Number range CHAPTER

**U.S. DEPARTMENT OF COMMERCE**

![](media/image1.wmf){width="1.5in"
height="1.5048611111111112in"}**National Oceanic and Atmospheric
Administration**

![](media/image2.wmf){width="1.5in" height="1.5in"}

**NATIONAL MARINE FISHERIES SERVICE**

**STRATEGIC PLAN FOR FISHERIES RESEARCH**

**December 2001**

**CONTENTS**

Preface 4

Legislative Background 8

Comprehensive Fishery Research Program 10

Research Components

I.  Research to support fishery conservation and management 11

    I.A. Biological research concerning stock abundance 12

    I.B. Social and economic factors affecting abundance levels 13

    I.C. Interdependence of fisheries or stocks of fish 13

    I.D. Identifying, restoring, and mapping of essential fish habitat
    (EFH) 16

    I.E. Impact of anthropogenic factors and environmental changes on

    fish populations 18 12

II. Conservation engineering research 21

III. Research on the fisheries 23

######  III.A. Social and economic research 23 

######  III.B. Seafood safety research 26 

######  III.C. Marine aquaculture 27 

###### IV. Information management research 28 

###### Major Fishery Research Goals and Objectives 29 

###### APPENDIX A. NMFS Scientific Enterprise 34 

###### Goals of the Scientific Enterprise 35 

###### NMFS Fisheries Science Centers 37

######  Alaska Fisheries Science Center (AFSC) 37 

Northwest Fisheries Science Center (NWFSC) 47

Southwest Fisheries Science Center (SWFSC) 55

Southeast Fisheries Science Center (SEFSC) 66

Northeast Fisheries Science Center (NEFSC) 73

APPENDIX B. Response to Comments on Public Draft of the NMFS Strategic
Plan for Fisheries Research 83

APPENDIX C. Abbreviations and Acronyms 86

APPENDIX D. Glossary 89

Literature Cited 95

**NATIONAL MARINE FISHERIES SERVICE**

**MISSION STATEMENT**

***Stewardship of living marine***

***resources for the benefit of the***

***Nation through their science-based***

***conservation and management and***

***promotion of the health of their***

***environment.***

**PREFACE**

The National Marine Fisheries Service (NMFS) is the agency responsible
for the science-based conservation and management of the Nation\'s
living marine resources and their environment. NMFS is part of the
National Oceanic and Atmospheric Administration (NOAA) within the
Department of Commerce. The agency's long-term commitment to scientific
excellence via internal and external peer-reviewed scientific journals
has materially advanced marine science and policy for over 125 years.

Since 1871, Federal fisheries scientists have collected, researched,
analyzed, and published peer-reviewed data on the Nation's living marine
resources, marine ecosystems, and the benefits that they provide.
Recently, NMFS has instituted a science quality assurance program to
consistently monitor and review NMFS research efforts to ensure that
they are of the highest quality. Further, this program identifies gaps
in infrastructure, facilities, and resources that are affecting the
productivity of NMFS scientists. Under this scrutiny, important agency
findings are published in many highly respected journals.

NMFS has established the position of Scientific Editor as well as the
Scientific Publications Office (SPO) to ensure the editorial and
scientific integrity of its research products. These and other regional
NMFS publication materials serve as the basis for agency scientific
reports, regulatory documents, and technical presentations to fishery
managers, industry and environmental groups, the information community
(media), and to the public and scientific community. Thus, the agency's
comprehensive scientific research and publishing efforts provide the
foundation for developing sound policies that govern the use,
protection, restoration, and conservation of living marine resources,
marine habitats, and other aquatic environments.

This document builds upon elements of previous significant planning
initiatives from both NMFS and NOAA:

• *NOAA Strategic Plan: A vision for 2005*

First released in 1993, this agency-wide Strategic Plan broadly covers
all the major programs and missions underneath NOAA and how they
contribute to the goal of bringing scientific information to bear on key
societal decisions. This Plan has evolved over time in response to
emerging issues and developing programs. The executive summary of the
latest edition of this Plan is available through the NOAA Web site at
[www.strategic.noaa.gov/](http://www.strategic.noaa.gov/).

• *Results of the Review of the NOAA Science Enterprise by the NOAA
Chief Scientist*

Released in 1995, this comprehensive review examined the quality of NOAA
research with respect to its methodological approaches, the relevancy
and adequacy of its science activities, and the strength and value of
partnerships between NOAA's programs and outside groups.

• *NOAA Fisheries Strategic Plan*

In 1997, NMFS published this Plan after extraordinary public
involvement, including 12 public meetings. This Plan describes specific
NMFS objectives and performance measures to fulfill all aspects of its
stewardship mission through a rational, scientific approach. This Plan
continues to serve as an outline to guide the agency and is available
through the NMFS Web site at
[www.nmfs.noaa.gov/om2/contents.html](http://www.nmfs.noaa.gov/om2/contents.html).

• *NMFS Strategic Plan for Fisheries Research (1998)*

Released in 1998 as a requirement of the Sustainable Fisheries Act of
1996, this original Plan was purposely framed to be consistent with
previous planning initiatives, yet with a more detailed focus on NMFS
research activities. In particular, the Plan functions as a subset of
the *NOAA Fisheries Strategic Plan*. Many of the objectives found under
the "Major Fishery Research Goals and Objectives" section of this Plan
(and this update) generally can be matched with strategies in the *NOAA
Fisheries Strategic Plan*. The 1998 NMFS Strategic Plan for Fisheries
Research is available for download at the NMFS Web site at
[[www.nmfs.noaa.gov/sfa/stratpln.pdf]{.underline}](http://www.nmfs.noaa.gov/sfa/stratpln.pdf).

• *NOAA Fisheries Data Acquisition Plan*

Released in September of 1998, this document represents a 5-year
strategy for meeting NMFS' rapidly growing at-sea data requirements. The
Plan provides an overview of the existing data acquisition program,
describes anticipated growth and changes to data requirements in the
future, details options available, and presents a suite of
recommendations for meeting these challenges, including the construction
of a fleet of modern Fisheries Research Vessels. Recommendations from
the Plan have become the basis for budget decisions relative to the
acquisition of at-sea data. This Plan is available from the NMFS Web
site at <http://www.st.nmfs.gov/st2/omb_link.html.>

In addition to the above internal planning documents, this Plan supports
and incorporates the following external reviews by the National Research
Council (NRC):

• *Improving Fish Stock Assessments*

Published in 1998, this report commissioned by NMFS reviews the agency's
current stock assessment methods and models and makes recommendations
for alternative approaches. The objective of the review was to produce
an authoritative report that documented the strengths and limitations of
stock assessment methods relative to the diversity of available data and
types of fisheries management systems. The report can be read online or
purchased at the National Academy Press Web site at
[www.nap.edu/](http://www.nap.edu/).

• *Sustaining Marine Fisheries*

Published in 1999, this NRC commissioned report explores the nature of
marine ecosystems and the complex interacting factors that shape their
productivity. The book documents the condition of marine fisheries in
1999, highlighting species and geographic areas that were under
particular stress. Challenges to achieving sustainability are discussed,
and shortcomings of existing fisheries management and regulation are
examined. The report calls for fisheries management to adopt a broader
ecosystem perspective that encompasses all relevant environmental and
human influences. It can be read online or purchased at the National
Academy Press Web site at [www.nap.edu/](http://www.nap.edu/).

• *Improving the Collection, Management, and Use of Marine Fisheries
Data*

Published in 2000, this NRC commissioned report assesses methods for
improving data for stock assessments and fisheries management. The
summer flounder fishery was used as a case study in this report because
it supported a fishery that spanned state and Federal waters over a vast
geographic area, both recreational and commercial fishermen targeted the
species, and there was an abundance of data available for assessments.
The report analyzed summer flounder stock assessments and the implicit
and explicit modeling assumptions that affected modeling outcomes. The
study also examined data collection and use and made 40 recommendations
to Federal and state fishery agencies, Congress, regional councils,
interstate commissions, and commercial and recreational fishermen with
the objective of improving fisheries data and management. This report
can be read online or purchased at the National Academy Press Web site
at [www.nap.edu/](http://www.nap.edu/).

• *Marine Protected Areas: Tools for sustaining ocean ecosystems*

Published in 2001, this NOAA commissioned report evaluates marine
protected areas (MPAs) as a tool to supplement conventional fishery
management. The report recommended networks of MPAs, some for fishery
management, embedded within broadly zoned management areas in the
coastal ocean. Additionally, the study indicated that the basic
knowledge gained through monitoring and evaluation of MPAs on the
structure, function, and variability in marine ecosystems would enhance
the design of reserves and allow more accurate evaluations of their
ecological and socio-economic consequences. Reserves would also allow
more accurate estimation of parameters such as natural mortality
rates---an essential variable in stock assessment models. This report
can be read online or purchased at the National Academy Press Web site
at [www.nap.edu/](http://www.nap.edu/).

The scope of the present document includes fisheries, habitat, and
protected species research that solely addresses requirements of the
Magnuson-Stevens Fishery Conservation and Management Act (MSFCMA). It
does not include the regulatory and enforcement components of the NMFS
mission. NMFS conducts a comprehensive program of fisheries research and
peer-reviewed publishing to make information available to industry,
environmental groups, resource managers, and others who are dependent on
fisheries science. This Plan, which updates the original *Strategic Plan
for Fisheries Research* released in 1998, covers what we do now and how
we expect to improve.

The research plans of NMFS are developed in constant communication with
our partners and constituents. NMFS research programs are periodically
reviewed by informal and formal program reviews. NMFS scientists serve
on Fishery Management Council Scientific Steering Committees where
research inadequacies are identified and then addressed through NMFS
programs. Regulatory and judicial proceedings also identify information
needs that are then incorporated in the research program. U.S. and
international scientists work together to identify means to fill
information gaps needed to manage both U.S. and high-seas fisheries of
interest to the American public and industries. In all respects, this
Plan is the ultimate integration of the broad fisheries research needs
of American society and its legislative, executive, and judicial
institutions.

**LEGISLATIVE BACKGROUND**

The United States Congress reauthorized the Magnuson-Stevens Fishery
Conservation and Management Act (MSFCMA), as amended by the Sustainable
Fisheries Act (SFA), on October 11, 1996. Section 404 (Fisheries
Research) of the MSFCMA requires the Secretary of Commerce to develop
and publish in the *Federal Register* a strategic plan for fisheries
research for the five (5) years immediately following such publication.
The Act stipulates that the plan:

• Identify and describe a comprehensive program with a limited number of
priority objectives for research in each of the research areas specified
below.

• Indicate goals and timetables for the program.

• Provide a role for commercial fishers in such research, including
involvement in field testing.

• Provide for collection and dissemination, in a timely manner, of
complete and accurate information concerning fishing activities, catch,
effort, stock assessments, and other research conducted under this
section.

• Be developed in cooperation with the fishery management councils and
affected states, and provide for coordination with the councils,
affected states, and other research entities.

The MSFCMA requires that the comprehensive program contain the following
areas of research:

• Research to support fishery conservation and management, including but
not limited to:

biological research concerning the abundance, trends, and life history
of stocks of fish,

the interdependence of fisheries or stocks of fish and their ecosystem,

the identification of essential fish habitat,

the impact of pollution on fish populations,

the impact of wetland and estuarine degradation, and

other factors affecting the abundance and availability of fish.

• Conservation engineering research, including:

the study of fish behavior,

the development and testing of new gear technology and fishing
techniques to minimize bycatch and any adverse effects on essential fish
habitat, and

the promotion of efficient harvest of target species.

• Research on the fisheries, including:

the social, cultural, and economic relationships among fishing vessel
owners, crew, fish processors, associated shoreside labor, seafood
markets, and fishing communities.

• Information management research, including:

the development of a fishery information base and an information
management system under Section 401 that will permit the full use of
information in the support of effective fishery conservation and
management

**[COMPREHENSIVE FISHERY RESEARCH PROGRAM]{.smallcaps}**

**Research Components**

The Magnuson-Stevens Fishery Conservation and Management Act (MSFCMA)
mandates strong action to conserve and manage fishery resources that
contribute to the food supply, economy, and health of the Nation. MSFCMA
provisions require NMFS to end overfishing, rebuild all overfished
stocks, and conserve essential fish habitat through research and
consultations on Federal and state actions which may adversely affect
such habitat. These are among our primary stewardship responsibilities.

NMFS is responsible for ensuring that management decisions are based on
the highest quality scientific information on the biological, social,
and economic status of the fisheries. Biologically, this includes
species\' responses to environmental changes, exploitation, and other
human activities that affect them and their habitat. This information
includes social, cultural, and economic behaviors and incentives that
influence human/marine interactions. All of the agency's information
must be comprehensive, objective, credible, and effectively
communicated. It is used not just for current management decisions, but
also to conserve resources and anticipate future trends, assure future
utilization opportunities, and assess the success or failure of the
agency's management efforts.

NMFS is also responsible for ensuring that this information, and thus
the management decisions for which it provides the foundation, is
understood and its validity accepted by user groups and other
constituents. To accomplish this, the MSFCMA has mandated that we
provide a role for commercial fishers in our fisheries research.

The research priorities of NMFS may be grouped into the four major areas
with several sub-areas defined by Congress (see **Legislative
Background**):

**I. Research to support fishery conservation and management**

**II. Conservation engineering research**

**III. Research on the fisheries**

**IV. Information management research**

**I. Research to support fishery conservation and management**

Living marine resources (LMRs) currently support extensive commercial,
recreational, and subsistence uses. In 2000, commercial landings by U.S.
fishers were 9.1 billion pounds valued at \$3.5 billion. The 2000 U.S.
marine recreational fish catch was an estimated 429 million fish taken
on an estimated 76.0 million fishing trips (NMFS, 2001). These represent
just some of the many benefits Americans derive from living marine
resources.

However, many marine species are under stress from overexploitation or
habitat degradation, or both. Over one-third of all fish stocks for
which we have scientific population information are overutilized, and
nearly half are below optimal population levels. Some populations are in
danger of extinction, and many more are threatened by various human
activities. There are many other species about which we have little
information. Many factors, both natural and human-related, affect the
status of fish stocks and their environment.

NMFS scientists are actively engaged in collaborative research to
protect and enhance fishery resources. These research efforts include
mapping, spatial analyses, geographic information systems (GISs), and
fishery and ocean habitat modeling and characterization, as well as an
evaluation of ecosystem approaches focusing on spatially-explicit models
and further research into trophic relationships. Additionally, with the
increasing need to seek new management approaches to enhance and
conserve essential fish habitat (EFH), NMFS is conducting studies on
adaptive/management techniques through the identification and use of
potential areas of refugia (i.e., using areas closed to fishing
activities for both recovery and research) and experiments on no-take
and limited take zones and time-area closures. NMFS is also exploring
the research potential of MPAs to facilitate important experiments in
marine ecology and to support recommendations made by the NRC (NRC,
2001). Further, NMFS is evaluating the potential negative/positive
impact of fishing gear on habitat and fisheries production.

NMFS' research efforts incorporate the use of innovative new
technologies and techniques. For example, NMFS in cooperation with NOAA,
is working to enhance survey capabilities through research and
development of an omnidirectional hydroacoustic system. This new system
will combine biomass assessments with the ability to acoustically
identify species, utilizing airborne LIDAR (Light Detection And Ranging)
laser technology as a biomass assessment tool for near-surface pelagic
species, and using underwater (laserline) technology for identification
of habitat types and species identification. Additionally, NMFS employs
manned submersibles and remotely-operated vehicles to directly evaluate
deepwater species and their habitat.

It is NMFS\' responsibility to provide fishery managers with the
information needed to make scientifically sound decisions. In order to
support fishery conservation and management, NMFS scientists are
actively pursuing the following areas of research.

**I.A. Biological research concerning the abundance and life history
parameters of fish stocks**

Activities in this area include collecting catch and effort data,
biological sampling, and developing bio-statistical analyses for a
variety of Fishery Management Plan (FMP) and non-FMP species of
exploited fish and invertebrates. Fishery-dependent and fishery
independent (i.e., resource survey) sources provide age and size
samples, catch composition, and indices of relative abundance. These
data are key inputs to stock assessments, fishery management
regulations, and the production of status reports for living marine
resources and their fisheries.

The complexity of any assessment is determined by the amount of
available data (i.e., tiers of data completeness) and by the type of
information required for scientific advice to fishery managers. Stock
assessments can be roughly grouped in order of increasing levels of
modeling effort and sophistication, each one incorporating the
underlying data requirements of all preceding levels.

**Assessment Levels:**

• **Index Only:** a time series of relative index of stock abundance
calculated as raw or standardized catch-per-unit-of-effort (CPUE) in
commercial, recreational, or survey vessel data; or a one-time
estimation of absolute abundance derived from tagging results, a
depletion study, or some form of calibrated survey.

• **Simple Life History Equilibrium Models:** typically applied to life
history information; for example, yield-per-recruit or
spawner-per-recruit functions based on mortality, growth, and maturity
schedules; catch curve analysis; survival analysis; or length-based
cohort analysis.

• **Aggregated Production Models:** data input for equilibrium and
non-equilibrium production models aggregated both spatially and over age
and size classes; these include the classic Schaefer model and the
Pella-Tomlinson model.

• **Size/Age/ Stage Structured Models:** techniques that include cohort
analysis, virtual population analysis, age-structured production
analysis, CAGEAN, stock synthesis, size or age-structured Bayesian
models, modified DeLury methods, and size or age-based mark-recapture
models.

• **Ecosystem Models:** assessments incorporating ecosystem
considerations with spatial and seasonal analyses. Ecosystem components
include one or more of the following: (1) one or more time-varying
parameters, either estimated as constrained series, or driven by
environmental variables; (2) multiple target species as state variables
in the model; or (3) living ecosystem components other than target
species included as model variables.

The biology and life history of species has taken on greater
significance in the managing the Nation's living marine resources.
Describing and understanding migration and distribution patterns,
habitat use, age, growth, mortality, age structure, sex ratios,
reproductive biology, and responses to environmental variability are key
to developing harvest strategies that produce high yields at low risk to
the long-term sustainability of the resource base. A variety of
scientific methods are employed, including aging using otoliths,
histological analyses of gonads, food studies, and observations of
spawning behavior. Studies of early life history and fishery
oceanography are necessary to understand recruitment dynamics, with the
aim of predicting incoming year-class strength. There is an increasing
need to identify and characterize discrete stocks. This will enable
scientists to correctly structure stock assessments and design
stock-specific management measures.

**I.B.** **Social and economic factors affecting abundance levels**

NMFS also recognizes the social, cultural, and economic diversity of the
fisheries, and the importance of recognizing those differences in
creating effective conservation measures. For instance, one critical
factor affecting stock abundance is the level of fishing effort. Type
and location of both commercial and recreational fishing effort vary
across different fishing fleets, groups of anglers, and communities.
Also, these groups will differ in their responses to alternative
strategies of effort control such as days-at-sea, closed areas, limited
access, and bag-limits. NMFS will need new data and models, and
modifications to existing models, to capture fully this diversity and
its interaction with biological diversity.

NMFS will therefore develop bio-socio-economic models and increase the
collection of data necessary to meet conservation goals and maximize net
economic and social benefits to the Nation from living marine resources.
For commercial fishing, these data include: vessel and plant level cost
and earnings data; ex-vessel prices; and data on social and
institutional constraints such as open access regimes or differing
ethnicity-based labor practices. For recreational and subsistence
fishing, these data include: information on expenditures, trip
characteristics, demographic descriptors, and social and cultural
influences on fishing behavior. Given that some of these data are newly
emphasized, national coordination and funding of these activities will
be especially important.

Coordinated bio-socio-economic research and analysis will add the
element of human behavior to stock variability, thus bringing the
parameters of our models closer to real world conditions. This, in turn,
will improve the predictive power of stock assessments and incorporate
fishers' incentives into the precautionary approach.

I.C. Interdependence of fisheries or stocks of fish

Living and non-living parts of an ecosystem are linked to each other
through physical and biological relationships---for example by food
chains or shared habitat use. This information is very important if we
are to successfully manage our living marine resources in a holistic
manner. The health of a fish stock and the merits of alternative harvest
strategies cannot be determined in isolation; an ecosystem-based
approach is needed to take into account the various factors that affect
the status of a stock and the importance of a stock to other components
of the ecosystem, as recommended in a report to Congress (EPAP, 1999).
The abundance, productivity, and spatial distribution of a fish stock
depends on a number of factors, including environmental conditions,
habitat quantity and quality, the abundance and health of its
competitors, predators, and prey, as well as its symbiotic
relationships.

The objective of the biological studies on ecosystem interdependence is
to understand the functional relationships among ecosystem components.
To do so requires that we determine consumption rates and the functional
form of feeding interrelationships of fish as well as the spatial and
temporal variability in abundance and habitat use. We will develop
recruitment and multi-species models that incorporate food web and
environmental information. The models can be used to help predict
long-term impacts of various harvest strategies and environmental trends
on yield potential and species composition as well as to investigate
effects of predation and compensatory population mechanisms on long-term
stability, production, and structure of fish communities under different
harvest strategies and environmental regimes. Research activities
include the following:

• Marine food web research through field and laboratory studies of fish
consumption rates, feeding selectivity patterns, food preference, and
nutritional values of various foods.

• Density-dependent and predator-prey dynamics.

• Fisheries oceanography research to determine how varying environmental
conditions create variability in biological components of the ecosystem.

• Food-web-based dynamic mathematical models are used to examine how
abundance of fish stocks, marine mammals, and other ecosystem components
react to changes in environmental conditions and alternative fishery
management measures.

To examine human activities in an ecosystem perspective, research is
required on the behavior of consumptive (e.g., commercial and
recreational fishers) and non-consumptive (e.g., whale watchers and
non-harvest divers) users of the resource. Some fishers target a single
species or species assemblage exclusively. Others fish for a variety of
different species by season (an annual round), sometimes switching
fishing gears to do so. Yet other fishers are part-time participants
only, working in land-based occupations for some portion of the year.
Other users of the ecosystem who, for example, swim with sharks or view
coral reef communities benefit from a rich and diverse habitat. Still
others who never see the resource value knowing that it exists.

Different fishing behaviors, based on use of different gear types and
vessel sizes among commercial or recreational fishers, appear more
likely to interact with the ecosystem differently and can negatively
impact the net benefits the ecosystem generates for a non-consumptive
user group. These different behaviors and the relative values attributed
to the ecosystem by different user groups imply different levels and
types of fishing effort applied to a resource stock and have differing
effects on their various target species, and are therefore important to
ecosystem management. For example, the development of a wetland for
industrial or residential purposes may impact water quality and thus
require that a water treatment plant be constructed to replace the
natural filtering action of a wetland, so that an offshore coral reef is
preserved. Some critical research areas include:

• The suite of fishing and non-fishing activities available to
commercial and recreational fishers for which they are qualified.

• The geographic range within which various consumptive and
non-consumptive user groups operate.

• The identification of all user groups, including but not limited to
consumptive and non-consumptive as well as those that value the
existence of the resource.

• Determination of the existence value of fishery resources in the
ecosystem by habitat type.

• Determination of the non-market value of fishery resources in the
ecosystem by habitat type for recreational and other non-consumptive
user groups.

• Determination of the market value of fishery resources in the
ecosystem by habitat type for commercial and other consumptive user
groups.

• Determination of the market incentives that determine behavior by
consumptive and non-consumptive user groups.

• Development of models that incorporate ecosystem relationships into
bio-economic models.

• Identification of the demographic, sociological, and anthropological
characteristics of different user groups who value fishery resources and
how do they differ between groups.

• The effect of point and non-point specific sources of pollution on the
ecosystem to determine trade-offs in costs and benefits of improving
ecosystems; e.g., hypoxia in the Gulf of Mexico.

• Establishment of safe minimum standards for fishery and other
resources in the ecosystems.

• Identification of the role of coastal settlements on ecosystems and
stocks of fish.

• Identification of the role of ecosystems and stocks of fish on
communities.

• Determination of the interactions and links between user groups and
fish stocks.

• Establishment of a national bio-socio-economic panel of experts to
advise NOAA and NMFS on ecosystems, habitat, fish stocks and their
interdependence with all affected user groups.

• The amount and value of subsistence, recreational, and part-time
fishing.

**I.D. Identifying, restoring, and mapping of essential fish habitat**
**(EFH)**

The long-term viability of living marine resources depends on
conservation and protection of their habitat. The effects of habitat
degradation are often insidious, and some losses are not well
understood. Others, however, are apparent. We know, for example, that
dams for hydroelectric power generation and water diversion for
agriculture have severely reduced some valuable anadromous fish runs,
and chemical contaminants cause neoplasm and reproductive dysfunction in
fish (e.g., winter flounder in Boston Harbor and English sole in Puget
Sound). We also know that habitat changes in Florida Bay and Chesapeake
Bay have resulted in continual changes in fish communities, and that
environmental variability, such as El Niño, changes the latitudinal
distribution, abundance, and recruitment dynamics of several species on
the west coast. It has become apparent that many changes to the habitat
are not only the result of natural processes, but also the direct result
of human interactions with the environment.

The Sustainable Fisheries Act of 1996 requires fishery management
councils (FMCs) to describe and identify EFH in FMPs, to minimize to the
extent practicable adverse effects of fishing activities on such
habitat, and to identify other actions to encourage the conservation and
enhancement of such habitat. It also requires that the Secretary of
Commerce initiate and maintain related research. MSFMCA defines EFH as
"those waters and substrate necessary to fish for spawning, breeding,
feeding, or growth to maturity. For the purpose of interpreting the
definition of EFH: \'waters\' include aquatic areas and their associated
physical, chemical, and biological properties that are used by fish, and
may include aquatic areas historically used by fish where appropriate;
\'substrate\' includes sediment, hard bottom, structures underlying the
waters, and associated biological communities; \'necessary\' means the
habitat required to support a sustainable fishery and the managed
species' contribution to a healthy ecosystem; and \'spawning, breeding,
feeding, or growth to maturity\' covers a species\' full life cycle.\"
(Federal Register, 2002).

NMFS will continue to conduct research, analyze data, and provide
consultation necessary to: (1) identify estuarine, coastal, and oceanic
habitats and their utilization by various life stages of living marine
resources for spawning, growth, and production, through comparative
studies of similar habitats in stressed and unstressed environs as well
as comparative studies of different habitats; (2) document the life
history of managed fish and determine factors that influence resiliency
or sensitivity to fishing; (3) increase NMFS' understanding of the role
of the benthic community in the overall ecosystem, the interaction of
target fish with benthic communities, and effects of fishing on benthic
communities; (4) determine the best methods for restoring LMRs injured
by human impacts including harmful spills, vessel groundings, material
disposal, and fishing; (5) develop population and habitat recovery
models; (6) describe seasonal changes in the character of the water
column and seabed, mega-invertebrates, and benthic infaunal communities
in estuaries and nearshore waters; (7) map EFH using remote sensing
platforms (satellite, aerial, and acoustic) along with ground truth and
algorithm development to assess habitat type and quality and
environmental parameters such as temperature, turbidity and salinity;
and (8) work cooperatively with fishers to gain information on existing
fishery habitats. The information resulting from these activities will
be used by fishery managers to identify, describe, conserve, and enhance
EFH.

The NMFS Centers' staff work closely with Regional Offices, FMCs, NOS
research facilities, the NOAA Damage Assessment and Restoration Program,
and other Federal and state agencies to provide timely habitat
information. NMFS works with the NOAA line offices and other agencies in
developing the Coastal Change Analysis Program and Coastwatch to apply
satellite imagery and aerial photography to habitat mapping, analysis of
change in coastal land cover, and assessment of water temperature,
color, and circulation.

These research areas and the specific EFH research described for each
Fishery Science Center will be used by NMFS and the FMCs to:

• Develop a comprehensive and coordinated base-funded habitat research
program in NMFS that interacts with and provides information to habitat
managers, the FMCs, and the Offices of Science and Technology,
Sustainable Fisheries, Habitat Conservation, and Protected Resources.

• Improve understanding of the distribution and habitat requirements of
early life stages of managed species and their prey species.

• Improve stock assessment capabilities and reduce uncertainty.

• Improve habitat conservation, protection, and enhancement capabilities
and improve assessment of threats to EFH and managed fishery stocks.

• Evaluate and predict how environment and climate signals change the
distribution and amount of EFH for important stocks.

• Synthesize research information needs nationally and prioritize
habitat research and funding across regions to refine EFH
identification, assess and minimize adverse effects of fishing
activities, and identify actions to encourage the conservation and
enhancement of such habitats as required by the MSFCMA.

• Develop a national database on habitat restoration measures and
designs that enhance recovery of biodiversity and value to fisheries.

• Map EFH for managed species in each region, and develop a national GIS
database on essential habitat.

• Provide GIS identification and mapping of habitat subject to adverse
impacts from fishing gear.

• Restore degraded habitat using restoration options that have a
scientific base.

• Cooperate with fishers in gathering information on habitat.

• Research current incentives for habitat protection, including
literature reviews of incentives for non-fishery activities such as
land-based non-point-source pollution.

**I.E. Impact of anthropogenic factors and environmental changes on fish
populations**

Changing conditions of the biotic and physical environment occupied by
fish, whether natural or anthropogenic, affect population productivity
through mechanisms ranging from sub-lethal effects to outright
mortality. Detecting such changes is an important task, but determining
causal relationships is complex. Anthropogenic effects may be confounded
by natural environmental changes or cycles. NMFS must conduct research
to unravel these complex relationships to better understand their role
in the sustainability of marine fish populations.

There is recognition in the scientific community that toxic contaminant
discharges to the coastal oceans can have a significant impact on the
viability of important fish populations. Contaminants can disrupt an
organism's early life stage development and growth that in turn can
affect their reproductive potential as adults. Such nonlethal effects
are not easily identified or characterized, and therefore, are difficult
to relate to the sustainability of the fishery populations. The
quantification and identification of deleterious changes is further
complicated by natural and uncontrolled variability within and between
fishery populations and their supporting food webs.

NMFS will continue to study the potential effects of contaminants on
important fishery species as well as the sources of variability. To
assess the risk to fish populations from different combinations of
stressors there must be a linkage made between understanding toxic
effects of contaminants to individual organisms and the factors, both
anthropogenic and natural, that influence fishery populations. There has
been growing recognition that marine pollution can disrupt the
development and function of the reproductive, endocrine, immune, and
nervous systems of marine animals, including fishes, affecting
reproductive and growth processes critical to population stability.
Because the effects are not always immediately visible, it is difficult
to establish the impact on fish populations. Environmental variation at
different temporal and spatial scales further complicates the picture.
NMFS will continue to study similar habitats in stressed and unstressed
anadromous streams, estuarine, and ocean environs in order to understand
the effects of pollution on LMRs and their habitats.

NMFS will also research social and economic causes of habitat
degradation, from fishery and non-fishery sources. This research
includes coordination with researchers studying land-based activities
such as non-point source pollution and urban development. NMFS also
engages in research to determine the effects of long-term changes in the
ocean climate on LMRs. This information helps assess the true impact of
human-induced factors.

Habitat loss and degradation affects riverine, estuarine, and coastal
ecosystems. The primary threats come from physical destruction of
wetland and other habitats, alteration of freshwater flows,
eutrophication, and destructive fishing methods. For example, logging
contributes to siltation and can destroy salmon spawning habitat upriver
and impede their migratory paths. Construction of marinas and docking
facilities as well as dredging and the disposal of dredged material in
estuaries and bays also cause significant habitat impacts. Loss of
aquatic habitat (e.g., coastal wetlands or seagrass and kelp beds)
resulting from development adversely affects a variety of food webs that
are important to adults and juveniles of many marine and anadromous
species. Propeller damage to shallow vegetated and non-vegetated
habitats not only causes a direct loss of habitat, but results in
destabilization of these areas, resulting in increased habitat loss and
increased sediment re-suspension and turbidity. Diminution in freshwater
volume and flow rates stem from damming and diversions of major rivers
impacting nearshore ecosystems adapted to seasonal discharges of
freshwater. Destructive fishing methods can damage EFH and coral reefs.

Nutrient enrichment and eutrophication have a major impact on fish
populations in estuarine and coastal waters. This impact is manifested
by hypoxia/anoxia accompanying the death of phytoplankton populations
(Gulf of Mexico dead zone off the Mississippi River and western Long
Island Sound) and loss of inshore habitat (replacement of eelgrass beds
by macroalgae or loss of eelgrass beds due to shading by epiphytes or
phytoplankton in Chesapeake Bay, Waiquiot Bay, and Lake Pontchartrain).
In addition, changes in nutrient dynamics can create harmful algal bloom
events that can lead to wild fish kills, shellfish harvest closures, and
mass mortalities of farmed salmon in the Northwest. Fishing activities,
if they alter food web structure, could change the population dynamics
of harmful algal species. A change in trophic webs that decreases
grazing on phytoplankton is a major factor in many blooms leading to
more or longer lasting bloom events. The potential effect of climate
change on harmful algal blooms events is also not known.

NMFS will engage in a variety of research initiatives to study the
effects of natural and man made environmental changes on living marine
resources and the related ecosystem, social, and economic causes and
effects, including:

• Examining the effects of mobile fishing gears, such as bottom trawls,
which disturb the sea bottom and damage fragile corals and other benthic
habitat.

• Determining the cumulative effects of watershed and regional land
cover and changes in that land cover on EFH.

• Ecosystem monitoring for habitat degradation and resource surveys by
satellite remote sensing and shipboard and moored instrumentation.

• Developing rationales/methodologies to detect and quantify habitat
loss.

• Establishing a GIS database to document and track habitat loss.

• Researching natural environmental variability at temporal and spatial
scales pertinent to marine fish populations.

• Developing methodologies to detect and quantify the effects of habitat
alterations on fishery populations.

• Conducting laboratory and field research to identify the probable
results of contaminant inputs and habitat alterations that significantly
affect important fishery species.

• Developing molecular genetic techniques to assess the fitness of
fishery organisms.

• Developing models (descriptive and predictive) to assess the risk
posed by contaminants and habitat alterations to fishery populations.

• Analyzing and synthesizing existing environmental and fishery data
that are available on fishery habitat types and fishery populations.

• Researching to separate the effects of natural versus human-induced
climate change.

• Developing methods to identify, map, and forecast harmful algal
blooms.

• Determining the effect of fishing on ecosystem trophic structure and
population dynamics of harmful algal species.

• Cooperating with fishers in assessing habitat changes over the past
decade.

• Assessing current economic and social incentives for habitat
protection or degradation.

# II. Conservation engineering research

Conservation engineering research is intended to make fishing gear more
efficient by decreasing fishing costs, bycatch mortality, and habitat
destruction. It is also intended to improve the data provided by
scientific surveys of fish populations. This area includes research on
gear performance and fish behavior used in the development of selective
fishing gear to reduce bycatch. Bycatch is responsible for the death of
millions of juvenile finfish, including red drum, red snapper, weakfish,
Spanish mackerel, and king mackerel. For example, prior to the
implementation of bycatch reduction devices (BRDs), it has been
estimated that between 15 to 50 million red snapper were annually taken
and discarded in the offshore shrimp fishery in the Gulf of Mexico. The
Food and Agriculture Organization (FAO) estimates that one-third of the
world\'s 16 billion lbs. of bycatch comes from shrimp fishing. The most
recent studies of bycatch estimate that the ratio of bycatch to shrimp
landed is 4:1 in the Gulf of Mexico. The worldwide bycatch ratio for all
fisheries is 0.35 lb. to 1 lb. of target species.

Since few discarded fish from trawls survive, bycatch constitutes a
problem for fishery managers because it represents both an unaccounted
mortality in fisheries and an economic loss to harvesters and the
Nation. For instance, fishers in another fishery might target the
discarded species, or fishers in the same fishery might be able to keep
those same fish when they are older or larger. Recreational discards are
another source of fishing mortality. Information is needed to determine
proportions of discards in different recreational fisheries and assess
associated release mortality. Additionally, NMFS will encourage research
on ways to increase the survival of recreational releases. Bycatch
reduction, then, is critical for the continued existence of healthy
fisheries, and is especially critical when the bycatch includes
protected species. Additionally, NMFS conducts research at several of
its laboratories on populations of ESA-listed species and marine
mammals. Stocks of listed species and marine mammals interact with
species managed under the MSFCMA (e.g., competition for food, bycatch).
As such, research conducted to support requirements of the
Magnuson-Stevens Act also make an important contribution to the
conservation and management requirements of the Endangered Species Act
(ESA) and the Marine Mammal Protection Act (MMPA). Along with incentives
and other management strategies, one solution to bycatch reduction is to
design and operate selective fishing gears, using knowledge of species
behavior, gear hydrodynamics, and fishing practices.

An important data collection method used by NMFS to conduct research on
fishing gear and its impact on fish stocks, protected species, and
habitat, is the deployment of marine resource observers on commercial
and recreational fishing vessels. Observers collect information on all
aspects of fishing gear operations, including what kind of gear is used,
how it is set, how long it is set, and how it is retrieved, as well as
information on fish catch and bycatch and incidental takes of protected
species. Observers also collect life history data on species of concern,
collect biological samples, and support research through tagging of
released animals and other activities. Observer data provide information
for stock assessment research, for the assessment of gear efficiency,
and for monitoring the relative impacts of various types of gear and
fishing methods on fish and protected species and marine habitats.
Currently, observers are deployed in only a fraction of the U.S.
commercial and recreational fisheries managed by NMFS or required to be
monitored under the MMPA, but there are initiatives underway to expand
the observer program into more fisheries and to more fully integrate
observers into fisheries research activities.

Bycatch levels and control measures continue to occupy the attention of
most fishery management actions of all regional FMCs. Even when apparent
solutions are found, the dynamics and abundance of marine species change
in time and area, which can shift the character of the problems and
require continuous adjustments to their solutions. NMFS will continue to
conduct studies to determine the magnitude of bycatch of overfished
stocks and options to reduce it. The options may require the design of
new types of fishing gear that are more selective for the targeted
species. This approach is known as \"conservation engineering\" and NMFS
will work in cooperation with the fishing industry and gear
manufacturers to find designs that meet conservation needs while
recognizing the financial constraints of fishers.

To determine when gear modifications are the most appropriate response
to bycatch problems, NMFS will study existing programs such as the
turtle excluder devices (TEDs) in the Gulf of Mexico and BRDs to exclude
finfish from Gulf shrimp trawls and from northern shrimp trawls in New
England. By understanding the successes and setbacks in these and other
settings, NMFS will be better able to coordinate gear research with the
social, economic, and institutional constraints of specific fisheries.

Experimental work with selective fishing gear involves considerable
field work on board fishing vessels working under actual fishing
conditions. Most trawl gear evaluation includes an alternate tow
approach, varying which net is fishing with the experimental gear and
comparing the catch results using statistical tests. Underwater cameras
allow for examination of the behavioral mechanisms and gear variations
that would account for the catch differences.

Growing controversy over the impact fishing gear is having on EFH has
resulted in a need to evaluate the impacts. Effects from fishing may
include physical disturbance of the substrate, and loss of and injury
to, benthic organisms, prey species and their habitat, and other
components of the ecosystem. Experiments are being designed to assess
the potential effects of all fishing gear types used in waters described
as EFH. These studies will include the use of remote underwater cameras,
divers, abundance studies, and perhaps research closure areas for
comparison. If an adverse effect is identified and determined to be an
impediment to reaching target long-term production levels, then the
research needed to quantify and mitigate that effect would be the next
logical step.

Growing concern over the impacts of bycatch on stocks resulted in the
development of a NMFS Bycatch Plan (NMFS, 1998a). Agency experts with
experience in fishery management, stock assessment, and social sciences
compiled this plan. It includes proposed national bycatch objectives,
specific recommendations concerning data collection, evaluation and
management actions necessary to attain the objectives, and a
comprehensive assessment of the state of bycatch in the Nation\'s marine
fisheries. The latter is intended to serve as a benchmark from which
progress in bycatch reduction can be measured.

NMFS is committed to maximizing the research contribution of the fishing
industry and other non-government participants in the fisheries. Across
the NMFS regions, the industry is providing advice in research planning,
in formal reviews of research programs, and, where possible, in research
operations. Examples of research involvement includes: (1) provision of
chartered vessels and crew for surveys and bycatch gear development; (2)
keeping logbooks of species catches, including bycatch; and (3) industry
efforts to develop gear, gear modifications, and fishing practices to
reduce bycatch.

The Saltonstall-Kennedy Grant Program has had direct industry
involvement and investment since its inception decades ago. Industry
members submit proposals, usually with strong cost sharing, to conduct
research in conservation engineering, to develop fisheries for
underutilized species to relieve pressure on traditional species, and to
improve the after-catch utilization of nearly all species.

# III. Research on the fisheries

In its fifth edition, Our Living Oceans (NMFS, 1999) reported (from
1995-97 data) that of 160 U.S. Exclusive Economic Zone (EEZ) fisheries
whose biological status could be assessed, 34% were classified as
overutilized and 47% were fully utilized. Nationwide an additional 43
fishery stocks were characterized as having \"unknown\" status. New
management measures, based on the Sustainable Fisheries Act (Public Law
104-297), have been implemented to halt the decline in stock levels in
many of these fisheries. Causes typically cited for the declines include
overfishing, deteriorating environmental conditions, loss of habitat,
and changing oceanographic conditions.

# III.A. Social and economic research

Social and economic information has become increasingly important in
addressing fishery conservation and management issues. Federal law,
Executive Orders, and NMFS policy require social and economic
assessments of proposed regulatory or policy changes. The U.S. fishing
industry, however, is quite diverse. Competition within and between
consumptive users of living marine resources, such as commercial and
recreational fishers, and non-consumptive users, who value the existence
of living marine resources, greatly complicates the resource allocation
decisions fishery managers face. Significant diversity exists between
firms within the commercial fishery, and can be seen by the variation in
the sizes and types of vessels between fisheries as well as between
geographic areas. In addition, oftentimes no clear distinction in an
actual fishery exists between commercial fishing firms and individual
recreational fishers. Instead, a continuum of activities separate two
extreme forms of fisheries exploitation including recreational fishers
who sell their catch, headboat and charterboat operations, meat fishers,
and catch-and-release fishers. Equally important are individuals who
value knowing a particular fish species exists or value the existence of
species dependent on a fish stock or stocks; e.g., whales, Steller sea
lions, and marine turtles. One consequence of the size and diversity of
the users of living marine resources is that the goal of managing U.S.
fisheries to maximize the present value of net benefits to the nation is
difficult to achieve.

The application of this broad-based policy to individual fisheries is
difficult because each fishery has unique biological, economic, and
sociological characteristics that require different types of regulatory
approaches. For example, vessel sizes, gear types, crew sizes, and
processing, marketing, and distributional arrangements vary
significantly among fisheries and geographic areas. Educational levels,
household dependence on fishing, preferred target species, and fishing
patterns differ across fisheries and fishing communities. Levels and
types of social, cultural, and economic dependence on fisheries vary by
community and region.

Management decisions must reflect the values as well as needs of many
different groups, including commercial and recreational fishers,
subsistence fishing communities, non-consumptive users, Pacific
Islanders, and Native American tribes (many of which have treaties with
the United States guaranteeing certain fishing rights).

Management by NMFS must be done within an economic framework that
considers economic efficiency and provides equity or fairness to all
resource users. This economic framework considers the transition time
associated with a proposed regulation to minimize adverse economic
impacts on fishing dependent communities, firms, and individuals.
Adequate consideration of these factors requires that NMFS collect and
analyze sufficient information about fishing communities, commercial and
recreational fishing firms or individuals, and other consumptive and
non-consumptive users of our living marine resources. Without sufficient
data and analyses, we will have inadequate social and economic
assessments and will be unable to determine if our management policies
are achieving their intended objectives.

To produce quality assessments will require new data and models on a
number of sectors, including the following:

• **The U.S. commercial harvesting sector:** Detailed social and
economic analyses of the majority of U.S. fisheries will be conducted in
conjunction with stock assessments to determine current social and
economic costs and benefits in the harvest of living marine resources,
and determine methods to maximize net benefits through innovative
management alternatives.

• **The U.S. recreational harvesting sector:** The recreational and
commercial fishing sectors are interdependent and have much in common.
Policies aimed at regulating one group almost always impact the other
and often affect other sectors of the marine fishing industry. NMFS will
assess the net economic and social benefits from various allocation
scenarios using estimates of anglers\' consumer surplus, commercial
fishers\' producer surplus, and, theoretically, the consumer surplus for
commercial catch as well.

• **The U.S. subsistence and traditional use fisheries:** NMFS will
conduct data collection to support empirical research using both
qualitative and quantitative techniques of fisheries economics,
including alternative sources of protein and cultural and ritual uses of
the harvested living marine resources, to model and assess social,
cultural, and economic factors related to community dependence on the
fishery.

• **The U.S. seafood processing/wholesale sector:** The processing and
wholesale sectors are an integral part of the seafood industry. As in
the harvesting sector, technological innovations advance the processing
and distribution of seafood. NMFS will continue to collect annual data
to determine the total number of processing and wholesaling plants, the
number of people employed, and the total volume and value processed.
NMFS will also increase data collection to support research on social
and economic relationships among fishing firms, processors, and
wholesalers to better understand the cultural and other institutional
influences on the structure of seafood markets (e.g., to develop
econometric models of the processing sector to determine the effect of
common property resources on capital investment).

• **The U.S. trade sector:** The U.S. plays a major role in the
international seafood market, importing and exporting billions of
dollars worth of seafood each year. The U.S. seafood trade market in
part determines conditions in its domestic fisheries. NMFS will conduct
an annual survey to determine our share of the international seafood
trade market from which econometric analyses of supply and demand
conditions in international markets can be developed to determine how
trade agreements impact our Nation\'s competitiveness in this arena.

• **Retail demand for seafood:** Social and economic forces in the
United States over time have influenced the current makeup of the
seafood industry. Population, real per capita income, and the prices of
substitutes are three factors that economic theory suggests should
explain the aggregate demand for seafood. NMFS will conduct studies to
gain a greater understanding of the responsiveness of consumers to
changes in prices, quantities, and product quality, their willingness to
substitute among various seafood products and other protein sources,
their readiness to purchase imported products, and the responsiveness of
fish and fishery product prices to changes in harvest levels.

• **Fishing communities:** NMFS will collect or acquire from other
sources qualitative ethnographic, demographic, and economic data
important for the social and economic profiling of fishing communities,
including opportunity costs, social structure, and ethnohistorical data,
and other data needed for the estimation of net benefits for use in
input-output models and analyses of distributional effects of
alternative management policies.

• **Economic impact analyses:** NMFS will collect economic data to meet
the requirements of Executive Order 12866, the National Environmental
Policy Act, regulatory flexibility analyses (RFAs), and fishery impact
statements for the MSFCMA.

• **Social impact assessment (SIA):** NMFS will collect ethnographic,
economic, and biological data related to fishing decision-making
processes of captains; investment decision-making processes of owners;
information flows within the fishery; and the differential effects of
management policies on various subsets of the fishing industry such as
absentee owners, captain-owners, and crew members, full-time and
part-time fishers, fishers with different household compositions, large
vessels and the undertonnage fleet, those who target single species or
complexes, and those who fish different gears and species by season.

• **Overcapacity:** NMFS will assess current levels of capacity of U.S.
commercial and recreational fishing fleets (i.e., charter/party
vessels), determine optimal levels, and develop approaches to solving
the problem of overcapacity.

• **Fisheries management:** NMFS will seek to integrate the existing
biological, economic, and other social sciences information into a
single bio-socio-economic framework from which information can be
generated to aid fishery managers in making decisions about our living
marine resources.

# III.B. Seafood safety research

Intra and extramural seafood science research is aimed at continuing the
integration of trophodynamic investigations relative to fishery resource
health and disease threats, and differential trophic level risk
evaluation effects resulting from such threats, be they to other fishery
resources, marine mammals, or human consumers. Studies are focused on
identifying and determining the characteristics of marine pathogens;
improving methods to detect, forecast, and evaluate the ecological
significance of harmful algal blooms; as well as developing and applying
biological and chemical analytical methods to measure toxic contaminants
to restore living marine resources and their habitats. Additionally,
when needed, specific highly focused research is rapidly directed to
address crisis situations dealing with animal and human health concerns,
such as that needed to perform a Risk Assessment to wild shrimp stocks
resulting from imported aquacultured shrimp products being infected with
various shrimp viruses or re-evaluating the human exposure rate from
mercury in seafoods. These research efforts are conducted primarily at
the National Seafood Inspection Laboratory in Pascagoula, MS, as well as
at the Northwest and Southeast Fisheries Science Centers.

# III.C. Marine aquaculture

The importance of marine aquaculture (mariculture), both in the U.S. and
throughout the world, is widely recognized. The production limits of
wild stock are being reached and most of the increased global production
of fisheries products for the last decade has come from aquaculture. In
many countries aquaculture is progressing more rapidly than in the U.S.,
and one-third of the global supply of food fish now come from
aquaculture (FAO, 2001). The annual U.S. trade deficit in edible fishery
products is \$7 billion. In the U.S., aquaculture production (1999
statistics) has reached over 380,000 metric tons per year, with a value
of \$987 million, but only about one-third of this is for marine
species. In addition, an estimated 150,000 metric tons of commercially
and recreationally caught fish with a value of about \$100 million
originate from marine stock enhancement, primarily for Pacific salmon
species. Although aquaculture accounts for 28% of the value of the total
U.S. landings, it makes up only 9% of the landed volume. There is
significant potential to increase U.S. marine aquaculture production.
However, there are technical, environmental, and socio-economic
impediments that need to be addressed by basic and applied research and
through an examination of policies. NMFS has scientific expertise that
can be applied to all of these issues. NMFS has had a long history in
aquaculture research and development, stretching back more than 100
years, and has made major contributions to the progress of aquaculture
both domestically and internationally. Also, NMFS has environmental
stewardship responsibilities and the expertise to assess the appropriate
role of mariculture and its potential impacts on wildstocks and habitat
quality. Finally, NMFS has responsibilities for permitting aquaculture
projects, and it is important to use good science as a basis for
establishing a clear policy for permitting decisions.

In addition to food production, aquaculture can also play a role in
enhancing wildstock populations, assisting in recovery plans for
protected species, and can be used to produce non-food products such as
ornamental fish, baitfish, and pharmaceuticals. Expanded mariculture
production in the U.S. has the potential to reduce the pressure on
wildstock harvest and help in the rebuilding efforts for those stocks.

To ensure that mariculture progresses in an environmentally sound
manner, NMFS will concentrate its mariculture research activities in the
following broad areas:

• Develop and evaluate commercially viable husbandry technologies for
new candidate species.

• Conduct research on the effects of marine aquaculture on habitat and
evaluate the risk to wild stocks from the introduction of cultured
stocks.

• Establish, with the help of stakeholders, uniform requirements for
aqua-culture development in the U.S. EEZ under a Code of Conduct for its
implementation.

• Develop effective enhancement strategies for aquatic species to help
in the recovery of wild-stock fisheries and endangered species.

• Integrate aquaculture development with the management of wild stocks,
particularly threatened and endangered species.

• Develop environmentally safe protocols for disease prevention.

• Assess the effectiveness of aquaculture as an alternative employment
source for fishers in over-exploited fisheries.

• Accelerate industrial implementation of aquaculture technologies
through demonstration, training, and extension projects for producers,
tribes, and community groups.

• Encourage coordination and collaboration of stakeholders to achieve
regional and national goals by establishing frameworks for regional
cooperation among the private and public sectors.

• Assist associations of producers to prepare best management practices
for their respective industries with scientific analysis and assessment
of risk.

# IV. Information management research

Title IV (Fishery Monitoring and Research) Section 401 (Registration and
Information Management) of the MSFCMA required the Secretary of Commerce
to deliver a proposal to Congress that recommended an implementation
strategy for the creation of a \"\...standardized fishing vessel
registration and fisheries information system.\" This report was
completed and delivered to Congress in December 1998, and outlined an
approach that integrated all fisheries information required under all
applicable National Marine Fisheries Service (NMFS) statutory and
regulatory requirements, including but not limited to MSFCMA, the Marine
Mammal Protection Act, the Endangered Species Act, and the Atlantic
Coastal Fisheries Cooperative Management Act (NMFS, 1998b). It also

includes all data collected under state authority for those states
willing to participate. This report was developed in consultation with
the U.S. Coast Guard, the states, the regional FMCs, the interstate
Marine Fisheries Commissions, other key governmental and non
governmental organizations, and interested stakeholders. Drafts of the
proposal were published in the Federal Register for public comment.

The proposed fisheries information system included information from both
commercial and recreational fisheries (the vessel registration component
was recommended to apply to only commercial vessels). The current
development of the fisheries information system is based on integrating
data collection and data management systems required by NMFS, and
linking them with existing state/Federal cooperative statistics programs
around the country (i.e., the Atlantic Coast Cooperative Statistics
Program (ACCSP); Gulf coast (GulfFIN); Pacific coast (Pacific RecFIN and
PacFIN); Hawaii and Pacific islands (WestPacFin); and Alaska (AkFIN)).
Linking regional systems will identify and satisfy mutual information
needs for states and the Federal government. In addition, gaps in
information needs not yet met by these programs will be identified
through consultation with industry and policy makers. The proposal
recommended the following:

• Standardization of vessel registration and information collection
systems contents as required by SFA and other state and Federal enabling
legislation, to include:

Establishing standardized units of measurement, nomenclature, and
formats for the collection, submission and management of data;
establishing procedures for requiring commercial and recreational
fishers and ex-vessel purchasers to participate in collection and
reporting of fisheries information;

Inclusion of all species and all commercial fishing vessels (including
charter fishing vessels) within the geographic areas of authority of the
FMCs; and

Assessing the desirability or necessity of creating a vessel
registration system for recreational fishing vessels (not including
charter fishing vessels).

• Integrating information collection programs under existing FMPs and
integrating other state, tribal, and Federal fishery information systems
to reduce/avoid duplication and minimize paperwork and other burdens on
affected parties.

• Improving stakeholder and industry participation in effectively
implementing new, integrated systems.

• Identifying costs and possible funding mechanisms and schedules
associated with implementing the recommendations for the system.

• Modifying several statutory impediments to enable implementation of
the system.

## Major Fishery Research Goals and Objectives 

All Federal agencies operate in an environment of increasing demands
competing for limited resources. To meet this challenge, NMFS is
increasing its partnering activities with other NOAA line offices and
their programs (e.g., Sea Grant, National Undersea Research Program,
Coastal Ocean Program), other Federal, state and local agencies,
universities, Native American tribes, Pacific Islanders, the commercial
and recreational fishing industries, environmental groups, and
international organizations. NMFS is committed to strengthening existing
relationships and building new ones.

The major fishery research goals and objectives are driven by the goals
and objectives in the NOAA Fisheries Strategic Plan (FSP), published in
May 1997. To facilitate cross reference, the corresponding FSP strategy
or foundation number follows each fishery research objective found
below.

GOAL 1: Provide scientifically sound information and data to support
fishery conservation and management. (Ongoing)

Objective 1.1: Periodically assess stocks to ascertain whether changes
in their status due to natural or human-related causes have occurred.
These stock assessments require adequate fishery monitoring and resource
surveys. (FSP Strategy 1.1.1)

Objective 1.2: Use stock assessments to predict future trends in stock
status. Forecasts will take into account projected biological
productivity, climatic information, economic markets, and other social
forces that will affect levels of fishing effort. (FSP Strategy 1.1.2)

Objective 1.3: Determine and reduce the level of uncertainty associated
with stock assessments through improved data collection and advanced
analytical techniques. (FSP Strategy 1.2.1)

Objective 1.4: Use stock assessment workshops, peer reviews, and other
fora to ensure that our information and advice are developed through an
open and collaborative process. (FSP Strategy 1.2.2)

Objective 1.5: Communicate our scientific information and advice, along
with the associated uncertainties, to the Councils, other management
authorities, and the public. (FSP Strategy 1.1.3)

Objective 1.6: Collaborate with the Councils and other management
authorities to explore and develop fishery management regimes and
alternative governance systems that will effectively control
exploitation and promote sustainability. (FSP Strategy 1.1.4)

Objective 1.7: Provide guidelines to assist the Councils in assessing
and specifying Maximum Sustainable Yield (MSY) for managed fisheries.
(FSP Strategy 1.1.5)

Objective 1.8: Work with the Councils to develop objective and
measurable criteria for each managed stock to determine if the stock is
overfished or approaching an overfished condition. (FSP Strategy 2.1.1)

Objective 1.9: For each stock which is overfished or approaching an
overfished condition, we will develop, in collaboration with the
Councils, measures to eliminate or prevent the overfishing. (FSP
Strategy 2.1.2)

Objective 1.10: Conduct additional research to provide needed
information to refine initial EFH designations and to help the Councils
minimize the adverse effects of fishing on EFH, as mandated by the SFA.
(FSP Strategy 2.3.1)

Objective 1.11: Establish an inventory of living marine resource
habitats (tied to Our Living Oceans series) and implement measures to
monitor the trends in habitat availability. (FSP Strategy 7.3.3)

Objective 1.12: Support recommendations provided by the NRC (NRC, 1999a)
and the Report to Congress (EPAP, 1999) by establishing criteria to
define and delineate marine, estuarine, and riverine ecosystems for
management purposes, and identify indicators for assessing the status
and detecting changes in the health of such ecosystems. (FSP Strategy
7.3.2)

Objective 1.13: Define the key aspects of vital habitat functions and
increase our understanding of how they affect marine and anadromous
species and how they are affected by human activities. This will involve
the development of new methods of evaluating the quality and
productivity of restored habitats, as well as improved restoration and
creation technologies, including contaminant remediation, to ensure that
created habitats are beneficial to fish populations. (FSP Strategy
7.3.1)

Objective 1.14: Incorporate assessments or indices of climate
variability into stock assessments.

Objective 1.15: Monitor climate change on inter-annual, decadal, and
centennial scales and its impact on currently sustainable fisheries.

GOAL 2: Through conservation engineering research contribute to efforts
to reduce bycatch and adverse effects on EFH, promote efficient harvest
of target species, and to improve the data from fishery surveys.
(Ongoing)

Objective 2.1: Identify and assess the magnitude of incidental takes of
protected marine species. (FSP Strategy 6.1.1)

Objective 2.2: Establish sustainable levels of takes for all protected
marine species and continue to improve the estimates of these levels
through ecologically sound research. (FSP Strategy 6.1.2)

Objective 2.3: Work through domestic and international cooperative
relationships with industry and environmental groups, including take
reduction teams, special task forces, and other needed scientific
collaborations. (FSP Strategy 6.1.3)

Objective 2.4: Explore, develop, and implement new technologies and
practices for reducing detrimental interactions. When such technologies
could reduce detrimental effects both to and from protected species in
other nations these technologies will be made available to those
nations. (FSP Strategy 6.1.5)

Objective 2.5: Establish a standardized reporting methodology to assess
the amount and type of bycatch occurring in each fishery covered by an
FMP. (FSP Strategy 3.4.1)

Objective 2.6: Work in cooperation with the fishing industry and gear
manufacturers to improve gear selectivity, design and field test new
gear designs and modifications, and evaluate gear regulations. (FSP
Strategy 3.4.2)

**GOAL 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. (FY 2003)**

Objective 3.1: Collect data and develop integrated bio-socio-economic
models to measure net benefits to the Nation from living marine
resources. (FSP Strategy 3.1.1)

Objective 3.2: Assist the Councils in reviewing optimum yield (OY)
levels for consistency with economic theory and with the revised
definition in the Sustainable Fisheries Act. (FSP Strategy 3.2.1)

Objective 3.3: Develop an integrated multi-disciplinary scientific
framework to collect sufficient economic, biological, and social data to
support recommendations made by the NRC on developing a national policy
for individual fishing quota programs (NRC, 1999b). (FSP Strategy 3.3.3)

Objective 3.4. Study new candidate species for culture through their
complete life cycle to determine which are economically and biologically
suitable for commercial culture or wild stock enhancement. (FSP Strategy
4.1.1)

Objective 3.5: Determine the bio-economic requirements for the siting of
aquaculture operations in the U.S. EEZ. (FSP Strategy 4.4.1)

Objective 3.6: Work with the aquaculture industry to develop, identify,
evaluate, and transfer technologies that are appropriate to both
economically efficient aquaculture production and environmental
protection. (FSP Strategy 4.5.1)

Objective 3.7: Evaluate the impacts of climate change on biological,
social, and economic conditions in fishing communities and commercial
and recreational sectors.

GOAL 4: Improve the fishery information system. (FY 2003)

Objective 4.1: Develop implementation strategy and annual operational
plans for creation of a national fisheries information system as
described in the December 1998 Report to Congress (NMFS, 1998b). (FSP
Strategy 3.3.2)

Objective 4.2: Develop implementation strategy and annual operational
plans for executing the days-at-sea requirements identified in the NMFS
Data Acquisition Plan (NMFS, 1998c).

GOAL 5: Improve the effectiveness of external partnerships with fishers,
managers, scientists, conservationists, and other interested groups.
(Ongoing)

Objective 5.1: Promote a cooperative network of partners in the
coordination of fisheries research.

Objective 5.2: Develop infrastructure for long-term, continuous working
relationships with partners to address fisheries research issues.

Objective 5.3: Sponsor symposia and conferences for partners to exchange
information and identify major fisheries research initiatives.

Objective 5.4: Solicit partners\' views on fisheries research needs.

## APPENDIX A. NMFS Scientific Enterprise 

The National Marine Fisheries Service is the NOAA line office
responsible for the stewardship of the Nation\'s living marine
resources. NMFS has five regional Science Centers, composed of about 30
laboratory facilities nationwide and over 1,500 scientific and support
personnel, which conduct a comprehensive, interdisciplinary science
program. The scope of their work is broad in time, space, and
discipline. These Science Centers provide the scientific knowledgebase
on which NMFS formulates stewardship policies through to its five
Regional Offices. Research at NMFS laboratories supports resource
managers in NOAA, fishery management councils, interstate fishery
commissions, and other agencies in making informed marine resource
management decisions for sustainable fisheries, protected resources,
endangered species, and habitat.

Because fisheries are managed on a regional basis, the focus of NMFS
research programs varies among the regional Science Centers. Each
Science Center Director and his/her Division Chiefs develop annual
research priorities, based upon regional and national needs, through
dialogue with his/her Regional Administrator, councils, the Program
Offices in NMFS headquarters, and with user groups and other interested
parties. Within each Science Center, teams of researchers work together
to develop research plans.

NMFS\' longer-term integrated research program is coordinated by
headquarters\' Office of Science and Technology. The Science Board,
composed of the five Science Center Directors and the Director of the
Office of Science and Technology, is responsible for ensuring the
integrity and quality of scientific research. The NMFS Science Board
addresses national science issues and programs and develops science
policy for the agency. All components of the science enterprise function
to provide the agency with information that is comprehensive, objective,
credible, and effectively communicated.

The NMFS science program has extensive collaborations with academia,
many through cooperative agreements and grants. These partnerships
enhance and extend NMFS\' research capability. Many NMFS scientists
serve as adjunct professors at nearby universities. This relationship
offers intellectual stimulation and challenges for agency scientists to
remain on the cutting edge, while expanding the teaching capability of
the university and bringing NMFS expertise into the academic community.
Academic scientists also play an important role in the periodic review
and evaluation of the quality and relevance of NMFS research programs.
The Science Centers work in cooperation with other Federal and state
agencies, international entities, non-governmental organizations, and
the private sector, including the fishing industry.

The scale and scope of NMFS research varies. Some major research
initiatives focus on the needs of the fishing industry and are performed
jointly with industry. For instance, joint studies of harvesting methods
and development of more effective fishing gear are underway to reduce
wasteful bycatch. Other research initiatives focus on needs of the FMCs
and NMFS Habitat Conservation field offices to meet their scientific and
management mandates under the EFH provisions of the MSFCMA.

## GOALS OF THE SCIENTIFIC ENTERPRISE 

The mission of NMFS scientific enterprise is to ensure that the science
products produced and disseminated by the National Marine Fisheries
Service is of the highest quality. During the next five years NMFS will
accomplish this by meeting the following goals and objectives:

# Improve Scientific Capability

• Implement NRC recommendations (NRC, 1998) to ensure state-of-the-art
resource assessments through our National Stock Assessment Improvement
Plan (NMFS, In press). (Ongoing)

• Continue to incorporate economic and social factors into our
decision-making. As part of this continuing effort, NMFS will publish
the next edition of the Our Living Oceans: The Economic Status of U.S.
Fisheries. The report will measure the economic health of U.S. fisheries
relative to current conditions versus desired future conditions of
long-term sustainability. (FY 2002)

• Increase our ability to predict natural living marine resource
variation through improved data collection, improved understanding of
how LMRs respond to environmental variability and climate change, and
coordinated bio-socio-economic modeling, which will result in more
accurate assessments and estimations of the uncertainty associated with
them. (Ongoing)

• Increase our ability to identify, conserve, protect, and restore those
habitats essential to managed fishery resources and to estimate the
impact of pollution, wetland and estuarine degradation, and fishing gear
on the abundance and availability of fish. (Ongoing)

# Increase Science Quality Assurance

• Implement policies to ensure that our science programs, analyses, and
products are sound, credible, and provide an objective basis for
management. (Ongoing)

• Improve our professional standards for research and scientific advice
by establishing national guidelines for technical program and staff
performance evaluations, performance award programs, and professional
career development opportunities. (Ongoing)

• Expand and improve our system for peer review of scientific advice by
establishing panels of knowledgeable scientists from both within and
outside government. (Ongoing)

• Solicit input from external scientists in topical areas when
identifying research initiatives for the various NMFS grant programs.
(Ongoing)

# Improve Fishery Research Capability

• Implement our fishery research vessel replacement plan (NMFS, 1998c)
that integrates government, university, and industry vessel capabilities
to provide the state-of the-art facilities necessary for the
accomplishment of our varied at-sea research programs. (FY 2008)

# Improve Data Collection

• Implement NRC recommendations (NRC, 2000) to improve our data
collection and analysis techniques and fishery data management systems.
(Ongoing)

• Provide a core fishery statistics program based on our strategic and
operational needs. (Ongoing)

# Increase Outreach/Information Dissemination

• Involve constituents in research programs. To the extent practicable,
NMFS will charter fishing vessels to participate in research projects,
invite constituents to participate aboard NOAA research vessels during
resource surveys, encourage frequent contact and cooperation between
scientists and constituents, and develop methods to incorporate
scientifically valid observations by fishers and others into fish stock
assessments and other analyses related to living marine resources and
their habitat. (Ongoing)

• Coordinate with the NMFS Constituent Affairs and Outreach Team to
develop an Internet Web-centralized resource for neutral science-based
information to educate the public and user groups and answer questions
on various topics on the status of our nation\'s fisheries, including
how NMFS research is conducted and how stock assessments are performed.
(Ongoing)

• Develop a new series of reports and presentations to communicate
scientific results in simplified language that is easier to understand
than traditional scientific publications. (Ongoing)

# Support International Fishery Science

• Participate in international scientific initiatives, such as the
United Nations Intergovernmental Panel on Climate Change (IPCC), Program
for the Conservation of Arctic Flora and Fauna (CAFF), Commission for
the Conservation of Antarctic Marine Living Resources (CCAMLR), Food and
Agriculture Organization of the UN (FAO), Global Oceans Observing
Program (GOOS), North Pacific Marine Science Organization (PICES),
International Council for the Exploration of the Seas (ICES),
International Whaling Commission (IWC), United Nations Atlas of the
Oceans, and Global Ocean Ecosystems Dynamics (GLOBEC). (Ongoing)

• Participate in bilateral scientific initiatives with neighboring
countries, Canada and Mexico, and in scientific exchange programs with
foreign countries which are developing their fishery resources.
(Ongoing)

### NMFS FISHERIES SCIENCE CENTERS 

The National Marine Fisheries Service is a world leader in fisheries
research. Each year the agency uses harvest and survey data to assess
the status and trends of more than 200 major commercially-valuable fish
and shellfish stocks. The NMFS Science Centers provide annual stock
assessment information and management advice to support the NOAA
stewardship mission for the living marine resources in their regions.
These cross disciplinary efforts are undertaken in cooperation with
other Federal and state agencies, international organizations, the
fishing industry, and academia, and are based on long standing
cooperative research agreements. In addition to these basic
responsibilities, each regional Science Center has unique capabilities
to focus on special research needs. The following is an overview of each
of the five NMFS Science Centers.

**ALASKA FISHERIES SCIENCE CENTER (AFSC)**

The Alaska Fisheries Science Center (AFSC) has research facilities in
Alaska (Auke Bay and Kodiak Island), Washington (Seattle), and Oregon
(Newport). Organizationally, the AFSC consists of the Auke Bay
Laboratory (ABL), the National Marine Mammal Laboratory (NMML), the
Resource Assessment and Conservation Engineering Division (RACE), the
Resource Ecology and Fisheries Management Division (REFM), and other
administrative units. The major survey platforms supporting the AFSC
include the NOAA fishery research vessels *Miller Freeman* and *John N.
Cobb*, and chartered vessels from the industry. External cooperators
include state and other Federal agencies, academic institutions, foreign
research institutions, the fishing industry, and resource conservation
organizations.

The Center has a permanent staff of about 325 employees who conduct
fisheries and marine mammal research in the coastal and offshore waters
off Alaska and the U.S. west coast. This marine region of nearly three
million square miles includes over 50% of the U.S. coastline and over
70% of the U.S. continental shelf. The region supports some of the most
important commercial fisheries in the world, particularly groundfish and
Pacific salmon species. It is host to some of the world\'s largest
populations of marine mammals and seabirds.

The Center conducts research on the following fishery resources that are
under active management:

• The groundfish fishery in the Bering Sea-Aleutian Islands region
involving 14 major species and 20 minor ones including walleye pollock,
Pacific cod, Atka mackerel, sablefish, yellowfin sole and other flatfish
species, Pacific ocean perch, and other rockfish species.

• The groundfish fishery in the Gulf of Alaska region involving 14 major
species and 37 minor ones including walleye pollock, Pacific cod,
sablefish, flatfish species, Pacific ocean perch, and a variety of slope
and shelf rockfish species.

• The king, tanner, and snow (*C. opilio*) crab fisheries in the Bering
Sea-Aleutian Islands region.

• The Pacific halibut fishery of Canada and the U.S.

• The scallop fishery off Alaska.

• The salmon fisheries off Alaska.

In addition to fishery research, the NMML conducts research on marine
mammals to determine their status, conservation needs, and potential
impacts of fishing activities on the populations. The Alaska region has
37 stocks of more than 25 species of marine mammals that may be grouped
as:

• Seals, sea lions, and walruses that include bearded seal, harbor seal,
northern fur seal, ribbon seal, ringed seal, and northern sea lion.

• Whales, dolphins, and porpoises that include beaked whale, beluga
whale, bowhead whale, Cuvier\'s beaked whale, fin whale, gray whale,
humpback whale, killer whale, minke whale, northern right whale, sperm
whale, Pacific white sided dolphin, Dall\'s porpoise, and harbor
porpoise.

# Recent Accomplishments and Research Priorities for FY 2001-2006

# I. Research to support fishery conservation and management

Recent Accomplishments:

Major research cruises conducted by the AFSC included: (1) a winter
hydroacoustic survey by the NOAA R/V *Miller Freeman* that estimated the
biomass and distribution of pollock in Steller sea lion critical habitat
on the Bering Sea shelf and in the Bogoslof area; (2) a spring
hydroacoustic survey by the NOAA R/V *Miller Freeman* to determine the
distribution and biomass of spawning pollock within the Shelikof Strait
area of the Gulf of Alaska; (3) a summer longline charter vessel survey
to assess the distribution and abundance of sablefish, rockfish, and
other commercially important groundfish resources in the Gulf of Alaska;
(4) a summer bottom trawl survey of Aleutian Islands groundfish with two
chartered fishing vessels to estimate the biomass and distribution of
groundfish and to collect other biological data; (5) a summer
hydroacoustic survey by the NOAA R/V *Miller Freeman* to determine the
distribution and biomass of pollock on the Bering Sea shelf; (6) a
summer bottom trawl survey of eastern Bering Sea shelf with two
chartered fishing vessels to estimate distribution and abundance of crab
and groundfish stocks, (7) a summer bottom trawl survey of Bering Sea
continental slope groundfish and crab with a chartered fishing vessel;
and (8) a fall bottom trawl survey of the west coast continental slope
by the NOAA R/V *Miller Freeman* to determine distribution of
groundfish.

The AFSC runs an ongoing Fisheries Observer Program to collect data from
the fishing industry. The data include the incidental takes of all
protected marine species such as marine mammals, seabirds, and
prohibited species of groundfish. The data collected by these observers
were used for stock assessments and real time management of the
fisheries.

The AFSC had the lead responsibility for analyzing the population
dynamics and status of most of the groundfish species managed by FMPs in
the Bering Sea-Aleutians and the Gulf of Alaska regions. The Center also
provided analysis of the Pacific hake resource off the Pacific Coast.

The AFSC, in cooperation with the Pacific Marine Environmental
Laboratory (PMEL), conducted some Fisheries Oceanography Coordinated
Investigations (FOCI) as part of GLOBEC and the Southeast Bering Sea
Carrying Capacity programs. These studies examine the environment and
biological factors affecting the recruitment of pollock in the Gulf of
Alaska and Bering Sea. Forecasts of future year class recruitment
strength are made for pollock stocks and in predicting future stock
levels.

The AFSC conducted studies on salmon ocean ecology, species life
histories, and historical data patterns to increase understanding of how
marine and anadromous species are affected by natural and human
activities.

The AFSC conducted restoration studies related to the Exxon Valdez oil
spill in Prince William Sound.

The NMML conducted research to determine the status, conservation needs,
and potential impacts of fishing activities on marine mammal
populations. The NMML worked closely with the Alaska Scientific Review
Group (ASRG) concerning recommendations regarding the status of marine
mammal stocks in Alaska. The ASRG had representatives from industry, the
tribal community, and the environmental community.

The AFSC (ABL) completed a three year radio-tagging study on Yukon River
fall chum salmon that documented spawning location, migration rates, and
estimated numbers crossing the border into Canada. This laboratory also
developed a genetic baseline information base on salmonids to identify
stocks or country of origin. AFSC scientists have been key partners in
Coastal Fish Habitat Restoration design and application of new aquatic
habitat restoration technology and in developing the database needed to
test the effectiveness of those restoration designs.

Research Priorities, FY 2001-2006:

I.A. Biological research concerning the abundance and life history
parameters of fish stocks

The following surveys are planned by the AFSC:

• Conduct an annual summer bottom trawl survey on groundfish and crabs
in the eastern Bering Sea shelf with chartered fishing vessels.

• Conduct midwater trawl-acoustic surveys to assess off-bottom component
of pollock stock in the Bering Sea every two years (2002, 2004, 2006)
and the Gulf of Alaska (2003, 2005) with the NOAA R/V *Miller Freeman*.

• Conduct an Eastern Bering Sea slope survey on groundfish every two
years (2002, 2004, 2006) with a chartered fishing vessel.

• Conduct an annual March survey on spawning pollock resources in the
Bogoslof Island area by the NOAA R/V *Miller Freeman* or with
cooperating foreign research vessels.

• Conduct an annual spring survey of pollock resources in the Shelikof
area by the NOAA R/V *Miller Freeman*.

• Conduct a summer bottom trawl survey on groundfish in the Gulf of
Alaska with chartered fishing vessels every two years (2001, 2003,
2005).

• Conduct a summer bottom trawl survey on groundfish in the Aleutian
Islands region with chartered fishing vessels every two years (2002,
2004, 2006).

• Conduct an annual summer longline survey on sablefish resources in the
Gulf of Alaska by a chartered vessel.

• Conduct a triennial summer bottom trawl survey on shelf groundfish off
the Pacific West coast with two chartered vessels in 2001.

• Conduct an autumn bottom trawl survey on slope groundfish off the
Pacific west coast with the NOAA R/V *Miller Freeman* in 2001.

• Conduct a triennial summer hydroacoustic-bottom trawl survey on
Pacific whiting off the Pacific west coast with the NOAA R/V *Miller
Freeman* in 2001.

• Conduct an annual April FOCI egg-larvae survey in the Gulf of Alaska
and a May survey on late-larvae by the NOAA R/V *Miller Freeman*.

• In addition to the above surveys, the AFSC is also planning to conduct
many field operations to study marine mammal-fish interactions, with
particular emphasis on sea lion-pollock/cod/atka mackerel interactions
in the Gulf of Alaska to the Bering Sea areas.

The following observer programs are planned for the groundfish fisheries
that occur off Alaska:

• 100% observer coverage of fishing and processing vessels longer than
125 feet.

• 100% observers coverage of most fish processing plants onshore.

• 30% observer coverage of fishing vessels that are 65-125 feet.

• 100% observer coverage (with multiple observers) of special category
vessels that engage in community development quota (CDQ) and American
Fisheries Act (AFA) fishing operations.

The AFSC will assess the status of stocks, estimate their biological
production potentials (MSY, acceptable biological catch (ABC),
overfishing levels), bycatch requirements, and other parameters required
for their management. The following stocks will be assessed annually and
be published in stock analysis and fishery evaluation (SAFE) reports:

• All Bering Sea-Aleutians and Gulf of Alaska groundfish stocks,
including pollock, cod, sablefish, atka mackerel, yellowfin sole, rock
sole, flathead sole, Greenland turbot, other flatfish, Pacific ocean
perch, and other rockfish species.

• King and tanner crabs in the Bering Sea.

The NMML will assess the population dynamics, ecosystem interactions,
and abundance of marine mammal stocks and their incidental take
requirements. Some specific programs and activities that will be pursued
are:

• Implement the Steller Sea Lion Recovery Plan.

• Implement the Steller Sea Lion - Fishery Interactions Research Plan.

• Implement the Northern Fur Seal Conservation Plan.

• Implement the Alaska Harbor Seal Research Plan.

• Analyze existing aerial survey data and harvest monitoring data on
Alaskan ice seals.

• Analyze data collected during the international Antarctic Pack Ice
Seal (APIS) cruise.

• Implement the Humpback Whale Recovery Plan.

• Implement the Northern Right Whale Recovery Plan as it pertains to the
North Pacific.

• Implement an extended five-year research and monitoring plan for the
eastern North Pacific gray whale.

• Analyze data collected during the 1997-1999 small cetacean surveys in
Alaska.

• Implement the west coast pinniped-salmonid research plan.

• Monitor the Makah gray whale harvest.

# I.B. Social and economic factors affecting abundance levels

• Expand sociological and economic research and incorporate results into
the fishery management process.

• Conduct research on vessel over-capitalization and impacts of their
fishing effort levels on fisheries.

• Compile and analyze data on harvesting and processing sector behavior.

# I.C. Interdependence of fisheries or stocks of fish

• Collect biological specimens of spawning pollock throughout its range
for genetic marker studies through DNA and other genetic techniques.
Cooperation with foreign scientists is required for sampling non-U.S.
waters.

• Analyze survey and observer data to determine spatial distributions of
different species clusters that would indicate separation or
interdependence of stocks.

• Develop genetic baseline information on salmonids to identify stocks
or area of origin.

• Conduct winter surveys to estimate distribution and abundance of
pollock (acoustic) and Pacific cod (bottom trawl) in Steller sea lion
critical habitat areas in southeast Bering Sea, Shumagin Islands, and
Kodiak Island to determine dependence of sea lions on localized food
supplies and assess feasibility of annual time series.

I.D. Identifying, restoring, and mapping of essential fish habitat (EFH)

• Conduct studies on the impacts of logging, urbanization, and mining on
coastal salmon resources in southeast Alaska. NMFS will work with the
Corps

of Engineers and local organizations to restore an urban impacted salmon
stream.

• Conduct restoration studies related to the Exxon Valdez oil spill in
Prince William Sound. The research will build upon the results reported
in the accomplishments section, including a study of the effects of oil
on the biology, homing, and survival of pink salmon.

I.E. Impact of anthropogenic factors and environmental changes on fish
populations

• Investigate mortality and pathogens of shellfish and groundfish.

• Conduct Fisheries Oceanography Coordinated Investigations (FOCI): a
cooperative research program with the Pacific Marine Environmental
Laboratory of NOAA\'s Oceanic and Atmospheric Research Office to
investigate the causes of variation in annual recruitment in fish
stocks.

• Assess effects of fishing on EFH and develop ways to minimize adverse
impacts.

# II. Conservation engineering research

Recent Accomplishments:

The AFSC conducted research to measure the direct effects of bottom
trawling on seafloor habitat in eastern and central Gulf of Alaska,
eastern Bering Sea, and the Aleutian Islands. Some of the major
accomplishments were: (1) the assessment of changes to the seafloor
caused by chronic long-term trawling in soft-bottom areas in the Gulf of
Alaska; (2) the examination of possible adverse effects of bottom trawls
on soft-bottom benthos in the eastern Bering Sea; (3) the evaluation of
acoustic technology for seabed classification; (4) the assessment of
impacts to habitat areas of particular concern (HAPC) such as gorgonian
corals; (5) the documentation of the effects of trawling on hard bottom
habitat in the Aleutian Islands and Gulf of Alaska; and (6) the mapping
of the areas by sediment types.

The AFSC worked cooperatively with the industry\'s Groundfish Forum by
chartering two fishing vessels to test a flexible grate system in bottom
trawls designed to reduce the bycatch of Pacific halibut in trawl
fisheries for Pacific cod. Preliminary results are very promising that
this technology will be successful in reducing bycatch of halibut. AFSC
has also worked with industry and the North Pacific Fishery Management
Council (NPFMC) to develop other bycatch management measures that would
provide substantial incentive for the development of more selective gear
types.

A workshop on fishing gear impacts and seafloor mapping was hosted by
the ABL of the AFSC and the NMFS Alaska Regional Office. The focus of
the workshop was to improve cooperation with other NOAA research
conducted by the U.S. Geological Survey, the National Undersea Research
Program, and the National Ocean Service. Plans for coordination were
developed at the workshop.

The NMML worked closely with the Northwest Regional Office and the Makah
tribe to develop methods for deterring the incidental mortality of
harbor porpoise in salmon gill nets. The recent development of an
acoustic pinger has resulted in a significant reduction in marine mammal
bycatch.

Live fish experiments at the Hatfield Marine Science Center in Newport,
OR, test fishing gear performance and fish behavioral studies to reduce
bycatch and bycatch mortality of prohibited, undersized, or unmarketable
species, and to understand performance of survey gear.

Research Priorities, FY 2001-2006:

• Continue to conduct research to measure direct effects of bottom
trawling on seafloor habitat according to a five-year research plan.

• Conduct fishing gear performance and fish behavioral studies to reduce
bycatch and bycatch mortality of prohibited, undersized, or unmarketable
species, and to understand performance of survey gear.

• Work with industry and the Council to develop bycatch reduction
techniques.

# III. Research on the fisheries

Recent Accomplishments:

The AFSC conducted socio-economic research to support fishery management
actions, particularly those of the NPFMC. The Center\'s principal
accomplishments

on socio-economic research were as follows:

• Developed a report on the economic status of the Alaska groundfish
fisheries and incorporated it as part of the SAFE reports for the Bering
Sea/Aleutian Islands (BSAI) and Gulf of Alaska (GOA) groundfish
fisheries.

• Identified and assessed economic consequences associated with
alternatives for the programmatic supplemental environmental impact
statement (SEIS)

for the BSAI and GOA groundfish fisheries.

• Analyzed economic consequences of fishery management actions including
additional restrictions on the atka mackerel, pollock, and Pacific cod
fisheries to provide additional protection for sea lions through the use
of trip limits, stacking groundfish permits, and changing time/area
closures to assess interactions between pollock fisheries and sea lions.

• Published research on the decision of fishers to choose fishing
locations, marine protected reserves, valuing recreational fisheries,
and behavioral modeling of Alaska groundfish fisheries.

The AFSC completed a qualitative assessment of excess fishing capacity
in federally managed fisheries off Alaska, assisted in a NMFS national
effort to define and measure excess capacity, and revised the guidelines
for economic analysis of fishery management actions.

Full utilization of groundfish is mandated by regulation in Alaska. The
AFSC contributed to research that led to a ban on roe-stripping and the
proper utilization of young fish. The research efforts now concentrate
on developing and incorporating aspects of uncertainties associated with
stock assessments and ecosystem interactions of the major component
species to assess the status, population dynamics, and biological
productivity of most of the major groundfish species managed by FMP\'s
in the BSAI and the GOA regions. For example, the effects of variable
recruitment and predation needs of marine mammals have been incorporated
to provide risk analyses of different exploitation strategies on the
Gulf of Alaska pollock stocks so that the stocks are properly utilized.

The AFSC also maintains a fish lab at the Hatfield Marine Science Center
at Newport, OR, that conducts research with live fish. The focus of the
research is to measure mortality resulting from the capture process of
Pacific halibut, sablefish, and juvenile pollock taken as bycatch in
trawl and longline fisheries. While the research is focused on impact
analyses of human activities on the fish, some of the lessons learned
may be useful for aquaculture research. For example, growth and
survivorship studies are conducted to study the influence of water
temperature on growth of young fish.

Research Priorities, FY 2001-2006:

# III.A. Social and economic research

• The AFSC has initiated a data collection program that will collect
cost, earning, and employment data for the Alaska groundfish fishery and
has worked with the NPFMC, Alaska Department of Fish and Game, and the
Alaska Fisheries Information Network (AKFIN) to identify the elements of
a broader program to collect economic and social data. This project is
continuing to build upon the economic database that is now available.

• Assess the economic impact of different fishing and conservation
strategies that are proposed throughout the year by NMFS and the
Councils.

• Compile the economic status of Alaska\'s groundfish fisheries as part
of the annual Groundfish SAFE reports.

• Assess economic performance of the Alaska groundfish and halibut
fisheries and research to improve these assessments.

# III.C. Marine aquaculture

• Study the growth, distribution, behavior, and early marine survival of
salmon; and conduct research on salmon biology and enhancement
technology in

Alaska.

# IV. Information management research

Recent Accomplishments:

The AFSC communicates its scientific information and advice, along with
the associated uncertainties, to the Councils, other management
authorities, and the public. For example, survey results of the AFSC
were disseminated to the user groups through the participation of
experts at meetings and submission of technical reports and published
papers. On a yearly basis, the AFSC publishes roughly 100 scientific
papers as well as over a dozen NOAA Technical Memos and Center Processed
Reports.

The AFSC and other research units of NMFS used stock assessment
workshops, peer reviews, and other fora to ensure that our information
and advice are developed through an open and collaborative process. The
stock assessment process of the AFSC undergoes periodic review
internally and externally throughout the years.

The AFSC provided guidelines to assist the Councils in assessing and
specifying MSY for managed fisheries. The AFSC (REFM Division) has the
lead role for defining and estimating the MSY levels for all the
groundfish stocks managed in the BSAI and GOA area. The information
helps the NPFMC determine the relative status of the stocks to
historical levels. The AFSC also has the lead role in defining and
estimating the overfishing levels for each of the groundfish stocks
managed in the BSAI and GOA area. These maximum fishing levels guide the
NPFMC to manage exploitation of the stocks within biologically safe
levels.

The AFSC (REFM) provided the technical lead role to develop objective
and measurable criteria for stocks that are overfished or approaching an
overfished condition. The definitions were used as uniform applications
throughout NMFS. These definitions would standardize the criteria for
determining depleted stocks due to fishing and other causes throughout
the nation.

The AFSC and the Alaska regional office took the lead in developing a
comprehensive Bering Sea ecosystem research plan. Two workshops were
held in Anchorage to bring together research experts from NMFS, other
elements of NOAA, different units from the Department of the Interior,
the Environmental Protection Agency, the Alaska Department of Fish and
Game, the University of Alaska, the University of Washington, Alaska
Native Groups, and other fisheries organizations to share in the
planning efforts. This comprehensive research plan can be found at the
Bering Sea and North Pacific Ocean Theme page under Interagency
Information Exchange at www.pmel.noaa.gov/bering/pages/inter-agency/.
Additionally a meta-data base of all the research of the different
research agencies now resides at www.pmel.noaa.gov/bering/mdb/.

Research Priorities, FY 2001-2006:

• Continue to build data infrastructure and resources for easy access
and data processing. The AFSC\'s key data bases are its survey data
bases from the 1950\'s (or earlier) and the scientific observer data
base that extends back to the foreign fishing days of the 1960s.

• Continue to provide information products based on experts and
technical data that support NMFS, the regional office, the Councils,
international scientific commissions, and the overall research and
management community.

**NORTHWEST FISHERIES SCIENCE CENTER (NWFSC)**

The Northwest Fisheries Science Center (NWFSC) conducts basic and
applied research to support the management, conservation, and
development of the Pacific Northwest region\'s anadromous and marine
fishery resources and their habitats. The NWFSC carries out its research
from its Montlake Laboratory headquarters in Seattle and from five
research stations located in Manchester, Mukilteo, and Pasco, WA, and at
Newport and Pt. Adams (Hammond), OR. The Center conducts both field and
laboratory research in coastal and estuarine environments of Washington
and Oregon, as well as in inland freshwater habitat populated by
anadromous species in Washington, Oregon, Idaho, and Montana. The Center
also supports annual and triennial groundfish surveys off the west
coast. The NWFSC has several small vessels for conducting field studies.
The R/V *Harold Streeter* serves Puget Sound and the R/V Sea Otter, R/V
*Nerka*, and the R/V *Columbia* serve Columbia River basin projects. The
NWFSC relies on the NOAA R/V *Miller Freeman* for some of its research
survey data, and also relies on privately chartered vessels and academic
research ships to supplement its research capability.

The NWFSC provides the scientific basis to conserve and recover
declining Pacific salmon and groundfish populations as well as to
address overarching issues such as the impacts of climate shifts,
biotoxins, including harmful algal blooms, and toxic chemical pollution
on anadromous and marine fishery resources. The NWFSC conducts multi
disciplinary research involving fisheries science, marine biology and
ecology, genetics, biochemistry, molecular biology, oceanography, and
aquaculture.

Center scientists conduct stock assessments, investigate the impact of
bycatch, describe essential fish habitat, and develop new seafood
technologies to reduce waste and maximize returns to fishers and
processors. Center scientists also develop quantitative models, genetic
tools, electronic monitoring devices, hatchery and captive-broodstock
rearing techniques, and strategies for safe migration of salmon to the
sea. The NWFSC\'s innovative and original research has helped establish
new aquaculture endeavors, seafood processing, dam passage equipment and
techniques, methods to detect and evaluate harmful algal blooms, and
technology to integrate and track important fisheries dependent data,
including fish catch and fish ticket data. The NWFSC\'s pioneering work
on evolutionarily significant units (ESUs) helped define the science of
salmonid stock identification under the Endangered Species Act (ESA).

NWFSC research supports critical management decisions on the
conservation and recovery of Pacific salmon and groundfish populations,
contaminant management, and seafood safety issues. Center scientists are
leading west coast recovery efforts for salmon listed under the ESA,
providing the scientific information necessary to determine whether
certain salmon and groundfish species should be listed as endangered or
threatened, understanding crucial links between habitat conditions and
species productivity, developing plans to rebuild overfished groundfish
stocks, and delivering the science necessary to develop or revise
national policies on contaminants, bycatch, fisheries dependent data
collection, fishery closures, harmful algal blooms, and other issues.
Center scientists are also conducting social and economic studies to
support the fishery management process.

Center research is used by the Pacific Fishery Management Council (PFMC)
to build and maintain sustainable fisheries through the development of
regional fishery management plans and subsequent amendments. NWFSC
scientists relay applicable research results through their participation
in committee meetings of the PFMC, Pacific Salmon Commission, and the
Pacific States Marine Fisheries Commission (PSMFC), as well as other
national and international fora, including National Stock Assessment
panels and workshops. NWFSC research also supports national and
international efforts, including the U.S. GLOBEC program.

The NWFSC nurtures and maintains strong collaborative relationships with
other Federal agencies, industry, environmental groups, Native American
tribes, individual fishers, universities, and other research and
academic institutions. The NWFSC conducts annual groundfish surveys in
collaboration with industry and provides west coast specific research
needed by other line offices within NOAA (e.g., National Ocean Service)
as well as other Federal agencies (e.g., the Bonneville Power
Administration and the Army Corps of Engineers). The NWFSC, working with
the Northwest Indian College (NWIC), the Department of Commerce, and
NOAA, established the National Indian Center for Marine and
Environmental Research and Education (NICMERE). NICMERE provides
training at the NWIC and NWFSC for students from the 40 tribes served by
the NWIC, and also to students from Tribal Colleges and Universities
(TCUs) throughout the nation through a distance learning network. The
Center also sponsors numerous students in marine research, technology,
and library science through cooperative research agreements with
regional universities and technical schools.

# Recent Accomplishments and Research Priorities for FY 2001-2006

# I. Research to support fishery conservation and management

Recent Accomplishments:

Comprehensive research plans for west coast groundfish and Pacific
salmon were developed to ensure that all relevant scientific information
is available to regional managers and policy makers. Scientists outside
the agency, as well as other NMFS Centers, reviewed and provided
comments on these documents.

The NWFSC conducted extensive assessments of west coast groundfish
species and analyzed the potential for rebuilding species classified as
overfished.

A new observer program for west coast groundfish was established. In
partnership with the PSMFC, this program is the first new coastwide
observer program launched from the NWFSC and implements a new electronic
system for capturing and communicating fishery-dependent data. NWFSC
also has begun management of the ongoing Pacific whiting observer
program.

Salmon Technical Recovery Teams (TRTs) were established in three
geographic regions Puget Sound, Willamette/Lower Columbia River, and the
Columbia Basin. TRTs are developing biological criteria for delisting
salmon populations and will assist in the development of recovery plans.
TRTs are chaired by NWFSC researchers and are composed of scientists
from Federal, state, county, city, tribal organizations, and
universities. The NWFSC also created a Recovery Science Review Panel,
composed of renowned external scientists, to help ensure integrity and
consistency in the scientific aspects of recovery planning.

Research Priorities, FY 2001-2006:

I.A. Biological research concerning the abundance and life history
parameters of fish stocks

• Develop biologically-based delisting goals for listed salmon and
steelhead. This action will be carried out by the Puget Sound,
Willamette/Lower Columbia River, and Columbia Basin TRTs for ESUs of
Pacific salmon that are listed as threatened or endangered under the
ESA.

• Evaluate the direct and indirect effects of nutrients derived from
salmon carcasses on salmon populations.

• Apply extinction risk estimates to salmonid populations to establish
rationally based priorities for recovery goals.

• Analyze data from trawl surveys, fishery catch, and life history
studies to produce reliable assessments of the status of groundfish
species.

• Explore and quantify the ecological linkages of salmon distribution
and survival in estuarine and near shore environments by studying
juvenile Pacific salmon in the Columbia River plume and at Oregon\'s
Cape Blanco.

• Improve west coast groundfish resource surveys and the scientific
assumptions on which assessments are based. This will ensure stock
assessments more accurately reflect population trends and provide for
economic viability of coastal communities, while preventing overfishing.

# I.B. Social and economic factors affecting abundance levels

• Expand sociological and economic research and incorporate results into
the fishery management process.

• Develop new economic models and analyses to support management
decisions.

# I.C. Interdependence of fisheries or stocks of fish

• Conduct Genetic Stock Identification (GSI) studies to help determine
stock allocation under the Pacific Salmon Treaty, analyze the
composition of chinook salmon fisheries in California, help elucidate
the ocean migration patterns of listed salmon stocks, and compare
different methods of stock identification through computer simulations.

• Develop quantitative and qualitative methods of classifying risk for
species of conservation concern through computer modeling and data
analysis.

• Assess both the positive and negative effects of hatcheries on wild
salmon populations by measuring the relative fitness of hatchery fish
and their descendants when they spawn in the wild, developing and
applying better models of phenotypic and genetic evolution in hatchery
influenced populations, characterizing the genetic consequences of
inbreeding within and interbreeding between salmon populations, and
developing and applying methods for addressing ecological risks
associated with artificial propagation programs.

• Better understand and quantify the importance of genetic diversity
within and among salmon populations. Research projects include: (1)
measuring the effects of in-breeding in Puget Sound chinook salmon; (2)
creating genome maps of chinook and coho salmon and identifying
chromosomal regions associated with traits important to adaptation and
fitness in species; and (3) determining the usefulness of molecular
tools for measuring natural selection and local adaptation.

• Further develop molecular techniques that identify salmon species
using DNA markers to identify individual populations within salmon
species.

• Use genetic analysis to further investigate the predator/prey
relationship between harbor seals and salmon as it relates to recovering
some listed salmon populations.

• Estimate the degree of genetic divergence among spawning populations
of Pacific hake in Puget Sound and the Strait of Georgia to support
decisions to determine the status of distinct population segments for
Puget Sound Pacific hake under the ESA, and conduct, if necessary,
additional genetic work to better elucidate the population structure of
these species.

I.D. Identifying, restoring, and mapping of essential fish habitat (EFH)

• Evaluate the effectiveness of habitat restoration efforts in
Washington and Oregon, including evaluating the extent to which
placement of structural elements in streams improves habitat quality and
increases salmon abundance.

• Develop statistical tools for recovery planning that meld economic
costs with biological benefits to ensure that conservation planning is
responsive to both economic considerations and biological needs.

• Develop monitoring and evaluation strategies to help determine the
rate and success of salmon recovery.

• Determine what aspects of estuarine conditions are critical to salmon
survival.

• Define essential fish habitat and assess the impact of fishing gear on
stocks by answering three questions: (1) which habitats are susceptible
to gear impacts; (2) what is the relationship between differing levels
of fishing activity and habitat degradation; and (3) how can current
fishing practices be modified to minimize risks to habitats.

I.E. Impact of anthropogenic factors and environmental changes on fish
populations

• Investigate the links between industrial waste, mining activity,
pesticide use, and other physical and chemical alterations of coastal
and urban habitats on decreased fisheries productivity. Establish
threshold values for contaminant effects so biological effects on
species can be predicted.

• Investigate the impact of ocean and marine climate variations on
salmon by studying salmon distribution, abundance, food habits, and
predator-prey

relations.

• Determine the impacts of non-indigenous species on salmon by
developing new statistical techniques, implementing food web modeling,
and conducting field studies and experiments.

• Investigate the effects of chemical contaminants on the growth,
development, reproduction, and survival of marine fish and mammals.

• Investigate how natural environmental variations and exposure to
contaminants affect juvenile salmon during their passage through
estuaries in Washington and Oregon, focusing on how natural and human
induced stresses alter growth, neurological function and behavior, and
induce disease-related mortality.

• Quantify how salmon use stream and river habitats by collecting
descriptive information as well as assessing population responses to
different watershed conditions.

• Explore how land use practices such as logging, farming, urban
development, and other human activities impact the recovery of
threatened and endangered Pacific salmon.

# II. Conservation engineering research

Recent Accomplishments:

The adult return of endangered Redfish Lake sockeye salmon was
significantly increased. Using captive broodstock technology, juveniles
produced from all returning fish (16) during the 1990s were reared and
released. Over 250 adults returned this year from the first year class.
A genetic marker for differentiating among strains of bacterial kidney
disease (BKD) was identified. Used in combination with other molecular
methods, this marker will be a powerful new tool for investigating
sources of infection and routes of transmission in both wild and captive
salmon.

Passive integrated transponder (PIT) tag technology was expanded in the
Columbia River Basin. As a result, it will be possible to install adult
salmonid PIT-tag detection systems in all fish ladders at Bonneville Dam
by 2002, allowing scientists to make precise estimates of ocean survival
of salmon and steelhead.

A collaboration with the net pen industry was established to conduct a
two-year risk benefit assessment of the Puget Sound net pen industry.

Research Priorities, FY 2001-2006:

• Develop conservation hatchery technology to aid recovery of ESA-listed
stocks of Pacific salmon. Further develop the Natural Rearing
Enhancement System (NATURES), a system for culture of Pacific salmon in
raceways that simulate natural environments to develop salmon with
characteristics and behavior more like their wild counterparts.

• Develop broodstock technology to restore depleted Pacific salmon
stocks. Improve captive broodstock rearing techniques and gauge the
potential of hatchery salmon to alter the genetics of wild populations.

• Develop methods to identify and control pathogenic microorganisms,
including BKD, that threaten fishery resources, by conducting genetic
studies of the bacterial pathogens, characterizing host-pathogen
interactions, and developing highly sensitive molecular techniques.

• Determine both the direct and indirect effects of hydropower
operations on salmon populations.

• Continue advancing PIT-tag technology to promote safe and efficient
fish passage through hydropower systems, and other unnatural barriers,
and to gain understanding of migration patterns upsteam and downstream.

# III. Research on the fisheries

Recent Accomplishments:

Over 5,000 juvenile lingcod were produced through culture techniques for
early life history and habitat preference research.

A new method was developed for producing surimi for human consumption
from fillet trimmings of cod, pollock, and underutilized species such as
arrowtooth flounder.

A regional aquaculture initiative was drafted to establish codes of
conduct and best management practices in coastal waters and the EEZ.

Research Priorities, FY 2001-2006:

# III.A. Social and economic research

• Analyze current and historical operating costs and activity patterns
in the fishing industry and indicate how each group would be
economically impacted by changes in fishing gear use and area
restrictions, limits on individual catch, and/or direct allocation
between user groups.

# III.B. Seafood safety research

• Explore more complete utilization of marine resources by developing
methods to recover more flesh from targeted fish species and to identify
and control naturally occurring microbial pathogens that limit shellfish
harvests.

• Develop methods to identify and analyze marine toxins and the algae
that produce them. Ascertain how these toxins are transmitted and their
effect on target organisms. Determine the health risks that biotoxins
pose for fish and shellfish.

# III.C. Marine aquaculture

• Develop laboratory aquaculture techniques for targeted marine species,
by studying aquaculture engineering, fish physiology, nutrition,
pathology, and developmental biology to relieve pressure on severely
depressed wild marine stocks.

# IV. Information management research

Recent Accomplishments:

The Alpha-level Electronic Fish Catch Logbook Project (EFCL) system was
demonstrated to the states of California, Oregon, and Washington and to
fishers and fish processors. Fishers requested that the NWFSC develop an
electronic system to allow better use of data that fishers and
processors are already required, by state law, to collect. Users wanted
to be able to enter fish catch landing data electronically and to use
computers to communicate and track fishing locations in real time, or
near-to-real time. This system can improve fisheries management and
support better fishing practices.

A salmon data team was created and launched to improve Pacific salmon
data management, data access, and data sharing between parties and
institutions.

Research Priorities, FY 2001-2006:

• Complete the current development effort of the EFCL with on-vessel
beta testing.

• Integrate all data on salmon stocks in Washington, Oregon, and
California generated by ESA status reviews with data maintained in the
StreamNet database. The NWFSC has created an interagency salmon data
team to develop a comprehensive management model. The model\'s purpose
is to anticipate multi-species impacts resulting from changes in
environmental and fishing regimes and to support tribal fishery managers
with data and analysis that focuses on maintaining long-term viability
and genetic diversity of local breeding populations.

• Develop statistical approaches to improve monitoring and evaluation of
threatened or endangered species.

• Improve Cumulative Risk Initiative web-based reporting system outputs
by strengthening links to raw data and other information sources.

• Provide support for area school systems interested in implementing
salmon genetics curricula as well as vocational programs for training
technicians.

**SOUTHWEST FISHERIES SCIENCE CENTER (SWFSC)**

The Southwest Fisheries Science Center (SWFSC) headquarters is located
in La Jolla, CA, and research is conducted at laboratories in La Jolla,
Santa Cruz, and Pacific Grove, CA, and Honolulu, HI. The current
staffing level involved in MSFCMA-related activities is at about 156
full-time equivalents (FTEs). An estimated 65% of total SWFSC resources
are assigned to direct MSFCMA activities. NOAA research vessels assigned
to fisheries research in the SWFSC are the NOAA R/V *Townsend Cromwell*,
assigned to the Honolulu Laboratory, and the NOAA R/V *David Starr
Jordan*, which has San Diego, CA, as its homeport. In addition about
two-thirds of the NOAA vessel *McArthur*\'s time is used by the Center.

The SWFSC is a world-class research organization which conducts
integrated, multi disciplinary research programs in biology,
mathematics, oceanography, and economics for the purpose of developing
scientific technology and information to support the management and
allocation of Pacific coastal, central and western Pacific insular,
coral reef, and high-seas fishery resources. These activities support
the scientific, statistical, and economic needs of the Western Pacific
and the Pacific Fishery Management Councils and international
commissions for large pelagic fishes and Antarctic resources. Center
programs also support efforts directed toward the reduction of protected
species interactions, fishery-related porpoise mortality, and a better
understanding of the biological and environmental factors affecting the
marine resources exploited by U.S. commercial and recreational
fisheries. The Center provides the scientific information necessary to
conserve and manage the following important fisheries in the Pacific and
Antarctic regions:

• Large pelagic fishes of the Pacific Ocean (tuna, billfish, shark, and
swordfish).

• Crustaceans of the central Pacific (lobster).

• Precious corals of the central Pacific.

• Bottomfish and seamount species of the western Pacific.

• Groundfishes of the west coast (Pacific hake, rockfishes, lingcod).

• Small coastal pelagic species of the west coast (northern anchovy,
sardine, mackerel, squid).

• Salmon of the west coast.

• Antarctic krill, crabs, squid, finfish including Patagonian toothfish.

The Southwest Fisheries Science Center specializes in fisheries of the
California Current, Pacific oceanic, and Antarctic regions. Research is
carried out on the ecology, population dynamics, fisheries, and stock
assessment of small coastal pelagic species, west coast groundfishes,
billfish, tunas and sharks, and California salmon. The Center maintains
and utilizes the largest database on tuna and tuna-related fisheries in
the world. The Center makes extensive use of biological and fisheries
data, which are collected by observers placed on fishing vessels by the
Southwest Region, to monitor interactions with protected resources to
achieve goals related to the MSFCMA. It is also considered a leader in
fish survey design, conducting surveys to monitor early recruitment
success of economically important fish stocks along the U.S. west coast.
It is a co-participant in the State-Federal California Cooperative
Fisheries Investigations, a comprehensive long-term study of the biology
and oceanography of the California Current. In the oceanic Pacific, the
Center is the leading source of stock assessment expertise on tropical
island and oceanic resources, especially bottomfishes, lobster, tunas,
sharks, and billfishes and cooperates with the University of Hawaii and
the Western Pacific Fishery Management Council (WPFMC) in undertaking
the Western Pacific Pelagics Research Program. The SWFSC is also leading
a multi-partner research and long-term monitoring effort to assess the
health of the Nation\'s largest coral reef resource and to mitigate the
impact of marine debris on the coral reef ecosystem of the Northwest
Hawaiian Islands (NWHI). In the Antarctic, the SWFSC leads U.S. research
directed at gathering ecological information to prevent overexploitation
of fish and krill and to protect Antarctic living marine resources. The
SWFSC provides oceanic environmental data and indices to the rest of
NMFS as well as to other Federal, state, academic, and foreign fisheries
scientists. Center scientists are leaders in the research and
development of fisheries-relevant environmental data products. The SWFSC
is home to two NOAA CoastWatch nodes at its Honolulu and La Jolla
laboratories.

SWFSC scientists have taken the lead in characterization of large- and
small-scale habitats that support groundfish and bottomfish populations
in deep water. This work requires an interdisciplinary approach from
fishery biologists, geologists, and ecologists and couples the use of
GIS with remote-sensing acoustic tools, *in situ* survey techniques
using submersibles, and spatial analyses. This approach is being applied
to the identification of EFH, the improvement of stock assessment
surveys, and the evaluation of MPAs as an effective supplement to
traditional fishery management. The National Ocean Service\'s MPA Center
is cooperatively co-located with the SWFSC\'s Santa Cruz Laboratory.

The SWFSC maintains an active communications network with constituents,
colleagues in the scientific professions, and the public to receive
input for research planning, execution, and results. The network
includes frequent dialogue with commercial and recreational fishers,
leaders of environmental groups, participants of fishery management
councils, state and Federal research agency staff, and outside
scientists in the United States and foreign countries. Supporting this
network is an infrastructure that includes cooperative agreements to
support collaborative work with researchers in state agencies,
universities, and foreign governmental agencies for collecting logbook
and other types of fisheries data and for shared research projects;
arrangements for data exchange; and contracts for charters of research
vessels and specialty expertise. The SWFSC and its laboratories maintain
up-to-date Internet sites that provide a range of information, including
scientific reports and summary data bases available to other researchers
as well as the general public.

The SWFSC provides scientific and research support for U.S. commitments
resulting from the following international arrangements and agreements
in the Pacific region: (1) Convention for the Conservation of Antarctic
Marine Living Resource (CCAMLR), which manages the marine living
resources of the Antarctic; (2) Inter-American Tropical Tuna Commission
(IATTC), which deals with tuna and tuna-like fishes, and the
tuna-dolphin issue of the eastern Pacific Ocean; (3) South Pacific Tuna
Treaty (SPTT), which provides tuna fishing access to the western Pacific
Ocean; (4) North Pacific Interim Scientific Committee for Tuna and
Tuna-like Species (ISC), which promotes research on tuna and tuna-like
species of the North Pacific Ocean; (5) Standing Committee on Tuna and
Billfish of the Secretariat of the Pacific Community (SCTB), which
facilitates collaborative research on tuna and billfish of the western
Pacific Ocean; (6) MEXUS Pacifico, which promotes joint U.S.-Mexico
research projects of mutual interest; (7) North Pacific Albacore
Workshop (NPALB), which promotes stock assessment research for north
Pacific albacore; (8) Commission on the Conservation of Highly Migratory
Fish Stocks in the Western and Central Pacific Ocean (MHLC), which will
manage the highly migratory fish resources of the western and central
Pacific Ocean; and (9) International Whaling Commission (IWC), which
promotes conservation of whale stocks. In addition, SWFSC scientists
periodically work jointly with other scientists on projects sponsored by
international organizations such as the UN Food and Agriculture
Organization (FAO), Global Ecosystem Dynamics (GLOBEC), and the North
Pacific Marine Science Organization (PICES).

The Southwest Fisheries Science Center maintains an exceptional
fisheries economic research capability. Special studies are undertaken
to help explain and evaluate the potential impacts of various management
options on components of the fishery or the public. In addition,
economic data collection and analyses are carried out to evaluate the
economic health of fisheries or components of the fisheries.

# Recent Accomplishments and Research Priorities for FY 2001-2006

# I. Research to support fishery conservation and management

Recent Accomplishments:

Studies on the basic biology, movement, and population status of North
Pacific swordfish were completed to provide the WPFMC up-to-date
information for the management of its longline fishery. Similar
information was provided on the status of the blue shark; in both cases
the stock assessments indicated these populations were being managed in
a sustainable manner. Subsequent analyses are underway for blue and
striped marlin, other tuna, and miscellaneous pelagic species. This work
has involved collaboration with fisheries scientists from around the
Pacific, particularly with Japanese scientists.

A multi-national synoptic survey of krill biomass of Antarctic
Statistical Subarea 48 (Peninsula, S. Orkney, S. Georgia, and S.
Sandwich) was completed. As a result of a five-year planning effort, one
ship from the U.S., United Kingdom, Japan, and Russia each conducted a
one-month acoustic/oceanographic survey of the above areas and the
open-ocean areas between each island group. This was a CCAMLR-sponsored
survey with the participation of scientists from the International
Whaling Commission. The U.S. convened a CCAMLR workshop to complete
analyses of survey data.

The Groundfish Program provided PFMC with stock assessments for bocaccio
rockfish, widow rockfish, canary rockfish (south), and lingcod (south),
as well as rebuilding analyses for bocaccio rockfish and Pacific ocean
perch. SWFSC staff initiated and convened a review of harvest rates for
west coast groundfish, resulting in significant revision of PFMC
management policy. Midwater trawl surveys provided annual indexes of
rockfish recruitment strength for use in stock assessments and analyses
of environmental influences.

A recent analysis of atmospheric observations in the North Pacific
revealed extensive decadal-scale variations in the mid-latitude winter
surface wind stress. In the decade after the winter of 1976, eastward
wind stress doubled over a broad area in the central North Pacific and
the core of the North Pacific Current was displaced about 360 nautical
miles southward. The result was that surface water entering the
California Current was of more subtropical origin in the post-1976
decade. All factors considered contributed to a multi-decadal
temperature pattern of warm, nutrient-poor surface waters in the
California and Alaska current regions. In association with the 1976
climatic shift, marine fishery production in the Oyashio, California,
and Alaska currents altered dramatically, suggesting that natural
environmental variation significantly alters the long-term yields from
many North Pacific fisheries.

Research Priorities, FY 2001-2006:

I.A. Biological research concerning the abundance and life history
parameters of fish stocks

• Conduct biological research by the U.S. Antarctic Marine Living
Resource Program concerning abundance and life history parameters of
fish stocks.

• Plan, conduct, and present results of annual predator/prey interaction
studies in waters around South Shetland Islands, Antarctica.

• Understand the stock dynamics and influence of environmental
conditions on the NWHI spiny and slipper lobster.

• Complete assessments of the coral reef ecosystems of the central and
western Pacific.

• Develop a new Bayesian method of stock assessment for application to
data-poor groundfish species.

• Develop a groundfish survey using chartered commercial fishing vessels
for the Southern California Bight.

• Develop a population genetic database of all anadromous California
salmonid stocks for determination of stock structure and as a baseline
for future monitoring efforts.

• Provide quantitative estimates of the take of listed salmon in the
California salmon harvest and evaluate proposals to minimize list
species take.

• Publish Rockfishes on the Northeast Pacific, a comprehensive book on
the identification, description, biology, distribution, conservation,
and

fisheries of 72 species of rockfishes recorded from Mexico to Alaska.

• Assist the California Department of Fish and Game in developing a
system of marine protected areas for California nearshore waters.

• Implement an archival tagging program for North Pacific albacore in
cooperation with the albacore fishing industry, Japanese fishery
agencies, and

other groups to trace their movements between fisheries and countries.

• Define unit stocks using genetics and otolith chemistry in highly
migratory species (albacore, thresher shark, and striped marlin), in
coastal pelagic species (sardine), and in groundfishes (cabezon, Puget
Sound and coastal brown rockfish, and other rockfishes).

• Conduct peer-reviewed assessments and statistical analyses on stocks
of groundfish, coastal pelagics, tunas, sharks, swordfish, salmon, and
other species.

• Develop a new generation of stock assessment models for highly
migratory species and coastal pelagic species stocks of the Pacific and
the state-of-the-art software to support them, using modern statistical
optimization techniques, Bayesian methods, and object-oriented
programming languages.

• Use pop-up satellite tags to identify forage and migration habitats of
exploited species and protected resources in the central and western
Pacific.

#### I.B. Social and economic factors affecting abundance levels 

• Expand sociological and economic research and incorporate results into
the fishery management process.

• Develop behavioral models of economic incentives affecting the level
and allocation of fishing effort in FMP fisheries.

• Initiate an economic survey of salmon commercial troll fishery.

• Enhance existing salmon harvest models to better predict fishing
effort response to changes in sport and commercial fishery regulations.

• Conduct RIRs and RFAs for management actions being considered for all
FMP fisheries.

• Evaluate growth in productivity for purse seine vessels harvesting
tuna in the western and central Pacific, paying special attention to the
effects of fish aggregating devices (FADs).

# I.C. Interdependence of fisheries or stocks of fish

• Complete research program under the International Dolphin Conservation
Protection Act to determine whether the chase and encirclement by the
fishery is having a significant adverse impact on depleted dolphin
populations in the eastern tropical Pacific.

• Design sampling surveys to analyze the impact of marine mammals on
listed salmon.

• Develop integrative oceanic environmental indices to improve
understanding of how environmental variability affects fish stocks.

• Extend analysis of factors affecting longline-turtle and longline-sea
bird interactions to include more detailed oceanographic, tagging, and
behavioral analysis.

• Evaluate the foraging ecology of the Hawaiian monk seal in terms of
its use of fishery resources such as lobsters and bottomfish.

• Initiate studies of trophic ecology and growth biology of billfish and
miscellaneous pelagic species (e.g., mahimahi, ono, moonfish).

• Integrate central Pacific pelagic ecosystem monitoring with stock
assessments.

• Use ecosystem models such as Ecopath with Ecosim to describe ecosystem
structure and dynamics for pelagic and insular ecosystems.

I.D. Identifying, restoring, and mapping of essential fish habitat (EFH)

• Participate in salmon EFH identification and protection.

• Develop and produce digital mosaics of seafloor habitats from
electro-optic images into a format compatible with other geo-referenced
data sets used in GIS.

• Develop approaches to evaluate essential habitat of pelagic fishes
based on satellite remote sensing and applications of archival and
pop-up satellite tags.

• Conduct baseline assessments and map major habitats of the coral reef
ecosystem in the central and western Pacific (American Samoa, Guam,
Hawaii, the Northern Mariana Islands, and remote Pacific islands).

• Investigate sources and ecosystem impacts of marine debris and
identify mitigation measures.

• Evaluate EFH and monitor marine resources in newly created \"no-take\"
marine reserves planned for the Channel Islands National Marine
Sanctuary.

• Define essential spawning habitat of market squid and the effects of
fishing gear on that habitat and the survivorship of demersal egg
capsules.

I.E. Impact of anthropogenic factors and environmental changes on fish
populations

• Estimate the impact of marine debris on the health of coral reef
ecosystems.

• Investigate relationship of juvenile salmon abundance and
physiological status with respect to oceanographic features (e.g.,
estuary plumes, upwelling centers, coastal jets, eddies, and fronts).

• Determine the effects of hatchery and aquaculture operations on
indigenous salmon and steelhead stocks in California by molecular
genetic analysis of museum specimens and previously collected scale
samples.

• Evaluate the effects of climate change of interannual, decadal, and
centennial scales on fisheries and fish habitat.

• Develop models of the impacts on salmon populations of natural
disturbances due to climatologies.

• Improve methods to identify pathways in estuarine ecosystems for the
bio-accumulation of contaminants in salmon.

• Examine the association of recruitment of young rockfishes and
climatic and oceanographic variables off central California.

• Investigate use of small estuaries on central California coast by
juvenile salmonids. Assess the effects of environmental variability,
particularly sandbar dynamics and water quality, on growth, development,
and survival.

• Investigate the linkage between the dynamics of oceanic features,
including eddies, fronts, and boundary currents, and the dynamics of
highly migratory fishes (tunas and billfishes) in the central and
western Pacific.

# II. Conservation engineering research

Recent Accomplishments:

A carefully constructed experimental design for testing alternative
methods to avoid longline interactions with sea birds was completed. It
identified several key methods for mitigating such impacts. These
results were combined with WPFMC-supported research aboard commercial
longliners to gain industry support of mitigation techniques and have
been proposed by the Council as management regulations.

A comprehensive multi-agency program was initiated to remove marine
debris from the NWHI coral reef ecosystem as a means to reduce impacts
on the corals and to reduce mortality of the Hawaiian monk seal. To
date, hundreds of tons of debris have been removed and the program will
continue for the next two years. The Habitat Restoration Cost Workshop
was convened in Portland, OR, in November 2000 to evaluate the
feasibility of developing and applying standardized methodologies for
estimating salmon habitat restoration costs, which would then be used
for salmon recovery planning. Restoration topics covered by the workshop
included road maintenance and road decommissioning, streambanks
stabilization, instream treatment, fish passages and fish screens, and
wetland creation and restoration. Presentations were made by engineers,
biologists, hydrologists, geologists, foresters, and economists
representing Federal, state, and local agencies and the private sector.

An analysis of acoustic backscatter from an acoustic Doppler current
profiler (ADCP) and surface temperature and salinity continuously
sampled in relation to the continuous underway fish egg sampler provided
a description of the sardine spawning habitat. This detailed
observational analysis shows, on a survey-by-survey basis, that eggs and
larvae are found in waters that are transitional between those that are
freshly upwelled and those of the California Current proper.

The SWFSC completed research to improve our understanding of fisheries
impacts on marine ecosystems. The study pioneered the use of the
combination of acoustic techniques, fishing information, and direct
submersible research to directly evaluate deepwater fisheries habitat.
Research published in the past year considered the potential of
side-scan sonar to enumerate the frequency of trawl tracks on soft
bottom environments, suggesting that acoustic remote sensing is a
promising independent approach to evaluate fishing effort on a scale
consistent with commercial fishing activities.

Research Priorities, FY 2001-2006:

• Undertake studies to determine the best methods to increase survival
of protected, prohibited, or sensitive species caught by longline and
troll vessels.

• Determine how to increase survival in the economic/regulatory discards
of undersized tunas, sharks, and other fishes.

• Create and test new trap designs for juvenile out-migrant salmon that
will minimize predation on juveniles from larger salmonids (in
cooperation with Humboldt State University).

• Investigate methods for reducing longline interactions with sea
turtles, including at-sea experiments with the commercial longline
fleet.

• Develop GIS applications for mapping the NWHI lobster and bottomfish
habitat, as well as identifying inter-relationship of precious (gold)
coral and Hawaiian monk seal habitat.

• Conduct baseline rapid environmental assessments of the condition and
health of some of the most remote and pristine coral reef ecosystems of
the U.S.-affiliated Pacific Islands.

• Assess and monitor, with remote sensing, the marine debris in the
NWHI.

• Establish a program to monitor the health of coral reef ecosystems,
including remote sensing.

• Develop advanced survey technology for monitoring abundance of fishes
including: (1) use of LIDAR for monitoring the abundance of CPS species;
(2) remote monitoring of FAD fish aggregations; and (3) species
identification algorithms for acoustic surveys.

• Develop advanced technology for automatic shipboard data logging of
bio acoustic and environmental data from standard equipment on
commercial fishing vessels and logging of catch. Develop algorithms for
processing and analysis of these data.

# III. Research on the fisheries

Recent Accomplishments:

The SWFSC initiated and led the efforts to evaluate MPAs as a
supplemental tool for groundfish management on the west coast. The
Center organized and convened the first workshop on marine harvest
refugia to conserve and manage rockfish and continued these discussions
in a special symposium on marine protected areas for California. The
published proceedings and reports are also being used by west coast
states in evaluating marine reserves as a strategy to conserve and
manage nearshore marine resources. Similar studies are underway in
Hawaii to evaluate State of Hawaii area closures designed to rebuild
populations of several commercially important bottomfish species.

General additive model (GAMs) were estimated from detailed observations
gathered from NMFS-SWR observers and high-resolution environmental data,
merged with fishery logbook data to assess the impact of time-area
closure alternatives on the Hawaiian longline fishery. The results from
these models were used in litigation concerning the impact of the
Hawaiian longline fishery on sea turtles and to propose efficient
regulatory alternatives. The analysis used a financial portfolio
analysis to estimate the efficacy of various scenarios.

Coho salmon production in the Pacific Northwest reached historically low
levels in the 1990s, which stimulated research examining whether changes
in ocean conditions were responsible for inter-annual variability in the
ocean survival of coho. Recent investigations focused on improving the
measures of ocean conditions using remotely sensed sea surface
temperature (SST) data and by weighting upwelling indices with sea
surface temperatures. The models generated from the analyses may have
the potential to be used for coho survival forecasting. Related research
evaluated how spatial patterns of environmental variability may
differentially affect parts of the coho populations.

The SWFSC completed an analysis of harvesting capacity in the Pacific
coast CPS limited entry finfish fishery. The Center also collaborated on
an analysis of harvesting capacity in the Pacific coast market squid
fishery. Multifan CL was applied to develop stock assessments for highly
migratory species.

Research Priorities, FY 2001-2006:

III.A. Social and economic research

• Initiate economic evaluation of salmon hatchery reform actions.

• Develop automated analytical templates integrated with current fishery
performance, cost, and price information for completing RFAs in an
efficient and timely basis. Augment these templates to include the basic
demographic information required to initiate preliminary SIAs.

• Conduct research to support the United Nations Implementing Agreement
(or Provision of the United Nations Convention on the Law of the Sea
(UNCLOS) Relating to the Conservation and Management of Straddling Fish
Stocks and Highly Migratory Fish Stocks).

• Research intra-industry linkages and develop input-output
relationships to describe and model the employment, income, and economic
activity impacts of management actions being considered for each of the
FMP fisheries and fishing communities.

• Develop methods to assess the efficacy of various MPAs, ecosystem
preserves, and other time-area closures in restoring fish stocks and
increasing sustainable yields.

# III.C. Marine aquaculture

• Develop techniques for culture of white abalone and other abalone
species for recovery of endangered stocks, stock enhancement, and
commercial production.

# IV. Information management research

Recent Accomplishments:

The SWFSC\'s Pacific Fisheries Environmental Laboratory (PFEL) provides
environmental data for fisheries research and management. Environmental
variability has been identified as a key feature in fish and marine
mammal population dynamics. PFEL\'s data holdings and related data
products provide fisheries relevant data that cover the entire spectrum
of the ocean environment-from surface or near-surface wind and pressure
data that can affect the ocean, to surface and subsurface measurements
of important oceanographic parameters. Over the last year, PFEL has
developed a system to make this information readily accessible to
fisheries scientists. Scientists can now obtain over the Internet most
of the PFEL\'s data holdings, for any location in the world. The data
can be sorted in both space and time, visualized on-line, and downloaded
in a variety of formats. Data and expertise were provided to researchers
working on salmon survivorship, hake catches and negotiations with
Canada, harmful algal blooms, rebuilding overfished fish stocks, benthic
fauna patterns in sanctuary areas, and marine mammal population
dynamics.

Data collected and processed from U.S. purse seiners fishing in the
central-western Pacific was computerized, edited, and submitted to the
Forum Fisheries Agency (Treaty Manager) as required under the SPTT. This
information was reported at the Annual Treaty meeting of the Forum
Fisheries Agency in Nuie and also presented at the meeting of the
Standing Committee of Tunas and Billfish in New Caledonia for use in
stock assessments of central-western Pacific skipjack, yellowfin, and
bigeye tuna stocks.

The SWFSC fielded three observers aboard U.S. troll vessels to collect
length measurements of albacore and bycatch estimates to verify and
supplement data taken by port samples and in logbook records. The data
was computerized and presented to the North Pacific Albacore Workshop in
Taiwan and used to assess the status of Pacific albacore stocks. This
data was also analyzed and distributed to U.S. albacore fishers.

Conductivity, temperature, and depth studies at a series of stations
along the NWHI were initiated in May 1999 to begin a long-term time
series of vertical structures of the physical environment affecting
fisheries. This information is being integrated in a GIS application
with fisheries information and NOAA R/V *Townsend Cromwell* information
to develop a series of applications for detailed location-referenced
studies.

Federal logbook and permit data from the rapidly growing American Samoa
longline fishery were developed into an integrated data management
system by the WpacFIN program which has allowed rapid use of the
information for assessing management measures considered for the fishery
by the WPFMC. The information is collected and compiled by the
government of American Samoa fisheries office where hands-on quality
control and delinquency analysis can be conducted in conjunction with
the NMFS Office of Enforcement. Data and statistics are then available
through Internet connections to the Honolulu Laboratory.

Research Priorities, FY 2001-2006:

• Implement an Oracle-based integrated system for storing and
distributing via the Internet all of the Honolulu Laboratory data
holdings, including fisheries dependent, research cruise, remote
sensing, laboratory, and video data.

• Develop automated systems for integrating data sets with common fields
(e.g., longline logbook and observer reports, the NOAA R/V *Townsend
Cromwell* cruise reports, and remote sensing).

• Develop GIS technology for mapping and spatial analysis of fisheries,
oceanographic, and habitat information.

• Automate quarterly and annual compilation of fisheries statistics and
annual reports on FMP fisheries.

• Develop and maintain web-based coastal salmon abundance database.

• Advance approaches of data fusion to combine fisheries data and
assessment model outputs with environmental data from ship, satellite,
and physical models.

**SOUTHEAST FISHERIES SCIENCE CENTER (SEFSC)**

The Southeast Fisheries Science Center (SEFSC) is headquartered in
Miami, FL. The SEFSC is responsible for scientific research on living
marine resources that occupy marine and estuarine habitats of the
continental southeastern United States, as well as Puerto Rico and the
U.S. Virgin Islands. Research is conducted at laboratories located in
Beaufort, NC (a joint NOS-NMFS facility); Miami, FL; Panama City, FL;
Galveston, TX; and Pascagoula, MS, with a field station at the Stennis
Space Center. Two NOAA vessels assigned to fisheries research are also
homeported in Pascagoula: the NOAA R/V *Oregon II* and the NOAA R/V
*Gordon Gunter*. SEFSC\'s current staffing level is 258 FTEs, with all
positions involved in MSFCMA-related activities. Approximately 80% of
all SEFSC resources are assigned to MSFCMA activities.

In general, SEFSC develops the scientific information required for: (1)
fishery resource conservation, (2) fishery development and utilization,
(3) habitat conservation, and (4) the protection of marine mammals and
endangered species. Impact analyses and environmental assessments for
management plans and international negotiations are also prepared, and
research is pursued to address specific needs in population dynamics,
fishery biology, fishery economics, engineering and gear development,
and protected species biology.

Each SEFSC laboratory is responsible for conducting research in specific
subject areas, however, there is extensive cooperative research between
SEFSC laboratories. Research activities conducted by the various
laboratories are as follows:

**Beaufort Laboratory:** habitat research; fishery biology and stock
assessments, especially for reef fish; population dynamics of menhaden,
weakfish, red drum, etc.; protected species research.

**Miami Laboratory:** stock assessments for species such as
snapper-grouper, mackerels, highly migratory species (e.g., sharks,
swordfish, tunas, and billfish), sea turtles, marine mammals, and other
endangered or threatened species; research on coral reefs, MPAs, and the
South Florida ecosystem restoration program.

**Panama City Laboratory:** fishery biology and life history
characteristics and essential fish habitat research.

**Mississippi Laboratories:** fishery-independent surveys; gear
development (TEDs and BRDs); environmental remote sensing; bycatch; and
endangered species research.

**Galveston Laboratory:** fishery biology and stock assessment of shrimp
populations; gear and bycatch evaluation studies; habitat research and
restoration;

and endangered species.

SEFSC provides scientific support for NMFS\' fishery management
activities for the South Atlantic Fishery Management Council (SAFMC),
the Gulf of Mexico Fishery Management Council (GMFMC), and the Caribbean
Fishery Management Council (CFMC), that involve 17 fishery management
plans covering the following major fisheries: spiny lobster,
snapper-grouper, reef fish, red drum, coastal migratory pelagic species,
coral, shrimp, stone crab, queen conch, and golden crab. SEFSC also has
significant interactions with the Gulf States Marine Fisheries
Commission (GSMFC), which administers the Fisheries Information Network
(FIN) statistics effort; and the Atlantic States Marine Fisheries
Commission (ASMFC), which administers the ACCSP and exercises fishery
management responsibilities through the Atlantic Coastal Fisheries
Cooperative Management Act. In addition, SEFSC maintains close ties with
state fishery programs and has funded the State/Federal cooperative
statistics program since 1983. Researchers at the SEFSC collaborate
extensively with other Federal agencies and academia.

Internationally, the SEFSC provides scientific support for U.S.
participation in: (1) the International Commission for the Conservation
of Atlantic Tunas (ICCAT), which manages Atlantic Ocean-wide fisheries
for tunas and billfishes; and (2) the International Oceanographic
Commission for the Caribbean (IOCARIBE), which coordinates fishery
oceanography studies among the approximately 30 islands and continental
countries in the region. SEFSC scientists also work jointly with the
government of Mexico on projects of mutual interest in the Gulf of
Mexico under the Mexus-Gulf research working group.

Constituents have the opportunity to provide input to SEFSC\'s research
programs through representation on FMCs, participation in Council public
hearings, and service on Council advisory committees. Input to the SEFSC
research program is also received via the activities of interstate
fishery commissions (the Atlantic and Gulf States Marine Fisheries
Commissions), joint agency planning groups, and cooperative programs
with state fishery agencies (GulfFIN). SEFSC responds to the information
needs of fishery management councils and has a formal procedure (Council
Operations Plan) for matching its research program to fishery management
plan requirements.

SEFSC\'s high caliber of research is maintained through periodic program
reviews by teams that include officials from industry, councils, state
agencies, universities, and other constituents. The Center also works
diligently to be responsive to the results of program reviews.

# Recent Accomplishments and Research Priorities for FY 2001-2006

# I. Research to support fishery conservation and management

Recent Accomplishments:

SEFSC has successfully incorporated \"risk assessment,\"
\"uncertainty,\" and the new SFA guidelines on \"overfished\" and
\"overfished status\" into stock assessment methodologies for numerous
species in the Gulf of Mexico, Atlantic, and Caribbean.

The development of the red snapper rebuilding plan was based on SEFSC
scientific efforts.

The Center is recognized for its expertise in the fields of habitat
research and restoration and has successfully developed criteria to
define and assess areas of EFH.

SEFSC completed baseline data collection essential for the successful
establishment of marine reserves in the Tortugas region for the Florida
Keys National Marine Sanctuary and for the Dry Tortugas National Park.

Research Priorities, FY 2001-2006:

I.A. Biological research concerning the abundance and life history
parameters of fish stocks

• Further efforts to improve the effectiveness of fishery resource
management programs by refining the definition of stocks (including the
\"management unit\" within species), and to determine data needs and
analytical methods required for applying refined definitions.

• Develop and maintain high quality fishery-dependent and fishery
independent long-term data sets for stock assessments. A main component
of this effort will be the expanded use of at-sea observers on
commercial and recreational fishing vessels to report on catch and
bycatch. Emphasis will be on collecting a wide range of information,
including biological and environmental data, gear type deployed, and
method of deployment.

• Incorporate marine ecosystems data into conceptual models of food webs
to link habitat to productivity and increase the Center\'s ability to
survey, inventory, and understand the dynamics of marine systems and
their biota.

• Continue to assess and monitor protected finfish species (e.g.,
jewfish and Nassau grouper).

• Conduct research on HMS stocks, particularly in the areas of stock
identification, life history, and precautionary approach methodologies.

• Develop basic life history information and conduct assessments on fish
stocks in support of management for the Councils (SAFMC, GMFMC, and
CFMC) and Commissions (ASMFC, GSMFC).

# I.B. Social and economic factors affecting abundance levels

• Expand sociological and economic research and incorporate results into
the fishery management process.

# I.C. Interdependence of fisheries or stocks of fish

• Increase our understanding of the interactions of protected species
(e.g., sea turtles, marine mammals: bottlenose dolphin and large whales)
and finfish candidate species (e.g., jewfish and Nassau grouper) with
ongoing fisheries in the Southeast Region.

• Prevent the extinction and promote the recovery of marine species and
at-risk populations through interventions and the continued development
of recovery strategies.

• Develop scientific methodology for multi-species or ecosystem
approaches towards the management of fishery resources, and where
appropriate, transition from single-species approaches.

I.D. Identifying, restoring, and mapping of essential fish habitat (EFH)

• Define and characterize EFH and develop an understanding of natural
and anthropogenic threats.

• Investigate downstream and coastal impacts of agricultural and urban
activities and provide the technical basis for designing and
implementing programs for ensuring sustainable coastal communities.

• Gain a better understanding of the structure and function of
estuarine, coastal, and marine systems to enhance the conservation and
restoration of wetland, benthic, and aquatic areas of EFH.

• Explore innovative techniques to determine the functional value of
natural habitats and to evaluate the restoration success relative to the
fish community rather than solely to the plant community.

• Develop restoration techniques for EFH including corals, salt marshes,
and seagrasses; and determine whether habitats created or restored with
such techniques are ecologically functional.

I.E. Impact of anthropogenic factors and environmental changes on fish
populations

• Continue to engage in joint efforts with state and other Federal
agencies to restore the ecological integrity and water quality in
Florida Bay, Galveston Bay, and other estuaries upon which fish depend.

• Continue research efforts under the South Florida Restoration Effort,
particularly in the areas of modeling fishery dynamics, recovery of
protected resources, restoring EFH, and providing support for the Coral
Reef Initiative.

• Derive more accurate assessments of fishing and other anthropogenic
impacts on living marine resources by incorporating risk and uncertainty
into models used to predict natural living marine resource variations.

• Develop techniques and scientific data necessary to support the
effective application of precautionary approaches to fisheries
management.

• Continue to evaluate the efficacy of marine reserves, no-take and
limited-take zones, and time closures as fishery management tools.

# II. Conservation engineering research

Recent Accomplishments:

Innovative approaches to BRD design have been developed. For example,
SEFSC has conducted in situ observations of red snapper behavior during
shrimp trawling to aid in the design of more effective BRDs and has
successfully led efforts to significantly reduce the bycatch of
non-target species such as red snapper in the Gulf of Mexico shrimp
fishery.

The development and use of improved TEDs is contributing to the recovery
of sea turtles, especially Kemp\'s ridley in the southeastern region.

A recovery model for impacted subtropical seagrass habitats was
developed and has been used successfully in court to demonstrate impacts
to sanctuaries.

Research Priorities, FY 2001-2006:

• Continue investigations on the importance of environmental cues in the
spatial orientation and migration behavior of sea turtles.

• Develop and test new gear technology and fishing techniques to
minimize bycatch. The SEFSC continues to explore options to reduce
bycatch and

mitigate mortality of sea turtles and other non-target species captured
in the distant water longline fisheries.

• Develop and test new gear technology and fishing techniques to
minimize adverse impacts on EFH. The Center will continue to document
the extent and assess the impact of various fishing gears on EFH in
support of conservation and management activities.

• Promote efficient harvest of target species. The Center will conduct
investigations into limited access options (e.g., individual
transferable quotas (ITQs)) as resource management alternatives that aid
increased harvest efficiency are continuing.

# III. Research on the fisheries

Recent Accomplishments:

Economic information, analyses, and evaluations were provided for
numerous proposed fishery management actions in the southeast.

SEFSC developed and assisted in the collection of economic data through
special surveys of the commercial snapper-grouper and mackerel
fisheries.

SEFSC, in conjunction with academic economists, contributed to the
development of random utility and contingent valuation models of the
South Atlantic and Gulf of Mexico recreational fisheries.

Research Priorities, FY 2001-2006:

# III.A. Social and economic research

• Include socio-economic related questions in the log book program and
increase the use of information such as cost and return data in
fisheries management.

• Design and implement procedures to collect socio-economic data on a
routine basis. Data would be used to better determine the effects of
regulation on commercial and recreational fishers.

• Develop better models of commercial and recreational fisheries to
evaluate proposed management alternatives, including limited access
systems.

• Estimate economic relationships such as demand curves, production
functions, import supply curves, and recreational benefit functions
needed to support the evaluation of management decisions.

# III.B. Seafood safety research

• Support research aimed at identifying and characterizing marine
pathogens, especially viruses, in aquacultured shrimp products, and the
extent of viruses in wild shrimp stocks.

• Continue to develop biological and chemical analytical methods for
toxic contaminants (e.g., mercury), assess their presence in seafood,
and define their impacts on marine ecosystems.

• Improve methods to detect, forecast, and evaluate the ecological
significance of harmful algal blooms and their impact on fish stocks,
marine mammals, and other protected species.

# III.C. Marine aquaculture

• Develop the scientific foundation and technical guidelines for
establishing ecologically responsible marine aquaculture.

• Continue to investigate the natural occurrence of shrimp viruses.

# 

# 

# 

# IV. Information management research

Recent Accomplishments:

SEFSC has developed and implemented a fully integrated Oracle-based
fisheries logbook system.

Research Priorities, FY 2001-2006:

• Develop a fishery database and information management system that will
allow the full use of information in support of effective fishery
conservation and management.

• Fully integrate the logbook system with the regional permit database.

• Increase collection of observer-based data on bycatch and improved
fishery-dependent data (e.g., via ACCSP\'s program with ASMFC).

• Secure access by constituents and the public to SEFSC information
resources via web-based technologies.

NORTHEAST FISHERIES SCIENCE CENTER (NEFSC)

The Northeast Fisheries Science Center (NEFSC) has facilities in Woods
Hole, MA; Narragansett, RI; Milford, CT; Sandy Hook, NJ (James J. Howard
Marine Laboratory space rental from the state of New Jersey), and
supports staff at the National Systematics Laboratory (housed at the
Smithsonian Institution in Washington, DC.). The NOAA R/V *Albatross IV*
and NOAA R/V *Delaware II*, berthed in Woods Hole, MA, support the
majority of the Center\'s fisheries survey and research cruises.
Periodically, the NOAA R/V *Gordon Gunter* and NOAA R/V *Oregon II*
(berthed in Pascagoula, MS) are utilized as supplemental sources for
either surveys or research cruises. Private fishing vessels and academic
research ships have been utilized on a periodic basis to support
ecosystem surveys on the northeast continental shelf.

The NEFSC research program runs the gamut from stock assessments on
finfish populations during the Spring and Fall Bottom Trawl Surveys
(conducted annually since the 1960s) to process-oriented research
projects such as studying the impacts of global climate change on the
coupling of zooplankton/cod and haddock larvae distribution and
predation on Georges Bank. Additional fisheries surveys are conducted
for ocean quahogs, surf clams, and sea scallops, and grant funds are
provided to support surveys of Gulf of Maine northern shrimp and finfish
surveys in state waters. Stock assessment workshops (SAWs) involving the
participation of fisheries experts from state, academic, and
non-government organizations (NGOs) use this survey data to develop
consensus estimates of stock size for managed species of finfish and
shellfish. The Mid-Atlantic Fishery Management Council (MAFMC) and the
New England Fishery Management Council (NEFMC) then uses this advice.

Long-term changes in the ecosystem supporting fisheries are monitored
through surveys of the Northeast Shelf Large Marine Ecosystem (LME) and
research is underway to convert such data into indices on the health of
the ecosystem. Additional process oriented research projects focus upon
the effects of pollution on winter flounder; recovery of herring and
Atlantic mackerel populations; trophic interactions between Atlantic
mackerel, juvenile cod, and haddock; biological characteristics of
selected shark species in the Northeast; and descriptions of EFH for
most coastal finfish species. The Center also conducts social and
economic research in support of the fishery management process.

Reliable information, critical to the development of regional FMPs and
subsequent amendments, and, ultimately, to the building and maintenance
of sustainable fisheries, is produced through the Northeast Regional SAW
process. This process is a cooperative effort of the NMFS/NEFSC and
Northeast Region Office (NERO), NEFMC, MAFMC, and the ASMFC. In the
northeast, peer review of stock assessments is conducted twice per year
within the Northeast Regional SAW process. The SAW process is guided by
the SAW Steering Committee (directors of NEFSC and NERO, MAFMC, NEFMC,
and the ASMFC) which determines the species to assess during a
particular SAW cycle and establishes the assessment terms of reference.
Each SAW cycle begins and ends with the meeting of the SAW Steering
Committee and includes Working Group meetings (where analyses are
prepared for review); a five-day Stock Assessment Review Committee
(SARC) meeting (where analyses are peer-reviewed and advice for managers
is developed); and a two-to-three-session Public Review Workshop held
during planned meetings of the MAFMC, NEFMC, and ASMFC. Participants in
this process include NMFS scientists and managers; representatives from
fishery agencies outside the region; MAFMC, NEFMC, and ASMFC
representatives; state fishery agency representatives from within the
region; academic and NGO participants; industry members; and
occasionally experts from the international community. SAW meetings are
open to the public and are widely announced. NEFSC personnel also
participate in various committee meetings of the Regional FMCs and the
ASMFC.

Much of the recent gear research in the northeast has been accomplished
through grants, with NERO oversight. These grants have gone to fishers,
or to organizations such as states and universities, which carry out the
research with the help and cooperation of the fishing industry. The NERO
Fisheries Engineering Group is also involved with data analysis for
exempted fishery permits and fishway engineering for anadromous fish.
Conservation engineering activities in the NERO have recently been
concentrated on the problem of entanglement of large whales in fixed
fishing gear (e.g., lobster traps and

gillnet gear). A resolution to this problem will allow fishing to
continue. The fishing industry aided this effort through its
participation in the Gear Advisory Group to the Atlantic Large Whale
Take Reduction Team to devise solutions, and by volunteering vessels and
time for observations and testing. Also, NERO and the Center are
collaborating on experiments using pingers and acoustic reflective nets
as deterrents to marine mammal entrapment in gillnets.

# Recent Accomplishments and Research Priorities for FY 2001-2006

# I. Research to support fishery conservation and management

Recent Accomplishments:

Rates of growth, development, and survival have been estimated for the
larval goosefish.

Rates of growth, development, survival, and how these vary with water
temperature, have been estimated for the egg, larval, and juvenile
stages of summer flounder and winter flounder.

The NEFSC has demonstrated that the technique of using scale texture for
sexing winter flounder is invalid.

Measures of egg quality and parental effects on offspring condition have
been quantified for summer flounder and winter flounder. The influences
of the timing and location of spawning of summer flounder on offspring
fitness have been estimated.

Data have been gathered on the timing and location of goosefish
spawning.

Field work in the U.S. GLOBEC program on Georges Bank has been
conducted. The program is investigating the environmental and biological
processes controlling the reproductive success of the cod and haddock
stocks on the Bank.

Winter flounder courtship and spawning behavior has been described
relative to estuarine habitats.

Development of a micro-constituent technique for stock identification of
bluefin tuna and other species was completed.

NEFSC demonstrated that diet influences otolith micro-constituent
composition in young-of-the-year bluefish.

The oceanographic conditions on the Northeast Shelf were measured and
the inter-annual variability was documented in a report each year. The
data were used in stock assessment activities and available to the
scientific community via the World Wide Web.

NEFSC completed the second year of a sampling program in the inner New
York Bight and lower Hudson-Raritan estuary studying the effects of
environmental/habitat variables on settlement and early post-settlement
processes of local fish species.

Bio-economic models were contributed to support fishery management
decisions. These models are designed to measure and project demand
conditions; evaluate direct impact of area-base management measures; and
to assess other regulatory tools such as trip limits.

Reports on the level of qualitative and quantitative harvest capacity in
the major fisheries of the region were completed.

Assistance in the design and evaluation of vessel buyback programs for
the groundfish fishery in the region was provided.

Biological parameters that potentially regulate foraging competition in
juvenile bluefish and striped bass were identified.

A series of 30 EFH Source Documents, summarizing life history, habitat,
and distribution/abundance information, was provided to NEFMC and MAFMC.

NEFSC completed a study of diets of 16 fish species in lower
Hudson-Raritan Estuary, as compared to other Middle Atlantic areas.

A study of functional equivalence of marshes replanted after EXXON
Bayway Oil Spill in Arthur Kill (NY/NJ) to oiled, but unrestored,
marshes and control marshes was completed.

The potential predation risks of juvenile summer flounder and winter
flounder in inshore habitats were quantified.

NEFSC demonstrated that nominal habitat classifications are inadequate
for defining and studying the functional value of those habitats.

NEFSC has conducted studies which demonstrated that habitats are
dynamic, defined by complex interactions of changing environmental
conditions, and yielding a space favorable to growth and survival that
continually expands, contracts, and changes position.

Environmental conditions and physical habitat within a shallow coastal
nursery area in Connecticut that supports young tautog were
characterized. The distribution and abundance of these fish has been
described and preliminary GIS-based spatial maps have been created.
Young tautog have been marked with coded wire tags in an effort, through
mark-recapture, to determining individual growth rates, population size,
and the extent of site-fidelity. Diets of young tautog and food habits
of predators have been investigated. These efforts will be valuable in
future attempts to release hatchery-reared tautog as they become
available from the Milford Aquaculture Program.

The effects of egg incubation temperatures on the development and
survival of summer flounder, winter flounder, windowpane, cod, and
haddock have been quantified through laboratory experiments.

A study was completed that indicated that the resuspension of
contaminated sediments is the dominant process in distributing
contaminants in the Hudson-Raritan and Navesink estuaries.

The uptake of trace metals and organic compounds into mussels from
Arthur Kill Sediments, including those tainted by oil spills, was
investigated.

Research Priorities, FY 2001-2006:

I.A. Biological research concerning the abundance and life history
parameters of fish stocks

• Continue to develop improved biological parameter estimates.

• Determine biological, environmental, and habitat processes controlling
the reproductive success of important fishery resources.

• Expand research in the development of micro-constituent chemical
analysis techniques for stock identification.

• Continue to monitor oceanographic and biological conditions on the
NortheastShelf and document ecosystem variability in order to determine
its role in the recovery and sustainability of depressed fish stocks.

**I.B. Social and economic factors affecting abundance levels**

• Expand sociological and economic research and incorporate results into
the fishery management process.

• Develop/refine models to evaluate the efficacy of area management
tools across a broad range of fisheries. This includes research into
alternative approaches to resource management such as area-based
resource portfolio management and the development of cooperatives.

• Investigate the impacts of latent (non-utilized) effort as stocks
recover, including the design, execution, and evaluation of latent
effort buyouts, and the factors affecting the reactivation and new
activation of latent effort pools.

• Continue to develop guidance on National Standard 8 and on social
impact assessments (SIAs). This includes examining approaches to rapid
assessment techniques and institutions as well as establishing coastal
cooperation in the supply of updated information relevant to SIAs on a
continuing basis.

• Investigate and develop design features to mitigate perceived failures
of individual fishing quota (IFQ), ITQ, and CDQ fishery regulations.

# I.C. Interdependence of fisheries or stocks of fish

• Continue to investigate the importance of trophic interactions between
the populations of bluefish and striped bass.

I.D. Identifying, restoring, and mapping of essential fish habitat (EFH)

• Identify and provide EFH information as required by the MSFCMA for
FMPs for the NEFMC and ASMFC.

• Continue to conduct research to determine the functional value to
estuarine and nearshore habitats, including restored sites, to the
sustainability

of fishery resources.

I.E. Impact of anthropogenic factors and environmental changes on fish
populations

• Conduct research to determine the effects of climate variability on
the sustainability of coastal and pelagic fishery resources.

• Investigate the transfer of contaminants within estuarine systems and
their effect on the growth and sustainability of fish populations.

# II. Conservation engineering research

Recent Accomplishments:

Through the recently established NEFSC Office of Cooperative Programs
Coordination, approximately 1,600 research fishing days were conducted
since the program\'s inception in September 2000. This multi-faceted
program is designed to explore ways to improve data upon which fishery
management decisions are made as well as to improve communications
between fishers, scientists, and fisheries managers. One of the key
elements of this program is in the area of conservation research (i.e.,
mesh selectivity, bycatch discard reduction, harvest efficiency, and
gear development).

The NEFSC Fishery Observer Program has made recent strides in the
development and deployment of more selective fishing gears by placing
scientific observers aboard commercial vessels. Specifically, in the
Gulf of Maine northern shrimp fishery, the Nordmore grate was tested and
subsequently implemented as a method to reduce the take of juvenile
groundfish. Sea sampling was used in the initial gear trials, and the
at-sea observer program continues to monitor the fishery following full
implementation of the grate requirement. The fishery observer data
indicate significant reductions in finfish bycatch after introduction of
the Nordmore grate in the shrimp fishery. Although reduced catches of
important groundfishes are in part due to their decreased abundance in
recent years, the grate has been effective in reducing the fraction of
finfish caught in this fishery, thereby reducing fishing mortality on
young groundfish.

Similar studies evaluating the effectiveness of acoustic alarms to deter
harbor porpoise from entering groundfish sink gillnets have also been
conducted through the Fishery Observer Program. These studies involved
alarm-equipped and control nets, fished in the vicinity of harbor
porpoise aggregations. Results from this work are currently being
evaluated to determine the efficacy of this method in reducing harbor
porpoise mortalities. Additionally, at-sea observers have been used in
other gear-related studies such as in the New England groundfish fishery
to evaluate the effectiveness of changes in trawl mesh size.

Three cruises were recently completed to evaluate the effect of gear on
habitat by comparing fish distribution/abundance and diets, benthic
communities, and sediment features in areas of Georges Bank that had
been closed to fishing for five years with conditions in adjacent open
areas.

Research Priorities, FY 2001-2006:

• Conduct research to develop and enhance gear performance and
characteristics.

• Conduct research aimed at reducing bycatch and marine mammal
mortalities.

• Conduct studies to evaluate the effects of gears on habitats.

# III. Research on the fisheries

Recent Accomplishments:

The NEFSC has recently completed development of a New England-wide
Input-Output model in collaboration with the Woods Hole Oceanographic
Institute\'s Marine Policy Center. This model is used to assess
distributional impacts of fisheries regulations.

The NEFSC has conducted collateral research with the Massachusetts
Institute of Technology\'s Center for Marine Social Sciences (CMSS).
CMSS is currently collecting socio-economic data on fishers and
fisheries-dependent communities. Information generated by this extensive
project will be the baseline from which the social impacts of regulatory
change will be measured. As a result, this project will help communities
and fisheries managers anticipate potential impacts and plan
accordingly.

The NEFSC has conducted Vessel Cost and Earning Surveys for all major
fisheries in the region. These \"snap-shot\" surveys contributed to the
design of the coast-wide pilot program for social science data used by
the ACCSP.

The NEFSC has produced a variety of socio-economic publications on the
fisheries to inform resource managers and the public. These works
address such issues as property rights, allocations between recreational
and commercial fisheries, rent-seeking behavior in fisheries, models of
recreational fisheries, and estimates of forgone national benefits as a
result of shortcomings in the management of groundfish. Additionally, in
support of two regional FMCs, the NEFSC has provided RIR/RFA analyses
for 17 FMPs and numerous amendments/framework actions.

The NEFSC\'s Office of Marine Ecosystem Studies has been active in the
monitoring and assessment of changes within the U.S. Northeast Shelf
ecosystem in relation to the recovery of depleted demersal fish stocks,
including cod, haddock, and yellowtail flounder and the unprecedented
population explosion of pelagic herring and mackerel stocks.

Several United Nations agencies are collaborating with the NMFS Office
of Science and Technology and Fishery Centers to introduce
ecosystem-based assessment and management practices leading to the
recovery of depleted fish stocks in Asia, Africa, Latin America, and
eastern Europe. A five module strategic approach developed and tested by
the NEFSC has been introduced to coastal countries bordering LMEs of the
Yellow Sea (China and Korea), the Benguela Current (Angola, Namibia,
South Africa), the Guinea Current (Benin, Cameroon, Ghana, Ivory Coast,
Nigeria, and Togo), and Baltic Sea (Denmark, Finland, Germany, Sweden,
Estonia, Latvia, Lithuania, Poland, and Russia). The five modules
provide advanced methodologies for monitoring and assessing the: (1)
productivity, (2) fish and fisheries, (3) pollution and health, (4)
socio-economics, and (5) governance of the LMEs.

Grants from the Global Environment Facility have been allocated over the
past five years to support the LME projects. In each of the LME
projects, joint international surveys are carried out measuring the
effects of changing ecosystem states on the recovery of depleted fish
stocks and the long term sustainability of biomass yields, ecosystem
health, and socio-economic benefits to the coastal communities.
Participating countries have created, under UNCLOS, Commissions and
other joint institutions to serve as governance bodies and to initiate
more sustainable ecosystem-based management protocols than have been
generally initiated and practiced during the past half century.

Tautog have been cultured successfully from egg to about 1-1.5 lbs., a
size especially desired for the live-market trade. Egg hatching rates
are high, but the larvae are extremely sensitive to handling. Research
efforts have focused on culture techniques that involved little or no
handling of these sensitive early stages. Once fish reach the juvenile
stage, survival rates are high. Optimum diets are being developed.

An integrated, micro-algal, shellfish nursery/wastewater treatment
system was designed, built, and tested. This land-based, pilot-scale
nursery for production of molluscan shellfish seed was based upon
seawater recirculation technology. This innovation in scientific and
engineering accomplishments represents an important step in developing
sustainable and environmentally-compatible shellfish aquaculture in the
U.S. and throughout the world.

A manuscript was published describing several years of field research
that investigated different strategies to enhance the bay scallop
population in a shallow coastal estuary in Connecticut. Part of the
project was a collaboration with volunteers from a local Shellfish
Commission. Low dissolved oxygen concentrations were found within some
eelgrass beds during midsummer, but environmental conditions were
generally favorable to support scallop growth. It was determined that
natural recruitment was too low to support spat collection-based
enhancement efforts. A transplant of large seed scallops in late fall
resulted in a spawning stock that released new larvae into the estuary
the following year. Use of suspension culture gear to rear, overwinter,
and provide spawner sanctuaries was also demonstrated.

The first biochemically-based feeding standards for molluscan shellfish
seed were developed. Using a custom designed and built
computer-controlled feeding apparatus, NEFSC scientists determined both
qualitative and quantitative nutritional needs of bay scallop seed for
optimal growth and feed-conversion efficiency. Feeding standards,
analogous to those used routinely in animal agriculture, were developed
for molluscan shellfish for the first time, marking a milestone in the
development of shellfish aquaculture.

Research Priorities, FY 2001-2006:

# III.A. Social and economic research

• Continue the development of ongoing coast-wide cost and earnings data
collection systems. This research includes the design of a fixed cost
sampling protocol and the exploration of wide-scale observer-supplied
economic data systems.

• Continue the development of a socio-cultural information gathering
system sufficient for National Environmental Policy Act, National
Standard 8, and SIA requirements for fisheries, marine mammals,
endangered species, critical habitat for designated species, and EFH
designations.

• Conduct additional research into multi-species management options
incorporating various levels of constituent species. Research will focus
on differential area treatment of gears, vessels, and effort based on
habitat and fishing mortality considerations as well as impacts of
variously defined MPAs.

• Conduct further exploration of applicability and utility of GIS
information on economic and socio-cultural assessments of area-based
management options including development of socio-economic and
governance modules for LMEs.

• Continue research efforts for price models, bio-economic models, rapid
social assessments techniques, rights-based fishing modes, annual round
fisheries, and other issues central to improving approaches to
management and the design and assessment of alternatives. Of particular
concern is the coming need for the estimation of non-use benefits and
cost minimization research for EFH, ESA, and MMPA issues.

• Extend input-output models to mid-Atlantic states for the management
of recreational fisheries. This expansion includes: (1) analysis of
effort and participation in specific recreational fisheries to better
assess impacts of regulations on recreational fishers; (2) development
of participation models to predict levels of activity 5-10 years into
the future; and (3) defining and exploring recreational/subsistence
fishing communities and their dependency and vulnerability to standard
management alternatives.

# III.C. Marine aquaculture

• Continue to conduct Aquaculture and Enhancement Division activities.

# IV. Information management research

Recent Accomplishments:

NEFSC oceanographic data sets are being served through a distributed
oceanographic data system (DODS) compliant server. In addition, data
collected as part of the U.S. GLOBEC program on Georges Bank are being
served through the GLOBEC data system, which is a DODS compliant system.

Research Priorities, FY 2001-2006:

• Continue to develop and expand DODS compliant client and server
libraries to support Internet access to NODC oceanographic data sets.

**APPENDIX B. Response to Comments on Public Draft of the NMFS Strategic
Plan for Fisheries Research**

In August 2001, NMFS published a Notice of Availability in the *Federal
Register* announcing the availability of the draft Strategic Plan for
Fisheries Research. Comments were received from 11 organizations and
individuals, representing a range of interests. The comments were
helpful in revising the plan and preparing the final document. This
appendix summarizes the comments and addresses each major comment. Some
commenters also identified inconsistencies in the draft plan and
suggested editorial or textual changes. These specific comments are not
addressed here. However, the final plan document incorporated these
suggestions as much as possible.

**Comment:** The Plan does not fully address stock assessment research.
It lacks specificity with regard to the development of better models to
estimate abundance, biomass, and mortality with limited data and does
not adequately detail methods to collect better data.

**Response:** The NMFS Strategic Plan for Fisheries Research is designed
to provide a common framework for research, not the specific details.
The details are to be elaborated in other plans such as the
soon-to-be-released NMFS Stock Assessment Improvement Plan.

**Comment:** The Plan should establish and outline research efforts to
explore alternatives to an MSY-based management system for fisheries.
Predictive management could be based on predator-prey relationships,
oceanographic conditions, and ecosystem-based interactions, but not
without supporting research.

**Response:** NMFS believes that the concept of maximum sustainable
yield (MSY) is an integral component of the MSFCMA and that it is
reasonable to retain as a key element of current fishery management
programs. It is worth noting that NMFS does not consider MSY, or the
fishing mortality rate that generates MSY, as a target for fisheries
management. Rather, NMFS interprets MSY as an upper bound on optimum
yield. This interpretation is shared by several intergovernmental and
national fisheries organizations as a central feature of the
precautionary approach to fisheries management. However, NMFS does agree
with the need to expand fisheries management to an ecosystem-based
approach and is working toward this end in several respects. The NMFS
Strategic Plan for Fisheries Research cites two prestigious committee
reports (EPAP, 1999; NRC, 1999a). The former contains recommendations
for the development of fishery ecosystem plans-a document that would
incorporate ecosystem principles, goals, and policies into current
fisheries management structure. The agency has formed a working group
that is evaluating the recommendations contained in these reports and
will begin developing technical guidelines for their implementation in
2002.

**Comment:** The Plan should provide a regional mechanism for soliciting
review of NMFS\' research programs, with an emphasis placed on
prioritizing, monitoring, and evaluating these programs and taking
corrective action when shortfalls occur. It is also important for this
Plan to outline how this mechanism would function and incorporate
knowledgeable fishers into the peer review process.

**Response:** NMFS agrees that peer review is an important component of
an effective science program. NMFS is in the process of formalizing its
science guidelines and procedures through the development of its Science
Quality Assurance program. This suggestion will be forwarded to the
development team so it can be considered for incorporation into their
plan.

**Comment:** For the SWFSC overview in Appendix A of this Plan, NMFS
does not adequately address research efforts to conduct baseline
assessments and map major habitats of the coral reef ecosystem in the
western Pacific region, despite the fact that this region contains most
of the U.S. coral reef areas. Additionally, the western Pacific region
might serve as a \"laboratory\" to investigate the impacts of fishing on
coral reefs, and in particular, research marine protected area impacts.

**Response:** NMFS agrees and has revised this section of the Plan to
more accurately reflect current research activities and priorities on
coral reefs and the research opportunities that MPAs provide in the
western Pacific region.

**Comment:** For the SWFSC overview in Appendix A of this Plan, NMFS
needs to expand on research efforts to evaluate the socio-economic
impacts of recent management measures affecting fishing industries in
the western Pacific region.

**Response:** NMFS agrees and has modified this section of the Plan to
more fully represent socio-economic research efforts and priorities in
the western Pacific region.

**Comment:** For the SEFSC overview in Appendix A of this Plan, NMFS
needs to list observer programs as a priority for the Southeast region.
Observer studies provide data that are not only critical to assessing
bycatch, but are an important component of the information needed for
reliable stock assessments.

**Response:** NMFS agrees and has revised this section and others in
this Plan to recognize the important role observers play in providing
data on species-composition of catch and bycatch, estimates of gear,
vessel and gear characteristics, fishing locations, biological samples,
and environmental parameters, all of which contribute to effective
fisheries management.

**Comment:** The Plan should include a study to identify the small
nucleus of anglers pursuing swordfish and gather their landing
statistics, catch rates, and size distribution in order to acquire more
accurate information on recreational landings by U.S. fishers for
swordfish.

**Response:** NMFS is very interested in conducting surveys to estimate
the landing of swordfish by recreational anglers. Identification of the
anglers who fish for swordfish is a difficult task because such anglers
are not required under any existing permit program to notify NMFS of
their intent to fish for this species. Compilation of a list of the
participants in the recreational swordfish fishery would be possible if
those participants were required to provide such notification. NMFS is
currently considering possible options for implementing such a
requirement. Once NMFS obtains a comprehensive list of these anglers
along with their telephone numbers and mailing addresses, it would
certainly be possible to use that list to conduct efficient surveys that
would accurately estimate their fishing effort, catch rates, and
landings with respect to swordfish.

**Comment:** The Plan should include research regarding post-release
mortality for billfish, sharks, and small swordfish caught on U.S.
longlines.

**Response:** The NMFS Strategic Plan for Fisheries Research cites and
supports research to implement the recommendations of the NMFS Bycatch
Plan which includes research on post-release mortality of billfish,
sharks, and small swordfish.

**APPENDIX C. Abbreviations and Acronyms**

ABC acceptable biological catch

ABL Auke Bay Laboratory

ACCSP Atlantic Coastal Cooperative Statistics Program

ADCP acoustic Doppler current profiler

AFSC Alaska Fisheries Science Center

AKFIN Alaska Fisheries Information Network

APIS Antarctic pack ice seal

ASMFC Atlantic States Marine Fisheries Commission

ASRG Alaska Scientific Review Group

BKD bacterial kidney disease

BRDs bycatch reduction devices

BSAI Bering Sea and Aleutian Islands

CAFF Conservation of Arctic Flora and Fauna

CCAMLR Commission for the Conservation of Antarctic Marine Living
Resources

CDQ community development quota

CFMC Caribbean Fishery Management Council

CMSS Center for Marine Social Sciences

CPS coastal pelagic species

CPUE catch-per-unit-of-effort

DNA deoxyribonucleic acid

DODS Department of Defense standard

EEZ Exclusive Economic Zone

EFCL electronic fish catch logbook

EFH essential fish habitat

ESA Endangered Species Act

ESU evolutionarily significant unit

FAD fish aggregating device

FAO Food and Agriculture Organization of the United Nations

FIN Fisheries Information Network

FMC fishery management council

FMP fishery management plan

FOCI Fisheries Oceanography Coordinated Investigations

FSP Fisheries Strategic Plan, NOAA

FTE full-time equivalent

GIS geographic information system

GLOBEC Global Ocean Ecosystems Dynamics

GMFMC Gulf of Mexico Fishery Management Council

GOA Gulf of Alaska

GOOS Global Oceans Observing Program

GSMFC Gulf States Marine Fisheries Commission

HAPC habitat areas of particular concern

HMS highly migratory species

ICCAT International Commission for the Conservation of Atlantic Tunas

ICES International Council for the Exploration of the Seas

IFQ individual fishing quota

IOCARIBE International Oceanographic Commission for the Caribbean

IPCC Intergovernmental Panel on Climate Change

ISC Interim Scientific Committee

ITQ individual transferable quota

IWC International Whaling Commission

LIDAR light detection and ranging

LME large marine ecosystem

LMR living marine resource

MAFMC Mid-Atlantic Fishery Management Council

MHLC Multilateral High Level Conference

MPA marine protected area

MSFCMA Magnuson-Stevens Fishery Conservation and Management Act

NEFMC New England Fishery Management Council

NEFSC Northeast Fisheries Science Center

NERO Northeast Regional Office

NGO non-government organization

NICMERE National Indian Center for Marine and Environmental Research

and Education

NMFS National Marine Fisheries Service

NMML National Marine Mammal Laboratory

NOAA National Oceanic and Atmospheric Administration

NODC National Oceanographic Data Center

NOS National Ocean Service

NPFMC North Pacific Fisheries Management Council

NRC National Research Council

NWFSC Northwest Fisheries Science Center

NWIC Northwest Indian College

PacFIN Pacific Fisheries Information Network

PFEL Pacific Fisheries Environmental Laboratory

PFMC Pacific Fishery Management Council

PICES North Pacific Marine Science Organization

PIT passive integrated transponder

PMEL Pacific Marine Environmental Laboratory

PSMFC Pacific States Marine Fisheries Commission

OY optimum yield

RACE Resource Assessment and Conservation Engineering Division, AFSC

RecFIN Recreational Fisheries Information Network

REFM Resource Ecology and Fisheries Management Division, AFSC

RFA regulatory flexibility analysis

RIR regulatory impact review

SAFE stock analysis and fishery evaluation

SAFMC South Atlantic Fishery Management Council

SARC Stock Assessment Review Committee

SAW stock assessment workshop

SEFSC Southeast Fisheries Science Center

SEIS supplemental environmental impact statement

SFA Sustainable Fisheries Act of 1996

SIA social impact assessment

SPO Scientific Publications Office Seattle, WA, NMFS

SPTT South Pacific Tuna Treaty

SST sea surface temperature

SWFSC Southwest Fisheries Science Center

TED turtle excluder device

UNCLOS United Nations Convention on the Law of the Sea

WPFMC Western Pacific Fishery Management Council

**APPENDIX D. Glossary**

**Acceptable biological catch (ABC):** The ABC is a scientific
calculation of the sustainable harvest level of a fishery as determined
by Federal fisheries biologists.

**Acoustic Doppler current profiler (ADCP):** An acoustic sensor that
measures the Doppler shift of acoustic scatterers in the water column
and estimates the magnitude and direction of 3-D motions of the
\"water\" versus depth, using the assumption that the scatterers are
passive tracers of the water mass. Fisheries scientists have applied
this sensor to look for biological constituents (i.e., eggs and larvae)
in the water column.

**Adaptive management:** A combination of stock assessments with prior
knowledge of the fishery coupled with quantitative modeling and
empirical management experimentation.

**Anadromous:** Fish stocks that migrate from saltwater to fresh water
to spawn.

**Anthropogenic:** Human caused; usually used in reference to risks
created to fish stocks by human activities.

**Atlantic Coastal Cooperative Statistics Program (ACCSP):** A
cooperative state-federal marine and coastal fisheries data collection
program. The goal of the program is to cooperatively collect, manage,
and disseminate fishery statistical data and information for the
conservation and management of fishery resources of the Atlantic coast
and to support the development and operation of a national data
collection and data management program.

**Benthic:** Refers to organisms which live at or near the bottom (see
Demersal).

**Biomass:** The total weight of organisms in a defined group, such as a
fish stock or year class.

**Broodstock:** Adult fish used to propagate the subsequent generation
of hatchery fish.

**Bycatch:** The Magnuson-Stevens Fishery Conservation and Management
Act defines **bycatch** as \"fish which are harvested in a fishery, but
which are not sold or kept for personal use, and includes economic
discards and regulatory discards\... \[But not\] fish released alive
under a recreational catch and release fishery management program.\"

**Bycatch reduction device (BRD):** Any of a number of implements that
have been certified to reduce the likelihood of capturing non-target
species.

**Catch per unit effort (CPUE):** The amount of fish that is caught by a
given amount of fishing effort. Typically, effort is a combination of
gear type, gear size, and length of time the gear is used.

**Charter fishing:** Fishing from a vessel carrying a passenger(s) for
hire who is engaged in recreational fishing.

**Commercial fishing:** Fishing in which the fish harvested, either in
whole or in part, are intended to enter commerce or enter commerce
through sale, barter, or trade.

**Conservation engineering:** The practice of determining the
modification in gear design that will meet conservation objectives, such
as decreasing bycatch and bycatch mortality by increasing the
selectivity of gear and increasing the survival of fish and other living
marine resources that fishing gear encounter inadvertently.

**Continental shelf:** Submerged margin of continent from low-tide line
to a point (generally between the 50 and 100 fathom isobaths) at which
there is a marked increase of slope (i.e., the continental slope) to
greater depth.

**Delisting criteria:** Determination as to what indicators need to
exist before stocks can be taken off the Endangered Species Act list of
endangered species. Typically, delisting criteria are elaborated by
policy decisions regarding various recovery activities, such as
reforming hatchery practices, reducing harvest, eliminating impacts of
dams or restoring habitat.

**Demersal:** Fish and animals that live near the bottom of an ocean.

**Endangered species:** A species is considered \"endangered\" if it is
in danger of extinction throughout a significant portion of its range;
it is considered \"threatened\" if it is likely to become an endangered
species.

**Endangered Species Act (ESA):** The Federal law, enacted by Congress
in 1973, to provide protection for, and promote recovery of, animal and
plant species considered as threatened or endangered because of natural
or anthropogenic conditions.

**Essential fish habitat (EFH):** The Magnuson-Stevens Fishery
Conservation and Management Act defines essential fish habitat as
\"those waters and substrate necessary to fish for spawning, breeding,
feeding, or growth to maturity.\"

**Evolutionarily significant unit (ESU):** An ESU represents a distinct
population segment under the Endangered Species Act that (1) is
substantially reproductively isolated from nonspecific populations and
(2) represents an important component of the evolutionary legacy of the
species.

**Exclusive Economic Zone (EEZ):** The zone contiguous to the
territorial sea of the United States, the inner boundary of which is a
line coterminous with the seaward boundary of each of the coastal states
and the outer boundary of which is a line drawn in such a manner that
each point on it is 200 nautical miles from the baseline from which the
territorial sea is measured. This zone was established by Proclamation
Numbered 5030, dated March 10, 1983.

**Exploitation rate:** The probability that a given fish will die during
the year because of fishing.

**Ex-vessel value:** The amount paid to vessel\'s owner or operator for
its catch, excluding any value added by at-sea processing.

**Fishery:** (a) One or more stocks of fish which can be treated as a
unit for purposes of conservation and management and which are
identified on the basis of geographical, scientific, technical,
recreational, and economic characteristics; and (b) any fishing for such
stocks.

**Fishery dependent data:** Data collected on a fish or a fishery from
sport fishers, commercial fishers, and seafood dealers.

**Fishery independent data:** Data collected on fish by scientists who
catch the fish themselves, rather than depending on fishermen or seafood
dealers.

**Fishery management council (FMC):** One of eight regional groups
established under Section 302 of the Magnuson-Stevens Fishery
Conservation and Management Act to prepare and oversee fishery
management plans for fisheries conducted principally within the
Exclusive Economic Zone.

**Fishery management plan (FMP):** A plan developed by a regional
fishery management council, or the Secretary of Commerce under certain
circumstances, to manage a fishery resource in the U.S. EEZ pursuant to
the Magnuson-Stevens Fishery Conservation and Management Act. Includes
data, analyses, and management measures for a fishery.

**Gillnet:** A flat net suspended vertically in the water used to
capture fish which entangle themselves in the net, usually by the
forward part of the body near the gills.

**Groundfish:** A species of fish, usually finfish, that live on or near
the sea bottom part of the time.

**Juvenile:** A young fish, usually resembling an adult in appearance,
but which has not yet become sexually mature.

**Krill:** Small abundant crustaceans that form an important part of the
food chain in Antarctic waters.

**Landings:** The number or poundage of fish unloaded at a dock by
commercial fishers or brought to shore by recreational fishers for
personal use. Landings are reported at the points at which fish are
brought to shore.

**Marine Mammal Protection Act (MMPA):** The MMPA is a statue which was
enacted in 1972 to protect marine mammals and their habitat. These
species include whales, dolphins, seals, seal lions, walruses, and
others.

**Mark-recapture:** The tagging and releasing of fish to be recaptured
later in their life cycles. These studies are used to study fish
movement, migration, mortality, and growth, and to estimate population
size.

**Maximum Sustainable Yield (MSY):** A management goal specifying the
largest long term average catch or yield (in terms of weight of fish)
that can be taken, continuously (sustained) from a stock or stock
complex under prevailing ecological and environmental conditions,
without reducing the size of the population.

**Metapopulation:** A group of partially isolated populations (or
subpopulations) belonging to the same biological species (or subspecies)
and connected by migratory pathways. These partially isolated
populations or subpopulations can exchange individuals, which are
potentially able to recolonize sites within the metapopulation from
which the species or subspecies recently became extinct.

**Pinger:** High-frequency acoustic devices that may keep marine mammals
from entering and becoming entangled in fishing nets.

**PIT-tag:** The passive integrated transponder (PIT) tag is an
electronic tag 10 mm long by 2.1 mm in diameter that can be coded with
one of 35 billion codes. The tag can be automatically detected and
decoded *in situ* and eliminates the need to sacrifice, anesthetize,
handle, or restrain fish during data retrieval. The tag has been
developed as a research and management tool for monitoring the movement
of juvenile and adult fish species.

**Plankton:** Plants (phytoplankton) and animals (zooplankton) which
float in the upper portion of the water column and provide the basic
constituents of the oceanic food web. Most planktonic organisms are
microscopic in size. Eggs and larvae of many fisheries species are also
components of the plankton community.

**Population:** A group of interbreeding organisms generally inhabiting
a given geographic area.

**Opportunity cost:** An amount a fisher could earn for his/her time and
investment in another business or occupation.

**Optimum yield (OY):** (a) The amount of fish which will provide the
greatest overall benefit to the Nation, particularly with respect to
food production and recreational opportunities, and taking into account
the protection of marine ecosystems; (b) is prescribed as such on the
basis of the maximum sustainable yield from the fishery, as reduced by
any relevant economic, social, or ecological factor; and (c) in the case
of an overfished fishery, provides for rebuilding to a level consistent
with producing the maximum sustainable yield in such fishery.

**Quota:** The maximum amount of fish that can be legally landed in a
time period. It can apply to the entire fishery, an individual fisher\'s
share under an individual fishing quota (IFQ) system, or refer to the
size of fish.

**Recovery Science Review Panel (RSRP):** A panel of scientists
established to ensure the consistency of salmon recovery efforts
throughout the western United States.

**Recreational Fisheries Information Network (RecFIN):** A cooperative
state-Federal effort among marine fisheries agencies to improve
collection and management of marine recreational fisheries statistical
information.

**Recruitment:** A measure of the weight or number of fish which enter a
defined portion of stock, such as the fishable stock or the spawning
stock.

**Regulatory impact review (RIR):** The part of a federal fishery
management plan that describes impacts resulting from the plan.

**Relative abundance:** An index of fish population abundance used to
compare fish populations from year to year. This does not measure the
actual numbers of fish, but shows changes in the population over time.

**Saltonstall-Kennedy Grant Program:** A competitive program that
provides funds through grants or cooperative agreements for research and
development projects to benefit U.S. fishing industry. The
Saltonstall-Kennedy Act, as amended \[15 U.S.C. 713 (c) (3)\], is the
program\'s statutory authority.

**Stakeholder:** One who is expected to receive economic or social
benefits from the conservation and management of living marine
resources.

**Stock:** A more-or-less discrete and identifiable unit of fish or
other exploited species, often referring to a management unit.

**Stock assessment:** The biological assessment of the status of the
resources. This analysis provides the official estimates of stock size,
spawning stock size, fishing mortalities, recruitment, and other
parameters.

**Stock assessment workshop (SAW):** A cooperative stock assessment
activity in which scientists from various agencies evaluate the status
of fish stocks.

**Subadult:** A developmental life stage when fish exhibit most but not
all traits of an adult fish.

**Subsistence fishing:** Fishing for personal consumption or
traditional/ceremonial purposes.

**Technical Review Team (TRT):** A panel of scientists set up to define
\"delisting criteria\" in specific geographic domains for endangered
salmon and steelhead species on the west coast.

**Trophic web:** The network that represents the predator/prey
interactions of an ecosystem.

**Turtle excluder device (TED):** An implement that has been certified
to reduce the likelihood of capturing turtles.

**Yield per recruit:** The average weight of fish ultimately harvested
for each fish that enters the fishery.

**Virtual population analysis:** A mathematical analysis in which catch
data are used to estimate absolute abundances of age-classes in a stock
and the fishing mortality that has been sustained by those age-classes.

**Literature Cited**

EPAP. 1999. Ecosystem-based fishery management: A report to Congress by
the Ecosystems Principles Advisory Panel, as mandated by the Sustainable
Fisheries Act amendments to the Magnuson-Stevens Fishery Conservation
and Management Act 1996. U.S. Dep. Commer., NOAA, Natl. Mar. Fish.
Serv., Silver Spring, MD, 54 p. Available electronically at
[[www.nmfs.noaa.gov/sfa/EPAPrpt.pdf]{.underline}](http://www.nmfs.noaa.gov/sfa/EPAPrpt.pdf).

FAO. 2001. The state of world fisheries and aquaculture, 2000. Food
Agric. Org. U.N., Rome, 142 p. Available electronically at
[[www.fao.org/docrep/003/x8002e/x8002e00.htm]{.underline}](http://www.fao.org/docrep/003/x8002e/x8002e00.htm).

Federal Register. 2002. Magnuson-Stevens Act Provisions; Essential Fish
Habitat, Final Rule, Federal Register, Vol. 67, No. 12, p. 2343,
Thursday, January 17, 2002.

NMFS. 1998a. Managing the nation\'s bycatch. Programs, activities, and
recommendations for the National Marine Fisheries Service. U.S. Dep.
Commer., NOAA, Natl. Mar. Fish. Serv., Silver Spring, MD, 174 p.

NMFS. 1998b. Proposed implementation of fishing vessel registration and
fisheries information system. Report to Congress submitted to the
Committee on Resources of the House of Representatives and the Committee
on Commerce, Science, and Transportation of the Senate. Available
electronically at
[[www.nmfs.noaa.gov/sfa/reports.html]{.underline}](http://www.nmfs.noaa.gov/sfa/reports.html).

NMFS. 1998c. NOAA Fisheries Data Acquisition Plan (September 1998)
available electronically at
[[www.st.nmfs.gov/st2/omb_link.html]{.underline}](http://www.st.nmfs.gov/st2/omb_link.html).

NMFS. 1999. Our living oceans. Report on the status of U.S. living
marine resources, 1999. U.S. Dep. Commer., NOAA Tech. Memo.
NMFS-F/SPO-41, 301 p. Available electronically at
[[http://spo.nwr.noaa.gov/olo99.htm]{.underline}](http://spo.nwr.noaa.gov/olo99.htm).

NMFS. 2001. Fisheries of the United States, 2000. U.S. Dep. Commer.,
NOAA, Natl. Mar. Fish. Serv., Curr. Fish. Stat. 2000, 126 p. Available
electronically at
[[www.st.nmfs.gov/st1/fus/fus00]{.underline}](http://www.st.nmfs.gov/st1/fus/fus00).

NMFS. In press. National Stock Assessment Improvement Plan. U.S. Dep.
Commer., NOAA Tech. Memo. NMFS.

NRC. 1998. Improving fish stock assessments. Natl. Res. Counc., Natl.
Acad. Press, Wash., DC, 188 p. Available electronically at
[[www.nap.edu/books/0309057256/html/]{.underline}](http://www.nap.edu/books/0309057256/html/).

NRC. 1999a. Sustaining marine fisheries. Natl. Res. Counc., Natl. Acad.
Press, Wash., DC, 184 p. Available electronically at
[[www.nap.edu/books/0309055261/html/]{.underline}](http://www.nap.edu/books/0309055261/html/).

NRC. 1999b. Sharing the fish: toward a national policy on individual
fishing quotas. Natl. Res. Counc., Natl. Acad. Press, Wash., DC, 436 p.
Available electronically at
[[www.nap.edu/books/0309063302/html/]{.underline}](http://www.nap.edu/books/0309063302/html/).

NRC. 2000. Improving the collection, management, and use of marine
fisheries data. Natl. Res. Counc., Natl. Acad. Press, Wash., DC, 236 p.
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[[www.nap.edu/books/0309070856/html/]{.underline}](http://www.nap.edu/books/0309070856/html/)

NRC. 2001. Marine protected areas: tools for sustaining ocean
ecosystems. Natl. Res. Counc., Natl. Acad. Press, Wash., DC, 288 p.
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