# FY 2007-2009 F&W Program Project Solicitation

# Section 10. Narrative

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**Project ID:** 2003-017-000

**Title:** Integrated Status and Effectiveness Monitoring Program
(ISEMP): The design and evaluation of monitoring tools for salmon
populations and habitat in the Interior Columbia River Basin.

A. Abstract

The Integrated Status and Effectiveness Monitoring Program is an ongoing
collaborative effort to design, test, implement and evaluate Status and
Trends Monitoring for salmon and steelhead populations and their habitat
and watershed-scale Effectiveness Monitoring for management actions
impacting salmon and steelhead populations and habitat in the Interior
Columbia River Basin. ISEMP takes a pilot-project approach to the
research and development of monitoring by implementing experimental
programs in several major subbasins of the Interior Columbia: the
Wenatchee, Entiat, John Day, South Fork Salmon and Lemhi River basins.
The overall goal of the project is to provide regional salmon management
agencies with the data, information and tools necessary to design
efficient and effective monitoring programs. Specifically, ISEMP will
generate quantitative guidance on and examples of: the robustness and
limitations of population and habitat monitoring protocols, indicators
and metrics; sampling design approaches for the distribution of
monitoring effort in time and space; analytical approaches to the
evaluation of monitoring data, information and programs; effective data
management and communication designs that support the use,
standardization and compilation of implementation, compliance, status,
trends and effectiveness monitoring data by regional data generators and
decision makers; and finally the design and implementation of
watershed-scale restoration actions to maximize the quantifiable
biological impact of the actions and learning from the design and
implementation strategy.

B. Technical and/or scientific background

**1.0 Introduction**

Monitoring and evaluation to support the management of anadromous
salmonid populations and ESUs (both ESA listed and not) is a critical
task of the resource's co-manager community. The monitoring required for
management purposes ranges from population assessments of various life
stages (e.g., adults, migrating and rearing juveniles) to the status of
fish habitat condition, to the effect of management and restoration
actions. These monitoring efforts are labor intensive, based on
extensive field observations across an enormous spatial extent,
undertaken seasonally and annually, relying on a vast network of
monitoring infrastructure and personnel, and as such, represent a major
investment by the co-manager community. However, the current monitoring
'program', if all salmonid population and habitat status and management
action effectiveness monitoring activities in the Columbia River basin
can be so described, did not develop as a result of a single intentional
design or evaluation process. Instead, the monitoring actions that
currently occur across the Columbia River basin for anadromous salmonids
arose from myriad projects and objectives, some with identified
performance metrics and data quality objectives, and others surviving
only due to inertial and historical artifact. As a result, the region
lacks a systematic approach to the implementation of population and
habitat status and management action effectiveness monitoring and, more
importantly, lacks a systematic approach to the design and assessment of
these monitoring activities.

This proposed work is the continuation of a monitoring and evaluation
design and testing project initiated in 2003 as a series of pilot
sub-basin scale test-beds for monitoring indicators and metrics,
sampling designs, evaluation procedures, data management and
communication processes, and large scale coordination and implementation
logistics. The overarching goal of this project, both during its initial
three-year phase and during the proposed continuation, is to act as a
major research and development structure for the development of
regionally supported status and effectiveness monitoring and evaluation
methods that directly meet the region's data and information needs with
regards to the management of anadromous salmonid populations and
habitat. In meeting this goal, the project also has established a series
of baseline data collection efforts in the Wenatchee and Entiat
Subbasins, the John Day Subbasin, and proposes the implementation of a
similar effort in the Salmon Subbasin. These efforts are necessary for
testing sampling design, data management, implementation and
coordination logistics and protocols. They serve a simultaneous need by
providing the co-manager community with extensive data-sets with well
defined objectives, scope and quality control metadata. The project has
also established itself as a resource for the development and testing of
data management and communication tools and skills, development and
testing of novel protocols, indicators and technologies, and the
development and testing of an experiment driven approach to monitoring
and evaluation design and implementation. Finally, the project has also
begun to tackle the issue of designing and testing approaches to
watershed-scale effectiveness monitoring, and it is this component of
the project that offers the most exciting new opportunities for the
collaborations developed so far.

To date this project has focused on generating data, information,
analyses and guidance to inform the design and implementation of status
and effectiveness monitoring; in all cases the underlying principal has
been to reduce, or at least quantify, the uncertainty associated with
each of these facets of a monitoring program. A piece-wise approach to
developing and improving monitoring tools is appropriate for status and
trends monitoring and some aspects of effectiveness monitoring; however,
several critical aspects of effectiveness monitoring will never be
addressed if monitoring program design guidance is developed in this
fashion. For aquatic habitat restoration, effectiveness monitoring is
the demonstration of a physical or biological effect of the restoration
actions. Demonstrating the effects of a restoration action depends on at
least three things: (i) the implemented action actually doing something
to physical or biological processes, both because the action addresses
an impaired, limiting factor, and the action really changes some part of
an impaired process, (ii) the action's impact being restricted to the
expected area/period of influence so that representative reference or
control locales can be identified, and (iii) that monitoring indicators
exist to quantify the effects and that they are collected at both the
treatment and reference locations in a manner that supports a
quantitative evaluation of the action's impact. Demonstrating the
action's effect depends critically on such that all are necessary, but
no combination short of the full compliment is sufficient. Because these
components represent a mixture of project implementation and monitoring,
successful effectiveness monitoring is not possible without the complete
integration of action and monitoring implementation and design.
Therefore, a piece-wise approach to the development and implementation
of effectiveness monitoring cannot be successful; a programmatic shift
must occur to simultaneously implement projects that result from and are
fully integrated with projects that can demonstrate their effect.

We propose a simple solution, though not one that we advocate for the
implementation of aquatic restoration programs region-wide -- allow the
implementation of on-the-ground restoration actions to be planned,
designed, identified, installed and monitored by a single project,
specifically a monitoring and evaluation project that has developed an
infrastructure to support the identification and quantification of
limiting factors, the monitoring of baseline conditions, the monitoring
of potential response variables, the design of evaluation frameworks for
watershed scale experiments, the quantification of expected restoration
action effect sizes, and most importantly, the development of local
participation, collaboration and buy-in such that simultaneous
implementation, monitoring and evaluation can occur in a single adaptive
experimental framework.[^1] The current model for the implementation of
aquatic restoration projects in the Columbia River basin may be
beneficial for fish, but the current model of effectiveness monitoring
will never demonstrate the projects' effects; decoupling the
implementation, implementation design/plan and the monitoring results in
the introduction of an overwhelming level of noise or uncertainty, and
as a result, little or no quantification of biological effect is
possible. The Integrated Status and Effectiveness Monitoring Project
provides the ideal test-bed for the development of watershed scale
restoration experiments that are designed to maximize the effect size of
restoration actions by identifying and controlling for critical
confounding factors, by identifying actions strategies that address
critical process limitations, and by implementing the actions in an
experimental context that maximizes the information content of the
monitoring.

**2.0 Key Questions Addressed by the Project**

The Integrated Status and Effectiveness Monitoring Program will address
the following questions:

1.  Status monitoring -- what are the design and implementation
    considerations for population and habitat status and trends
    monitoring for anadromous salmonids in their tributary environment
    such that it meets the data and information needs of co-manager
    decision making processes, is amenable to program evaluation and
    assessment, is robust to statistical analysis, and is practical and
    cost effective?

2.  Adult abundance -- how can random sampling and ongoing index-area
    based sampling to be combined to generate a cost effective adult
    abundance metric that: has known statistical properties, that
    estimates the entire population, and that is sensitive to changes in
    population size (#) and extent (area)?

3.  Juvenile abundance -- how can cost effective estimates of juvenile
    (rearing and migrating) population size be generated such that the
    data can also be used to estimate freshwater productivity as a
    function of habitat condition?

4.  Population productivity -- how to best estimate the annual
    population productivity of an entire watershed?

5.  Freshwater (tributary) productivity as a function of habitat
    condition -- how to estimate the effect of habitat condition on
    freshwater productivity of salmonid populations?

6.  Freshwater (tributary) habitat condition -- what aspects of
    freshwater habitat are important determinants of biological and
    physical processes that impact salmonid population processes, and do
    we have cost effective monitoring indicators that describe them?

7.  Effectiveness monitoring -- how can effectiveness monitoring be
    treated as a controlled experiment from the initial
    conceptualization of a restoration action through to the
    demonstration of that action's physical and biological effect?

8.  Effectiveness monitoring -- how can monitoring data be collected to
    support the demonstration of project effectiveness short of
    implementing an intensively monitored watershed experiment?

9.  Factors limiting (freshwater habitat and ecology) population
    productivity -- how can status monitoring be used to determine and
    test hypothesized factors that limit freshwater population
    productivity?

10. Impact of anthropogenic habitat manipulation on population
    productivity -- how can physical habitat monitoring and mechanistic
    models be used to generate expectations for the physical impact of
    habitat manipulations in a manner that can be tested and
    incorporated into restoration planning?

11. Mechanistic connection between freshwater habitat and population
    productivity -- how can limiting factor hypotheses, coupled with
    mechanistic models generate restoration scenarios that are testable
    through the implementation of effectiveness monitoring experiments?

12. Landscape scale effects (covariates) on freshwater habitat condition
    -- are landscape scale features important determinants of freshwater
    habitat condition and aquatic processes and can these features be
    described with remote sensing data and standard landscape data
    reduction and classification tools?

13. Data management infrastructure to support data compilation, analysis
    and distribution -- how can data management systems be constructed
    that facilitate both data communication and information access?

14. Evaluation of monitoring data and information to support regional
    co-manager community -- how can a standard set of data reduction and
    analysis tools be developed that arise from, and ultimately feed
    back on to refine the design of, regional status and effectiveness
    monitoring programs?

These questions form the conceptual framework that guides and motivates
this project's overall design, analysis and implementation. The
resulting project is implemented to meet seven key objectives -- the
outcome of these objectives will be the data, information, experience
and products used to answer the framework's guiding questions.

**3.0 Specific Project Objectives**

> **Subbasin-scale**
>
> **1. Programmatic coordination, design, planning and
> implementation** - *Establish contacts and coordinate current
> monitoring and evaluation activities*
>
> **2. Indicators and metric development and testing** - *Establish
> causal relationships between ecological processes that control fish
> production, and develop metrics and indices to better capture these
> mechanisms.*
>
> **3. Protocol development, refinement and testing -** *Determine the
> accuracy and precision of information we need collected through
> different protocols.*
>
> **4. Sampling design development and testing** - *Given what we
> learned about the accuracy and precision of different protocols,
> develop a sampling design.*
>
> **5. Effectiveness and status and trend monitoring experimental design
> and implementation** - *Determine the effectiveness of restoration
> actions through effectiveness monitoring or an experimental management
> framework, such as the Intensively Monitored Watershed studies.*
>
> **Program-scale**
>
> **6. Evaluation tools development and testing** -- *Develop monitoring
> data analysis tools and tools to evaluate monitoring programs and
> approaches*.
>
> **7. Data management tools development and testing** -- *Develop
> databases, data communication templates, data and information output
> tools, and populate databases with current and historic monitoring
> data.*

Tasks one through five are primarily addressed via implementation of
subbasin scale Pilot Projects in the Wenatchee/Entiat, John Day, and
Salmon subbasins as described in greater detail in following sections.
Within each subbasin, task one is satisfied by the establishment of a
technical advisory group, consisting of local and regional researchers
that coordinate research activities, and provide technical input to the
Pilot Project study designs to ensure that they address information
needs and do not duplicate existing efforts. Tasks two through five are
satisfied by the completion of subbasin scale study designs, constructed
in collaboration with the subbasin technical advisory groups. Upon
completion, subbasin study designs are reviewed by the ISRP for adequacy
and implemented for a trial period. Tasks six and seven are largely
approached at the scale of the entire ISEMP using the information
collected by the implementation of subbasin study designs.

The key questions and associated objectives and will be addressed by
implementing Pilot Effectiveness and Status and Trend Monitoring
projects in three subbasins:

1.  Wenatchee and Entiat Rivers;

2.  John Day;

3.  Salmon River

This proposal is structured geographically around the three subbasins,
and within each subbasin section, by the project objectives. In all
sections below, the work to date is used to explain the objective's
implementation in each subbasin, followed by proposed new or continuing
implementation of these tasks.

**4.0 Wenatchee and Entiat**

The ISEMP Program has been developing two novel monitoring and
evaluation programs in the Wenatchee and Entiat subbasins since FY04,
including: (i) subbasin-scale pilot status and trend monitoring efforts
for anadromous salmonids and their habitat, and (ii) effectiveness
monitoring for suites of habitat restoration projects. The ISEMP Program
has integrated existing and new monitoring and evaluation activities in
the Wenatchee and Entiat to help ensure that provisions of the 2000
National Marine Fisheries Service Federal Columbia River Power System
Biological Opinion (BiOp) are satisfied. Monitoring being implemented
under the ISEMP Program is following protocols specified in Hillman
(2004; the *Upper Columbia Monitoring Strategy*). The ISEMP Program
addresses a complex and large set of scientific uncertainties underlying
status, trend, and effectiveness monitoring programs at many spatial and
temporal scales. The ISEMP Program also examines scientific
uncertainties underlying selected monitoring methodologies. For these
reasons, multiple entities have been enlisted to conduct aspects of this
program, in many cases by building upon existing monitoring efforts and
sharing costs with other programs, and in all cases by using the expert
staff that each agency is able to provide.

**4.1. Programmatic coordination, design, planning and implementation**

> ***Accomplishments (FY04-06)***

-   Facilitated unprecedented collaboration among county, state,
    federal, tribal, and private agencies at the programmatic scale: for
    the first time agencies from all levels are working together on a
    joint approach to monitoring as compared to the previously disjunct
    or competitive monitoring approach of the past.

-   Coordinated over a dozen tribal, state, federal and private
    contractors implementing components of ISEMP in the Wenatchee and
    Entiat subbasins, including insuring that budgets and scopes of work
    were appropriately designed, scientifically defensible, and within
    budget.

-   Facilitated unprecedented collaboration among multiple agencies
    working at the field level, for example: U.S. Forest Service (USFS)
    and Washington Department of Ecology (WDOE) conduct snorkel and
    habitat surveys within 48 hours of each other at over 50 random
    locations per year while the Chelan County Conservation District
    facilitates landowner access permission affording these agencies
    unprecedented access to sites on private lands; this project
    encouraged Washington Department of Fish and Wildlife (WDFW), Yakama
    Nation, and USFWS to standardize smolt trapping operations, data
    collection, and data management throughout the Upper Columbia; WDFW
    and USFS jointly conducted both index-area and randomized steelhead
    surveys in tight coordination.

-   Explored and refined novel ways to communicate and share ideas,
    avoid and recover from mistakes, and manage large groups of
    collaborators from diverse backgrounds and agencies in a fashion
    that could reduce "ramp-up" time when lessons from ISEMP are
    expanded to other parts of the Columbia. We are working to develop a
    community with a common language for monitoring, a basic set of
    tools and skills for data communication and management, and a shared
    set of goals and objectives. We feel that by actively fostering this
    community we will ultimately be able to progress further and faster
    in the design and implementation of a subbasin scale monitoring and
    evaluation program. To facilitate the development of a community of
    practice we have developed workshops, training sessions and
    technology transfer approaches.

-   Enlisted the Upper Columbia Regional Technical Team (RTT)[^2] as the
    technical advisory committee for ISEMP in the Wenatchee/Entiat;
    ISEMP staff have coordinated the RTT's monitoring effort for the
    past two years.

-   Completed a Monitoring Strategy for the Upper Columbia (which
    includes Wenatchee/Entiat and two other subbasins).

-   Completed an Implementation Strategy for ISEMP in the Wenatchee that
    describes how ISEMP will implement and analyze monitoring activities
    over the next 20 years.

-   Developed a "living" Tracking Document that captures all
    institutional decision-making since the inception of the ISEMP in
    the Wenatchee. This record will be crucial in light of the adaptive
    design of each monitoring element: as we learn, we change the
    monitoring work adaptively, and this document provides a clear
    record of these changes and the underlying rationales.

-   Completed a Study Design for the effectiveness monitoring of the
    "Bridge-to-Bridge" restoration project in the Entiat.

-   Coordinated protocol standardization throughout the Upper Columbia
    ESU, for example: are analyzing differences in protocols, and
    recommending standardized approaches, between two BPA projects in
    the Wenatchee/Entiat and Okanogan subbasins.

> ***Proposed Work (FY07-09)***

-   Continue to facilitate collaboration among county, state, federal,
    tribal, and private agencies at the programmatic scale and at field
    and analytical levels in the Wenatchee.

-   Expand the multi-agency programmatic collaboration to the Entiat.

-   Continue the coordination and collaboration described above in
    "accomplishments for FY04-06"

-   Revise, as necessary, the Monitoring Strategy for the Upper Columbia
    and the Implementation Strategy for the Wenatchee.

-   Complete an Implementation Strategy for ISEMP in the Entiat.

-   Expand the Entiat effectiveness monitoring study design (and include
    this in the Implementation Strategy) to appropriately monitor
    changes resulting from the planned implementation of nearly 80
    habitat actions in the Entiat under the Recovery Plan.

-   Expand the use of the Tracking Document to include ISEMP work
    conducted in the Entiat.

-   Continue to promote protocol standardization throughout the Upper
    Columbia ESU based on analytical results of protocol comparisons
    being conducted under ISEMP.

**4.2, 4.3 and 4.4 Development and Testing of Indicators and Metrics,
Protocols, and Sampling Designs**

> ***Accomplishments (FY04-06)***

-   Developed, in the Upper Columbia Monitoring Strategy, a list of 67
    monitoring indicators, and identified a similar list of protocols to
    measure these indicators, that are monitored by ISEMP in the
    Wenatchee. To review this list see the Upper Columbia Monitoring
    Strategy at ***CEJ web address.***

-   Designed sampling regimes for each of 67 indicators/protocols, often
    at multiple spatial and temporal scales, and have been implementing
    the monitoring of these indicators since FY04.

-   Testing multiple protocols and sampling designs in a coordinated
    fashion within the Wenatchee/Entiat to identify feasible and
    effective alternatives to legacy monitoring approaches. For example:
    we are quantifying temporal variability in snorkel surveys at
    12-hour, 24-hour, 7-day, and 30-day time scales; comparing bias and
    variability between index-area and randomized steelhead redd
    surveys; comparing between crew bias and variability in habitat
    surveys; examining patterns of variability in continuous smolt
    trapping and water quality collection to suggest ways to reduce
    effort by subsampling in time; comparing ground-based and
    remotely-sensed data collection for riparian and stream channel
    habitat. For many other examples, see \<ISEMPDataAnalysisPriorities
    '05-06.ppt\> at ***CEJ web address.*** These protocol comparisons
    will be used to inform monitoring programs throughout the Columbia,
    but in particular, within the Upper Columbia ESU.

-   Tested ISEMP protocols in the PNAMP "Side-by-Side" protocol
    comparison experiment in 2005.

-   Designed and are implementing an effectiveness monitoring program
    for the "Bridge-to-Bridge" habitat restoration project in the
    Entiat.

> ***Proposed Work (FY07-09)***

-   Continue implementing ISEMP in the Wenatchee subbasin. This will
    allow continued exploration of the use of these 67
    indicators/protocols/sampling designs and, possibly, the development
    of new ones when suggested by ISEMP analysis or other scientific
    advancements. Many of the protocol comparisons we are conducting
    require long term data sets and are scheduled to be completed in
    FY09 after 5 years of ISEMP data collection since FY04, or later as
    necessary. Some analyses identified in the Implementation Strategy
    require at least 20 years of data collection. Hence, we have a need
    to rely, primarily, on the indicators already developed.

-   Expand the monitoring of this list of indicators in the Entiat as a
    first step in implementing pre-treatment monitoring of the Entiat
    Recovery Plan habitat action implementation (see Objective 5 below).

-   Continue the implementation of effectiveness monitoring of the
    "Bridge-to-Bridge" restoration project in the Entiat to elucidate
    reach-scale changes in habitat/biology, as compared to
    subbasin-scale changes that are discussed in the next two bullets.

**4.5**. **Effectiveness and status and trend monitoring experimental
design and implementation**

> ***Accomplishments (FY04-06)***

-   ISEMP has been designed and implemented to quantify the effects of
    changes resulting from restoration actions between watersheds and is
    currently operating in a manner to capture "pre-treatment" data in
    anticipation of future habitat action implementation. While no
    watershed-scale habitat restoration actions have been implemented to
    date, they may occur in the future. However, ISEMP is currently
    implemented to detect changes resulting from, for example: the
    differential impacts of hatchery programs on populations in the
    various watersheds of the Wenatchee subbasin; and differential
    preservation/conservation actions at the watershed-scale. We
    anticipate, but have no control over, the development of
    watershed-scale restoration actions. For example, several agencies
    are beginning to design a watershed-scale habitat restoration action
    in Nason Creek with predicted impacts at a magnitude that ISEMP is
    designed to resolve.

-   Developed and initiated effectiveness monitoring of the
    "Bridge-to-Bridge" habitat restoration project in the Entiat at the
    reach-scale. Much of this work (e.g. snorkel/habitat surveys of
    restoration sites) will provide "pilot" knowledge when designing
    watershed-scale monitoring of habitat actions in the Entiat. Other
    elements of this work (e.g. initiation of habitat monitoring at an
    "annual panel" of sites in FY05 and FY06) will be directly useful in
    the implementation of watershed-scale monitoring of habitat actions
    in the Entiat.

-   Facilitated the coordination of Entiat restoration project planning
    and implementation at the subbasin-scale within the monitoring
    framework of the ISEMP project.

> ***Proposed Work (FY07-09)***

-   Continue implementing ISEMP in the Wenatchee subbasin, collecting
    pre-treatment data for watershed-scale effectiveness comparisons,
    while watershed-scale restoration projects are contemplated,
    designed, and implemented.

-   Initiate the implementation of ISEMP in the Entiat subbasin
    collecting pre-treatment data for subbasin-scale effectiveness
    monitoring in anticipation of imminent implementation of
    subbasin-scale habitat restoration actions as part of an accelerated
    Entiat Recovery Plan Implementation Schedule. Effectiveness
    monitoring at the subbasin-scale in the Entiat under ISEMP is ideal
    for several reasons: implementation of subbasin-scale habitat
    restoration actions is imminent yet enough time remains to begin
    pre-treatment data collection; ISEMP activities in the Wenatchee
    provide an excellent, real-world scientific control complete with
    robust, well-designed data sets; the Entiat has fairly static
    landuse and fish management regimes, and limited influence from
    hatcheries -- all of which should optimize resolution of changes due
    to the habitat restoration actions. Please refer to the following
    text box for details regarding the planned project in the Entiat.
    The specific sampling design for this effectiveness will largely
    follow that of the ISEMP project in the Wenatchee but has not yet
    been written (it is proposed, above, in Objective 1).

Table 4.1. All habitat diversity / riparian recovery actions in the
Lower Entiat (above and below Mad River) and Middle Entiat Assessment
Units

  -------------------- ------------------------- ------------------------------
  Habitat              Implementation Plan       Implementation Plan End Goal
  Diversity/Riparian   Proposed Approach         
  Implementation                                 
  Action                                         

  Instream Structures  Implement EDT Alternative Up to 75 rock and/or wood
  / LWD Restoration    5, focusing on pool       structures as identified in
                       forming structures        WRIA 46 Plan and supplemental
                                                 analyses

  Floodplain           Implement Ecosystem       All potential (possibly 5)
  Restoration          Diagnosis and Treatment   off-channel opportunities
                       (EDT) Alternative 5       reconnected.
                       related to side-channel   
                       options                   

  Riparian Restoration Implement riparian        40,000 lineal feet as
                       planting projects with    identified in WRIA 46 Plan and
                       willing landowners        supplemental analyses (SNTEMP,
                                                 ground truthing, etc.)

  Riparian Protection  Work with willing         Larger undisturbed riparian
                       landowners to protect     areas are preserved in a
                       larger, undisturbed       manner that does not adversely
                       riparian areas by first   impact community tax base
                       pursuing conservation     
                       easement, lease, and      
                       options other than        
                       outright property         
                       acquisition               
  -------------------- ------------------------- ------------------------------

**5.0 John Day**

The John Day was chosen for a pilot project because (1) the John Day
basin is represented by several populations of the Mid-Columbia
Steelhead ESU, listed as threatened by NMFS in 1999 (64 FR 14517); (2)
there is an opportunity to build quickly on current research in the
basin to develop answers to key management questions; (3) past
information suggests that focused research should address water supply,
temperature, and sediments as potential key limiting factors; (4) there
is little influence of hatchery fish in the basin; (5) the basin has key
sites where fish traps can be effectively located; and (6) the
information from the research is likely to be transferable to other
ESUs. The John Day RME program will focus on two anadromous fish
species: spring/summer chinook (*Oncorhynchus tshawytscha*) and rainbow
trout/Steelhead (*Oncorhynchus mykiss*).

The John Day pilot project has outlined a plan to investigate modifying
current RME efforts in the basin to address local agency goals as well
as the three programmatic goals of Federal Tributary RME program: 1) to
assess the 'health' or status of populations and their environment; 2)
to identify and prioritize restoration actions to increase freshwater
production as a means of increasing overall life-cycle survival; and 3)
to quantify the degree to which restoration actions are achieving its
goals (Jordan et al. 2003). The project relies on the collaboration of
researchers and managers to: consolidate current and historic
information; define information needs; design research and monitoring
programs to establish status and trends, and causal relationships; and
synthesize RME information to determine limiting factors to prioritize
and design restoration actions. Another major component of the pilot
project is to design methods to evaluate the effectiveness of monitoring
programs. The John Day pilot project is planning on evaluating project
effectiveness in an experimental management framework. Factors limiting
fish production in watersheds will be assessed, restoration actions will
be designed to address these problems, actions will be implemented as a
large scale experiment (e.g. BACI design), and intensive monitoring and
research will evaluate the success of the action. This study design is
referred to as the Intensively Monitored Watershed (IMW) study, and is
not only a powerful approach to evaluate action effectiveness, but a
small-scale example of the process required to develop a basinwide RME
program.

The development of the John Day RME pilot project is expected to be a
long term process whereby lessons learned through research and the
Intensively Monitored Watershed studies will influence current and
future monitoring efforts. We are working closely with personnel
implementing current monitoring programs in the John Day as changes to
current programs will not likely be accepted unless we provide strong
justification of the benefit of action revisions to salmonid management
in the basin. Therefore, the RME pilot approach in the John Day is to
develop a monitoring framework developed as a cohesive, basin-wide RME
program that will be agreed upon by the multiple monitoring entities in
the basin.

**5.1 Establish contacts and coordinate current activities** (Objective
1). The John Day Basin is large and crosses multiple jurisdictional
boundaries. There are over 150 people from over 30 agencies and
institutions that are connected with monitoring, restoration, or
management associated with fisheries in the basin. Historic and current
monitoring programs have collected over 25 years of fish, habitat, and
water quality data within the basin. One objective of the pilot project
is to become well aware of current and historic efforts, coordinating
current efforts to reduce duplication, compile associated data and make
it available to all researchers (Objective 7), and to use this process
to further working relationships with local RME personnel.

[To Date:]{.underline} In 2003, the Analytical Framework Group (AFG),
made up of approximately 30 people representing several agencies, was
formed to identify information needs and coordinate the development of
research and monitoring projects. The AFG and the Habitat, Fish, and GIS
AFG subgroups continued to meet in 2005. In addition, pilot project
coordinators have met with approximately 100 local RME-related
personnel, exposing them to pilot project objectives, gathering existing
project information and data, and assessing monitoring needs within the
basin.

[Proposal:]{.underline} We plan to further engage and broaden
collaboration with personnel from USFS, CTWSRO, CTUIR, SWCD, and other
local agencies. Subbasin workgroups comprised of agency biologists and
restoration and management personnel will be formed to increase
communication and create a strong network among monitoring agencies. For
example, a Middle Fork John Day workgroup was formed in 2005 by USFS
personnel and we plan to initiate similar workgroups for the North Fork,
the South Fork and Upper John Day subbasins. An annual monitoring
meeting is also planned to coordinate development of a basin-wide
monitoring study design, incorporating current and legacy monitoring
activities of local agencies.

*Summarize current RME activities.* Current status and trend fish and
habitat monitoring programs are implemented by state, tribal, and local
agencies and these agencies are represented in the AFG. Activities
include annual steelhead spawner surveys (ODFW), water quality (USFS,
BLM, ODEQ, OSU, CTWS and Monument SWCD), and in-stream habitat surveys
(EMAP and EPA). Their monitoring efforts have been described in Bouwes
(2004, 2005) as well as their initial proposals and annual reports
(cite?)

*Determine what information we need to inform goals.* While there are a
large number of agencies and people conducting monitoring and research
in the John Day, the size and complexity of the basin ensures that large
information gaps will exist within any single monitoring program. An
objective of the pilot projects is to assess multiple monitoring
programs to determine which information is essential, yet lacking, to
reach status and trend monitoring goals for the basin. Collaborations
among agencies within the AFG and review of the John Day Subbasin Plan
(CITE) have determined information gaps within current monitoring
actions.

[To Date:]{.underline} Examples of information needs include, but are
not limited to: population structure and distribution information (e.g.
genetic data) for salmon and steelhead; hatchery/wild fish interactions,
especially in areas with large percentages of hatchery origin salmon and
steelhead strays; fish passage monitoring; movement patterns of rearing
salmon and steelhead parr; high resolution remote sensing and riparian
vegetation mapping; spatial gaps in water quality monitoring;
invertebrate monitoring; predation and food web interactions;
understanding spatial and temporal variability of collected samples;
compliance monitoring; implementation monitoring and project inventory;
and effectiveness monitoring. The pilot project and collaborators have
initiated or are planning studies to address these particular needs.

[Proposal:]{.underline} We plan to continue to query biologists in the
John Day Basin, review Biological Review Team and TRT products, and use
current RME analyses to help identify further information needs.

**5.2 Establish causal relationships between ecological processes that
control fish production, and develop metrics and indices to better
capture these mechanisms** (Objective 2). If we can understand the
mechanistic relationships between fish and their environment, we will
more likely be successful in managing these populations. Our
understanding of factors limiting freshwater salmonid production will
increase, and defining causal relationships will assist our development
of metrics and indices that capture relevant ecological processes. The
wealth of fisheries literature and past and current intensive research
in the John Day Basin, in part funded by other agencies (e.g. BOR), will
help define these causal relationships across multiple spatial and
temporal scales. Several monitoring projects in the John Day collect
spatially and temporally overlapping fish and habitat information that
can be used to test causal relationships or generate new hypotheses. We
expect RME efforts and IMW studies will continue to discover and refine
causal relationships.

[To Date:]{.underline} Several studies are currently underway in the
John Day pilot project to determine causal relationships and metrics
that capture these relationships, such as fish movement and water
temperature relationships (OSU 2005) *John Day Basin Sediment
Assessment* (EPA) is evaluating sediment input sources, such as land
use, road crossings, and channel morphology, which are considered major
limiting factors for fish production in the basin (John Day Subbasin
Plan). The *EMAP- Western Regional Pilot Project* is evaluating
relationships between physical and biotic factors and the ability to
predict current 'health' of fish habitat. High stream temperature is
considered another major limiting factor in the John Day, and the *John
Day TMDL process* is measuring several morphological and riparian
vegetation characteristics to parameterize the Heatsource model (Boyd,
Matthew and Kasper, Brian, 2002,
[www.heatsource.info](../www.heatsource.info)), a mechanistic model
relating these inputs to stream temperature. This model will also
evaluate how changes to factors such as flow and riparian vegetation
through restoration might impact temperature.

*Push-up dam removal evaluation- The South Fork Intensively Monitored
Watershed study.* BOR has funded the Oregon Cooperative Fish and
Wildlife Research Unit at Oregon State University (OSU) to conduct the
South Fork John Day IMW. This IMW was designed to evaluate whether
habitat and temperature attributes can explain changes in fish behavior
(e.g. densities and movement), growth and other physiological indices,
survival, and ultimately production. This also included plans to
evaluate the effects of push-dams and their removal on these fish
responses as an IMW (Li et al. 2005).

*Invertebrate Productivity Monitoring***.** NOAA-Fisheries and Eco
Logical Research/Utah State University are currently evaluating
macroinvertebrate metrics that potentially predict fish growth when
coupled with temperature metrics. The objective of this project is to
evaluate integrated metric approaches to estimate food availability for
salmonids, rather than exclusively using water quality and
macroinvertebrate monitoring methods. Project outcomes may include easy
metric additions to habitat monitoring programs that reflect food
availability.

[Proposal:]{.underline} *Landscape Changes and Patterns Project:
Exploring Landscape Scale Influences on In-Stream Water Temperature*. An
existing time series of in-stream water temperature data will be
evaluated against the newly derived metrics of landscape complexity to
assess how landscape scale factors relate to measured in-stream
variables.

*Predation and food web interactions***.** Several species of native and
non-native fish species live in the John Day system. Very little is
known about how these species interact with anadromous fish. Some of
these are warm water species that are potential predators to juvenile
salmonids, such as smallmouth bass, catfish, and pikeminnow, especially
in the migration corridor through which all anadromous species must
pass. Others, such as dace, shiners, and young pikeminnows, might
compete with juveniles for food resources. If so, parr density alone may
not be the most relevant response variable, if inter-specific
competition is just as important as intra-specific competition. Many
warm water species seem to be expanding their range, which may further
complicate the success of some restoration actions. Conversely,
restoration actions that decrease temperature may decrease warm water
species use of certain habitats and may provide an added benefit to
these types of actions. ODFW, the Subbasin Plan (2005), and the
ISAB/ISRP (2004a) have suggested that monitoring programs need to
address these interactions. We propose collecting diets and tissue or
blood (non-lethal) stable isotopes samples for all fish species and
macroinvertebrates as a potential monitoring tool to describe general
food web patterns. Stable isotopes can describe general prey types
consumed for up to months. Collection of these samples during times of
outmigration through the lower mainstem, or times of high thermal stress
above, at, and below the interface of species overlap may elucidate
these food web patterns.

**5.3 Determine the accuracy and precision of information we need
collected through different protocols** (Objective 3)**.** The ability
for a sample to provide accurate and precise information depends heavily
on the protocol used to collect that sample. Therefore, monitoring
programs need to adopt protocols that are the most informative yet are
still affordable (e.g. time, money, effort, etc.). This requires testing
the accuracy and precision of several protocols. Currently, there are
multiple monitoring protocols to measure the same general
characteristic. Often these protocols differ enough that, although they
are attempting to describe the same general characteristic, they produce
different information. These differences produce inconsistencies that
make detection of changes difficult or information that is not even
comparable across areas where multiple protocols are implemented. Effort
is being spent in the John Day to use habitat, invertebrate, and fish
sampling protocols that provide reliable information and are reasonable
to implement. Many protocols that are used in the current RME program
were tested in 2005. Testing of protocols will continue throughout the
life of this project but is expected to diminish as protocol differences
are defined.

[To Date:]{.underline} *Comparison of satellite remote sensing
information collected at different levels of resolution.* As part of the
*Landscape Changes and Patterns Project*, remote sensing data derived
from the LANDSAT 5 Thematic Mapper sensor is being compared against
IKONOS high resolution multispectral imager. While this information has
higher resolution, the temporal coverage is limited, and it is much more
expensive than LANDSAT 5 images. The objectives of this analysis is to
determine what information is lost by using coarser resolution yet less
expensive LANDSAT 5 data, and whether the coarser resolution is adequate
to describe changes in landscape and landuse patterns evaluations used
in the pilot projects.

*Comparison of Aquatic Survey Protocols Used to Measurement of Physical
Habitat Attributes within the John Day Basin Oregon.* This study was led
by the USFS PIBO program in collaboration with the Pacific Northwest
Aquatic Monitoring Program (PNAMP), and the John Day pilot project.
Several of the most widely used stream survey protocols within the
Columbia River Basin were used to survey a common set of sites. To
ensure sufficient data to evaluate crew variability, at least three
crews from each program collected habitat and physical information at
each site. A total of 12 sites in the John Day drainage were surveyed
with these protocols; four sites falling into each of the following
geomorphic reach types; 1) step-pool, 2) pool-riffle, and 3) plane bed.
In addition to these protocols a remote sensing approach (LiDAR) was
compared and a more precise method (engineering survey) was conducted to
establish a benchmark or 'truth'. Results from this study will describe
the precision and accuracy of, and to help RME programs decide on, the
protocols used to collect habitat information.

As part of the *South Fork IMW study* conducted by OSU, the following
protocols were evaluated. *Devising less stressful fish capturing
techniques.* Three alternative methods of counting and capturing fishes,
believed to be less stressful to the fish, were compared to
electrofishing: (1) visual counts by divers, (2) divers chasing fish
into bag seines ("snorkel-herding") (3) chasing fish into bag seines
using an electrical probe that emits an irritating electrical field, but
not one set to stun ("electro-herding"). All the new techniques
demonstrated to be less intrusive. *Diver effects on fish behaviors.*
The response of *O.mykiss* parr to snorkel surveyors was assessed by
placing a remotely controlled video camera in the stream and waiting 30
minutes before attempting to enter the stream again. They found that
fish will scatter into cover even when a diver enters the stream two
pools below the pool to be inventoried. *Calibration of fish sampling
techniques.* OSU conducted a calibration study in an attempt rectify the
biases of different gears to count fishes described above. Preliminary
results suggest that approximately 25%, 35%, 45% of the mark-recapture
estimated population size were detected by visual counts,
snorkel-herding, and electro-herding, respectively. In addition, rotary
screw traps are being calibrated against, PIT tag antennas that have
been installed just above the screw trap as part of the South Fork John
Day IMW. They are evaluating impacts of release time and location of
marked fish used estimate trap efficiency. Difference in these
treatments might suggest that attention should be given to capture
induced behavioral modification on trap efficiency calculations.

The *Invertebrate Productivity Monitoring study* is evaluating the
spatial and temporal variability of drift and benthic invertebrate
metrics. Drift samples were taken with 2 to 4 replicate nets in each
riffle, with 1-3 riffles sampled at each of seven sentinel sites to
describe the spatial variability within riffle, within site and between
sites, respectively. Samples were also collected during the morning,
mid-day, and evening over 3 days consecutive days for 3 sample dates to
describe temporal variability within days, between days, and throughout
the season, respectively. This information will be used to determine the
level of effort (samples size and design) needed for a monitoring
program to estimate relevant stream invertebrate information.

[Proposal:]{.underline} Many of these studies have just been completed
or are still in progress. We plan to analyze this information and based
on results, provide recommendations to monitoring programs. In addition,
several of these studies will be repeated to see if these sources of
variability are similar between years (e.g. calibration of fish and
macroinvertebrate sampling techniques).

We plan to also evaluate the level effort or resolution required to
estimate a metric. For example, in the *South Fork IMW* approximate
8,000 juvenile *O. mykiss* have been PIT tagged. These tagged fish must
migrate past the rotary screw trap (set daily) and a set of PIT-tag
antennas just upstream from the trap. If the ratio of tagged to untagged
fish remain relatively constant (an assumption of mark-recapture
methods), then analysis of this paired information may suggest that
continuous reading of the antennas can be used to estimate production of
the subbasin, with much less effort spent collecting outmigrants in the
screw trap. We will also test this assumption in the *Bridge Creek IMW*.
Further review of screw trap data may also suggest that daily operation
is not required, even in the absence of antennas. Additionally,
subsampling and comparison of high and low resolution LiDAR data can
lead insight into the level of resolution needed to provide accurate
estimates of stream characteristics relative to other habitat monitoring
protocols.

We will also evaluate the ability to create cross walks between
different sampling protocols. For example, ODFW is willing to substitute
LiDAR information in lieu of habitat surveys, if LiDAR can provide the
same information. This will allow ODFW to increase snorkel survey reach
lengths to estimate of juvenile salmonid abundance and distribution for
the same level of effort (the same crews conduct habitat and snorkel
surveys). Also, in the *Invertebrate Productivity Monitoring study*, we
have collected benthic and drift samples. PIBO collected drift samples
with their standard benthic invertebrate monitoring. If a relationship
between these two methods can be developed and we develop a metric that
relates to fish growth, standard benthic invertebrate monitoring samples
may be available to predict fish growth.

**5.4 Given what we learned about the accuracy and precision of
different protocols, develop a sampling design** (Objective 4)**.**
While accuracy and precision of a sample is needed, the ability to
extrapolate a collection of samples to provide an accurate assessment at
the appropriate scale is dependent on the sampling design. The sampling
design describes, when, where, and how much to sample for a given sample
area. The design is highly dependent on the protocols used to collect
the information and how the information will be used. Protocol testing
and variability comparisons will be used to improve monitoring program
design in the basin..

[To Date:]{.underline} In conjunction with the RME monitoring program
within the target basins, NOAA-Fisheries has initiated a *Watershed
Classification* project to group similar 6^th^ field watersheds
(Hydrologic Unit Code 6, HUC 6) in the Pacific Northwest according to
watershed characteristics. MCLUST software will be used to classify
spatially continuous GIS data such as precipitation, temperature,
watershed topography, geology, and hydrography metrics into discrete
classes. This regionally continuous classification of watersheds can be
used to determine if the selected Intensively Monitored Watersheds
equally represent the landscape diversity. In addition, this
classification scheme may be provide a way to stratify monitoring sites
for analyses, and as a means to extrapolate the results beyond the
boundaries of the study.

A similar classification approach to describe reaches was applied to the
*South Fork John Day IMW*. In 2004, a census of habitat and the
distribution of fishes was conducted in the SFJD, Black Canyon, Deer,
and Murderers creeks. Data were gathered from FLIR imagery, LiDAR images
depicting vegetation structure, channel morphology and basin topology,
aerial photographs of push-up dams, multispectral satellite imagery and
maps identifying patterns of public ownership. This information was used
to define discrete reaches that formed the sampling strata that greatly
reduced sample variance. Sentinel sites (defined as a 5 pools sequence)
or sites that would be sampled repeatedly, were established based on
this strata. These six sentinel sites represent the range of thermal and
habitat characteristics in the study streams and allow for contrasts to
be made between different habitat features to elucidate their influence
on the different fish responses. Bootstrapping procedures were used to
sample the census information to determine the number of samples
required to produce an accurate picture of the census area with a
defined level of statistical power.

[Proposal:]{.underline} Based on the results of the testing of protocols
and information from current monitoring efforts, we will assess the
level of effort (i.e. sample sizes) sufficient to detect defined
differences. Status and trend monitoring information has been collected
by ODFW for 2 years and therefore the ability to address inter-annual
variability and its implication on sample designs is limited. We will
use studies identifying causal relationships and limiting factors to
help describe where monitoring efforts need to be focused. We will also
conduct analyzes like the reach classification approach described above
to develop effectiveness monitoring designs. We will continue to refine
sample designs over the life of this project as new information becomes
available.

Putting all the pieces together that result from implementing tasks
under objectives 1 -- 4 allows us to determine factors limiting
populations in order to prioritize and develop restoration programs and
as hypotheses to test. There are few examples of effective restoration
actions in the Columbia River basin, and this is partially because
actions often do not address the limiting factor within the study area
(Roper et al. 1997). Causal relationships, as defined by current
research and pertinent literature, between fish production and habitat
variables should be assembled into a framework (e.g. models) that allows
us to assess factors limiting fish production in the John Day Basin.
Creation of basin specific evaluation tools will be a synthesis of all
lessons learned in specific John Day pilot projects.

[To Date:]{.underline} We are working with the John Day subbasin
planning participants that have implemented the Ecosystem, Diagnostic,
and Treatment (EDT) model to assess limiting factors and prioritize
restoration efforts. EDT results have been summarized for each watershed
in 2005. Some shortcomings to this general model's application to the
John Day have been identified, and recommendations to produce more basin
specific models have been made (Subbasin Plan 2005). Sediment
assessments and TMDL efforts are expected to completed in 2007 and
provide addition information on limiting factors in the John Day Basin.

[Proposal:]{.underline} The John Day pilot project has initiated or
collaborated on several studies that are evaluating relationships
between environmental factors and/or how these environmental factors
govern fish populations across multiple scales. At the landscape scale,
satellite remote sensing information, summarized in GIS, is being used
to describe *Landscape Changes and Patterns* and its potential impact on
in-stream temperatures. Landscape information is also being used to
estimate in-stream *Sediment Assessment*, habitat quality, and fish
distribution. *Airborne LiDAR and TIR Remote Sensing* collects data at a
much higher resolution at a watershed/reach scale and is being used to
inform these analyses as well as the *TMDL project*. The *TMDL project*
and the *Sediment Assessment project* are relating riparian habitat
information to in-stream temperature and sediment loading, respectively.
At the reach level, the *South Fork IMW* is relating temperature and
habitat characteristics to growth, density, survival, and production of
juvenile *O. mykiss* across different seasons. At this scale, the
*Invertebrate Productivity Monitoring study* is relating invertebrate
abundance to fish growth. These projects have the potential to be
synthesized in a hierarchical fashion to estimate limiting factors
across several scales. We propose to use structural equation modeling
(SEMs) and hierarchal models to synthesize this information across
several scales We plan to use this set of integrated relationships to
describe data collected through basin-wide monitoring to produce a
limiting factor analysis.

The above synthesis will require completion of a number of projects and
thus will not be available in the near term. Therefore, other models
that focus on a reduced set of potentially limiting factors (as judged
by researchers in the John Day) might be constructed for short term use.
For example, stream temperature patterns are a consequence of the
interaction of important physical and ecological processes acting within
the landscape (Ward 1985). The HeatSource model used in the TMDL
process, describes many of this physical processes to define a heat
budget for a reach. Watershed Sciences is developing algorithms to
process LiDAR information that can be used as direct inputs into the
HeatSource model. As is done in the TMDL process, impacts of different
scenarios, such as the increase of the riparian canopy through a
riparian fencing project or increased discharge by purchasing instream
water rights, on stream temperature can be estimated with the HeatSource
model. The *Invertebrate Productivity Monitoring study* is developing a
relationship between prey density and temperature dependent consumption
rates (as estimated by the bioenergetics models) as has been observed
with other fishes (Budy et al. 1996, Budy et al. 2005). This simple
relationship could be used to estimate growth potential of different
stream reaches based on invertebrate and temperature data. Incorporated
with the HeatSource model, which describes temperature regimes under
restored and current conditions, this set of models could identify where
temperature and invertebrate production limits fish production.
Restoration activities addressing these factors can then be prescribed
for these reaches.

**5.5 Determine the effectiveness of restoration actions through
effectiveness monitoring or an experimental management framework, such
as the Intensively Monitored Watershed studies** (Objective 5)

*Intensively Monitored Watershed Restoration Project-Bridge Creek*

We propose a pilot restoration project along approximately 4 km of
Bridge Creek, sufficient to cause a population-level impact to the
steelhead that utilize the system. We will monitor the results, treating
Bridge Creek as an intensively monitored watershed/restoration site.
This is consistent with the purposes of IMWs, one of which is to test
the impacts of restoration projects, with the goal of detecting
population-level effects on targeted species (Bilby et al 2004, PNAMP
2005). Monitoring will be designed to gather responses to the
manipulation as well as covariates unaffected by the manipulation. The
results will be analyzed and used to inform whether the restoration
action was beneficial to the population (the original goal of the
Biological Opinion) while revealing important causal mechanisms.

![](media/image1.pct){width="3.811111111111111in"
height="5.324305555555555in"}The Bridge Creek subbasin is a 710 km^2^
watershed draining directly into the lower John Day River. Bridge Creek
and its tributaries are utilized by a run of Middle Columbia steelhead
that are part of the ecologically distinct Lower John Day population
which occupies the lower, drier Columbia Plateau ecoregion within the
John Day Subbasin, and are listed under the Endangered Species Act
(CBMRC 2005, p. 75). The John Day Subbasin Plan (JDSP) has designated
Bridge Creek as a priority watershed for restoration because its
salmonid production and abundance potential is high (CBMRC 2005, pp. 83,
249). The JDSP also identifies habitat quantity, temperature, sediment
load, habitat diversity and flow as limiting factors in Bridge Creek
(CBMRC 2005, p.83). Analysis of the John Day and other subbasins in the
interior Columbia River basin suggest that incision is a widespread
phenomenon affecting as much as half of all the fish bearing streams in
a watershed (Beechie and Pollock, unpublished data). Historical records
suggest that Bridge Creek and nearby watershed incised deeply in the
early 1900s, shortly after Europeans began to settle the area (Buckley
1992, Peacock 1994). The mainstem incision depth in Bridge Creek
typically ranges from 1-3 m, sufficient to disconnect the stream from
the former floodplain (Figure 5.1). This has resulted in the lowering of
floodplain water tables,

the loss of off-channel habitat and

[]{.mark}

Figure 5.1. Typical sequence of stream incision in the semi-arid region
of the Columbia River basin, showing the lowering of groundwater levels
and the subsequent loss of riparian forest.

riparian forest and a general simplification of stream habitat (Figure
5.1, Elmore et al. 1994). Stream temperatures in the summer frequently
exceed 27 ^0^C, and late summer streamflows are less than 5 cfs (Anna
Smith BLM Hydrologist, personal communication). Not surprisingly, it is
on the 303(d) list of temperature impaired streams (CBMRC, 2005 p. 40).
Due to the erosive nature of some of the geologies and in particular,
the large number of incised, failing stream banks, sediment loads are
high in Bridge Creek, especially during peak flow events. Annual
suspended sediment loads may exceed 19,000 m^3^ (Pollock and Beechie,
unpublished data).

The purpose of the project is to engage in watershed restoration at a
scale sufficient to cause a detectable, population-level impact to the
steelhead and that utilize this watershed. This project proposes to take
a process-based approach to restoration of Bridge Creek to cause
aggradation of approximately 4 km of incised mainstem stream bed and
lower tributary reaches. Such aggradation should raise floodplain water
tables and lead to increased summer streamflows, decreased stream
temperatures, a narrower and more sinuous stream channel, and a vastly
expanded riparian forest. Thus we propose to restore one process
(aggradation), which in turn will trigger a series of positive feedback
loops that restore other biological and physical processes that maintain
stream ecosystems. Comparison of observed parr densities in Bridge Creek
with densities in nearby healthy watersheds suggests that the restored
reaches will potentially increase steelhead rearing capacity
approximately 30 fold. Using available parr and smolt survival estimates
for the John Day River, we calculate that the project will result in an
additional 79 steelhead adult spawners in Bridge Creek. The existing
population is poorly documented because spawner surveys are infrequent,
but based on the very limited, available spawner survey data from ODFW,
which is the best data we have, we estimate that our efforts would
roughly double the current population.

*5.5.1 Proposed actions*

![](media/image2.jpeg){width="3.50625in"
height="2.6326388888888888in"}Presently, aggradation is already
occurring behind reaches where the small, existing beaver population has
constructed dams. Some of these dams have backfilled completely with
sediment, allowing for riparian vegetation such as willows to colonize
(Figure 5.2) and create a stable, elevated stream bed and floodplain.
High sediment loads and rapid riparian colonization in this system has
resulted in a rapid aggradation process (\<10 yr). This process has
locally elevated the stream bed by as much as 1.5 m in some places, but
more typically by less than 0.5 m.

Figure 5.2. View of an aggraded reach upstream of a 1.5 m high beaver
dam on Bridge Creek, Oregon. The pond has almost completely backfilled
with (approximately 7500 m^3^) of sediment. Willows, cattails and other
riparian vegetation have colonized the new surface. Additionally,
willows have recently replaced sagebrush on the adjacent terrace where
water tables have risen to within 0.5 m of the surface. The dam is just
beyond the patch of open water in the upper left of photograph.

Unfortunately, many of the beaver dams fail before the upstream sediment
wedge and dam can be stabilized by riparian vegetation. Dams appear to
fail primarily because of the lack of large diameter woody vegetation
(e.g. willow and cottonwood stems) to provide sufficient strength to
withstand high flows (Michael Pollock, personal observation).

We propose 3 restoration structures that mimic strong, long-lasting
beaver dams, in order to accelerate aggradation processes. These
include: (1) Beaver dam assisting devices or post-pile fences: insertion
of vertical posts or poles across the incised trench to provide key
members for beaver to build dams off of (Figure 5.3); (2) construction
of small diameter log bundles placed perpendicular to the stream in a
series of steps (Figure 5.4); and (3) construction of a series of rock
steps. Each strategy should result in elevated water tables sufficient
to expand the riparian gallery forests and thus create a long-term
supply of structural material for the construction and maintenance of
more beaver dams. All of these structures should become "invisible" in a
relatively short time period as aggradation and vegetative colonization
occurs. The three strategies range between the relatively low cost
option of enhancing habitat so that beaver will build stable dams versus
the higher cost option of actually constructing sediment aggrading
structures. We have identified two general areas along the mainstem of
Bridge Creek totaling approximately 4 km in length where criteria is
appropriate and the likelihood of success is high (Figure 5.5). Criteria
selection included stream gradient, incision depth, floodplain width and
presence of upstream sediment supplies.

![](media/image3.pct){width="2.8229166666666665in"
height="3.6354166666666665in"}[Post-pile fence.]{.underline} This
strategy is simple in concept, and lowest in cost. A series of posts or
poles are pounded into the bed substrate perpendicular to the flow of
the stream (Figure 5.3), preferably near natural constrictions with
low-gradient upstream reaches. These posts provide key structural
support that can then be used by beaver to build durable dams better
able to withstand high flow events until the area behind the dam can
backfill with sediment and be colonized by woody riparian vegetation. A
series of posts lines will be placed in close proximity to mimic typical
frequencies and heights of beaver dams. An idealized beaver dam sequence
might be a primary dam 1-1.5 m high with a smaller 0.5-1 m dam 20-50 m
downstream of the primary dam and 2-3 intermediate-sized (0.5-1 m) dams
upstream of the primary dam, and spaced perhaps 30-100 m apart,
depending on stream gradient, creating a series of connected pools. We
will also provide piles of

[]{.mark}

Figure 5.3. Schematic of a post-pile fence design to facilitate beaver
dam construction-a "soft engineering" approach for causing aggradation
of an incised stream bed.

cottonwood and willow branches for beaver during the dam-building season
(summer) to supplement food and building material. We will work with
ODFW to relocate nuisance beaver (of which there is a steady supply) to
our sites. Such a strategy has been successfully employed elsewhere to
trap sediment in streams (Scheffer 1938, Apple 1983).

![](media/image4.pct){width="2.84375in"
height="3.6354166666666665in"}[Bundled log steps.]{.underline} This
strategy employs bundles of small diameter (30 cm) poles to create a
series of steps sufficient to raise the stream bed to the desired
height, usually 1-2 m (Figure 5.4), to raise the nearstream water table
close to the level (\< 0.5 m) of the floodplain. The structure is
designed such that it will be covered with vegetation and sediment,
particularly once the area

behind it backfills with sediment. Riparian plantings (willow and
cottonwood staking) will be used to aid in the "visual recovery" of the
project. Thus within a relatively short time frame (\< 10 yrs) the
project structure will be invisible, and in a longitudinal profile of
the stream will appear as a locally steepened section (Figure 5.4).
These structures are designed to mimic (very strong) beaver dams in
terms of size and function. These are much higher in cost than the
post-pile fences, and therefore will be limited to fewer locations.

Figure 5.4. Schematic of an idealized bundled-log complex dam-a "soft
engineering" approach for causing aggradation of an incised stream bed.

[Rock steps.]{.underline} This strategy employees the use of large rock
to create a series of steps that will cause aggradation, similar in
design to the bundled log steps (see Figure 5.4). Basalt rock is a
common feature throughout much of the watershed, so indigenous materials
can be used.

Within each of the project areas, we will construct two series or
complexes of aggradational structures. The complexes will be designed
with robust centerpiece structures, either the bundled log steps or the
rock steps, with a series of downstream and upstream post pile fences.

![](media/image5.jpeg){width="4.024305555555555in"
height="2.8409722222222222in"}

Figure 5.5. Map of Bridge Creek showing approximate locations of
proposed restoration and control reaches and proposed PIT tag detectors
and smolt traps. Smolt and adult traps will measure watershed and
subwatershed abundances, and PIT tag detectors will be used to describe
movement between reaches and survival information.

*5.5.2 Expected impacts on O. mykiss*

The restoration actions implemented should restore floodplain processes
that will result in increased baseflow, lower summer temperatures,
decreased sediment loads and greater habitat complexity such as more
off-channel habitat, more riparian vegetation, and more frequent and
deeper pools. These increases in habitat quality and quantity should
increase the carrying capacity of the system. Greater habitat complexity
also provides refuge from predation, interference competition, and high
velocity current. The expected decrease in temperature should also
reduce predation by warm water species such as the exotic smallmouth
bass found in this system either through thermal displacement or
lowering energetic demand. Decreased temperatures should also provide a
thermal environment closer to the energetic optima of *O. mykiss*,
resulting in an increase in growth rates. In addition, allocthonous
inputs should increase with an increase in floodplain connectivity and
riparian vegetation, boosting primary and secondary production, and
increasing growth rates of fishes. Decreases in energetic expenditures
(e.g. temperature and refuge, increases in energetic inputs (e.g.
production), and decreases in mortality (e.g. predation) are expected to
increase survival and production. Decreased sedimentation should lead to
a decrease in gravel and cobble embeddeness, providing increases in
suitable spawning gravels, and habitat complexity for periphyton,
benthic invertebrates, and parr. Egg survival is also expected to
increase as entombment of eggs by sediments is decreased.

To evaluate whether fish are responding to changes in habitat as
expected we will monitor several response variables: 1) Spatial
distribution (juvenile steelhead, and other fish species); (2) smolts
per redd or per spawner (steelhead); (3) migratory timing and size
(steelhead parr and smolts); (4) population abundance (steelhead parr,
smolts, and other fish species); (5) parr-to-smolt survival (steelhead
); (6) smolt-to-adult ratio (SAR- steelhead); and (7) recruiting adults
(R/S- steelhead). The experimental and monitoring program will be
designed to address the hypotheses whether changes in these response
variables are a result of the restoration actions, after accounting for
the number of spawners, natural disturbances, climate indicators, and
habitat conditions not-impacted by the actions (i.e. covariates).

*5.5.3 Experimental Design*

The experimental design attempts to maximize our ability to detect
responses as a function of the restoration action. We plan to do this by
comparing a time series of responses prior to the manipulation to a
series after the manipulation. Intervention Analysis (IA) have been used
for these types of comparisons (Box and Tiao 1975, Steward-Oaten 1986,
Carpenter et al. 1989). A Before-After-Control-Impact (BACI) approach is
an IA with non-manipulated sites used as a covariate, thus the
"controls" are used to reduce variation but are not used to measure it
as do true experimental controls (Steward-Oaten and Bence 2001).
Basically, the difference between the manipulated and the control
responses are calculated for every sample event and these are averaged
for the pre- and post-treatment periods, or Ď(PRE) and Ď(POST),
respectively. The test statistic is [׀]{dir="rtl"}Ď(PRE)- Ď(POST)
[׀]{dir="rtl"} and is compared to a theoretical distribution (e.g. BACI;
Steward-Oaten et al. 1986) or a distribution of random permutations of
the observed sequence of treatment and control differences (e.g. a
Randomized Intervention Analysis; Carpenter et al. 1989). The latter of
these is not constrained by the assumptions of parametric statistics
(for a comparison of BACI and RIA see Cloutman and Jackson 2003). By
evaluating the difference in treatment and control, shared
characteristics (e.g. climatic conditions, geology and vegetation types,
and monitoring crews) tend to cancel out. Thus, the benefit of a control
as a covariate, capturing multiple parameters, becomes more apparent. If
treatment and control watersheds differ substantially in a
characteristic as to swamp the effect of the treatment then these can be
used as covariates to aid in partitioning these sources of variability
from the differences caused by the treatment. Techniques are available
to select useful covariates from a list of potential covariates measured
throughout the study period (Milliken and Johnson 2001, Kershner et al.
2004). Further refinement to statistical models can account for temporal
autocorrelations, cyclic effects, and gradient effects (Draper 1984,
Steward-Oaten and Bence 2001).

We describe what we believe is a powerful design to detect the impacts
of these restoration projects on steelhead, *O. mykiss*. Ultimately,
everything describe below would be implemented, however, reality may
prove otherwise. Because of the scale and complexity of the system we
are proposing to study, we view the gathering of pre-treatment data as
attempt to implement this plan fully and as a scoping process necessary
to determine what is and is not feasible. Potential limitations include
denied permission by land owners, the ability to capture enough juvenile
*O. mykiss* to PIT tag, natural disturbances (e.g. flood events or
debris flows), vandalism, and other unforeseen events.

Depending on feasibility, the experimental approach will be implemented
in the Bridge Creek study over multiple scales: the watershed,
subwatershed, and reach scales (Figure 5.5). At the watershed scale,
Bridge Creek will be compared to nearby Murderer's Creek, where ongoing
monitoring of steelhead populations is already occurring. Within Bridge
Creek, comparisons will be made between Bear Creek, Gable Creek and the
mainstem. Within the mainstem of Bridge Creek comparisons will be made
between control and manipulated reaches, separated by enough distance to
reduce movement between reaches by parr.

Habitat surveys will also be collected in the same areas as the fish
surveys (see below). This information will be used in conjunction with
LiDAR information already collected to describe physically distinct
reaches, as has been done to define sentinel reaches in the South Fork
John Day IMW (Bouwes 2005). This will allow us to better pair control
and treatment reaches for this and further experimental designs. A
minimum of 4 reaches, 2 treated (manipulated) and 2 untreated (control)
reaches, would need to be defined in the mainstem Bridge Creek. More
reaches may be defined to provide more control reaches to bracket
treatment conditions or to conduct other specific research projects
attempting maximize contrast.

Although this hierarchical design may appear redundant, we will attempt
this approach for several reasons. First, by including multiple controls
at different scales, we are protecting against the possibility that
something could go wrong with the one control approach, such as a large
scale disturbance. Second, we are uncertain to the degree restoration
may impact downstream reaches. Although a comparison of multiple reaches
may be more powerful because of higher replicability and the ability to
accurately describe a reach versus a watershed or subwatershed, these
sites may not be independent from each other depending on the degree of
movement by *O. mykiss*, and the degree to which physical impacts from
treated reaches propagate into the next study reach. Third, hierarchical
models such as structural equation modeling, may be able to capture
small scale mechanistic relationships and how larger scale process form
the template for these processes (Shipley 2005). This study will provide
the information to parameterize such models. A better understanding of
the ecological processes that act across scales to ultimately impact
fish populations advances fish management (Fausch et al. 2002). Fourth,
we are also evaluating the degree of variability and statistical power
associated with each scale. This will provide insight into the scale at
which future restoration actions should be monitored. This hierarchical
design will also lend itself to the testing and development of causal
relationships pursued in monitoring and research programs currently
being implemented in the John Day RME pilot program.

*5.5.4 Monitoring Design*

[Steelhead monitoring.]{.underline} After the experimental design has
been determined, implementation monitoring (monitoring to ensure the
restoration action is still in place) and effectiveness monitoring
programs need to be designed. This will likely include a combination of
fixed and probabilistic randomized sample sites (e.g. EMAP approach),
pre- and post-manipulation in control and treatment watersheds. Fixed
sites will reveal responses more quickly than randomized sites (Roper et
al. 2002), but will likely not detect some responses such as increases
in juvenile distribution. A mechanistic understanding of how restoration
actions influence habitat and fish will help determine where fixed
samples sites will be located. In some watersheds or reaches, whole
census can be conducted negating the need for a design to select sample
sites. Described below is the general monitoring program we will take to
estimate before and after treatment fish responses in the control and
treatment areas across multiple scales for each response variable. We
will monitor several life-stages throughout the study areas, including
parr (age 0 to pre-smolt which range in age from 1-4 yrs old), smolts,
and adults.

This study will take advantage of recent advances in PIT tag technology,
including the use of extended length PIT tag detectors that can be
deployed to obtain nearly complete detection efficiency of tagged fish
that pass through the antennas. The placement of PIT tag detectors
between distinct reaches which include treated and untreated reaches. It
is unclear how many parr can be captured and PIT tagged in the different
areas. Up to 3,000 tagged fish per watershed are needed to provide
watershed specific SAR estimates. PIT tag antennas will document the
amount of independence of reaches on fish distribution, habitat use,
growth, and parr-to-smolt survival. In addition, the movement
information will describe the importance of the potomandromous (seasonal
movement between mainstem and tributaries) life history strategy as
observed in the South Fork of the John Day IMW. This strategy is thought
to occur because of an interaction between behavioral thermoregulation
and density dependent interactions, where a percentage of the population
uses cooler tributaries in the summer, migrates out in the fall to rear
in the warmer mainstem John Day, and potentially returns to the
tributaries as mainstem temperatures become too warm in the summer
(Hiram Li, OSU Personal Communication). The use of tributaries for
thermoregulation is a life-history strategy for steelhead that requires
further investigation (CBMRC 2005, Tim Unterwegner and Jim Ruzycki of
ODFW, personal communication).

Parr abundance and distribution will be estimated through a combination
of snorkeling surveys, snorkel-herding and electro-herding
(electroshocker set to a low setting that is irritating but will not
stun) into bag seines. Snorkel- and electro-herding will be used to
capture fish to PIT tag as well as to calibrate snorkel surveys that are
used by ODFW. These methods have been calibrated in the South Fork John
Day IMW (Bouwes 2005). A census using snorkel/herd-seining surveys may
be conducted over the entire study area. In some areas these surveys
will not be logistically feasible, such as in beaver ponds where
disturbance of sediments will preclude visual estimates, or in shallow
waters that cannot be reasonably observed. In such instances, 3-pass
electroshocking or mark-recapture Peterson abundance estimates will be
conducted for each habitat unit. Surveys will be conducted at the
beginning and the end of the summer field season. Habitat surveys will
be conducted at these sites as well. Changes in fish density will be
used to assess changes in habitat quality, with the assumption that fish
select for higher quality habitat as a means to increase fitness. These
surveys can be used to address reach scale comparisons or rolled up to
assess larger scale comparisons. Further sampling may be done to capture
more fish to increase the sample size of PIT tagged fish.

A redd census and carcass survey will also be conducted in Bridge Creek,
Bear Creek and Gable Creek. As adults begin to return from the first
cohorts of PIT tagged juveniles, carcasses will also be scanned for PIT
tags. In addition, fixed reaches and ten 1 km long reaches selected in a
random probabilistic design will be visited every two weeks throughout
the season to quantify cumulative redd counts at each site, as is done
for the ODFW steelhead surveys.

The number of smolts leaving and adults entering a watershed or
subwatershed will be compared in this experiment as this gets to the
most direct measure of interest, freshwater production or smolts per
spawner. A removable two-way trap will capture outmigrating juveniles
and incoming adults. The trap will be deployed daily to once a week and
checked the next day. PIT tag antennas will be deployed above the traps
to describe trap efficiency. The ratio of tagged to untagged fish may
remain rather constant negating the need to deploy the trap on daily
basis (this is currently being evaluated in the South Fork John Day
IMW). All outmigrating juveniles will be scanned using a hand-held PIT
tag detector or tagged if no tag is detected for further survival
estimates (SARs). These traps will be operated during the migration
seasons when possible. The traps will be used to capture adults
migrating upstream to the spawning grounds. Adults will measured, aged,
sexed and scanned for tags as well during the spawning season. This
information will be used estimate recruits per spawner or overall
life-cycle survival.

Cormack-Jolly-Seber (CJS) models of mark-recaptured PIT tag fish will be
used to estimate seasonal parr survival, parr-to-smolt survival, smolt
reach survival in the mainstem John Day and Columbia River, and
smolt-to-adult survival between reaches, subwatersheds and watersheds.
PIT tag detected at PIT tag antennas in the study watersheds, smolt and
adult traps, and John Day and Bonneville dams on the Columbia River will
be used to make these estimates. Multiple CJS type models can be
compared to evaluate influence other covariates such as; time at
release, size, number of times recaptured, and habitat features on
survival rates (White et al. 1999).

The size, timing, and age of out-migration smolts may provide
information about changes to habitat quality. Length and weights of parr
captured for tagging will be measured. Juveniles recaptured at the traps
or in later juvenile surveys will also be measured to describe a change
in biomass or growth. Growth rates will then be compared between
reaches, subwatersheds, and watersheds throughout the study.
Bioenergetics model can be used to further partition these changes in
growth to changes in temperature and prey production. Growth rates and
other information are a more proximate response to habitat quality than
measures of survival allowing for a finer resolution evaluation of the
impacts of these restoration actions on juvenile salmonids. Also,
changes in the amount of time spent rearing in the different study areas
will also provide us a more mechanistic understanding of impacts of
restoration to this population.

[Habitat monitoring]{.underline} --LiDAR and 3-band digital aerial
photography remote sensing has already been conducted for Bridge Creek
and Murderer's Creeks. When analyzed these data will provide baseline
data on stream and riparian habitat conditions within the restored and
control reaches. Using these data, habitat parameters that will be
quantified within the restored and control reaches include: aerial
extent of riparian vegetation, sorted by dominant vegetation type (e.g.
willows, cottonwoods, emergent graminoids), stream geomorphology,
including cross-section geometry, planform sinuosity and longitudinal
gradient profile, and the location and size of beaver dams. Our goal is
to repeat these remote sensing surveys over the study area every 3 yrs
after completion of the project to measure changes in habitat quality
and quantity. Because LiDAR does not easily penetrate water, we will
also measure and monument stream cross-sections at the restored and
control sites so as to provide data on aggradation rates and volumes
behind the structures relative to control sites, as well as providing
detailed information on changes in the channel cross-section geometry.
Additionally, in FY 2006 we (NOAA Fisheries) will be installing water
level monitoring well fields along the proposed restoration and control
sites to measure the anticipated changes in floodplain groundwater
levels upstream and downstream of the aggradational structures,
including "control" locations where beaver dams already exist. Automatic
water level recorders/temperature monitors will be installed in the
wells. In FY 2006 we will also install temperature data loggers within
the restored and control reaches, which will remain in place before,
during and after completion of the restoration project.

**5.6 Learn and adapt**

Given what we learn from implementing the above 5 steps, we will be able
to provide rationale and suggestions on how to change current monitoring
designs to best address goals in the John Day River basin. While we are
working on completing the above steps, we will be working with current
monitoring efforts to determine near term alterations that may need to
be implemented to provide necessary information. Ultimately, we would
like to apply what we have learned through completing the above steps to
develop a well-coordinated and comprehensive monitoring program in the
John Day Basin as an example of how other basins should develop an RME
program. The success of the pilot project will be dependent on the
ability to develop and maintain working relationships with those who
will ultimately be conducting the RME program. Collaboration and
demonstration of how the RME process can be improved will likely result
in an adoption of these suggestions. While this is not a fast track
process, we believe that this will lead to a longer term, well
coordinated RME program than if we immediately insisted on
implementation of a theoretical RME plan.

**6.0 Salmon River Basin**

**6.1 South Fork Salmon River**

The South Fork Salmon River (SFSR) was selected to part of the ISEMP
because: 1) it represents a substantial contributor to Snake River
spring/summer Chinook salmon production and 2) ongoing monitoring
activities are accompanied by a substantial time series and present an
opportunity to evaluate sampling alternatives in a "common garden." The
initial phases of ISEMP implementation in the SFSR will emphasize status
and trends monitoring development to take best advantage of a developed
monitoring infrastructure and historical data collection efforts.
Subsequent development of effectiveness monitoring opportunities will be
explored as the watershed's potential is more fully understood.

The SFSR supports listed stocks of native summer-run Chinook salmon and
B-run steelhead (Matthews and Waples 1991). Historically, the South Fork
Salmon River (SFSR) was the single most important summer Chinook salmon
spawning stream in the Columbia River basin, accounting for
approximately 50% of the summer Chinook salmon redds enumerated in Idaho
(Mallet 1974). Declines in natural escapement within the SFSR have
paralleled those of other Snake River stocks, resulting in their listing
under the Endangered Species Act (ESA). The Interior Columbia River
Basin Technical Recovery Team (ICBTRT) identified three populations of
spring/summer Chinook salmon in the SFSR, including the mainstem SFSR,
the Secesh River, and the East Fork SFSR (EFSFSR; ICBTRT 2003); together
forming a single Major Population Group (MPG).

The ICBTRT also identified two steelhead populations in the SFSR (one in
the Secesh River, and the other inhabiting the mainstem and EFSFSR;
ICBTRT 2003). The TRT (ICBTRT 2003) commented on the inadequacy of
existing data to determine: 1) spawner distribution; 2) general life
history information; and 3) population and stream level abundance data.

A substantial number of Research, Monitoring, and Evaluation (RME)
projects are currently underway in the SFSR, primarily aimed at
assessing the effectiveness of artificial propagation at increasing the
abundance of adult spring/summer Chinook salmon. These ongoing
activities, managed by the NPT and IDFG, utilize substantial
infrastructure (Figure 6.1). In addition, the NPT and IDFG conduct
spawning ground surveys that cover nearly all of the known range of
spring/summer Chinook salmon spawning habitat.

However, existing projects in the SFSR (with the exception of the Secesh
River for spring/summer Chinook salmon) primarily address subpopulations
(e.g., the Johnson Creek component of the EFSFSR spring/summer Chinook
salmon population, the Lake Creek component of the Secesh River
spring/summer Chinook salmon population, and the upper mainstem SFSR
component of the mainstem SFSR spring/summer Chinook salmon population).
These subpopulation level estimates may or may not adequately represent
the larger population, and data currently cannot be aggregated to yield
an MPG level population estimate due to gaps in existing data collection
(e.g., in the lower mainstem SFSR area). In addition, much of the
available data for steelhead and resident salmonids is collected
opportunistically by projects targeting spring/summer Chinook salmon,
thus it is unclear how effectively these data portray the status and
trends of these non-target species/life-histories. Finally, the SFSR
lacks an integrated and standardized habitat monitoring component.

The SFSR Status and Trends Pilot Project has developed a coordinated
study design (QCI 2005) that utilizes information from existing projects
and proposes additional monitoring effort and infrastructure in the
South Fork Salmon River that develops; information needs, power analyses
to define tagging requirements, estimators of common precision metrics
among methods, validation metrics, and multiple methods for estimating
life-stage specific abundance and survival -- this plan is currently
under review by regional technical teams (e.g. ISRP).

[]{.mark}

![](media/image6.pct){width="4.521527777777778in"
height="4.624305555555556in"}

**Figure 6.1.** Location of existing (black) and proposed (red) juvenile
and adult sampling infrastructure in the SFSR.

The proposed SFSR status and trends work will generate habitat and
population status and trend data for spring/summer Chinook salmon at the
reach, population, and MPG spatial scales; and steelhead and resident
salmonids (e.g., rainbow trout) at the reach and population scale. As
summarized below, the precision and reliability of estimates generated
using proposed methods will be compared to existing methods following
standardization of data. Habitat sampling effort will be allocated to
fixed (trend) and probabilistically (status) selected sites, building
when possible on existing fixed site surveys. A response design and
habitat attributes will be selected based on the results of the habitat
protocol comparison project (PNAMP 2005).

The ability to generate status and trend information at multiple spatial
scales is constrained by: 1) logistical and technological limitations;
2) the fact that most of the existing monitoring projects are designed
to evaluate a management action that occurs at a specific spatial scale;
and 3) data collection and analysis methodologies are not routinely
standardized among projects. The SFSR provides an opportunity to
leverage substantial existing infrastructure and effort to evaluate and
validate alternative designs capable of providing status and trend
information at multiple spatial scales with relatively minimal
additional cost.

In short, existing infrastructure within the SFSR will be supplemented
by a combination of additional juvenile and adult sampling devices and
extended length PIT tag arrays (Figure 6.1). PIT tag arrays will have
two sets of antennas (A and B; one upstream and one downstream)
separated by a distance of approximately five meters, attached to a
common reader. Juvenile PIT tagging will occur in each major tributary
(mainstem SFSR, the Secesh River and the EFSFSR) via probabilistically
distributed and fixed site electrofishing effort (which may also
simultaneously serve a habitat monitoring function). Adults will be PIT
tagged at the fishwheel located near the confluence of the SFSR and
mainstem Salmon River. Proposed infrastructure will enable estimates of
juvenile and adult Chinook salmon and anadromous steelhead abundance at
the scale of the SFSR MPG (for spring/summer Chinook salmon), individual
populations, and reaches (in the case of Lake Creek spring/summer
Chinook salmon). Abundance, productivity, and life-stage specific
survival estimates generated by the proposed infrastructure will be
validated by comparisons to estimates derived from existing and proposed
infrastructure.

*6.1.1 Juvenile Abundance and Survival Estimates*

Population specific and aggregate estimates of juvenile abundance and
survival will be estimated using information obtained from the recapture
of juveniles PIT tagged during electrofishing surveys in each major
tributary (mainstem SFSR, the Secesh River and the EFSFSR). Recapture
data for tagged individuals will be derived from repeat electrofishing
surveys, interrogations at extended length PIT tag arrays, via recapture
at the proposed lower mainstem rotary screw trap, and at existing
tributary rotary screw traps. Efficiency estimates for rotary screw
traps will be generated in two ways:

1.  via marking a subsample of captured juveniles for release upstream
    of the trap and performing a simple mark-recapture and

2.  using the proportion of previously PIT tagged juveniles (e.g.,
    tagged during electrofishing surveys) that are detected at the
    extended length PIT tag arrays downstream of the screw traps that
    passed the traps without capture.

Efficiency estimates of extended length PIT tag arrays will be generated
using two methods:

1.  via the proportion of juveniles PIT tagged at upstream rotary screw
    traps that are not recorded at the PIT tag arrays during passage and

2.  mathematically by calculating the probability that a PIT tag would
    not be detected given the numbers of PIT tags detected at the
    upstream span of the tandem array (A), but not the downstream span
    (B), the number detected B but not at A, and the number detected at
    both A and B.

Expanding the previous example to the entire SFSR, fish tagged in each
of the major tributaries (Mainstem SFSR, EFSFSR, and the Secesh River)
will be detected at the lower mainstem rotary screw trap and via PIT tag
interrogations at tributary specific PIT tag arrays and the PIT tag
array located on the lower mainstem SFSR. Population specific juvenile
abundance estimates obtained via proportional partitioning of the SFSR
estimate will serve two purposes:

1.  to compare the precision of partitioning an SFSR scale juvenile
    abundance estimate versus tributary specific estimates generated
    using rotary screw traps and

2.  to evaluate the proportion of juvenile production not sampled by
    existing infrastructure due to the placement of that infrastructure
    above varying fractions of the spawning and rearing habitat.

*6.1.2 Adult Escapement Estimates*

Adult escapement estimates are currently generated by a Dual-frequency
IDentification SONar (DIDSON) array in the Secesh River, a video weir in
Lake Creek, a temporary picket weir in Johnson Creek, and a reinforced
weir located in the upper mainstem SFSR. The enumeration sites on the
Secesh River have been extensively validated and escapement estimates
are accompanied by variance estimates. The weirs operated on Johnson
Creek and the upper mainstem SFSR utilize mark-recapture (via marking
adults at the weir and recovering marks during carcass surveys) to
provide efficiency estimates, thus enabling variance estimation for
total escapement past the weirs. None of these sites is currently
operated to enumerate steelhead escapement, and the estimates provided
by enumeration sites on the mainstem SFSR, Johnson Creek, and the Secesh
River are located above varying fractions of the spawning habitat
utilized by spring/summer Chinook salmon. Because existing
infrastructure does not enumerate total escapement for any of the SFSR
populations (with the possible exception of the Secesh River),
population level escapement estimates and estimates of escapement for
the SFSR spring/summer Chinook salmon MPG cannot be calculated. In
addition, escapement of steelhead is not currently estimated for either
of the SFSR populations. We propose the operation of a fishwheel on the
lower mainstem SFSR to collect, PIT tag, and visually mark returning
adult spring/summer Chinook salmon and steelhead. Total escapement to
the SFSR for each species will be generated using the efficiency of the
fishwheel to expand captures. Efficiency estimates for the fishwheel
will be generated using two methods:

1.  calculating the proportion of PIT tagged adults (originally tagged
    as juveniles via proposed electrofishing surveys and at existing
    rotary screw traps) detected at the extended length PIT tag array
    located below the fishwheel that escape the fishwheel and

2.  by releasing a subsample of the adults captured and tagged at the
    fishwheel downstream of the fishwheel and calculating the proportion
    that are detected at the PIT tag array, but are not recaptured at
    the fishwheel.

Method one is preferred, as it limits handling stress, however the
number of returning adults with a PIT tag may be insufficient to
generate efficiency estimates across strata that are expected to effect
efficiency (e.g., changes in flow).

Tributary and reach specific Chinook salmon and steelhead escapement
will be estimated via interrogation of PIT tagged adults at extended
length PIT tag arrays located in each tributary. Efficiency estimates
for the tandem extended length PIT tag arrays will be generated as
discussed under juvenile survival and abundance estimation above.
Escapement estimates for spring/summer Chinook salmon generated via
parsing of the total SFSR estimate will be validated using the proposed
lower Secesh River DIDSON site, which will enumerate total escapement to
that tributary for both spring/summer Chinook salmon and steelhead.

The monitoring program development work piloted in the SFSR hinges on
the ability to perform retrospective statistical analyses to provide
variance estimators for historical time series data, and the development
of statistical relationships between estimators derived from proposed
versus existing infrastructure and analytical methods. Thus the SFSR
Pilot Project is moving beyond the side-by-side
protocol/indicator/metric tests underway in the Wenatchee and John Day
Pilots to experiment with an entirely new status and trends monitoring
approach designed top-down from the resource data management needs. For
example, IDFG has completed redd surveys for spring/summer Chinook
salmon in index areas of the mainstem SFSR, Johnson Creek, the Secesh
River, and Lake Creek since the late 1950's. Surveys cover non-randomly
selected reaches located in "important" spawning areas for spring/summer
Chinook salmon that are surveyed in a single pass timed to correspond
with the peak of spawning (Hassemer1993). These data provide an
important time series of redd abundance trend data, that have been
widely utilized in listing decisions and risk analyses (Holmes 2001,
2004a, 2004b, Hyun and Talbot 2004, McClure et al. 2003). Nonetheless,
these data are not accompanied by variance estimates, and the degree to
which these redd counts represent the "population" of redds within a
given year is largely unknown. Finally, the expansion of redds to
estimate adult escapement is accompanied by numerous assumptions (Roger
and Schwartzberg 1986). We propose to use the validated adult escapement
estimates generated by this proposal to evaluate the utility of the IDFG
redd count time series as a measure of relative abundance. Observed
variance in the relationship between escapement and IDFG redd counts
will be used, if possible, to retrospectively evaluate the precision of
the time series. If a significant relationship can be developed,
managers could elect to implement escapement methods developed by this
proposal as a possible replacement for single pass or extensive redd
surveys.

As discussed previously, the infrastructure currently operated to
provide juvenile and adult abundance estimates within the SFSR watershed
generally provide suboptimal information for steelhead, and Chinook
salmon estimates are generally applicable to some fraction of targeted
populations, and these data cannot be aggregated for MPG level
estimates. While proposed infrastructure enables reach, population, and
MPG level estimates, managers may be justifiably hesitant to replace
existing infrastructure without developing a relationship between the
proposed estimators and existing estimators. Thus the following
relationships will be developed:

1.  escapement estimates generated for the EFSFSR (generated using the
    proposed methods) versus estimates currently generated for Johnson
    Creek (the primary EFSFSR tributary);

2.  escapement estimates for the entire mainstem SFSR (generated using
    the proposed methods) versus those currently generated for the upper
    SFSR;

3.  escapement estimates for the Secesh River (generated using the
    proposed methods) versus those generated from the existing DIDSON
    site; and

4.  juvenile emigrant abundance estimates currently generated by
    infrastructure in the Secesh River, upper mainstem SFSR, and Johnson
    Creek versus those generated by the proposed design.

Finally, the SFSR Pilot project seeks to evaluate the efficacy of the
proposed infrastructure for providing juvenile and adult abundance,
survival, and productivity estimates independently of all existing SFSR
infrastructure. If implementation and validation of proposed
infrastructure and estimates are acceptable for management purposes
(i.e., are reliable and provide adequate precision), the deployment of a
similar study design and associated infrastructure may enable reach,
population, and MPG level status and trend monitoring, for relatively
low cost, in locations that currently lack such estimators (e.g., the
Middle Fork Salmon River). Thus the proposed design and associated
infrastructure will be evaluated for its potential as a template that
can be applied elsewhere.

**6.2 Lemhi River Habitat Action Effectiveness Monitoring**

The Lemhi River is a tributary to the upper Salmon River, located in
central Idaho State. There are a total of 31 tributaries to the Lemhi
River. With the exception of Hayden Creek and Big Springs Creek, in most
years all are dewatered in their lower reaches, and are therefore
isolated from the Lemhi River. Tributaries contain habitat that is
believed to be important for the persistence of fish in the Lemhi basin.
Grassroots concern over the widespread habitat degradation within the
Lemhi River watershed resulted in its designation as a Model Watershed
(e.g., ISCC 1995).

Habitat restoration activities in the Lemhi are guided by the Lemhi
Conservation Plan (LCP). The LCP is an evolving document that has
benefited from a wealth of information on historical productivity,
life-stage specific survival, and carrying capacity (Bjornn 1978);
contemporary juvenile density, abundance, distribution, and the
distribution and magnitude of adult spawning (Venditti et al. 2005); and
habitat attributes (Trapani 2002) including habitat and discharge
relationships (Sutton and Morris 2005) available for the Lemhi. Ongoing
and proposed habitat actions have been targeted to address the limiting
factors deduced by these studies and are aggressive, and anticipated to
result in measurable biological responses, both in terms of physical
habitat attributes (e.g., quality and quantity of accessible habitat)
and fish vital rates (survival/productivity, distribution, and
abundance) both at the scale of individual reaches and at the scale of
the watershed. These habitat actions are the primary mechanism intended
to stimulate the delisting of the ESA listed TRT identified population
of spring/summer Chinook salmon (*Oncorhynchus tshawytscha*) and
steelhead trout (*O. mykiss*) as well as bull trout (*Salvelinus
confluentus*) populations that reside in the Lemhi River subbasin.

Actions proposed in the LCP are intended to:

1.  Remove or reduce upstream and downstream migration barriers to fish
    and provide access to available spawning and rearing habitat by:

    a.  providing flow to maintain hydraulic and ecological connectivity
        between the mainstem and tributaries so that fish have access to
        historically productive habitat;

    b.  providing flow in the lower reach of the Lemhi River so that
        adults and juveniles can freely migrate in and out of the Lemhi
        subbasin;

    c.  removing physical obstructions (e.g. irrigation berms and
        push-up dams) that limit localized movements of upstream and
        downstream migrating fish; and

    d.  minimizing entrainment into irrigation ditches that do not
        provide adequate rearing habitat and do not functionally
        reconnect with the Lemhi River or its tributaries.

2.  Maintain or enhance riparian conditions characteristic of good
    habitat to ensure that adequate vegetation persists to provide
    shade, increase bank stability and protection, decrease sediment
    input, and promote the recruitment of large woody debris.

3.  Decrease sediment, temperature, provide quality substrate, increase
    the abundance and quality of off-channel habitat, and increase pool
    frequency and quality to improve productivity and survival.

Because ongoing and proposed habitat actions in the Lemhi watershed are
targeted to efficiently address limiting factors that have a predefined
spatial structure (e.g., reconnection of tributaries) and since these
actions require significant landowner cooperation, there is a limited
ability to randomly allocate habitat actions. Thus, evaluation of the
effectiveness of many of the habitat actions will take the form of
design-based experiments (ISRP 2005). The primary goal of the Lemhi
Habitat Action Effectiveness Pilot Project is to identify and quantify
the effects of classes of habitat actions (e.g., channel reconnection,
flow augmentation, physical changes in channel morphology etc.) on the
abundance productivity/survival, condition, and distribution of
anadromous and resident salmonids within the Lemhi watershed. Because
multiple habitat actions may be collocated, assessing the individual
affects of classes of habitat actions will require a modeling approach.
In addition, because the LCP uses a phased implementation approach,
wherein the effectiveness of Phase I habitat actions are used to
identify and prioritize Phase II actions, the model-based approach will
be useful for conducting *a priori* simulations to estimate the
potential effects of different suites of proposed Phase II habitat
actions. A statistical framework developed for the Lemhi Pilot Project
produced the following tools:

1.  Development and application of a watershed model to evaluate
    survival, productivity, and carrying capacity by life-stage as a
    function of habitat availability and quality, with a simulation
    component to estimate life-stage specific benefits from increased
    habitat availability and/or quality.

2.  Development and implementation of a study design that utilizes
    reach-specific empirical measures of productivity, juvenile
    survival, condition, and distribution across habitat classes, in
    treated and untreated areas, to determine whether tributary
    reconnection and other habitat actions have provided high quality
    habitat that benefits fish vital rates (survival, growth etc.).

3.  Development and implementation of a design that evaluates the
    movement and distribution of anadromous and resident salmonids to
    address the following questions:

    a.  Are anadromous fish utilizing reconnected habitat?

    b.  Have the reconnections changed the distribution and connectivity
        of resident fish?

The following sections summarize functions of the model and design-based
features of the Lemhi Pilot Project Study Design ([QCI 2005]{.mark}),
and describe a sampling design to meet the information needs of the
approach.

Tool one takes the form of a watershed model (based on Sharma et al.
2005) that views fish vital rates (survival/productivity, abundance, and
condition) as a function of the quantity and quality of available
habitat. These functions are constructed using both coarse (e.g.,
Geographic Information Systems (GIS)) and fine (e.g., reach) scale
habitat measures (Figure 6.2). Once validated via the collection of
empirical data within habitat classes, the model provides a statistical
framework to assess the effects of different classes of habitat actions
on life-stage specific vital rates (productivity/survival and condition)
of anadromous and resident salmonids.

The information needs of the watershed model are addressed by a sampling
design (Tool 2) that yields reach specific and aggregated estimates of
life-stage specific juvenile abundance, productivity/survival,
condition, and distribution as well as adult escapement across habitat
classes and within treated and untreated stream reaches. The use of
tandem extended length PIT tag arrays within the study design provide
information necessary to determine whether habitat actions (e.g.,
channel reconnection) have increased population connectivity, and
whether anadromous salmonids utilize newly available habitat (Tool 3).

**Figure 6.2.** Schematic illustrating how the model develops
relationships between habitat quantity (capacity) and quality
(survival/productivity) and stage-based abundance, productivity, and
survival. Grey boxes indicate those life stages for which metrics will
be inferred, notation in parentheses refers to model parameters, and
numbers within the boxes refer to equations in the Lemhi Study Design
([QCI 2005]{.mark}).

Existing data collection efforts within the Lemhi River are insufficient
to satisfy the reach and life-stage specific information needs of the
Lemhi Pilot Project. The following sections summarize those information
needs and propose methods for data collection.

*6.2.1 Adult Escapement*

There are currently no fixed point (e.g., weir based) counts of adult
escapement to the Lemhi River. We propose to generate escapement
estimates for anadromous salmonids (and possibly adfluvial residents) by
modifying an existing mainstem irrigation diversion (L6) to serve as a
trap or as a location for a video monitoring station (Figure 6.3). A
trap is preferred, as that would enable adults to be PIT tagged.
Aggregate escapement will be partitioned into reach specific estimates
via the interrogation of PIT tagged adults at mainstem and tributary
tandem extended length PIT tag arrays (Figure 6.3). Efficiency estimates
for the mainstem fish trap will be generated using two methods:

1.  calculating the proportion of PIT tagged adults (originally tagged
    as juveniles via proposed electrofishing surveys and at existing
    rotary screw traps) detected at the extended length PIT tag array
    located below the trap that escape the trap and

2.  by releasing a subsample of the adults captured and tagged at the
    trap downstream of the trap and calculating the proportion that are
    detected at the PIT tag array, but are not recaptured at the trap.

If adults cannot be captured at the L6 diversion, tributary extended
length PIT tag arrays would be accompanied by video weirs or DIDSON
arrays to enable partitioning of adult escapement.

*6.2.2 Juvenile Abundance, Survival, and Distribution*

Some of the habitat actions proposed in the LCP are anticipated to
primarily effect survival at specific life stages. For example,
augmentation of pool habitat might be expected to exert the greatest
influence on juvenile overwinter survival, thus measures of survival
from the presmolt to smolt life-stage may be most sensitive to the
effects of that habitat action. The collection of life-stage specific
vital rates provides a means to potentially separate the effects of
collocated habitat actions. Thus, methods to generate life-stage
specific juvenile productivity/survival, abundance, and condition are
required. Juvenile abundance estimates (primarily targeting emigrating
spring Chinook salmon) are currently generated via rotary screw traps at
two sites in the Lemhi watershed. We propose to operate an additional
screw trap in Hayden Creek (Figure 6.3) and extend the operating period
of the existing screw trap in the upper Lemhi mainstem to better
estimate steelhead emigration. These efforts will be useful in
generating population level juvenile emigrant abundance estimates,
estimating survival from earlier life-stages, and in determining the
proportion of juvenile production that occurs in Hayden Creek, a
potential reference stream.

Estimates of pre-migratory juvenile abundance and survival in
reconnected versus currently available habitat will be generated using
PIT tags and visual marks, deployed via electrofishing at fixed and
probabilistically selected sites throughout the Lemhi watershed (e.g.,
in currently available, reconnected, and isolated habitat). Recaptures
of PIT tagged juveniles will occur during repeat electrofishing surveys,
at extended length PIT tag arrays, and at rotary screw traps. Efficiency
estimates for screw traps will be derived by marking and releasing a
fraction of each days catch above the trap and calculating the fraction
that are recaptured at the screw trap. Efficiency estimates for extended
length PIT tag arrays will be derived in two ways:

1.  by calculating the number of juveniles tagged in a given tributary
    that are detected at downstream sites (e.g., the mainstem PIT tag
    arrays and screw traps) that were not detected at the tributary PIT
    tag array and

2.  mathematically by calculating the probability that a PIT tag would
    not be detected given the numbers of PIT tags detected at the
    upstream span of the tandem array (A), but not the downstream span
    (B), the number detected B but not at A, and the number detected at
    both A and B.

It is anticipated that PIT tags can be deployed in both anadromous and
resident salmonids (e.g., rainbow trout). Juvenile survival will be
estimated by evaluating overall systemwide recapture efficiency,
generated by common PIT tag detections at upper and lower screw traps,
determining the fraction of fish that passed PIT tag arrays (using the
efficiency estimates described above), and via repeat electrofishing
surveys. Juvenile distribution and movement will be evaluated by
scrutinizing recaptures of tagged fish during repeat electrofishing
surveys, by interrogations at extended length PIT tag arrays, and via
capture at rotary screw traps.

**Figure 6.3.** Location of existing (black) and proposed (red)
infrastructure for the Lemhi River watershed.

*6.2.3 Habitat Sampling*

Habitat sampling effort will be allocated to fixed (trend) and
probabilistically (status) selected sites. A response design and habitat
attributes will be selected based on the results of the habitat protocol
comparison project (PNAMP 2005). Because the design requires estimates
of habitat availability for specific life-stages of juvenile resident
and anadromous salmonids, habitat surveys will incorporate temporal
replication to achieve seasonal estimates of habitat availability.

*6.2.4 Evaluation*

Evaluations of the effectiveness of habitat actions within the Lemhi
River follow the following summarized framework:

1.  potential productivity (capacity), survival, and realized
    productivity are compared within sites before and after the
    implementation of habitat actions;

2.  potential productivity (capacity), survival, and realized
    productivity are compared across treatment and reference sites
    within the Lemhi watershed and among different treatment types and
    extents using a cross-sectional design; and

3.  at the scale of the Lemhi watershed, a combination of empirical
    survival (via PIT tag interrogation) and modeling will be used to
    continuously assess changes in population growth rate over the
    course of the LCP implementation.

Four primary questions have been identified by the Lemhi Pilot Project:

1.  have tributary reconnections changed habitat availability and what
    are the affects of tributary reconnections on stage-based carrying
    capacity (i.e., potential productivity);

2.  have other habitat actions (e.g., creation of pool habitat) changed
    stage-based productivity/survival;

3.  have tributary reconnections changed fish distribution; and

4.  is fish condition similar in reconnected versus existing habitat
    (i.e., what is the quality of reconnected tributary habitat relative
    to existing habitat)?

Since the sampling design will provide multiple replicate estimates of
stage-based abundance and survival within land-use classifications, we
can implement a binomial test using Generalized Linear Models (GLM; R
software) with the logit link to determine whether carrying capacity
varies as a function of land-use and whether reconnections changed
survival/productivity, using a pre/post test (Question 1).

A number of other habitat actions (e.g., increased flow) will be
occurring in addition to (or as a result of) tributary reconnections
(Question 2). Since data are cross-sectional (e.g., measures are
replicated under varying flows), and assuming a given watershed variable
of interest has sufficient contrast then we can show how manipulations
in a certain watershed trait (e.g. flow or predator-density) will affect
potential productivity.

Measures of juvenile abundance by life history stage corrected for
spawner abundance within a given habitat classification will be used in
a pre/post treatment analysis (Question 3). For each life cycle stage
and location, a model is implemented in GLM (R-software), and the
results are analyzed using an Analysis of Covariance.

Pre-experiment data on fish attributes (e.g., size, weight, or condition
factor) before reconnections, versus the same measures after
reconnection, collected at rotary screw traps and during electrofishing
surveys, enables a test of the effects of reconnections on these
attributes (Question 4). If pre-treatment data for fish condition are
unavailable, the effects of differing levels of stream connectivity on
fish condition can be evaluated in a treatment versus control framework.

**7.0 ISEMP overall project components (Objectives 6 & 7)**

**7.1 Develop monitoring data analysis tools and tools to evaluate
monitoring programs and approaches (Objective 6).** Data analysis
objectives for 2007-2009 capture four facets of the RME project:
standard data reduction of status and trend monitoring data, evaluation
of monitoring protocols and overall design, determination of mechanistic
linkages among habitat condition and response variables and evaluation
of population limiting factors at a HUC 6 watershed scale. Outcomes of
these objectives will provide feedback to the RME program to streamline
monitoring design and data processing, facilitating the identification
of habitat conditions important for ESA and non-ESA species. Data
compiled and generated within RME pilot basins during proposed
(2007-2009) and past (2004-2006) funding years will be used for the
proposed analyses. Analysis objectives encompass multiple data types
generated for the RME project, including water quality, multiple fish
life stage populations (juvenile, smolt, and adults), macroinvertebrates
and riparian and in-stream habitat metrics.

[To Date:]{.underline}

The data collection process in the Wenatchee basin has been used as a
testing scenario for evaluating the data reduction process. We have
outlined data reduction and storage goals based on commentary from fish,
habitat, and water quality data providers in both the Wenatchee and John
Day basins. Data provider goals include: simple and easily modified
database storage, straightforward database communication with analysis
tools, guideline development for data quality, and the development of
consistent and relevant data analysis tools.

Additionally, our completion of historical dataset compilation in the
John Day basin and continuing work in the Wenatchee and Salmon basins
has developed a process for the locating, identifying, prioritizing,
processing, and storing historical datasets. Although this compilation
process is still in progress, historical datasets in the John Day are
available for use in analysis tool development.

[Proposal:]{.underline}

The development of data analysis tools and RME evaluation will improve
local agency data manipulation and feedback to the RME pilot program.
Data analysis tool development will focus on the creation of a standard
process to reduce status and trend monitoring data generated by the
pilot project, calculate standard habitat metrics, calculate statistical
summary metrics, and develop indicators of habitat metrics relevant to
biological populations of interest. Standard habitat metrics, such as
those used by EPA's EMAP program are previously defined and common
summary metrics for habitat variables. Although these metrics
significantly reduce data, they do not always capture the functional
importance of the measured metric. Therefore, we propose to test and
develop of indicators that capture biological significance and describe
multiple habitat variables. Field measured and calculated variables
require statistical calculations, such as mean, maximum, minimum and
variation, and graphical representations prior to hypothesis testing.
Our analysis tool development will include programmed calculation of
these standard summary formats within databases, aiding data providers
and researchers by reducing data reduction workload. The construction of
RME data management infrastructure and storage tools will consider the
needs, structure, and process of the data reduction process. Both
analysis and storage tools will facilitate data sharing, analysis, and
management at local and regional scales, encouraging further analysis
tool development within the RME program.

The RME pilot project was designed to evaluate both status and trend
monitoring and effectiveness monitoring program designs. Data collection
protocols, site selection procedures, sample sizes, and spatial
considerations of project designs are all factors that influence the
type and quality of data generated by monitoring programs. Our proposed
analysis efforts will evaluate protocol comparisons conducted in the
Wenatchee and John Day basins in 2004-2006, investigate the partitioning
of environmental and spatial site variability and develop effective
methodologies for determining sample sizes for field sampling efforts
with respect to program goals. Analysis and data reduction tools will
prepare data for statistical comparisons of data collected within
protocol testing scenarios. Further determination of sample size and
spatial sampling designs will be tested by comparing data variability at
multiple spatial scales, answering questions related to landscape
representation (e.g. What attributes of the landscape are captured with
current monitoring sample designs?)

Modeling and a basic regression approach will be used to determine
mechanistic linkages among habitat condition and response variables.
Regression analyses will identify habitat and response variables
potentially linked through cause and effect at multiple spatial scales.
Determining influential factors and relationships at the fish population
scale will be of particular interest and will require extensive
attention during the 2007-2009 funding cycle. By using mechanistic
modeling we will be able to investigate whole ecosystem dynamics and can
test specific hypotheses through scenario manipulations. Scenarios
related to human impacts, change over time, and change with respect to
landscape variability can be investigated. Data generated for RME
projects will be used to evaluate mechanistic models used by recovery
and subbasin planning efforts (e.g., SHIRAZ, SWAM, HeatSource, EDT) to
predict fish distribution based on limiting factors of basins.

We have started, and are proposing to continue, characterizing the
inherent potential and human impacts throughout the Columbia River Basin
using multiple GIS approaches. The effectiveness of any stream
restoration strategy will be heavily dependant on the landscape level
context in which the project is implemented. For example, an in-stream
wood enhancement project may produce insignificant contributions to
watershed scale fish populations, if upslope or riparian processes are
outside of their natural range of variability. To be able to interpret
the effectiveness of a restoration strategy, we need to place
restoration sites within the context of the site's inherent fish
production potential and human impacts to fish production.

**7.2 Develop databases, data communication templates, data and
information output tools, and populate databases with current and
historic monitoring data** (Objective 7). For a monitoring program at
the scale of the Columbia River Basin to be truly successful, a strategy
utilizing strong yet flexible lines of communication needs to exist
between project coordinators and local collaborators and should be
mirrored within the data management tools developed for the program. The
assembly of existing data sources and locations allows the
identification of both spatial and content gaps in current monitoring
efforts and will provide a framework for designing supplemental
monitoring projects within the basin. Data assimilation efforts have
also helped facilitate the coordination of local agencies, their
monitoring designs and current data storage methods. We are using
multiple approaches to collect, summarize, and store both tabular and
spatial information. Each approach is unique in the type information it
provides, the input data, cost of production, repeatability across the
basin, and utility in interpreting restoration monitoring data. For
example, aerial photo interpretation provides detailed, site specific
information, however, is expensive and requires thousands of subjective
decisions. DEM analysis can be conducted inexpensively and consistently
across large areas, however, is limited to describing only the
geomorphic context. Investigation of these questions and the development
of financially reasonable and feasible data storage tools is critical to
the sustainability of a monitoring project.

[To Date:]{.underline} An extensive collection of historical tabular
datasets, spatial datasets and current monitoring programs have been
inventoried for the pilot basins. These collection methods have been
tested in the John Day (tabular data) and Wenatchee (spatial data), and
all methods will be extended to all pilot basins in future years.

In the John Day basin, agencies participating in data standardization
and monitoring designs include local, state, and federal agencies, such
as ODEQ, BLM, USFS, ODFW, USGS, SWCD, CTWSRO, Oregon Water Resources
Division, UW, OSU, National Oceanic and NOAAF, and BOR. A basin-wide
meeting in 2005 of 10 agencies concluded that there is a need for
basin-wide coordination of monitoring efforts and increased
communication between agencies. Datasets supporting the conceptual plans
of potential John Day IMWs were the priority for collection efforts and
assimilation into databases. Local agency knowledge and the Pacific NW
Salmon Habitat Project Tracking Database (NOAA-Fisheries, NWFSC) have
been the primary source of restoration project knowledge in the pilot
basins. Extensive inventories of GIS, tabular, and restoration project
data are available upon request.

Efforts in the Wenatchee and Upper Columbia Basin have focused on
spatial data compilation and collection. We contracted Pacific
Biodiversity Institute (PBI) to delineate the landscape and stream
network using traditional classification schema. PBI assembled GIS
layers representing eco-regions, land ownership, and geology.
Additionally, Strahler order, gradient, Niaman valley type, Rosgen
channel type, and riparian vegetation was determined for all stream
segments in the basin. Riparian vegetation was classified from ASTER
satellite images and further delineated using aerial photos. These
traditional classification schemas provide landscape and site level
context for interpreting site restoration and are based on a solid
foundation within the scientific literature.

Topographic relief and precipitation exert primary controls on hillslope
processes and in-stream habitat forming processes. Using established
geomorphic relationships, valley and reach scale habitat characteristics
can be accurately predicted from digital elevation models and digital
precipitation data. Earth Systems Institute (ESI) was contracted to
derive a suite of metrics from the National Elevation Dataset and PRISM
precipitation dataset for the Upper Columbia Basin. A multitude of
metrics was calculated for basins, reaches, and tributary junctions. The
dataset includes over 7,500,000 reaches, 180,000 tributary junctions,
and 450 basins. ESI's derived products should prove beneficial in
understanding the relationships between landscape processes, stream
habitat, and fish production; for understanding the influence for
tributary junctions; and for understanding the influence of basin shape
and basin rugosity.

In fiscal year 2005 the NOAA Northwest Fisheries Science Center started
to develop a pilot data management system for the Wenatchee Subbasin.
The goals for this Status and Trend Monitoring Database (STM), pilot
effort were to develop a database structure to store salmonid and other
status and trend data, store stream habitat status and trend data, track
the protocols used to collect this data, and link this database directly
to a GIS system to support spatial analysis. By the end of 2005 this
database management system was developed and populated with the 2004
Wenatchee field data. The design of the database is not geographically
restricted but is intended to accommodate the full range of drainages
and subbasins across the Columbia River Basin.

In order to analyze and monitor the effectiveness of restoration sites
in the Wenatchee it was critical to establish a GIS system to maintain
the locations of the monitoring sites and the restoration sites that are
being investigated. For the 2004 data, the GPS coordinates were
converted into GIS point locations and were incorporated into a
hydrologic model based on the USGS 1:100,000 NHD dataset. Since these
locations participate in a GIS based hydrologic network, tools to trace
and store the relationships of survey sites along the network were
developed.

With additional financial support from NOAA/NMFS, we have begun a
multi-dimensional classification of the Columbia River Basin and the
coast range of Oregon and Washington. During the past year and a half,
we have generated 12 GIS data layers that represent climatologic,
geologic, topographic, and stream network characteristics as continuous
surfaces for the entire study area. The characteristics were selected
based on their influence on inherent fish production and include, mean
annual precipitation, month of maximum precipitation, temperature range,
growing degree day, hardness index of surficial geology, generic erosion
potential, elevation, stream density, tributary junction density,
percent of network comprised of response channels, percent of network
comprised of transport channels, and network distance to saltwater.
Additionally, the continuous surfaces have been summarized for the 9000
sub-watershed that comprise the study area.

In order to be able to use data collected by various agencies throughout
the Columbia Basin, it is recognized that tracking the protocol that was
used to collect the data is essential. Previous funding has been used to
establish a "Protocol Manager/Library", developed by BOR, which will
house the various data collection protocols used to collect monitoring
data within the John Day Basin and other project basins and areas within
the Pacific Northwest. Protocol Manager will be useful in describing
which collection characteristics and methods are relevant and pertain to
specific attributes and indicators used within various protocols, such
as those defined and practiced by data collection agencies using EMAP
and PIBO.

[Proposal:]{.underline}

Previous monitoring programs have built central data warehouses with
web-based applications for uploading and downloading monitoring data;
however, have tended to leave local data contributors to develop their
own data management strategies. A central data warehouse needs to
support and be supported by small-scale applications that can be
implemented on the desktops of local collaborators. The RME Status and
Trend Monitoring data warehouse has been optimized to manage large
volumes of data and associated metadata, to ensure data access
privileges are properly allocated, and to provide rapid distribution of
data across the Internet. However, to maximize the usefulness of the RME
Status and Trend Monitoring data warehouse, we need small-scale
applications that can support efficient data entry, storage, uploading,
and analyses. Distributing these applications to the desktops of local
collaborators will help ensure clear communication of data and analyses
between local collaborators and the central data warehouse.

To address complications arising from multiple agency database storage
devices, or sometimes lack of database storage devices, we propose
developing small-scale database templates for storing tabular data and
basin specific geo-spatial databases for storing GIS data layers. These
databases will help ensure consistency of data management at the local
scale and provide a mechanism for exporting more complex data structures
that can support advance level analyses. Databases can be modified to
fit the needs of each agency, yet share common data storage formats that
will be supported throughout the region.

Data structures and relationships common to multiple agencies collecting
monitoring data are the basis for proposed database templates that will
store and manage water quality, fish habitat, fish abundance, and
invertebrate abundance data. The templates will be built from attributes
already defined within the RME Status and Trend Monitoring data
warehouse. As a result, the templates will provide a useful format for
data collectors and local agencies to enter and store their data. The
templates will be a container where data downloaded from the warehouse
(raw data, derived metrics, descriptive statistics, or summary graphs)
can be stored and analyzed. Having a direct link between the central
warehouse and local databases is essential for efficient transfer of
field data and for analysis of data exported from the central warehouse.
Building tools that allow project collaborators to efficiently interact
with the central warehouse will increase its utility and support the
success of the monitoring program as a whole.

With the proliferation of geo-spatial data and the increasing complexity
of analyses being performed on geo-spatial data, more advanced data
structures are needed to manage these data and perform the analyses.
Geo-databases provide the structures necessary to store large numbers of
GIS data layers, to control projections, define relationships between
data layers, define attribute domains, and set data validation rules.
Additionally, geodatabases have the ability to build data structures
(geometric networks) that understand the relationships between features
within hydrologic networks. Using geometric networks, we can define the
relationship between monitoring points or reaches and their upstream
catchments, identify all streams or catchments upstream or downstream of
points on the network, and calculate network distance between monitoring
points. The ability to create these relationships and perform these
analyses is essential to answering the question being proposed by
regional scale monitoring programs and can be addressed via a
geo-database scheme developed for managing and analyzing geo-spatial
water resources data (The ArcHydro database scheme). In addition to
supporting advance level analyses, we will use the ArcHydro geo-database
model as the standard format for distributing geo-spatial data to
sub-basin project collaborators. Maintaining central control of
geo-spatial data will help ensure data consistency throughout the basin.
Distribution of small-scale, basin specific geo-databases to project
collaborators will capitalize on the board range of expertise available
in the basin and increase buy-in from project collaborators.

Future work on the GIS classification process includes completing the
unsupervised classification on both the continuous and summarized data
layers (12 data layers). Classification of the continuous data layers
will produce a landscape classification while the summarized data layer
will produce a watershed classification. Additionally, we are developing
statistics that will be used to determine the number of naturally
occurring classes within each dataset. In addition to completing the
multi-dimensional classification of inherent fish production potential,
we hope to perform a similar analysis on human impacts to fish
production. This will require developing appropriate data layers
representing human population density, road density, forest age,
agricultural clearing, and stream reaches influence by dam, barriers, or
other hydro modifications. Being able to contrast the landscape in terms
of inherent fish production and human impacts will prove beneficial in
interpreting basin wide monitoring data and be useful for plan future
location of restoration projects.

C. Rationale and significance to regional programs

**NPPC (2000) Fish and Wildlife Program:** Strategies identified under
the Research, Monitoring and Evaluation subsection (NPPC 2000)
identifies the primary strategies of RM&E as: 1) identify and resolve
key uncertainties for the program, 2) monitor, evaluate, and apply
results, and 3) make information from this program readily available.
Given that habitat restoration plays a critical role in the Fish and
Wildlife Program, it follows that the information generated by the Pilot
Projects will provide the information necessary to evaluate the
potential effectiveness of habitat actions and to prioritize among
habitat actions.

**Final UPA for the FCRPS Biological Opinion on Remand**: The UPA states
that "*Available science cannot quantify the increased fish survival
attributable to each habitat action for each ESU"* (Page 24). This is
largely a result of the fact that "*...the science that would allow us
to quantify and predict juvenile survival improvements from specific
habitat projects or types of habitat projects is still in its infancy"*
(Page 25). RM&E strategy 1 states the need for a regional network of
status monitoring programs, specifically citing the need to continue the
Pilot Projects initiated in the Upper Columbia Basin, John Day subbasin,
and a third location - for which the Salmon River was selected (Page
88). RM&E monitoring substrategy 1.2 (tributary monitoring) specifically
supports the continuation of the tributary habitat status monitoring
project in the John Day subbasin, and another to be determined -- for
which the Salmon subbasin has been selected.

**Draft Columbia River Basin Research Plan (NWPPC 2005)**: The plan
identifies three primary information needs required to effectively
implement the research plan:

*1 What pattern and amount of habitat protection is needed to ensure
long-term survival of*

*fish and wildlife populations in the face of variable environmental
regimes?*

*2. Can the benefits of on-the-ground habitat restoration and
protection*

*measures be quantified?*

*3. What are the most effective Best Management Practices for protecting
and restoring habitat?*

These information needs largely parallel the Effectiveness Monitoring
and Status and Trend Monitoring functions of the Pilot Projects, a fact
noted on Page 42 of the document "*it will be important to continue
supporting the Upper Columbia, John Day, and Salmon Pilot Studies as
testing areas for comparing protocols and sampling methods*."

**Wenatchee Subbasin Plan:** The Wenatchee Subbasin Plan explicitly
recognizes that ecosystem restoration is an evolving science, requiring
that implemented actions be monitored such that their effectiveness can
be evaluated (Page 229). Thus, the plan requires that "statistically
rigorous" monitoring must accompany habitat actions to enable
partitioning of the effects of habitat actions from environmental
variation in evaluations of population responses (Page 238). Section 7.7
(Page 255) develops the need for the implementation of a coordinated
status and trend and habitat action effectiveness monitoring program for
the Wenatchee Subbasin, and Section 7.8.1.5 (Page 303) provides a
summary of proposed and ongoing actions within the Wenatchee Subbasin
that require monitoring. At a minimum, the Subbasin Plan requires that
such a program address the following information needs (Section 8.1.1,
Page 307):

1.  What are the current habitat conditions and abundance, distribution,
    life-stage survival, and age-composition of ESA-listed fish in the
    Wenatchee Basin (status monitoring)?

2.  How do these factors change over time (trend monitoring)?

3.  What effects do tributary habitat actions have on fish populations
    and habitat conditions (effectiveness monitoring)?

The Wenatchee Pilot Project directly addresses both the Status and Trend
and Effectiveness Monitoring requirements of the Subbasin Plan, and the
need for coordination among monitoring entities and activities (through
participation in the Regional Technical Team, assembled for the purpose
of coordinating implementation and monitoring of recovery activities).

**Entiat Subbasin Plan:** The Entiat Subbasin Plan (Page 169) recognized
that ecosystem recovery is a developing science, and proposes that
monitoring and evaluation are required in order to adaptively manage and
optimize the effectiveness of recovery plans. This approach to ecosystem
recovery is underscored by Goal 6 (Page xii), which indicates the need
for "*improved coordination for long-term monitoring of fish and
wildlife population and habitat and development of the required
institutional infrastructure to better insure consistency and efficiency
with other local, tribal, state and federal monitoring protocols:*

*• Develop and employ a trend monitoring program based on
remotely-sensed data obtained from sources such as aerial photography or
satellite imagery;*

*• Develop and implement a long-term statistically-based monitoring
program to evaluate the status of fish populations and habitat (this
requires probability-based statistical site selection procedures and
establishment of standard protocols and data collection methods.); and*

*• Implement experimental research monitoring at selected locations to
establish the underlying causes for the changes in habitat and
population indicators*."

Following the guidance provided by the ISAB (2003), the subbasin plan
(Page xxvi) indicates that restoration actions in the Entiat Subbasin
will be accompanied by:

1.  a trend monitoring program based upon remotely-sensed data obtained
    from sources such as aerial photography and/or satellite imagery;

2.  a long-term statistical monitoring program to evaluate the status of
    fish populations and habitat; and

3.  experimental research monitoring at selected locations to establish
    the underlying causes for the changes in habitat and population
    indicators.

The Wenatchee/Entiat Pilot Project has played a key role in the
development and implementation of Status and Trend and Effectiveness
Monitoring activities in the Entiat Subbasin. Coordination among
monitoring entities and activities, including the Wenatchee/Entiat Pilot
Project is ensured by joint participation in the Regional Technical
Team.

**John Day Subbasin Plan:** The John Day Subbasin Plan based many of its
conclusions on the Ecosystem Diagnosis and Treatment (EDT) model. The
writers acknowledge that the assumed benefits of habitat based
biological objectives presented within the document are in many cases
qualitative, owing to uncertainties in habitat-fish interactions (Page
241), and the fact the EDT model has limitations that potentially
decrease its value in identifying restoration actions (Page 317). The
document identifies a number of information needs, including:

1.  estimates of production capacity (Page 314);

2.  intensive monitoring of selected restoration actions to enable
    quantitative evaluation of the effects of those actions on
    productivity (Page 314);

3.  studies of local ecological processes, enabling modeling exercises
    to better represent the conditions typical of the John Day Basin
    (Page 317);

4.  the need for better analytical tools to identify and prioritize
    restoration actions; and

5.  coordination with local and regional efforts aimed at evaluating
    Tier 1 and 2 monitoring, with an emphasis on standardization with
    other regional efforts (Page 319).

The authors further indicate that the existing subbasin plan should be
viewed as a dynamic document; and that the results of ongoing and
proposed monitoring and evaluation will be employed to adaptively change
proposed actions and priorities every five years (Page 17). The John Day
Pilot Project is explicitly mentioned (Page 318) as contributing to the
adaptive management strategy recommended in the document.

**Salmon Subbasin Plan**: The Salmon Subbasin Plan notes (page 41) that
there is very little information available to determine the effects that
habitat actions will have on fish populations. This uncertainty is
reflected in Aquatic Objective Strategies 2A3, 2A4, 3C2, and 3C3; which
are aimed at assessing population productivity, abundance, and survival
of focal anadromous species. Both the Lemhi and SFSR study designs
directly evaluate status and trends in the productivity, abundance, and
survival of anadromous and resident salmonids. In both locations,
information generated on these vital rates is related to the status and
trends of habitat attributes, thus providing information on how vital
rates are affected by habitat actions.

D. Relationships to other projects

**Umbrella Pilot Project**

> **Collaborative System-Wide Monitoring and Evaluation project (CSMEP)
> (Project No. 200303600)**: The CSMEP group has been actively involved
> in metadata surveys and the evaluation of strengths and weaknesses of
> available information. These evaluations contributed substantially to
> the design of the Salmon River Pilot Project. The design tasks
> assigned to the CSMEP Status and Trends and Habitat subgroups provided
> a draft monitoring design for the Lemhi River and South Fork Salmon
> River, providing a basis for further refinement within the Salmon
> Pilot Project study design. At a larger scale, the CSMEP workgroup and
> technical review teams within Pilot Project subbasins share common
> membership. Thus, the implementation of Pilot Projects can efficiently
> and effectively act as a test-bed for the evaluation of CSMEP design
> components.
>
> **Pacific Northwest Aquatic Monitoring Partnership:** PNAMP provides
> the regional forum for the technical and policy components of large
> scale monitoring programs to be discussed, designed, and evaluated --
> ISEMP serves as a vehicle for testing some of the ideas discussed by
> this group. Specifically, PNAMP has coordinated protocol compilations
> and tests, and ISEMP has participated in these tasks. PNAMP is also
> serving to coordinate discussions of data management and communication
> standardization, and ISEMP has demonstrated some database products
> developed to meet project and collaborator needs as examples to help
> move the regional discussion forward.

**Wenatchee/Entiat**

> **Upper Columbia Regional Technical Team** -- Approximately 15 state,
> federal, tribal and private agencies pay for staff to participate as
> members of the RTT. Overseeing the ISEMP program requires a
> substantial commitment of the RTT's time in attending meetings and
> reviewing documents or other products. This staff time is donated by
> each agency at a value of approximately \$36,000 per year.
>
> **Wasington Department of Ecology (WDOE) Ambient Monitoring Program**
> -- WDOE operates and maintains 15 flow stations and four continuously
> recording water quality stations that provide data which ISEMP would
> otherwise have to obtain through contracts. In-kind cost share value
> of \$96,000 in 2005.
>
> **WDOE RIVPACS Modelling** -- WDOE will be creating a
> subbasin-specific model for analyzing macroinvertebrate communities
> that will be useful to ISEMP.
>
> **WDOE Contributions to Habitat Surveys** -- In addition to the amount
> contracted to WDOE for habitat surveying, WDOE provided extra funding
> for salaries, training, and equipment at a value of \$28,924 in 2005.
>
> **NOAA Fisheries Snorkel Surveys --** NOAA Fisheries has supplemented
> ISEMP's BPA funding to roughly double the number of site visits that
> are conducted by the USFS as part of snorkel surveys at an annual
> value of \$100,000.
>
> **Wasington Department of Fish and Wildlife SSHEAR Program** -- ISEMP
> will be relying exclusively on WDFW for all the data regarding habitat
> access; WDFW's SSHEAR program will be conducting surveys of barriers
> and habitat access in the Wenatchee for a one-time cost with an
> approximate value of \$200,000.
>
> **U.S. Forest Service** **Depth Fines Sampling** -- USFS has provided
> baseline depth fines sampling in the Wenatchee and Entiat at an annual
> value of about \$50,000 per year.
>
> **U.S. Forest Service Entiat Monitoring Planning and Coordination** --
> USFS has provided technical oversight and coordination of restoration
> project planning and monitoring in the Entiat subbasin at an annual
> value of about \$10,000 per year.
>
> **U.S. Forest Service** **Contributions to Snorkelling,
> Reconnaissance, and Redd Surveys**-- In addition to the amount
> contracted to USFS for these ISEMP elements, the USFS provides extra
> funding for salaries, training, and equipment that directly supports
> these contracted elements, in addition to the review and development
> of other elements of the ISEMP program outside their contracted
> scopes-of-work, at an annual value of about \$20,000.
>
> **Smolt Trapping: Various Related Programs --** ISEMP benefits from
> cost sharing from multiple sources for the operation of smolt traps:
> for the operation of the lower Wenatchee smolt trap, approximately
> \$35,062 will come from the BPA Reproductive Success study and
> \$119,544 will be provided by Chelan PUD Monitoring and Evaluation
> Program in 2006; Chelan PUD will contribute \$29,712 to the operation
> of the upper Wenatchee smolt trap and pays for the entire operation of
> the Chiwawa River trap at an approximate annual value of \$100,000;
> BPA's coho reintroduction study jointly funds the Nason Creek smolt
> trap at an approximate annual value of \$33,000.
>
> **Spawning Ground Surveys** -- ISEMP directly utilizes spawning ground
> survey information funded by a variety of sources. Chelan PUD funds
> the bulk of steelhead index-area spawning ground surveys in the
> Wenatchee at about \$60,245 per year; Chelan PUD funds all summer
> chinook spawning ground surveys in the Wenatchee at about \$100,000
> per year; NOAA Fisheries has funded steelhead spawning ground surveys
> in the Entiat at about \$100,000 per year; and another outside funder
> pays for all summer chinook surveys in the Entiat at about \$100,000
> per year; other outside funders pay approximately \$100,000 each in
> Entiat and Wenatchee to survey for spring chinook.
>
> **PIT Tagging Programs** -- PIT tagging is useful to multiple
> angencies and ISEMP benefits from cost sharing from at multiple
> partners: Chelan PUD will be contributing in-kind labor cost sharing
> in the Wenatchee valued at approximately \$120,000 per year; NOAA
> Fisheries will be contributing approximately \$120,000 in start up
> money for deployment of tag detection arrays in the Wenatchee and
> another \$120,000 in the Entiat.
>
> **Genetic Sampling** -- ISEMP will rely exclusively on genetics data
> collected from the WDFW/NOAA spring chinook pedigree study (annual
> value of approximately \$200,000) and sampling done as part of the
> Chelan PUD Monitoring and Evaluation studies at an unknown value.

**John Day Pilot Project**

> **Analytical Framework Group (AFG) and coordination with other
> participants**
>
> Approximately 15 state, federal, tribal and private agencies pay for
> staff to participate as members of the AFG and coordinate with the
> pilot project. Overseeing the ISEMP program requires a substantial
> commitment of the these staffs\' time in attending meetings and
> reviewing documents or other products. This staff time is donated by
> each agency at a value of approximately \$39,000 per year.
>
> Bureau of Reclamation
>
>  
>
> **Data dictionary and protocol manager development -** Bureau of
> Reclamation (BOR)
>
> Using the John Day basin as test basin, the BOR is funding the
> development of a database application to house protocols and data in
> spatial database. This project has collaborated closely with the John
> Day pilot project and has been funded at near \$100,000/yr but will
> drop to \$50,000/yr.
>
> **Evaluation of Push-up Dam Replacements in the South Fork John Day
> Basin.** Bureau of Reclamation-1434-03HQRU1584
>
> This project is conducted by Oregon Cooperative Fish and Wildlife
> Research Unit (USGS-BRD), and is the South Fork Intensively Monitoried
> Watershed study. The pilot project works closely with this project and
> this project will provide framework and the control watershed for the
> Bridge Creek Intensively Monitored Watershed study. Cost-share This
> project is funded at nearly \$250,000/yr.
>
> **Salmonid Productivity, Escapement, Trend, and Habitat Monitoring in
> the John Day Basin** (BPA Project Number 1998-016-00).
>
> ODFW operates juvenile rotary screw traps, conducts juvenile PIT
> tagging, and conducts redd and carcass surveys for salmon and
> steelhead, conducts juvenile snorkel survey and habitat surveys
> throughout the John Day Basin. This project supplies much of the
> basinwide salmonid information. ODFW is one of the principal
> collaborators for the pilot project. This project has a budget of
> approximately \$998,000/yr.
>
> **John Day Basin TMDL Development -** Oregon Department of
> Environmental Quality
>
> Oregon Department of Environmental Quality is developing a TMDL model
> to evaluate the effects channel characteristics on temperature. We
> collaborated closely with ODEQ and will be using this model to
> prioritize restoration efforts. This project requires nearly a full
> FTE plus considerable travel
>
> **ODEQ-EMAP Western Regional Pilot Project** - Oregon Department of
> Environmental Quality
>
> This project was initiated by ODEQ in 2000 and data collection was
> completed in 2004. Data from this project is being used in the
> Sediment Assessment project of the John Day pilot project. Data on
> channel morpholgy, riparian vegetation, substrate, macroinvertebrates,
> other biological indicators were collected. We plan to use information
> from this effort.
>
> **USFS-PACFISH-INFISH Biological Opinion (PIBO) Effectiveness
> Monitoring Program --** USFS, BLM
>
> This project is conducted by the US FS over the Columbia River Basin.
> This project collects channel morpholgy, riparian vegetation,
> substrate, macroinvertebrates from watersheds throughout the CRB,
> including the John Day. We have collaborated closely with the PIBO
> project and plan to use information collected from this program for
> the pilot projects.

**Salmon River Subbasin Pilot Project**

> **The Chinook Salmon Adult Abundance Monitoring Project (BPA Project
> Number 199703000)**: This project funds the operation of a video weir
> on Lake Creek (a tributary to the Secesh River in the South Fork
> Salmon River) and a DIDSON enumeration device on the mainstem Secesh
> River. Escapement estimates generated by this project will be used to
> validate proportional escapement estimators developed within the
> proposed Salmon Pilot Project.
>
> **Idaho Supplementation Studies (BPA Project Numbers 19890800 and
> 198909802)**: The Idaho Supplementation Studies (ISS) operates
> juvenile rotary screw traps, conducts juvenile PIT tagging, and
> conducts redd and carcass surveys in Lake Creek, the Secesh River, and
> the Lemhi River. Juvenile abundance estimates generated by this study
> will be used to validate proportional estimators developed by the
> Salmon Pilot Project in the South Fork Salmon River and Lemhi River.
> Information obtained from redd and carcass surveys will likewise be
> used to validate survival estimates and age composition estimates
> generated by the Salmon Pilot Project. Redd count data will be used by
> the Pilot Project to retrospectively assess the precision of redd
> count time series' and develop a relationship between enumerated redds
> and total escapement. Finally, ongoing PIT tagging, funded by the ISS
> project, decreases the number of additional PIT tags that would
> otherwise be requested for the Salmon ISEMP.
>
> **The Johnson Creek Summer Chinook Salmon Monitoring and Evaluation
> Project (BPA Project Number 199604302)**: This project monitors adult
> escapement, juvenile abundance, productivity, out-of-subbasin
> survival, and life-history attributes of the Johnson Creek component
> of the East Fork South Fork Salmon River spring/summer Chinook salmon
> population. Adult escapement, juvenile abundance, and productivity
> estimates generated by this project will be used to validate
> proportional estimators developed by the Salmon Pilot Project. Ongoing
> PIT tagging, funded by the Johnson Creek project, decreases the number
> of additional PIT tags that would otherwise be requested for the
> Salmon ISEMP. In their review of the Johnson Creek RM&E plan the ISRP
> strongly recommended the collocation of the Salmon River Pilot Project
> with the Johnson Creek M&E project (ISRP 2005-6).
>
> **Idaho Natural Production Monitoring (BPA Project Number
> 199107300)**: This project comprehensively evaluates age structure of
> adult spring/summer Chinook salmon in the Salmon Subbasin and provides
> run reconstructions. In addition, this project generates parr density,
> species presence, and habitat information at fixed sites throughout
> the Salmon Subbasin. Age structure estimates generated by this study
> will be used to validate age structure estimates generated by the
> Salmon Pilot Project. Likewise, the times series of juvenile density,
> species composition, and habitat attributes will be utilized by the
> model developed for the Salmon River Pilot Study. Finally, where
> possible, fixed sampling sites surveyed by this study will be
> incorporated into the Salmon Pilot Project, potentially decreasing the
> number of habitat sampling sites required by the study design.
>
> **Implementing Salmon and Steelhead Conservation actions in the upper
> Salmon Subbasin (PCSRF Project Number 01404SA)**: This project funds
> participation by the IDFG to identify information gaps, implement
> conservation plans, and support RM&E activities in the Lemhi River
> Watershed. The Salmon River Pilot Project directly interacts with this
> project through the RM&E Technical Oversight Committee, ensuring that
> Pilot Project planning and RME implementation addresses information
> needs of the LCP and ensuring that RME activities proposed by the
> multiple agencies operating in the Lemhi are coordinated. **This
> project can be viewed as a direct cost-share, with the PCSRF
> contributing \$128,633 and the State of Idaho contributing \$42,878.**
>
> C**omprehensive effectiveness monitoring and evaluation of habitat
> improvement projects in the Lemhi River watershed (PCSRF Project
> Number 01504SA)**: This project evaluates changes in adult escapement,
> and juvenile abundance within the Lemhi River for the purpose of
> evaluating habitat actions. The project provides funding for redd
> counts, carcass surveys, and the operation of a rotary screw trap on
> the mainstem Lemhi River. Efforts implemented under this project are
> coordinated with the proposed Salmon Pilot Project, and it is
> anticipated that the two projects will cooperatively enable an
> intensive Habitat Action Effectiveness Monitoring project in the Lemhi
> River watershed. **This project can be viewed as a direct cost-share,
> with the PCSRF contributing \$99,970 and the State of Idaho
> contributing \$124,928.**
>
> **Reconnect Big Eight Mile Creek, Big Timber Creek, and Bohannon Creek
> (PCSRF Project Number 00804SA)**: This project seeks to maintain
> hydraulic connectivity between the named tributaries and the mainstem
> Lemhi River through improved water management and the removal of
> passage obstructions. The Salmon Pilot Project will evaluate the
> effects of these tributary reconnections on fish vital rates.
>
> **Hawley-Eighteenmile Siphon (PCSRF Project Number 01204SA)**: This
> project will improve passage at an irrigation withdrawal, which is
> expected to enable access by anadromous and resident salmonids. The
> Salmon Pilot Project will evaluate the effects of improved passage on
> fish vital rates.
>
> **L-6 to S-14 Water Diversion Transfer (PCSRF Project Number
> 01104SA)**: This project will decrease diversions at the L-6 diversion
> on the lower mainstem Lemhi by 15 CFS, by instead providing conveyance
> from the S-14 diversion on the mainstem Salmon River. The Salmon Pilot
> Project will evaluate the effects of increased mainstem flow,
> resulting from this project, on juvenile fish survival and adult
> passage.
>
> **Fence Replacement on the Mainstem Lemhi River (PCSRF Project Number
> 01304SA)**: This project will replace 1,800 feet of riparian fencing
> abutting the primary Chinook salmon spawning grounds in the mainstem
> Lemhi River. The Salmon Pilot Project will evaluate the effects of
> this action on habitat attributes and fish vital rates within the
> affected area.

E. Project history (for ongoing projects)

**Integrated Status and Effectiveness Monitoring Program**

Project number: 2003-017-000

Project initiation -- FY2003

Project spending to date:

> FY 2003 \$79,230
>
> FY 2004 \$676,482
>
> FY 2005 \$1,273,240
>
> FY 2006 (est) \$2,310,000

ISEMP seeks to develop two novel monitoring and evaluation programs and
the rule set that guides these programs development, evaluation and
assessment: (i) subbasin-scale pilot status and trend monitoring efforts
for anadromous salmonids and their habitat in the Wenatchee, John Day
and Salmon River basins, and (ii) effectiveness monitoring for suites of
habitat restoration projects in selected watersheds within the three
target subbasins. Project progress to date has focused on the
development of standardized status monitoring designs and protocols,
effectiveness monitoring designs and conceptual gap analyses for
Intensively Monitored Watersheds (IMWs), inventory and compilation of
existing agency data and coordination efforts, and the development of
data management tools for agency and subbasin scale projects.

Implementing the subbasin scale intensive monitoring projects has
involved contracting with numerous individuals and agencies. A
coordination staff has been assembled for each subbasin BioAnalysts and
Terraqua (Wenatchee), Eco Logical Research and NMFS/NWFSC (John Day),
and Quantitative Consultants and NMFS/NWFSC (Salmon River). Project
coordination staff have been responsible for securing contracts with
agencies for project implementation, plan writing and productivity
monitoring component development, statistical design/analysis
development, and monitoring indicator development.

RME progress within pilot basins has varied due to different resources
and project trajectories within basins. To date, efforts within the
Wenatchee basin have focused on the development of spatial status and
effectiveness monitoring designs for the entire basin and Entiat IMW,
comparison of habitat and invertebrate field protocols and evaluation of
fish population distributions and field metrics (e.g. trap
efficiencies). In the John Day basin we have compiled a comprehensive
library of spatial and tabular data (historical and recent), compared
multiple in-stream habitat and sedimentation protocols, developed
conceptual IMWs and field studies for fish production (SF John Day IMW)
and sediment transport-incision (Bridge Creek IMW) projects and
collaborated with remote sensing and basin-wide sedimentation modeling
projects (University of Washington and Oregon State University). In the
Salmon basin, initial effectiveness monitoring strategies and sites for
channel reconnection restoration projects in association with the Lemhi
Habitat Conservation Plan have been discussed for full design and field
implementation in 2006.

Data management and the development of data communication tools has also
been a major focus of the project. Progress to date has included the
development of an Oracle database and adjacent Status and Trend
Monitoring internet data access page (Wenatchee pilot project), the
completion of a comprehensive Data Dictionary and Protocol Manager (John
Day pilot project), and spatial GIS data compilation and standardization
for both the John Day and Wentachee projects.

All project supporting documents, contract progress reports, data
communication tools, and other project products are available via the
project website (under project links \--
<http://www.nwfsc.noaa.gov/research/divisions/cbd/mathbio/index.cfm>).
Data management products will be linked to this site when data sharing
agreements are in place.

The Integrated Status and Effectiveness Monitoring Program is a key part
of the region's move towards adaptive management and salmon recovery.
Adaptive management requires explicit links between decisions, scenarios
and performance metrics -- all of which are critically underpinned by
monitoring data with known information content, data management and
communication, and programmatic assessment metrics and tools that
quantitatively link actions to outcomes. Only by developing monitoring
tools in this context can monitoring data be useful to resource managers
-- ISEMP represents the quantitative infrastructure to design, test and
document monitoring and management approaches that meet the region's
needs. ISEMP has begun to build the collaborations, data collection
processes and analytical/communication tools that are required for
adaptive management strategies; however, the next three years will be
critical as the program expands beyond passively measuring environmental
and population conditions to actively manipulating on-the-ground
conditions to develop metrics and methods to document restoration action
progress and success.

**Wenatchee**

The ISEMP Program has been developing two novel monitoring and
evaluation programs in the Wenatchee and Entiat subbasins since 2003,
including: (i) subbasin-scale pilot status and trend monitoring efforts
for anadromous salmonids and their habitat, and (ii) effectiveness
monitoring for suites of habitat restoration projects. The ISEMP Program
has integrated existing and new monitoring and evaluation activities in
the Wenatchee and Entiat to help ensure that provisions of the 2000
National Marine Fisheries Service Federal Columbia River Power System
Biological Opinion (BiOp) are satisfied. Monitoring being implemented
under the ISEMP Program is following protocols specified in Hillman
(2004; the *Upper Columbia Monitoring Strategy*). The ISEMP Program
addresses a complex and large set of scientific uncertainties underlying
status, trend, and effectiveness monitoring programs at many spatial and
temporal scales. The ISEMP Program also examines scientific
uncertainties underlying selected monitoring methodologies. For these
reasons, multiple entities have been enlisted to conduct aspects of this
program, in many cases by building upon existing monitoring efforts and
sharing costs with other programs and in all cases by using the expert
staff that each agency is able to provide.

**John Day**

In the John Day, the pilot project has developed a framework for a RME
program. An explicit goal of the RME program development is that it must
deliver reliable and relevant information that is logistically feasible
and affordable to collect. The second part of this statement is, of
course, a constraint to every RME program that most everyone is aware
of. The first part of this statement, however, is often not stated or
tested. Estimates and comparison of the reliability, or the accuracy and
precision, of information collected through different protocols is
rarely determined. Also, RME programs often do not demonstrate that the
metrics collected are relevant to questions related to project goals or
that all relevant information is being collected. For example, many
monitoring programs are implemented under the pretext that the
information collected will be used to inform the above goals for ESA
listed fishes. Many of these programs collect macroinvertebrates
samples; however, the metrics that are derived from these samples are
mainly used to describe water quality. Little research has been
conducted that demonstrates that these invertebrate metrics correlate to
fish production even though that is justification for this monitoring.
Therefore, in the John Day pilot project, much emphasis has been place
on determining and developing monitoring protocols that produce reliable
and relevant information. Identification of information that should be
collected and programs to do this is another component of the program.

Synthesis of this research will be captured in the hierarchical
framework to describe the causal relationships of ecological processes
across several scales throughout the John Day Basin. This information
will be used to identify and prioritize stream reaches that would
produce the greatest response for the level of effort in restoration.
This information can also be used to design mitigation experiments and
form the expectation of responses from these actions. As a means to test
these approaches, the pilot project has initiated and is developing
Intensively Monitored Watersheds studies. The synthesis of information
collected from current RME activities are used to help describe limiting
factors of watersheds in the John Day. These studies will test a set of
restoration actions in a watershed in an experimental management
framework. Intensive monitoring and research will be used to describe
the impacts of these actions on fish and their habitat. The steps in
executing an IMW are similar to the steps required to implement a
comprehensive and well coordinated basin-wide RME program, and thus the
IMW will be extremely informative to the pilot project efforts.

Development of the John Day RME pilot project is a long term process
whereby lessons learned through research and the Intensively Monitored
Watershed studies will be used as the rationale to suggest changes to
current monitoring efforts. Monitoring programs are already in place in
the John Day and we are working closely with the personnel implementing
these monitoring programs. Changes to these programs will likely not be
accepted unless we can demonstrate a strong justification of why this
would be beneficial to the management of salmonids in basin. Thus, the
current approach in John Day pilot project is the development of a
framework that describes the multiple tasks that must be completed
before the final RME plan will be determined and agreed upon by the
multiple entities conducting monitoring in the basin.

**Salmon River**

The Salmon River Pilot Project was initiated in August 2005 to:

1.  develop a habitat action effectiveness monitoring plan for the Lemhi
    River and

2.  develop a habitat and population status and trend monitoring plan
    for the South Fork Salmon River (SFSR).

The Lemhi and SFSR Pilot Projects are intended to directly address key
evaluation gaps that currently limit effective recovery planning and
complicate the aggregation of population and habitat status and trends
information to higher spatial scales. Implementation of the Lemhi and
SFSR Pilot Studies is anticipated proceed as follows:

1.  define primary study objectives and formulate a statistical
    framework and data requirements to evaluate the objectives
    (completed in 2005);

2.  utilize existing monitoring data and the technical expertise of
    action agencies to evaluate the logistical feasibility and scope
    (i.e., does the framework address data needs on temporal and spatial
    scales useful for management as well as the information needs
    addressed in previous paragraphs) of the statistical framework
    (scheduled for completion in early 2006);

3.  implement proposed monitoring and infrastructure on a trial basis to
    evaluate feasibility and information quality that could be expected
    from long-term implementation (scheduled for 2006);

4.  revise the statistical framework and implementation plan based on
    results of the trial implementation (2007-2009);

5.  implement the revised study design.

A draft study design (QCI 2005) was completed in September 2005 is
currently under review by the ISRP. A research Monitoring and Evaluation
Technical Oversight Committee (RMETOC) consisting of researchers from
the Nez Perce Tribe, Idaho Department of Fish and Game, NOAA Fisheries,
the Shoshone-Bannock Tribes, the United States Fish and Wildlife
Service, and the Idaho Department of Water Resources was convened in
October 2005 to review preliminary study designs for the Lemhi and SFSR.
If the draft Lemhi and SFSR study design receives a positive ISRP
review, trial implementation will begin in 2006. This proposal seeks
funding to continue implementation and adaptive revision of the study
design during the Fiscal Year 2007-2009 period.

F. Proposal biological objectives, work elements, and methods

  ------------------ ----------- ----------------------------------------- ---------
  **Objective(s)**   **Work      **Method**                                **Start
                     Element**                                             End**

                                                                           

  **Umbrella ISEMP**                                                       

  1, 5               118         Coordinate sampling, and data collection, 2007 -
                                 analysis, and reporting                   2011

  1, 5               119         Administer project funds and subcontracts 2007 -
                                                                           2011

  6, 7               160         Develop and maintain a database to house  2007 -
                                 project metadata and data                 2011

  6, 7               162         Develop modeling tools to support project 2007 -
                                 data assessment                           2011

  6, 7               162         Develop modeling tools to support         2007 -
                                 evaluation of monitoring programs         2011

  6, 7               162         Analyze project data to adaptively manage 2007 -
                                 the project                               2011

  1, 5, 6, 7         174         Determine adequacy of sampling, metrics,  2007 -
                                 indicators, and data management: annually 2011
                                 update designs, models and management     
                                 tools.                                    

  1, 5, 6, 7         174         Update program design document annually   2007 -
                                                                           2011
  ------------------ ----------- ----------------------------------------- ---------

  ------------------ ----------- --------------------------------------------- ---------
  **Objective(s)**   **Work      **Method**                                    **Start
                     Element**                                                 End**

                                                                               

  **Wenatchee and                                                              
  Entiat Subbasins**                                                           

  2, 3, 4, 5         70          Install rotary screw traps in lower mainstem  2007
                                 Entiat                                        

  2, 3, 4, 5         70          Purchase PIT tags for installation at four    2006 -
                                 smolt trapping sites and in tributary habitat 2011
                                 upstream of these sites in the Wenatchee      
                                 Subbasin (has been WE 182)                    

  2, 3, 4, 5         70          Install PIT tag arrays at six locations in    2006 (or
                                 the Entiat Subbasin (installation maybe       2007) -
                                 funded by NOAA in 2006, otherwise BPA in      2011
                                 2007)                                         

  2, 3, 4, 5         70          Purchase PIT tags for installation at two     2005 -
                                 smolt trapping sites and in tributary habitat 2011
                                 upstream of these sites in the Entiat         
                                 Subbasin (work in 2005 and 2006 is funded by  
                                 NOAA; has been WE 182)                        

  1, 5               118         Coordinate sampling activities, data          2003 -
                                 collection, data analysis, and reporting with 2011
                                 local researchers                             

  1, 5               119         Administer project funds and subcontracts     2003 -
                                                                               2011

  **Objective(s)**   **Work      **Method**                                    **Start
                     Element**                                                 End**

  **Wenatchee and                                                              
  Entiat Subbasins                                                             
  Continued**                                                                  

  1, 5               156         Develop QA/QC procedures for any new          2007 -
                                 indicators developed under objectives 2, 3,   2010
                                 4, and 5.                                     

  2, 3, 4, 5         157         Survey habitat conditions and collect         2004 -
                                 macroinvertebrates at 50 locations plus 5     2011
                                 re-samples per year in the Wenatchee          

  2, 3, 4, 5         157         Survey habitat conditions and collect         2005 -
                                 macroinvertebrates at 50 locations plus 5     2011
                                 re-samples per year in the Entiat (a          
                                 subsample was started in 2005 to be expanded  
                                 in 2006 or 2007)                              

  2, 3, 4, 5         157         Survey fish populations through snorkeling at 2004 -
                                 50 locations plus 5 re-samples per year in    2011
                                 the Wenatchee                                 

  2, 3, 4, 5         157         Survey fish populations through snorkeling at 2006 -
                                 50 locations plus 5 re-samples per year in    2011
                                 the Entiat                                    

  2, 3, 4, 5         157         Survey fish populations through snorkeling at 2005 -
                                 13 \"Bridge-to-Bridge\" treatment and control 2011
                                 sites                                         

  2, 3, 4, 5         157         Survey habitat conditions and collect         2005 -
                                 macroinvertebrates at 13 \"Bridge-to-Bridge\" 2011
                                 treatment and control sites                   

  2, 3, 4, 5         157         Conduct reconnaissance and obtain landowner   2004 -
                                 permission for 50 random locations used in    2011
                                 snorkel and habitat surveys in Wenatchee      

  2, 3, 4, 5         157         Conduct reconnaissance and obtain landowner   2005 -
                                 permission for 50 random locations used in    2011
                                 snorkel and habitat surveys in Entiat         

  2, 3, 4, 5         157         Identify macroinvertebrates collected in      2004 -
                                 Wenatchee                                     2011

  2, 3, 4, 5         157         Identify macroinvertebrates collected in      2005 -
                                 Entiat (a subsample was started in 2005 to be 2011
                                 expanded in 2006 or 2007)                     

  2, 3, 4, 5         157         Sample depth fines in Wenatchee and Entiat    2005 -
                                                                               2011

  **Objective(s)**   **Work      **Method**                                    **Start
                     Element**                                                 End**

  **Wenatchee and                                                              
  Entiat Subbasins                                                             
  Continued**                                                                  

  2, 3, 4, 5         157         Sample water quality continuously at 5        2004 -
                                 locations in Wenatchee                        2011

  2, 3, 4, 5         157         Sample steelhead redds at random sites and    2004 -
                                 index areas in Wenatchee                      2011

  2, 3, 4, 5         157         Operate smolt traps at four locations in      2004 -
                                 Wenatchee                                     2011

  2, 3, 4, 5         157         Operate smolt traps at two locations in       2007 -
                                 Entiat                                        2011

  2, 3, 4, 5         158         Install PIT tags at four smolt trapping sites 2006 -
                                 and in tributary habitat upstream of these    2011
                                 sites in the Wenatchee Subbasin               

  2, 3, 4, 5         158         Install PIT tags at two smolt trapping sites  2005 -
                                 and in tributary habitat upstream of these    2011
                                 sites in the Entiat Subbasin (work in 2005    
                                 and 2006 is funded by NOAA)                   

  2, 3, 4, 5         157         Operate PIT tag arrays at six locations in    2006 -
                                 the Wenatchee (installation to be funded by   2011
                                 NOAA)                                         

  2, 3, 4, 5         157         Operate PIT tag arrays at six locations in    2006 (or
                                 the Entiat Subbasin (installation maybe       2007) -
                                 funded by NOAA in 2006, otherwise BPA in      2011
                                 2007)                                         

  2, 3, 4            160         Develop and maintain a database to house      2006 -
                                 project metadata and data                     2011

  6, 7               162         Update model annually with empirical data     2006 -
                                                                               2011

  1, 5               165         Complete permit applications for handling     2004 -
                                 listed species                                2011

  1, 5               174         Develop and adaptively update study design    2004 -
                                 documentation                                 2011
  ------------------ ----------- --------------------------------------------- ---------

  ------------------ ----------- ------------------------------------------ -----------
  **Objective(s)**   **Work      **Method**                                 **Start
                     Element**                                              End**

                                                                            

  **John Day                                                                
  Subbasin**                                                                

  5                  29          John Day Pilot Project -- Bridge Ck Reach  2008
                                 #17070204000307. Construct bundled log     
                                 step, centerpiece structure                

  5                  29          John Day Pilot Project -- Bridge Ck Reach  2008
                                 #17070204000307. Construct bundled log     
                                 step, centerpiece structure                

  5                  29          John Day Pilot Project -- Bridge Ck Reach  2008-2009
                                 #17070204000307. Construct upstream post   
                                 pile fences, secondary structure           

  5                  29          John Day Pilot Project -- Bridge Ck Reach  2008-2009
                                 #17070204000307. Construct downstream post 
                                 pile fences, secondary structure           

  5                  29          John Day Pilot Project -- Bridge Ck Reach  2008
                                 #17070204000305. Construct rock step,      
                                 centerpiece structure                      

  5                  29          John Day Pilot Project -- Bridge Ck Reach  2008
                                 #17070204000305. Construct rock step,      
                                 centerpiece structure                      

  5                  29          John Day Pilot Project -- Bridge Ck Reach  2008-2009
                                 #17070204000305. Construct upstream post   
                                 pile fences, secondary structure           

  5                  29          John Day Pilot Project -- Bridge Ck Reach  2008-2009
                                 #17070204000305. Construct downstream post 
                                 pile fences, secondary structure           

  5                  29          John Day Pilot Project -- Bridge Ck Reach  2008
                                 #17070204000299. Construct rock step,      
                                 centerpiece structure                      

  5                  29          John Day Pilot Project -- Bridge Ck Reach  2008
                                 #17070204000299. Construct rock step,      
                                 centerpiece structure                      

  5                  29          John Day Pilot Project -- Bridge Ck Reach  2008-2009
                                 #17070204000299. Construct upstream post   
                                 pile fences, secondary structure           

  5                  29          John Day Pilot Project -- Bridge Ck Reach  2008-2009
                                 #17070204000299. Construct downstream post 
                                 pile fences, secondary structure           

  5                  29          John Day Pilot Project -- Bridge Ck Reach  2008
                                 #17070204000298. Construct bundled log     
                                 step, centerpiece structure                

  5                  29          John Day Pilot Project -- Bridge Ck Reach  2008
                                 #17070204000298. Construct bundled log     
                                 step, centerpiece structure                

  **Objective(s)**   **Work      **Method**                                 **Start
                     Element**                                              End**

  **John Day                                                                
  Subbasin                                                                  
  Continued**                                                               

  5                  29          John Day Pilot Project -- Bridge Ck Reach  2008-2009
                                 #17070204000298. Construct upstream post   
                                 pile fences, secondary structure           

  5                  29          John Day Pilot Project -- Bridge Ck Reach  2008-2009
                                 #17070204000298. Construct downstream post 
                                 pile fences, secondary structure           

  5                  175         John Day Pilot Project-Design              2007
                                 specifications for Bridge Creek instream   
                                 structures                                 

  2, 3, 4, 5         70          Purchase PIT tags for installation at two  2006 - 2011
                                 smolt trapping sites and in tributary      
                                 habitat upstream of these sites in the     
                                 Bridge Creek (has been WE 182)             

  2, 3, 4, 5         70          Install PIT tag arrays at six locations in 2006 (or
                                 the Bridge Creek                           2007) -
                                                                            2011

  1, 5               118         Coordinate sampling activities, data       2003 - 2011
                                 collection, data analysis, and reporting   
                                 with local researchers                     

  1, 5               119         Administer project funds and subcontracts  2003 - 2011

  1, 5               156         Develop QA/QC procedures for any new       2007 - 2010
                                 indicators developed under objectives 2,   
                                 3, 4, and 5.                               

  1, 5               156         Calculate estimates of population metrics  2006 - 2011
                                 (e.g., escapement) generated using         
                                 proposed methods, and develop methods to   
                                 retrospectively apply variance to time     
                                 series data (e.g., redd counts)            

  1, 5               156         Develop methods to estimates of population 2005 - 2011
                                 metrics generated using proposed           
                                 methods/locations to existing              
                                 methods/locations to enable continuation   
                                 of existing time series data               

  1, 5               156         Continue development and adaptive          2005 - 2011
                                 refinement of statistical design and       
                                 analytical methods                         

  2, 3, 4, 5         157         Survey habitat conditions and collect      2005 - 2011
                                 macroinvertebrates at random and fixed     
                                 locations in Bridge Creek                  

  2, 3, 4, 5         157         Survey fish populations through snorkeling 2006 - 2011
                                 at random and fixed locations in Bridge    
                                 Creek                                      

  2, 3, 4, 5         157         Identify macroinvertebrates collected in   2005 - 2011
                                 Bridge Creek                               

  2, 3, 4, 5         157         Sample water quality continuously with     2004 - 2011
                                 hydrolabs at 3 locations in John Day       

  **Objective(s)**   **Work      **Method**                                 **Start
                     Element**                                              End**

  **John Day                                                                
  Subbasin                                                                  
  Continued**                                                               

  2, 3, 4, 5         157         Sample steelhead redds at random sites and 2004 - 2011
                                 index areas in Bridge Creek                

  2, 3, 4, 5         157         Operate smolt traps at two locations in    2007 - 2011
                                 Bridge Creek                               

  2, 3, 4, 5         157         Operate PIT tag arrays at six locations in 2006 (or
                                 the Bridge Creek                           2007) -
                                                                            2011

  2,3,4              157         Sample stable isotopes from all fish       2006 - 2011
                                 species present and macroinvertebrate      
                                 samples, plus diet samples from collected  
                                 fish at random and non-random selected     
                                 sites in the John Day                      

  2,3,4              157         Monitor grazing practices as the relate to 2006 - 2011
                                 compliance grazing guidelines throughout   
                                 the John Day                               

  2, 3, 4, 5         158         Install PIT tags at two smolt trapping     2005 - 2011
                                 sites and in tributary habitat upstream of 
                                 these sites in the Bridge Creek            

  2, 3, 4            160         Design and implement a database to capture 2006 - 2011
                                 metadata and data from project activities  

  2, 3, 4            160         Develop, maintain, and adapt a database to 2006 - 2011
                                 house project metadata and data            

  6, 7               162         Analyze recapture data for PIT tagged      2006 - 2011
                                 juveniles generated by PIT tag arrays,     
                                 repeat electrofishing, and at rotary screw 
                                 and smolt traps,                           

  1, 5               174         Develop and adaptively update study design 2004 - 2011
                                 documentation                              

  1, 5               174         Update study design document and model     2006 - 2011
                                 annually                                   

  2,3,4              174         Estimate sources of sampling variability   2006 - 2011

  6,7                174         Develop analytical framework and models to 2006 - 2011
                                 evaluate limiting factors                  

  6,7                174         Evaluate data for causal relationships     2006 - 2011
  ------------------ ----------- ------------------------------------------ -----------

  ------------------ ----------- ------------------------------------------ -----------
  **Objective(s)**   **Work      **Method**                                 **Start
                     Element**                                              End**

                                                                            

  **Salmon River                                                            
  Subbasin - South                                                          
  Fork Salmon                                                               
  River**                                                                   

  2, 3, 4            70          Install rotary screw trap in mainstem SFSR 2006 - 2011

  2, 3, 4            70          Install adult trap in mainstem SFSR        2006 - 2011

  2, 3, 4            70          Install DIDSON in Secesh River             2006 - 2011

  2, 3, 4            70          Install PIT tag arrays in mainstem SFSR,   2006 - 2011
                                 Secesh and East Fork SFSR                  

  2, 3, 4            70          Purchase PIT tags for deployment during    2006 - 2011
                                 electrofishing surveys and at juvenile and 
                                 adult traps                                

  1, 5               118         Coordinate sampling activities, data       2006 - 2011
                                 collection, data analysis, and reporting   
                                 with local researchers                     

  1, 5               119         Administer project funds and subcontracts  2006 - 2011

  1, 5               156         Calculate estimates of population metrics  2006 - 2011
                                 (e.g., escapement) generated using         
                                 proposed methods, and develop methods to   
                                 retrospectively apply variance to time     
                                 series data (e.g., redd counts)            

  1, 5               156         Develop methods to estimates of population 2005 - 2011
                                 metrics generated using proposed           
                                 methods/locations to existing              
                                 methods/locations to enable continuation   
                                 of existing time series data               

  1, 5               156         Continue development and adaptive          2005 - 2011
                                 refinement of statistical design and       
                                 analytical methods                         

  2, 3, 4            157         Operate rotary screw trap in mainstem SFSR 2006 - 2011

  2, 3, 4            157         Operate adult trap in mainstem SFSR        2006 - 2011

  2, 3, 4            157         Operate DIDSON in Secesh River             2006 - 2011

  2, 3, 4            157         Increase temporal span of operations of    2006 - 2011
                                 the lower Secesh River rotary screw trap   

  2, 3, 4            157         Operate PIT tag arrays in mainstem SFSR,   2006 - 2011
                                 Secesh, and EFSFSR                         

  2, 3, 4            157         Conduct probabilistic and fixed site       2006 - 2011
                                 electrofishing surveys throughout the      
                                 SFSR.                                      

  2, 3, 4            157         Conduct probabilistic and fixed site       2006 - 2011
                                 habitat surveys throughout the SFSR.       

  **Objective(s)**   **Work      **Method**                                 **Start
                     Element**                                              End**

  **Salmon River                                                            
  Subbasin - South                                                          
  Fork Salmon River                                                         
  Continued**                                                               

  2, 3, 4            158         PIT tag juveniles collected at rotary      2006 - 2011
                                 screw traps and during electrofishing      
                                 surveys                                    

  2, 3, 4            158         PIT tag and visually mark adults collected 2006 - 2011
                                 at the mainstem fish trap                  

  2, 3, 4            160         Design and implement a database to capture 2006 - 2011
                                 metadata and data from project activities  

  2, 3, 4            160         Develop, maintain, and adapt a database to 2006 - 2011
                                 house project metadata and data            

  6, 7               162         Compare estimates derived from proposed    2006 - 2011
                                 methods to estimates derived from existing 
                                 methods (e.g., tributary specific juvenile 
                                 abundance generated from rotary screw      
                                 traps versus proportional estimation from  
                                 SFSR aggregate).                           

  6, 7               162         Apply retrospective variance estimators to 2006 - 2011
                                 time series data                           

  6, 7               162         Apply methods to maintain continuity of    2006 - 2011
                                 current time series data                   

  6, 7               162         Evaluate whether proposed infrastructure   2011-2011
                                 can reliably meet information needs        
                                 without relying on existing                
                                 infrastructure.                            

  6, 7               162         Analyze project data annually to           2006 - 2011
                                 adaptively manage collection and evaluate  
                                 methods                                    

  1, 5               165         Complete permit applications for handling  2006 - 2011
                                 listed species                             

  1, 5               174         Update study design document and model     2006 - 2011
                                 annually                                   
  ------------------ ----------- ------------------------------------------ -----------

  ------------------ ----------- -------------------------------------------- ---------
  **Objective(s)**   **Work      **Method**                                   **Start
                     Element**                                                End**

                                                                              

  **Salmon River                                                              
  Subbasin - Lemhi                                                            
  River**                                                                     

  2, 3, 4            70          Install rotary screw trap in mainstem Lemhi  2006 -
                                                                              2011

  2, 3, 4            70          Install rotary screw trap in Hayden Creek    2006 -
                                                                              2011

  2, 3, 4            70          Install adult trap in mainstem Lemhi         2006 -
                                                                              2011

  2, 3, 4            70          Install PIT tag arrays in Lemhi mainstem and 2006 -
                                 reconnected tributaries                      2011

  **Objective(s)**   **Work      **Method**                                   **Start
                     Element**                                                End**

  **Salmon River                                                              
  Subbasin - Lemhi                                                            
  River Continued**                                                           

  2, 3, 4            70          Purchase PIT tags for deployment during      2006 -
                                 electrofishing surveys and at juvenile and   2011
                                 adult traps                                  

  1, 5               118         Coordinate sampling, and data collection,    2006 -
                                 analysis, and reporting                      2011

  1, 5               119         Administer project funds and subcontracts    2006 -
                                                                              2011

  1, 5               156         Continue development and adaptive            2005 -
                                 modification of watershed model              2011

  1, 5               156         Continue development and adaptive refinement 2006 -
                                 of methods                                   2011

  2, 3, 4            157         Operate rotary screw trap in mainstem Lemhi  2006 -
                                                                              2011

  2, 3, 4            157         Operate rotary screw trap in Hayden Creek    2006 -
                                                                              2011

  2, 3, 4            157         Operate adult trap in mainstem Lemhi         2006 -
                                                                              2011

  2, 3, 4            157         Operate PIT tag arrays in Lemhi mainstem and 2006 -
                                 reconnected tributaries                      2011

  2, 3, 4            157         Conduct probabilistic and fixed site         2006 -
                                 electrofishing surveys throughout the Lemhi  2011
                                 watershed                                    

  2, 3, 4            157         Conduct probabilistic and fixed site habitat 2006 -
                                 surveys throughout the Lemhi watershed.      2011

  2, 3, 4            158         PIT tag juveniles at rotary screw traps and  2006 -
                                 during electrofishing surveys                2011

  2, 3, 4            158         PIT tag and visually mark adults collected   2006 -
                                 at the mainstem fish trap                    2011

  2, 3, 4            160         Develop and maintain a database to house     2006 -
                                 project metadata and data                    2011

  6, 7               162         Update model annually with empirical data    2006 -
                                                                              2011

  6, 7               162         Analyze recapture data for PIT tagged        2006 -
                                 juveniles generated by PIT tag arrays,       2011
                                 repeat electrofishing, and at rotary screw   
                                 traps                                        

  6, 7               162         Analyze project data to adaptively manage    2006 -
                                 the project                                  2011

  1, 5               165         Complete permit applications for handling    2006 -
                                 listed species                               2011

  **Objective(s)**   **Work      **Method**                                   **Start
                     Element**                                                End**

  **Salmon River                                                              
  Subbasin - Lemhi                                                            
  River Continued**                                                           

  1, 5               174         Determine adequacy of sampling, annually     2005 -
                                 update sampling design and model             2011

  1, 5               174         Update study design document and model       2006 -
                                 annually                                     2011
  ------------------ ----------- -------------------------------------------- ---------

G. Facilities and equipment

ISEMP has not purchased major equipment other than Rotary Screw Trap
cones (and custom made pontoons) for the Wenatchee Pilot Project. The
project, however, depends on the collaborative participation of numerous
other programs who operate juvenile and adult trapping and tagging
facilities and equipment. In addition, the project depends on the
laboratory facilities of several subcontractors where water quality
chemistry and macro invertebrate sample processing is performed.

H. References

+-----------------------------------------------------------------------+
| > Apple, L.L. 1983. The use of beavers in riparian/aquatic habitat    |
| > restoration in a cold desert, gully-cut stream system: a case       |
| > history. Annual Proceedings, American Fisheries Society, Colorado   |
| > Wyoming Chapter 18:29-35.                                           |
+-----------------------------------------------------------------------+
| Beechie, T. and M. Pollock. Northwest Fisheries Science Center,       |
| NOAA-Fisheries. Personal communication of unpublished data            |
+-----------------------------------------------------------------------+
| > Bilby, R.E., W.J. Ehinger, C. Jordan, K. Krueger, M. McHenry, T.    |
| > Quinn, G. Pess, D. Poon, D. Seiler, and G. Volkhardt. 2004.         |
| > Evaluating watershed response to land management and restoration    |
| > actions: intensively monitored watersheds (IMW) progress report.    |
| > Submitted to the Washington Salmon Recovery Funding Board by the    |
| > IMW Scientific Oversight Committee. 72pp.                           |
| > <                                                                   |
| http://www.iac.wa.gov/Documents/SRFB/Monitoring/IMW_progress_rpt.pdf> |
+-----------------------------------------------------------------------+
| > Bjornn, T.C. 1978. Survival, production, and yield of trout and     |
| > chinook salmon in the Lemhi River, Idaho. University of Idaho,      |
| > Bulletin 27, Moscow.                                                |
+-----------------------------------------------------------------------+
| > Bouwes, N. ed. 2004. Research, monitoring, and evaluation           |
| > coordination in the John Day basin, 2004-2005 status report.        |
| > Compiled and edited by Eco Logical Research, Inc. Providence, UT    |
| > for NOAA Fisheries Service and the Bonneville Power Administration. |
| >                                                                     |
|  <http://www.nwfsc.noaa.gov/research/divisions/cbd/mathbio/index.cfm> |
+-----------------------------------------------------------------------+
| > Bouwes, N. ed. 2005. Integrated status and effectiveness monitoring |
| > John Day pilot program, 2005 draft annual report. Compiled and      |
| > edited by Eco Logical Research, Inc. Providence, UT for NOAA        |
| > Fisheries Service and the Bonneville Power Administration.          |
| >                                                                     |
|  <http://www.nwfsc.noaa.gov/research/divisions/cbd/mathbio/index.cfm> |
+-----------------------------------------------------------------------+
| > Box, G.E.P. and G.C. Tiao. 1975. Intervention analysis with         |
| > applications to economic and environmental problems. Journal of the |
| > American Statistical Association 70:70-79                           |
+-----------------------------------------------------------------------+
| Boyd, M. and B. Kasper. 2002. HeatSource Model. www.heatsource info   |
+-----------------------------------------------------------------------+
| Buckley, G.L. 1992. Desertification of the Camp Creek drainage in     |
| central Oregon, 1826-1905. MA. University of Oregon.                  |
+-----------------------------------------------------------------------+
| > Budy, P., T. Haddix, and R. Schneidervin. 2005. Zooplankton size    |
| > selection relative to gill raker spacing in rainbow trout.          |
| > Transactions of the American Fisheries Society 134:1228-1235.       |
+-----------------------------------------------------------------------+
| Carpenter, S.R., T.M. Frost, D. Heisey, and T.K. Kratz. 1989.         |
| Randomized intervention analysis and the interpretation of            |
| whole-ecosystems. Ecology 70:1142-1152.                               |
+-----------------------------------------------------------------------+
| > CBMRC (Columbia-Blue Mountain Resource Conservation and Development |
| > Area). 2005. John Day Subbasin Plan. Prepared for the Northwest     |
| > Power and Conservation Council, Portland, Oregon                    |
+-----------------------------------------------------------------------+
| Cloutman D.G. and D.C. Jackson. 2003. A comparison of randomized      |
| intervention analysis and two-factor analysis of variance for         |
| analysis of angler effort in a floodplain river fishery. Fisheries    |
| Management and Ecology 10:173-177                                     |
+-----------------------------------------------------------------------+
| > Columbia-Blue Mountain Resource Conservation and Development Area.  |
| > 2005. John Day subbasin revised draft plan. Prepared for the        |
| > Northwest Power and Conservation Council.                           |
| > <http://www.nwcouncil.org/fw/subbasinplanning/johnday/plan/>        |
+-----------------------------------------------------------------------+
| > CSMEP. Collaborative Systemwide Monitoring and Evaluation Program.  |
| > [http://www.                                                        |
| cbfwa.org/committees/csmep/](http://www.cbfwa.org/committees/csmep/ ) |
+-----------------------------------------------------------------------+
| > Draper, D. 1995. Assessment and propagation of model uncertainty    |
| > (with discussion). The Journal of the Royal Statistical Society B   |
| > 57:45-97                                                            |
+-----------------------------------------------------------------------+
| > Ecovista. 2004. Salmon Subbasin management plan. Prepared on behalf |
| > of the Nez Perce Tribe Watershed Division and Shoshone-Bannock      |
| > Tribes for the Northwest Power Planning Council. 851 SW Sixth       |
| > Avenue, Suite 1100, Portland, Oregon, 97204. 21 pp.                 |
+-----------------------------------------------------------------------+
| Elmore, W., B. Kauffman, M. Vavra, W. A. Laycock, and R. D. Pieper.   |
| 1994. Riparian and watershed systems: degradation and restoration.    |
| Ecological implications of herbivory in the west.                     |
+-----------------------------------------------------------------------+
| EMAP, Enivironmental Monitoring and Assessment Program, US EPA,       |
| <http://www.epa.gov/emap/>                                            |
+-----------------------------------------------------------------------+
| Fausch, K.D., C.E. Torgersen, C.V. Baxter, H.W. Li. 2002. Landscapes  |
| to Riverscapes: Bridging the Gap between Research and Conservation of |
| Stream Fishes. Bioscience 52(6):483-498.                              |
+-----------------------------------------------------------------------+
| Johnson, R., C. McKinstry, R. Mueller, \"Chinook Salmon Adult         |
| Abundance Monitoring; Hydroacoustic Assessment of Chinook Salmon      |
| Escapement to the Secesh River, Idaho\", 2002-2004 Final Report,      |
| Project No. 199703000, 34 electronic pages, (BPA Report               |
| DOE/BP-00000652-17).                                                  |
| <http://www.efw.bpa.gov/publications/U00000652-17.pdf>                |
+-----------------------------------------------------------------------+
| Hassemer, P. 1993. Salmon spawning ground surveys 1989-92. Pacific    |
| Salmon Treaty Program. Award Number NA17FPO168-02.                    |
| <https://research.idfg.idaho.gov/>.                                   |
+-----------------------------------------------------------------------+
| Hesse, Jay, Billy Arnsberg, \"Salmon Supplementation Studies in Idaho |
| Rivers; Idaho Supplementation Studies\", 1993 Annual Report, Project  |
| No. 198909802, 26 electronic pages, (BPAReport DOE/BP-00004127-2)     |
| <http://www.efw.bpa.gov/publications/A00004127-2.pdf>                 |
+-----------------------------------------------------------------------+
| Hillman, T.W. 2004. Monitoring Strategy for the Upper Columbia Basin. |
| Draft Report prepared for Upper Columbia Regional Technical Team.     |
| BioAnalysts, Inc. Eagle, ID.                                          |
+-----------------------------------------------------------------------+
| Holmes, E.E. 2001. Estimating risks in declining populations with     |
| poor data. Proceedings of the National Academy of Science USA 98:     |
| 5072-5077.                                                            |
+-----------------------------------------------------------------------+
| Holmes, E.E. 2004a. Beyond theory to application and evaluation:      |
| Diffusion approximations for population viability analysis.           |
| Ecological Applications. *In press*.                                  |
+-----------------------------------------------------------------------+
| Holmes, E.E. 2004b. Review of methods, process and cross-validation   |
| studies pertaining to population trend and risk assessment for        |
| Columbia River salmonids. *FCRPS Biological white paper*.             |
+-----------------------------------------------------------------------+
| Hyun, S., and A. Talbot. 2004. Status of Snake River spring/summer    |
| Chinook salmon and steelhead by an integrated risk metric. Bonneville |
| Power Administration (BPA) contract report.                           |
+-----------------------------------------------------------------------+
| ICBTRT. 2003. Independent populations of chinook, steelhead and       |
| sockeye for listed evolutionarily significant units (ESUs) within the |
| interior Columbia basin.                                              |
| <http://www.nwfsc.noaa.gov/trt/trt_pop_id.htm>                        |
+-----------------------------------------------------------------------+
| ID OSC (Idaho Governor's Office of Species Conservation). 2004.       |
| Cottom Lane Fence Project (PCSRF Project Number 01304SA).             |
+-----------------------------------------------------------------------+
| ID OSC (Idaho Governor's Office of Species Conservation). 2004.       |
| Effectiveness Monitoring and Evaluation or Habitat Projects in the    |
| Lemhi River, (PCSRF Project Number 01504SA)                           |
+-----------------------------------------------------------------------+
| ID OSC (Idaho Governor's Office of Species Conservation). 2004.       |
| Hawley-Eighteenmile Siphon (PCSRF Project Number 01204SA)             |
+-----------------------------------------------------------------------+
| ID OSC (Idaho Governor's Office of Species Conservation). 2004.       |
| Implementing Salmon and Steelhead Conservation Actions in the Upper   |
| Salmon Subbasin (PCSRF Project Number 01404SA)                        |
+-----------------------------------------------------------------------+
| ID OSC (Idaho Governor's Office of Species Conservation). 2004. L-6   |
| to S-14 Water Diversion Transfer (PCSRF Project Number 01104SA)       |
+-----------------------------------------------------------------------+
| ID OSC (Idaho Governor's Office of Species Conservation). 2004.       |
| Reconnect Big Eight Mile Creek, Big Timber Creek, and Bohannon Creek  |
| (PCSRF Project Number 00804SA)                                        |
+-----------------------------------------------------------------------+
| ISAB. 2003. Comments on draft NOAA Technical Recovery Team documents  |
| identifying independent salmonid populations within evolutionarily    |
| significant units.                                                    |
| <http://www.nwcouncil.org/library/isab/isab2003-4.htm>                |
+-----------------------------------------------------------------------+
| ISCC (Idaho Soil Conservation Commission). 1995. Model watershed      |
| plan: Lemhi, Pahsimeroi, and East Fork of the Salmon River. Prepared  |
| for U.S. Department of Energy Bonneville Power Administration         |
| Division of Fish and Wildlife P.O. Box 3621 Portland, OR.97208-3621   |
+-----------------------------------------------------------------------+
| ISRP/ISAB (Independent Scientific Review Panel and Independent        |
| Scientific Advisory Board). 2004a. A Joint ISAB and ISRP Review of    |
| the Draft Research, Monitoring & Evaluation Plan for the              |
| NOAA-Fisheries 2000 Federal Columbia River Power System Biological    |
| Opinion. <http://www.nwcouncil.org/library/isab/isab2004-1.htm>       |
+-----------------------------------------------------------------------+
| ISRP/ISAB (Independent Scientific Review Panel and Independent        |
| Scientific Advisory Board). 2004b. Scientific review of subbasin      |
| plans for the Columbia River Basin fish and wildlife program.         |
| <http://www.nwcouncil.org/library/isrp/isrpisab2004-13.htm>           |
+-----------------------------------------------------------------------+
| ISRP 2005. Independent Scientific Review Panel Retrospective Report   |
| 1997-2005. Northwest Power and Conservation Council, 851 SW 6th       |
| Avenue, Suite 1100, Portland, Oregon 97204. Available at:             |
| [www.nwcouncil.org/library/isrp/isr                                   |
| p2005-14.htm](http://www.nwcouncil.org/library/isrp/isrp2005-14.htm). |
+-----------------------------------------------------------------------+
| ISRP 2005-6. Step review of the Johnson Creek artificial propagation  |
| enhancement project, 1996-043-00.                                     |
| <http://www.nwcouncil.org/library/isrp/isrp2005-6.htm>                |
+-----------------------------------------------------------------------+
| Johnson, J. Editor. 2004. Wenatchee subbasin plan. Prepared for the   |
| Northwest Power and Conservation Council.                             |
| <http://www.nwcouncil.org/fw/subbasinplanning/wenatchee/plan/>        |
+-----------------------------------------------------------------------+
| Jordan, C.E., J. Geiselman, M.                                        |
| Newsom, and J. Athearn (editors). 2003.\                              |
| Draf                                                                  |
| t Research, Monitoring & Evaluation Plan for the NOAA-Fisheries 2000\ |
| Federal Columbia River Power System Biological Opinion.  9.11.03.\    |
| [www.salmonrecovery.gov/r                                             |
| eports_and_papers/reserach/docs/RME_Plan_09-2003.pdf](http://www.salm |
| onrecovery.gov/reports_and_papers/reserach/docs/RME_Plan_09-2003.pdf) |
+-----------------------------------------------------------------------+
| Kershner, JL., BB. Roper, N. Bowes, R. Henderson, and E. Archer.      |
| 2004. An analysis of stream habitat conditions in reference and       |
| managed watersheds on some federal lands within the Columbia River    |
| Basin. North American Journal of Fisheries Management. 24:1363-1375.  |
+-----------------------------------------------------------------------+
| Kiefer, R.B. and J.N. Lockhart - Idaho Department Of Fish And Game,   |
| 1995, Intensive Evaluation And Monitoring Of Chinook Salmon And       |
| Steelhead Production, Crooked River And Upper Salmon River Sites      |
| Annual Progress Report January 1, 1993 - December 31, 1993, Report to |
| Bonneville Power Administration, Contract No. 00005862, Project No.   |
| 199107300, 64 electronic pages (BPA Report DOE/BP-00005862-3)         |
| <http://www.efw.bpa.gov/publications/I00005862-3.pdf>                 |
+-----------------------------------------------------------------------+
| Leth, B., T. Holubetz, D. Nemeth - Idaho Dept. Fish & Game,           |
| Evaluation and Monitoring of Wild/Natural Steelhead Trout Production  |
| Annual Progress Report, January 1, 1996 - December 31, 1996, Report   |
| to Bonneville Power Administration, Contract No. 00005862, Project    |
| No. 199107300, 11 electronic pages (BPA Report DOE/BP-00005862-2).    |
| <http://www.efw.bpa.gov/publications/I00005862-2.pdf>                 |
+-----------------------------------------------------------------------+
| Li, H.W. Proposal: Effects of push-up dams on redband/steelhead (*O.  |
| mykiss*) production in the mid-Columbia basin.                        |
| <http://www.nwfsc.noaa.gov/research/divisions/cbd/mathbio/index.cfm>  |
+-----------------------------------------------------------------------+
| Luecke C., W.A. Wurtsbaugh, P. Budy, H.P. Gross and G. Steinhart.     |
| 1996. Simulated growth and production of endangered Snake River       |
| sockeye salmon: assessing management strategies for the nursery       |
| lakes. Fisheries 21:18-25                                             |
+-----------------------------------------------------------------------+
| Mallet, J. 1974. Inventory of salmon and steelhead resources,         |
| habitat, use and demands. Idaho Department of Fish and Game, Project  |
| F-58-R-1, Boise.                                                      |
+-----------------------------------------------------------------------+
| Matthews, G.M. and R.S. Waples. 1991. Status review for Snake River   |
| spring and summer chinook salmon. NTIS Number PB91-218065. Pp. 75.    |
+-----------------------------------------------------------------------+
| McClure, M.M., E.E. Holmes, B.L. Sanderson, and C.E. Jordan. 2003. A  |
| large-scale, multispecies status assessment: Anadromous salmonids in  |
| the Columbia River Basin. Ecological Applications 13 (4): 964-989     |
+-----------------------------------------------------------------------+
| Milliken, G.A. and D.E. Johnson. 2001. Analysis of messy data, Volume |
| III: Analysis of Co-variance. CRC Press. Boca Raton, Florida.         |
+-----------------------------------------------------------------------+
| Nemeth, D., K. Plaster, K. Apperson, J. Brostrom, T. Curet and E.     |
| Brown - Idaho Dept. of Fish and Game, 1996, Idaho Supplementation     |
| Studies, Annual Report 1994, Report to Bonneville Power               |
| Administration, Contract No. 1989BP01466, Project No. 198909800, 66   |
| electronic pages (BPA Report DOE/BP-01466-4A).                        |
| <http://www.efw.bpa.gov/publications/A01466-4A.pdf>                   |
+-----------------------------------------------------------------------+
| NPPC 2000. Northwest Power Planning Council. Columbia River Basin     |
| fish and wildlife program.                                            |
| <http://www.nwcouncil.org/library/2000/2000-19/Default.htm>           |
+-----------------------------------------------------------------------+
| NWPPC. 2004. Northwest Power Planning Council 1994/95 Columbia River  |
| Basin Fish and Wildlife Program.                                      |
| <http://www.nwcouncil.org/library/1994/>                              |
+-----------------------------------------------------------------------+
| NWPPC. 2005. Northwest Power Planning Council. Draft Columbia River   |
| Basin Research Plan.                                                  |
| <http://www.nwcouncil.org/library/2005/draftrme.htm>                  |
+-----------------------------------------------------------------------+
| ODEQ TMDL, Total Maximum Daily Load Program. Oregon Department of     |
| Environmental Quality.                                                |
| <http://www.deq.state.or.us/wq/TMDLs/TMDLs.htm>                       |
+-----------------------------------------------------------------------+
| Peacock, K.A. 1994. Valley fill and channel incision in Meyer's       |
| Canyon, Northcenteral Oregon. M.S. Oregon State University.           |
+-----------------------------------------------------------------------+
| PACFISH/INFISH Biological Opinion, USFS,                              |
| <http://www.fs.fed.us/biology/fishecology/emp/>                       |
+-----------------------------------------------------------------------+
| Peven, C., B. Rose, W. Trihey, and S.M. Walker. 2004. Entiat subbasin |
| plan. Ed. Jean Johnson. Prepared for the Northwest Power and          |
| Conservation Council.                                                 |
| <http://www.nwcouncil.org/fw/subbasinplanning/entiat/plan/>           |
+-----------------------------------------------------------------------+
| PNAMP (Pacific Northwest Aquatic Monitoring Partnership. 2005.        |
| Habitat coordination and survey design.                               |
| [http://www.reo.gov/PNAMP/workgroup                                   |
| s/PNAMP%20WS.htm.](http://www.reo.gov/PNAMP/workgroups/PNAMP WS.htm.) |
+-----------------------------------------------------------------------+
| QCI. Quantitative Consultants, Inc. 2005. Study design for habitat    |
| and population status and trend monitoring for the South Fork Salmon  |
| River, Idaho and habitat action effectiveness monitoring for the      |
| Lemhi River, Idaho. Prepared for National Oceanographic and           |
| Atmospheric Administration, Department of Fisheries, Northwest        |
| Fisheries Science Center. 61pp.                                       |
+-----------------------------------------------------------------------+
| Rich, B.A., R.J. Scully, C.E. Petrosky, 1990. Idaho Department Of     |
| Fish And Game, Idaho Habitat/Natural ProductionMonitoring, Part I:    |
| General Monitoring Subproject, Annual Report 1990, Report to          |
| Bonneville Power Administration, Contract No.1984BP13381, Project No. |
| 198300700, 63 electronic pages (BPA Report DOE/BP-13381-7).           |
| <http://www.efw.bpa.gov/publications/H13381-7.pdf>                    |
+-----------------------------------------------------------------------+
| Ricker, W.E. 1954. Stock and recruitment. Journal of the Fisheries    |
| Research Board of Canada. 11:559--623                                 |
+-----------------------------------------------------------------------+
| Roger, P.B. and M. Schwartzberg. 1986. Observations on the accuracy   |
| of redd counting techniques used in the Columbia River Basin.         |
| Columbia River Inter-Tribal Fish Commission. Technical Report 86-2.   |
| [www.CRITFC.org](http://www.CRITFC.org/)                              |
+-----------------------------------------------------------------------+
| Roper B.B., J.J. Dose, and J.E. Williams. 1997. Stream restoration:   |
| is fisheries biology enough? Fisheries 22:6-11.                       |
+-----------------------------------------------------------------------+
| Roper, B.B., J.L. Kershner, E. Archer, R. Henderson and N. Bouwes.    |
| 2002. An evaluation of physical stream habitat attributes used to     |
| monitor streams. Journal of the American Water Resources Association  |
| 38:1637-1646.                                                         |
+-----------------------------------------------------------------------+
| Russell, B. K. Kiefer, and A. Forster. 1990. Idaho Habitat/Natural    |
| Production Monitoring Pare II: Intensive Monitoring Subproject,       |
| Annual Progress Report 1990, Report to the Bonneville Power           |
| Administration, Project Number 83-7 Contract Number                   |
| DE-BI79-84BP13381. <http://www.efw.bpa.gov/publications/H13381-8.pdf> |
+-----------------------------------------------------------------------+
| Scheffer, P.M. 1938. The beaver as an upstream engineer. Soil         |
| Conservation **3**:178-181.                                           |
+-----------------------------------------------------------------------+
| Sharma, R., A.B. Cooper, and R. Hilborn. 2005. A quantitative         |
| framework for the analysis of habitat and hatchery practices on       |
| Pacific salmon. Ecological Modeling. 183: 231-250                     |
+-----------------------------------------------------------------------+
| Shipley, B. 2000 Cause and correlation in biology. A user's guide to  |
| path analysis and structural equations and causal inferences.         |
| Cambridge University Press, Cambridge, UK                             |
+-----------------------------------------------------------------------+
| Stewart-Oaten, A., W.M. Murdock, and K.R. Parker. 1986. Environmental |
| impact assessment: \"pseudo replication\" in time? Ecology            |
| 67:929-940.Tait, C.K., J.L. Li, G.A. Lamberti, T.N. Pearsons, and     |
| H.W. Li. 1994. Influences of riparian cover on benthic community      |
| structure in high desert streams. Journal of the North American       |
| Benthological Society 13(1):45-56                                     |
+-----------------------------------------------------------------------+
| Stewart-Oaten A. and J.R. Bence. 2001. Temporal and spatial variation |
| in environmental impact assessment. Ecological Monographs 71:305-339  |
+-----------------------------------------------------------------------+
| Sutton, R. and C. Morris. 2005. Flow characterization study. Instream |
| flow assessment Big Eighteenmile Creek, Bohannon Creek, and Hayden    |
| Creek, Idaho. U.S. Department of the Interior, Bureau of Reclamation, |
| Snake River Area Office, Boise, ID.                                   |
| <http://id.water.usgs.gov/projects/salmon_streamflow/index.html>      |
+-----------------------------------------------------------------------+
| Trapani, J. 2002. Stream habitat inventory report fro the Lemhi,      |
| Pahsimeroi, and East Fork Salmon River, Idaho. Upper Salmon Basin     |
| Watershed Project                                                     |
+-----------------------------------------------------------------------+
| Venditti, D.A., K. Apperson, A. Brimmer, N. Brindza, C. Gass, A.      |
| Kohler, and J. Lockhart. 2005. Idaho supplementation studies brood    |
| year 2002 cooperative report.                                         |
| <http://fishandgame.idaho.gov/cms/tech/reports/>                      |
+-----------------------------------------------------------------------+
| Waples, R.S. 1991. Pacific salmon, *Oncorhynchus* spp., and the       |
| definition of "species" under the endangered species act. Marine      |
| Fisheries Review 53(3):11-22                                          |
+-----------------------------------------------------------------------+
| Ward J.V. 1985. Thermal characteristics of running waters.            |
| Hydrobiologia 125:31-46                                               |
+-----------------------------------------------------------------------+
| White, G.C. and K. P. Burnham. 1999.  Program MARK: Survival          |
| estimation from populations of marked animals. Bird Study 46          |
| Supplement, 120-138                                                   |
+-----------------------------------------------------------------------+
| Wiley, D., M. Garriott and J. Ruzycki. 2004. \"Implementation of the  |
| Environmental Monitoring and Assessment Program (EMAP) Protocol in    |
| the John Day Subbasin of the Columbia Plateau Province\", 2003-2004   |
| Technical Report, Project No. 199801600, 56 electronic pages, (BPA    |
| Report DOE/BP-00015113-1)                                             |
| <http://www.efw.bpa.gov/publications/A00015113-1.pdf>                 |
+-----------------------------------------------------------------------+

I. Key personnel

Key personnel section is limited to ISEMP coordinator (Chris Jordan --
NMFS) and the ISEMP-Pilot Project subbasin coordinators (Mike Ward --
Wenatchee/Entiat; Nick Bouwes -- John Day/Bridge Ck; Chris Beasley --
SFSalmon/Lemhi). The entire group of project participants (contractors,
TOC members, and technical staff) is more than 100 -- all of them key to
the success of the project.

**Chris Jordan**

Program Manager

Mathematical Biology, Systems Monitoring and Cumulative Risk Initiative

NOAA-Fisheries/Northwest Fisheries Science Center

Newport Research Station

Newport, OR 97365

**Education:**

University of Washington Ph.D. 1994 Zoology

University of Chicago B.A. 1985 Biology

**Positions Held:**

Program Manager NOAA-F/NWFSC, Seattle 2002 - present

Operations Research Analyst NOAA-F/NWFSC, Seattle 1999 - 2002

Research Assistant Professor Washington State Univ., Pullman 1999 -
present

Assistant Professor University of Colorado, Boulder 1995 - 1999

Research Associate University of Chicago, Chicago 1994 - 1995

Research/Teaching Assistant University of Washington, Seattle 1987 -
1994

**Related Publications:**

McClure, M. M., Sanderson, B. L., Holmes, E. E. and Jordan, C. E. 2003.
A large-scale, multi-species risk assessment: Anadromous salmon in the
Columbia River Basin. Ecol. App. 13: 964-989

Roni, P., M.C. Liermann, C.E. Jordan, and A.E. Steel. 2004. Monitoring
design: important considerations for developing monitoring of aquatic
restoration. In *Monitoring stream and watershed restoration,* P. Roni
ed. AFS Press, *In Press*

Courbois, P. Katz, S, Jordan, C., and A.E. Steel. (In Review) Sampling
Strategies for Chinook Spawning Populations.

Sholz, N, Hecht, S, Laetz, C, Jordan,C. and T. Collier. (in Review)
Problem formulation for Risk Assessments involving pesticides and
threatened or endangered pacific salmon. Ecol. Appl.

**Technical Reports:**

Jordan, C.E. (ed). 2003. Research Monitoring and Evaluation for the 2000
FCRPS Biological Opinion, 2003. Prepared for NOAA-F NWR Hydro Division
and Action Agencies

Jordan, C.E. and 15 co-authors 2002. Mainstem/Systemwide Province Stock
Status Program Summary. Guidelines for Conducting Population and
Environmental Status Monitoring. February 22, 2002. Prepared for the
Northwest Power Planning Council.

MICHAEL B. WARD

Senior Fisheries Ecologist

Terraqua, Inc.

**EDUCATION**

Univ. of Washington, M.Sc. Fisheries, 1993.

Humboldt State Univ., B.Sc. Fisheries, 1989.

Wa. State DNR Watershed Analysis, 1996.

Wa. State DNR Stream Survey Protocol, 1997.

**PROFESSIONAL AFFILIATIONS**

Upper Columbia Regional Technical Team

American Fisheries Society

American Inst. of Fisheries Research Biologists

Gilbert Ichthyological Society

Pacific Fisheries Biologists

######### **PROFESSIONAL SUMMARY**

> Mr. Ward has been active in the field of fisheries ecology since 1986
> and has been consulting on hydropower/fisheries interactions since
> 1989. Mr. Ward has been vice-president/senior fisheries ecologist of
> Terraqua Inc. since January 1995. Mr. Ward is an expert in fisheries
> populations and habitat assessments, monitoring and study designs, and
> resource management planning. His research has focused on the
> relationships between fisheries, water quantity, and fish habitat in
> watersheds impacted by fisheries restoration projects, hydroelectric
> power generation, water diversions, and land-use.
>
> Mr. Ward has coordinated ISEMP activities in the Wenatchee and Entiat
> subbasins since 2003. He has developed much of the project planning
> and design documentation pertaining to these subbasins and has led
> specific elements of ISEMP field work and analysis.

**GENERAL FISHERIES EXPERIENCE**

[Vice-President/Fisheries Ecologist,]{.underline} Terraqua, Inc.,
Wauconda, Wa. 1/95 - present.

Managing a growing environmental consulting business. Coordinating the
design and implementation of monitoring studies for Bonneville Power
Administration's ISEMP Project; representing the Battle Creek Watershed
Conservancy in policy arenas pertaining to the management of Coleman
National Fish Hatchery and the land and waters of Battle Creek,
California; and providing planning services to U.S. Bureau of
Reclamation for the Battle Creek Restoration Project. Other recent
clients have included: Metropolitan Water District of Southern
California, PacifiCorp, California Fish and Game, Grant County P.U.D.,
Seattle City Light, Hoopa Valley Tribe, Pacific Gas and Electric, and
Colville Confederated Tribes.

[Aquatic Ecologist]{.underline}, Harza, Inc., Bellevue, Wa. 7/93 - 2/95.

Conducted habitat assessments and identified the impacts of the North
Umpqua River Hydroelectric Project, Or. on trout and salmon fisheries.
Studied the effects of heavy metal pollution and water quality problems
on urbanized fish populations.

[Research Assistant]{.underline}, Fisheries Research Institute, Univ. of
Washington, Seattle, Wa. 9/90 - 7/93.

[Fisheries Biologist]{.underline}, Steiner Environmental Consulting,
Potter Valley, Ca. 8/89-12/90.

[Project Manager]{.underline}, California Dept. of Fish and Game, U. S.
Forest Service, Arcata, Ca. 5/88-5/90.

[Fishery Technician/Intern]{.underline}, U. S. Fish and Wildlife
Service, Ashland, Wi. 5/85-5/86.

**Nicolaas W. Bouwes, Jr.**

**EDUCATION**

Ph.D.- Aquatic Ecology, Utah State University. January 1999.

M.S.- Aquatic Ecology, Utah State University. March 1995.

B.S.- Zoology- University of Wisconsin, Madison. December 1989.

**RECENT PROFESSIONAL EXPERIENCE**

[Environmental Consultant. Owner.]{.underline} Eco Logical Research,
Inc.. 2000-present. Selected projects:

> 2005-Present -- Research Coordinator for the Columbia River Basin
> Federal Research Monitoring and Evaluation (RME) program's John Day
> pilot project.
>
> 2003-Present-Collaborative System-wide Monitoring and Evaluation
> Project administered through the Columbia Basin Fish and Wildlife
> Authority, Portland OR.
>
> 2003 -- present. Technical review of the modeling processes used in
> the FERC relicensing of PacifiCorp's hydroelectric projects in the
> Klamath River, Oregon.
>
> 2003 - 2005 Analytical Framework administered by the Bureau of
> Reclamation. Development of the study plan to assess mitigation
> response for chinook and steelhead in the John Day River basin of
> Oregon.
>
> 2000 - 2002. The Comparative Survival Study (CSS) administered by the
> Fish Passage Center, Portland Oregon. Analytical support.
>
> 2000 - 2003. PACFISH-INFISH Biological Opinion (PIBO) Effectiveness
> Monitoring Program conducted by the US Forest Service. Analytical
> support.

[Adjunct Faculty.]{.underline} Department of Aquatic, Watershed, and
Earth Resources, Utah State University, Logan, Utah 84322-5210.
2001-present.

[Biometrician/Modeler, Natural Resource Specialist 4.]{.underline}
Oregon Department of Fish and Wildlife, 2501 SW First Avenue. P.O. Box
59, Portland, Oregon 97207. 1999-2000.

[Fish Population Analyst, Natural Resource Specialist 3]{.underline}.
Oregon Department of Fish and Wildlife, 2501 SW First Ave. P.O. Box 59,
Portland, OR, 97207. 1998-1999.

**PUBLICATIONS** (8 journal articles and 36 technical reports). Selected
articles

Kershner, J.L, B.B. Roper, N. Bouwes, R. Henderson, and E. Archer. 2004.
An analysis of stream habitat conditions in reference and managed
watersheds on some federal lands within the Columbia basin. *North
American Journal of Fisheries Management* 24:1363-1375.

Roper, B.B., J.L. Kershner, E. Archer, R. Henderson, and N. Bouwes.
2002. An evaluation of physical stream habitat attributes used to
monitor streams*. Journal of the American Water Resources Association*
38(6):1637-1646.

Budy, P., G.P. Thiede, N. Bouwes, C. Petrosky, and H. Schaller. 2002.
Evidence linking delayed hydrosystem mortality of Snake River salmon to
their earlier hydrosystem experience. *North American Journal of
Fisheries Management* 22:35-51.

I have experience in stock assessment, biometric and data analyses,
modeling, experimental and monitoring design, fisheries research and
aquatic ecology and my past experience has given me detailed knowledge
of the salmon, steelhead, and bulltrout issues in the Columbia River and
Klamath River basins. I was previously employed first as a fish
population analyst and later as a biometrician/modeler for Oregon
Department of Fish and Wildlife (ODFW). I aided in the development of
analytical models and statistical methods to assess population status
and impacts of management alternatives for salmon and steelhead in the
Columbia River basin and advised the ODFW, their commissioners, Oregon's
Northwest Power Planning Council (NPPC) members, and the Governor's
Natural Resource Office on the effects and risks of various complex
management strategies of Columbia basin fish populations. Recently, I
have been summarizing and synthesizing current research and monitoring,
collaborating with researchers and managers, and further developing RME
programs in the John Day Basin. Other current projects include CSMEP
(see above) working collaboratively with state, federal, and tribal
fisheries agencies to review and develop status and effectiveness
monitoring programs addressing NOAA and USFWS Biological Opinions and
Recovery Plans and the NPPC Fish and Wildlife Program throughout the
Columbia River Basin. I am also currently reviewing the Ecosystem
Diagnosis and Treatment (EDT) model and KlamRAS model in assessing
anadromous species population responses to current habitat conditions
and different management alternatives evaluated in the FERC relicensing
of Pacific Corps hydroelectric projects in the Klamath River.

**Christopher A. Beasley**

Fisheries Scientist

My focus is the conservation and restoration of aquatic resources. I use
applied conservation genetics and risk analysis to evaluate population
status and weigh the risks and benefits of alternative management
actions, and employ adaptive experimental designs to evaluate whether
risks or benefits of implemented actions have been realized. I have
designed and implemented conservation and restoration projects at the
scale of individual populations, metapopulations, and evolutionarily
significant units. I have substantial field sampling experience, thus I
understand the logistical realities that limit the effectiveness of
alternative sampling designs, and the impact of those limitations on the
quality and biological interpretation of resulting data. Finally, I have
contributed to a number of projects seeking to address questions at
larger spatial and temporal scales through the accumulation and
coalescence of existing disparate projects operating at smaller scales.

**Selected Projects**

**Collaborative System-wide Monitoring and Evaluation Project, WA, ID,
OR; Columbia Basin Fish and Wildlife Foundation** **--** Evaluation of
the bias, accuracy, and precision of Columbia River Basin research,
monitoring, and evaluation data to determine whether those data can be
combined to evaluate the effectiveness of recovery actions prescribed by
NOAA Fisheries in the 2000 Biological Opinion on the Federal Columbia
River Power System.

**Johnson Creek Artificial Propagation Enhancement Project Benefit Risk
Analysis, ID; Nez Perce Tribe** - Employed stochastic models using
demographic and genetic data pertinent to Snake River spring/summer
Chinook salmon as a means to determine the benefits and risks associated
with a proposed conservation facility for Johnson Creek spring/summer
Chinook salmon. Analyses identified minimum population sizes necessary
to maintain genetic diversity in hatchery and natural settings, and
established rates of gene flow among hatchery and natural groups aimed
at minimizing domestication potential and maximizing the retention of
genetic variation.

**Evaluation of Methow River Spring Chinook Salmon Stock Structure, WA;
Yakama Tribe --** Used Bayesian and maximum likelihood based statistical
models to evaluate coancestry of three putative populations of natural
origin spring Chinook salmon and three hatchery facilities affecting
spring Chinook salmon in the Methow River subbasin of Washington State.
Non *a priori* data analyses in conjunction with historical management
data were used to determine the number and relatedness of putative
populations of natural and hatchery origin spring Chinook salmon in
order to define conservation priorities and guide the management of
hatcheries.

**Russian River Fish Facilities Impact Assessment, CA; Sonoma County
Water Agency/Entrix, Inc.** -- Provided conservation plans for Russian
River coho, steelhead, and Chinook salmon; evaluated alternative
management plans including risk metrics for management alternatives.
Construction of these management plans required the ability to
pragmatically apply conservation genetics theory to rapidly declining
isolated stocks of historically abundant species.

**Employment**

**1998 -- 2003 Fisheries Scientist, Columbia River Inter-Tribal Fish
Commission, Production and Restoration Research Group** - Employed
population genetics, abundance simulations, and GIS to define
restoration programs for tribal aquatic resources. Developed risk
analysis methodologies to minimize deleterious impacts of artificial
propagation. Prescribed research, monitoring and evaluation protocols to
address critical uncertainties and implement adaptive management. Acted
as technical liaison between tribes and state and federal agencies
regarding tribal restoration programs and methodologies.

**2003 -- 2004 Project Leader, Nez Perce Tribe, Idaho Supplementation
Studies** - Quantitatively evaluated time series data spanning 14 years
in 31 tributaries of the Salmon and Clearwater River subbasins
(tributaries of the Snake River in Idaho state) to determine the
statistical power of adult escapement, spawner escapement, and juvenile
abundance data as applied to an assessment of the effectiveness of
artificial propagation. This project required the compilation of data
from two federal agencies, one state agency and two Native American
tribes. Evaluations required substantial data standardization and
familiarity with the statistical limitations accompanying the
application of study designs in the field.

**2004 -- 2005 Fisheries Scientist, FishPro** -- Employed principles of
conservation genetics to guide the implementation of a refuge for the
endangered Rio Grande Silvery minnow. Completed a master plan to guide
the reintroduction of coho salmon to the Clearwater River subbasin
(tributary to the Snake River in Idaho). Completed bioengineering
designs for the Nez Perce Tribal Hatchery, Mescalero Apache Fish
Hatchery, Northeast Oregon Hatchery Project, and the Baker River
Hatchery.

**2005 -- Present President, Quantitative Consultants** - In early 2005
I started my own company to meet a perceived need for the application of
quantitatively rigorous methods to evaluate population status and
provide meaningful methods to guide the implementation of conservation
actions. In short, my company is dedicated to comprehensive data
analysis, study design, and quantitative evaluation of uncertainties and
potential benefits of alternative management responses aimed at
population recovery. In short, we quantitatively evaluate risk, provide
a comprehensive analysis of the benefits and risks of management
alternatives, and construct monitoring designs to determine whether
benefits or risks are realized. Current projects include National
Oceanographic and Atmospheric Administration Pilot Projects,
Collaborative Systemwide Monitoring and Evaluation Project, Benefit/Rick
Analysis for Chinook salmon propagation in the Middle Fork Salmon River
subbasin, Bioengineering Analysis of the Muckleshoot Hatchery, and
development of a fully recirculating shellfish hatchery for the
Skokomish Tribe.

[]{.mark}

**Education and Training**

North Carolina Institute of Statistical Genetics (Continuing Education)

M.S. Zoology, North Carolina University

B.S. Systematics and Ecology, University of Kansas

**Contact**

Office Phone: (360) 297-4813

Mobile: (360) 620-2883

Email: <chris@qcinc.org>

[^1]: We do not advocate the region-wide adoption of this experimental
    approach for several reasons: (i) the synergies that allow the
    development of an experimental design for situating a restoration
    strategy do not exist everywhere, and therefore should not constrain
    the implementation of restoration actions more broadly; (ii)
    effectiveness monitoring should not be necessary for all projects at
    all times, rather only the ideal situations to test project types
    should be exploited for this purpose; and (iii) implementing a
    project to demonstrate restoration action impact is a complex
    process requiring the compilation of a skill set far beyond the
    implementation of an action alone, and as such is neither reasonable
    to impose on all restoration action proponents, nor feasible to
    achieve. None-the-less, this experimental approach is necessary to
    properly study the efficacy of effectiveness monitoring.

[^2]: The RTT serves the Upper Columbia Salmon Recovery Board in
    technical matters and consists of members who possess a strong
    technical background and knowledge of salmonids and their habitats
    in the Upper Columbia Region. The RTT's membership consists of
    employees of private, tribal, public utility, and government
    entities, but is not representational of these entities.