation models used to
characterize flows, water stage, and water velocities at locations within the riverine and
tidal regions of the Delta. Section 2 also provides information on the relationship
between SWP and CVP export operations and changes in water velocities and flows at
various locations in relation to Delta inflows, installation and operation of some Delta
barriers (e.g., Head of Old River, and the Delta Cross Channel gates), and tidal conditions.
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Section 3 describes information on the relationships between water project driven
changes in Delta hydrodynamic conditions and the behavior of juvenile salmonids
migrating through the Delta channels (e.g., migration rate and route selection).
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Section 4 describes information on the relationship between water project driven changes
in migration behavior and subsequent survival of juvenile salmonids based on results of
both coded wire tagging and more recent acoustic tagging survival studies.
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Section 5 addresses the eight primary management questions that were provided to the
SST by CAMT (as listed in Section 1.1.4 above).
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Section 6 presents a summary of findings and recommendations for potential funding and
implementation as next steps in the salmonid assessment process.
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Literature cited in preparing the report is documented in Section 7.
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The report also includes several technical appendices that serve as additional background
information for the gap analysis including a description of water project facilities and
operations considered in the analysis (Appendix A), a comparison of available
hydrodynamic models (Appendix B), and a comparison of predicted changes in water
velocities and flows at a variety of locations in the Delta generated by the 1-D DSM2 and
2-D RMA hydrodynamic simulation models with actual field measurements (Appendix
C).
1.2
GENERAL BACKGROUND
1.2.1
Central Valley Chinook Salmon and Steelhead
The historic Delta system (Figure 1-1) and Central Valley tributaries supported one of the
most diverse aquatic fauna in North America (Moyle 2002). This biodiversity includes four
runs of Chinook salmon (winter-run, spring-run, fall-run, and late fall-run Chinook salmon)
and Central Valley steelhead. Three of these genetically distinct salmonid runs, identified as
Evolutionarily Significant Units (ESU; see McElhany et al. 2000, Waples 1995, Lindley et al.
2007, National Marine Fisheries Service (NMFS) 2014), have been listed for protection under
the federal Endangered Species Act (ESA) and/or California Endangered Species Act (CESA)
including winter-run (ESA endangered/CESA endangered), spring-run (ESA
threatened/CESA threatened), and steelhead (ESA threatened). Fall-run Chinook salmon,
which support an important commercial and recreational fishery are a Species of Concern
and considered impacted and vulnerable to extinction (Katz et al. 2013). Late fall-run
Chinook salmon have also been designated a Species of Concern due to limitations in both
demographics and genetic diversity. All of these salmonids inhabit Central Valley rivers and
use the Delta as a migratory corridor and juvenile rearing habitat. Anadromous salmonids
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(Figure 1-2) spawn in upstream freshwater habitat and juveniles begin rearing in those same
waters, continuing as they migrate downstream through the Delta to enter coastal marine
waters where they rear typically for 1 to 4 years before migrating upstream through the
Delta to inland spawning habitat.
Figure 1-1. Map of the Sacramento-San Joaquin.
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Figure 1-2. Generalized Life History of Central Valley Salmon and Steelhead (Source: Vogel 2011)
1.2.2
The Delta
The Delta is the estuarine transition habitat between coastal marine waters, where salmonids
rear and grow for a substantial proportion of their lifecycles, and freshwater habitats in rivers
that serve as spawning and juvenile rearing habitat. All juvenile Chinook salmon and
steelhead from the Central Valley must move through the Delta to reach the ocean. The
Delta serves as both a migration corridor and as rearing habitat. For the purposes of this Gap
Analysis, we focused primarily on the Delta as a migration corridor. Juvenile salmon of all
runs occur throughout the Delta, although at slightly different times of the year, at different
sizes, and with significant overlap (Fisher 1994, Table 1 in Yoshiyama et al. 1998, Pyper et al.
2013).
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Over the past 150 years the Delta ecosystem has been extensively modified through
reclamation of areas that were historically shallow tidal wetlands, and which produced food,
velocity refugia, and complex rearing habitat for juvenile salmonids. The channels passing
through the Delta have been leveed and armored with rip-rap to support water conveyance
and flood protection purposes. They now provide little shallow water channel margin,
seasonally inundated floodplain, or tidal wetland habitat for juvenile rearing and foraging
(Whipple et al. 2012).
Physical changes have also facilitated shifts in species composition and trophic dynamics that
favor the introduction and expansion of non-native fish, macroinvertebrates, and aquatic
plants. Introduced species such as striped bass and largemouth bass prey upon juvenile
salmonids and other fish inhabiting the Delta. Extensive expansion of submerged aquatic
vegetation (SAV), increased water clarity, and seasonally elevated water temperature also
provide advantages to introduced predators. How these physical changes have been
facilitated by water project operations is an area of needed study (Brown and Michniuk
2007).
1.2.3
Effects of SWP and CVP Operations
Operation of the SWP and CVP can affect habitat conditions in the Delta but the magnitude
and geographic footprint of these effects has not been clearly identified or described.
Depending on Delta inflows, tidal conditions, and the rate of diversions in the Delta, the
direction and magnitude of Sacramento River or San Joaquin River flows into the Delta as
well as flows in interior Delta channels and at channel junctions can be altered in a number
of ways. These effects are discussed in general in Section 2 of this report. Altered
hydrodynamic conditions can affect the distribution, behavior, and survival of juvenile
salmonids during their migration through the Delta. Some of these effects are described in
Sections 3 and 4 of this report.
1.2.4
Individual and Population Effects
The vast majority of the existing survival studies in the Delta have focused on survival of
individual fish to Chipps Island as part of experimental release groups. They have not been
used to quantify the cumulative effect of water project related impacts (lethal and sublethal)
on the overall population dynamics, abundance, or resilience of the species. Some attempts
to estimate the proportion of the population suffering mortality as a result of direct
entrainment at the export facilities have been made for different runs (Kimmerer 2008; Zeug
and Cavallo 2014). However, it is important to note that these estimates do not account for
mortality that may occur within the rivers and Delta prior to encountering the export
facilities (e.g. due to enhanced predation), which may or may not be affected indirectly by
water project operations. When Zeug and Cavallo (2014) estimated mean relative mortality
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attributable to exports, San Joaquin River releases had mortality estimates of more than
double that of Sacramento River releases at both state and federal facilities. Losses were
greater at SWP than at the CVP (Zeug and Cavallo 2014).
Information on the population-level consequences of various sources of juvenile mortality is
limited, and the relationship of those sources to water project operations is a major gap in our
understanding of salmon biology in the Delta. The NMFS is currently developing a Central
Valley Chinook salmon lifecycle model. The original model was developed for Sacramento
River winter-run Chinook but is now being expanded to also include consideration of other
salmon runs on both the Sacramento and San Joaquin Rivers (Hendrix et. al. 2014). Once the
lifecycle model has been calibrated and validated, as well as peer reviewed, it is expected to
be a valuable tool for investigating the population level effects of project related entrainment
and other sources of mortality on Central Valley Chinook salmon.
1.2.5
Gap Analysis Approach
The SST started with a broad conceptual model developed by the South Delta Salmon
Research Collaborative Effort (Figure 1-3). The SST then developed a series of refined
conceptual models to address the narrower scope of work described in Section 1.1.2.
For the purposes of this gap analysis, the SST focused explicitly on potential relationships
between flows and water project exports and Delta hydrodynamics, behavior (specifically
migration route and migration rate), and salmonid survival. A series of Driver-LinkageOutcome (DLO) conceptual models (DiGennaro et al. 2012) were established to depict how
specific actions would propagate through different biotic and abiotic pathways (mechanisms)
to ultimately affect salmonid survival (Figure 1-4). The conceptual models identify
hypothesized mechanisms that can be tested and either: (1) supported by results of the
analysis; (2) refuted by lack of a relationship if data are sufficient to do so; or (3) identified as
a gap for consideration as a potential priority for future research and analysis.
The SST divided into three sub-teams corresponding to water project operational effects on
hydrodynamics, behavior and survival. The sub-teams were individually responsible for
evaluating the DLOs by and summarizing the literature and doing developing supporting
analyses. Because the number of permutations of DLOs was large and increased after specific
geographic reaches were incorporated into the DLOs, each of the different sub-teams was
responsible for identifying focal relationships while coordinating with the other sub-teams.
Due to the limited scope of the gap analysis, as discussed above (Section 1.1.3), and time
constraints, the DLOs included in the analysis reflect a subset of the array of factors that
affect juvenile salmonid migration behavior and survival within the Delta. The SST
examined a subset (limited by time and scope) some of the available scientific data and
analyses that could be used to support or refute hypothesized linkages (mechanisms) between
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project operations and ambient hydrodynamic conditions in the Delta, juvenile salmonid
migration, and survival. The SST acknowledges that there are additional DLOs related to the
potential impacts of water exports on salmon survival and populations that may warrant
investigation and prioritization.
Upon receipt of the 13 management questions from CAMT, the SST’s original, very
mechanistic, DLO approach (relating migration rate to velocity or flow in general, rather
than to management actions such as OMR management or I:E ratio) broadened to include
linkages of hydrodynamics, behavior, and survival to specific management actions and
CVP/SWP operations elements, listed in section 1.1.2.
Figure 1-3. Conceptual Model from the South Delta Salmonid Research Collaborative Effort Describing
Factors Affecting Survival of Juvenile Salmonids in the South Delta
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Figure 1-4. Prioritized Focal Areas and Framework Considered by SST to Evaluate Knowledge Gaps
1.2.6
Identification of Data and Knowledge Gaps
The gap analysis relies on the underlying framework of conceptual models and available
analysis for depicting and evaluating hypothesized relationships, or linkages between water
project export operations as drivers, and salmonid survival as an outcome. Knowledge gaps
may exist regarding a hypothesized linkage between a specific driver and an outcome where
the existence or strength of the linkage requires further evaluation. Knowledge gaps may
also involve an unknown driver of a known outcome, or a hypothesized outcome from a
known driver based on several potential linkages.
This framework provides a basis for identifying testable hypotheses that can be used to assess
the strength of the linkage between a driver and an outcome. Delineating those portions of
the cause-and-effect relationship that are supported by evidence (e.g., available literature and
data) or lack of evidence or information helps to frame potential gaps and identify testable
hypotheses that can be used to assess the strength of linkages between drivers and outcomes.
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The linkage between a driver and outcome is likely to be complicated by other factors and
determining the importance of the gap requires characterizing it in more detail.
Tables 1-1 through 1-3 depict specific DLO models developed by the SST.
Table 1-1. Hydrodynamics DLO Components for Analysis (DLOs not included in the analysis
are shown in red italics text)
Drivers
Linkages
Outcomes
 Exports
 Proximity to Exports
 Instantaneous velocities
 River Inflow;
 Channel Configuration/Barrier
or flows
Sacramento and
Deployment
 Net Daily Flow
San Joaquin
 Clifton Court Forebay
 Sub-Daily Velocity
 Tide
Operation radial gate
 Percent Positive Flow
 Channel
operations (e.g., opening to fill  Water Temperature
Morphology
CCFB and then closing to
 Salinity
isolate the pumping plant
 Residence Time
operations from the Delta)
 Source/Origin of Water
Table 1-2. Behavior DLO Components for Analysis (DLOs not included in the analysis are
shown in red, italics text)
Drivers
Linkages
Outcomes
 Instantaneous
 Physiological and
 Individual outcomes:
flow/velocity (channels)
behavioral responses to
 Migration rate
 Instantaneous
hydrodynamic or water
 Migration route
flow/velocity (junctions)
quality conditions,
 Migration Timing
 Water quality
gradients, or variability,
 Timing of Delta entry
(e.g., temperature, DO,
such as:
 Delta residence time
salinity, turbidity,
 Rearing
 Rearing location
contaminants
 Active swimming
 Population outcomes:
 Hydraulic residence time
 Lateral distribution
 Population scale
 Spatial/temporal
in the channel
outcomes depend on
heterogeneity of
 Passive displacement
the spatial/temporal
hydrodynamic/water
 Diel Movements
heterogeneity of
quality drivers
 Energy expenditure
individual outcomes
 Small-scale
 Selective Tidal
hydrodynamics as
affected by
structures/bathymetry
Stream Transport
Notes: DO = dissolved oxygen
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Table 1-3. Salmonid Survival DLO Components for Analysis
Drivers
Linkages
 Migration route
 Exposure to variables (e.g., habitat and
selection
predators) that affect differential survival
 Migration rate
between routes or between years for the
same route
 Duration of exposure to route-specific
conditions that affect survival
1.2.7
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Outcomes
Mortality
Variation, Uncertainty, and Statistical power
The Delta is a complex network of interconnected channels and channel junctions that is
characterized by highly variable water quality and hydrodynamic conditions, only some of
which are due to water project operations. In addition to the spatial variation and
complexity of the system, juvenile salmonids exhibit highly variable life history strategies
(e.g., extended residence periods for rearing versus rapid migration) and behavior in response
to environmental conditions such as water quality, hydrodynamics, habitat suitability, and
others.
The hydrodynamic and biological temporal variation that occur within the Delta includes
variation within a day (in response to factors such as tidal conditions), over weeks (in
response to factors such as spring and neap tidal cycles), over seasons (in response to
hydrology), and over years (in response to factors such as non-native species introductions
and long-term trends in population dynamics, ocean conditions, climate, and ecosystem
alteration). Given these conditions, numerous experimental studies of salmonid migration
and survival in the Delta under variable, and preferably explicitly manipulated,
environmental covariates such as Delta inflow or changes in water project operations need to
be tested to better understand potential cause and effect relationships and associated
mechanisms. These studies may involve large, and/or small scale experiments designed to
address specific questions.
Using statistical power analysis in developing the experimental designs for testing factors
affecting Delta survival and migration and in analyzing results can help to provide important
context for meaningful interpretation of results. For example, it would be useful if study
results included some measure of the effect size (e.g. change in survival or migration rate)
that could have been detected under the experimental conditions.
1.2
SUPPLEMENTAL EXPERT INPUT AND REVIEW
The analysis process has been augmented by the contributions of non-SST scientists familiar
with Delta hydrodynamics and hydrologic simulation modeling. Outside experts were
engaged to assist in developing data summaries and data visualization methods from
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commonly used hydrodynamic simulation models. Outside experts that contributed to the
analysis included John DeGeorge and Stacie Grinbergs from Resource Management
Associates (RMA), Jon Burau from USGS, Tara Smith and Xiaochun Wang from DWR, Paul
Hutton from MWD, Alison Febbo from the State Water Contractors, Tom Boardman from
Westlands Water District and Brad Cavallo from Cramer Fish Sciences. These outside
experts also assisted in the analysis, presentation, and interpretation of available data,
assessed the appropriate application of modeling tools and their limitations and constraints,
and provided internal review of synthesis and summary of information related specifically to
hydrodynamic modeling (Section 2 and Management Questions 1 and 7) developed by the
SST as part of the gap analysis technical report. The SST greatly appreciates the input from
these external contributors.
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1