Planning Today for Tomorrow's Science; The NWFSC's Research Planning Priorities

PLANNING TODAY FOR TOMORROW’S SCIENCE:
The Northwest Fisheries Science Center’s Research Planning Priorities

2010 Research Plan Update
Original Research Plan:
December 20071

Research Council

Michelle McClure
Barry Berejikian
Patricia Burke
Edmundo Casillas
Mike Ford
Brad Hanson
Aimee Keller
Kathi Lefebvre
Regan McNatt
Rohinee Paranjpye
Mindi Sheer

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The Research Planning Team was the author of the original Research Plan: Michelle McClure, Phil Levin,
Tim Beechie, Barry Berejikian, Ric Brodeur, Owen Hamel, Jeff Hard, Chris Jordan, Todd Lee, Dawn
Noren, Nat Scholz, Penny Swanson, John Williams.

I. EXECUTIVE SUMMARY .......................................................................................... 4
1. Ecosystem Approach to Management for the California Current Large
Marine Ecosystem:........................................................................................................ 4
2. Habitats to Support Sustainable Fisheries and Recovered Populations: ........ 5
3. Recovery, Rebuilding and Sustainability of Marine and Anadromous
Species: ........................................................................................................................... 5
4. Oceans and Human Health: ................................................................................. 6
Near Term Priorities......................................................................................................... 6
Necessary Tools ................................................................................................................. 7
Implementation Strategy .................................................................................................. 7
II. VISION AND PURPOSE OF THE NWFSC RESEARCH PLAN .......................................... 9
Vision and Role of the Northwest Fisheries Science Center ......................................... 9
Background and Purpose of this Research Plan ............................................................ 9
III. DRIVERS OF THE NWFSC RESEARCH PLAN............................................................ 11
Mandates and Legislative Drivers ................................................................................... 11
Administration and NOAA Priorities .............................................................................. 11
Regional Priorities ........................................................................................................... 12
National Priorities for Ocean Research .......................................................................... 12
IV. Research Themes and Foci .................................................................................... 16
Theme 1: Ecosystem Approach to Management for the California Current Large
Marine Ecosystem ........................................................................................................... 20
Theme 2: Habitats to Support Sustainable Fisheries and Recovered Populations .. 24
Theme 3: Recovery, Rebuilding and Sustainability of Marine and Anadromous
Species .............................................................................................................................. 27
Theme 4: Oceans and Human Health ......................................................................... 32
V. Near-Term Priorities ................................................................................................ 35
Near Term Priority 1: Conduct an integrated ecosystem assessment of Puget Sound as a
pilot project ....................................................................................................................... 36
Near Term Priority 2: Case study – Salmon, people, and instream flows under climate
change ............................................................................................................................... 37
Near Term Priority 3: Evaluate and implement new and alternative survey and
monitoring methods for groundfish .................................................................................. 39
Near Term Priority 4: Predict population and ESU-level response to management,
climatic and other impacts across the life-cycle of species of concern ............................ 40

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Near Term Priority 5: Develop rapid detection and improved prediction methods to
identify pathogens, biotoxins, toxics and other marine impacts on human health ........... 41
Near Term Priority 6: Initiate an ecosystem-based aquaculture research program .......... 43
Near Term Priority 7 (Currently in development): Predicting effects of ocean
acidification on coastal species of Washington and Oregon though experiments, modeling
and targeted monitoring .................................................................................................... 45
VI. Necessary Tools........................................................................................................ 45
Technologies: ................................................................................................................... 45
Models and the Data to Support Them: ....................................................................... 46
Infrastructure:................................................................................................................. 48
VII. Conclusions ............................................................................................................. 49
ACRONYMS .................................................................................................................... 50
REFERENCES: ................................................................................................................ 51
APPENDICES ................................................................................................................. 52
APPENDIX A: Drivers for the NWFSC Research Plan .................................................. 53
APPENDIX B: Relationship Table ................................................................................. 57
APPENDIX C: Details of Policy Drivers for the NWFSC.............................................. 59
Appendix D: Strategic Science and Research Planning Charter ................................. 66
APPENDIX E: Necessary Tools for implementation...................................................... 79

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I. EXECUTIVE SUMMARY
The Northwest Fisheries Science Center fills a unique role for NOAA as the liaison
between scientists engaged in long term oceanographic and ecosystem research, and
regional managers faced with daily decisions on the stewardship of living marine
resources and their habitats in the Pacific Northwest. In 2007, the Center’s managers
requested a plan to ensure that research priorities not only reflect current scientific
knowledge and methods, but are relevant to the resource management decisions being
made by NOAA and others. Additionally, research at the Center should utilize a holistic
approach to ecosystem management as called for by national and international oceans
commissions. The Research Planning Team met with Center scientists and regional
offices and identified 18 research foci for the next two to ten years. These foci are
designed to support the mission of NOAA and conduct research that will emphasize
ocean health and a renewed human relationship with ocean ecosystems. The Research
Council, which is the group that implements the plan, has recently reviewed the 2007
research themes, and is in the process of redefining and broadening one of these (Oceans and
Human Health), and will report on this in the next research plan update. The research foci
are grouped into four themes:

1. Ecosystem Approach to Management for the California Current Large Marine
Ecosystem: The ecosystems of the California Current LME range from alpine
streams where salmon spawn and rear, to mainstem rivers, wetlands, estuaries,
continental shelves, and deep-ocean waters. The cumulative impacts from growing
human populations in coastal communities have led to complex management issues
from competing sectors, and the linkages of human actions and ecosystem response
are not well understood. The Ecosystem Approach research theme is a shift away
from current management efforts that tend to be fishery- or species-specific,
compartmental, and short term, toward a future-oriented approach that will fully
integrate various scientific disciplines and account for interactions within and across
ecosystems. Research foci emphasize the need to conduct a comprehensive
assessment of ecosystem components and develop appropriate measurement
indicators; characterize the linkages and interactions between physical processes,
species, and human activities; and provide a basis to measure and predict ecosystem
responses and socio-economic benefits from management actions. The careful
assessment and forecasting of ecosystem indicators will form a sound scientific basis
to shape management practices that are flexible and sensitive to changing conditions
and new information.
“Although ‘ecosystem-based management’ is clearly a national priority, we need to
shed some light on what it actually means and how to go about it.”
---- Comment from the draft research plan review

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2. Habitats to Support Sustainable Fisheries and Recovered Populations: Critical
habitat areas impact the survival of species at every life-stage and influence the function
of ecosystems as a whole. More regional information is needed about physical, chemical
and biological habitat features by location, extent, persistence, and condition.
Furthermore, NOAA Fisheries and other natural resource managers need to understand
what long-term processes form and sustain riparian, riverine, estuarine, and ocean
environments. In order to manage the living resources of the California Current Large
Marine Ecosystem in a sustainable fashion, habitat conditions must be linked to their
biological impact on species at the nested scales of the individual organism, population,
community and ecosystem. Research foci include: the linkage of habitat features to lifestage survival, growth and productivity of organisms; mapping the footprint of human
activities and their impacts to species of interest; and developing restoration techniques
that are compatible with large-scale processes to create diverse and dynamic habitats. As
with other research themes, the development of metrics and evaluation models are needed
to identify trends, improve predictive capability, and develop sustainable management
approaches to habitat.
“Research at the Northwest Fisheries Science Center provides the basis for many of the
management actions taken by NOAA Fisheries and other natural resource agencies as they
strive to protect and recover aquatic ecosystems and living marine resources.”
--- excerpt from the full narrative of Theme 2

3. Recovery, Rebuilding and Sustainability of Marine and Anadromous Species:
Approximately 39 marine species (including anadromous fishes, marine mammals,
and sea turtles) listed as endangered or threatened under the Endangered Species Act
(ESA) occur in the Pacific Northwest. Seven Pacific Northwest marine invertebrate
and fish species are designated as “Species of Concern.” Moreover, seven West
Coast marine fish stocks are classified as “overfished” under the Magnuson-Stevens
Act. Each listing under the ESA or Magnuson-Stevens creates substantial socioeconomic impacts to the region and nation by restricting activities, requiring
permitting, and undertaking recovery, conservation and rebuilding measures. The
populations of concern are subject to variations from natural ecosystem fluctuation,
the harvest and propagation of marine organisms, and a host of human changes to the
environment. Recovery and rebuilding efforts are impeded by a lack of measurement
parameters and predictive models that can assess progress against this variable
background. Additionally, some species are long-lived, compounding the challenge
of developing effective and measurable recovery strategies. Research foci include:
the characterization of vital physiological, behavioral, and demographic information
for key species (e.g. data on temperature responses, nutritional requirements, prey
species, response to contaminants); development of models to forecast cumulative
effects on species productivity and ecosystem health; investigation of alternative
management strategies and governance structures; and the role of artificial
propagation in recovery efforts.

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“An ecosystem approach to management is a critical agency objective, but it creates tension with some
of the statutory responsibilities of NOAA which are specific to a particular species. Balancing these
directives will require back-and-forth discussion between managers and researchers on an ongoing
basis.”
--- Comment from the draft research plan review

4. Oceans and Human Health: Residents and visitors to the Pacific Northwest enjoy
various forms of recreation on the waters, beaches and coastal communities, along
with nutritious seafood and other benefits of the marine ecosystem. However,
pathogens, toxins from harmful algal blooms (HABs) and chemical contaminants
pose significant risks to humans and wildlife. The Northwest Fisheries Science
Center serves as the host institution to NOAA’s West Coast Center of Excellence for
Oceans and Human Health. The Center’s research includes ocean and climate factors
affecting the distribution, abundance and toxicity of pathogens and bio-toxin
producing organisms, and studies of sentinel or surrogate species to measure the
effects of contaminants. Research foci for Oceans and Human Health were derived
from plans developed by OHH investigators, with the focus of Center scientists on
pathogens, HABs, chemical contaminants and sentinel species. Research foci also
include the investigation of technologies to improve seafood safety and quality, and
the relationship between human exposure to pathogens, toxins and contaminants, and
the resulting health and socio-economic effects.
“The Center is at the forefront of emerging technologies and long term research on oceans and human
health, but we must remain poised to address immediate and critical questions when hot issues come
up.”
---- Comment from the draft research plan review

Near Term Priorities
Six near-term research priorities were developed by the Research Planning Team and
Center staff based on three primary criteria: 1) issues that are identified as urgent or of
critical management importance in the near term; 2) projects that are likely to provide
important technical or conceptual advances; and 3) compatibility with the immediate
capabilities of the Center. The six near term priorities have been shaped into pilot
projects, case studies, and focused research questions. Additionally, all six share a
common need to consider emerging challenges to marine ecosystems from climate
change and human population growth in the future. Currently, one additional near term
priority, “Ocean Acidification” is under review for inclusion as the Center’s next priority.
A draft writeup of this is included in section IV. The current near-term priorities are:
•
•
•

Conduct an integrated ecosystem assessment of Puget Sound as a pilot project.
Case study - salmon, people, and instream flows under climate change.
Evaluate and implement new and alternative survey and monitoring methods for
groundfish.

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•
•
•

Predict population and ESU-level response to management, climatic and other
impacts across the life-cycle of species of concern.
Develop rapid detection and improved prediction methods to identify pathogens,
biotoxins, toxics and other marine impacts on human health.
Initiate an ecosystem-based aquaculture research program.

Necessary Tools
The implementation of the research priorities will require the active development and
improvement of technologies and models, as well as changes to agency infrastructure to
ensure that information is easily disseminated and accessible. Ocean environments are
notoriously challenging to observe, and the species that inhabit them occupy varying
habitats across wide areas that are difficult to access. Emerging and enhanced
technologies for research include large-scale observation systems such as geo-spatial
remote sensing, Autonomous Underwater Vehicles (AUVs), tagging and remote sensing
for individual organisms, and genetic techniques. Faster recording systems for fish catch
and observer data are needed to improve the accuracy and timeliness of fisheries
management decisions, particularly for groundfish. Socio-economic models addressing
fisheries and ecosystem management provide decision-makers with information about
impacts of alternative management regimes on net national benefits, effects on particular
participant groups, and provide a common valuation basis to assess tradeoffs for human
activities and ecosystem health. Ecological and evolutionary models can be used to
prioritize sites for conservation, estimate future populations due to species interaction or
climate change, and simulate food web dynamics. Infrastructure needs include largescale systematic improvements to data management, enhanced laboratory facilities, and
operation of an array of large and small vessels, gear, and storage facilities to facilitate
field research.

Implementation Strategy
The Research Planning Team developed the original NWFSC Research Plan in 2007 (this
document is an update of that plan). Recommendations from the plan were presented to
the Center Directorate in January of 2008. The Directorate briefed the Center
Management Team, and decided to hold an implementation research planning
implementation retreat. The retreat was held in March of 2008 and retreat participants
included Division Directors, Deputies, Division Coordinators, Program Leaders,
members of the Research Planning Team, and staff from the Science Director’s office
and the Operations, Management and Information (OMI) Division. Some important
outcomes of this retreat were:
• an operational model for NWFSC strategic science and research planning ,
• a charter documenting roles, reporting, and decision-making processes of each
element in this operational model

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• designation of a new research planning team, the NWFSC Research Council to
manage and guide future implementation of the Research Plan
Details on the Research Council and the charter that guides research planning at the
NWFSC can be found in Appendix D.
“Our annual budgeting and reporting should be closely linked to our progress on the
research priorities, rather than treating these as separate processes.”
--- Comment from the draft research plan review

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II. VISION AND PURPOSE OF THE NWFSC RESEARCH PLAN
Vision and Role of the Northwest Fisheries Science Center
The Northwest Fisheries Science Center operates under the vision expressed on the
Center’s website that “scientists at the Northwest Fisheries Science Center conduct
leading-edge research and analyses that provide the foundation for management
decisions to protect, recover, restore, and sustain ecosystems and living marine resources
in the Pacific Northwest.” NWFSC researchers are dedicated to producing scientific
products that will strengthen decision-making at all levels, enhance socio-economic
benefits, support sustainable resource use, and conserve biological diversity. The work
of the Center is encompassed in two key roles:
•

•

Provide current, relevant information to support science-based stewardship
of natural resources. The primary mission of the NWFSC is to provide
multi-disciplinary scientific and technical information to the Northwest
Regional Office of NOAA Fisheries, other NOAA line offices, co-managers,
stakeholders and other constituents to inform decision and policy-making
processes.
Foster scientific literacy and expertise. In order to achieve the national
missions of NOAA, the NWFSC must ensure that Center research results
reach the broader science, education, and public communities within the
region and beyond. The Center has the additional responsibility to help train
the next generation of fisheries scientists.

Background and Purpose of this Research Plan
NWFSC Management formed the Research Planning Team (RPT) in 2005 to develop this
research plan with two primary goals:
•

•

Identify areas of research that are the most important for the NWFSC in
achieving national goals and regional science needs of NOAA/NMFS, other
federal agencies, and external constituents. These include legally-mandated
investigations, science support for other NOAA offices, and contributions to
emerging regional and national scientific issues.
Identify areas of investigation that will move critical areas of scientific inquiry
and discovery forward.

The RPT solicited considerable staff input and identified priorities and challenges for the
Center in the short to moderate term (2 to 10 years) as well as long term research that will
remain critical for the foreseeable future. The plan supports several key internal goals
and external functions as described in Box 1. The RPT followed several criteria in
developing the research plan, including: staff participation and grass roots input;
emphasizing integrative, multi-disciplinary research; ensuring that research is relevant to
management objectives; building on Center strengths; and utilizing approaches that are

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proactive, independent, innovative, imaginative, and which foster excellence in scientific
inquiry and communication.

Box 1.
The NWFSC Research Plan is intended to support a number of key internal
objectives of the Center, including:
• Link specific research objectives and national or agency-wide goals;
• Provide benchmarks for implementation and evaluation;
• Contribute to a transparent process of allocating resources within the Center;
• Develop and strengthen the Center’s capability to support innovative research and
respond to emerging issues;
• Develop and strengthen inter-disciplinary and collaborative scientific research;
• Promote flexible research planning.
External uses of the NWFSC Research Plan include:
• Communicate links with scientific research at regional, national and international
forums;
• Improve coordination to ensure that the results of NWFSC scientific research provide
useful support to the Northwest Region, and are appropriately incorporated into
management;
• Provide support for efforts to respond to emerging issues;
• Establish or enhance mechanisms to disseminate the products and accomplishments
of the Center’s research efforts.

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III. DRIVERS OF THE NWFSC RESEARCH PLAN
The NWFSC provides the science and research necessary to support decisions for
management of NMFS trust resources, including marine and coastal ecosystems of the
United States and the human communities dependent on them for health and well-being.
The geographic scope of NWFSC’s work is generally focused on the resources of the
United States Pacific Northwest; however, the scientific work of the Center frequently
has an impact on work done in other regions and parts of the world. This section of the
strategic science and research plan is to illustrate connections between research programs
at the NWFSC and the international, national, and regional policy directives and
initiatives that guide them (figure 1; Table 1; Appendices A and B).
The drivers and activities for this NWFSC research originate from Congressional
Legislation, priorities of the Administration, judicial directives, international agreements,
and other emerging priorities. Work activity can also be driven by short or long-term
events that cannot be predicted in advance. Table 1 presents an overview of the drivers
and crosscutting Near Term Priority research topics (See Appendix A for drivers of major
research Themes described in this report), and Figure 1 depicts the connections between
drivers, research themes and foci, and NWFSC’s research activities. Major research
theme drivers are in Appendix A, and background, definitions, and specific details on
drivers are in Appendices B and C.
Mandates and Legislative Drivers
Legislative requirements or mandates from the United States Congress direct much of the
work of the NWFSC and can only change by an act of Congress. The administration (the
Executive Branch including NOAA and NMFS) is responsible for implementing the
intent of these laws. Regulations are also promulgated to provide clarity on specific
actions that that agency will take to implement the laws. Three primary legislative
drivers are: the Endangered Species Act (ESA), the Magnuson Stevens Fishery
Conservation and Management Act (MSA), and the Marine Mammal Protection Act
(MMPA). The ESA provides for the conservation of species that are endangered or
threatened throughout all or a significant portion of their range, and the conservation of
the ecosystems on which they depend. A major focus of the MSA is to take immediate
action to conserve and manage the fishery resources found off the coasts of the United
States, and the anadromous species and Continental Shelf fishery resources of the United
States. The MMPA protects all marine mammals and prohibits, with certain exceptions,
the "take" of marine mammals in U.S. waters and by U.S. citizens on the high seas, and
the importation of marine mammals and marine mammal products into the U.S.
Administration and NOAA Priorities
Each Administration sets national priorities at the level of the President and appointed
designees, including the Secretary of Commerce, Administrator of NOAA, and Assistant
Administrator of NMFS. The mission of the Department of Commerce (DOC) has

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evolved from its historic mission "to foster, promote, and develop the foreign and
domestic commerce" to include responsibilities in environmental stewardship and
statistical research and analysis. Current NOAA-level guidance that directs NWFSC
work originates from the 2009 NOAA Annual Guidance Memorandum (AGM). The
current NMFS Strategic Plan for Fisheries Research provides national level goals for
NMFS science and research. The upcoming NOAA Next Generation Strategic Plan
(2010-2025) sets the vision for upcoming research and emphasizes ecosystem-based
assessments as a foundation for management.
Regional Priorities
The NWFSC’s Science and Research Director is a “Federal Lead” for the Department of
Commerce on The West Coast Governors’ Agreement on Ocean Health, and is helping to
provide support to this collaborative effort. This agreement is intended to increase
regional collaboration to protect and manage the ocean and coastal resources along the
entire West Coast, as called for in the recommendations of the U.S. Commission on
Ocean Policy and the Pew Oceans Commission. The NWFSC also collaborates with both
the Pacific Fisheries Management Council (See MSA above) and the Western States
Water Council to improve understanding of the connections between harvest, people,
water, and fish. The Puget Sound Partnership is a Washington State agency with
responsibility to create an Action Agenda that will lead to the recovery of the Puget
Sound Ecosystem by 2020. The NWFSC participates in the Partnership by loaning staff
and completing projects that help to inform management decisions, participates in the adhoc Puget Sound Federal Caucus and provides input to the Puget Sound Partnership’s
advisory Science Panel.
National Priorities for Ocean Research
The past, present, and future status of our nation’s oceans were recently reviewed by both
the U.S. Commission on Ocean Policy (USCOP 2004) and the Pew Oceans Commission
(Pew 2003). These reviews called for a change in our nation’s stewardship of the oceans
and the pursuit of an ecosystem-based approach to ocean management. In response, a
number of national efforts have been launched to improve the scientific basis for resource
management, such as the formation of the Joint Subcommittee on Ocean Science and
Technology (JSOST). The report, Charting the Course for Ocean Science in the United
States for the Next Decade: An Ocean Research Priorities Plan and Research Strategy,
was released by the JSOST in January 2007, and identified three critical scientific
elements to advance the nation’s relationship to our oceans:
ƒ
ƒ
ƒ

the development and deployment of ocean observing systems
the capability to forecast key ocean-influenced processes and phenomena
the central role of science in an ecosystem approach to natural resource
management

Additional national priorities for ocean research have been identified in the Climate
Change Strategic Plan (CCSP 2003), and the Earth Observation System Plan

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(CNER/IWGEO 2005). These complementary plans will contribute to local, regional and
global climate forecasting and the interactions of climate with other environmental
factors.
The USCOP and PEW Oceans Commissions represented the most comprehensive
reviews in the decades since the National Oceanographic and Atmospheric
Administration was founded as an agency. In order to align research priorities at the
Northwest Fisheries Science Center (National Marine Fisheries Service) with national
and NOAA goals, this Research Plan and (and updates) was prepared to guide scientific
research, advance ocean stewardship, and provide information for regional and national
decision-making.

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Research Theme
Divisions

Research Foci

Example

DRIVERS

Ecosystem Management
of the California Current

Example

Research
Activities
Food web dynamics

CB, FRAM, FE

Population structure

Marine Mammal
Protection Act

Characterize marine, freshwater, terrestrial links
Describe human effect on ecosystem status
Characterize climate-biotic linkages
Inter/intraspecific ecological interactions
Conduct IEAs

MSA

Recovery,
Rebuilding, Sustainability

Support ESA Processes
(Sect. 7, etc)

MMPA

MagnusonStevens Act

ESA

Endangered
Species Act

NOPTF

National Ocean
Policy Task Force

CB, FRAM, FE, REUT

Describe human impacts on species status
Investigate effects of management strategies
Characterize vital rates for managed species
Clarify the role of artificial propagation
Predict population responses

Habitats

EC, FE, FRAM
Characterize habitat effects on ecosystem processes
Describe human effects on habitat quality, distribution
Develop habitat restoration techniques

Physiology

Status reviews and
Stock assessments
Hydro passage
Effects of climate
change
Social & Economic
drivers and effects
Aquaculture and
Artificial propagation
Habitat restoration

PSP

Puget Sound
Partnership

Oceans and Human Health

Toxin distribution and
effects

Evaluate the effects of pathogens and toxins
Evaluate socio-econ. effects of health threats
Determine climate -human health links
Ensure seafood safety and quality
Monitor sentinels for ocean health

HABS and
Pathogens

REUT, EC, CB

Figure 1. Schematic of primary drivers for NWFSC research themes, with example activities for each (subset of all activities).
Acronyms are center organizational divisions: CB (Conservation Biology), EC (Environmental Conservation), FE (Fish Ecology),
FRAM (Fishery Resource Analysis and Monitoring), REUT (Resource Enhancement and Utilization Technologies),
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Table 1. Relationship of specific NWFSC Near Term Priorities (refer to NPT section of the plan
plan for full names and descriptions) to legislative, regional, national, international, and NOAA-level
drivers. Appendices A and B illustrate drivers for the Themes and Foci described in this plan.
Puget
Sound
IEA2

Salmon,
People,
and
Flows3

ESU and
Groundfish Population
Level5
Surveys4

Marine
Impacts6

Aquaculture
Ocean
Research7 Acidification8

Legislative
ESA
MSA
MMPA

Regional, and Local Government
Puget Sound
Partnership
West Coast
Governor’s
Agreement
Pacific
Fisheries
Management
Council

International
PICES
Pacific
Salmon
Treaty

NOAA
NOAA’s Next
Generation
Strategic Plan
Ocean
Research
Priority Plan

National
NMFS
Strategic
Science Plan
National
Ocean Policy
Taskforce
GPRA
Measures
U.S. COP
Ocean Action
Plan

2

Puget Sound Integrated Ecosystem Assessment
Case Study -- Salmon, People, and Instream Flows Under Climate Change
4
Evaluate New and Alternative Methods for Groundfish Surveys
5
Predict ESU and population level responses to natural and anthropogenic impacts for
species of concern
6
Develop rapid detection and improved prediction methods to identify marine impacts on
human health
7
Initiate an aquaculture research program
8
15
Ocean Acidification
3

IV. RESEARCH THEMES AND FOCI
To identify research foci for the NWFSC, several factors were considered that were
similar to those used by the Joint Subcommittee on Ocean Science and Technology in the
development of the 2007 national ocean research plan: a) potential to enable significant
advances for science and its application; b) high priority for ongoing and emerging
management issues; c) builds appropriately on capabilities at the NWFSC; and d)
provides critical support for the wise stewardship of our ocean resources. Eighteen
research foci within four major themes emerged from staff input and discussion (Table
2). Themes are areas of scientific inquiry to guide the Center’s research and that can be
used to align this research with national directives and are crafted to be broad and have a
relatively long life-span (10-20 years). Research foci are more specific areas within
themes that are particularly relevant for the NWFSC to pursue, given our geographic
location, regional science needs and similar considerations. These specific areas are also
relatively long-term. The eighteen research foci support both national and regional
science goals, and relate clearly to the goals of NOAA and the findings of the US
Commission on Oceans Policy (Appendix A). Elements common to these major themes
include a holistic approach to ecosystem management, the improvement of predictive
capability by characterizing linkages and advanced modeling, and providing scientific
information to management practitioners within NOAA and across the nation and region.
Near-term priorities are discrete and typically interdisciplinary research projects that
will 1) provide results of immediate management relevance; and 2) provide significant
advances in one or more identified theme areas and one or more research foci. These
near-term priority projects are intended to be finite, produce results and disband in a 2-3
year time frame.
Global climate change is arguably the defining environmental, social and even economic
issue of our day. It is almost certain to have profound effects on the distribution and
abundance of the marine and anadromous species for which NOAA Fisheries has
responsibility and the Northwest Fisheries Science Center conducts research. It will alter
the chemistry and temperature of our marine waters, while affecting the timing and
magnitude of flows in freshwater systems. These changes are likely to have cascading
effects throughout the marine, estuarine, nearshore and freshwater habitats, foodwebs and
ecosystems and thus on the full range of human benefits we derive from the natural
world.
NOAA’s mission is to “understand and predict changes in weather, climate, oceans,
and coasts, to share that knowledge and information with others, and use it
to improve society’s conservation and management of marine resources.” Toward that
end, NMFS’s Science Centers are charged with providing the critical science to support
effective management of our living marine resources, whether they be protected or
harvested, as well as ensuring benefits to human well-being from those marine and
anadromous species. In this context, climate change is a perturbation (albeit an
overwhelming perturbation) to our ecosystems, and we investigate its consequences and

our ability to adapt to its effects as we investigate other natural and anthropogenic
changes to the ecosystems on which we depend. Each of our research themes – which
focus on ecosystem management; species and population biology; habitats for sustainable
populations and oceans and human health (or human well-being) – has as one of its key
components exploring both the effects of climate change and the most effective methods
to respond to those changes.
The NWFSC considers climate change a topic of the utmost urgency. We have included
it within each of the four research themes to emphasize its important in these broader
topics that we are mandated to address.
Determining success at coordinating and implementing research planning at NWFSC
requires up-to-date information on budgeting, staffing, research projects descriptions,
accomplishments and publications for every Theme, Focus, and Near Term Priority. The
Research Council is in the process of completing a NWFSC Project Database, which will
capture this information for every NWFSC project and become the primary mechanism
for describing activities and accomplishments. The web interface will allow entry and
editing of projects, queries, reporting, exporting, and mapping of projects and associated
data. The every project will be categorized into one or more of the 4 themes and 18 foci.
The database includes budget information, allowing projects to be linked to NOAA
budget programs and strategic goals. The database is being designed to be compatible
with eAOP, although it is independent at this point. Plans for Phase II (next year) include
exploring the feasibility of linking directly to the eAOP system.

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Table 2: Summary of 18 major research foci for the NWFSC grouped into four
themes.
Ecosystem Management Approach for the California Current Large Marine
Ecosystem
1. Conduct integrated ecosystem assessments that produce metrics and criteria that will improve ecosystem
forecasts and predictions.
2. Describe the interaction between human activities and ecosystem status and resilience.
3. Characterize linkages between climatic conditions and biotic responses.
4. Characterize ecological interactions (e.g. predation, competition, parasitism, disease, etc.) within and
among species.
5. Characterize the interaction between marine, freshwater and terrestrial ecosystem components.

Habitats to Support Sustainable Fisheries and Recovered Populations
6. Characterize habitat effects on ecosystem processes, ecological interactions, and the health of
organisms.
7. Characterize the interaction of human use and habitat distribution, quantity and quality.
8. Develop effective and efficient habitat restoration and conservation techniques.

Recovery, Rebuilding and Sustainability of Marine and Anadromous Species
9. Describe the relationship among human activities and species recovery, rebuilding and sustainability.
10. Investigate ecological and socio-economic effects of alternative management strategies or governance
structures.
11. Characterize vital rates and other demographic parameters for key species, and develop and improve
methods for predicting risk and viability/sustainability from population dynamics and demographic
information.
12. Develop methods to use physiological, biological and behavioral information of organisms to predict
population-level processes.
13. Clarify the role of artificial propagation (including aquaculture) in recovery, rebuilding and
sustainability.

Oceans and Human Health
14. Characterize the exposure to and effects of pathogens, chemical contaminants, and marine biotoxins on
humans and other species.
15. Determine how ecosystem variables, such as climate, affect the distribution, abundance and toxicity of
microbial pathogens and bio-toxin producing organisms.
16. Ensure seafood safety and improve seafood quality.
17. Monitor the health of fish and marine mammals as sentinels for ocean health and develop new species
as mechanistic models.
18. Evaluate the effects of changes in the distribution, abundance and virulence of threats such as marinetoxin producing phytoplankton or microbial pathogens to human health or socio-economic indicators.

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Theme 1:
Ecosystem Approach to Management for the California
Current Large Marine Ecosystem
Relevance to national and regional ocean issues:
The California Current LME provides abundant products and
services essential for fisheries, climate regulation, pollution
control, energy production, transportation and recreation. Yet,
ensuring the resiliency and productivity of California Current
ecosystems will require understanding their structure,
function, and vulnerability to anthropogenic actions.
Increased population growth in coastal communities from
diverse, often competing sectors complicates management
strategies.
Role of the NWFSC:
The Northwest Fisheries Science Center provides science
support for moving resource management toward a more
holistic, ecosystem-based strategy. The NWFSC's ecosystem
approach promotes a shift away from current management that
often focuses in the short-term on a single species. The new
approach focuses on interactions within and among
ecosystems, offers long-term perspectives, and fully integrates
analyses across a range of scientific disciplines.

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Theme 1:
Ecosystem Approach to Management for the California Current Large Marine Ecosystem
Research Focus 1. Conduct integrated ecosystem assessments that produce metrics and
criteria that will improve ecosystem forecasts and predictions.
An Integrated Ecosystem Assessment (IEA) is a synthesis and analysis of all available
information on relevant physical, chemical, ecological and human processes in relation to
specified ecosystem management objectives. IEAs provide an efficient, transparent
means of summarizing the status of ecosystem components, screening and prioritizing
potential risks, and evaluating alternative management strategies against a backdrop of
environmental (e.g., temporal and spatial) variability. They also provide a means of
evaluating tradeoffs in management objectives among potentially competing ocean-use
sectors. The California Current LME lacks such an assessment. To achieve one will
require the development of test indicators and input from a broad range of stakeholders
and scientists. Careful assessment and forecasting of ecosystem indicators will provide a
powerful means for assessing management efficacy and a basis for adapting and
improving management practices.
Research Focus 2. Describe the interaction between human activities and ecosystem
status and resilience
Humans are an integral component of the ecosystems they inhabit and exploit. They
receive goods and services from these systems and may manipulate them to purposefully
enhance some features. Anthropogenic actions may change systems inadvertently
through the type, variety or magnitude of demands which are placed upon them.
Understanding the nature of these interactions will require observational and
experimental studies aimed at identifying ecosystem-level responses to human activities,
both individually and cumulatively. Improved prediction and adaptive management of
ecosystems will require integrating that information with socio-economic analyses of
human responses (economic valuation, governance structures, etc.).

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ECOSYSTEM
STRUCTURE AND
FUNCTION

Direct and Indirect
Drivers of Change

geology--climate--physical
processes--habitat--species
--terrestrial/marine linkages

HUMAN ACTIONS

ECOSYSTEM GOODS &
SERVICES

resource extraction--water
diversions--pavement--shoreline
development--transportation--- introduction of non-native
species--contaminants

Direct Use and
Non-Use Values

Ecological Production

provisioning of food & fiber-regulation of air & water

VALUES/HUMAN
WELL-BEING

Economic or Social
Valuation

Human health, cultural heritage,
biodiversity, aesthetic enjoyment

Figure 1: Relationship of Ecosystem Structure and Function and Human Well-Being
(adapted from National Research Council 2004 and Millennium Ecosystem Assessment
2005).

Research Focus 3. Characterize linkages between climatic conditions and biotic
responses
Identifying ecosystem management foci in the California Coastal Current LME requires
an understanding of how climate change and variation will alter riverine, estuarine, and
marine habitats. Models may then be used to develop predictions of how those changes
will affect ecosystem status and function. Key research elements include understanding
sensitivity of key species and biotic communities to expected habitat changes. These
changes could include decreasing stream flow, increasing stream temperature, sea level
rise, ocean acidification, shifts in ocean currents, and changed frequency and extent of
deoxygenated zones. A secondary goal is to improve understanding of the effects of yearto-year and decadal climate variability on population dynamics and ecosystem variability.
Achieving this goal will require identifying ‘sensitive’ and ‘resilient’ ecosystems, and
providing NOAA and state and local governments the knowledge and tools needed to
incorporate climate variability into decisions about living marine resources.
Research Focus 4. Characterize ecological interactions (e.g. predation, competition,
parasitism, disease, etc.) within and among species to support an ecosystem approach to
management of species of concern and the habitats they use.

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Understanding ecological interactions at various trophic levels provides important insight
into factors limiting the productivity of freshwater and marine species. Predator-prey
interactions, inter- and intra-specific competition, and parasites and pathogens can
influence the survival, growth, and reproductive success of anadromous and marine
fishes, marine mammals and other marine organisms. Moreover, anthropogenic stressors,
for example pollution and fishing, can change natural interactions among species. The
extremely complex nature of these interactions makes it difficult to obtain useful data and
prioritize research. Addressing questions about ecological interactions will require field
and laboratory studies that complement new models including:
• conducting gut content analysis of utilized and unutilized species during surveys
or harvest;
• examining direct and indirect ecological effects of fishing activities
• analysis of otolith microchemistry to assess fish growth rates and habitat use;
• use of stable isotope analysis to determine predator-prey relationships;
• integration of sample collection efforts with those of the Pacific Coastal Ocean
Observing System (PaCOOS) and with the various ocean productivity indicators
(e.g., PDO, ENSO, coastal upwelling);
• determination of how pollution and other environmental stressors (e.g. biotoxins,
poor nutrients, low oxygen, pH) alter interactive processes such as infectious
disease;
• examination of how evidence for compensatory and depensatory processes
change under variable exploitation, climatic and ecosystem scenarios.
From a holistic standpoint, individual animal tracking over extended distances and
durations in the marine environment will improve understanding of the spatial and
temporal overlap among species and potential for competition, predation or transfer of
pathogens on an ecosystem scale.
Research Focus 5. Characterize the interaction between marine, freshwater and
terrestrial ecosystem components
Within the California Current LME, many species undergo dramatic habitat shifts as they
move from fresh or estuarine to marine waters. Further, habitat conditions in both marine
and freshwater areas are strongly influenced by flows of water, sediment, and nutrients
between the two environments. While species migrations among these habitats are well
known, freshwater, estuarine, and marine environments are commonly studied and
managed as separate ecosystems. Moreover, many threats (e.g., pollution, habitat loss,
climate change, etc.) to marine organisms cross land-sea boundaries. Successful
management of marine systems thus requires an understanding of:
• the linkages among the freshwater and marine environments;
• how specific habitats (e.g., headwaters, floodplains, submerged aquatic
vegetation, nearshore zones, plumes and frontal regions) contribute to the
productivity and capacity of ecosystems; and
• how to prioritize habitat protection or restoration within the context of the entire
freshwater-estuarine-marine ecosystem.

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Theme 2:
Habitats to Support Sustainable Fisheries and Recovered
Populations
Relevance to national and regional ocean issues:
Healthy oceans and natural coastal and riverine habitats
provide the foundation for aquatic resources that society uses
daily. Coastal habitats often overlay oil and gas resources,
and also serve as transportation corridors, recreational venues,
waste receptors, and prime sites for residential use and
manufacturing, creating intense competition between marine
resources and other societal needs and values. The
examination of the environmental impacts of resource use and
extraction, combined with increased understanding of the
factors influencing overall ecosystem health, can help balance
the pressures placed on freshwater, estuarine, coastal and
offshore marine ecosystems. Research will enable the
restoration of degraded habitats, and ultimately, support
coordinated ecosystem approaches to management and
governance strategies for sustainable resource use.
Role of the NWFSC:
Habitat has tremendous influence on ecosystem structure and
functioning. The ability to define the state of an ecosystem
requires insight into the natural processes within habitats that
form and maintain aquatic and marine ecosystems, and how
anthropogenic actions on these processes can alter ecosystems
and affect living marine resources. NOAA Fisheries and
other natural resource managers need to understand what
processes form and sustain riparian, riverine, estuarine, and
ocean environments. These processes include the transport of
sediment, water, and organic material from terrestrial areas
through streams, to rivers, through estuaries, and into the
ocean, or actions from extraction that alters benthic marine
habitat. Research at the NWFSC provides the basis for many
of the management actions taken by NOAA Fisheries and
other natural resource agencies as they strive to protect and
recover aquatic ecosystems and living marine resources.

Randy Johnson photo

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Theme 2: Habitats to Support Sustainable Fisheries and Recovered Populations
Research Focus 6. Characterize habitat effects on ecosystem processes, ecological
interactions and the health of organisms.
In the northern California Current, the Essential Fish Habitat for groundfish, coastal
pelagic species, anadromous salmonids, marine mammals and other marine species
include all marine waters and bottom habitat from the shoreline along the coasts of
California, Oregon, and Washington offshore to the Exclusive Economic Zone. The
upper 10-20 m of the water column across the continental shelf and slope is the primary
habitat for many non-benthic species. Essential Fish Habitat for anadromous salmonids
(and other diadromous species) extend inland to include the watersheds that these species
utilize for spawning, rearing and migration. Characterizing how and when these species
use habitat in the CCLME is important to establishing land-use and fishing policies that
promote a sustainable ecosystem. Research needs include:
• Developing spatially explicit population dynamic models;
• Linking habitat features and conditions to key life-history stages, life-stage survival
rates, and other demographic parameters such as growth rate;
• Tracking the movement, growth and survival of individuals across habitats;
• Mapping key habitat features by location, extent, persistence, quality and condition;
• Development of statistical modeling approaches to illuminate patterns in distribution
and habitat data;
• Development of landscape classification approaches in quantifying and describing
habitat;
• Continued development of tagging and tracking technologies to document the
movement patterns of individual organisms through time and space.
Research Focus 7. Characterize the interaction of human use and habitat distribution,
quantity and quality.
An enormous diversity of human activities directly and indirectly impacts critical
freshwater, estuarine, and marine habitats. Degradation of river and stream habitats
occurs from land uses and water withdrawal. Estuarine habitats are adversely impacted
by contaminant runoff, industrialization, and dredging. The degradation of marine
habitats is due to pollution, some fishing practices and climate change (e.g. ocean
acidification). Characterizing how this collection of human activities degrade habitats,
and which habitats humans are most prone to use and degrade, is critical to establishing
land-use and fishing policies that promote a healthy ecosystem. To best manage the
CCLME in a sustainable fashion, it is necessary to map the footprint of human activities
and their direct and indirect spatial and temporal impacts, and review the potential
biological impact on each species of interest. Measurement parameters will need to be
developed to determine the full range of human impacts on habitat using spatial data and
improved habitat classification approaches.

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Research Focus 8. Develop effective and efficient habitat restoration and conservation
techniques
Maintaining and re-establishing viability and sustainability of living marine resources
often requires conservation and rehabilitation or restoration of habitats upon which
species depend. However, available techniques for rehabilitating riverine, nearshore, and
marine habitats are often only modestly effective on a small scale, and advances in
understanding how to restore long-term dynamic and diverse habitats are sorely needed.
Common habitat restoration approaches and techniques often presume that habitats are
static features of the environment, and that creation of stable habitats is a desirable
restoration strategy. However, riverine, nearshore, and marine habitats are created and
sustained by dynamic landscape, climatic, and oceanographic processes and biota are
adapted to changing habitats. Hence, current restoration strategies often have limited
success, in part because they fail to recognize larger scale processes that drive habitat
degradation, and in part because they fail to recognize intrinsic habitat potential of
individual restoration sites. The main goals of this research focus are to: improve
understanding of how large-scale processes create diverse and dynamic habitats that
support living marine resources, better understand how human activities alter habitatforming processes and alter habitats, develop new restoration techniques that are
compatible with sustainable habitat-forming processes, and understand the variety of
actions needed to adequately conserve intact critical habitats.

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Theme 3:
Recovery, Rebuilding and Sustainability of Marine and Anadromous Species
Relevance to current national and regional priorities:
Approximately 39 marine species (inclusive of anadromous fishes, marine mammals, and
sea turtles) listed as endangered or threatened under the Endangered Species Act (ESA)
occur in the Pacific Northwest. Seven Pacific Northwest marine invertebrate and fish
species are designated as “Species of Concern.” Moreover, seven West Coast marine fish
stocks are classified as “overfished” under the Magnuson-Stevens Act. Many of these
species, such as Pacific salmon and killer whales, are iconic symbols of the Pacific
Northwest. Others form the basis of critical human economies, and are harvested directly
(e.g., salmon), while others are an important food source for other commercially exploited
species (e.g., herring). Human sustenance, economic benefits, and ways of life are
dependent upon these species. Improving their status so that they are recovered or rebuilt,
and sustainable fisheries can be maintained, is essential both regionally and nationally.
The economic burdens of listing species under either the ESA or Magnuson-Stevens
statutes are significant. Endangered Species Act listings require additional permitting for
and restrictions on a variety of activities as well as the implementation of recovery and
conservation actions. Similarly, species or stocks identified as overfished or experiencing
overfishing under the Magnuson-Stevens Act are subject to harvest restrictions, and
rebuilding measures must be undertaken for overfished species.
Role of the NWFSC:
NOAA and other resource managers and decision-makers carry the responsibilities for
preventing extinctions, improving stewardship, and managing harvest for the communities
that depend on it. However, effective recovery, rebuilding, and sustainable fisheries are
impeded by limitations in our ability to predict population-level responses to natural
environmental variation and human alterations to the environment. NWFSC research is
needed to thoroughly characterize species and population interactions with human activities
and socio-economic indicators, and develop operative models for predicting population
responses. The information and models would contribute to decision making, and provide
benchmarks for assessing progress toward recovery.

26

Theme 3: Recovery, Rebuilding and Sustainability of Marine and Anadromous Species
Research Focus 9. Describe the relationship among human activities and species
recovery, rebuilding and sustainability
Humans have substantially altered the ability of natural ecosystems to support key marine
and anadromous species by degrading habitats, harvesting marine organisms, artificially
propagating selected species, and altering climate. In order to recover, rebuild, or sustain
declining species, it will be essential to understand the extent to which humans have
affected physical, biological, and chemical processes in ecosystems, and the magnitude
and pace of change that will be needed to restore or retain ecosystem function. Models
are needed that replicate how natural and anthropogenic changes and their interactions
have occurred, and which can also forecast the changes (and their interactions) that will
be needed to improve conditions in the future. Restoration and recovery of declining
species will also require the development of new ecosystem dynamics models that span
multiple trophic levels.

Research Focus 10. Investigate ecological and socio-economic effects of alternative
management strategies or governance structures
Management strategies and governance structures have a large influence on the
efficiency, practicability, sustainability and distribution of natural resources used by
humans. It is therefore important to understand the effects of alternative management
structures such as management scale (e.g., local versus regional management), ecosystem
management, and limited access privileges. Several variables including the nature of the
resource, current incentive structures, and the ability to transform institutional
frameworks determine whether changes can be made to management structure with
positive gains. To investigate these relationships it is necessary to form collaborative
research teams drawing expertise from a variety of natural and social science fields, as
well as policy and management experts. It is also vital to include stakeholders in the
process to understand the motivations and constraints faced by their constituents.
Research Focus 11. Characterize vital rates and other demographic parameters for key
species, and develop and improve methods for predicting risk and viability/ sustainability
from population dynamics and demographic information
The sustainability of a healthy ecosystem—as well as its recovery when under threat—
depends heavily on the viability of key species (and vice-versa). Identifying these key
species and the factors that limit their viability is necessary to understand the
consequences of environmental perturbation on ecosystem structure and function.
Estimates of the major demographic parameters or vital rates (e.g., birth and death rates,
immigration and emigration rates, fertility, age of maturity, and age structure) necessary
to assess viability in these key species are an essential step in identifying constraints on
ecosystem structure and function. These estimates are difficult to obtain in free-living

27

organisms because controlled experimentation and replication are not feasible in many
natural systems. Observational and empirical studies, as well as advanced modeling of
population dynamics of key species, will help to characterize the most serious threats to
ecosystem structure and function and encourage more effective management and
conservation. Research priorities focus on improving the characterization of
demographic parameters for key species. Determining how variation in parameters such
as age-specific survival, maturation, and fecundity affect population growth rates in
pristine and degraded ecosystems is needed. It is also necessary to link variation in vital
rates to variation in abundance and productivity and to stability of the structure of aquatic
ecosystems. For ecosystems in which particular species are heavily affected by harvest,
discards, and other human actions, it is essential that research focus on the ability of these
species to withstand these impacts and their consequences on the abundance,
productivity, and life history characteristics of the affected species.
Because multiple factors influence the status (including risk and viability/sustainability)
of a species, population, stock or ESU, understanding the whole spectrum of causes and
consequences and their complex interactions is difficult. Models are currently being used
for a range of management and recovery actions such as stock assessment, fishing
impacts, and habitat diagnostics, but these generally have limited capabilities in
incorporating risk factors and modeling interactions and cumulative impacts. Where
possible, models should, for example, incorporate climate data and predictions of future
conditions and variability, including risks of associated recruitment failure or mass
mortality events. A thorough review of the assumptions, sensitivities, uncertainties, and
statistical properties of current stock assessment models is needed. This will include
simulation modeling of complications such as highly variable recruitment, spatial
structure, changing life-history traits, and multiple stocks or populations modeled as a
single stock. Other conflicting assumptions and realities about demographic rates or the
relationship of survey, fishery, monitoring, and escapement data to population parameters
will need to be incorporated. All of this will aid in quantifying uncertainty in stock
assessments and predictive models, in defining optimal spawning stock
biomass/escapement, and in creating protocols for assessing populations for which
limited data exist or are infeasible to collect.
Research Focus 12. Develop methods to use biological, physiological and behavioral
information of organisms to predict population-level processes.
Continuing to understand the intricate biological processes occurring within organisms is
a fundamental component of identifying factors that may affect those organisms. Needed
data include those on the genetics, development, physiology, ecology and behavior of
organisms. Integrating this information is vital to predict how populations will respond
to natural or human perturbations to the environment, and to assess the impediments to or
potential success of rebuilding efforts. For example, data on thermal tolerance and
physiological responses to changes in environmental temperature can be used to assess
such issues as potential changes in reproductive behavior and productivity, viability,
movement patterns, preferred habitat selection, and population dynamics caused by shifts
in climate. Likewise, data on levels of contaminants that impact the immune system,

28

growth, development, reproduction, and general health of organisms is critical in
determining how these compounds affect population level processes and population
dynamics. Information on nutritional and energy requirements can be used to assess how
competition (from humans and other species) for prey resources impacts population
dynamics and carrying capacity. Other factors that should be incorporated into models to
predict population-level processes and dynamics are the effects of disease, parasites, and
anthropogenic perturbations in the environment. Much of the information and data listed
above is in the process of being collected for several species of concern, and the effort
should continue and expand, particularly for protected and endangered species as well as
other key species. Development of methods to incorporate these data into models in
order to predict population-level processes and dynamics is needed.
Research Focus 13. Clarify the role of artificial propagation (including aquaculture) in
recovery, rebuilding and sustainability.
There is considerable debate within the scientific community over whether artificial
propagation programs benefit or cause harm to natural populations and recovery efforts,
and under what conditions. The debate is complicated by the fact that such programs
vary widely in size, rearing practices, and goals (e.g., harvest augmentation or
aquaculture production vs. conservation). Aquaculture programs, which can replace or
augment commercial fisheries, are also a subject of controversy, and vary widely in scale
and impact. Additional information on the influence of artificial propagation on the
population dynamics, growth rate, ecology of infectious disease, and the evolutionary
fitness of wild fish and other marine organisms is a critical need, as is information on the
impacts of aquaculture on fishing pressure and practices, and on the surrounding
environment and wild fish, shellfish and marine mammals. Critical questions related to
artificial propagation programs that release fish include: 1) How do broodstock
management (integrated versus segregated), culture protocols, and release strategies (life
history stage) influence the relative reproductive success of artificially propagated and
wild fish; 2) What are the long-term effects of artificial propagation on natural population
productivity, abundance, diversity (phenotypic and genetic) and spatial distribution; and
3) Do the effects differ for programs with contrasting objectives (e.g., supporting harvest
vs. conservation)? Hatchery experiments conducted on an ecosystem scale, with
replicate populations or locations which do or do not receive hatchery fish, are necessary
to accommodate spatial and temporal variability that can confound investigations of
hatchery effects. Methods to control or eliminate infectious disease transmission from
hatchery to wild fish are also needed. Research efforts will provide data for ongoing
hatchery reform activities to guide hatchery operations with respect to genetics,
demographics, and ecological health, endangered species issues, legislated sustainable
fisheries and treaty trust responsibilities. Critical questions related to aquaculture
programs include: 1) What are the effects of aquaculture programs, including culture
protocols, engineering and facility design, species reared, and waste disposal on species
composition, habitat quality and biological and physical processes (such as nutrient
cycling) of the surrounding ecosystem; 2) What practices both maximize ecological
integrity of surrounding ecosystems and permit economically viable production. For both
artificial propagation/hatchery and aquaculture programs, there is also a need to identify:

29

1) when and where programs could be initiated and terminated; 2) where programs
should not be permitted to occur; and 3) programs that are terminating or being initiated
so that appropriate experiments can be crafted around them to evaluate their effects.

30

Theme 4:
Oceans and Human Health
The research council is currently in the process of redefining and broadening the Oceans and
Human Health research theme. The new theme will be described and reported on in the next
research plan update or progress report.
Relevance to national and regional ocean issues:
In the Pacific Northwest, much of the population lives at the coastal interface of terrestrial and
marine ecosystems, with an increasing trend in the coming decades (1.4 million more residents
are predicted in the Puget Sound region by 2020). The ocean and coastal environments
provide numerous benefits to humans, including nutritious seafood, various
pharmaceuticals and natural products, and opportunities for a multitude of recreational and
commercial activities. However, pathogens, toxins from harmful algal blooms (HABs) and
chemical contaminants present in marine ecosystems pose significant risks to health of both
humans and wildlife. Critical gaps exist in our knowledge of what those risks are, how to
forecast them, and identification of means to mitigate their impacts.
Role of the NWFSC:
In recognition of the relationships between the health of ocean ecosystems and human
health, multidisciplinary research teams of Federal, academic, and non-governmental
institutions were assembled by NOAA to address these critical information gaps. The
Northwest Fisheries Science Center serves as host institution to NOAA’s West Coast
Center of Excellence for Oceans and Human Health (OHH). NOAA’s research includes
studies on ocean and climate factors that directly impact human health through their effects
on pathogens and harmful algae blooms, and studies using sentinel or surrogate species to
measure the impacts of chemical contaminants or other anthropogenic and natural stressors
on human health. The research priorities listed below are largely derived from plans
developed by OHH investigators, with the focus of Center scientists on pathogens, HABS,
chemical contaminants and sentinel species.

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THEME 4: OCEANS AND HUMAN HEALTH
Research Focus 14. Characterize the exposure to and effects of pathogens, chemical
contaminants, and marine biotoxins on humans and other species
A variety of threats to human health are found in marine environments. These include
microorganisms, chemical contaminants and marine biotoxins. Disease-causing
microorganisms in aquatic environments with the capability of causing disease in humans
are often introduced from terrestrial sources, or are natural inhabitants in marine waters.
These pathogens pose risks to human health by exposure on beaches or ingestion of
seafood. Chemical contaminants are ubiquitous in aquatic environments and can pose
risks to humans either via consumption of contaminated seafood or from contact with
polluted waters. Many contaminants, including flame retardants and other emerging
chemicals of concern, are not routinely monitored because of lack of methodologies for
detection and quantification and lack of information on potential hazards posed to aquatic
ecosystems and humans. Outbreaks of marine toxin-producing harmful algal blooms are
unpredictable, and they pose an ongoing risk for seafood consumption. For each of these
distinct threats to human health, improved sensor technologies and environmental
monitoring is needed. Moreover, targeted research using biomedical models and key
marine species (e.g., shellfish) is needed to more accurately define the adverse impacts of
these agents on human health and other socio-economic indicators.
Research Focus 15. Determine how ecosystem variables, such as climate, affect the
distribution, abundance and toxicity of microbial pathogens and bio-toxin producing
organisms
Ocean and estuarine ecosystems can directly and indirectly impact the extent to which
humans are exposed to pathogens or marine biotoxins originating from harmful algal
blooms. The marine environment serves as a reservoir for emerging human pathogens
and harmful algae whose numbers can be affected by anthropogenic inputs, climate and
other environmental factors. Seafood safety thus needs to be examined in an ecosystem
context, including the role of anthropogenic factors, climate cycles and climate change in
the virulence of pathogens, toxicity of phytoplankton that contaminate seafood, or
bioavailability and trophic transfer of toxic chemical contaminants. Research aimed at
determining how virulence of microorganisms is linked to ecosystem variables (e.g.,
seasonal variation, water temperature, water chemistry, algal blooms) and climate cycles
and trends in global climate change is needed. An understanding of the pathways by
which these pathogens interact with other aquatic species is also needed. The extent to
which large-scale environmental factors influence changes in assemblages of toxic algae,
and the magnitude and duration of toxic blooms should be examined. This information is
essential to develop environmental indicators that will provide predictive capabilities for
human exposure. Models linking environmental data to seafood contamination should
also be developed to enhance predictive and risk assessment capabilities.

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Research Focus 16. Ensure seafood safety and improve seafood quality
The availability and safety of food sources from marine ecosystems or aquaculture industries
are essential to maintain and maximize human health. Fish are an important source of high
quality protein and contain omega-3 fatty acids, which have a variety of health benefits.
However, consumption of seafood (wild or farmed) poses some health risks to humans
because of accumulation of chemical contaminants in fish and shellfish tissues, and
potential contamination with pathogenic bacteria, viruses, or biotoxins. Improved
methods for monitoring presence of pathogens, toxins and contaminants in seafood
products are needed. This includes development of molecular-based assays, sensors,
micro-arrays and other techniques to detect and quantify levels of specific contaminants
of concern (pathogens, harmful algal toxins, chemical pollutants) in seafood from all
sources, that can be applied in the field and used by fish markets, fish wholesalers and
restaurants. Technologies to remove chemical contaminants from fish feed and to
enhance the nutritional content of aquaculture products are also needed to ensure a safer,
higher quality product is available to the consumer. Since the source of contaminants in
cultured fish is largely from fish meal and oil used in producing artificial fish diets,
research efforts should also include evaluation of substitutes for fish meal and oil, such as
materials derived from plants and microbes. The net economic benefits of improved
seafood safety and quality should also be determined.
Research Focus 17. Monitor the health of fish and marine mammals as sentinels for
ocean health and develop new species as mechanistic models
A variety of marine species and habitats are excellent indicators or sentinels of
environmental stress and potential health threats for humans. Biological observing
systems can serve as integrative indicators of: 1) the movement of toxics and pathogens
through marine ecosystems; 2) the effectiveness of pollution control measures; and 3)
emerging or unexpected threats. The scope and sensitivity of these observing systems
needs to be improved. Marine organisms also serve as informative animal models for
investigations related to human physiology and mechanisms of toxicity or disease
processes. Research should focus on optimizing existing marine animal models for
investigations that lead to improved understanding of human disease processes and health
effects. Efforts should also be directed toward developing new species as mechanistic
models for study of diseases, toxicology, physiological and biochemical processes
relevant to human health. Research should integrate the use of microarray or molecular
technology into sentinel surveillance systems by expanding the use of genomic and
proteomic tools for rapid detection of multiple microbes and toxicants. This information
is needed to unravel mechanisms of ocean-related health effects in sentinel species that
are particularly indicative of likely human effects.
Research Focus 18. Evaluate the effects of changes in the distribution, abundance and
virulence of threats such as toxin-producing phytoplankton or microbial pathogens to
human health or socio-economic indicators

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The consumption of certain types of seafood (sometimes within specified quantity
restrictions) has been documented to have positive health effects, while consumption of
other types of seafood and exposure to the marine environment is detrimental. It is
important to develop a better understanding of the relationship between human exposure
to pathogens, toxins and contaminants and the resulting health effects. These
relationships should then be analyzed and mapped with socio-economic indicators such
as loss or gain of commercial and recreational values, community impacts, and changes
in health status or mortality rates.

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V. NEAR-TERM PRIORITIES
The RPT in collaboration with Center researchers, developed six near-term (2–5 years)
priorities, each with equal weight, to focus initial research efforts. However, these efforts
do not preclude other activities towards all 18, longer-term (2–10 years) research
priorities. These near-term priorities were chosen based on three primary criteria: 1) a
sense of urgency or critical management importance in the near-term; 2) the project
provides technical or conceptual advances important for a range of identified research
priorities; and 3) Center capabilities support the rapid development of the project.
Opportunities for collaboration across NOAA line offices are present within the near term
priorities, and each of the priorities reflects scientific, national, regional and local
considerations. The Research Council was tasked with reviewing, selecting, and
coordinating implementation of the NTPs. Additional information about the relationship
of the near term priorities to the 18 overall research foci NOAA program components,
and national plans is included in Table 1 and the Appendix.
These near-term priorities share a common need for the development of alternative future
scenarios. For example, climate change is predicted to decrease stream flows, increase
stream temperatures, raise sea level, lead to ocean acidification and alter ocean current
patterns in the region. At the same time, human population growth will lead to increased
loading of toxic pollutants as well as increased demands by coastal communities for clean
sources of water and protection from erosion. An emerging challenge for NOAA and
other natural resource management agencies at all levels is to make appropriate decisions
in the face of these changes. Developing likely scenarios for future climate change, sealevel change, ocean acidification, patterns of human population growth, and other critical
environmental characteristics that can be included or integrated with life-cycle,
population dynamic, ecosystem, HAB and other related models is an integral part of each
of these near-term priorities

35

NEAR TERM PRIORITY 1:
Conduct an integrated ecosystem assessment of Puget Sound as a pilot project

Near-Term Priority
1:
Conduct an Integrated
Ecosystem Assessment
(IEA) for Puget Sound

Scientific Considerations
An Integrated Ecosystem Assessment is an important cornerstone of
implementing an ecosystem approach to management. A fully quantitative
IEA has yet to be conducted. Initiating and completing one will provide key
structure and guidance for future efforts. New scientific tools to determine
ecosystem risk must be developed. Determination of appropriate
benchmarks for ecosystem metrics is crucial and has never been attempted.
There is a solid body of ecological information about the region that could
underpin an IEA; similarly, it is tractable in scale.
National Considerations
IEAs have been identified as a NOAA-level priority and the focus of intense
efforts by the Ecosystem Goal Team and the NOAA Priority Area Task
Team. The NOAA Strategic Plan highlights the importance of ecosystem
approaches to management, and the NOAA Ecosystem Goal Team has
made IEAs a cornerstone of this effort
Regional Considerations
Current state-level efforts focus on Puget Sound restoration through the
Puget Sound Partnership. NOAA's Western regional team has identified
Puget Sound as the best location to conduct a Pilot IEA. The Western
Governors' Agreement has also highlighted the need to develop a Puget
Sound IEA as a means to address ecosystem concerns under their
governance.
NWFSC Considerations
All NWFSC divisions have projects focusing on Puget Sound. The NWFSC
is a leader in quantitative risk assessment and ecosystem modeling. NWFSC
staff both wrote the IEA guidance documents for NOAA and led a multiagency effort to describe the Puget Sound ecosystem and identify key
research gaps. The Southern Resident Killer Whale Research Plan identifies
understanding predator prey relationships as a key research need.

Both the NOAA 2006-2011 Strategic Plan and the Ocean Research Priority Plan
highlight the importance of incorporating ecosystem principles in resource management.
Specifically, a critical agency objective is to “Protect, Restore, and Manage the use of
Coastal and Ocean Resources through an Ecosystem Approach to Management (EAM)”
(NOAA, 2005). Integrated ecosystem assessments (IEAs) are a critical element of an
EAM strategy. An IEA is a tool to synthesize a range of physical, chemical, ecological
and socio-economic information through integrated analysis and ecosystem modeling.
An IEA is also a product for managers and stakeholders who rely on scientific support
for policy and decision making, as well as for scientists who want to enhance their
understanding of ecosystem dynamics. Finally, an IEA is a process that begins with
involvement of stakeholders to identify management priorities and objectives, moves to a
quantitative assessment, and proceeds with an evaluation of management strategies.
Through adaptive management, the process advances full circle by triggering an update
of the assessment and identifying information and management gaps.

36

Puget Sound is well suited for a pilot IEA for several reasons. It provides easy access to
the NWFSC, its scale is not overwhelming, and sufficient previous work in the Sound has
been conducted to support substantial short-term progress. Additionally, it is currently
the object of several state and regional efforts to improve ecosystem health. Finally, it
will provide a means of testing how best to nest or link sub-sets of a large marine
ecosystem to an IEA of the entire California Current LME.
The pilot IEA for Puget Sound will result in the following components:
1. Assessment of baseline conditions of the ecosystem
2. Assessment of stressors on the ecosystem
3. Forecast of ecosystem status with no management action
4. Forecast of ecosystem status under different management strategies
5. Evaluation of the success of management actions
IEAs will serve as a forum for integration of information collected by the NWFSC with
other regional entities including other Federal agencies, states and academic institutions.
IEAs will also identify critical data gaps, which, if filled, would greatly reduce
uncertainty and improve our ability to fully employ ecosystem approaches to
management.
NEAR TERM PRIORITY 2:
Case study – Salmon, people, and instream flows under climate change

Near-Term Priority
2:
Case study – Salmon,
people, and instream
flows under climate
change.

Scientific Considerations
A key element of ecosystem approaches to management is the inclusion of
human needs, impacts and behaviors. This is particularly true for
management of resources, like water, that play a fundamental role for both
humans and other species of concern, such as salmon. Assessing changes
in water supplies in both an ecological and a human context can provide an
example for future efforts to incorporate humans into ecosystem analysis.
Additionally, the effect of climate change on environmentally functional
flows has not been fully explored.
National Considerations
Nationally, changes in summer water supplies will diminish throughout
much of the US; examples of how to predict ecological and agricultural
consequences and devise restoration strategies that enhance multiple
ecosystem services are in high demand.
Regional Considerations
Climate change effects on water supplies are high priorities for
municipalities and irrigators in the Pacific Northwest. In addition, these
factors have been identified as potentially limiting for anadromous
salmonids in a variety of recovery plans.
NWFSC Considerations
NWFSC staff have expertise in assessing impacts on salmonids; in
addition, the newly-developed socio-economic team provides expertise in
evaluating drivers of human behavior. Improving collaborations between
these disciplinary areas will strengthen our ability to contribute to
implementation of ecosystem approaches to management.

37

The rebuilding and recovery of Pacific anadromous salmonids is a major priority for
NOAA Fisheries, and an important area of expertise at the NWFSC. In this region,
competition between salmon and humans for freshwater flows, particularly in the
summer, is likely to increase in the very near term as the relatively simultaneous effects
of climate change and increasing human population growth are felt. Importantly,
assessing appropriate management strategies for these fish and the streams and rivers
they rely on is not dependent on biological information alone. Socio-economic factors
such as patterns of population growth, economic development, and land use strongly
influence the types of management actions that will ultimately be successful. A critical
challenge is framing and evaluating the tradeoffs decision makers will face in balancing
the conservation of freshwater ecosystems and flows for anadromous salmonids with
human demands for safe drinking water, crop irrigation, recreation, and flood control.
Resolving this fundamental tension will require that NOAA develop sound physical,
biological and ecosystem models allowing the prediction of likely impacts on
anadromous fishes, as well as social and economic models that provide valuation systems
(e.g., the cost effectiveness of water recovery systems versus the ecological consequences
of extracting larger amounts of freshwater for agriculture, power generation or industrial
purposes). This project will work to develop and integrate these models to inform
decisions regarding allocations of a diminishing resource under alternative climate
change scenarios.
Products of this research will include:
1. Evaluation of climate change impacts on water availability in Pacific Northwest river
systems.
2. Evaluation of present water diversions and withdrawals from regional rivers and their
impacts on salmon populations.
3. Predictions of increased water demands for human uses.
4. Prediction of combined effects of climate-altered flows and water uses on salmon
populations.

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NEAR TERM PRIORITY 3:
Evaluate and implement new and alternative survey and monitoring methods for
groundfish

Near-Term Priority
3:
Evaluate and implement
new and alternative
survey and monitoring
methods for groundfish.

Scientific Considerations
Many of the species for which NMFS has responsibility are difficult or
impossible to survey using currently available methods. This, in turn,
precludes both immediate management needs, such as data-based assessments
and catch-limits, and the information needed to include these species in
models of ecosystem structure and function.
National Considerations
The Magnuson-Stevens Sustainable Fisheries Act was recently renewed, and
includes requirements for science-based Annual Catch Limits for a total of
532 species. For 261 of these species, data to support these legally mandated
ACLs are unavailable, often due to the challenges of conducting surveys.
Regional Considerations
The largest group of species in the Pacific Northwest for which large-scale
surveys are difficult or impossible is groundfish. Efforts to develop catch
limits on any time scale, or to assess species status, are extremely limited as a
result.
NWFSC Considerations
Leadership for West Coast groundfish surveys has rested to date largely at the
NWFSC.

The vast majority of groundfish stock assessments rely heavily upon bottom-trawl data
from surveys or fisheries or both. However, many groundfish species use rocky or
topographically complex habitat that is not effectively sampled by bottom-trawl surveys.
Evaluating the status of groundfish stocks is thus hindered by the limited knowledge
concerning groundfish habitat use and an inability to conduct trawl survey samples in
areas that are topographical complex. Additionally, there are concerns about the effects
of research trawling on benthic habitat, and the occasional large catch of overfished
species by the bottom trawl survey can result in fishery restrictions. The use of alternative
survey methods that are viable in untrawlable habitat, non-lethal, or that target early life
history stages will greatly improve the coverage and completeness of groundfish surveys
and reduce their ecological impacts. In recent years, feasibility studies and small–scale
surveys have been conducted using Autonomous Underwater Vehicles (AUVs),
Remotely Operated Vehicles (ROVs), submersibles, acoustic surveys, advanced tagging
technologies, towed cameras, LIDAR, hook and line gear, and egg and larval sampling.
The comparative costs and utility of these alternative survey methods for groundfish
assessment are still being evaluated and significant further research and testing is needed.
This analysis will coincide with continued work on habitat mapping, thus allowing the
design of habitat-stratified sampling programs, An additional need is more rapid
availability (from collection to dissemination) of both survey and fishery data. This
would improve the ability of managers to respond to events, and would enhance the
ability of stock assessment scientists to incorporate the most recent data into their

39

evaluations. An integrated electronic recording system for fishticket and logbook
information would allow for such real-time estimates of landings and discards.
Products of this research will include:
1. Information on the feasibility of alternative resource surveys and the usefulness of
the resultant data.
2. The implementation and improvement of new and ongoing surveys for groundfish
as well as other benthic organisms and habitats.
3. More rapid and accurate transmittal of monitoring data to managers and analysts.
NEAR TERM PRIORITY 4:
Predict population and ESU-level response to management, climatic and other impacts
across the life-cycle of species of concern

Near-Term Priority
4:
Predict population and
ESU-level response to
management, climatic
and other impacts
across the life-cycle of
species of concern.

Scientific Considerations
Management of ESA-listed and other species of concern has been limited by a
lack of information about the response of species (or subunits) to specific
human or natural impacts across a range of conditions. This information can
also support multi-species prioritization efforts.
National Considerations
Several laws, including the Endangered Species Act, call for recovery of
species of concern, and for jeopardy analysis of proposed actions.
Understanding likely responses to proposed actions and conservation
measures underlies these efforts.
Regional Considerations
Recovery planners for listed anadromous salmonids require information about
the efficacy of restoration efforts and the impact of both anthropogenic and
climatic changes to plan and implement recovery actions appropriately.
NWFSC Considerations
NWFSC staff have worked with NW Region staff in the development of both
recovery plans and jeopardy analyses. This priority is intended to allow the
NWFSC to approach these issues more systematically and support a multispecies perspective. Southern Resident Killer Whale Research and Recovery
Plans identify these research areas as critical.

A critical question in salmon recovery and rebuilding is: “What management actions are
necessary to achieve conservation goals?” Answers to this question depend on which
species are the focus of restoration efforts, as conflicting priorities may emerge when
comparing single-species analyses. This research priority is a Management Strategy
Evaluation -- it couples modeling with empirical research and directed field studies to
compare the likely outcomes of alternative management or restoration strategies (e.g.,
habitat restoration, pollution reduction, hatchery reform, harvest reform, altering
hydropower operations) across a range of species and life stages. The tools for this
research include life-cycle models that evaluate the diverse and dynamic habitats used by
salmon throughout their life cycle, as well as interactions among species. Tagging of
individuals reveals habitat use and preferences for particular life stages. Combined
computer models and field studies will assist in evaluating the relative importance of

40

alternative restoration strategies to the recovery and persistence of individual listed
species, life history diversity, and potential tradeoffs among species. Studies that assess
the health of individual animals (e.g., in response to environmental conditions, pathogens,
toxic chemicals, etc.) and extrapolate this information to the population scale will help
resource managers understand the extent to which degraded water quality can limit the
recovery potential of species at risk of extinction. Products of this research will include:
1. A logical approach for evaluating multi-species benefits of river restoration
actions
2. A suite of modeling tools that will enable use of the approach
3. Novel methods for incorporating the health and performance of individual
animals into population-scale evaluations
4. Two applied examples of the approach and models culminating in a formal
Management Strategy Evaluation for these two examples.
Results of this research will allow stakeholders to more realistically prioritize restoration
or recovery actions, evaluate cost-effectiveness, and identify critical population
bottlenecks.
NEAR TERM PRIORITY 5:
Develop rapid detection and improved prediction methods to identify pathogens,
biotoxins, toxics and other marine impacts on human health

Near-Term Priority
5:
Develop rapid detection
and improved
prediction methods to
identify pathogens,
biotoxins, toxics and
other marine impacts on
human health

Scientific Considerations
Pathogens, biotoxins, and toxics pose a substantial risk to human health, and
provide indicators of ecosystem status. These events can occur rapidly, and
have effects on human health shortly thereafter. Developing prediction and
detection methods will assist with both human health concerns and in
evaluating overall ecosystem conditions. It can also potentially contribute to
more precise and/or reduced impacts of closures on the shellfish industry.
National Considerations
The Harmful Algal Bloom and Hypoxia Amendments Act of 2004 reaffirms
and expands the mandate for NOAA to advance the scientific understanding
and ability to detect, monitor, assess, and predict HABs and to develop
programs for research into the methods of prevention, control, and mitigation
of HABs. The implementation of this act is also called for in the President’s
U.S. Ocean Action Plan.
Regional Considerations
The Pacific Northwest, and Puget Sound in particular, are likely to face
multiple pressures (climate change and human population growth) that have
the potential to increase risks of HAB events, toxic accumulation and
pathogens.
NWFSC Considerations
The NWFSC has been designated as a Center of Excellence for Research in
Oceans and Human Health, with strong research programs in toxics,
biotoxins, microbiology and disease.

The development and implementation of new technologies to ensure a safe and healthy
supply of seafood has been a core scientific mission at the Center for decades. Recent
advancements in the fields of genomics, proteomics, bioinformatics, sensor technology,

41

analytical chemistry, and ocean observing systems have greatly expanded the potential
for rapid and sensitive detection of pathogenic organisms, marine biotoxins, and chemical
contaminants. As indicated by the Center’s coordinated response to Hurricanes Katrina
and Rita, the timely analysis of seafood quality can be critical for coastal economies (e.g.,
reopening the shrimp fishery in affected areas of the Gulf of Mexico). To continue to
meet the regional and national analytical needs of NOAA, the Center must remain at the
forefront of emerging technologies. This will require scientific expertise that spans
nearly the full spectrum of biological organization, from genes to organisms to coastal
ecosystems. Ongoing investments in analytical infrastructure, such as those made
possible by NOAA’s Oceans and Human Health Initiative, will be necessary. Moreover,
the Center must meet the complex challenges posed by bioinformatics – that is, the need
to navigate vast genomic, transcriptional and proteomic datasets. To this end, expanded
collaborations with academia and other partners will be essential. A broad aim will be to
develop new diagnostic tools and then integrate these into in situ monitoring programs
and ocean observing systems. Components of this research include:
1. The deployment of remote sensing systems;
2. The development of more sensitive laboratory methods to detect harmful agents
in water and tissues;
3. The biologically-based monitoring of sentinel species in estuaries and the
nearshore marine environment.
4. Equally important is the need to develop new and more accurate forecasting
capabilities. This includes forecasting over the near term (e.g., seasonal beach
and shellfish closures in response to HABs, pathogens or contaminants).
Over longer timescales, the Center should continue to monitor and forecast emerging
threats to human health. These emerging threats include, for example, the persistent
bioaccumulation of brominated flame retardants at increasingly higher trophic levels in
the marine food web.

42

NEAR TERM PRIORITY 6:
Initiate an ecosystem-based aquaculture research program

Near-Term Priority
6:
Initiate an aquaculture
research program

Scientific Considerations
Improving culture techniques for marine fish larvae, juveniles and adults will
also support production of fish for laboratory studies on high priority areas
such as effects of ocean pH on marine organisms, bioenergetics and nutrition
of marine fish, reproductive biology of marine fish, and effects of
contaminants on fish behavior, growth, development, physiology,
immunology, disease resistance, & reproduction. This information will be
valuable to management of fish in their native habitat as well as development
of aquaculture technology. Additionally, research and improved technologies
focused on ‘best practices’ (in terms of sustainability, genetics, invasive
species, and environmental impacts) are needed because these issues are not
being addressed in many other countries with rapidly growing aquaculture
industries.
National Considerations
The recently-passed National Offshore Aquaculture Act mandates the
development of aquaculture in U.S. waters, with strict environmental
guidelines. Given this high priority for development of marine aquaculture in
the US, it is critical that NOAA Fisheries take a lead role in assessing risks
and benefits, assist in development of fish culture practices that minimize
negative ecological impacts, and provide science needed for regulation of this
developing industry. Both the NOAA-Strategic Plan and Ocean Research
Priority Plan identify marine aquaculture as a priority research area.
Regional Considerations
Recovery plans for listed species in the Pacific Northwest call for additional
analysis of the ecological effects of aquaculture, and incorporation of
aquaculture into ecosystem and species-specific models.
NWFSC Considerations
The Center is in a unique position to make contributions in marine
aquaculture research because of its facilities for marine fish culture and
expertise of staff in fish nutrition, behavior, husbandry, physiology,
ecotoxicology, and marine ecology. The NWFSC has capabilities to address
technological development as well as issues related to regulation. The Center
is doing more aquaculture-related work than any other science center within
NOAA-Fisheries and has a responsibility to take the lead in this area within
the Agency.

Demand for seafood in the United States and worldwide is rapidly expanding and
creating an incentive to increase harvest rates to meet the growing markets. The
development of sustainable, ecologically-sound marine aquaculture in the United States
is one of the highest priorities within the Department of Commerce. Aquaculture is a
matrix program at NOAA, and Center scientists have been included on the matrix
management team since its inception. The National Offshore Aquaculture Act is the top
agency legislative priority. Innovative approaches to develop ecologically sound
commercial aquaculture industries are needed to provide seafood for a growing human

43

population, particularly in view of current recommendations for increased fish
consumption to promote human health. Expansion of the national aquaculture industry
requires research on a number of topics to ensure a minimum of ecological risk and a
maximum of opportunities for economically viable development. In particular, recent
proposed legislation points toward development of aquaculture in the Exclusive
Economic Zone (EEZ), which will present new technological and regulatory challenges.
Aquaculture systems must be secure, efficient, cost-effective, and reliable, and their
products must be healthy, free of disease and chemical contamination, lack deformities,
and perform well in grow-out systems. Furthermore, aquaculture programs must be able
to quantify their impacts on the natural environment within a risk management
framework. The United States lags behind Europe and Asia in marine aquaculture
technology and investment. There is currently no coordination in the sector in the United
States and few aquaculture facilities operate above a laboratory scale. Commercial
marine aquaculture finfish species that have greater potential than currently valued
include Atlantic salmon, sablefish, lingcod, Atlantic and Pacific cod, red snapper, the sea
breams and bass, flatfishes, mullets, and now some ocean pelagic fishes. Additional
areas of important research include assessing the ecological risk of aquaculture, and
identifying positive and negative links between human health and aquaculture practices.
The products of aquaculture research will include:
1. Development of culture techniques for a variety of cultured finfish and shellfish
that ensure economic efficiency, seafood safety and quality.
2. Development of sustainable feeds that will reduce reliance on fish meal and fish
oils as they become limiting for expansion of fish culture.
3. Development of environmental and monitoring guidelines to ensure sustainability
and minimize ecological risks associated with aquaculture programs.
4. Scientific evaluation of the potential for responsible enhancement of marine
stocks.

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NEAR TERM PRIORITY 7 (CURRENTLY IN DEVELOPMENT):
PREDICTING EFFECTS OF OCEAN ACIDIFICATION ON COASTAL SPECIES OF WASHINGTON AND
OREGON THOUGH EXPERIMENTS, MODELING AND TARGETED MONITORING

VI. NECESSARY TOOLS
Implementing these research priorities will require the active development and
improvement of Center capabilities in three areas: 1) technologies that allow scientists to
observe and analyze ocean environments; 2) models to evaluate alternative scenarios and
effects; and 3) some targeted changes in the data management, laboratory facilities, and
field sampling infrastructure of the Center. A detailed description of the specific tools
that the Center will need to develop is provided in Appendix C based on these three
categories.
Technologies: Ocean environments and the organisms that inhabit them are notoriously
challenging to observe –the scales are large, the organisms are often fragile, cryptic or
unknown, and the habitat is a demanding and expensive one for humans to occupy for
prolonged periods of time. Technology development that enables us to gain information
remotely about oceanographic or other environmental conditions and about organisms
across wide areas or in inaccessible habitats is clearly a high priority. Other key
technologies include those that allow us to understand the interaction between organisms
of interest, their habitats and humans.
•

Large-scale observational systems and techniques such as ocean observation systems,
remote sensing (satellites, multi-beam, LIDAR, hyperspectral imagery, etc), and
remote and autonomous underwater vehicles facilitate the observation and mapping
of ocean conditions at the ecosystem scale, and provide mechanisms for groundtruthing where access is difficult and costly.

•

Tagging and remote sensing technologies for individual organisms have progressed
rapidly over the past several decades as the power of computers has increased,
electronic components have decreased in size, and the ability to detect signals
remotely has increased. The ability to detect and identify individual animals greatly
enhances the ability to track movement, survival rates and other demographic and
behavioral information. These data are needed to make decisions on altering
management strategies for protecting listed stocks.

•

Population structure and patterns of movement can be determined by recent advances
in genetic techniques, isotopes, and the identification of parasites.

•

Landed catch, bycatch and discard has not been systematically monitored for some
West Coast fisheries until recently. The West Coast Groundfish Observer Program

45

(WCGOP) was established in 2001 to improve estimates of total catch and discard in
West Coast fisheries. The program deploys over 40 observers and collects at-sea data
from limited-entry trawl and fixed gear fleets as well as from open access, nearshore,
prawn, and shrimp fleets. An integrated electronic recording system for fishticket and
logbook information for the Pacific coast would vastly improve the ability to track
groundfish catches in season and to produce real-time estimates of landings and
discard needed for timely management decision-making.
•

Geographically or spatially linked analysis and interpretation: Marine and
freshwater research efforts increasingly rely on large geospatial data sets to address
issues such as individual and population-level movement patterns, climate change
effects on stream flows, ocean circulation patterns, and patterns of current and future
land use. Maintaining up-to-date GIS capabilities, including software, databases and
support staff, will be a critical element of conducting the landscape (and oceanscape)
scale analyses that contribute to multiple goals.

•

Socio-economic surveys are the primary means of collecting information and data
used to describe the interactions between humans and living marine resources. Two
important policy themes for socio-economic analysis are commercial and recreational
fisheries, and conservation and ecosystem management.

•

Bioinformatics include advances in genomic technologies; sensors that can be used
for the rapid detection of pathogens, harmful algae, and toxins; and associated
instrumentation. Molecular techniques that have been used to identify species and
stock structure can also be used to assess gene expression patterns in the assessment
of ecosystem function. Development of shared computational bioinformatics tools
requires hardware, software and personnel with specific expertise. Presently the
Center has hardware and software for a bioinformatics core facility. Personnel with
specific expertise in bioinformatics are needed.

Models and the Data to Support Them: Modeling provides a framework in which to
describe a system in detail or in general, to evaluate the effects of alternative actions, and
to characterize the sensitivity of a system to perturbations – all of which are key for
effective management. However, it is critical that these models are supplemented by
experiments, directed observational studies and other research efforts to develop the data
to establish parameters and evaluate the models. Several types of models are being used
or developed at the Center:
•

Socio-economic models are necessary to measure the benefits provided by natural
resources, and how those benefits may changes as resource flows changes. Economic
valuation and behavioral are needed to evaluate both use and non-use values, as well
and regional economy, community and social impacts. These models should be
linked to biological and ecological models of habitat distribution, abundance and
quality.

46

•

Risk assessment models attempt to analyze biological information in the face of
limited data, and are limited by the difficulty of capturing biological complexity
through models with many parameters. Research is needed to incorporate additional
biological information into simple models, and to develop methods for incorporating
or specifying uncertainties.

•

Population dynamic models can be quite sophisticated, but substantial improvement
in their utility can be achieved by developing ways of including information on
spatial dynamics, the role of size and age composition in population demographics,
and demographic and environmental stochasticity. At the ecosystem level, forecasting
these impacts requires understanding complex dynamics controlling: 1) productivity
of populations within various trophic levels, 2) predator-prey interactions, 3)
connectedness of sub-populations, 4) impacts of natural climate variation and change,
and 5) anthropogenic pressures.

•

Evolutionary models may be valuable for analyzing population dynamics of, and
genetically-based changes in, exploited species or key components of disturbed
ecosystems. Evolutionary approaches to this problem should link multivariate
genetic models of life history variation to analyses of population dynamics and
viability.

•

Models to support ecosystem approaches to management have generally fallen into
three categories: 1) models aimed at prioritizing sites for conservation, 2) data-driven
statistical models that estimate population or community dynamics, and 3) food web
simulations.

•

Models treating habitats and landscapes contribute to effective recovery planning by
analyzing how habitat restoration actions will affect population viability and
sustainability. Few models are available to simulate how natural processes form and
sustain habitat. Integration of data on the quantity, quality and spatial distribution of
habitat can improve the predictive powers of assessment models and guide fishery
management.

•

Essential Fish Habitat (EFH) designation and delineation models are being
developed in response to the requirement of the Magnuson-Stevens Fishery
Conservation and Management Act that regional management councils describe EFH
in their fishery management plans. The councils must minimize impacts on this
essential habitat from fishing activities, and councils and other Federal agencies must
consult with the National Marine Fisheries Service about activities that might harm
EFH.

•

Integrated modeling approaches overcome many of the limitations described above
and achieve the crucial goal of integrating physical, chemical, ecological, and
fisheries dynamics in a three-dimensional, spatially explicit domain. In these models,
ecosystem dynamics are represented by spatially-explicit sub-models that simulate

47

hydrographic processes (light- and temperature-driven fluxes of water and nutrients),
biogeochemical factors driving primary production, and food web relations among
functional groups. These models represent key exploited species at the level of detail
necessary to evaluate direct effects of fishing, and they also represent other
anthropogenic and climate impacts on the ecosystem as a whole.

Infrastructure: The Center maintains the infrastructure for many critical data
management functions, laboratory facilities, and field sampling.
•

Data management responsibilities of the NWFSC are enormous, and are used to
efficiently generate science guidance products such as ESA status reviews, MSFCMA
stock assessments and IEAs. The Center must also have the capacity to archive,
compile and inter-relate numerous independent data types running into the millions of
records. A standardized protocol for data security needs to be developed and
supported to protect the Center’s huge investment in electronic data. The entire
Center staff needs to be involved in a discussion of how to identify and support Data
Stewards for research and corporate data that are maintained by Center staff; and the
Center needs to develop a data management strategy that meets the needs of multiple
scales of data management.

•

Laboratory Facilities are important in achieving research goals. Although many
facilities are already operational, mechanisms to improve access and provide
adequate technical support are needed. Some identified needs include:
o Diet and tissue analysis laboratories and support personnel
o Wet labs
o Fish culture facilities

•

Field sampling support: Large-scale, interdisciplinary ocean research requires the
use of large, sophisticated research vessels capable of extended cruises in rough sea
conditions. The broad nature of oceanographic sampling requires many sensors of
atmospheric and ocean conditions and the ability to deploy and retrieve many gear
types. Estuarine and riverine sampling do not pose the logistic limitations in ship size
as does ocean sampling, but these other habitats also face shortages of small vessels.

•

Gear storage needs for sampling gear including ATVs, equipment, boats, nets, trawls
and other gear have become more acute in recent years.

The Center has made substantial investments into the tools necessary for long term
research that will greatly benefit the near-term priorities for research. While some
upgraded and new laboratory facilities, equipment and personnel are needed to achieve
research objectives, the evaluation and possible reorganization of existing facilities and
gear availability can help facilitate research.

48

VII. CONCLUSIONS
Preparing the Center to provide scientific leadership as the U.S. and the Pacific
Northwest begin to implement ecosystem approaches to management of ocean systems
can fortunately build on the strong research programs that have been developed within
the organization. The Center is also fortunate to have a scientific and administrative staff
that is committed not only to improving the Center, but also to making a difference—in
the management of our natural resources, in the scientific community, and within our
region and nation. As the Center moves forward in implementing this plan, we hope that
it will reinforce and enhance this commitment, and in so doing, allow us all to contribute
meaningfully to the stewardship of our interconnected environment.

49

ACRONYMS
AOP
AUV
CCLME
ECC
EEZ
EFH
ENSO
EOP
ERP
ESA
ESU
GIS
GPRA
HAB
HP
IEA
JSOST
LIDAR
LME
LMR
MSFCMA
NWFSC
OHH
PaCOOS
PAHs
PCBs
PDO
PPBES
PSP
RPT
WCGOP

Annual Operating Plan
Autonomous Underwater Vehicle
California Coastal Large marine Ecosystem
Emerging Chemical Contaminant
Exclusive Economic Zone
Essential Fish Habitat
El Nino Southern Oscillation
Ecosystem Observation Program
Ecosystem Research Program
Endangered Species Act
Evolutionarily Significant Unit
Geographic Information System
Gov’t Paperwork Reduction Act or Government Performance & Result
Act
Harmful Algal Bloom
Habitat Program
Integrated Ecosystem Assessment
Joint Subcommittee on Ocean Science and Technology
Light Detection and Ranging
Large Marine Ecosystem
Living marine resources
Magnuson-Stevens Fishery Conservation & Management Act
Northwest Fisheries Science Center
Oceans and Human Health
Pacific Coastal Ocean Observing System
Polycyclic Aromatic Hydrocarbons
Polychlorinated Biphenyls
Pacific Decadal Oscillation
Planning, Programming, Budgeting, and Execution System
Puget Sound Partnership
Research Planning Team
West Coast Groundfish Observer Program

50

REFERENCES:
Climate Change Science Program and the Subcommittee on Global Change Research,
2003. The U.S. Climate Change Science Program. Vision for the Program and
Highlights of the Scientific Strategic Plan. 41 p.
Climate Change Science Program and the Subcommittee on Global Change Research,
2003. Strategic Plan for the U.S. Climate Change Science Program. 364 p.
Committee on Environment and Natural Resources/Interagency Working Group on Earth
Observations, 2005. Strategic Plan for the US Integrated Earth Observation
System. USGEO. Washington, DC.
Joint Subcommittee on Ocean Science and Technology, 2007. Charting the Course for
Ocean Science in the United States for the Next Decade: An Ocean Research
Priorities Plan and Research Strategy. Washington, D.C.
National Marine Fisheries Service, 2004. NMFS Strategic Plan for Fisheries Research.
U.S. Dep. Commerce, NOAA Tech. Memo. NMFS F/SPO-61, 148 p.
Washington, D.C.
National Oceanic and Atmospheric Administration (U.S. Department of Commerce),
2005. New Priorities for the 21st Century -- updated for FY2006 to FY2011.
http://www.ppi.noaa.gov/pdfs/STRATEGIC%20PLAN/Strategic_Plan_2006_FIN
AL_04282005.pdf Washington, D.C.
Pew Oceans Commission. 2003. America’s Living Oceans: Charting a Course for Sea
Change. A Report to the Nation. Arlington, Virginia.
U.S. Commission on Ocean Policy (USCOP). 2004. An Ocean Blueprint for the 21st
Century. Washington, D.C.

51

APPENDICES

Appendix A: Table of drivers for the NWFSC Research Plan themes and foci.
Appendix B: Table of detailed tasks, GPRA measures, and driver priorities related to
NWFSC Research Plan themes, foci, and near-term priority research
Appendix C: Background and definitions of policy drivers associated with the NWFSC
Research Plan
Appendix D: NWFSC Strategic Science and Research Planning Charter (2008)
Appendix E: Necessary Tools for implementing research

52

APPENDIX A: Drivers for the NWFSC Research Plan. In general, all of these drivers call for work in the areas highlighted in the NWFSC’s research
themes and foci. In this table, dark shading in a box indicates that the theme or focus is in direct and specific support of elements of the driver. Light
shading indicates that the research focus or theme is clearly in support of the driver, even though the specific element may not be laid out in detail in
that document. For more specifics, please refer to Appendix B.
Legislative
Regional, and Local Government
International
Focus

ESA

Ecosystem Approaches to Management for the California
Current LME
Conduct integrated ecosystem assessments to improve
1 ecosystem predictions
2

Describe interaction between human activities and
ecosystem status

3

Characterize linkages between climatic conditions and
biotic responses

4
5

Characterize ecological interactions
Characterize interaction between marine, freshwater and
terrestrial ecosystem

Habitats to Support Sustainable Fisheries and Recovered
Populations
Characterize habitat effects on ecosystems, ecological
6 interactions, and organism health
7

Characterize interaction between human use and habitat
distribution and quality

8

Develop effective habitat restoration and conservation
techniques

Recovery, Rebuilding and Sustainability of Marine and
Anadromous Species

53

MSA MMPA

Puget
Sound
Partnership

West Coast
Governor’s
Agreement

Pacific
Fisheries
Management
Council

PICES

Pacific
Salmon
Treaty

Legislative
Focus

ESA

9

Describe the relationship between human activities and
species recovery

10

Investigate ecological and socio-economic effects of
alternative management structures

11

Characterize demographic parameters for key species;
improve methods for predicting risk

12

Develop methods to use physiological information to
predict population processes

13

Clarify role of artificial propagation in recovery, rebuilding
and sustainability

Oceans and Human Health
14

Characterize exposure/effects of pathogens,
contaminants and biotoxins on humans and other species

15

Determine how ecosystem variables affect bio-toxin
producing organisms

16

Ensure seafood safety and improve seafood quality

17

Monitor the health of fish and marine mammals as
sentinels for ocean health

18

Evaluate effects of changes in abundance and virulence
of health threats on socio-economic indicators

54

MSA MMPA

Regional, and Local Government
Puget
Sound
Partnership

West Coast
Governor’s
Agreement

Pacific
Fisheries
Management
Council

International
PICES

Pacific
Salmon
Treaty

NOAA
NOAA’s Next
Generation
Strategic Plan

Focus
Ecosystem Approaches to Management for the California
Current LME
Conduct integrated ecosystem assessments to improve
1 ecosystem predictions
2

Describe interaction between human activities and
ecosystem status

3

Characterize linkages between climatic conditions and
biotic responses

4
5

Characterize ecological interactions
Characterize interaction between marine, freshwater and
terrestrial ecosystem

Habitats to Support Sustainable Fisheries and Recovered
Populations
Characterize habitat effects on ecosystems, ecological
6 interactions, and organism health
7

Characterize interaction between human use and habitat
distribution and quality

8

Develop effective habitat restoration and conservation
techniques

Recovery, Rebuilding and Sustainability of Marine and
Anadromous Species
Describe the relationship between human activities and
9 species recovery

55

NMFS
Strategic
Science Plan

National
GPRA
Measures1

U.S. COP
Ocean
Action
Plan2

National
Ocean
Policy
Taskforce

Ocean
Research
Priority
Plan3

NOAA
NOAA’s Next
Generation
Strategic Plan

Focus
10

Investigate ecological and socio-economic effects of
alternative management structures

11

Characterize demographic parameters for key species;
improve methods for predicting risk

12

Develop methods to use physiological information to
predict population processes

13

Clarify role of artificial propagation in recovery, rebuilding
and sustainability

NMFS
Strategic
Science Plan

National
GPRA
Measures1

U.S. COP
Ocean
Action
Plan2

National
Ocean
Policy
Taskforce

Oceans and Human Health
14

Characterize exposure/effects of pathogens,
contaminants and biotoxins on humans and other species

15

Determine how ecosystem variables affect bio-toxin
producing organisms

16

Ensure seafood safety and improve seafood quality

17

Monitor the health of fish and marine mammals as
sentinels for ocean health

18

Evaluate effects of changes in abundance and virulence
of health threats on socio-economic indicators

1

GPRA - light shading indicate foci that relate to at least one GPRA measure; foci with dark shading relate to more than one measure (see Appendix B for which measures).
Ocean Research Priority Plan - light shading indicates foci that link with 1-4 numbered priorities; dark shading indicates a link with more than four distinct priorities in this Plan.
3U.S. COP Ocean Action Plan - light shading indicates a link with identified themes, and dark shading means a link with specific tasks in the Plan.

2

56

Ocean
Research
Priority
Plan3

APPENDIX B: Relationship of themes, foci to the Ocean Research Priority Plan (numbers refer to priority themes identified in that
plan); the U.S. Commission on Ocean Policy Ocean Action Plan (text refers to identified themes, numbers refer to specific tasks);
NOAA Programs and Components as identified in the NMFS Strategic Plan (codes refer to Program and numbered component); and
GPRA measures (text refers to individual measures).
Themes
Ecosystem Approaches to Management for the California
Current LME

1

2

3

Describe the relationship between human activities and
species recovery

Investigate ecological and socio-economic effects of
alternative management structures

Characterize demographic parameters for key species;
improve methods for predicting risk

Ocean
Research
Priority Plan

U.S. COP Ocean
Action Plan

1, 2, 4, 5

Achieving
Sustainable
Marine Fisheries
EOP-1
ERP-1,2
HP-1
CEP-1,2
ERP-1,2
PSP-1,2
HP-1
CEP-1,2,3
EOP-2
PSP-1,2,5
CEP-1,2,3

1, 7, 11, 12,
16, 20

3, 5, 14, 15,
20
5, 6, 11, 13,
14

Develop methods to use physiological information to
predict population processes
4

5

Clarify role of artificial propagation in recovery, rebuilding
and sustainability

Habitats to Support Sustainable Fisheries and Recovered
Populations

6

7

Characterize habitat effects on ecosystems, ecological
interactions, and organism health

Characterize interaction between human use and habitat
distribution and quality

57

NOAA Programs
and Program
Components

GPRA Measures

% LMR with adequate
assessments

% LMR with adequate
assessments

2, 6, 14

ERP-1,2
PSP-1,2
CEP-1,2,3

% LMR with adequate
assessments;
Commercial fisheries
with insignif. marine
mammal mortality

2, 7, 14

ERP-1,2
PSP-1,2
HP-1
CEP-1,2,3

% LMR with adequate
assessments

1, 2, 4, 5

1, 2, 6,
13,14,16
3, 14, 15, 20

Conserve and
Restore Coastal
Habitat
ERP-1
PSP-1
HP-1,2,3
CEP-1,2,3
EOP-5
HP-1,2,3

% LMR with adequate
assessments
Habitat acres restored

Themes
8

Develop effective habitat restoration and conservation
techniques

Recovery, Rebuilding and Sustainability of Marine and
Anadromous Species

9

Describe the relationship between human activities and
species recovery

10

Investigate ecological and socio-economic effects of
alternative management structures

11

Characterize demographic parameters for key species;
improve methods for predicting risk

12

Develop methods to use physiological information to
predict population processes

13

Clarify role of artificial propagation in recovery, rebuilding
and sustainability

Oceans and Human Health
14

Characterize exposure/effects of pathogens,
contaminants and biotoxins on humans and other species

15

Determine how ecosystem variables affect bio-toxin
producing organisms

16

Ensure seafood safety and improve seafood quality

17

Monitor the health of fish and marine mammals as
sentinels for ocean health

18

Evaluate effects of changes in abundance and virulence
of health threats on socio-economic indicators

58

Ocean
Research
Priority Plan

U.S. COP Ocean
Action Plan

3, 14

59

1, 2, 4, 5

Enhance
Conservation of
Protected Species

NOAA Programs
and Program
Components
PSP-2,4
HP-1,2,3,4
CEP-3

ERP-2
PSP-1,2
CEP-1,2,3

3, 7, 14

EOP-8
FMP-1
PSP-1,2
EOP-1,3
FMP-1
PSP-1,2
FMP-1
PSP-1,2
ERP-2
FMP-1
PSP-1,2
AP-1,2

3, 15
1, 6, 13, 16,
20
1, 2, 16

3, 14, 20

1, 2, 6

Reduce Coastal
Water Pollution

3, 7, 14, 18

12, 52

PSP-1
HP-1.2

5, 6, 7, 13, 14,
17, 20

12, 52

ERP-2
CEP-1,2,3

3, 4, 7, 17, 18

FMP-2

1, 6, 7, 14, 16,
18, 20

ERP-2
PSP-5

3, 7, 15, 19,
20

12

EOP-8

GPRA Measures

Habitat acres restored

Plans to rebuild stocks,
Protected species with
increase or stable
population numbers
Protected species with
increasing or stable
population numbers
% LMR with adequate
assessments
% LMR with adequate
assessments

Habitat acres restored

APPENDIX C: DETAILS OF POLICY DRIVERS FOR THE NWFSC
Legislative Requirements
Endangered Species Act (ESA)
http://www.nmfs.noaa.gov/pr/laws/esa/
The ESA provides for the conservation of species that are endangered or threatened
throughout all or a significant portion of their range, and the conservation of the
ecosystems on which they depend. Species that are endangered or threatened in the
Pacific Northwest include salmon species such as the Puget Sound Chinook and marine
mammals such as the Orca. The NWFSC is involved in providing input for decisions
under the Act on the status and range of salmonid populations and the conservation of
ecosystems.
NOAA’s jurisdiction for ESA determinations includes anadromous fish, marine
mammals and other marine species.
As a part of statutory obligations under the ESA, the NWFSC established Salmon
Recovery Teams, now known as Recovery Implementation Science Team (RIST) to
provide scientific support about the status and trends of salmon populations, the impact of
activities on those populations and actions that are most likely to lead to recovery of
populations and other matters.
Magnuson Stevens Fishery Conservation and Management Act (MSA)
http://www.nmfs.noaa.gov/sfa/magact/
The first purpose of the MSA is to take immediate action to conserve and manage the
fishery resources found off the coasts of the United States, and the anadromous species
and Continental Shelf fishery resources of the United States. Other purposes establish
Regional Fishery Management Councils to exercise sound judgment in the stewardship of
fishery resources. The NWFSC provides scientific information to the NMFS NW
Regional Office to help the Office and the Council decision-making process.
The central importance of scientific data is outlined in the Act: “The Secretary [of
Commerce] shall make determinations … solely on the basis of the best scientific and
commercial data available to him after conducting a review of the status of the species.”
Marine Mammal Protection Act
http://www.nmfs.noaa.gov/pr/laws/mmpa/
All marine mammals are protected under the MMPA. The MMPA prohibits, with certain
exceptions, the "take" of marine mammals in U.S. waters and by U.S. citizens on the high
seas, and the importation of marine mammals and marine mammal products into the U.S.

59

There are no fewer than 111 references to the use of ”scientific data” for the purposes of
supporting actions allowed under the MMPA. The NWFSC is involved in providing
scientific input to resource managers to protect marine mammals under the MMPA.
NWFSC scientists provide scientific advice to the regional office concerning requests to
“take” protected marine animals, develop scientific recommendations concerning the
status of populations and the need or otherwise for protection under ESA regulations and
develop scientific information about the marine mammals and impacts and threats to their
populations.
Other Legislation
Other legislation that affects the work of the NWFSC is defined in Appendix A.
Judicial Requirements
Judicial decisions and orders also affect the work of the Center. While it is unusual for
the work of the Center to be directly impacted by the judicial process we are indirectly
affected by decisions or orders that apply to the resource management and regulatory
offices of the NMFS. For example, the management of Threatened and Endangered
species of salmon in the Columbia River has been a matter of legal action and the
Judiciary has directed the NMFS NWRO to take certain actions which in turn can affect
the Center’s need to provide information, scientific analysis or testimony.
National Administration Priorities
Presidential Priorities
National Ocean Policy Taskforce (and by reference USCOP and Pew Commission).
http://www.whitehouse.gov/administration/eop/ceq/initiatives/oceans
On June 12, 2009, President Obama sent a memorandum to the heads of executive
departments and federal agencies establishing an Interagency Ocean Policy Task Force,
led by the White House Council on Environmental Quality. The Task Force is charged
with developing a recommendation for a national policy that ensures protection,
maintenance, and restoration of our nation’s oceans, coasts and the Great Lakes. It will
also recommend a framework for improved stewardship, and effective coastal and marine
spatial planning. The recommendations are expected have implications for the work
conducted at the NWFSC. Final recommendations are due on Dec. 9, 2009. Note: When
released, relevant recommendations will be added here.

Ocean Research Priorities Plan: Charting the Course for Ocean Science in the United
States: Research Priorities for the Next Decade
The Ocean Research Priorities Plan and Implementation Strategy (ORPP) (released Sept
2006) provides high level guidance on how the various ocean science sectors

60

(government, academia, industry, and non-government entities) can and should be
engaged, individually or through partnerships, to address the areas of greatest research
need and opportunity. It identifies national ocean research priorities for the next ten
years to ensure that the management, use, and protection of our ocean ecosystem is based
on the strongest available science to promote health and sustainability. The document
was developed with extensive input from the constituents and interest groups concerned
about the ocean and identifies research priorities about the interactions between society
and the ocean. This document is under review pending the results of the new
administration’s Ocean Policy Taskforce.
The four near-term research priorities articulated in the ORPP are:
1) Response of Coastal Ecosystems to Persistent Forcing and Extreme Events to
provide better forecasts of coastal response to a variety of natural events and
human influenced processes, such as hurricanes and non-point source pollution.
2) Comparative Analysis of Marine Ecosystem Organization to understand the
complex dynamics of marine ecosystems and use that understanding to improve
management of these critical areas and their resources.
3) Sensors for Marine Ecosystems to develop the tools needed to collect key, but
elusive, scientific information on various biological and chemical processes
necessary to better understand marine ecosystems.
4) Enhance ongoing efforts to observe, understand, and predict changes in ocean
circulation in the Atlantic Ocean, the “Meridional Overturning Variability” a key
driver of climate variability and change.
In addition, the six societal themes defined in the ORPP are as follows:
•
•
•
•
•
•

Stewardship of Natural and Cultural Ocean Resources
Increasing Resilience to Natural Hazards
Enabling Marine Operations
The Ocean’s Role in Climate
Improving Ecosystem Health
Enhancing Human Health

Department of Commerce Priorities
http://www.osec.doc.gov/bmi/budget/Strategic07-12.htm
The historic mission of the Department of Commerce (DOC) is "to foster, promote, and
develop the foreign and domestic commerce" of the United States. This has evolved, as a
result of legislative and administrative additions, to a broad mandate to advance
economic growth and jobs and opportunities for the American people. It has cross
cutting responsibilities in the areas of trade, technology, entrepreneurship, economic
development, environmental stewardship and statistical research and analysis. NOAA
and NMFS activities, and the work conducted by the NWFSC, must strive to contribute
to this broad mission.

61

Within the DOC’s 2007-2012 Strategic Plan, Strategic Goal 3, Promote Environmental
Stewardship, applies to NOAA. Four objectives are cited under this goal, the first two of
which are most applicable to the NWFSC:
Objective 3.1 - Protect, restore, and manage the use of coastal and ocean
resources
Objective 3.2 - Advance understanding of climate variability and change
Objective 3.3 - Provide accurate and timely weather and water information
Objective 3.4 - Support safe, efficient, and environmentally sound commercial
navigation

NOAA Priorities
NOAA Annual Guidance Memorandum.
http://www.ppi.noaa.gov/PPI_Capabilities/agm.html
Every year the NOAA Administrator issues an Annual Guidance Memorandum (AGM).
The Memorandum is a vehicle for the Administrator of NOAA to set organizational
priorities across all NOAA Line offices. The 2009 AGM includes guidance that relates
to the mission of the NWFSC and has the potential to guide the direction of our work.
Strategic Priorities for FY12-16 are below, with the first three most applicable to
NWFSC:
•
•
•
•
•

Enhance NOAA's climate services and support the establishment of a National
Climate Service
Support Comprehensive Marine Spatial Planning
Ensure the Sustainability of Marine Fisheries
Strengthen Arctic Science and Service
Sustain Satellite-based Earth Observations

NOAA Next Generation Strategic Plan
http://www.ppi.noaa.gov/ngsp.html
The NOAA Next Generation Strategic Plan, covering 2010-2025, is in preparation.
Delivery is expected in early 2010. A summary of results from the sustainable fisheries,
species, and habitat breakout group in the National Stakeholder Forum included the
following goals:
1) Science is a priority: enhanced data collection, monitoring and at-sea observing
2) Improved outreach, education and customer service with general public, stakeholders and
partners
3) Increase amount of protected/restored areas
4) Statutory requirements are met to recover overfished stocks and end overfishing
5) Ecosystem-based assessments are used as a foundation for management

NMFS Priorities
NMFS Strategic Plan
http://www.nmfs.noaa.gov/mb/strategic/

62

The NMFS Strategic Plan 2005-2010 outlines the steps necessary toward achieving
effective and efficient ecosystem-based conservation and management of living marine
resources in collaboration with our NOAA, Federal, tribal, state and local partners. It
maps NMFS programs to three of NOAA’s goals: 1) Protect, restore, and management
the use of coastal and ocean resources through an ecosystem approach to management, 2)
Understand climate variability and change to enhance society’s ability to plan and
respond, and 3) Provide critical support for NOAA’s mission. It will be revised in 2010
in light of NOAA’s Next Generation Strategic Plan.
NMFS Strategic Science Plan
http://www.st.nmfs.noaa.gov/
The NMFS Strategic Plan for Fisheries Research provides national level goals for NMFS
science and research along with associated objectives. The plan also includes priorities
of each of the NMFS regional science centers, in an effort to recognize regional priorities.
The six national-level priorities are listed below:
1) Provide scientifically sound information and data sufficient to support
ecosystem-based fishery conservation and management.
2) Through conservation engineering research contribute to efforts to reduce
bycatch and adverse effects on essential Fish Habitat, promote efficient harvest
of target species, and improve the data from fishery surveys.
3) Through economic and ecological research on marine communities and
ecosystems, provide scientific data and information to increase long-term
economic and social benefits to the nation from living marine resources.
4) Provide scientific information and assessments to guide the development of a
sustainable and environmentally sound marine aquaculture, including research on
environmental impacts, and technologies to improve marine aquaculture
operations.
5) Improve the Fishery Information System
6) Improve the effectiveness of external partnerships with fishers, managers,
scientists, conservationists, and other interested groups.

International Priorities
PICES
http://www.pices.int/
The North Pacific Marine Science Organization (PICES) is an intergovernmental
scientific organization, established in 1992 to promote and coordinate marine research in
the northern North Pacific and adjacent seas. Its present members are Canada, Japan,
People's Republic of China, Republic of Korea, the Russian Federation, and the United
States of America. The NWFSC participates as a representative of the United States and
contributes relevant data and scientific findings leading to management advice.
Pacific Salmon Treaty
http://www.psc.org/
On June 30, 1999, the United States and Canada signed a new Pacific Salmon
Agreement. The agreement concluded 7 years of negotiations and established new fishing
regimes under the 1985 Pacific Salmon Treaty to protect and rebuild salmon stocks. The

63

long-term agreement secures a management and harvest-sharing framework for the next
decade. Science conducted by the NWFSC provides technical and scientific basis for
allocation decisions made by each country under this treaty.

Regional Priorities
West Coast Governors’ Agreement on Ocean Health.
http://westcoastoceans.gov/
The agreement is intended to increase regional collaboration to protect and manage the
ocean and coastal resources along the entire West Coast, as called for in the
recommendations of the U.S. Commission on Ocean Policy and the Pew Oceans
Commission. The collaboration has created Action Coordination Teams for Climate
Change, Integrated Ecosystem Assessment Marine Debris, Ocean Awareness and
Literacy, Polluted Runoff, renewable Ocean Energy, Seafloor Mapping, Sediment
Management, Spartina Eradication and Sustainable Coastal Communities. The
NWFSC’s Science and Research Director is a “Federal Lead” for the Department of
Commerce, is helping to provide support to this collaborative effort, along with the EPA
and the Department of Interior and is a member of the Washington Coast Governor’s
Agreement Executive Committee. Individual NWFSC staff are also involved in some of
the Action Coordination Teams.
Pacific Fisheries Management Council (See MSA above)
http://www.pcouncil.org/
Western States Water Council
http://www.westgov.org/wswc/
Driver for Regional Collaboration

Puget Sound Partnership
http://www.psp.wa.gov/aboutthepartnership.php
The Puget Sound Partnership is a Washington State agency with responsibility to create
an Action Agenda that will lead to the recovery of the Puget Sound Ecosystem by 2020.
The NWFSC participates in the Partnership by loaning staff, completing projects that
help to inform management decisions and helping to support the ad-hoc Puget Sound
Federal Caucus. The Center also provides input to the Puget Sound Partnership’s
advisory Science Panel that creates and maintains a Biennial Science Work Plan and a
State of the Sound report. The Partnership is also responsible for implementing Salmon
Recovery plans for Puget Sound Chinook Salmon.

64

Other Drivers – Unanticipated Needs
Strategy evaluation, planning and subsequent work activity can also be driven by short or
long -term events that cannot be predicted in advance.
No legislation or judicial activity can fully anticipate all needs, events or circumstances.
There is some discretion within legislative and administrative arrangements for the
NWFSC to help support some scientific work needed for important emerging issues,
concerns or emergencies.
An example of an emerging issue is the recently released NOAA strategic document “A
Vision for Climate Services in NOAA”. The thrust of this vision is that climate impacts
all of what we do, affecting the environment we live in and our safety and wellbeing.
Because NOAA’s mission is to “understand and predict changes in Earth’s environment
and conserve and manage coastal and marine resources to meet our nation’s economic,
social and environmental needs,” the document notes that “NOAA has the scientific
underpinnings, infrastructure, and delivery mechanisms required to develop coordinated
and integrated agency-wide ‘end to end’ climate services strategy.
If NOAA establishes a Climate Service Office, it is likely that the Center’s work with
NOAA and our partners would change with an increasing emphasis on studying the
impact of climate change on the management and protection of our trust obligations.
Examples of unplanned work needed to respond to emergencies include urgent requests
to provide support following oil spills, hurricanes and flood events.
Regardless of the source of change to mission the Center needs to endeavor to anticipate
these challenges and be flexible and ready to respond accordingly.

65

APPENDIX D: STRATEGIC SCIENCE AND RESEARCH PLANNING CHARTER

Northwest Fisheries Science Center
Strategic Science and Research Planning Charter
Version 1.3 (2008-11-18)

1.0 Background
At year end 2007 the NWFSC Research Planning Team9 (RPT), with valuable input and
suggestions from many staff, developed a Strategic Science and Research Plan for the Center.
The Strategic Science and Research Plan can be found at the following website:
https://inside.nwfsc.noaa.gov/insiderinfo/omi/research_planning_team.cfm.
The plan identified several key needs at the Center:
i.
ii.
iii.
iv.
v.
vi.

Efficient oversight and coordination of scientific themes and near-term priorities
No “meeting overload”
Increased transparency in budgeting
Efficient review and revision of plan elements
Ensuring that innovative science is supported
Promoting high quality science and creative problem solving

In January 2008 Dr. Michelle McClure and other RPT members presented recommendations for
implementation of the Research Plan to the Center Directorate: Drs Usha Varanasi, Bob
Iwamoto, and John Stein. After reviewing the recommendations, the Directorate arranged for a
briefing of the Center Management Team (CMT) and the CMT began a work group to plan an
implementation retreat.

2.0 Retreat Goal
The Center Directorate provided a Retreat Goal:
The near term goal is to fully integrate near term priorities within the Center's
research programs, including budgeting and administrative functions, by the
beginning of FY 2009.
9

Tim Beechie (EC), Barry Berejikian (REUT), Ric Brodeur (FE), Owen Hamel (FRAM), Jeff Hard (CB), Chris Jordan
(CB), Todd Lee (FRAM), Phil Levin (FRAM), Michelle McClure (OMI), Dawn Noren (CB), Nat Scholz (EC), Penny
Swanson (REUT), and John Williams (FE). 9
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2.1 Retreat
The Center hired an organizational facilitator, Tamie Kellogg, to help plan and facilitate an
implementation retreat and develop a retreat methodology (below).
On March 21, 2008 a group of 40 NWFSC staff, including Division Directors, Deputies and
Coordinators, Program Leaders, members of the Research Planning Team and OMI/SD staff met
for a one-day retreat, facilitated by Ms. Kellogg, to develop a model mechanism and agree on
other arrangements for implementing the Strategic Research Plan.
Retreat Methodology
Participants developed and agreed on a list of goals and functions that the eventual
model/s for implementation of the Plan should address:
a. Oversight and scientific coordination of themes
b. Implementation, oversight and execution of near-term priority projects (NTPs)
c. Review and renewal of plan elements, particularly science themes and NTPs
Within each of those areas the following elements should be considered:
1. Provision of resources (staff, funding, facilities, etc.)
2. Prioritization of projects/efforts
3. Effective coordination of effort within the Center (note: this includes duplication
of effort)
4. Reporting to Headquarters EAOP, PPBES/other accounting systems
5. Accountability: Internal milestones for individuals and the organization
6. Input to annual research planning retreats
7. Education and outreach
8. Human resources development
9. Information management, knowledge management and data management
10. Promote quality science and creative problem solving

2.2 Retreat Outcomes
The retreat participants (see Appendix A) agreed to use the Retreat Methodology (above) to
develop practical mechanisms: to provide resources, to prioritize projects, to efficiently report or
respond to Headquarters, and to manage other logistical issues.
Retreat outcomes included:
1) Development of a NWFSC Strategic Science and Research Plan Operational Model (below).
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At the retreat a generic model was developed similar to that above. The generic model was then
developed further after consideration of NOAA’s Executive Decision Process10 and through
discussion with the Center Executive and Division Directors.
2) A Strategic Research Plan Transition Team.
During and after the retreat volunteers were invited from across the Center to participate and
help as needed in the Retreat Transition Team. Membership includes Bob Iwamoto, John Stein,
Michelle McClure, Paul Aebersold, Penny Swanson, Tim Beechie, Mike Ford and Stewart
Toshach.
The task of the Transition Team is to build off the findings of the retreat and recommendations
of the Research Planning Team to develop procedures and processes to implement the Strategic
Science and Research Plan at the NWFSC.
3) A List of Needed Next Steps and a Preliminary Time-line.

10

NOAA Decision Coordination Office www.dco.noaa.gov

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3.0 NWFSC Strategic Science and Research Planning and Operational
Charters
The following charters describe the role, membership, meeting frequency, reporting and decision
making process for each of the groups in the operational model above.
Senior staff meetings will be convened on a weekly basis or as needed by the NWFSC Science
and Research Director, the NWFSC Deputy Science and Research Director or the Director of
OMI.

3.1 NWFSC Executive Council
Role: The Executive Council will:
Make decisions and provide directions on key NWFSC issues, e.g., policy, resources,
annual operating plan and Strategic Science and Research Plan approval.
Membership:
NWFSC Science and Research Director (Chair)
NWFSC Deputy Science and Research Director
NWFSC Director OMI
Participants:
NWFSC Division Directors
Depending on the topic, and with the permission of the Chair, the Research Council,
External Strategic Research Plan Review Board or other staff may be invited to attend
applicable portions of Executive Council meetings. At times the Council will meet in
executive session.
Meeting Frequency:
The Executive Council will meet monthly or at discretion of Chair.
Reporting: The agenda, related products, and a brief record of decisions and directions
(other than those covered by confidentiality requirements) will be maintained and will be
reviewed by the Executive Council Chair and made available to Center Staff within 7
working days of meetings.
Decision Making Process:

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Decisions will be accomplished by informed consensus. The Chair (NWFSC Science and
Research Director) will strive for consensus on every issue. The Chair maintains 51% of
the vote so the Chair makes the final decision when consensus is not achieved. The
Division Directors advise but do not vote. If consensus is not reached opinions will be
documented.

3.2 NWFSC Executive Panel
Role: The NWFSC Executive Panel will:
1) Provide information and advice to the Executive Council on relevant issues relating to
implementation of the Science and Research Plan, the day-to-day operations and
management of NWFSC programs including cross-program coordination;
2) Coordinate management of the Near Term Priorities including budgetary review and
staffing recommendations;
3) Coordinate management where needed of ongoing theme-based work efforts and
implementation of performance reporting across Divisions related to meeting Strategic
Science and Research Plan objectives; and,
4) Complete Strategic Science and Research Plan evaluation, review and implementation.
5) Review all proposed decisions to hire full time permanent staff for consistency with
the high priority research and near term priorities identified in The Center Research Plan.
In its deliberations the Executive Panel will strive to consider and balance near term
priorities, “must dos”, and long term research goals, as well as advice of the Succession
Team. The Executive Panel makes a recommendation to the Executive Council, which
then makes the final decision. Appendix B - Decision Making Process for Executive
Panel Hiring Evaluations describes the process in detail).
Membership:
NWFSC Deputy Science and Research Director (Chair)
NWFSC Division Directors:
Conservation Biology (CB)
Environmental Conservation (EC)
Fish Ecology (FE)
Fishery Resource Analysis and Modeling (FRAM)
Resource Enhancement and Utilization Technologies (REUT)
Operations Management and Information (OMI), (alternate Chair)
Depending on the topic, and with permission of the Chair, staff may be invited to attend
applicable portions of Executive Panel meetings.

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Meeting Frequency:
The Executive Panel will meet monthly or at the discretion of the Chair.
Reporting:
The agenda, related products, and a brief record of decisions and directions (other than
those covered by confidentiality requirements) will be documented and reviewed by the
Executive Panel Chair and made available to Center Staff within 7 working days of the
meeting.
Decision Making Process:
Decisions will be accomplished by consensus. The Chair will strive for consensus on
every issue. The Chair will maintain 51% of the vote so the Chair will make the final
decision when consensus is not achieved.

3.3 NWFSC Research Council
Role: The NWFSC Research Council will:
1) Develop and maintain a 3-5 year PPBES compliant organization-wide Strategic
Science and Research Plan to ensure that NWFSC research activities are: of the highest
scientific quality, meet long-range societal needs, take advantage of emerging scientific
and technological opportunities, shape a forward-looking research agenda, are consistent
with NOAA goals, and, can be accomplished in an efficient and cost effective manner;
2) Review and make an EAOP compliant annual Research Plan from the Divisions;
3) Make recommendations for new research that is based on a fiscal planning target from
the Executive Council, consistent with the 3-5 year Science and Research Plan and
addresses the NTP’s;
4) Review Succession Team information and advice, and include necessary work or
program elements into Science and Research Plans;
5) Review Education and Outreach Team information and advice and include necessary
work or program elements into Science and Research Plans, and;
6) Provide annual reporting on progress of the Science and Research Plan to the
Executive Council.
Membership

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Membership will be comprised of 13 NWFSC staff. Nominations will be sought via
Center-wide recruitment. The ideal is a mix of research scientists and Division Directors.
One member will represent Center information management. One to two members will
be selected to represent each theme.
One member, appointed by the Director of OMI, will function as a Research Planning
Coordinator. The Research Planning Coordinator will work with the Research Council,
Executive Panel and Executive Council to organize and schedule meetings and to provide
coordination between the Research Council, Executive Council and Executive Panel. The
Coordinator will also collaborate with the Research Council and the Executive Panel to
develop a reporting system that effectively meshes with NOAA/NMFS reporting
obligations to PPBES, EAOP and other systems.
Membership will be up to 3 years. The Executive Panel will select 12 staff to serve on the
Research Council and the Executive Council will have final approval of this selection.
The Chair will be selected by the Executive Council.
The Research Council will determine how to organize to complete its work, using
subcommittees for each Theme as necessary. The Research Council may form short term
work groups to achieve specific tasks. These work groups may include persons who are
not members of the Research Council, but Research Council members must be a part of
all such work groups and will be responsible for work group products.
Meeting Frequency:
The Research Council will meet every three months, or at discretion of the Chair. It is
expected that the Research Council work will require more frequent meetings for annual
plan review or other intensive tasks.
Reporting:
The agenda, related products, and record of decisions and directions (other than those
covered by confidentiality requirements) will be documented by the Coordinator and
reviewed by the Research Council Chair and made available to Center Staff within 7
working days of the meeting.
Strategic Research Plans or drafts, when conveyed to the Executive Council for their
approval, will include an Executive Summary highlighting any issues of particular
concern or interest and summarizing the major significance of the plan to operations.
Decision Making Process:
Decisions will be accomplished by consensus. The Chair will strive for consensus on
every issue. When consensus is not achieved a brief minority and majority report will
be prepared.
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3.4 Succession Team
Role: The NWFSC Succession Team will:
1) Work with OMI and Division staff to identify the future skills and expertise most
likely to be needed for the plan elements; review the likelihood of upcoming retirements
and departures; consider programs to fill gaps caused by departures and new challenges;
identify staff training and development needs related to the plan and develop a training
proposal to meet these needs.
2) Provide information and advice related to succession needs to the Research Council.
The Council will review this information and advice and include necessary work or
program elements into the Center Strategic Science and Research Plan. The Research
Council and the Succession Team will collaborate on an agenda to provide timely
provision of needed information.
Membership:
The Succession Team will be composed of at least three members of the Executive Panel,
and at least three additional members of the Research Council. The Panel will be chaired
by the OMI Division Director. Membership will be determined by the Director of OMI
and the Chair of the Research Council.
Frequency of Meetings:
The Succession Team will meet at least four times annually.
Reporting:
The agenda, related products, and record of decisions and directions (other than those
covered by confidentiality requirements) will be documented, reviewed by the Team
Chair, and made available to Center Staff within 7 working days of the meeting.
Decision Making Process:
Decisions will be accomplished by consensus. The Chair will strive for consensus on
every issue. The Chair maintains 51% of the vote so the Chair makes the final decision
when consensus is not achieved.

3.5 Education & Outreach Team
Role: The NWFSC Education and Outreach Team will:

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1) Work with the Research Council to provide review and advice regarding development
and implementation of the Center’s education and outreach program including:
development of an education and outreach plan component; tracking and evaluation of
Center activities related to education and outreach; critical review and guidance regarding
the scientific content for targeted education and outreach activities (e.g., curricula);
advancement of cooperative efforts (e.g., by helping Center scientists include education
and outreach activities in their grant applications); and, annual submission of at least one
education focused funding proposal (e.g., to NOAA Education Office).
2) Provide information and advice related to Education and Outreach to the Research
Council. The Research Council will review this information and advice and include
necessary work or program elements into the Center Strategic Science and Research Plan.
The Research Council and the Team will collaborate on an agenda to provide timely
provision of needed information.
3) Use information from Strategic Research Planning retreats, the Strategic Science and
Research Plan, contact with staff working on NTP’s, themes and other program elements,
and other relevant sources.
Membership:
The Team will be chaired by the OMI Communications Supervisor. Additional
membership will consist of up to five staff scientists, striving for one from each Division.
Team members shall serve a two year appointment with the potential for renewal for
additional terms.
Members shall have prior experience with education and/or outreach and a particular
interest in advancing the Center’s efforts in these areas. Membership will be determined
by the Director of OMI in consultation with the Executive Panel.
Meeting Frequency:
The Education and Outreach Planning Team will meet at least four times annually.
Reporting:
The agenda, related products, and a brief record of decisions and directions (other than
those covered by confidentiality requirements) will be documented, reviewed by the
Education and Outreach Planning Team, and made available to Center Staff within 7
working days of the meeting.
Decision Making Process:
Decisions will be accomplished by consensus. The Chair will strive for consensus on
every issue. The Chair maintains 51% of the vote so the Chair makes the final
decision when consensus is not achieved.
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3.6 NWFSC External Review Board
Role:
The NWFSC External Review Board will:
1) Complete an independent review of NWFSC Strategic Science and Research Plan for
the NWFSC Science and Research Director. The review will be in writing and completed
before the Plan is submitted to the NWFSC Executive Council11. The Research Council
will provide planning, support and assistance to the External Review Board as necessary.
2) Complete the review in response to the following terms of reference and in writing:
whether the Strategic Science and Research Plan is of the highest scientific quality; will
meet NOAA and NMFS Strategic Plan goals and objectives; will take advantage of
emerging scientific and technological opportunities; will shape a forward-looking
research agenda; is consistent with long-range societal needs; and, can be accomplished
in an efficient and cost effective manner.
Membership:
The Board will consist of at least 4 members. Two members will be scientists external to
the Agency, one member will be from the NMFS NWRO and one member will be from
the NMFS Head Office. The Research Planning Coordinator will serve as an ex-officio
member.
The Board will elect a Chair. The Chair will be the primary contact for communications.
Recommendations for Board membership will be made by the Research Council. Final
approval of members and invitations to them will be made by the NWFSC Director of
Science and Research.
Meeting Frequency:
The Board will be convened on a 3-5 year recurring basis.
Reporting:
The Board will report to the Executive Council.
Decision Making Process:
Decisions will be accomplished by consensus with minority opinions or
recommendations where necessary.

11

The Draft 2007 NWFSC Draft Research Plan was reviewed by the NOAA-NWRO and the NOAAF Head Office
Director of Science Programs and Chief Science Advisor.

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Charter Appendix A: Invited Retreat Participants - March 21, 2008
Usha Varanasi

Exec

SD

John Stein
Bob Iwamoto
Stewart Toshach
Tom Hom
Michelle McClure
Julie Peddy
Diane Stanger
Mary Nolting
Kathleen Jewett
Diane Tierney
Jim Herkelrath
Richard Kang
Alicia Matter
John Ferguson
Doug Dey
Ed Casillas
John Williams
Ric Brodeur
Elizabeth Clarke
John Turrell
Phil Levin
Aimee Keller
Jim Hastie
Owen Hamel
Walt Dickhoff
Cyndy Masada
Penny Swanson

Exec
Exec
Nat Res Spec.
PL
RPT
PL
Budget
Budget
Grants
Admin
Facilities
Data Mgmt
IT
DD
DDD
PL
PL
RPT
DD
DC
PL
PL
PL
RPT
DD
DC
RPT

SD
OMI
OMI
OMI
OMI
OMI
OMI
OMI
OMI
OMI
OMI
OMI
OMI
FE
FE
FE
FE
FE
FRAM
FRAM
FRAM
FRAM
FRAM
FRAM
REUT
REUT/EC
REUT

Barry Berejikian

RPT

REUT

Mark Strom
Mike Ford
Paul Abersold
Mark Plummer
Jeff Hard
Chris Jordan
Tamie Kellogg
Tracy Collier
Peggy Krahn
Vera Trainer
Nat Scholz
Tim Beechie
Casey Ralston
Rick Brown
Helen Brandling-Bennet

PL
DD
DC
PL
RPT
RPT
Facilitator
DD
DDD
PL
RPT
RPT
Info & Ed.
Nat Res Spec.
Budget

REUT
CB
CB
CB
CB
CB
EC
EC
EC
EC
EC
OMI
OMI
OMI

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Charter Appendix B: Decision Making Process for Executive Panel Hiring
Evaluations
The Executive Panel will follow the following process for reviewing proposed hiring
of staff:
•

•
•
•

•

When an FTE becomes available either due to new funding or to attrition, the OMI
Director shall notify each Division Director of the available FTE and any potential
constraints on its use due to the source of funds. The past use of an FTE for a particular
topic or tasks, on its own, will not be considered a constraint. The OMI Director shall
also describe the funding attached to the FTE. As a general rule, the funding associated
with an FTE created from attrition will be the amount of permanent NOAA funding paid
in salary, benefits and overhead in the most recent fiscal year, taking into account any
known future budget changes. Budget constraints may mean that not all positions lost due
to attrition will create an available FTE. Along with this notification, the OMI Director
shall set a date by which any Divisions that are interested in the FTE shall submit
proposals to the OMI Director for use of that FTE. Except for the case of expedited
review (see below), the OMI Director shall strive to allow a reasonable amount of time
for the Divisions to prepare proposals.
The Executive Panel will meet to review proposals. All proposals will be distributed to
the Executive Panel by the OMI Director at least 5 business days prior to the scheduled
meeting. Late submissions will not be reviewed.
Similar to the PMAC, decisions will be accomplished by majority vote, however the
Chair will strive for consensus when possible.
The decision making process must be kept strictly to the formal panel meetings and
members must not discuss upcoming decisions outside of this process. Each proposal
must be reviewed on its own its own merits, and Panel members are not allowed to trade
or sell votes.
Expedited review:
o An expedited review process shall be available for emergency hires and for hires
that are unlikely to be subject to competing proposals. The latter might include,
for example, positions that are funded with very specific mandates, or positions
funded on reimbursable funds.
o In an expedited review, the Division wishing to conduct the expedited hire shall
notify the OMI Director as soon as possible and explain in writing the rationale
for the expedited review. The OMI Director shall review the request, and if he or
she agrees that the request for expedited review is reasonable, shall forward the
request by email to the Executive Panel. The Executive Panel will not meet, but
each panel member has 24 hours to consider the request and to object via an email
to the OMI Director to the expedited review. Failure to respond will be considered
a vote of approval. If a majority of the Executive Panel objects to the expedited
review, the proposed hire must go through the full review process described
above.

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Positions hired on non-NOAA funds
Some Center FTE’s are paid on non-NOAA funds obtained through grant
proposals, contracts, or other similar processes. By their nature, such funds are
highly constrained, and it makes no sense for the Divisions to compete for the
FTE positions hired using non-NOAA funds. However, except when an expedited
review is needed (see above), the Executive Panel shall review hires on
reimbursable funds for consistency with the Research Plan and as a mechanism to
determine if there are existing permanent staff who could fill the proposed
positions. Approval of hiring a FTP will be a rare occurrence.
Temporary/seasonal hires
Executive Panel review is not required for temporary or term positions with
terms < 1 year. Executive panel review is also not required for simple term
extensions. Term renewals that require a new position announcement and job
applications do need to go through Executive Panel review like any other new
hire.
Quorum
At least 80% of the Executive Panel members or their designees must be present
to make a decision

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APPENDIX E: NECESSARY TOOLS FOR IMPLEMENTATION

Implementing these research priorities will require the active development and
improvement of technologies and models, as well as some targeted changes in
infrastructure. We have identified several specific needs in these areas that the Center
will need to develop to make progress on the identified research priorities.
Technologies
Ocean environments and the organisms that inhabit them are notoriously challenging to
observe –the scales are large, the organisms are often fragile, cryptic or unknown, and the
habitat is a demanding and expensive one for humans to occupy for prolonged periods of
time. Technology development that enables us to gain information remotely about
oceanographic or other environmental conditions and about organisms across wide areas
or in inaccessible habitats is clearly a high priority. Other key technologies include those
that allow us to understand the interaction between organisms of interest, their habitats
and humans.
Large-scale Observational Systems and Techniques
Ocean observation systems. Both the U.S. Commission on Ocean Policy
(USCOP 2004) and the recent Ocean Research Priorities Plan (JSOST 2007)
have called for increased effort in observing ocean conditions as a vital
component of the research needed to understand and predict the effects of
changing ocean conditions on marine ecosystems and their resources. This has
led to the establishment of several networks involving agency and academic
scientists that initiate and maintain ocean observing systems. These systems
include ships of opportunity, dedicated research cruises, land and ocean-based
sensors, and remote sensing technologies working in tandem to observe and
measure changing ocean conditions. One such network, PaCOOS (Pacific
Coastal Ocean Observing System), covers much of the California Current; the
northern part of that system is monitored as part of a regional network, NANOOS
(Northwest Association of Networked Ocean Observing Systems) that is
responsible for designing the regional observatory and providing data products.
Continuing work aimed at developing autonomous samplers of the water column
and remote interdisciplinary cabled seabed observatories can increase our ability
to monitor ocean conditions without the need for costly ship time. These will be
particularly useful as data from these observatories are made available in near
real-time through live-access servers for rapid interpretation and assimilation into
ocean models.
Remote sensing (satellites, multi-beam, LIDAR, hyperspectral imagery etc.).
Technology is rapidly expanding in the field of remote sensing of freshwater and
marine habitats. Many satellite sensors offer the potential to synoptically survey

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entire ecosystems but present technology often provides data only for the surface
of the ocean which may not be relevant to bottom-dwelling organisms. LIDAR
from airplanes may penetrate up to 50 m of the water column and provide rapid,
near-synoptic surveys of pelagic fishes and invertebrates that can be related to
oceanographic variables measured from the plane or satellites. Multifrequency
ship acoustics continue to develop and presently play an important role in stock
assessment of pelagic fishes. Seabed habitat characterization and mapping using
side-scan sonars and multibeam sounders play a critical role in establishing MPAs
and other habitats of concern. All of these technologies are beyond the normal
training background of most fisheries biologists and will require collaboration
with specialists in these fields to maximize their utility.
AUVs, ROVs and other remotely controlled observing methods. Autonomous
Underwater Vehicles (AUVs) have the ability to provide comprehensive scientific
information for management of West Coast ecosystems. AUVs, individually or
jointly with vessels using acoustics and other observational tools, are the excellent
tools for comprehensive surveys including in untrawlable habitat. AUVs can be
used to augment vessel coverage of established acoustic surveys and other routine
assessment surveys and improve efficiency. AUVs also will allow closer
observations of target fish to determine their acoustic backscatter and identity and
can provide scouting capabilities during surveys as an adaptive sampling
technique. In situ autonomous drifters or gliders are providing useful information
on water column properties that may affect fish distributions. As vessel and fuel
costs increase, ship time for sea truthing of remote sensors such as satellites,
acoustics, or LIDAR will become more costly. Simultaneous deployment of
several AUVs either from shore or from small vessels can provide a cost effective
method to provide sea truthing. AUVs, when combined with other tools (e.g.,
sidescan and multibeam sonars, CTD, ADCP, ROVs), also provide an important
means of assessing fish habitat and groundtruthing existing habitat maps. As the
importance of structure forming benthic invertebrates becomes clearer, there is an
increasing interest in their protection. However, information on the distribution
and abundance of cold-water corals, sponges and other invertebrates off the West
Coast remains sparse. AUVs will simultaneously provide information on the
occurrence of corals and their associations with commercially important fish.
AUVs will be used as cost effective scouting tools to identify high priority sites
for directed sampling from more expensive platforms such as ships or ROVs.
AUVs also offer additional capabilities for other initiatives that include the
development of non-extractive fish population assessments, use as platforms to
observe interactions between fish and fishing gear and evaluation of systems
designed to reduce bycatch, and as a vehicle for observing and quantifying fish
responses to vessel noise.
Tagging and remote sensing technologies for individual organisms
Technology related to tagging and remote sensing of marine and freshwater organisms
has progressed rapidly over the past several decades as the power of computers has

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increased, electronic components have decreased in size, and the ability to detect signals
remotely has increased. The ability to detect and identify individual animals greatly
enhances our ability to track movement, survival rates and other demographic and
behavioral information, information often needed to make decisions on altering
management strategies for protecting listed stocks. Several technologies for tracking
individuals or groups are undergoing ongoing development.
PIT-tags. Passive integrated transponder (PIT)-tag receivers that can detect
individual fish in fresh and sea water have been recently developed and deployed
in support of individual research projects. Further research is ongoing to increase
the detection range of receivers, which will decrease the number of receivers
needed and increase our ability to detect fish in large areas such as estuaries.
Radio tags. The increased power of batteries of miniature size, along with
decreases in size of electronic parts and chips has led to the miniaturization of
radio tags down to a size that is usable on nearly all sizes of fishes and marine
mammals. Faster ping rates also allow a larger number of uniquely-identifiable
fish to be tagged.
Acoustic tags. New miniaturized batteries have made possible the ability to
develop very small acoustic tags that also provide the capability to follow
individual fish through freshwater and into seawater. Strategically placed
acoustic arrays can also provide 3-D locations of fish allowing the ability to
determine organismal behavior in varying habitats.
Satellite tags. These tags are generally larger than radio tags and require that
animals come to the water’s surface so that data can be downloaded via satellite.
This technology is used on marine mammals, some larger fish and turtles and can
provide a range of data including, ocean temperature profiles, diving profiles, and
geographic locations while the animal is still at sea.
Passive acoustic monitors. Moored passive acoustic monitors that stay in place
for several months can record organismal and ambient sounds. These can
contribute to our understanding of both organismal biology and anthropogenic
impacts on the acoustic environment.
Improved physiological observation techniques. While advanced sensors for
acquiring physical and chemical data are being developed and deployed (ocean
observing systems), development of sensors and systems for biological data on
ecosystems are lagging behind. However, because of rapid advances in
nanotechnology, it is anticipated that hand-held biosensors for near -instantaneous
species identification in the field will be developed within a decade. Biosensors
detecting specific DNA could be used to rapidly differentiate species and stocks
in stock assessment surveys. Such technology could rapidly identify eggs and
larvae of commercially important marine species. Additional applications include
species identification of processed fish samples (forensics), and analysis of the
physiological/health status of animals (stress, growth, disease status,
reproduction). In addition to important fish species, the technology could be

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easily applied to marine microbes, phytoplankton and zooplankton. The Center
should promote and participate in the development of this technology to enhance
stock assessment and, ecosystem science and observation capabilities.
A key need, given the rapid development of these technologies, and their current
deployment on a project-by-project basis is a coordination effort that would distribute
receivers for maximum efficiency across projects.
Determining Population Structure and Patterns of Movement
Genetic techniques. Recent developments in molecular genetics have
revolutionized our ability to detect patterns of population structure resulting from
migration and reproductive isolation. DNA-based technologies based on
evaluating non-coding DNA variation at the sequence level include minisatellites
and microsatellites, randomly amplified polymorphic DNAs (RAPDs), and
variable number of tandem repeats (VNTRs); these methods have proven
indispensable in characterizing evolutionary processes of migration and genetic
drift. In particular, patterns of DNA microsatellite variation that reflect variable
numbers of tandem repeats in base sequence are proving extremely useful in
detecting these processes, identifying breeding aggregations and patterns of
dispersal and gene flow on short time scales. Tools such as single nucleotide
polymorphisms (SNPs) provide direct sequence information with fewer
ambiguities, and they can detect very small differences between putative groups.
Rapid developments in gene mapping, in identifying quantitative trait loci (QTL)
associated with phenotypes of interest, in integrating quantitative and molecular
genetics, and in the detection and measurement of gene expression are making
possible the ability to improve our understanding of the link between genotype
and phenotype—the “holy grail” of evolutionary genetics. Future efforts to
develop and improve these techniques should also focus on coordinating efforts
and samples and standardizing protocols at independent genetic laboratories to
facilitate scientific exchange and to uncover broad evolutionary patterns.
Novel Uses of Population Movement Information – Seafood Safety and Fish
Health. There is a growing concern among consumers about what species they
are purchasing. Instrumentation used for species identification of fish sampled in
the marketplace could easily be modified to detect toxic chemicals and biotoxins.
Thus, this technology could improve seafood safety and boost consumer
confidence in the nation’s seafood supply.
Isotopes and parasites. Other promising techniques are also being explored and
merit additional support, particularly evaluation of ratios of stable isotopes in hard
parts that deposit calcified tissue incrementally with age, such as fish otoliths, and
identification of parasites and measurement of parasite load and diversity. Both
of these techniques can yield information regarding locations individuals resided
in or passed through, and thus patterns of movement over time

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Monitoring of fishing catch, bycatch and discard
It is crucial to document and quantify total fisheries removals, including landed catch and
discards. Fishery-dependent sampling provides a measure of the directed and bycatch
removals, and, in limited circumstances, an additional measure of the trend in stock
abundance. Until recently, at-sea discard had not been systematically monitored outside
of the at-sea processing hake fleet and isolated research projects. The West Coast
Groundfish Observer Program (WCGOP) was established in 2001 to improve estimates
of total catch and discard in West Coast fisheries. The program deploys over 40
observers and collects at-sea data from limited-entry trawl and fixed gear fleets as well as
from open access, nearshore, prawn, and shrimp fleets. West Coast groundfish landings
have long been documented by state fishery agencies, however this data is generally not
available in what is considered a timely fashion. An integrated electronic recording
system for fishticket and logbook information for the Pacific coast would vastly improve
the ability to track groundfish catches inseason and to produce real-time estimates of
landings and discards. An electronic fishticket system is needed to provide real-time
landings data. Logbooks are used with fishtickets and WCGOP data to reconcile the total
catch by area and determine bycatch rates in association with target species. Logbook
data availability can lag by as much as a year, which delays input data to bycatch models
and the total catch reconciliation process. Electronic logbooks, like electronic fishtickets,
would increase the accuracy and timeliness of critical data needed for good management
decision-making.
Geographically or spatially linked analysis and interpretation
Marine and freshwater research efforts increasingly rely on large geospatial data sets to
address issues such as individual and population-level movement patterns, climate
change effects on stream flows, ocean circulation patterns, and patterns of current and
future land use. Maintaining up-to-date GIS capabilities, including software, databases
and support staff, will be a critical element of conducting the landscape (and oceanscape)
scale analyses that inform our multiple goals.
Socio-economic surveys
Socio-economic surveys are the primary means of collecting information and data used to
describe the interactions between humans and living marine resources. Several different
types of data collection efforts need to be developed or enhanced to better understand
these relationships. The surveys should cover a broad range of socio-economic fields,
answer important policy questions, and use state-of-the-art methods. The fields of study
include economics, anthropology and sociology. Each of these disciplines provides
useful information for sound management decisions. Even though the fields are related,
the questions and approaches used by each field are different; and, thus, their data
requirements are not completely overlapping. Socio-economic surveys should support
the analysis of two general themes of policy questions: commercial and recreational
fisheries, and in situ conservation and ecosystem management. Commercial and

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recreational fisheries data should address issues such as community profiles, community
impacts, fleets costs and earns, impacts on participants, alternative management regimes
(e.g., closed areas, changes in seasons, rebuilding plans, and limited access privileges),
effects of environmental change (e.g., climate change, coastal dead zones, and harmful
algal blooms), and seafood safety. In situ conservation and ecosystem management data
should address issues such as the value of ESA listed species, the market and non-market
value of ecosystem goods and services, the interaction of human activities and ecosystem
characteristics, and management strategy evaluation. The Center should use state-of-theart data collection methods that are appropriate for the issues being addressed. These
include electronic data collection to increase timeliness and accuracy, methods to obtain
high response rates (e.g., contacting respondents through personal communication inperson or over the telephone), work closely with constituents, and use local knowledge.
The data required to support economic behavioral models is more complex and detailed.
To serve these needs data should be collected through time and space, and include more
frequent observations.
Bioinformatics
Genomics technologies. Significant advances in our understanding of ecosystem
structure and function can emerge from the rapid development of genetic
technologies. For example, development of genomic libraries to advance
understanding of food web dynamics and other ecosystem processes, as well as
species abundance and distribution, is now possible. Among the valuable tools in
this category are in situ sensors for rapid detection of pathogens, harmful algae,
and toxins, and methods to integrate biosensor data with other ocean observations.
Genomic tools and supporting bioinformatics infrastructure can now be designed
to elucidate effects of multiple environmental stressors on marine organisms.
Efforts should focus on developing, enhancing, and applying new methods and
tools at laboratories and other facilities with specialized instrumentation (e.g., for
large-scale gene expression analysis) and computational resources in genomics,
proteomics, and bioinformatics to expand surveying and screening capabilities for
assessment of impacts to ecosystems from biotoxins, pathogens, and other
sources. Work to integrate genomic, in situ biological, chemical, and bio-optical
field observations, remote sensing, and numerical models into diagnostic tools for
regional to global investigations is also a high priority. These efforts can be
linked with developing coastal and offshore observatory efforts to maximize
stakeholder participation, input, and use of the advances. In addition to using
molecular techniques for identification of species/stock structure, similar
approaches can be used to assess gene or protein expression patterns in marine
animals to assess ecosystem function. Stress genes have been identified and
related to such functions as adaptation to temperature extremes, hypoxia, lack of
food, and chemical toxins among other environmental stressors. Gene expression
may also indicate relative states of growth and reproduction. Individuals from
populations can be analyzed to indicate which stressors may be acting to affect
population growth and juvenile recruitment.

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Global assessment of gene expression is more advantageous than studies surveying
a few genes, because many physiological processes including impacts of toxins
typically involve a cascade of gene interactions rather than a change in a few or in
single genes. If a sufficiently diverse set of genes is monitored, toxicant and mode of
action-specific responses can be identified and used as a molecular fingerprint for
environmental monitoring. However, there has been minimal application of these
techniques to marine shellfish and finfish, which are more suitable for environmental
monitoring and ecotoxicological testing. This is due to the limited knowledge of the
genome of most fish and shellfish. The recent development of high-density fish
DNA microarrays has allowed exploration of this technology for bioassessment of
contaminants. Research should be directed toward, expanding development of DNA
arrays, laboratory assessments, and validation for field monitoring.
Develop capabilities for biological computational analyses (bioinformatics). The
advances in biotechnology mentioned above also present distinct challenges. As a
result of the rapidly changing scientific environment, regulatory agencies must
quickly develop the capability to adopt these new methodologies and evaluate the
quality of data generated both within the Agency and by the scientific community
at large. The significance of specific changes and performance characteristics of
new methods, as well as their strengths and limitations, must be fully understood
to avoid misinterpretation of data that could lead to inappropriate conclusions. As
these applications and their uses expand, there is an ever-increasing need for
computational analyses and subsequently computational power, along with data
and database storage, sharing, and retrieval. Biological computational analyses,
generically called bioinformatics, include storage, comparisons and
characterizations of DNA and protein (amino acid) sequence data, and analysis of
microarray expression data. Although different research groups throughout the
Agency approach research topics through a variety of directions and disciplines,
research data analyses often intersect at the level of bioinformatics. Therefore,
there is a need to have these resources and tools available to NOAA scientists.
Development of shared computational tools for biological applications
(bioinformatics), requires hardware, software and personnel with specific
expertise. While there is no single central repository or server of bioinformatics
applications (software applications, data and database storage and retrieval), many
tools are available through web-based servers hosted by university research
groups or government agencies. While this resource is extremely powerful, the
growing server loads are resulting in increasing times for the analyses to be
carried out. Development of a centralized bioinformatics core facility is more
cost-effective and efficient. Presently the Center has hardware and software for
the bioinformatics core facility. Personnel with specific expertise in
bioinformatics are needed.

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Models and the Data to Support Them
We emphasize model development in this section because modeling provides a
framework in which to describe a system in detail or in general, to evaluate the effects of
alternative actions, and to characterize the sensitivity of a system to perturbations – all of
which are key for effective management. However, it is critical that these models are
supplemented by experiments, directed observational studies and other research efforts to
develop the data to parameterize and evaluate the models. These experiments and studies
are implicitly included in the discussion of needed models.
Integrating social and biological sciences
Economic participation and valuation models. Economic valuation models are
needed for both use and non-use values. Examples of use values include
recreational fishing, whale watching, recreational enjoyment of the ocean or
associated ecosystems, and viewing a pristine environment. These models rely on
revealed or stated preference data. It will be important to be able to map changes
in resource characteristics or availability to changes in valuation estimates. This
will provide a link between the state of the resource, changes in participant
values, and the effect of management actions. These models should also include
participation estimates, and be able to forecast changes in participation associated
with changes in resource characteristics or availability. Changes in participation
should then be linked to regional input-output models to forecast changes in
economic activity. The valuation of human health or health risks is another type
of use value. These values could be positive (e.g., the positive heath effects of
seafood consumption) or negative (e.g., the effect of mercury consumption
through seafood). Non-use values include resource and ecosystem existence
value. Examples include the value of protecting ESA listed species and habitat
protection. These models rely on stated preference data. Similar to use value
models, these models should provide a link between changes the level of the good
being valued and changes in the level of the non-use value.
Socio-economic models linking habitat distribution, abundance and quality with
human activities. Humans interact with the environment in a dynamic process.
Humans not only affect the distribution, abundance and quality of habitat, but are
also affected by these same habitat characteristics. These relationships are not
well understood and much progress could be made in increasing our
understanding of them. Behavioral models that forecast changes in human actions
associated with changes in habit need to be developed. These types of models
require either a long time-series of data that capture observed changes in human
behavior, or stated preference data. The most fruitful avenue of research is likely
the construction of a model that combines both types of data. These models also
require observational habitat data that quantifies the state or changes in habitat
variables such as distribution, abundance and quality. In addition, it is necessary
to model the link between changes in habitat and changes in variables that drive
human action (e.g., species distribution and abundance). It is also necessary to

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develop a model that relates changes in human action to changes in habitat.
Completing this type of integrated model will require the collaborative work of
social scientists, ecologists, biologists and stock assessors.
Risk assessment models
There are two critical problems facing the state-of-the art for quantitative risk
assessments. First is data limitation. Capturing biological complexity means building
models with many parameters, but most biologists feel very uncomfortable building a
model that relies on parameters for which they have no direct data for the species in
question. Collection of more data is often not feasible, and statistical approaches to risk
assessments are needed. These approaches rely on estimation of relationships between
environmental drivers and population responses without building intricate models. In
addition, we need much more research to understand both the implications of ignoring
biological detail and how to incorporate the biological detail we know. Currently the
only option to incorporate more biological information is to use a more complex model,
which usually entails additional—often untested—assumptions. How to incorporate
additional biological information to improve a simple model is largely unknown.
Additionally, much more work needs to be conducted on methods for incorporating
uncertainty into risk assessments, specifying uncertainty, and making decisions under
uncertainty.
Population dynamic models
Population dynamic models can be quite sophisticated, but substantial improvement in
their utility can be achieved by developing ways of including information on spatial
dynamics, the role of size and age composition in population demographics, and
demographic and environmental stochasticity. At the ecosystem level, research should
facilitate application of quantitative frameworks to data sets to synthesize dynamics
across ecosystems and to conduct investigations with theory, design, observations, and
experiments to interpret the ecosystem and socioeconomic impacts of alternative
strategies. Ecosystem approaches emphasize interactions among components and the
impacts that various human activities have on productivity and organization. Forecasting
these impacts requires understanding complex dynamics controlling: 1) productivity of
populations within various trophic levels, 2) predator-prey interactions, 3) connectedness
of sub-populations, 4) impacts of natural climate variation and change, and 5)
anthropogenic pressures. Because the dynamics of marine ecosystems are complex, a
variety of approaches are warranted. First, viability and extinction risk models that
incorporate assessment of abundance, productivity, genetic and phenotypic diversity, and
spatial structure are useful in identifying limits to viability at the population and species
levels. Application of various classes of energy-budget and dynamic models at the
ecosystem level can improve understanding of the impacts of human activities on
ecosystem structure and function by contrasting biomass changes according to trophic
level. Another valuable approach is to compare systems where managed areas have been
enacted to conserve species, habitats and ecosystems. Such comparisons should include

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before and after area designation contrasts where sufficient data are available, and inside
versus outside comparisons for established managed ecosystems.
Evolutionary models
The importance of evolutionary processes in population dynamics is still widely
underappreciated, particularly for exploited species or key components of disturbed
ecosystems. Evolutionary approaches to this problem should link multivariate genetic
models of life history variation to analyses of population dynamics and viability.
Promising models include linking genetic covariance structures for traits under natural or
artificial selection (e.g., through sexual selection on breeding grounds or through sizeselective fishing) to size- and age-structured population dynamic structures such as
projection matrices, and exploring the consequences of selection on size or age for 1)
evolutionary change in life history, 2) pre-harvest abundance, 3) breeding abundance and
4) sustainable yield. When they directly incorporate genetic information, such approaches
can provide a useful glimpse into how adaptation will affect future abundance and
productivity. Analyses like these can support management strategy evaluation by
identifying alternative management strategies that maintain yield without compromising
viability.
Models to support ecosystem approach to management
Models are mathematical or conceptual caricatures of reality, and as such are tools that
allow us to project the future state of an ecosystem or guide further inquires. Attempts to
develop tools to support ecosystem approaches to management have generally fallen into
three categories: 1) models aimed at prioritizing sites for conservation, 2) statistical
models that estimate population dynamics within the context of species interactions or
changes in climate-driven demographic rates, and 3) food web simulations.
Site Prioritization Models. Site prioritization models are used for siting marine
protected areas based on algorithms that attempt to maximize biodiversity targets.
Such models operate by finding efficient solutions to the problem of selecting a
system of spatially cohesive sites that meet a suite of conservation goals (e.g.
biodiversity). While these models have proven useful in selecting sites for
conservation action, they are based only on a data ‘snapshot.’ As a result, they
cannot take ecological interactions or dynamics into account, and therefore do not
attempt to predict future ecosystem states under different management regimes.
Statistical Models. Statistical models have traditionally been used to estimate
trends in population size of single species can be augmented with predator or prey
abundance or environmental correlates. Examples include stock assessments that
are improved by inclusion of climate indices or including predator and prey
abundance as predictors of the abundance of single target species. Statistical
models have also been extended to estimate the abundance of a few target species.
However, the complexity of such models is severely limited by the need to
estimate many parameters from limited, noisy data.

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Food web simulations. Food web simulations are theoretical models that are
more complex than statistical models, and do not involve estimation of parameters
such as abundances or rates of growth or reproduction. Instead, parameters are
estimated outside the model and then used as model input. The added complexity
of the models allows increased realism, but this comes at the cost of increasing
the uncertainty of predictions. Among these models, Ecopath with Ecosim (EwE)
is especially notable. EwE considers changes in food consumption and predation
that might accompany changes in food web structure and how those changes alter
the productivity of harvested stocks. Other simulation models include nutrientphytoplankton-zooplankton models of the whole food web and biogeochemical
system models. In the past, typical implementations of any of these modeling
frameworks involved simplifications such as aggregating species at lower trophic
levels, a lack of spatial resolution, and crude representations of oceanography,
nutrients, and fleet dynamics. Nonetheless, these models are useful for generating
hypotheses about past and future impacts of altered fishing and predation rates,
and for screening potential management policies.
Models Treating Habitats and Landscapes
Landscape process models, particularly at a range of scales. Effective recovery
planning for ESA-listed anadromous species requires that we understand how
habitat restoration actions will affect population viability and sustainability.
However, there are few models available to simulate how natural processes form
and sustain riverine habitats, or how watershed or stream restoration actions will
alter processes and habitats at reach scales. Development of such models is a
critical component of cost-effective habitat restoration for anadromous species.
Integration of habitat into assessment models. Integration of data on the quantity,
quality and spatial distribution of habitat can improve the predictive powers of
assessment models and guide fishery management. The necessary data are
difficult to obtain because of practical limitations of observation, controlled
experimentation and replication in natural systems. Before habitat can be
integrated into assessment models, relationships between the distribution, quantity
and quality of habitats and demographic rates will have to be investigated.
Investing in observations, process studies, and advanced modeling will expand
current understanding of impacts at appropriate temporal and spatial scales, and
help identify crucial data and process-understanding gaps. The Pacific Coast
Groundfish FMP has recently been amended to describe Essential Fish Habitat
(EFH) for the managed groundfish stocks as well as all waters and substrates
within areas with a depth less than or equal to 3,500 m as well as seamounts in
depths greater than 3,500 m. In addition to EFH, Habitat Areas of Particular
Concern (HAPC) are identified along the coast based on the importance of the
ecological function provided by the habitat, the extent to which the habitat is
sensitive to human-induced environmental degradation, whether and to what
extent development activities are or will be stressing the habitat type, and the
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rarity of the habitat type. More detailed mapping and linking of habitats to the
species that use them is needed before the relative importance of different benthic
habitats can be determined. Of particular importance in the future will be the
determination of the distribution and abundance of biogenic species and their role
and importance to the groundfish ecosystem, as well as the integration of ocean
habitat conditions into salmon assessment models.
Essential Fish Habitat (EFH) designation and delineation models. The
Magnuson-Stevens Fishery Conservation and Management Act requires that
regional management councils describe EFH in their fishery management plans,
that Councils minimize impacts on this essential habitat from fishing activities,
and that Councils and other federal agencies consult with the National Marine
Fisheries Service about activities that might harm EFH. The Magnuson Act
defines “essential fish habitat” as “those waters and substrate necessary to fish for
spawning, breeding, feeding, or growth to maturity.”
Presently, the definition of EFH in the Coastal Pelagic Species, Highly Migratory
Species, and Salmon Fisheries Management Plans is quite broad. For instance,
the definition of essential fish habitat for Coastal Pelagic Species is based on the
temperature range where they are found, and on the geographic area where they
occur at any life stage, and takes into account where these species have been
found in the past, and where they may be found in the future. Thus, the EFH for
the Coastal Pelagic Species Fisheries Management Plan includes all marine and
estuary waters above the 10o thermocline, from the coast to the limits of the
Exclusive Economic Zone. Similarly, freshwater EFH for the salmon
management plan includes all the lakes, streams, ponds, rivers, wetlands, and
other bodies of water that have been historically accessible to salmon. To identify
EFH for groundfish, NMFS used a GIS-based assessment model that looked at the
occurrence of groundfish in relation to depth, latitude, and substrate type. Despite
the complexity of the model, a lack of data resulted in EFH including all waters
from the high tide line to 3,500 m in depth. Simple assessments that produce
broad EFH designations may have heuristic appeal, but do not aid, and may
actually hinder, the work that needs to occur. We need to develop tools and
datasets that allow us to understand what habitats fish use, the demographic rates
associated with these habitats, and the factors that make some habitats more
valuable than others. While initially such approaches may be rough, they
acknowledge that successful management of fisheries resources depends not only
on protecting sites where animals occur, but also on protecting the ecological
processes that allow populations to persist or expand.
Integrated modeling approaches
Integrated modeling approaches overcome many of the limitations described above and
achieve the crucial goal of integrating physical, chemical, ecological, and fisheries
dynamics in a three-dimensional, spatially explicit domain. In these models, ecosystem
dynamics are represented by spatially-explicit sub-models that simulate hydrographic

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processes (light- and temperature-driven fluxes of water and nutrients), biogeochemical
factors driving primary production, and food web relations among functional groups.
These models represent key exploited species at the level of detail necessary to evaluate
direct effects of fishing, and they also represent other anthropogenic and climate impacts
on the ecosystem as a whole.
These sorts of models are intended as a strategic management tool that allows one to
identify tradeoffs between species, fleets, and management goals, and to identify effects
of management policies. They are ideal tools for management strategy evaluation
(MSE), in which management scenarios are tested against simulations that represent a
real ecosystem and its complexities. In this framework, these models are useful in that
they reproduce qualitative behavior of the system, and exhibit a range of dynamic
responses similar to that observed in the ecosystem. The ecosystem model can thus serve
as a filter to identify which policies and methods are promising and which appear flawed.

Infrastructure
Data management
The Center has important and critical data management needs and responsibilities. We
must effectively manage the enormous amount of information necessary to efficiently
generate science guidance products such as ESA status reviews, MSFCMA stock
assessments and IEAs. We must also have the capacity to archive, compile and interrelate numerous independent data types running into the millions of records. If we also
consider the data management challenges inherent in applying GIS-based analysis tools,
Center staff routinely manipulate terabytes of data – ignoring the institutional
requirements that such activities present today will certainly handicap the Center
tomorrow. Fortunately the Center has invested in enterprise-level data management and
IT tools and the staff to design and implement them. These investments have paid off
with a number of important data management products developed for the region;
however, a much stronger parallel effort needs to be applied to the mid-level or subenterprise data management needs of Center staff. Desktop computer based data
management products must be available for staff as: bridges towards enterprise level
products as individual databases scale up; designs or scoping templates for future
enterprise level efforts; or, simply for data management needs that will not ever be at the
enterprise level. While the software to generate desktop scale databases is readily
available to staff, the expertise to use these products in a manner consistent with standard
database design theory and practice is not in the typical skill-set of Center research staff.
Therefore, the Center should support access to the power of relational databases through
a multi-level program of designing both desktop and enterprise level data management
tools. Currently staff engage with the Center data management group for the design of
enterprise databases and contract externally for smaller, individual scale databases – we
can be more efficient at Center-wide data management if the Center Data Management

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and IT teams could support a multiple-scale approach to the development and
implementation of data management tools.
In addition to large-scale systematic enhancements to our approach to data management,
there are a number of items that could be acted on in the short-term that would make
significant contributions to staff. To raise the awareness and level of sophistication that
Center staff have of designing and implementing effective data management systems the
Center could establish formal data management design working groups for both spatial
and tabular data users. There is a large body of expertise and experience within the
Center with respect to the use and management of spatial and tabular data – formalizing
the sharing of this knowledge and developing an infrastructure for the dissemination of
knowledge and training will be very beneficial to all. Large volumes of data are regularly
shared or transferred in and out of the Center; having an effective method, such as an
FTP-site, to perform these tasks safely and efficiently would be very useful to staff.
Millions of dollars have been spent on data collection at the Center and most of this data
is in an electronic format. A standardized protocol for data security needs to be
developed and supported to protect our huge investment in electronic data. Finally, the
entire Center staff needs to be involved in a discussion of how to identify and support
Data Stewards for research and corporate data that we agree to maintain; the Center needs
to develop a Data Management Strategy that meets the needs of multiple scales of data
management within the Center, outlines a consistent and scaleable approach to
maintaining these databases, and is compatible with our ongoing and projected needs for
data sharing at the Center and with our collaborators and constituents.
Laboratory Facilities
A number of laboratory facilities were identified as being important to achieving these
goals. Many of these facilities do exist, at least in part. However, mechanisms to provide
access to the facilities and to provide adequate technical support for those facilities are
greatly needed.
Diet and Tissue Analysis Laboratories and Support Personnel. Details of the life
history and other characteristics of marine species are difficult to observe in their
natural habitats. Recent advances in the use of new methods and technologies to
investigate the physiology, foraging ecology, susceptibility to lethal contaminants,
and other life history details of marine species are providing new and important
information. The ability to fully utilize these powerful methods would be greatly
improved by a dedicated diet and tissues analysis laboratory and support. This
laboratory should allow identification of species or processing of tissues in a
variety of ways:
• Morphological examination of digested prey parts;
• Genetic identification;
• Chemical analysis of tissues for contaminants, stable isotopes and other
techniques that can inform diet analysis, demographic studies, nutritional
status and studies aimed at human health, as well as other novel uses of
chemicals as indicators;

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•

Otolith analysis, both morphological and chemical.

Many components of this laboratory are already present at one or more of the
NWFSC’s facilities. However, making them more readily accessible to Center
scientists is important.
Wet Labs. The Center’s laboratory facilities were the focus of an external panel
review in July of 2005 that highlighted the need for freshwater and marine flowthrough systems. Establishing this capacity (possibly at Mukilteo) remains a
critical need for experiments relying on fish culture.
Fish culture facilities: The ability of Center scientists to address several issues in
fish biology and conservation would be enhanced by improved access to fish
culture facilities that can support fresh- and salt-water rearing. Scientific
questions that can be addressed using fish culture techniques includes many in in
reproductive biology, behavior, inheritance and evolution of phenotypes, and
nutrition. As key projects are identified, support for facilities providing an
adequate supply of high-quality water, rearing containers (tanks, raceways, and
ponds), food storage, and sampling and diagnostic facilities will be important.
Field sampling support
Large-scale, interdisciplinary ocean research requires the use of large, sophisticated
research vessels capable of extended cruises in rough sea conditions. The broad nature of
oceanographic sampling requires many sensors of atmospheric and ocean conditions and
the ability to deploy and retrieve many gear types. Although chartered commercial
fishing vessels can still be used for trawl surveys which require little sampling besides
trawling and a minimum of scientific crew, many oceanographic programs require
deployment of physical and biological sensors and multiple gears sampling everything
from plankton to large nekton. Large survey vessels capable of extended diel operations
and containing sufficient laboratory space to process samples at sea are critical to this
work.
Estuarine and riverine sampling do not pose the logistic limitations in ship size as ocean
sampling, but these other habitats also face shortages of sampling platforms. Small boats
can be towed on trailers to various sites but often have conflicts in scheduling and may
need to be modified depending on the needs of various investigators. Having a small
fleet of such vessels that can be quickly modified and deployed to various systems will
allow greater flexibility in sampling many smaller systems.
Gear storage
Over the past several years, broadening research needs along with increased staffing have
required acquisition of a variety of new gear types, including ATVs and well-drilling
equipment for freshwater research, small boats, nets, and trailers for nearshore research,
and plankton gear, trawls and camera sleds for marine research. Space for maintenance

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and storage is required to protect substantial monetary investments in this equipment, but
space at the NWFSC is at a premium. Particularly acute needs include garage storage
space for small boats, well drilling equipment, ATVs, and trailers, and covered spaces for
net drying and storage. Storage and maintenance spaces for a variety of small gear types,
including tagging and sensor equipment and dive gear, are also needed.

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