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Puckett, Kathryn J

From: Puckett, Kathryn J


Sent: Wednesday, August 26, 2009 2:58 PM
To: DUANE.MECHAM@sol.doi.gov; Gayle.N.Lear@usace.army.mil; Peters, Rock D NWD;
Stier,Jeffrey K - KE-4; Grabowski, Stephen J; Personius, Timothy L; McDonald, John (Bill);
McNary,Sarah R - A-7
Subject: triggers appendix
Attachments: appendices 2-7 8-21-09.docx

Attorney client work product 
Prepared for litigation 
 
Rock, Jeff (Sarah), Steve, 
 
Enclosed are my comments on the 8‐21 draft of the triggers (starting on page 29).  I'd like to have the AAs have a 
coordinated response to NOAA if possible.  I am trying to be sensitive to NOAA's needs.   Below are the principles behind 
my enclosed remarks: 
 
1. AAs need to balance the time and effort we spend on triggers w RPA implementation.  Money re‐routed to triggers 
development is money away from implementation.    
 
2. The triggers should be simple and transparent.  There should be a maximum of 3 triggers ‐ Severe Decline, Early 
Warning, and Juvenile.  Juvenile is to be evaluated as to whether it is possible and we don't send the court a bunch of 
ideas.   Anything we commit to in the future is a refinement of these triggers ‐ we're not adding additional triggers; 
we're refining those we already have.  I want to avoid 15 early warning triggers ‐ this is silly and chaotic.   Again, time 
spent in process w RIOG is time away from implementation; some is necessary ‐ there needs to be an appropriate 
balance.  
 
3. Triggers are at the ESU level (w some exceptions).  We do have to monitor at the MPG and population levels.   
 
Please call when you get a chance to coordinate on this.  thx, Kate 

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Appendix 2: Summary of the Reasonable and Prudent Alternative

2.1 Adaptive Management

2.1.1 Introduction

Using the Collaboration Framework, the Action Agencies identified Biological Objectives,
Recovery Strategies, and Actions for ESUs affected by the operation of the FCRPS – supported
by specific commitments for hydro, habitat, hatcheries, predation management, and harvest. In
the biological analyses of these commitments, the Action Agencies estimated benefits to fish
species listed under the ESA and considered aggregated, cumulative effects on “gravel-to-
gravel” lifecycle survival and recovery under the ESA. The Action Agencies evaluated multiple
measures of survival and recovery, including extinction risk, productivity (recruits per spawner),
abundance trend, population growth rate or lambda (λ) (the measure primarily used in the 2000
BiOp), and the Collaboration Framework gaps (allocation of long-term recovery responsibility
by sector). This analysis is addressed in the referenced Comprehensive Analysis.

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Figure 2-1. Proposed RPA Strategy Overview

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The Action Agencies’ analysis is based on the best available scientific information. However, as with any
analysis for a species with a complex lifecycle, there is uncertainty associated with this evaluation of
survival, recovery, and biological benefits. These issues are described in more detail in the discussions of
the biological analyses, climate change and ocean conditions, and latent mortality.

The Action Agencies’ RPA incorporates an adaptive management structure of checks and balances
similar to the 2000 BiOp, to ensure accountability for results in the face of uncertainty and risk. This
section summarizes the Action Agencies’ performance standards and targets, reporting and adaptive
management approach, continued collaboration and oversight, and contingencies.

Accountability for Results


Action Commitments: The Action Agencies' specific commitments, including funding,
presented in the form of the Proposed RPA, provide the first means to gauge results.
Performance Targets and Standards: Commitments to action are reinforced by
performance targets (long-term goals) and performance standards (benchmarks for
results). These will help track and gauge the effectiveness of our actions.
Planning and Reporting: A key aspect of our accountability structure is implementation
plans, reporting and check-ins. The Action Agencies will report annually on progress of
implementation and performance results to inform and signal appropriate adaptations or
adjustments to our actions, and provide cumulative check-ins at 5 and 8 years.
Research, Monitoring, and Evaluation (RM&E) and Adaptive Management: Using a
program of extensive and robust RM&E, the Action Agencies will assess compliance,
effectiveness, and critical uncertainties. Adaptive management will be used to modify
our actions and ensure that they continue to track performance expectations, based on the
best available scientific information.
Oversight: Continued collaboration and oversight of implementation by the sovereign
parties is provided, including review of how listed fish are progressing toward recovery
and “All-H” (i.e., Hydropower, Hatchery, Habitat, and Harvest) diagnosis of emerging
issues.
Contingencies: Consistent with the 2000 BiOp, the Action Agencies will provide specific
and general contingencies in case more aggressive adaptive management changes are
called for based on evaluation of our performance in years 5 and 8.

2.1.2 Performance-Based Framework

As in the 2000 and 2004 BiOps, performance targets and standards and RM&E remain central to the
success of the Proposed RPA. Commitments to specific actions are reinforced by a performance-based
framework that will help the Action Agencies track and gauge the effectiveness of specific actions, as
well as inform adaptive management actions.

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The Action Agencies have identified performance measures (metrics) that will be monitored and
evaluated relative to performance standards (benchmarks) and performance targets (longer-term goals) to
assess progress and inform adaptive management actions. Performance standards will be monitored
frequently to ensure accountability and adherence to Proposed RPA with potential contingencies or other
time-critical corrective actions. Performance targets will be evaluated over longer time periods as new
information and learning is applied through analytical models to check for progress toward expected life
stage survival improvements and trends in population performance. Performance targets will inform
longer-term adaptive management decisions and prioritization of options across populations with different
relative needs.

The Action Agencies will monitor two aspects of performance:

Programmatic performance standards, tracked through project implementation and compliance


monitoring, and
Biological and Environmental performance standards or targets, tracked and evaluated through status
monitoring, action effectiveness research, and critical uncertainty research in combination with
existing and developing quantitative models.
Descriptions of biological/environmental performance standards and targets are outlined for adult
abundance, hydropower, predation, habitat, and hatchery performance in the following sections.

Programmatic performance standards are also discussed below, but specific programmatic standards
are, or will be, identified by the specific actions and associated projects committed to within the
Proposed RPA and in subsequent 3-year Implementation Plans.

Reporting on achievement of performance standards and progress toward longer-term targets will
take place annually and through two comprehensive evaluations in years 2012 and 2015. The
proposed reporting structure includes changes made through monitoring and adaptive management, as
well as clear signals if performance standards are not being met. If there is a failure to achieve
performance standards, the Action Agencies commit to explore specific contingencies, in
coordination with States and Tribes. These discussions will occur through the Regional
Implementation Oversight Group (RIOG) described in Section 2.1.4.3.

Performance targets: Performance goals for actions. These are generally the survival
improvements from the lifecycle modeling, and will continue to be assessed using a modeling
approach. The performance targets represent long-term goals, which are not necessarily
achievable by this Proposed RPA/BiOp alone.
Performance standards: Results or benchmarks for accountability for FCRPS actions. They may be
biological, physical, programmatic, or a combination. This Proposed RPA establishes
contingencies to address failure to meet performance standards.
Performance metrics or measures: Units of measurement for assessing performance targets or
performance standards.
All-H Reporting metrics: Broad-level measurements that the Action Agencies may report, but
which are not the exclusive performance responsibility of the FCRPS (e.g., adult trends).

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2.1.2.1 Adult Abundance and Trends (All-H Reporting Metrics)

Adult abundance and trends reflect the most accessible currency in which to evaluate the
progress in region-wide recovery efforts over multiple years. They give an indication of how
both the naturally spawning and hatchery-based portions of a listed species are doing.

Adult trends are also indicators of variability in ocean survival conditions, which can
significantly affect the numbers of adult anadromous fish over multiple years. Because adult
trends are so critical to understanding the progress of listed fish toward recovery, the Action
Agencies will regularly track and report available data on overall adult abundance and trends for
the ESUs. Adult abundance and trends represent an overarching performance target, not just for
the FCRPS, but also for the collective actions by all parties in the Columbia River Basin for the
conservation and recovery of listed fish. Specifically, this overarching performance target is a
positive trend in adult abundance.

Based on examination of adult abundance and trends, including NMFS’ expected updates of
ESU status in 2009 and 2014, the Action Agencies may determine that some ESUs and
populations require greater or less immediate attention as implementation of the Proposed RPA
is advanced, particularly related to more “local” mitigation such as habitat improvements and
hatchery reforms. This approach makes best use of available resources for those ESUs in
greatest need.

2.1.2.2 Hydrosystem Performance

The primary benchmark for assessing progress of FCRPS actions for conservation of ESA-listed
fish is adult and juvenile survival through the hydrosystem. The Action Agencies have the
greatest influence on this outcome, and it is less confounded by actions of others. Hydrosystem
performance will be tracked and evaluated through adult reach survival and juvenile dam
survival performance standards, and through a juvenile system survival performance target.

Adult Survival Standards


For adult fish, the Action Agencies have largely achieved or exceeded the performance standards
identified in the 2000 BiOp (Ruff 2004). Because the Action Agencies do not expect the
Proposed RPA to reduce adult upstream passage survival, they will continue that operation and
monitor adult passage. The intent of this standard is to demonstrate that current high levels of
adult survival are being maintained.

The performance standard for Snake River Chinook salmon ESUs (including Spring/Summer
and Fall), will be based on PIT-tag detections at Bonneville and Lower Granite dams. Past
estimates have yielded an upstream survival estimate of 90 percent for Snake River Spring
Chinook salmon, 94 percent for Snake River Summer Chinook salmon and 92 percent for Snake

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River Fall Chinook salmon. The Action Agencies propose to use these as estimates as the
standard. For the Upper Columbia Chinook salmon ESU, the standard would be measured from
Bonneville Dam to McNary Dam and would be 92 percent. Adult performance standards are
summarized by ESU in Table 2-1. A more detailed discussion and the methods for calculating
adult performance are located in Attachment B.2.6-2.
 
Table 2-1. Adult Performance Standards
Adult 
ESU  Standard  Reach  Rationale 
Snake River Spring Chinook  90%   Bonn. to Lower  Longest migratory route 
Salmon  Granite 
Snake River Summer Chinook  94%  Bonn. to Lower  Longest migratory route 
Salmon  Granite 
Upper Columbia Spring  92%  Bonn. to McNary  Longest migratory route 
Chinook Salmon 
Snake River Fall Chinook  92%  Bonn. to Lower  Longest migratory route 
Salmon  Granite 
Willamette River Chinook  None  None  Low Encounter Rate 
Salmon 
Lower Columbia River Chinook  None  None  Surrogate of upriver ESU 
Salmon 
Snake River Steelhead  N/A  Bonn. to Lower  Unaccounted harvest leads to 
Granite  uncertainty in calculations 
Upper Columbia River  N/A  Bonn. to McNary  Unaccounted harvest leads to 
Steelhead  uncertainty in calculations 
Mid‐Columbia River Steelhead  N/A  Variable  Unaccounted harvest leads to 
uncertainty in calculations 
Lower Columbia River  None  None  Upriver Steelhead ESU 
Steelhead  surrogate 
Willamette River Steelhead  None  None  Low Encounter Rate 
Snake River Sockeye Salmon  None  None  Uncertainty in data 
Lower Columbia River Coho  None  None  Upriver Chinook ESU surrogate 
Salmon 
Columbia River Chum Salmon  None  None  Low Encounter Rate 

Juvenile Dam Passage Survival Standards


The Action Agencies propose specific performance standards of 96 percent average relative dam
survival for spring migrating fish and 93 percent average relative dam survival for summer
migrating fish, with averaging/tradeoffs allowed between dams. Any survival averaging or
tradeoffs between dams may occur among the Snake River dams or among the lower Columbia
River dams, but not between Snake and Columbia River dams. Definitions and methods for
calculating juvenile performance are located in Attachment B.2.6-2.

One mechanism for adaptive management to improve performance, when necessary, will be the
Configuration and Operation Plans (COP) that the Corps prepares to evaluate and develop
hydrosystem project improvements. The Corps has prepared COPs to lead to improvements

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including surface passage (e.g., RSWs) and other dam passage improvements at each of the
lower Columbia River and Snake River projects. A COP is being/has been developed for each
dam in close coordination with the Region at the technical level. Each COP will recommend the
ultimate configuration and operation for that project.

The COP considers alternatives and performance standards, and several other components as
described in the Draft Snake and Columbia River Surface Passage Strategy prepared by the
Corps in July 2005. Following installation of dam passage improvements, an evaluation will be
conducted to determine the success of the action in meeting the performance standard. If the
standard is not met, the Corps will update the COP coordinated through the Regional Forum to
determine additional potential actions.

Juvenile System Survival Targets


In the biological analyses, the Action Agencies have assessed the expected juvenile system
survival to the Bonneville tailrace under current conditions (2006 hydrosystem configuration and
the operation plan that were identified in the 2004 BiOp) and under the prospective conditions of
our proposed hydrosystem actions through 2017. The Action Agencies propose to use the
relative improvement in direct system survival from the 2004 base level conditions to the 2017
Proposed RPA conditions, as the system survival performance targets. Further explanation is
provided in Appendix B.2.6-2 and tables in Appendix B of the Comprehensive Analysis.

Achievement of Performance Standards


Once the Action Agencies meet adult survival and juvenile dam survival performance standards,
they will move from detailed actions to maintenance of the performance standard, subject to
regular monitoring to ensure continued performance. The choice of tools needed to maintain
performance will be at the discretion of the Action Agencies. The juvenile system survival target
is a longer-term goal that will be used to inform broader lifecycle improvement assessments

2.1.2.3 Predation Management Performance


Management of piscivorous and avian predation of juvenile salmonids is an effective means of
increasing juvenile fish survival (Beamesderfer et al. 1996, Roby et al. 1998, NMFS 2000, Good
et al. 2004). The Action Agencies will pursue focused measures that reduce predation mortality
in the near and long term. These measures will be monitored annually for programmatic-level
standards.

For both piscivorous and avian predation, estimates of juvenile fish survival improvements
associated with the 2007 to 2017 Actions (3.1 percent for Chinook salmon, 4.4 percent for
steelhead, and 1.7 percent for fall Chinook salmon) will serve as long-term performance targets.
Additional performance metrics that will be reported and included into modeling assessments
will include monitoring results on predator exploitation rates and changes in estimated annual
predation rates. As described above for juvenile system survival measures, comprehensive
evaluations using modeling will take into account any improvements in predation management

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over the 2004 BiOp baseline condition (i.e., current survival benefits associated with ongoing
predation control).

Research and monitoring results on predation will continue to be incorporated into these juvenile
survival analyses and used to evaluate progress and achievement of expected survival
improvements from predation actions.

2.1.2.4 Tributary and Estuary Habitat Performance


For the Tributary and Estuary Habitat Actions, the Action Agencies estimated survival and
productivity benefits using methods developed and discussed in the Habitat and Estuary
Workgroups. This approach, although not as precise as preferred, applies the best available
scientific information to estimate benefits from habitat actions. The performance targets and
standards derive from this approach.

Tributary Habitat
Benefits for Tributary Habitat Actions were estimated for individual populations and also were
used in the biological analyses for the FCRPS BA. These estimated benefits, in the form of
changes in habitat quality linked to limiting factors, provide the performance targets to be
achieved by 2017 for individual populations. Performance standards will be initially based on
annual progress reports of specific habitat projects that were identified for 2007 to 2009
implementation. Subsequent performance standards will be based on specific projects and
actions identified in 3-year cycles from 2010 to 2017. Those projects will be selected from the
menu of actions compiled in the Remand Collaboration Process in coordination with Council and
recovery planning processes. Performance metrics such as cubic feet per second of streamflow
improvement, miles of access restored to spawning and rearing habitat, diversions screened,
acres of riparian habitat protected or enhanced, and miles of channel complexity improvement
will be compiled and reported on an annual basis.

RM&E will be used to confirm and improve the understanding of the relationships among
different habitat actions, environmental improvements, and survival and productivity
improvements. As this information is developed, it will be considered in the selection and the
priorities of projects for 2010 to 2017 to meet the habitat quality improvement targets.

Estuary Habitat 
Biological benefits for Estuary Habitat Actions that will be implemented by the Action Agencies
from 2007 to 2017 have been estimated for ESUs depending on life history and use of the
estuary, and applied within the biological analysis in the FCRPS BA. Estimates are 5.7 percent
for stream-type fish and 1.9 percent and 5 percent for ocean-type fish. These estimates have
been based on a review of the menu of potential recovery actions developed in the Remand
Collaboration Process, consideration of which projects might be feasible and estimated
improvement of habitat functions linked to key limiting factors, developed in coordination with
local biological input. The estimated improvements in habitat function based on Estuary Habitat
Actions provide the long-term biological performance targets for estuary habitat.

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Programmatic performance will be assessed by monitoring implementation of the specific


projects identified to meet the habitat function targets on a 3-year cycle. Standard habitat
performance measures such as acres of habitat restored will also be compiled on a rolling basis.

RM&E will be used to confirm and improve the understanding of the relationships between
different estuary habitat actions, the environment, and the survival and productivity performance
measures. As this information is developed, it will be considered in the selection and the
priorities of projects for 2010 to 2017 to meet the habitat quality targets.

2.1.2.5 Hatchery Performance Standards


The Action Agencies have developed Hatchery Actions that are expected to reduce extinction
risk and increase abundance and productivity of several ESUs. The Hatchery Actions identify
targeted populations and factors to be improved. Programmatic performance standards will be
used, based on Action Agency commitments and implementation plans, to track implementation.

Although ongoing hatchery RM&E has targeted many of the research needs described in the
Hatchery Action, existing information remains insufficient to quantitatively estimate the effects
of many of the actions proposed in the Hatchery Action, a view confirmed by the
Hatchery/Harvest Workgroup. The expected benefits of the Action were qualitatively assigned
as high, medium, or low value. These benefits represent the performance targets for adaptive
management. Hatchery Action effectiveness research will be used to help confirm and update
the qualitative expectations of these benefits as new information becomes available.

These benefits (performance targets) are relative to the following objectives of the Hatchery
Actions:

Safety-net programs reduce extinction risk for target populations in Snake River Sockeye
Salmon, Snake River Spring/Summer Chinook Salmon, Mid-Columbia River Steelhead,
Lower Columbia River Steelhead, and Columbia River Chum Salmon ESUs.
Conservation hatchery programs increase abundance of target populations in Snake River
Spring/Summer Chinook Salmon, Snake River Fall Chinook Salmon, and Upper
Columbia River Steelhead ESUs, thereby reducing the time to recovery.
High-priority hatchery reform actions (i.e., those needed to address hatchery programs that
are considered major limiting factors by NMFS), result in improved abundance,
productivity, diversity, and/or spatial structure of target populations.
Future implementation of additional hatchery reforms identified through Columbia River
Hatchery Scientific Review Group’s hatchery review process, combined with use of best
management practices (BMPs) at FCRPS hatchery facilities, improve abundance,
productivity, diversity, and/or spatial structure of target populations, depending on the
nature of the reform.

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Hatchery effectiveness monitoring and research will be used in the 2012 and 2015
comprehensive evaluations to test and update the expectations of these benefits and gauge
the progress. As BMPs are adopted for specific hatchery programs, these will provide
additional performance measures that Action Agencies will track and report.

2.1.2.6 Summary of Performance Targets and Standards


Table 2-2 provides a summary of performance targets, standards, monitoring, and reporting
under the performance-based framework.

2.1.2.7 The Role of Cost Effectiveness


Comprehensive performance management is critical to success in achieving ESA goals, but cost-
effectiveness is also a consideration. Consistent with the approach described in the Northwest
Power Act, clearly defined performance standards and biological objectives should be met
through cost-effective alternatives, so that fish receive the greatest benefits possible for the
region’s financial investment.

The Action Agencies will use the adaptive management framework to achieve performance
standards in a cost-effective manner and may seek changes or propose alternative
implementation options if they will achieve equal or better survival improvements at lower cost.
The Action Agencies will continue to engage in regional discussions of any potential or proposed
cost effectiveness initiatives.

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Table 2-2. Outline of Performance Tracking and Reporting


Performance Targets  Performance Standards Monitoring  Reporting 
Fish Population Metrics 
Positive trends in    Context for prioritization of  Comprehensive 
abundance  actions and adaptive  Evaluations [using 
management needs  NMFS Biological 
Review Team (BRT) 
Status Report] 
Hydrosystem 
Percent system survival – by    Juvenile Passage RM&E and  Comprehensive 
ESU or DPS  System Survival Modeling  Evaluations 
Hydrosystem Action  Project Implementation and  Annual Progress 
Programmatic  Compliance Monitoring  Reports and 
Standards  Comprehensive 
Evaluations 
Juvenile Dam Survival  Juvenile Passage Monitoring  Comprehensive 
Standards (96 percent  and Dam Survival Modeling  Evaluations 
average for spring 
migrants and 93 
percent average for 
summer migrants) 
Flow, gas, and temperature  Juvenile and Adult  Environmental Monitoring at  TMT Annual Water 
levels (adjusted to reflect  Hydrosystem  Mainstem Dams  Management Plan 
annual and seasonal water  Environmental and  Reports 
conditions)  Physical Configuration 
Standards 
Adult Hydrosystem  Adult System Survival  Annual Progress 
Survival (no significant  Monitoring  Reports and 
change from current  Comprehensive 
average survival levels)  Evaluations 
Tributary Habitat 
Percent habitat quality    Intensively Monitored  Comprehensive 
improvement – by  Watersheds, Status  Evaluations 
population for actions  Monitoring, and Project‐
implemented from 2007  Level Monitoring informs and 
through 2017  updates modeling 
Tributary Habitat  Project Implementation and  Annual Progress 
Action Programmatic  Compliance Monitoring  Reports and 
Standards (3‐year cycle) Comprehensive 
Evaluations 
Estuary Habitat 
Percent function    Status Monitoring and  Comprehensive 
improvements for Stream  Project‐Level Monitoring  Evaluations 
Type and Ocean Type ESUs  informs and updates 
for actions through 2007  modeling 
and through 2017  Estuary Habitat Action  Project Implementation and  Annual Progress 
Programmatic  Compliance Modeling  Reports and 
Standards  Comprehensive 
Evaluations 
Hatchery 

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Low, Medium or High    Status Monitoring and  Comprehensive 
benefits relative to  Project‐Level Monitoring and  Evaluations 
objectives – by target  updates Lifecycle Modeling 
populating  Hatchery Action  Project Implementation and  Annual Progress 
Programmatic  Compliance Monitoring  Reports and 
Standards; site‐specific  Comprehensive 
BMPs  Evaluations 

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Table 2-2. Outline of Performance Tracking and Reporting (continued)
Performance Targets  Performance Standards Monitoring  Reporting 
Predation 
Percent survival increase for    Predation Action  Comprehensive 
spring and for summer  Effectiveness Research and  Evaluations 
migrants  Status Monitoring 
  Predation Exploitation rates  Comprehensive 
Evaluations 
Predation Action  Project Implementation and  Annual Progress 
Programmatic  Compliance Monitoring  Reports and 
Standards  Comprehensive 
Evaluations 

2.1.3 Planning and Reporting


The Action Agencies will provide a transparent and regular examination of their performance
under the new FCRPS BiOp through implementation and progress reporting, using the
milestones identified in Table 2-3.

Table 2-3. Overview of Planning and Reporting Milestones


Comprehensive 
Year  Implementation Plans  Evaluations  Annual Reports 
Sept. 2009 Report on Jan. 
2009  Dec. 2009 Plan for 2010‐2012   
2008‐Dec. 2008 
Sept. 2010 Report on Jan. 
2010  ‐  ‐ 
2009‐ Dec. 2009 
Sept. 2011 Report on Jan. 
2011  ‐  ‐ 
2010‐Dec. 2010 
June 2012 Report on 
2012  Dec. 2012 Plan for 2013‐2015  ‐ 
info. Thru Dec. 2011 
Sept. 2013 Report on Jan. 
2013  ‐  ‐ 
2012‐Dec. 2012 
Sept. 2014 Report on Jan. 
2014  ‐  ‐ 
2013‐Dec. 2013 
June 2015 Report on 
2015  Dec. 2015 Plan for 2016‐2018  ‐ 
info. Thru Dec. 2014 
Sept. 2016 Report on Jan. 
2016  ‐  ‐ 
2015‐Dec. 2015 
Sept. 2017 Report on Jan. 
2017  ‐  ‐ 
2016‐Dec. 2016 

2.1.3.1 Implementation Plans

Adaptive Management Action 1- Implementation Plans


The Corps, BPA, and Reclamation will submit to NMFS Action Implementation Plans by the
end of December 2009, December 2012, and December 2015 that detail commitments to
implement RPA actions during the subsequent 2-3 years. Specifically, the Action
Implementation Plans will describe the tributary and estuary habitat actions that will be funded
during the 2010 to 2012, 2013 to 2015, and 2016 to 2017 periods. The Action Implementation

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Plans will also detail any changes in Proposed RPA Actions for hydro, predation management,
hatchery, or RM&E from the actions described in the BA for each time period. This information
will assist NMFS in determining if the Proposed RPA is being implemented as identified in this
BA or, conversely, if re-initiation triggers defined in 50 CFR 402.16 have been exceeded.

For the Proposed RPA, the Action Agencies have identified specific details for the first 3 years of the
BiOp term (2007 to 2009). This specific information represents the initial 3-year implementation plan for
the new BiOp. BPA will maintain a BiOp database to provide project- and action-level detail for
planning and reporting purposes. This information will be updated and summarized in subsequent 3-year
implementation plans to be submitted to NMFS in December 2009 for Fiscal Year (FY) 2010 to 2012 (i.e.
October 2010 to September 2012), December 2012 for FY 2013 to 2015, and December 2015 for FY
2016 to 2017 during the life of the BiOp. The December submittal will allow for regional discussion of
the results of the comprehensive evaluations provided in June of that year.

The Action Agencies will coordinate implementation plan with other appropriate regional processes. This
includes coordination related to statutory provisions for the Federal government [BPA/Northwest Power
and Conservation Council (Council)], voluntary coordination among Federal agencies (Federal Caucus),
and coordination with regional processes for Federal/non-Federal engagement [Technical Management
Team (TMT), System Configuration Team (SCT), Pacific Northwest Aquatic Monitoring Partnership
(PNAMP), Northwest Environmental Data (NED) network, and others]. The collaboration described in
the Oversight section (see Section 2.1.4.3) is intended to support continued interaction among the
sovereigns regarding the effectiveness of the Proposed RPA and the need to alter or adjust actions in
response to documented successes or failures.

2.1.3.2 Annual Progress Reporting

Adaptive Management Action 2- Annual Progress Reports


The Corps, BPA, and Reclamation will submit to NMFS Annual Progress Reports in September of all
years except 2012, and 2015. The reports will cover operations for the previous calendar year. These
Annual RPA Progress reports will describe the status of implementing all actions as of the end of the
previous calendar year. For example, the 2009 RPA Progress report will describe the status of RPA
Actions through December 2008. In addition to RPA Action implementation status, the Annual RPA
Progress Reports will describe the status of physical or biological metrics monitoring (as described in the
RM&E). This information will assist NMFS in determining if the RPA is being implemented as
anticipated in this BA or, conversely, if re-initiation triggers defined in 50 CFR 402.16 have been
exceeded.

As noted previously, the Action Agencies will monitor implementation and compliance, or
programmatic performance, for all of the identified action commitments in the Proposed RPA
and as further defined by Implementation Plans in 2009, 2012, and 2015. In addition, the Action
Agencies will track biological and environmental performance metrics such as juvenile and adult
hydrosystem passage through monitoring and annual reports of hydrosystem survival conditions,

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and performance metrics for non-hydrosystem actions. Finally, to provide context for the
performance in aggregate with others’ actions, the Action Agencies will report on adult
abundance for listed ESUs using available information. The results of the progress reports will
inform adjustments in future year actions through adaptive management.

The Action Agencies will prepare annual progress reports and provide them to the RIOG. The
annual reports will document progress on specific performance standards. For example, some
types of actions specify anticipated dates for implementation (e.g., for installation of RSWs).
The Action Agencies consider project milestones as benchmarks for implementation. Annual
reports will identify the status of achievement of these benchmarks.

The Annual Progress Reports will describe the progress on implementation of all of the Actions
in the Proposed RPA, the status and results of the RM&E on juvenile and adult survival
improvements, and adjustments made on specific actions through the Regional Forum within the
reporting year. The Annual Progress Reports are not intended to assess the overall re-assessment
of the Proposed RPA to compare with the estimated survival improvements included in the
Comprehensive Analysis. This overall analysis is addressed in the following Comprehensive
Evaluations.

2.1.3.3 Comprehensive Evaluations

Adaptive Management Action 3­ Comprehensive RPA Evaluations 
 
The Corps, BPA, and Reclamation will submit to NMFS Comprehensive Evaluations of multi-
year implementation activities by the end of June 2012, and June 2015. The Comprehensive
Evaluations will review all implementation activities through the end of the previous calendar
year (as would be covered in the Annual Progress Report) and compares them to scheduled
completion dates as identified in the BA or modified in the Implementation Plans in 2009, 2012,
and 2015. The Comprehensive Evaluations will also describe the status of the physical and
biological factors identified in this BA, and compare these with the expectations in the survival
improvements identified in the Comprehensive Analysis. The Comprehensive Evaluation will
include a discussion of Action Agencies plan to address any shortcomings of current estimated
survival improvements as compared to the original survival estimates identified in the
Comprehensive Analysis referenced in this BA. This information will assist NMFS in
determining if the RPA is being implemented as anticipated in this BA or, conversely, if re-
initiation triggers defined in 50 CFR 402.16 have been exceeded.

Comprehensive Evaluations are a tool to ensure that the Action Agencies and regional parties step back
and take a comprehensive and cumulative check on implementation of FCRPS actions. This allows the
opportunity to both build on successes and make mid-course corrections where necessary.
Comprehensive Evaluations are also a juncture to examine the broader context of recovery, looking at the
status of listed fish, actions by others across the salmon lifecycle, and environmental or other changes.

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The Action Agencies will prepare Comprehensive Evaluations in 2012 and 2015. The evaluations will
include a cumulative review of both progress in implementation and updated information on ESU status
and trends by the NMFS BRT (now scheduled for 2009 and 2012).

The evaluations will describe progress on programmatic (compliance) standards to determine whether the
cumulative implemented actions remain consistent with the objectives identified for the new BiOp and an
assessment of progress toward biological/environmental performance standards and targets.

Regarding programmatic standards, the evaluations will summarize the cumulative accomplishments; and
propose corrective actions where the Proposed RPA may be off track programmatically.

Regarding biological performance standards and targets, progress toward the performance standards and
targets for hydro, habitat, hatcheries and predation management will be reported on in the Comprehensive
Evaluations, and used to inform adaptive management decisions. This report will also address any
significant new information from RM&E results.

The results of the evaluations will be used to guide adaptive management of the Proposed RPA and to
ensure that Action Agencies are making adequate progress on achieving the strategies and performance
standards, as well as to inform the 2012 to 2015 implementation plan. If it is determined that course
changes are necessary in order to achieve expected performance, the Action Agencies will discuss those
changes with NMFS and the Collaboration parties prior to implementation.

Coordination with the RIOG in connection with the Comprehensive Evaluations will include
consideration of adaptive management and contingencies (described in more detail below). The RIOG
may utilize a diagnostic performance framework described in Figure 2-2 to assess FCRPS and broader
regional progress for listed fish.

2.1.3.4 Reporting Clear Signals for Adaptive Management


As part of the 2012 and 2015 Comprehensive Evaluations, the Action Agencies will use the following
Green-Yellow-Red signals to gauge their success, challenges, and failures:

Green—Standard Met or Exceeded: If performance tracking shows that compliance or performance


standards for a particular strategy have been met, the strategy will be maintained. If performance tracking
shows that compliance or anticipated performance standards for a particular strategy has been exceeded,
the strategies may also be adjusted.

Yellow—Obstacles or Delays in Meeting Standards: If performance tracking shows that issues are
hindering or delaying achievement of performance standards, modifications of approach or schedule may
be necessary to get back on track.

Red—Compliance/Standard Not Met: If performance tracking shows a failure to achieve compliance


or performance standards for a particular strategy, a response will be necessary. This response may

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involve modification of the specific strategy not meeting expectations, or implementation of other cost-
effective strategies. Depending on degree, more aggressive contingencies might be pursued. In the
alternative, re-consultation might be necessary.

Red and yellow signals will be discussed with the RIOG.

2.1.4 Contingencies
Contingencies are alternative actions, plans, or approaches for addressing failure to meet performance
standards, in other words a “Red” signal as described above.

2.1.4.1 Specific Contingencies


The Action Agencies have committed to explore specific contingencies they have been able to identify
through coordination with States and Tribes, in advance of knowing whether they will actually need to be
deployed:
For dam modifications, COPs include specific Phase 2 actions to be pursued in the event initial
actions do not achieve performance standards for juvenile dam passage (see Appendix B.2.1).
For Snake River Sockeye Salmon safety-net production, the Action Agencies are investigating
alternatives to the current expansion program, including lower river production and Wallowa
Lake production, in the event that the expansion effort is not successful.
For tributary and estuary habitat, the failure of an individual project to be implemented would lead to
a replacement project of equal or greater biological value being implemented.

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Tier 1
ESU Trigger Analysis

Upper Columbia River Mid-Columbia River Snake River Lower Columbia River
Populations Populations Populations Populations

Technical Assessment
Greater than 30%-50%
of an ESU’s populations
have decreasing abundance trend
Return-per-spawner, Lambda?

If YES, then
Trigger Tier 2
Diagnosis

Tier 2
All H Diagnosis

Environmental
and Ocean Conditions

Hydro Predation Hatchery Habitat Harvest


Relative to FCRPS Relative to Status Relative to Hatchery Relative to FCRPS Relative to 2004
Performance Targets of Predation Policy and BMP Implementation and Other Agency Targets Harvest Levels

Technical Assessment

Policy Recommendations

Resolution

Action

Figure 2-2. Performance Diagnosis Framework

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Other Contingencies
The Action Agencies acknowledge the need to consider other contingencies in the event that actions
under this new BiOp do not prove successful, even after adaptive management. As a result, the Action
Agencies commit to the following approach in coordination with States and Tribes:

In the course of the 2012 and the 2015 Comprehensive Evaluations, the Action Agencies will include
the All-H diagnosis described in Figure 2-2.
Tier 1 of this approach includes consideration of the status of abundance, trends, and productivity of
the ESUs. Tier 2 includes consideration of whether the actions of the FCRPS are on track to meet
All-H specific performance targets by 2017, as well as progress through broader regional actions.
Contingencies under this section may be advisable if ESA-listed fish are not making expected progress
toward recovery goals and the All-H diagnosis confirms that the FCRPS is a significant factor.

Based on this review, the Action Agencies will coordinate with States and Tribes using the RIOG process
to identify, evaluate, and develop proposed schedules for contingent actions to be implemented after
2017. Contingent actions will:

Address the appropriate limiting factors identified in the All-H diagnostic analysis with a high
likelihood of enhancing fish survival;
Consider both biological effectiveness and cost effectiveness; and
Ensure the RIOG consideration is guided by the All-H diagnosis process presented in Figure 2-2.
Once contingencies are identified, the Action Agencies will evaluate them for biological, economic,
technical, and institutional feasibility. If feasible, the Action Agencies will proceed with pre-planning,
design, and funding/authorization as appropriate, so that the actions can be implemented on schedule.

2.1.4.3 Collaboration and Oversight of Implementation


The Federal agencies, States, and Tribes would like to continue to collaborate and oversee
implementation of recovery actions across the salmon and steelhead lifecycle. Acknowledging the value
gained from the Remand Collaboration Policy Work Group, the Action Agencies will support a RIOG to
oversee the implementation of the FCRPS BiOp, in aggregate with the conservation and recovery actions
of others.

Like the Policy Work Group, the Action Agencies recommend that the RIOG consist of senior policy
representatives, representing Federal, State, and Tribal sovereigns, appointed by:

Federal executives to represent the following Federal agencies: NMFS, BPA, Reclamation, the
Corps, and the U.S. Fish and Wildlife Service (USFWS);
The Governors representing the States of Montana, Idaho, Washington, and Oregon; and
Tribal governments appointed by Tribal councils.

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A memorandum of agreement (MOA) to memorialize the RIOG would be desirable to provide operating
principles and protocols. The RIOG may form subcommittees to oversee the hydrosystem and predation
management, estuary and tributary habitat, hatchery, harvest, and RM&E.

Responsibilities of the RIOG would include:

Review implementation of FCRPS ESA actions and results;


Review implementation of lifecycle recovery actions by others, including States and Tribes;
Discuss and attempt to resolve salmon and steelhead issues in ways that minimize or result in no
adverse impact on other Columbia River Basin fish and wildlife;
Clarify, address, and narrow policy issues and differences relating to implementation;
Promote coordinated funding and partnerships;
Emphasize “on-the ground” actions that meet or exceed legal requirements and provide accountability
for results in a biologically effective and cost-efficient manner;
Coordinate regarding the annual and comprehensive progress reports prepared by the Action
Agencies, including adaptive management decisions and consideration of contingencies;
Hold an annual meeting to review how well actions by the FCRPS and others have been implemented
and the success in meeting the appropriate performance standards; and
Coordinate implementation and oversight of the Proposed RPA with other regional processes [e.g.,
Council; Regional Forum; U.S. v. Oregon; NMFS recovery process] to minimize duplication and
promote efficiencies).
In year 10 (2017), the RIOG will consider the effectiveness of the BiOp. It will also consider whether a
new RPA is desirable, or whether an extension of the current Proposed RPA/BiOp would be appropriate,
taking into account that biological benefits of FCRPS actions from 2007 to 2017 will continue to be
expressed in adult returns and other measures in the next decade.

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Appendix 3: Proposed Estuary MOA with the State of Washington

Through funds provided by BPA, Washington Department of Fish and Wildlife (WDFW) is a


cost-sharing partner with the Corps under its Section 536 authority to implement ecosystem
restoration projects that support salmonids. This new partnership will produce major projects to
be implemented in the out-years between 2013 and 2017; however, some of these projects will
likely be implemented in the 2010 – 2012 timeframe.

Project Selection and Benefits

In identifying the projects for inclusion in the Estuary MOA, the WDFW identified a suite of
potential projects, which were later refined to the 21 listed in Attachment 1: Estuary MOA
Projects. Projects were then evaluated based upon a scoring process that was consistent with the
method used in the 2008 FCRPS BiOp.

A potential benefit score was assigned by WDFW for each of the 21 projects. The scores ranged
from a high of 5 and a low of 2. The average potential benefit score for the projects was between
3 and 4 points.

The Hump - Fisher Island Restoration is an example of project that was evaluated before
inclusion in the Estuary MOA. The 337 acre site is located in the mainstem downstream of
Longview. Hump – Fisher Island is co-owned by the Washington Department of Fish & Wildlife
and the Department of Natural Resources. The site contains important juvenile salmonid rearing
habitat in a complex of channels and mosaic of tidal and upland wetlands adjacent to Fisher
Slough (see Figure 1 existing habitat arrow). The proposed project at Hump – Fisher Island is to
enhance the existing embayment wetlands to improve hydrology and tidal and upland wetland
habitat complexity within and around the existing embayment.

FIGURE 1
Hump – Fisher Island Restoration, Columbia River Estuary

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The Hump – Fisher Restoration project concept was developed by the WDFW and the Army
Corps of Engineers – Portland District. Hump – Fisher received a high score (4) for certainty of
success and a very high score (5) for potential benefit.

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Attachment 1: Estuary Habitat WA MOA projects  

Project Description

Abernathy Tidal IMW Treatment Plan identifies two projects in the tidal reaches of Abernathy Cr
Restoration (1A and 2A). The projects would enhance 500' of off channel habitat and 2200'
of mainstem through ELJ, LWD riparian enhancement and floodplain
reconnection. Conceptual designs have been completed for these projects.

Germany Tidal IMW Treatment Plan identifies two projects in the tidal reaches of Germany Cr
Restoration (2A, 2B, 2C). The projects would enhance 600' of mainstem habitat, stabilize
350' of eroding bank, and enhance 7 acres of riparian area. Conceptual
designs have been completed for these projects.

Lower Kalama Tidal LCFEG recently completed a Lower Kalama Offchannel Habitat Assessment
Restoration that identified five projects in the tidal reaches of the Kalama. Three of these
scored in the fundable range when subjected to the LCFRB criteria (KRL 0.1,
KRR 0.7, and KRL 1.4). These projects would create or enhance existing off-
channel habitat. Conceptual designs and cost estimates have been completed
for KRR 0.7.

Acquisition of Acquire 2.29 acre property located within the Wood's Landing Columbia River
Chaney chum salmon spawning site. It has old growth cedar forest and has a segment
Parcel at Wood's of an essential habitat, Erskine's Creek, that supports the chum spawning
Landing and springs to the east - in front of a parcel currently owned by Columbia Land
Restoration Trust. The parcel is crucial both for its microclimate/hydrological support for the
of Chum Salmon habitat as a whole, but also for its stream segment and riparian values. This
Spawning Tributary parcel contains the last unprotected habitat for the genetically distinct "I-205
population" of chum salmon. If protected, restoration efforts could bring salmon
back up Erskine's Creek, where they historically spawned. Site also has Native
American cultural values and functioning riverine wildlife community.

Ft Columbia Tidal Replace culvert to allow reconnection of salt water tidal wetland and provide
Reconnection fish passage into wetland.

Fish - Hump Island Modify dredge spoils to improve flushing flows within the Hump - Fisher Island
Restoration embayment; plant additional riparian vegetation (Hump Island); revegetate
meadow on Fish Island (5-10 acres); remove piling/add LWD.

Paradise Point Restore and enhance approximately 1000 lineal feet of side channel habitats
Wetland within a tidally influenced forested/emergent/scrub-shrub wetland complex;
Enhancement construct mainstem LWD structures juvenile rearing and adult holding habitat
during low tributary flows, low Columbia River flows, and periods of low tide.

Austin Point LWD Restore riparian habitat and construct ELJs on the right bank of the North Fork
Complexing Lewis River at the confluence with the Columbia River, to provide instream
cover and complexity, and cold-water refuge for outmigrating salmonids.

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Project Description

Elochoman Tidal CLT was funded to purchase 200 acres of high quality intertidal forested
Restoration riparian and wetland habitat along the Elochoman River and Elochoman
Slough. The property is adjacent to the JBH Refuge and 210 acres already
owned by CLT on Nelson Creek. The property includes over 7000' of off
channel habitat. Potential restoration activities on the property include culvert
removal, tidegate removal, road abandonment, invasive treatment, and riparian
enhancement.
Willow Grove Tidal CLT has recently purchased over 200 acres of intertidal wetland and off-
Restoration channel habitat along the Columbia River and Coal Creek. Potential restoration
activities include restoration of native wetland communities, invasive control,
and enhancing the hydrologic connection of the site to the mainstem, possibly
via Fisher slough.
Shillapoo Wildlife Construct setback levees at Shillapoo Wildilfe Area and Post Office Lake to
Area/Post Office reconnect historic Columbia River floodplain (Note: Further discussions with
Lake WDFW, COE and USFWS needed to determine feasibility and scope and scale
Setback Levees of project).
Duncan Creek Fish Modify existing dam and outlet structure and construct backwater elevation
Passage control berm/roughened channel to improve steelhead, coho and chum
Restoration passage during Columbia River low flow periods.

Pile Dike Removal Remove pile dike structures based on existing and ongoing assessment work,
to increase availability and access to side channel and wetland habitats, and
reduce adverse changes on sediment and nutrient dynamics.

Lower Washougal Construct ELJs on the Lower Washougal river delta at the Columbia River
Delta confluence to provide instream cover and complexity, and cold-water refuge for
Habitat Complexing outmigrating juvenile salmonids and migrating adults.

Lower Kalama Delta Construct ELJs on the Lower Kalama river delta at the Columbia River
Habitat Complexing confluence to provide instream cover, complexity and holding; coldwater refuge
for outmigrating juvenile salmonids and migrating adults; and to reduce
predation by pinnipeds during low flow conditions.

Chinook River Project would include additional acquisition of estuarine wetland contiguous
Estuary with previous acquisitions. The project would re-establish the hydrologic link
Restoration between the river channel and the floodplain over the entire acquisition area,
including the removal of tidegates at the mouth of the Chinook, and setback
levee construction.

Lower Cowlitz Tidal The Lower Cowlitz River and Floodplain Habitat Restoration Project Siting and
Restoration Design report identifies 6 potential projects in the tidal reaches of the Lower
Cowlitz and Coweeman Rivers (1 0L 0 5R C3 5R C4 0B 3 0L 4 5R). These
projects include removal of dredge material, riparian enhancement, side
channel creation and/or enhancement, riprap removal, and LWD placement.
(Note: when scored by LCFRB, these projects did not all fall within the fundable
range, but out-of-basin/estuary benefits were not included at that time).
Lewis River A large parcel of land on the lower Lewis River will be purchased by Clark
Restoration County in 2010. This property has potential for future side channel and
floodplain reconnection.

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Project Description

Port of Kalama Restore and enhance tidal slough channel habitats at the Port of Kalama's
Offchannel Northport mitigation site; remove or modify pile structures.
Wetland
Enhancement

Cottonwood/Howard Reconnect and construct backwater channels.


Island Tidal Channel
Connection

Barlowe Point Contour beach profile through beach nourishment to reduce fish stranding
Beach (Note: should be associated with subsequent effectiveness monitoring).
Nourishment
  
Attachment 2

<placeholder for map of the 21 estuary MOA projects>

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Appendix 4: Key Elements of the Life -cycle Model

The 2008 BiOp used a combination of life-cycle modeling and passage modeling (COMPASS)
for evaluation of impacts and All H actions. These analyses provided state of the art evaluations
based on the best available scientific information on fish status, hydropower effects, mitigation
actions, and ocean/climate scenarios to estimate how changes in life-stage specific survival affect
long term viability metrics (productivity, mean abundance and probability of quasi-extinction).

The Action Agencies and NOAA will be jointly funding enhanced, data-driven lifecycle
modeling for contingencies, building off of the current BiOp modeling. Based on newly
available and emerging data, the existing models can be expanded further in order to explicitly
evaluate a variety of other factors, described below. The primary purpose of this revision is to
allow the federal agencies to better evaluate short and long term contingency actions, including
dam breaching.

These model revisions will be developed through regional collaboration and go through an
independent science review process and review by the Northwest Power and Conservation
Council. The goal of the effort would be to develop models that are well grounded in empirical
data and the latest research, and to identify data gaps that are a high priority for regional R,M&E
coordination.

As part of this effort, the Interior Columbia Technical Recovery Teams (ICTRT) stochastic life-
cycle models will be updated to incorporate most recent population data (abundance of adults
and juveniles, stage-specific survival, etc.) and expand the number of populations considered
where possible (Snake River spring/summer Chinook; Snake River steelhead; Upper Columbia
spring Chinook; and Middle Columbia steelhead). Data availability will be explored and data-
supported models will be developed for populations within ESUs that have not been modeled to
date (Snake River fall Chinook; Snake River sockeye; and Upper Columbia steelhead). Second,
the current models will be enhanced to address the following:

1. Climate – Sensitivity of ESUs. Analyzing the potential effects of climate change is a key
element to the Adaptive Management Plan of the BiOp. Ultimately, as part of the spatially
explicit modeling discussed below, it would be helpful to identify which ESUs are most
sensitive to climate variability and which restoration actions are most resilient to climate
change. Results will be used to guide BiOp implementation decisions and determinations
regarding cost effectiveness.

2. Climate – Adaptive Management. The effects of climate variability and change will be
evaluated by incorporating observed climate conditions, such as freshwater conditions (e.g.,
snow pack), mainstem conditions (flow and temperature), and ocean conditions on survival
through the life cycle. Longer term effects of climate will be modeled based on model studies

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of biological responses to projected changes in freshwater and marine climate conditions from
various scenarios (IPCC, NOAA Fisheries, UW-CIG). Outputs will be considered
qualitatively in the context of the running 4-year averages in adult escapement “triggers” in
the Adaptive Management Plan and used to further judge trend patterns.

3. Hatchery Effects. A critical uncertainty is the effect of hatchery spawners on the success of
wild spawners, the impact of hatchery releases on wild populations, and density-dependent
effects of hatchery production on the productivity of wild fish. Each of these issues has been
evaluated to some degree, and the effects of hatcheries on populations will be modeled under
various ocean productivity regimes and climate scenarios. This will provide a sensitivity
analysis of the potential role of hatchery production in recovery and to possibly identify
alternative production release timing strategies that increase survival of wild fish and hatchery
fish.

4. Habitat Actions & Monitoring. The potential effects of habitat improvements on population
viability metrics will be incorporated into the life cycle models as the information becomes
available from IMWs and RM&E activities. Results of analyses of key assumptions on how
fish populations respond to habitat alterations will be used to guide future RM&E and IMW
activities, and used qualitatively as part of the 2-year early warning and 4-year trigger
components of the Adaptive Management Plan.

5. Spatially Explicit Modeling. As stated above, the number of populations and ESUs
considered in Leslie matrix models, will be expanded as available data allow. This
comparative approach will allow better identification of similarities and differences in how
populations respond to factors such as variability in freshwater and marine productivity,
differing levels of habitat restoration across watersheds, and influences of total hatchery
composition on the wild component of the ESU.

6. Inter-species Interactions. Available data will be evaluated on the effects of other native
species (competitors, piscivorous and avian predators, and prey), invasive species
(competitors, predators, or pathogens), or other salmon populations (i.e., tradeoffs among
ESUs) on target salmon populations. If sufficient data exist, the potential effects through food
web or bioenergetics models, or other analyses, will be evaluated to estimate the magnitude of
their impact.

7. John Day MOP <do we need a bullet for this one, or delete?>

8. Dam Breach Module

Gayle will rework this sentence: During the Administration’s recent independent science


review, the scientists noted uncertainty about the short-term biological effects that may impede
the long-term effects of dam breaching. The new life-cycle model will use existing information
as well as new information being developed for evaluating effects of sediment, contaminants,

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construction, trap and haul, habitat changes, and changes in hatchery production to provide a
comprehensive assessment.

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Appendix 5: Development of Severe Decline and Early


Warning Triggers

Introduction

As part of the administration’s review of the 2008 FCRPS BiOp (BiOp), scientists suggested that Comment [K1]: Pls seek legal review 
on whether this wording regarding the 
a refinement of the BiOp’s adaptive management and contingency planning processes could scientists is appropriate 
provide additional assurance that the RPA is implemented in a precautionary fashion through Deleted: surety
2017. Specifically, the scientists suggested that additional triggers be developed that would be Deleted: BiOp
sensitive to 1) unexpected declines in adult abundance and 2) environmental disasters or Deleted: 8
environmental degradation (either biological or environmental) in combination with preliminary
abundance indicators. They further advised suggested that these triggers should be based on Comment [K2]: shouldn't we avoid 
this word?  
simple metrics that are readily available.

In response to these recommendations the administration has decided to develop and implement
triggers that, if tripped, would invoke additional actions. These triggers represent refinements of Deleted: a system of

the adaptive management and contingency planning processes in the 2007 Biological
Assessment and RPA . The first type of trigger – Severe Decline –will precipitate immediate Deleted: BiOp

actions. The principle underlying the Severe Decline trigger is that the conditions represented by
this trigger would be significant deviations from the biological expectations in the 2008 BiOp
and, if they were to persist despite the AMIP’s short and long term contingency actions, could
result in a reinitiation of consultation. The second type of trigger – Early Warning - will serve as
an alert to focus more attention on potentially vulnerable species1. These triggers should rapidly Deleted: or Major Population Groups
(MPGs) within the species
detect when a species falls to a dangerously low level and be easily interpretable and transparent.
Deleted: or MPG (or population)
In addition, the triggers should be developed to avoid erroneous conclusions.
Comment [K3]: This sentence is not 
The initial Severe Decline triggers are based on four-year rolling averages of adult abundances of consistent with our chart (Figure 2).   
naturally produced fish. Refined triggers based on trends will be developed in 2010 in Comment [K4]: This is not consistent 
coordination with the Regional Implementation and Oversight Group (RIOG). Early Warning w our chart.  We talk about short term 
rapid responses.  
Triggers, to be fully developed in 2010 in coordination with the RIOG, would rely on adult
Deleted: Once tripped, the responsive
abundance and trends, but also utilize information relating to environmental conditions, actions would be implemented and
significant catastrophic events, and potentially on juvenile parameters (e.g., abundance and body remain in effect until the precipitating
condition has passed
size).
Deleted: .¶
Deleted: Additional
It is important to remember that triggering the proposed Severe Decline or Early Warning
Triggers within the term of the BiOp is not an expected or even likely outcome. Indeed, under
the BiOp the abundance of the species on average are expected to increase over time. However,
                                                            
1
Salmon species are designates as Evolutionarily Significant Units (ESUs) and steelhead are designated as Distinct
Population Segments (DPSs); however, for simplicity’s sake, all of the listed ESUs or DPSs will be referred to in
this document as species.

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inclusion of these triggers as part of the RPA's adaptive management and contingency Deleted: BiOp

implementation processes provides additional assurances that the RPA is implemented in a Deleted: BiOp

precautionary fashion from the perspective of the ESA-listed salmon and steelhead species.

Adult Triggers

A consideration in the development of triggers is how quickly the data will become available and
the magnitude of sampling error associated with the data. In general, the most quickly available
data that have relatively low sampling error are counts of adults, which are typically enumerated Deleted: is

at dams. Unfortunately, these data can inform decisions at the species scale, but they do not
typically discern among MPGs or populations. Population-level data have primarily been based
on redd counts, which are less timely and more prone to sampling error. Accordingly, one of the
main activities associated with the early warning triggers is to provide additional resources to
monitor more rigorously and quickly at the MPG and population level.

It will be difficult to monitor the status of MPGs, which are amalgamations of populations, of
which only some are monitored. There is currently no mechanism in place to define which
populations should be monitored to represent an MPG. Accordingly we do not present here a
mechanism to define triggers at the MPG level. However, we recommend that establishing
monitoring protocols at the MPG level should be a high priority for RME. Deleted: Once these protocols are
established, we can apply similar
The triggers described below are based on adult abundance and trend estimates. One techniques to MPGs.¶
complication with this type of data is that salmon abundances are notorious for being highly
variable (Paulsen et al. 2007), and thus short-term trends can be difficult to discern. Because of
this, our abundance-based triggers are derived from four-year running averages, which smooth
abundance time series (Holmes 2001). The choice of a four-year running average has several
justifications and precedents. First, it approximately corresponds to the generation time of most
salmon speciess in the interior Columbia River basin, and the International Union for
Conservation of Nature (IUCN) recommends examining population declines over a time period
representing one generation (Mace et al. 2008). Furthermore, the ICTRT risk assessments
incorporated a quasi extinction threshold expressed in terms of a 4-year sum of abundance
(ICTRT and Zabel 2008).

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Severe Decline Trigger for Chinook Salmon and Steelhead

The purpose of the Severe Decline Trigger is to detect unexpected and severe declines in the
abundance of listed species2 so that rapid response actions can be implemented in a timely
fashion to minimize or mitigate for an unforeseen downturn. Many salmon and steelhead
populations experienced extremely low abundances in the 1980s and 1990s, and the triggers are
designed to help head off future declines to these levels. The interim Severe Decline Trigger is
based on recent average abundance estimates of naturally produced fish at the species level.
Triggers based on a combination of abundance and trend will be developed in 2010 in
coordination with the RIOG. A combination trigger is desirable because salmon populations
exhibit a significant amount of variability, and thus large increases in abundance are typically
followed by declines, which can be heightened by density-dependent processes. By combining a
trend and abundance metric, the triggers will not be tripped in cases where declines have
occurred, but the population or species is still at a relatively high abundance level.

Information is sufficient to suggest critical levels for the abundance component of the Severe
Decline Trigger for Chinook salmon and steelhead,3 based on frequencies of returns at various
abundance levels observed in historic time series. However, additional analysis is necessary
before suggesting specific trigger points for trend estimates, so only limited examples of
potential trend-based trigger points are described at this time. We anticipate that, for both the
abundance and trend components of the Severe Decline Trigger, additional analyses will be
performed and, following review of new information and discussions with co-managers, the
interim Severe Decline Trigger may be modified.

Short-term population abundance will be measured as a four-year running average. Short-term


trend will be measured with a metric such as the geometric mean of four consecutive years of
relative abundance, where relative abundance is defined as the abundance in year t divided by the
abundance in year t-1. The relative abundance metric has advantages for representing trend,
compared to alternatives such as “four years in a row of decline,” because it protects against
strings of declines interrupted by slight upturns that would mask the overall decline.

The trend and abundance metrics estimated during implementation of the RPA will be compared Deleted: BiOp

to the distribution of these metrics represented by the historic data. In this way, the current

                                                            
2
Species-level (i.e., ESU or DPS) adult abundance information is the most readily available information at present - Deleted: Future refinements of the
excepting Mid-Columbia steelhead for which the Yakima River MPG data is most readily available. Severe Decline trigger could potentially
be extended to the Major Population
3 Group (MPG) or the population level.
The administration does not propose any triggers for Snake River Sockeye salmon at this time. This species, after
falling to extremely low levels in the early 1990s, is effectively managed under ongoing contingency actions at the
present time. The contingency actions include continuation of the safety net hatchery program; further expansion of
the sockeye program (up to 1 million fish released as smolts), investigation the feasibility of transporting adults from
Lower Granite Dam to Sawtooth Valley lakes or artificial production facilities; and investigation of highly variable
juvenile mortality rates between Stanley Basin and Lower Granite Dam.

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year’s value can be compared to the historic distribution to determine the proportion of historic
years that the current value equals or exceeds, and the triggers will be based on these exceedence
proportions.

Abundance Component of the Severe Decline Trigger

A quantitative description of the Unexpected Sever Decline Trigger was developed, based on the
following steps:

Step 1: Identify Available Data. For species level data, the proposed approach applies data (the
estimated number of naturally produced adult Chinook Salmon4 and steelhead passing a specific
dam) generated by state and tribal co-managers for use in US v. Oregon Technical Advisory
Committee (TAC) run reconstructions. Counts at Lower Granite Dam are used for Snake River
speciess, counts at Priest Rapids or Rock Island dams are used for Upper Columbia River
speciess and counts at Prosser Dam are used for the Yakima River MPG of Mid-Columbia River
steelhead.5 The available data varies by species within the 1975 to 2008 time frame. Where
estimates of naturally produced adult returns at the species level are not readily and publicly
available, we will work with fisheries managers to develop protocols for the regular production
and dissemination of this information.

Step 2: Establish Distributions of Historical Abundances During the Time Periods Considered
by the BiOp. The approach uses four-year rolling averages of abundances. Based on the
historical period evaluated in the BiOp (approximately 1980 to present), the observed four-year
rolling averages were sorted from high to low and plotted to create exceedence curves
(cumulative density functions). These depict the percent of years in the data set in which the
four-year rolling average was greater than a particular level. See Figure 1 for Chinook salmon
species abundances and Figure 2 for steelhead species abundances.

Step 3: Identify Abundance Levels That Were Not Expected in the BiOp. An examination of the
resultant exceedence curves for Chinook salmon species abundances (Figure 1) indicate that, of
the observed four-year average abundances, about 15-25% are relatively high, about 5-15% are
relatively low, and the remainder are close to average, showing relatively little variation. The
pattern is less clear for steelhead species abundances, whose distributions are more continuous
(Figure 2).

                                                            
4
Chinook “Jacks” are excluded from this data as they are predominantly small males which return to spawn after
spending only a single year in the ocean and generally represent a minor contribution to the viability of a population.
5
Mid Columbia River steelhead populations pass 1-4 mainstem dams and cannot be distinguished at those dams
from other listed species traveling further upstream. Prosser Dam is an adult counting site on the Yakima River that
does provide a census of adults in this MPG. We acknowledge that the Yakima River MPG is a single MPG and
Deleted: In addition to the Yakima
may or may not be representative of the DPS as a whole and therefore this trigger will initiate a rapid review to River MPG, it may be possible to develop
determine whether the problem is limited to the MPG or represents a DPS-wide decline. MPG level indices for other MPGs in the
relatively near future.

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Step 4: Specify the Triggers. For average abundance, we propose that the 90th percentile (dashed
vertical line on Figures 1 and 2) be used as the trigger for implementing Rapid Response Actions
(see Contingency Planning and RM&E Document); and the 80th percentile (dotted vertical line
on Figures 1 and 2) be used as an Early Warning trigger that would engage closer examination
and potential readying of Rapid Response actions for more rapid implementation if the species(s)
in question continue to decline.

The 90th percentile exceedence level of abundance was selected as a threshold level because this
is a level below which mean four-year abundances for naturally produced Chinook salmon
dropped rapidly (Figure 1). This level represents a marked departure from median abundance
levels (especially for Chinook salmon), but is also somewhat above the lowest observed four-
year period for both naturally produced Chinook salmon and steelhead (the 1990 levels that led
to ESA listings). While falling to these levels is a cause for concern, they are precautionary in
that they represent species abundance that is at least 3-4 times higher than the abundance if all
populations dropped to the 50 fish quasi-extinction threshold.

As an additional precaution, abundance at the 80th percentile will serve as an Early Warning
trigger requiring closer examination of the available data and the readying of Rapid Response
actions for more rapid implementation if the species(s) in question continue to decline.

Table 1 summarizes the four-year average abundance levels of naturally produced fish
corresponding (closest value or average of two nearest values rounded to the nearest 25 fish) to
the 90th and 80th percentiles in Figures 1 and 2.

Table 1. Summary of species-Specific Severe Decline Triggers (Average 4-year Abundance of


Naturally Produced Adults).

Species 90th Percentile Trigger 80th Percentile Trigger

SR fall Chinook 350 400


SR spring/summer Chinook 4,850 7,575
UCR spring Chinook 450 1,125
SR steelhead (A-Run) 6,800 7,825
SR steelhead (B-Run) 1,350 1,850
UCR steelhead 975 1,100
MCR steelhead (Yakima R.) 775 975

Trend Component of the Severe Decline Trigger

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As described above, quantitative triggers have not yet been defined for the trend component of
the Severe Decline Trigger, but will be developed in coordination with the RIOG in 2010. The
trend metric will be one that is indicative of short term trend consistent with the timeframe used
for the abundance metric. The same approach used for defining specific abundance triggers
would also be used for defining a trend trigger. Steps 1-3, in particular, would be identical to
those described above, except that a trend metric would be derived from the basic adult return
data and exceedence curves would be based on the trend metric.

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Example of a Potential Trend Trigger:

For illustrative purposes only, Figure 3 displays the percentile exceedence level for 4-year
geometric means of relative abundance in the historical record for the naturally produced Snake
River spring/summer Chinook species (the 90th percentile is represented by the dashed vertical
line). If the 90th percentile exceedence threshold was adopted as an Severe Decline trend trigger,
this figure indicates that four-year geometric mean relative abundances would be about 0.7. The
geometric mean of 0.7 indicates a decline in abundance of about 76% (1- 0.74) from the start
until the end of the four-year period. The additional use of the trend metric can result in triggers
that are more precautionary than those based on abundance metrics alone. For example, in the
case of SRSS Chinook in the 1990s, a 90% exceedence trend-based trigger would have been
tripped two years earlier than the abundance trigger alone. In this case, the populations
continued to decline to dangerously low levels, and the implementation of rapid response actions
at that time as an extra precaution would have been beneficial.

Figure 3. Example of exceedence chart for four-year geometric means of the relative abundance
for naturally produced Snake River spring/summer Chinook salmon (vertical dashed line
indicates the 90th percentile exceedence value).
Potential Combination of Abundance and Trend Triggers

Combinations of abundance and trend metrics can be used to further define Severe Decline and
Early Warning triggers. Figure 4 is a conceptual example of one method of combining the two
types of metrics. In this example:

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 the Severe Decline Trigger would be tripped if the abundance metric dropped to below
the 90% exceedence OR the trend metric dropped to below the 90% exceedence and the
abundance metric was below the 80% exceedence; and

 the Early Warning Trigger would be tripped if the abundance metric dropped to below
the 80% exceedence OR the trend metric dropped to below the 90% exceedence.

While other approaches are possible, this example demonstrates the types of considerations that
are relevant to a combination of abundance and trend components of the Severe Decline Trigger.

Figure 4. Example of Severe Decline and Early Warning triggers based on combinations of 4-year
running averages of abundance and a trend metric, such as 4-year geometric means of trend.

Early Warning Trigger for Chinook Salmon and Steelhead

The purpose of the Early Warning Trigger is to detect factors indicating that the Severe Decline
species6 abundance levels are likely to be reached within one to two years so that rapid response
actions can be implemented in a timely fashion to minimize or mitigate for an unforeseen
downturn. It is intended to be a failsafe that could be triggered before the Severe Declines triggers
are exceeded.
                                                            
6
Species-level adult abundance information is the most readily available information at present. Where feasible,
future refinements of the Early Warning trigger could be informed by MPG or population level information.

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One Early Warning Triggers, based on 80th percentile values of four year average abundances of Comment [K5]: What I do not want 
to buy here is multiple triggers for each 
naturally produce adults, was described above. Refined Early Warning Triggers would also ESU ‐ that will simply get to complicated 
evaluate whether a species is likely to have substantially reduced abundance (and productivity) in and cause too much process.  We can 
refine a trigger to incorporate these 
the future, based on two years of adult return information, preliminary biological information and other factors.   
environmental indicators or known environmental disasters. These indicators may included, but Deleted: Additional
are not limited to, low jack counts or juvenile migrants (biological), indicators of ocean conditions
predicting very low abundance of adult returns for recent outmigrants (environmental indicators),
or wide-spread forest fires, increased distribution and virulence of pathogens, new invasive
species, prolonged severe droughts etc. (environmental disasters).

Initial assessments suggest that juvenile monitoring (numbers, sizes, condition, etc.) of interior
Columbia River basin species (or MPGs or a subset of populations) at dams and in tributaries
would likely provide information that could complement the adult monitoring information and
further enhance the Early Warning Trigger in the future. Additional work will be required in order
to inventory the current monitoring program, determine what additional monitoring might be
needed, and assess how best to collect and use this information to inform the Early Warning
Trigger at the species scale. Deleted: , MPG, or population

Other than the 80th percentile average abundance trigger, specific Early Warning Triggers have not
yet been defined. The Action Agencies and NOAA have committed to refining these triggers in Deleted: d

2010. Definition and implementation of the Early Warning Trigger would involve the following
steps:

Step 1: Determine if the most recent two-year average of adult returns is near the threshold levels
used for the Severe Decline Trigger (above).

Step 2: Determine if there are any biological or environmental indicators that would suggest that
species are likely to experience low abundance in the next two or more years. This information
could include, as an example, extremely low jack counts (a preliminary biological indicator that
next year’s returns will be much lower than average) and ocean indicators (both biological and
environmental) that indicate that recent outmigrants are likely experiencing extremely poor ocean
conditions that would be expected to result in substantially reduced numbers of naturally produced
adults in the next two years.

Step 3: Assess whether there have been any "environmental disasters" such as wide-scale forest
fires, volcanic eruptions, rapid increases in the distribution or virulence of fish pathogens, or mud-
slides that would be likely to substantially reduce the productivity of freshwater habitat or severely
limit the ability of adults or juveniles to migrate to or from this habitat. Responses to impacts
affecting a specific MPG or subset of populations would be tailored to the appropriate scale.

After evaluating each of the factors in steps 1-3, a determination would need to be made as to
whether or not there is a reasonable likelihood that future adult returns would fall to levels

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triggering the Severe Decline Trigger (see above) or the existing BA/RPA trigger. If the Deleted: BiOp

determination is affirmative, then the Rapid Response Actions would be implemented.

Development of Future Juvenile Triggers

The Action Agencies and NOAA Fisheries also will evaluate development of a future Severe
Decline and Early Warning Triggers based on information from juvenile salmon and steelhead.
This is a longer-term task because additional monitoring will be required to implement a juvenile
trigger. Steps in the process of developing this trigger and some of the properties of a useful
juvenile trigger are described below.

Establish a juvenile monitoring program for Interior Columbia basin species could provide
information relevant to future Severe Decline or Early Warning triggers with respect to changes in
juvenile production or survival at the species, major population group, or population level. In
addition to abundance based metrics, the program would monitor changes in parr/smolt size or
timing that might translate into changes in cumulative life cycle survival or productivity. Comment [K6]: Suggest ending this 
section here.   

Development of Future Juvenile Triggers

Future juvenile outmigrant metrics would complement adult based measures and should provide
an early opportunity to detect patterns or trends than adult based approaches that might otherwise
be masked by the relatively high year to year variation in ocean survival rates typical of salmon
runs. The primary objectives for a juvenile monitoring program would be to:

 Enable detection of within species (specific to particular MPGs, populations, major life
history groupings) sudden downturns in natural production levels.
 Complement environmental measures, jack return metrics etc. to detect sudden downturns
in abundance at the species/MPG level.
 Detect changes in size, timing other condition factors that could be early warning signs of
regional environmental impacts (e.g., local or subregional climate change impacts, etc.)

The approach would incorporate at least three types of juvenile monitoring efforts. At the
species or major population group level, the monitoring framework would incorporate estimates
of aggregate juvenile abundance or productivity generated through updated sampling programs
targeting the aggregate wild run from an species or MPG (e.g., Lower Granite Dam smolt
sampling, Rock Island Dam juvenile sampling, Prosser Dam outmigrant monitoring in the lower
Yakima River. Sampling programs designed to estimate juvenile production from a specific
tributary would also be included (e.g., Grande Ronde River sampling programs, Yanke et al,
2007). A third major program component would include out-migrant marking/downstream
monitoring designed to collect information on the timing/size of migration from a given reach
(e.g., Achord, et al. 2007). The tributary production and out-migrant evaluation programs
generate information on the size and timing of annual outmigrants. The size individuals attain
during the juvenile life stage has direct consequences for fitness through size-selective mortality

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in later life stages (e.g., Zabel and Williams 2002) and enhanced reproductive success of larger
individuals (Kingsolver & Huey 2008). Further, migration timing is related to growth, with
larger individuals within a population out-migrating earlier than smaller ones (Achord et al.
2007). Thus, juvenile fish size is an indicator of habitat quality, particularly for higher elevation,
lower nutrient streams found in the interior Columbia River basin. Deviation from long-term
average fish size is potentially an indicator of deterioration in conditions related to juvenile fish
growth.

Monitoring fish size at a specific time in the season can provide several benefits:
1) A general indication of the fish and habitat status.
2) An early indication that habitat conditions have changed for the worse and further actions Formatted: Bullets and Numbering

are required.
3) An indication of whether habitat actions are effective.

Each population has different growth patterns, and thus annual measures of fish size should be
compared to long-term patterns for the population.

Annual results from a structured juvenile monitoring program would serve as inputs into early
warning assessments. Life cycle assessment tools would incorporate results from annual
juvenile modeling along with environmental indices and recent adult return data to generate
probability based projections of near term risks (see Life Cycle Modeling attachment). A second
general application would be to detect or confirm changes in production among populations
within species. For example, patterns in smolt per spawner or population size characteristics
could indicate impacts of changing climate conditions or the effects of local changes in habitat
conditions, etc.

Implementation of Future Juvenile Triggers

As a first step, ongoing juvenile monitoring efforts will be inventoried and evaluated as potential
contributors to the annual juvenile trigger program. Some of these metrics have been employed
for past evaluations or could be implemented with information from ongoing studies. Those
metrics would be verified and updated for application beginning with the 2010 out-migration.

This step would also include defining explicit technical guidelines for metrics and triggers Comment [K7]: We are making this 
exercise extremely complicated ‐ seems 
considering each of the categories of juvenile monitoring listed above. The trigger guidelines for entirely unmanageable and therfore 
juvenile monitoring would include an evaluation of alternative criteria applicable to each unuseable.   These are long term goals. 

category. For example, annual indices of total natural origin smolt production from a given
region that are generated from an effort with a relatively long historical series might incorporate
a trigger based on a statistical analysis of the time series or on stochastic modeling. The same
general approach could also be used to define specific criteria based on the size distribution of
migrants or on timing metrics. Smolt per spawner metrics could be evaluated against minimums
based on past performance or estimates generated by stochastic population modeling.

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The inventory of current juvenile monitoring activities would also be a starting point for
identifying opportunities for expanding on the initial set to ensure appropriate coverage at least at
the major population group level across each species in the Columbia River basin. The review
would be used to identify additional monitoring sites or metrics for implementation, specifically
identifying opportunities that could begin to generate information prior to 2013
status/implementation check-in called for in the FCRPS Biological Opinion. Selecting and
implementing additional monitoring actions for the program could be carried out in conjunction
with the ongoing process to develop annual population level fish-in fish-out monitoring
(described in accompanying attachment Fish In/Fish Out monitoring support to BiOp
contingency planning). The guidelines for early warning trigger metrics and criteria will inform
the design and selection of additional monitoring actions through that effort.

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Appendix 6: Rapid Response Actions from 8-10 version

A. Rapid Response Hydro Actions

The 2008 FCRPS BiOp provides a systematic approach to achieving dam passage performance
standards at the mainstem dams, with accountability for specific survival results. Species
response to spill, bypass and transport varies from dam to dam therefore the RPA is structured to
apply the most effective operation at each dam factoring in species migration timing. To improve
fish survival and meet BiOp performance standards and metrics (e.g. 96% dam survival for
spring migrants, etc.), the RPA spill, bypass, and transport operations at mainstem Snake and
Columbia River projects are adaptively managed annually based on results of biological studies.
These results are discussed and operations modified in collaboration with sovereign
representatives to ensure targets are being met based on the best available scientific information.

In 2009, spill and transport operations under the adaptive management provisions of the BiOp
were modified to continue spill for two weeks in May at the Snake River collector projects as a
result of an ISAB recommendation and agreement with RIOG. This was done for one year
despite concern about adverse affects on Snake River steelhead. The adult return information
will be reviewed in fall 2009 to determine future years’ operation based on the best available
science.

The RPA also requires the use of Configuration and Operational Plans (COPS) to describe
existing dam configuration and operations, and identify additional dam improvements needed to
achieve the performance standards. These plans are based on the best available scientific
information in collaboration with sovereign representatives. Following installation and testing of
planned fish passage features dam passage survival will be evaluated to determine if
performance standards are being met. In the event performance standards are not being met,
Phase II contingency actions will be discussed and implemented as long term contingency
actions. Phase II measures may include, for example, additional surface passage and other
juvenile passage improvements. In addition to the BiOp provisions, the Fish Accords include
“no backsliding” metrics for forebay delay and spill passage efficiency.

If a biological trigger is tripped, the Action Agencies and NOAA Fisheries, in collaboration with
RIOG and appropriate technical groups (hydro coordination team), will review the current status
of the biological research at the dams and discuss where additional project survival benefits
could be gained in relation to the specific ESU in question. This will include assessing whether
there are potential spill and/or transport operational adjustments that could be made to address
the problem contributing to the decline or the condition affecting survival, in order to maximize
additional survival benefits.

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This discussion will inform the spill and transport operations the Action Agencies will
implement. If triggered, this rapid response could call for short-term changes in spill operations
that would exceed the dam passage performance standard, or transport changes. This rapid
response goes further than what is described as the current activity in that it would make changes
intended to exceed the performance standard.

The planned testing of dam passage improvements currently anticipated in the BiOp will include
assessment of the SPE and forebay delay to ensure “no-backsliding” occurs consistent with the
Fish Accords. The assessment will also consider adult passage, water quality, and other potential
environmental effects. This information will be useful in the event a rapid response is triggered
to ensure an informed quick response operation will not degrade other environmental conditions.
If the new operation has not been previously tested, the operation being implemented would
likely require a test program to confirm the operation is producing the expected increased
survival.

B. Predation Management Rapid Response Actions

The FCRPS BiOp RPA identified specific actions that will be undertaken with respect to avian,
piscivorous fish, and sea lions to reduce the take on juvenile and adult listed salmon and
steelhead. The following delineates the specific measures being taken and related Rapid response
Actions.

Sea Lions

The BiOp RPA calls for the Corps to install and improve as needed Sea Lion Excluder Devices
in the fishways at Bonneville annually. It also requires support for hazing actions by NOAA
Fisheries, Tribes, and the States of Oregon, Washington, and Idaho. The BiOp assumed the
continuing impact of pinnipeds at the Bonneville tailrace to be approximately 3% for spring
Chinook and 7.6% for winter run steelhead. The removal action initiated in 2008 and 2009
should further reduce pinniped take on adult salmon and steelhead.

Avian Predation

The current RPA identifies both on the ground actions as well as RM&E to reduce the impact of Comment [k8]: These comments 
from FWS do not appear to fit here.  
avian predators on listed juvenile salmon and steelhead (BiOp RPA Actions 45, 46, 47, and 48). Someone needs to call Dan and see what 
Several of the avian predation actions are underway. The BiOp calls for reducing tern habitat in he intended.  I’ll reply to his e‐mail to me 
to this effect and ask him to call Rock.   
the estuary consistent with the EIS on Caspian Terns. The EIS considered creation of new
habitat outside of the Columbia River which will allow for reduction in tern habitat in the estuary
from 6 acres to 1.5 to 2.0 acres. The result of this action will likely reduce terns to
approximately 2,500 to 3,125 breeding pairs. Comment [U9]: The EIS set this as a 
goal based on the available habitat, but I 
don’t think anyone is thinking that we 
The BiOp RPA requires additional actions on double-crested cormorants (RPA 46 and 47). would consider direct population 
management of terns if there are more 
Cormorant numbers have been increasing in recent years with a corresponding significant take than 3,125 pairs in the 1.5 acres. 

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on juvenile salmon and steelhead. Information is currently being gathered to allow for the
development of alternative actions to reduce cormorant predation both in the estuary and inland
areas. With respect to cormorant take on listed salmon and steelhead, the BiOp analysis was
based on maintaining the current level of take. Further actions on cormorants will require
coordination with partners and NEPA documentation which will identify future potential actions.
Cormorant management issues must be coordinated with other partners to avoid causing
resource conflicts elsewhere.

The BiOp RPA 48 requires the Corps to continue to implement and improve avian deterrent
programs at all lower Snake and Columbia River dams. Gulls and other avian scavengers and
predators feed in the near vicinity of spillways and juvenile bypass outlets to feed on moribund
and passing juvenile salmon and steelhead as well as other fish species. Wire arrays are also in
place at all dams to reduce avian predation in the immediate tailrace areas. They are effective in
reducing avian activity where they are in place. Avian hazing at McNary and Lower Snake
River dam currently occurs from 1 April through 1 July, up to eight hours per day at each dam.
Activity is land based using pyrotechnics.

Rapid Response efforts will include increasing hazing at projects. These measures will use boats
to carry out hazing efforts, increase the hours conducted per day, and the season will be extended
though July. Additionally, increasing the coverage of wire arrays at dams will increase juvenile
survival by limiting gull and tern access to juvenile salmonids that are rolled to the surface or
disoriented below the dams. Lethal measures may also be employed if authorized under permit
after all non-lethal measures have been exhausted.

Pikeminnow Sport Reward Fishery

BPA and the Corps of Engineers are committed to the ongoing implementation of the enhanced
Northern Pikeminnow Management Program (NPMP), as articulated in RPA Action 43. This
commitment includes a general increase in the reward structure of the sport-reward fishery and
an evaluation of the effectiveness of focused removals (dam angling) at lower Columbia FCRPS
projects. The Action Agencies will work with Pacific States Marine Fisheries Commission,
Oregon Department of Fish and Wildlife, WDFW, and USDA (Animal Damage Control (Dam
Angling)) to ensure full implementation of this program.

The current NPMP deploys USDA employees to conduct dam angling in forebay and tailrace
areas at two FCRPS projects. Increasing the dam angling effort at more FCRPS projects as a
Rapid Response Action will increase the overall catch to contribute to the program’s exploitation
rate and potentially improve within year dam passage survival of outmigration juvenile salmon.
There is also a small increased benefit of removals at the dam relative to the general public
fishery because pikeminnow removed from these areas tend to be larger and therefore able to
consume more juvenile salmonids. The proposal would increase the dam angling program from
one crew to three crews with the mobility and flexibility to fish all eight mainstem dams.

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C. Rapid Response Harvest Actions

Terminal Fisheries

In the event of an early warning or severe decline, all terminal fisheries that affect the
populations or ESUs of concern would be reviewed to assess whether existing harvest
management provisions provide protection appropriate for the circumstances. Changes to
existing terminal fishery regulations can be targeted to the populations, MPGs, or ESUs of
concern. NOAA Fisheries can affect these changes through their ESA authority.

Terminal fisheries generally refer to those that occur in areas above Lower Granite Dam on the
Snake River and McNary Dam on the upper Columbia River. These are managed by the states
and tribes and are outside of the scope of the current U.S v. Oregon Agreement. Terminal
fisheries are generally directed at hatchery-origin fish, are often mark-selective and located in
place and time to target hatchery fish, and are highly responsive to changes in abundance. There
are nonetheless some incidental impacts to natural-origin fish. The level of harvest that may
occur when abundance is very low will be populations specific depending on the location of
remaining fisheries. Impacts in terminal fisheries will be on the order of 0% to 2%.

U.S. v Oregon Fisheries

U.S. v. Oregon refers to a settlement agreement between five tribes, three states, and the federal
government. The agreement establishes rules for managing harvest and hatchery production in
the Columbia Basin in areas above Bonneville Dam. The agreement is a stipulated order and
operates under the continuing jurisdiction of the federal court. The U.S v. Oregon agreement and
all its provisions are central to the overall settlement in the FCRPS litigation, particularly for the
tribes, and cannot be changed unilaterally in any detail without substantive consultation and
agreement with the affected parties.

Fisheries under the jurisdiction of the U.S v. Oregon Agreement generally occur in the mainstem
Columbia River from the river mouth up to McNary Dam. UCR spring Chinook and SR
spring/summer Chinook are caught in spring season fisheries. Under the current abundance
based management framework harvest rates vary between 5.5% and 17%. At the lowest level of
abundance, fisheries are scaled back under the agreement to 5% to provide limited opportunity
for tribal ceremonial and subsistence fisheries.

All SR fall Chinook harvest in the Columbia River occurs in fall season fisheries that are subject
to the U.S. v. Oregon agreement. SR fall Chinook in the Columbia River are managed subject to
an abundance-based harvest rate schedule. Under the current schedule harvest rates on SR fall
Chinook vary between 21.5% and 45%. At the lowest level of abundance, fisheries for fall
Chinook are allocated 1.5% to the non-Treaty fishery and 20% to the Treaty fishery.

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Most of the harvest of upriver steelhead in the Columbia River occurs in fall season fisheries
subject to the U.S v. Oregon agreement (additional harvest occurs in terminal fisheries as
discussed above). Under the agreement, non-Treaty fall season fisheries are subject to a 2%
mortality limit for steelhead. Treaty Indian fisheries are subject to an abundance base harvest
rate for “B-run” steelhead. B-run steelhead are a component of the SR steelhead DPS. The
allowable harvest rate ranges from 13% to 20%. Harvest rates on “A-run” steelhead that return
to the UCR DPS and parts of the Snake River are lower, generally less than 10%.

Harvest rates on Snake River sockeye are limited to 1% in non-Treaty fisheries and 5% to 7% in
Treaty fisheries.

An early warning or severe decline may suggest the need for a harvest response affecting
fisheries subject to the U.S v. Oregon agreement. In that event, NOAA Fisheries will work
within the U.S. v. Oregon framework to seek consensus on modifications of the agreement.

Ocean Fisheries

Of the seven ESUs and DPSs considered here SR fall Chinook is the only one caught in ocean
fisheries. SR fall Chinook are caught in fisheries in Alaska, Canada, and off the
Washington/Oregon coast. Ocean fisheries are subject to provisions of the Pacific Salmon
Treaty; fisheries off of Washington/Oregon are also subject to regulation through the PFMC and
NOAA Fisheries. Roughly half of all harvest impacts to SR fall Chinook occur in ocean
fisheries.

<Needs further discussion with SFD—Does NOAA have authority to reduce OR/WA
coastal harvest under Magnuson Stevens Act> If the early warning or severe decline applies
to SR fall Chinook and NOAA Fisheries determines that a harvest response is required, NOAA
Fisheries will engage the U.S. v Oregon parties as described above, take action to reduce harvest
in U.S. ocean fisheries, and seek to negotiate further reductions in Canadian fisheries through
emergency provisions of the PST agreement

D. Rapid Response Safety Net Hatchery Actions

Under RPA 41 and 42 of the FCRPS BiOp, BPA will fund ongoing and new safety net and
conservation hatchery programs to preserve genetic resources, reduce short-term extinction risk
and promote recovery of ESA-listed populations of Snake River sockeye salmon, Snake River
spring/summer Chinook salmon, Upper Columbia spring Chinook salmon, Upper Columbia
steelhead, Middle Columbia steelhead, and Columbia River chum salmon. Under RPA Action
39, the Action Agencies will continue funding FCRPS mitigation hatcheries in accordance with
existing programs and will adopt programmatic funding criteria for funding decisions.

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During FY 2010, the Action Agencies and NOAA Fisheries in consultation with the RIOG will
develop Rapid Response Contingency Plans for each ESU and DPS of the interior Columbia
basin. These plans will include mitigation actions that will immediately enhance fish survival
and for which the needed regulatory process is already largely in place. If triggered, actions will
be implemented relatively quickly and provide immediate survival benefits. Most, if not all
contingencies included in the Rapid Response Plans are intended to be temporary in nature.

The following are immediate actions that should be taken to prepare for using hatcheries as a
safety net.

 Determine whether any additional safety net programs are needed. Because there are already
numerous programs designed to conserve and propagate listed salmon species in the
Columbia River Basin there may be at most a limited need for expansion of the existing
programs. Hatchery propagation entails risks as well as benefits to listed species, so for ESUs
with numerous populations there are both genetic and ecological reasons to “spread the risk”
by identifying some populations that would remain free of supplementation under all
circumstances.

 NOAA Fisheries, the Action Agencies and the co-managers will develop a Plan of Action
(POA) for using safety net hatcheries as part of the rapid response plan, to include the
following:

1. Identity of the species or population that has reached the “trigger” for use of a safety net
program.

2. Action, location, anticipated production needs and goals, monitoring plan, funding authority,
cost estimate and risk assessment.

3. Approval of the safety-net conservation action by NOAA, state and tribal authorities.

4. Annual reporting requirements

5. Adaptive management plan

If necessary, the Rapid Response Plan could call for either (1) the reactivation of closed
hatchery facilities (central and/or satellite) as safety-net hatcheries and/or (2) retro-fit of existing
safety-net hatcheries in order to supplement and/or enhance fish production capabilities.

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