willingness to share data sets with NMFS but, again, a
standard, interactive access system with uniform data code
and format is needed to use this information effectively.
IDIMS will not be a repository for all these data, but will
provide an index of sources of data stored elsewhere, and
contain condensed files of certain Center data ina
relational data base.

IDIMS, the foundation of the Framework, will be a major
component of the Center’s complete data management system,
which will allow interaction among inshore, and between
inshore and offshore, data sets. Once developed, IDIMS will
enable NMFS personnel to generate rapid and comprehensive
responses to requests for information and advice on major
issues affecting living resources in inshore waters. IDIMS
will be capable of producing information summaries that are
necessary to develop credible NMFS positions on effects of
proposed habitat alterations and fishery management
strategies, and will allow hazard assessments to be performed
that are focused on particular species or geographic areas.

An obvious advantage of IDIMS is that information
produced in response to one request (e.g., habitat require-
ments of species in a fishery management plan) is stored and
may be used for other purposes (e.g., biological effects of
proposed habitat alterations on those same species). IDIMS
will also be used to track the Center’s inshore research
projects, and to help coordinate research efforts with the
many organizations involved with the Center in inshore
research.

The goal of the data and information management system
component of the Framework is to establish and maintain a
system for the storage, retrieval, and interactive
(relational) analyses of inshore data and information.

To accomplish this goal, it is necessary to: (1)
identify the essential core of environmental, biological,
economic, and fisheries data to be incorporated in the
integrated and operational data base; (2) evaluate the
relative importance of the various types of data, the
adequacy of available data sets for answering information
needs of users, the quality assurance procedures to be
followed, and the methods of accessing particular data sets;
(3) develop an interim plan for data archiving until the
system is fully developed and operational; (4) develop data
base criteria for systematic inputs to the system; (5)
develop and apply techniques and software for creating
compatibility among assembled inshore data bases (i.e.,
create a relational data base), ensuring that IDIMS is
compatible with its eventual offshore counterpart; (6)
develop tutorials for NMFS staff and other users; and

-12-


Current information on several species (e.g., winter
flounder) considers all stocks together in the fisheries.
Separate stocks or subpopulations should be identified, using
standard methodologies (suitably modified for inshore areas
and species, if necessary), before attempting to determine
the effects of fishing on offshore aggregations of fish that
utilize inshore waters during certain periods of their lives.
Methods available include tagging studies, multivariate
statistical analyses of meristics and morphometrics, image
analysis of scales and otoliths, electrophoresis and
isoelectric focusing, and monoclonal antibodies.

Products anticipated from these efforts include:

o Designs for collecting fisheries statistics usable by
NMFS and/or states, emphasizing comparability and
quality assurance of all data used in stock
assessments.

o Fisheries statistics networking system.

o Assessments of inshore fishery stocks and endangered
species of national or regional importance.

o Plans for surveillance and monitoring programs and
special research projects.

© Relational data base and software package.

o Input to habitat requirements and use studies and to
IDIMS.

o Comparison of the relative abundance of species in
inshore and offshore areas.

o Comparison of recreational fish catches and value
(e.g., expenditures by fishermen) in inshore and
offshore areas.

o Comparison of commercial fish landings and value of
fish caught in inshore and offshore areas, and
distinction between sources of fish harvested.

o Identification of stocks or subpopulations inhabiting
or harvested in inshore and offshore areas.

o Comparative effects of fishing mortality on inshore
and offshore stocks and fisheries.

-33-


anthropogenic mortality; (5) create a relational data base
and software, and prepare data for IDIMS; and (6) link
findings (products) to research planning.

Existing tested and evaluated models will be used first,
and any new models that are developed will be tested,
modified, and verified to ensure that they adequately reflect
the system chosen for modeling.

The biomass of a population can be characterized as a
balance between gains realized through growth and
recruitment, and losses from several types of "competing"
mortalities. These mortalities include natural mortality
from predation or disease and anthropogenic mortality from
fishing, pollution, and habitat alteration and loss. Stock
assessment research attempts to partition and determine the
levels of each of these mortalities, and to examine the
effects of each on population levels, anticipating that
different mortalities affect distinct life history stages of
the individuals in a population. For instance, predation
mortality may primarily affect early life history stages
(eggs, larvae, juveniles) because potential predators of
smaller individuals are more numerous. In contrast, fishing
mortality is concentrated on adults, and sometimes juveniles,
of most exploited species. Pollutant-related stresses may
affect population levels by reducing fecundity or the
viability of the ova; by decreasing the survival of larvae,
postlarvae, and juveniles; and by increasing mortalities on
the recruited population by increasing the incidence of
disease and vulnerability to predation.

Additional comprehensive studies need to be conducted to
determine the long-term, cumulative effects of habitat
degradation and fishing on (1) populations of inshore-
dependent living resources (including changes in habitat or
biomass of prey organisms) and (2) catches of recreational
and commercial fish. These studies will involve evaluating
and utilizing various conceptual approaches (models) to
evaluate the population- and fishery-level effects of
competing mortalities, and to partition the levels of
mortality from natural and anthropogenic causes.

Complex inshore ecosystems include living marine
resources from microorganisms to apex predators, all under
the influence of their habitat. Models are used to integrate
various hypotheses about the functioning of an ecosysten,
assure that research hypotheses are internally consistent and
are focused on the problems at hand, test whether or not they
are contradicted by available information, determine the
relative importance of various processes and controlling
factors, determine the types of data needed, and make
predictions.

-29-


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-38-


Table 1. (Cont’d).
Center
Brief Project Title sitel Cooperator? Lead?
Coastal Habitat Assessment, Regional ORNL EPD
Research, & Mensuration
(CHARM) Program
Historical Trends in Benthos NYB,HRE, LIS EPD
Biomass
Limits to Production of Middle Atlantic EPD
Estuarine Shellfish
Behavior of Marine Fishes & Regional OSsU,EPA EPD
Invertebrates
Chesapeake Bay Stock Assessment CB MD,VA,DC, RPAC
Program PSU
NOAA Status & Trends -- National S&T Sites OAD
Benthic Surveillance Project:
o Analysis of Extractable cuUD
Organic Compounds
o Histopathological Analysis FED
o Heavy Metals Analysis EPD
o Benthos Studies EPD
Cytogenetic Effects of
Contaminants on Mackerel Eggs Regional EPD
Massachusetts Inshore Survey MA MA FED,
cuD
Northern Shrimp Survey Gulf of MA,NH,ME FED,
Maine cuD
Maine Herring Survey ME ME FED,
cuD

1pH: Boston Harbor, BB:
Long Island Sound, HRE:
NYB: New York Bight, CB:

2pws: Fish and Wildlife

Buzzards Bay, NB: Narragansett Bay, LIS:
Hudson River Estuary, RB: Raritan
Chesapeake Bay, S&T: Status and Trends

Bay,

Service, EPA: U.S. Environmental

Protection Agency, FVSC: Fort Valley State College, OAD: Ocean
Assessments Division, NURP: National Undersea Research Program,
ORNL: Oak Ridge National Laboratory, OSU: Oregon State Univ.

3see Figure 1 for acronym definitions

~6-


Information Services Section
Northeast Fisheries Center
National Marine Fisheries Service, NOAA
Water St.

Woods Hole, MA 02543

it

—
US.MAIL
eo

POSTAGE ANO FEES PAID
US. DEPARTMENT OF COMMERCE
com210

THIRD CLASS MAIL

NOAA SCIENTIFIC AND TECHNICAL PUBLICATIONS

The National Oceanic and Atmospheric Administration was established as part of the Department of Commerce
on October 3, 1970. The mission responsibilities of NOAA are to assess the socioeconomic impact of natural and
technological changes in the environment and to monitor and predict the state of the solid Earth, the oceans and their
living resources, the atmosphere, and the space environment of the Earth.

The major components of NOAA regularly produce various types of scientific and technical information in the

following kinds of publications:

PROFESSIONAL PAPERS—Important definitive
research results, major techniques, and special
investigations.

CONTRACT AND GRANT REPORTS—Reports
Prepared by contractors or grantees under NOAA
sponsorship.

ATLAS—Presentation of analyzed data generally in the
form of maps showing distribution of rainfall, chemical
and physical conditions of oceans and atmosphere,
distribution of fishes and marine mammals, iono-
spheric conditions, ete.

TECHNICAL SERVICE PUBLICATIONS—Reports
containing data, observations, instructions, etc. A
Partial listing includes data serials; prediction and
outlook periodicals: technical manuals, training
Papers, planning reports, and information serials: and
miscellaneous technical publications

TECHNICAL REPORTS—Journal quality with extensive
details, mathematical developments, or data listings.

TECHNICAL MEMORANDUMS—Reports of pre-
liminary, partial, or negative research or technology
results. interim instructions, and the like.

Information on availability of NOAA publications can be obtained from.

National Technical intormation Service
5285 Port Royal Road
Springfield, VA 22161


of the inshore research program. The in situ analysis of
contaminant effects proposed by FED as part of the winter
flounder case study, which requires start-up support for
developing prototype study chambers and for evaluating
potential study sites in the Northeast, is an example of the
type of research project that should qualify for reimbursable
funding.

3. Begin studies recommended _in the Habitat
Requirements and Use section of the Framework for Inshore
Research as soon as possible. Habitat requirements and use
information is a high priority need of the Region’s Habitat
Conservation Branch; this information is used during
evaluation of habitat-altering projects, as well as for
preparation of habitat sections of fishery management plans.
The Center and the Region should begin the tasks necessary to
achieve the objectives outlined in this section with internal
funds if monies are not otherwise available.

4. Accelerate and expand cooperative efforts to develop
and_ implement a fisheries statistics network with the states
and continue cooperative semi-annual stock assessment
workshops. The Center’s inshore research efforts should be
directed toward determining: (a) the relationship between
the inshore and offshore abundance and yield of winter
flounder and lobster, (b) the origin of stocks contributing
to fisheries in inshore and offshore areas, and (c) the long-
term implications of inshore fishing mortality to recreation-
al and commercial fisheries.

5. Develop operational approaches for accomplishing the

Framework’s objectives, with or without additional funding.
The lead Center unit for each of the Framework’s components

should immediately begin to develop these approaches so that
appropriate Center units can conduct the necessary inshore
research. The operational plans should include contingencies
for supporting the Center’s inshore research efforts if the
FY89 budget initiative is not funded, or is funded only
partially or incrementally.

-44-


Conservation Branch and State Federal Relations Branch, as
well as in other NMFS Centers and Regions, other NOAA
components (OAD, Sea Grant, NESDIS, etc.), other federal
agencies (FWS, EPA, COE, etc.), state agencies, the ASMFC,
Fishery Management Councils, and academic groups such as the
Northeast Area Remote Sensing System (NEARSS) and Sea Grant
institutions. Experts in these groups will be relied upon
for basic biological and environmental information, and for
consultation during the peer review and product development
processes.

The Center will rely on NMFS Headquarters for assistance
in product development, and in coordinating the Center’s
efforts with NOAA components such as EPO, OAD, NESDIS, and
Sea Grant. RPAC, in consultation with DMS and NESDIS, will
monitor contracts for developing a relational data base and
associated software.

3.0 Biological Effects of Inshore Habitat Degradation

Understanding the effects of various kinds of habitat
alterations on living marine resources, especially the
ultimate effects on their populations, requires knowledge of
the natural chemical, physical, and biological processes
controlling dispersal and uptake of contaminants and
pathogens, as well as information on the habitat requirements
of the affected species. Consequences of continued inshore
habitat degradation can only be assessed and predicted with
knowledge of how, and to what degree, natural environmental
processes may counteract man-caused habitat degradation.

The sources of habitat degradation to be studied at the
Center are: (1) contaminants, including (a) toxic chemicals
(synthetic organics, petroleum hydrocarbons, heavy metals),
(b) nutrient overenrichment (causing eutrophication and
hypoxia), and (c) diseases and pathogens; (2) physical
habitat alteration and loss; and (3) cumulative effects of
(1) and (2) in the presence of fishing mortality.

The ultimate goal of biological effects studies is to
link effects on individual organisms to effects on
populations and fishery yields. Accomplishing this goal
involves the difficult task of determining the mortality rate
due to a given source of habitat degradation. Source-
specific mortality rates, combined with source-specific
effects on growth, behavior, and reproduction, are necessary
for examining the effects of cumulative stress due to habitat
degradation and fishing.

-16-


In cooperation with state fish and wildlife agencies,
FWS, academic institutions, NMFS Headquarters, and fishermen,
the Center (CUD) collects and archives recreational and
commercial fishery statistics information (Fishery Statistics
and Economics Branch), organizes and participates in stock
assessment workshops (Population Dynamics Branch), and
monitors inshore and offshore stocks (Population Biology
Branch). These three Branches will share the Center lead for
accomplishing the objectives of this component of the
Framework, and will coordinate with other Center elements as
necessary. The Center will rely on the Region’s State
Federal Relations Branch to monitor grants to states for
collection of fisheries statistics and stock monitoring
information.

C. COORDINATION OF THE CENTER’S INSHORE RESEARCH INSIDE
AND OUTSIDE NOAA

Coordination of information exchange is an important
part of the Center’s inshore research program, and may in
fact be the key to its ultimate success. The Center must
interact with many other agencies and institutions interested
in the condition of inshore living resources and their
habitats. The scientific purpose of these interactions is
three-fold: (1) to obtain baseline information on historical
and projected trends in habitat degradation; (2) to
participate in collaborative studies; and (3) to provide
other agencies and institutions with scientific knowledge
necessary for successfully conducting their research
programs.

Formal interactions to date have been with NMFS’s
Northeast Regional Office, NMFS Headquarters, other NMFS
Regional Offices and Fisheries Centers, other NOAA components
(e.g., EPO, OAD, Sea Grant), other federal agencies (e.g.,
EPA, COE, FDA, NCI), the National Science Foundation and
National Academy of Sciences, the coastal states (in stock
assessment workshops, etc.), and academia (e.g., the NEARSS
Association). Data and information transfer activities
related to inshore research are also conducted informally on
a scientist-to-scientist level, as well as on a national and
international level.

An overriding problem facing the Center in coordinating
its inshore research activities is the necessity to provide
information for use within the management and research
structure of other agencies, specifically EPA, that are not
based on a regional perspective. Although only 7 percent of
the Center’s inshore research is supported by EPA in FY87,
Center scientists have to deal with separate, often

-34~


EXECUTIVE SUMMARY

I.

II.

III.

TABLE OF CONTENTS

INTRODUCTION......
THE CENTER’S FRAMEWORK FOR INSHORE RESEARCH.......... 8
A. THE ROLE OF THE CENTER IN INSHORE WATERS.........8
B. THE CENTER’S INSHORE RESEARCH PROGRAM......... re)
1.0 Inshore Data and Information Management
System (IDIMS)........... ee 8
2.0 Inshore Habitat Requirements and Use....... 14
3.0 Biological Effects of Inshore
Habitat Degradation.............0 eee e enone 16
3.1 Effects of Contaminants...............19
3.1.1 Effects of Toxic Chemicals..... 22
3.1.2 Effects of Nutrient
Overenrichment..........eeeeee- 23
3.1.3 Effects of Pathogens
and Disease.... ane 24
3.2 Effects of Physical Habitat
Alteration...
3.3 Cumulative Effects of Habitat
Degradation and Fishing Mortality..... 28
4.0 Fishery Statistics and Stock Assessments...31
C. COORDINATION OF THE CENTER’S INSHORE RESEARCH
INSIDE AND OUTSIDE NOAA......ceeeeeeees eee ee ee 34
IMPLEMENTATION OF THE INSHORE RESEARCH PROGRAM...... 36
A. IMPLEMENTATION OPTIONS......--2eeceececees oe 36
B. IMPLEMENTATION SCHEDULE..........ceeeeeeceeeee 237
C. PROGRAM PRIORITIES....... eee eee eee twee eee eee 42
1.0 New Projects...... See rs 42
2.0 Ongoing Projects.............. ren 5)
D. RECOMMENDED ACTIONS........22-0-- eee eee ee eens 43


economically and ecologically valuable functions of lost
habitat are replaced is poorly documented, and information on
the processes that lead to successful replacement or
enhancement is generally lacking. This knowledge is needed
for effective management of habitats through the COE’s
regulatory program.

FED’s Ecosystem Dynamics Branch will take the Center
lead for studies on the functional value of habitats,
comparability of habitat functional values, and evaluation of
alternative mitigation and enhancement techniques. EPD’s
Environmental Assessment Branch, FED’s Manned Undersea
Research and Fisheries Engineering Branch (MURFE) and
Experimental Biology Branch, and CUD’s Population Biology
Branch will conduct studies on the reaction of organisms to
habitat availability; conduct studies on habitat usage,
importance, and denial; and contribute to studies on habitat
functional value and evaluations of alternative mitigation
and enhancement techniques. CUD’s Fisheries Statistics
Branch will perform economic analyses. RPAC will help
develop and monitor contracts for evaluating mitigation and
enhancement techniques, participate in product development,
and help coordinate research with cooperating agencies.

The Center will rely on the Region’s Habitat
Conservation Branch to: (1) collect, archive, and analyze
data on habitat availability and rates of loss; (2) provide
advice on habitat types and areas of most importance for
study; (3) participate in field studies and ground-truthing
activities; (4) provide liaison with other agencies regarding
habitat-altering projects; (5) provide advice on non-monetary
valuation, habitat evaluation procedures, and mitigation and
enhancement techniques; and (6) participate in peer review
and product development. The Center also will rely on NMFS
Headquarters for help in coordinating with other NOAA
elements, and for advice on product development.

The Center will rely on the Southeast Fisheries Center
and Southeast Region, especially during the early stages of
these studies, for: (1) cooperative studies and assistance
in study design, collection of samples, and data analysis and
interpretation; (2) consultation on habitat availability and
functional values, comparability of habitats and functional
values, non-monetary habitat evaluation techniques, and
product development; and (3) peer reviews.

The Center will rely on other NOAA elements (e.g., OAD,
EPO, and Sea Grant) and other federal agencies (e.g., FWS,
COE, and EPA) for cooperative studies, consultation on
habitat status and trends, habitat evaluation procedures,
mitigation and enhancement techniques, and participation in
peer review and product development; state agencies for

-27-


(7) evaluate the usefulness of IDIMS and the resulting
products, and make necessary improvements.

Anticipated IDIMS products include:
o System design.

o Interim plan for data archiving until system is fully
developed and operational.

o Data base format criteria for systematic input.
o Techniques for interactive analysis.

o Software for interaction and relational analysis of
data bases.

o An accessible, user-friendly system that may be
accessed by Center scientists and administrators, and
by other users.

o Inventories of accessible data sets, tabular and
graphic representations of data sets, and integrated
products such as periodic atlases and information
syntheses for particular geographic areas, species,
and time periods.

Expected Center participants include DMS and RPAC staff
who will develop and monitor private sector contracts for
system development, and coordinate Center participation by
appropriate CUD, FED, and EPD staff.

Definition of products and identification of data bases
will be done in cooperation with NMFS’s Northeast Region;
Regional Fishery Management Councils; state agencies; the
ASMFC; NMFS’s Washington Office; academic institutions; other
NOAA components such as the National Environmental Satellite,
Data, and Information Service (NESDIS), the National Ocean
Service’s Ocean Assessments Division (OAD), the Office of Sea
Grant and Extramural Programs (Sea Grant), and the Estuarine
Programs Office (EPO); and other federal agencies such as
EPA, the U.S. Fish and Wildlife Service (FWS), the U.S. Army
Corps of Engineers (COE), the U.S. Geological Survey, the
Federal Energy Regulatory Commission, the Minerals Management
Service, the U.S. Coast Guard, the U.S. Nuclear Regulatory
Commission, and the U.S. Department of Energy.

-13-


3.1 Effects of Contaminants

Human activities and the wastes associated with these
activities contribute many different contaminants to inshore
waters. These contaminants include potentially toxic
chemicals, as well as nutrients and pathogens.

Although many of the chemical contaminants occur
naturally, human activities alter the rates and amounts of
these materials cycling in inshore environments to such a
profound extent that potentially harmful levels are often
reached in marine organisms and their habitats in Northeast
inshore waters. Other chemicals, such as synthetic organic
compounds, are, by definition, present in the environment
only because they are produced by the chemical industry and
released into the environment through human activities.

Contaminants may affect population dynamics of living
marine resources in two ways: (1) directly, by causing an
increase in mortality during one or more life stages,
changing spawning or migrational behavior patterns, or
changing the genetic fitness of the population; or (2)
indirectly, by reducing the available habitat, or by causing
bans on fishing and on consumption of fishery products to
protect human health. Events that may cause organisms to
avoid normally preferred habitats include (1) hypoxia or
anoxia caused by nutrient overenrichment, (2) chronic
poisoning brought about by industrial and municipal
discharges, and (3) urban and agricultural runoff and its
effects on (1) and (2).

To what extent and in what manner these events may
affect the biological processes of inshore-dependent fishery
resources and endangered species is a subject of major
concern to recreational and commercial fishermen, seafood
consumers, conservationists, government workers, and others
whose livelihood depends on the sea, who use or otherwise
enjoy the inshore environment and its living resources, or
who are responsible for pollutant discharge regulation,
fishery management, habitat conservation, and recovery
programs for endangered species.

The anthropogenic additions of halogenated organic
compounds, petroleum hydrocarbons, heavy metals, nutrients,
and pathogens to inshore waters can cause problems by
threatening ecosystems or contaminating sea food. Metals and
organics are potentially toxic to marine organisms, and to
humans when these chemicals are bioaccumulated in fishery
products. Many of the contaminants (e.g., polychlorinated
biphenyls, dioxins, and organotins) are persistent in the
environment, and are toxic to marine organisms and humans at
extremely low concentrations; i.e., at parts per billion to

-19-


various life history stages; (3) food requirements, food
availability, and predator-prey interactions in inshore
habitats; (4) the relationship of physiological requirements
and behavioral characteristics to environmental
characteristics of inshore habitats (e.g., sediment type,
vegetation, water temperature, salinity, circulation and
exchange patterns); and (5) the effects of natural
environmental variations on survival, growth, maturation,
behavior, reproduction, and movements.

Once this information is summarized and evaluated,
additional research necessary to fill critical information
gaps should be determined, research plans should be developed
for conducting the highest priority studies, and planned
research should be conducted in cooperation with other
agencies and institutions. Techniques for creating
compatibility among the data bases developed for IDIMS should
be evaluated and applied to create a relational data base,
and a software package should be created for storage and
retrieval of habitat information to be entered on IDIMS.

Anticipated habitat-related products include:

o Matrix of status of knowledge for species’ inshore
habitat requirements and use.

o Research plans and research to fill gaps in matrix.

o Summaries of information on important habitat types
and conditions.

o Contributions of local inshore habitats to regional
population abundance (i.e., "inshore-dependency" of
species and stocks).

o Relational data base on habitat requirements and use.

o Information storage and retrieval software package
for relational data base.

o Input to biological effects and to IDIMS.

o Maps, atlases, and inventories of habitat usage for
selected species.

© Zoogeographic (e.g., RAP "Water Management Unit")
characterizations.

FED’s Ecosystem Dynamics Branch, the lead Center unit
for this component of the Framework, will depend on
considerable help from species and habitat experts within the
Center (EPD, FED, CUD, and NSL) and the Region’s Habitat

-15-


cooperative studies, consultation on availability of habitat
types, habitat usage; the academic sector (e.g., the NEARSS
Association) for information on habitat status and trends;
and the private sector through contracts for mitigation and
enhancement studies.

Products anticipated from the physical habitat
alteration component of the program include:

o Status and trends in quantity and quality of inshore
habitats.

o Functional (ecological) valuation of inshore
habitats.

o Comparison of the functional values of habitat types
along the Atlantic coast.

o Assessment and modification of habitat evaluation
procedures.

o Relative impacts of loss of habitat types on fishery
stocks and endangered species in presently used and
potential alternative areas.

o Mortality rates due to physical habitat alteration
and loss for use in studies on the cumulative effects
of habitat degradation and fishing.

© Relational data base and software.

o Input to habitat requirements and use studies,
cumulative effects studies, and IDIMS.

o Recommendations for mitigation/enhancement
techniques.

3.3 Cumulative Effects of Habitat Degradation and Fishing
Mortality

The goal of the cumulative effects studies is to
evaluate, develop, and use conceptual approaches (models) for

linking effects on organisms caused by habitat degradation to
effects on populations and fisheries yields.

The objectives associated with these studies are to:
(1) evaluate available conceptual approaches, and develop and
implement new approaches, as necessary; (2) use models to
determine the types of information needed from biological
effects studies; (3) use models to assess and predict
cumulative effects; (4) partition levels of natural and

-28-


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-10-


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base and software, and prepare data for IDIMS; and (8)
evaluate alternative management measures to limit the spread
of pathogens and outbreak of disease.

Anticipated products of the studies on pathogens and
disease include:

o Spatial and temporal occurrence of disease outbreaks
on a regional scale.

o Summaries of available information on life cycles
(including intermediate hosts) of the most common
pathogens, habitat conditions favoring pathogens, and
pathogen ranges and transport media.

o Research plans to fill gaps in knowledge and address
priority issues.

o Relationship of pathogen occurrence to other sources
of organism stress.

© Mortality rates due to disease for use in studies of
cumulative effects of habitat degradation and
fishing.

o Relational data base and software package.
o Recommendations for disease prevention and
control strategies.
3.2 Effects of Physical Habitat Alteration
The goal of the physical habitat alteration studies is
to relate trends in the amount and condition of inshore

habitat types to effects on inshore and offshore populations
of living marine resources.

The major objectives of this component of the Framework
are to: (1) obtain reliable information on the current
availability (quantity and quality) of various habitat types
and the rates of loss or gain; (2) determine species usage
and importance (functional value) of individual habitats to
total populations (inshore and offshore); (3) determine the
similarity and comparability of habitats and habitat
functional values along the Atlantic coast, and the extent to
which research results can be extrapolated from one area to
another; (4) determine the reaction of organisms to inshore
habitat denial (behavior, density-dependent effects on
survival, ability to locate and use alternative sites, etc.);
(5) evaluate existing non-monetary assessment techniques for
natural and artificial habitats, and adapt them to inshore

-25-


3.1.1 Effects of Toxic Chemicals

The goal of the studies on biological effects of toxic
chemicals is to relate concentrations in the inshore
environment to effects on living resources.

The objectives for achieving the goal are to: (1)
define the pathways and rates of uptake from food, water, and
sediments, and the fates of toxic chemicals and metabolites
within target organisms (i.e., determine exposure, uptake,
and retention); (2) determine direct and indirect biological
effects on target species; (3) create a relational data base
and software, and prepare data for IDIMS; and (4) evaluate
alternative strategies for mitigating adverse effects on
living marine resources.

To accomplish these objectives, the Center needs to:
(1) rank classes of toxic chemicals to be studied and
determine the order of priority of contaminants within each
class, based on cooperatively developed, agreed-upon criteria
(e.g., toxicity, persistence, bioavailability,
bioaccumulation); (2) choose representative study sites and
target species; (3) summarize and evaluate existing
knowledge; (4) determine research required to fill gaps in
knowledge; (5) conduct a regional survey of levels of toxic
chemicals and associated gross abnormalities in tissues of
target species; and (6) design and conduct appropriate field
and laboratory studies.

Direct and indirect effects that need to be addressed
include effects on: physiology (cellular level--micro-
biology, genetics); reproduction (gonadal development,
fertility, maturation rate, egg viability); development
(embryology, metamorphosis, etc.); subsequent generations
(i.e., filial effects); behavior, feeding, growth, morbidity,
and mortality; susceptibility to pathogens and disease;
cumulative and synergistic effects of more than one chemical;
recovery rates of degraded areas following clean-up or
cessation of dumping or discharge. (Priorities must be
established, and detailed plans must be developed for those
effects actually chosen for study.)

Anticipated products from the toxic chemical studies
include:

o Ranking of priority chemicals to study.
o Summaries and evaluations of available information.
o Research plans to fill gaps in knowledge and address

priority issues.

-22-


EXECUTIVE SUMMARY

The role of the Northeast Fisheries Center in inshore
waters is to integrate scientific information and conduct
research necessary to support fishery conservation and
management goals and objectives for species that move between
inshore (generally inside three miles) and offshore habitats,
or that occur alongshore over a major portion of the Atlantic
coast from Maine through Virginia.

As a component of the National Marine Fisheries Service
(NMFS), the federal agency with primary responsibility for
conserving and managing living marine resources and their
habitats, the Center takes a broad, regional perspective of
the status and condition of living marine resources that
depend on inshore habitats.

The primary users and beneficiaries of the products
generated by the Center’s inshore research program are the
NMFS’s Northeast Region and the Regional Fishery Management
Councils. Many other agencies and organizations will also
benefit through implementation of an efficient, responsive,
and cost-effective program. The success of the program
depends on coordination and cooperation with state and local
governments, academia, the Atlantic States Marine Fisheries
Commission (ASMFC), other components of the National Oceanic
and Atmospheric Administration (NOAA), other federal
agencies, the marine recreational fishing community, and
various public and private organizations.

The Center’s Framework for Inshore Research embodies the
Regional Action Plan (RAP) concept by identifying the highest
priority habitat issues and threats to living marine
resources in the Northeast, setting priorities for needed
information syntheses and new research, and laying the
foundation for addressing the highest priority issues using
all appropriate NMFS components.

The inshore research program focuses on addressing the
threats to living marine resources caused by various forms of
contamination (toxic chemicals, nutrient overenrichment,
pathogens, and disease), physical habitat alteration and
loss, and fishing, as well as on garnering knowledge of the
causes of and trends in natural system variability, so that
changes related to these threats can be detected.

The Framework provides criteria for choosing species and
study sites, and lists products that need to be developed to
accomplish the program’s objectives. It also describes the

-v-




agency, or to other potential collaborators, such as Sea
Grant institutions, with which cooperative activities can be
planned.

Step 4 is to modify ongoing Center research projects, as
necessary, and conduct additional research. This step
involves procuring equipment, developing techniques, and
conducting field, laboratory, and in situ studies.

Steps 5-8 involve combining and interpreting the results
of these studies, recording the data on a data base
management system that permits interactive analyses and
creation of integrated products, and developing and
distributing interim products that represent an initial
attempt to summarize the information. Interactive analyses
should then be conducted, integrated products developed and
distributed, and necessary program adjustments made.

Research plans and products should be modified as
deficiencies are identified during synthesis efforts, or as a
result of feedback from users.

Obviously, the process is dynamic and flexible. Many of
the steps occur simultaneously, the process recycles as more
information becomes available, and not all research areas
have to begin at step 1.

1.0 Inshore Data and Information Management System
(IDIMS)

Fish and wildlife resource managers and regulatory
agencies constantly need answers to questions about various
species’ inshore habitat requirements and habitat usage
patterns, the biological and economic importance of inshore
populations relative to entire populations, and the
biological effects of inshore habitat degradation.

A prerequisite to the Center’s providing the scientific
basis for answering such questions is the ability to combine
habitat information with biological and economic data, and to
summarize and display such information in appropriate formats
and time frames for the Region and other users. However, the
existing data management systems in the Center do not allow
easy access to this type of integrated information because
the individual data bases are frequently bonded to, and are
accessed only through, particular data base management
systems.

Important data sets are also held by academic
institutions, the states, other components of NOAA/NMFS,
other federal agencies, and several industrial and consulting
firms. Some of these organizations have indicated a

-11-


I. INTRODUCTION

Many federal laws authorize NOAA to address virtually
all facets of research, assessment, and resource use in
estuarine, nearshore, and offshore waters of the United
States. Recognizing the great importance of estuaries to our
society, the U.S. Congress recently passed the Water Quality
Act of 1987 that, among other things, establishes a National
Estuary Program. Implementation of this program will be a
cooperative effort of NOAA and the U.S. Environmental
Protection Agency (EPA). NOAA has already responded to
several of the problems identified in connection with the
designated estuaries through its Chesapeake Bay Study and
EPA-funded efforts in other estuaries. NOAA’s Estuarine
Framework also addresses many of the needs of the National
Estuary Program.

The Magnuson Fisheries Conservation and Management Act
(MFCMA), Marine Mammal Protection Act, Endangered Species
Act, and other laws give NMFS the primary responsibility for
conserving and managing living marine resources. Over 20
U.S. Department of Commerce, NOAA, and NMFS policies also
affect the direction of NMFS’s research programs, including
the National Program for Marine Fisheries, the Estuarine
Policy, the Fisheries Development Policy, the Marine
Recreational Fisheries Policy, the Habitat Conservation
Policy, the Habitat Alterations Policy, and Guidelines for
Fishery Management Plans.

The NMFS’s Northeast Fisheries Center conducts,
coordinates, and supports scientific investigations relevant
to resolving issues concerning productivity and harvest of
fishery resources throughout their range. The Center is
composed of a Center Directorate, supported by Research
Planning and Coordination (RPAC), Program Support, and Data
Management Support (DMS) staffs; three Divisions --
Conservation and Utilization (CUD), Fisheries Ecology (FED),
and Environmental Processes (EPD); and the National
Systematics Laboratory (NSL) (Figure 1). Center scientists
at laboratories in Woods Hole MA, Gloucester MA, Narragansett
RI, Milford CT, Sandy Hook NJ, and Oxford MD conduct research
in several inshore areas along the northeast U.S. coast, as
well as in the offshore ecosystem.

Waters within three miles of the Northeast coast provide
essential spawning and nursery habitat for many important
living marine resources. Noteworthy species dependent on

1 "NOAA Estuarine and Coastal Ocean Science Framework."
Manuscript. NOAA Estuarine Programs Office, Washington, D.C.

-1-


The Center initially will focus its biological effects
studies on species selected using the following criteria:
(1) the species is a known or suspected indicator of inshore
habitat degradation; (2) inshore habitat is essential to the
life cycle of the species; (3) the species has socio-economic
importance; (4) the species’ range covers a major part of the
Northeast inshore habitat; (5) comprehensive research
programs on biological effects on the species are not being
undertaken by others; and (6) significant information gaps
exist for the species that are not likely to be filled
without Center involvement.

Species recommended for current biological effects
studies, based on the above criteria, are winter flounder,
hard clam, American lobster, American oyster, and soft shell
clam. Species for future studies (including anadromous fish,
endangered species, and food chain organisms) will be
selected based on information needs then considered most
important, according to the above criteria.

Geographic areas for study should be selected based on
any or all of the following criteria: (1) the assumed
importance of the area to living marine resources of greatest
concern to NMFS; (2) the presence of habitat types (e.g.,
salt marsh, intertidal mudflat, submerged aquatic vegetation
beds) for which the Region has the most critical need for
information regarding their functional value; (3) the
presence of relatively clean, unmodified habitats in the
area, and the likelihood that human activities will
significantly alter these habitats in the near future; (4)
the presence of degraded habitats that are amenable to long-
term biological effects and ecosystem recovery studies; (4)
the degree to which the area has been studied previously, and
the likelihood that EPA, FWS, Sea Grant, the states, or
others will conduct the needed research there in the near
future; (5) the existence of relevant, good quality,
accessible data and information for the area; (6) the
proximity of the area to NMFS laboratories, the availability
of suitable equipment and trained personnel, and the cost-
effectiveness of the proposed studies; and (7) the likelihood
that Center research efforts will contribute to solving
resource management problems.

The Center is already conducting studies in several
inshore areas (Table 1). Additional studies may be conducted
in these same general areas, or in other areas based on the
above criteria.

-17-


nT OF
Pe Coy,

i)

NOAA Technical Memorandum NMFS-F/NEC-49

te eS
Pea. a

Northeast Fisheries Center

Framework for Inshore Research

U.S. DEPARTMENT OF COMMERCE
National Oceanic and Atmospheric Administration
National Marine Fisheries Service
Northeast Fisheries Center
Woods Hole, Massachusetts

* July 1987


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proportionally smaller component. In the 1980s, however,
renewed Congressional interest in water quality and NOAA/NMFS
policies and directives related to habitat conservation led
toward a greater research emphasis on those factors affecting
the productivity of living resources in inshore environments.

The Center conducts independent investigations and
participates in cooperative research and monitoring programs
that relate fishing and inshore and offshore habitat
alterations to biological effects and fishery yields (Table
1). An interagency agreement with EPA provides for
cooperative research on the biological effects of
contaminants in Long Island Sound and Narragansett Bay.
Cooperative agreements with Maryland, Virginia, the District
of Columbia, and Pennsylvania State University provide for
joint development of a program to examine the combined
effects of fishing and pollution on the fishery resources of
Chesapeake Bay.

The Center’s Fiscal Year 1987 (FY87) inshore research
projects (Table 1) focus on the biological effects of habitat
degradation, particularly those associated with contaminants,
and on several species that support inshore fisheries (winter
flounder, hard clam, oyster, and lobster). Field and
laboratory work includes examination of the biological,
physical, and chemical processes that affect growth and
reproduction. Studies range from those on cytogenetic
effects of pollution on development of fish and shellfish to
broad-scale examination of the effects of contamination on
recruitment success of species in several estuaries. The
relationship between contaminant loadings and the occurrence
of pathogens in fish and shellfish is also being examined,
and cooperative inshore surveys and stock assessment programs
are being conducted in New England coastal waters and in
Chesapeake Bay, Long Island Sound, Buzzards Bay, and
Narragansett Bay. The Center supports or conducts these
studies in cooperation with state agencies, other elements of
NOAA, other federal agencies, and academic institutions.

Because of the collective desire of federal, state, and
private institutions to understand the factors affecting
productivity and utilization of inshore waters, a clear
statement of the Center’s research program in these systems
is necessary. The purpose of this document is to present
such a statement, putting it in the context of the Center’s
role in inshore waters and the "Core emphasis" of the
Center’s research program.

The inshore research program outlined in this document
is consistent with the NOAA Estuarine and Coastal Ocean
Science Framework, and provides a framework for the
Northeast’s contribution to a cost-effective and responsive

-4-


these inshore waters during at least part of their life cycle
include anadromous and catadromous fish (e.g., striped bass,
American shad, blueback herring, menhaden, alewife, Atlantic
salmon, American eel); coastal migratory fish (e.g.,
bluefish, scup, weakfish, black sea bass, summer flounder,
windowpane flounder); fish and shellfish common to, and
residents of, a wide geographic range of inshore waters
(e.g., winter flounder, American oyster, hard and soft shell
clams, bay scallop, blue mussel, American lobster, blue
crab); marine species commonly harvested in inshore waters
(e.g., Atlantic cod, pollock, silver hake, sharks, squids) ;
and marine mammals and endangered species (e.g., harbor and
gray seals, Kemp’s ridley and loggerhead sea turtles,
shortnose sturgeon).

Fishing and hunting pressure and deterioration of
inshore habitats have contributed to decreased abundance and
yields of many species. Moratoria have been declared on
harvesting of some species to help their populations recover.
Shellfish areas have been closed due to contamination by
human pathogens discharged from municipal sewage treatment
plants and other sources. Fish kills have been caused by
contaminants and hypoxia that, in turn, are linked to
accidental spills, waste discharges, agricultural and urban
runoff, and other factors. Degraded environments have been
linked to increased incidence of disease and abnormalities in
demersal fish and shellfish. Several species contain levels
of contaminants in edible tissues that are serious cause for
public concern. Commercial sale of some species has been
banned, and health advisories have been issued to
recreational fishermen. Construction of dams and freshwater
diversions has denied anadromous fish access to historic
spawning areas; altered salinity profiles in estuaries; and
possibly expanded the range of diseases, parasites, and
predators associated with higher salinities. Impoundments
may restrict natural tidal flows, reduce transport of
detritus and nutrients to and from salt marsh wetlands, and
impede movements of fish and shellfish. Dredging, filling,
and in-water construction activities continue to destroy
valuable wetland areas and degrade water quality at a rate
commensurate with human population growth and activities
along the coast.

The federal laboratories conducting marine fisheries
research in the Northeast have been involved in inshore
research activities throughout their 100-year history. Some
laboratories (Oxford, Sandy Hook, and Milford) were
established specifically to conduct research in inshore
waters. In 1976, the NMFS laboratories were consolidated
into the Northeast Fisheries Center, and more emphasis was
placed on addressing problems and issues associated with
passage of the MFCMA; the inshore research program became a

-3-


III. IMPLEMENTATION OF THE INSHORE RESEARCH PROGRAM

A. IMPLEMENTATION OPTIONS

The level of involvement of the Center in research
activities associated with inshore living resources in FY88
and beyond could follow one of three possible options: (1)
reduce or eliminate involvement in inshore research in favor
of expanding research activities dealing with offshore living
resources; (2) maintain the current level of inshore
research, and consider reprogramming some inshore research
activities; or (3) expand the current level of inshore
research, through (a) reprogramming, (b) seeking
reimbursables, or (c) submitting budget initiatives.

Option 1 (reduce or eliminate involvement) is not a good
choice due to the present desires of Congress and NOAA for
NMFS to participate more fully in intra- and interagency
inshore research programs, such as the National Estuary
Program and the Status and Trends Program.

Adopting Option 2 (maintain current level of
involvement) would lead to development of some of the
products listed in the Framework, but would not encourage a
well-integrated, long-term approach to inshore research that
has consistency in terms of priorities, relationships among
projects, satisfaction of information needs, and timeliness
of products.

The Center does not have the base funds necessary to
expand its inshore research efforts by reprogramming from
other research areas (Option 3a). Reprogramming would reduce
to an unacceptable level the Center’s capabilities to respond
to MFCMA and related offshore information needs. Since these
needs are expected to grow, further reprogramming to enhance
inshore research is not a realistic option.

Additional reimbursables could be sought from other
agencies, such as EPA and COE, to expand the Center’s inshore
research program (Qption 3b). Coordination and cooperation
among federal agency line offices is desired, but the one-
year reimbursable mode creates difficulties in Center
planning and management of the projects. These difficulties
are particularly apparent when several agency reimbursables
are involved. Because longer-term transfer of funds is
currently not the policy, reimbursables are not suitable to
support the long-term Center commitment that is required.
Furthermore, products from reimbursed projects may suit the
funding agencies and perhaps satisfy other needs, but may be
unsuitable for developing and enhancing the inshore data and
information base that is the backbone of the Center’s inshore

-36-


Anticipated products of nutrient overenrichment studies
include:

o A description of the regional extent and severity of
existing and potential biological problems associated
with nutrient overenrichment.

o Summaries of existing knowledge of effects and
mechanisms for effects.

o Research plans for studies to fill gaps in knowledge
and address priority issues.

o Mortality rates due to effects of nutrient
overenrichment for use in studies of cumulative
effects of habitat degradation and fishing.

o Species’ threshold levels for dissolved oxygen.

o Relationship of dissolved oxygen levels to species
productivity.

o Relationship of disease and abnormalities to various
nutrient levels and concomitant eutrophication and
hypoxia.

o Relational data base and software package.

o Input to cumulative effects studies and to IDIMS.

o Evaluations of alternative management strategies for
improving nutrient enrichment conditions, including
risk assessments and recommendations for remedial
action.

3.1.3 Effects of Pathogens and Disease
The goal of the studies on pathogens and disease is to

determine relationship among disease outbreaks, presence of
pathogens, and habitat degradation.

The objectives necessary to achieve this goal are to:
(1) define the spatial and temporal occurrence of disease
outbreaks in inshore waters; (2) identify habitat conditions
that favor pathogens productivity and movement; (3) identify
intermediate hosts (life cycles) for pathogens; (4) identify
ranges and transport media for pathogens; (5) determine
effects of disease on survival, growth, and reproduction at
organism- and population levels; (6) establish association
with other types of organism stress (contaminants, nutrient
overenrichment, habitat loss}; (7) create a relational data

~24-


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o Distribution of body burdens of toxic materials
in key organisms on a regional scale.

o Relationships of concentrations of chemicals in
environment to concentrations in organisms.

o Fates and effects of toxic chemicals in target
organisms (i.e., exposure, uptake, and retention).

o Relationship of disease and other abnormalities to
toxic chemical concentrations in environment and
organisms.

o Mortality rates due to individual toxic chemicals, as
well as combinations of chemicals, for use in studies
of cumulative effects of habitat degradation and
fishing.

o Relational data base on toxic chemicals.
o Input to cumulative effects studies and to IDIMS.

o Evaluations of alternative management schemes to stop
pollution or remove contaminants, including risk
assessments and recommendations for remedial action.

3.1.2 Effects of Nutrient Overenrichment

The goal of the nutrient overenrichment studies is to
determine organism- and community-level responses to changes
in inshore systems due to events associated with excessive
nutrient input to inshore waters (e.g., eutrophication,
hypoxia, or anoxia, increased turbidity, and altered plankton
species composition).

The objectives associated with this goal are to: (1)
define the scope of the nutrient overenrichment problem for
selected species, by geographic region; (2) determine effects
of the events associated with nutrient overenrichment on
species distribution, movement, and migration; (3) determine
changes in feeding relative to impacts of the events on food
supply; (4) determine effects of the events on reproduction
and recruitment; (5) identify physiological and developmental
effects (e.g., on growth); (6) determine the relationship of
nutrient overenrichment to susceptibility of species to
disease; (7) create a relational data base and prepare data
for IDIMS; and (8) determine probable mechanisms for effects
from the events, and evaluate alternative strategies for
mitigating the events.

-23-


various phases through which each of the major inshore
research activities should progress, and indicates the
linkages among the objectives and products associated with
each major component of the Framework.

The Center’s inshore research program is aligned with
conservation and management needs of the Region and Center
that fall into four major categories: (1) data and
information management, (2) habitat requirements and use, (3)
biological effects of habitat degradation, and (4) fishery
statistics and stock assessments.

The top priority for implementing new projects proposed
in the Framework is completion of the tasks associated with
creating and using the Inshore Data and Information
Management System (IDIMS). Assembly, synthesis, and
evaluation of available information that defines inshore
habitat requirements and use by important living marine
resources is the next highest priority.

The highest priority ongoing projects are: (1) research
on the population- and fishery-level effects of contaminants
on the reproductive success of winter flounder and American
lobster; and (2) cooperative state/federal efforts to develop
a shared network of fisheries statistics data, and to conduct
stock assessment workshops that deal with inshore species on
a regular basis.

Major products include: (1) improved knowledge on the
relationships among inshore habitats, human activities,
living marine resource populations, and fishery yields; (2)
summaries and evaluations of available knowledge; (3) an
interactive data and information management system; (4)
improved capability for predicting abundance and availability
of fishery resources; (5) risk assessments and evaluations of
alternative management strategies; and (6) research plans to
fill gaps in knowledge.

The Framework recommends that the Center: (1) prepare a
major budget initiative for FY89 that expands the capability
of the Center, Region, and cooperators to address the
Framework’s objectives; (2) begin consolidating present
inshore research projects into a cohesive program; (3) begin
assembling and evaluating information on habitat requirements
and use; (4) accelerate and expand cooperative efforts to
develop and implement a shared fisheries statistics network
with the states, and continue cooperative semi-annual stock
assessment workshops; (5) develop operational approaches for
accomplishing the Framework’s objectives, with or without
additional funding (i.e., develop detailed research plans and
conduct the necessary inshore research) .

-vi-


2.0 Inshore Habitat Requirements and Use

Effective conservation and management of inshore-
dependent marine organisms depends on achieving a better
understanding of the role that the quantity and quality of
inshore habitats plays in the continued productivity and
well-being of these species. Documentation of the importance
of inshore habitats to selected species is essential to
understanding why some inshore areas are more productive than
others, and what the effects of any given habitat loss or
alteration might be on living resource populations.

Much of the functional or ecological value of inshore
habitats is related to the presence of spawning and nursery
areas, but the extent to which the productivity and well-
being of living marine resources are linked to the quality,
quantity, and productivity of their habitats generally
remains to be quantified. Similarly, although considerable
research has been done, little is known about the nature of
the relationships among stock size, recruitment, and
production of marine organisms. Additional research is
needed on the ecological factors that determine abundance and
survival of larvae and juveniles. Information generated by
these studies is crucial to understanding recruitment
variability and the natural variability in the populations.
This knowledge will help resource managers and scientists
undertake risk assessments and establish criteria to protect
the characteristics of inshore areas that provide for
continued optimum production of living marine resources.

The goal of the habitat requirements and use component
of the Framework is to develop a basic knowledge of the
inshore habitat requirements, habitat preferences, and

habitat usage patterns of selected species.

Major objectives associated with this goal are to: (1)
define habitat requirements, preferences, and usage patterns
for selected species; and (2) determine the importance of
inshore habitats to marine species and populations. Species
to be studied may include those of ecological importance
(e.g., food organisms), as well as representative species
(probably 15-20) for which NMFS bears mandated responsibility
(i.e., commercial and recreational species of fish and
shellfish and protected species of mammals, turtles, and
fish).

To accomplish these objectives, relevant information
should be assembled, evaluated, and summarized on: (1)
species’ distribution, patterns of movement or migration,
subpopulation or stock definition, and abundance; (2) the
degree of "inshore-dependency" of marine species, including
residence time in, and seasonal usage of, inshore habitats by

-14-


o Relative importance of sources of mortality by
species and habitat type.

o Risk assessments and recommendations.

4.0 Fishery Statistics and Stock Assessments

The goal of this component of the Framework is to
determine the contribution of inshore biological processes to
total fisheries yield potential.

The major objectives associated with this goal are to:
(1) improve the accuracy, completeness, and timeliness of
commercial and recreational harvest statistics for inshore
waters; (2) participate in, and contribute to, joint
Center/State assessments of fishery stocks of regional
importance and of endangered species found in inshore
habitats; (3) determine the relationship between the inshore
and offshore abundance and yield of selected species; (4)
determine the origin of stocks contributing to fisheries in
inshore and offshore areas; (5) determine the long-term
implications of inshore fishing mortalities to recreational
and commercial fisheries; and (6) create a relational data
base for inshore fisheries statistics and stock assessment
data, and input relevant data to IDIMS and other inshore
studies.

Better documentation of the characteristics of inshore
fisheries, particularly the recreational fisheries, is
necessary to support fishery management and habitat
conservation objectives throughout the range of each species.
Fisheries statistical information should be improved to
document the importance of inshore areas, and to support
analyses of mortalities and the effects of fishing on inshore
fish stocks.

Catch, effort, and economic data need to be collected
and analyzed more quickly and accurately for all major
recreational and commercial species in inshore areas. A
fisheries network among NMFS, the Fishery Management
Councils, and the coastal states needs to be developed and
maintained. Ongoing cooperative efforts with the states to
collect better statistics on inshore fisheries need to be
accelerated and expanded, especially for the recreational
fisheries.

Stock assessments are regularly performed for several
species exploited in both inshore and offshore waters. Stock
assessment workshops that consider inshore fish populations
are now conducted each fall by the Center, with state and

-31-


academia participation. Recommendations are carried forward
immediately to the ASMFC.

To determine the long-term implications of anthropogenic
mortalities on inshore stocks to recreational and commercial
fishing, additional research is needed on the relationship
between effective fishing effort and the fishing mortality
generated on multispecies assemblages and component species
in fisheries conducted in inshore waters, and on endangered
species that frequent inshore waters (e.g., shortnose
sturgeon and Kemp’s ridley sea turtle).

Stock assessments for species subjected to inshore
fisheries should include information on: (1) present status
of stocks in relation to historical record; (2) evidence for
trends in status of stock abundance or catch; (3) evaluation
of proposed or existing management regulations; (4) effects
of habitat degradation on status of stocks and fisheries; (5)
short-term and long-term projections for status of stocks;
(6) plans for surveillance and monitoring programs, and for
special research projects; and (7) special assessments on
marine mammals and endangered species.

Combined fishery-independent resource survey data from
each of the state and federal surveys conducted in inshore
waters need to be analyzed and evaluated to determine
abundance levels, distribution patterns, migration or
movement patterns, and residence times of the species. In
some areas, inshore surveys must be expanded or created to
provide the information needed.

Given the uncertainties involved with the adequacy of
the available catch and effort data for inshore species,
survey indices play an important role in the analysis of
trends in abundance of these species. Statistical methods
(time series models, etc.) for combining and analyzing the
data must be determined or developed before the combined
survey data will be applicable to assessment activities.

Many inshore-dependent fish species migrate and are
caught away from home waters; therefore, controlling fishing
to ensure optimum utilization of a fishery resource requires
an understanding of the origin of the stocks contributing to
that fishery, knowledge of the inshore waters from which the
stocks originate, and knowledge of the migratory patterns of
the species. It is also important to know the geographic
range and the extent to which an inshore-dependent stock
contributes to coastal fisheries, so that risk of exposure to
humans can be assessed if that stock is contaminated with
toxic compounds. EPA and the states are particularly
interested in using this information to set water~, air-, and
land-use standards.

-32-


parts per million levels. Other contaminants (e.g., cadmium)
may be toxic not only by themselves, but may become more or
less toxic in the presence of other metals (e.g., copper,
iron, manganese) or organic carbon.

Nutrient overenrichment can cause shifts within the
biological community to less desirable species, and can
stimulate nuisance growths of algae and cause oxygen
depletion when these growths decay, frequently resulting in
mortalities of fish and other biota.

Pathogens and diseases introduced from municipal
outfalls, land drainage, and other sources can increase rates
of morbidity in marine organisms, and create public health
problems as well.

The degree to which an organism is contaminated by a
toxic substance depends on the concentration of the
contaminant in the environment, the form of the contaminant,
the length of time the organism is exposed to the
contaminant, the level and source of exposure (water,
sediments, or food), which part of the organism accumulates
the contaminant, and the rate at which the organism can purge
the contaminant from its system. If the source is water or
sediments, the normal movements, distribution, and habits of
the organism need to be fully understood; if the source is
its food, the trophic dynamics of the system need to be
studied, including the rate and total amount of
bioaccumulation of toxic substances as they pass through the
food chain.

Migrating fish and shellfish (e.g., lobster), and
shellfish transplants, may play an important role in the
dispersal of contaminants from an estuary, or in the
introduction of contaminants to an estuary. This phenomenon
can only be assessed through knowledge of migratory behavior
and the factors that affect it, as well as the impact of
emigration/immigration on the bioenergetics of the estuarine
system. Migrations and shellfish transplants may also result
in transfer of infectious disease agents (pathogens) among
inshore and offshore waters.

FED’s Experimental Biology Branch will be the lead
Center unit for studies on the effects of toxic chemicals.
Contributing Center units include EPD’s Chemical Processes
Branch and Environmental Analysis Branch (fates of toxic
chemicals in coastal ecosystems), CUD’s Population Dynamics
Branch (collection of samples, analyses of growth and
maturation effects), FED’s Ecosystems Dynamics Branch
(recruitment effects) and Pathobiology Branch (relationship
of toxic chemicals to pathogens and disease), and RPAC
(consultation on toxic chemicals to be studied, major problem

-20-




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research program. Therefore, the option for a Center base-
funded program would better serve to achieve the objectives
of the Framework, including promoting regional cooperation.

Once the program is fully implemented, reimbursables
should only be accepted for "packaging" information on
inshore living resources in a product form requested by the
funding agency. The design, collection, and analysis of
information related to inshore living resources under the
purview of NMFS should be conducted by Center scientists
under base~funded projects; in this way, the Center can
maintain full management control over its long-term
information base, and provide stable funding to develop top
quality professional staff.

Finally, under Option 3c, the Center could seek
additional base-level funding through a budget initiative (or
initiatives). The initiative could include any or all parts
of the Framework. Within the initiative, it would be
important to identify products for each year’s activities,
and to relate these products to the objectives established
for each research area in the Framework. The initiative
should also provide allowance for additional support ceiling.

B. IMPLEMENTATION SCHEDULE

Activities necessary to accomplish the objectives of
each of the Framework’s components will be conducted in
several "phases" (Table 2). The duration of any one phase
could be weeks to years, depending on such variables as the
availability of funds and personnel, the duration of the
sampling program, and the availability of information
required from other studies within the program and from
outside sources.

The status of knowledge relative to certain components
of the Framework (e.g., Effects of Toxic Chemicals) is more
advanced than for other components (e.g., Effects of Physical
Habitat Alteration and Loss). Thus, some of the steps
depicted in Figure 2 and Table 2 may already be accomplished
or underway, whereas work must begin at the basic stage of
information assembly and evaluation for other components.

Although the phases for any one component are
sequential, the phases may also be interrelated among
components. For example, studies on Cumulative Effects of
Habitat Degradation cannot begin until information is
assembled from the studies dealing with the individual

-37-


national estuarine program for the 1990s. Detailed research
plans will be developed for each component of the Center’s
program once funding is assured.

Products generated through implementation of the
Center’s inshore research program will benefit a variety of
agencies and organizations. NMFS’s Northeast Region will
gain more complete and timely information for use in
evaluating alternative habitat conservation and fisheries
management strategies. NOAA will have an integrated regional
program that provides timely and accurate predictions of
potential impacts of habitat degradation on the status and
harvest of living resources in inshore waters. Other federal
agencies will be able to use the information on inshore
living resources in their environmental impact analyses and
hazard or risk assessments. State and local governments in
the Northeast will gain a regional perspective of the status
and condition of the resources they conserve and manage. The
Fishery Management Councils and the ASMFC can use the
information to satisfy their requirements for addressing
habitat issues in their fishery management plans. The marine
recreational fishing community, which focuses primarily on
inshore species, will benefit from the improved accuracy,
completeness, and timeliness of fishery statistics and stock
assessments, as well as information related to contamination
and habitat loss. The recreational and commercial fishing
industries can use this information to document the
importance of their fisheries, and to plan business
operations in a more efficient and cost-effective manner.


utilize these resources or their habitats and those who wish
to conduct other developmental activities in inshore areas.
The Center does not have the funding or personnel necessary
to address all potential conflicts; therefore, research
priorities must be established.

The Northeast Regional Action Plan (RAP), implemented in
1985, identified several threats to living marine resources
and habitats that are of immediate concern in inshore areas.3
Pollution and inshore habitat alteration associated with (1)
urban and port development, (2) non-point source pollution,
and (3) ocean disposal were identified as being the highest
priority threats. The Center’s inshore research program
focuses on addressing these threats to selected species and
their habitats, and on obtaining general knowledge of the
causes of and trends in natural system variability, so that
changes related to these threats can be detected.

B. THE CENTER’S INSHORE RESEARCH PROGRAM

Formulation of an inshore research program to address
the effects of pollution and habitat alteration should be
based on the types of information needs that the program is
expected to fulfill. The most important inshore information
needs suggest four major components for the Center’s inshore
research program: (1) data and information management, (2)
habitat requirements and use, (3) biological effects of
habitat degradation, and (4) fishery statistics and stock
assessments. The information and research needs, goals,
objectives, products, and participants for these four
components are discussed in the following sections.

The general approach to achieving an identified research
objective involves several steps (Figure 2). Step 1 is to
identify issues or problems and select species, areas, and
habitats to study. Step 2 is to assemble, evaluate, and
summarize available information. The use of generic data,
which result from studies done in other temperate waters, is
extremely important.

Step 3 is to develop research plans for new studies to
be conducted by the Center, based on apparent information
gaps. If for some reason the Center cannot produce certain
missing information, or if that information is more
appropriately produced by others, the criteria to meet the
need should be specified and provided to the responsible

3 “Regional Action Plan: Northeast Regional Office and
Northeast Fisheries Center." 1985. NOAA Technical
Memorandum NMFS-F/NEC-37. ix + 20 p., 8 app.

“Qa


we ose,

NOAA Technical Memorandum NMFS-F/NEC-49

This TM series is used for documentation and timely communication of
preliminary resuits, interim reports, or special purpose information, and
has not received complete formal review, editorial control, or detailed
editing

Northeast Fisheries Center
Framework for Inshore Research

Research Planning & Coordination Staff
Northeast Fisheries Center

U.S. DEPARTMENT OF COMMERCE

Maicolm Baldrige, Secretary

National Oceanic and Atmospheric Administration
Anthony J. Calio, Administrator

National Marine Fisheries Service
William E. Evans, Assistant Administrator for Fisheries

Northeast Fisheries Center
Woods Hole, Massachusetts
July 1987


Existing fisheries models can be used as a starting
point to develop new models to assess the effects of
anthropogenic stress and natural factors on important inshore
fishery resources. These models need to be evaluated and
modified as appropriate, and sub-models need to be built. To
implement this approach, a substantial body of traditional
fisheries data is required to estimate catch, growth,
mortality, recruitment, and reproductive parameters. This
information presently exists for only a few populations.

Available information needs to be surveyed, including
existing habitat types and trends, levels of toxic chemicals,
and environmental factors (temperature, salinity, oxygen,
substrate composition, etc.). Hypotheses need to be
developed, refined as necessary, and tested in controlled
experiments (e.g., mesocosms) and, ultimately, at various
representative sites in the field. This approach provides a
framework that should make it possible to quantify the
effects of fishing and habitat degradation in a "common
currency," whereby the effect of a particular type of habitat
degradation (or several types together) can be expressed in
terms of the equivalent stress on a population in units of
fishing mortality or loss in fishery yield.

FED’s Ecosystems Dynamics Branch and CUD’s Population
Dynamics Branch will share the lead for developing and
executing population and community models, and for
identifying additional data needs. Contributing Center units
include all Branches presently or potentially involved in
studies on the biological effects of contaminants, nutrient
overenrichment, pathogens and disease, and physical habitat
alteration. Assistance in developing models also is expected
to come from Sea Grant, FWS, state resource management
agencies, and the academic sector.

Anticipated cumulative effects studies products include:

© Methodologies for determining cumulative effects.

o Relative importance to populations and fisheries of
sources of mortality due to habitat degradation and
fishing.

o Mortality rates due to the combined effects of toxic
chemicals, nutrient overenrichment, pathogens and
disease, and physical habitat alteration.

o Additional data collection needs for habitat
degradation studies.

o Assessments and predictions of cumulative effects.

-30-


Biological effects studies should be conducted using the
following guidelines:

1. Focus on relationship of laboratory experiments to
in-situ field observations, especially macro-
cosm/mesocosm/microcosm studies and exposures to
multiple stress.

2. Choose experimental study sites where impacts of
habitat degradation are known, suspected of being
most extreme, or seem inevitable, and where long-
term effects can be assessed.

3. Where possible, study gradients of degradation
or use multi-factorial designs to assess the
relative significance of physical or
chemical factors (e.g., study the synergistic
effects of multiple contaminants), derive
response rates, and identify the relative
contribution of the factors to observed
effects.

4. Study an adequate number of representative sites,
stations, and samples to permit meaningful
comparisons and analyses.

5. Work cooperatively with states, other NOAA
components, and other federal agencies, where
appropriate.

6. Develop research plans after available information is
synthesized, and information gaps and research needs
are clearly identified.

7. Undertake biological studies of individual sources of
habitat degradation with methods to examine
cumulative effects in mind, so that experimental
designs and data analyses for the individual
biological effects studies will provide appropriate
information for examination of cumulative effects.

-18-


NOAA TECHNICAL MEMORANDUM NMFS-F/NEC

Under the National Marine Fisheries Service's mission to "Achieve a
continued optimum utilization of living resources for the benefit of the
Nation," the Northeast Fisheries Center (NEFC) is responsible for planning,
developing, and managing multidisciplinary programs of basic and applied
research to: (1) better understand the living marine resources (including
marine mammals) of the Northwest Atlantic, and the environmental quality
essential for their existence and continued productivity; and (2) describe and
provide to management, industry, and the public, options for the utilization and
conservation of living marine resources and maintenance of environmental quality
which are consistent with national and regional goals and needs, and with
international commitments.

The timely need for such information by decision makers often precludes
publication in formal journals. The NOAA Technical Memorandum NMFS-F/WiC series
provides a relatively quick and highly visible outlet for documents prepared by
NEFC authors, or similar material prepared by others for NEFC purposes, where
formal review and editorial processing are not appropriate or feasible.

However, documents within this series reflect sound professional work and can be
referenced in formal journals. Any use of trade names within this series does
not imply endorsement.

Copies of this and other NOAA Technical Memorandums are available from the
National Technical Information Service, 5285 Port Royal Rd., Springfield, VA
22161. Recent issues of WOAA Technical Memorandum NMFS-F/NEC are noted below:

35. Annual NEMP Report on the Health of the Northeast Coastal Waters, 1982. By
John B. Pearce, Carl R. Berman, and Marlene R. Rosen, eds., and Robert N. Reid
(benthos), Catherine E. Warsh (water quality), and Edith Gould (biological
effects), topic coords. January 1985. xi + 68 p., 29 figs., 5 tables. NTIS
Access. No. PB85-219129/AS.

36. Growth and Survival of Larval Fishes in Relation to the Trophodynamics of
Georges Bank Cod and Haddock. By Geoffrey C. Laurence and R. Gregory Lough.
January 1985. xvi + 150 p., 67 figs., 15 tables, 1 app. NTIS Access. No. PB85-
220093/a~S.

37. Regional Action Plan: Northeast Regional Office and Northeast Fisheries
Center. By Bruce E. Higgins, Ruth Rehfus, John B. Pearce, Robert J. Pawlowski,
Robert L. Lippson, Timothy Goodger, Susan Mello Roe, and Douglas W. Beach.
April 1985. ix + 84 p., 4 figs., 6 tables, 9 app. NTIS Access. No. PB85-
219962/AS.

38. The Shelf/Slope Front South of Nantucket Shoals and Georges Bank as
Delineated by Satellite Infrared Imagery and Shipboard Hydrographic and Plankton
Observations. By J. B. Colton, Jr., J. L. Anderson, J. E. O'Reilly, C. A.
Evans-Zetlin, and H. G. Marshall. May 1985. vi + 22 p., 14 figs. NTIS Access.
No. PB85-221083/AS.

(continued on inside back cover)


sources of habitat degradation (contaminants and physical
habitat alteration and loss). As such, research required to
achieve the Framework’s objectives must be closely
coordinated within and among the major components.

Implementation of the inshore research program will
bring the inshore studies now underway into a more cohesive
program for FY88 and beyond. Many of the objectives
identified in the Framework are already being addressed at
some level by Center scientists; however, the Framework
provides a mechanism for tracking progress and assuring that
the Center’s inshore research is being directed toward
clearly defined goals. Timelines for tasks and products will
be developed in the early implementation phase of the
program, as will the description of information flow from
data gathering and analysis to final products.

A schedule for products will be determined by RPAC in
consultation with the Center Division Chiefs, the Regional
Office, and all other major user groups, especially the
States, ASMFC, Fishery Management Councils, NMFS
Headquarters, and NOAA/EPO.

C. PROGRAM PRIORITIES
1.0 New Projects

The top priority for implementing the inshore research
program is completion of the tasks associated with creation

and_use of IDIMS. Development
key to the program’s success.

entire RAP effort, and to more
Habitat Conservation Policy in

IDIMS will link all areas
research program by functioning
data and information produced b
retrieved, and evaluated. Once
facilitate interactive analyses
information, and development of
maps, atlases, inventories, and
also provide information useful
studies under any particular pr
others involved in research pla
coordination.

and implementation of IDIMS is
IDIMS is important to the
fully implementing NMFS’s

the Northeast.

of the Center’s inshore
as the mechanism by which
y the program are assembled,
IDIMS is operational, it will
of inshore data and
integrated products such as
characterizations. It will
to scientists conducting
ogram element, and RPAC and
nning, evaluation, and

-42-


areas or develop additional techniques for inshore habitats,
as necessary; (6) create a relational data base and software,
and prepare data for IDIMS; and (7) evaluate various habitat
mitigation/enhancement technigues for ameliorating habitat
loss.

Resource and habitat managers need quantitative cause-
and-effect information that defines, to the extent possible,
the relationship between inshore habitat alteration and
productivity of inshore-dependent populations. Understanding
this relationship requires knowledge of each species habitat
requirements and its ability to adapt to changes in its
habitat. (This knowledge will be developed by studies on
habitat requirements and use.)

Dredging, wetland filling, bulkheading, and dam
construction are human activities that obviously result in
physical habitat alteration or loss. The total amount of
habitat proposed for alteration each year in the Northeast is
relatively small (e.g., compared with the Southeast): In
FY86, for example, NMFS reviewed about 1,633 applications
from individuals, private businesses, and state and federal
agencies for COE permits for dredging, filling, and
impounding a total of about 5,866 acres of habitat; only
about 6 acres of marine habitat were lost in FY86 because
NMFS recommendations were not included in 16 permits issued
over NMFS objections. Although this loss seems small, and
perhaps insignificant, it is important to keep in mind that
most of the natural inshore habitat. along the Northeast coast
has already been altered or lost, less suitabie habitat
remains in the Northeast each year tc support living marine
resource populations (despite the existence of fairly
effective state and federal regulatory programs to protect
wetlands), population pressure along the Northeast coast is
increasing, and the cumulative effects of habitat alteration
and loss on living marine resource populations are generally
not known.

NMFS‘s ability to assess and predict the long-term
effects of habitat alteration depends on knowledge of how
habitats function, and on quantitative information on the
extent and effects of habitat alteration and loss. These
needs can be satisfied only by evaluating the functional
relations between organisms and their habitats, and by
determining the present status and rates of change of various
inshore habitat types.

Much effort has gone into attempting to develop
mitigation and enhancement approaches to ameliorate habitat
loss through the COE’s regulatcry program for proposed
construction and dredge-and-fill activities in coastal and
inland waters. However, the degree to, and rate at which,

-26-


independent management and research entities for each of the
four estuaries presently in EPA’s program in the Northeast
(i.e., Long Island Sound, Buzzards Bay, Narragansett Bay, and
Chesapeake Bay). Each estuary has a Management Committee, a
Technical Advisory Committee, a Citizens Advisory Committee,
and sundry working groups. The Water Quality Act of 1987
adds New York-New Jersey Harbor and Delaware Bay to the
National Estuary Program, and directs EPA to assess the
principal factors adversely affecting environmental quality
in Boston Harbor and to develop and implement a management
program to improve the water quality of Boston Harbor and
adjacent areas. The Center will be expected to take
advantage of these additional opportunities for interagency
research planning and coordination.

Many of the Center’s interactions with other federal
agencies are initiated through the Region in conjunction with
reviews of federally authorized projects that pose
significant environmental impacts. These reviews usually
involve helping the Region summarize available information,
rather than conducting research. The Region will continue to
handle most such information summaries, in consultation with
Center scientists as necessary, and will continue to maintain
liaison with the states, other federal agencies, and Fishery
Management Councils on habitat-altering projects that may
affect inshore living marine resources.

The primary benefit of these many interactions with
other agencies and institutions is cost effectiveness:
Cooperative studies maximize the use of the federal dollar by
avoiding redundancy in data collection and research programs,
especially among federal agencies. The Center will pursue
cooperative efforts to the maximum extent possible to achieve
the most efficient and effective use of human and fiscal
resources.

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areas and issues, and coordination of efforts to evaluate
alternative strategies).

EPD’s Chemical Processes Branch will be the lead Center
unit for the nutrient overenrichment biological effects
studies. Contributing Center units include EPD’s Physical
Oceanography Branch and Environmental Analysis Branch
(identification of potential areas of anoxia, biological
effects), and CUD’s Population Dynamics Branch (population
and fishery effects) and Population Biology Branch (resource
surveys).

FED’s Pathobiology Branch is responsible for studies on
effects of pathogens, and disease, including pathogen life
cycles, and will be the lead Center unit for this component
of the Framework. Assistance will be provided by CUD’s
Population Biology Branch (collection of samples) and
Population Dynamics Branch (population and fishery effects).

Other NOAA/NMFS participants are expected to be the
Region’s Habitat Conservation Branch (interagency
coordination, consultation on priorities of toxic chemicals,
major contaminant problem areas and issues, strategies for
mitigating adverse impacts, and product development), NMFS
Headquarters (consultation on product development,
coordination with headquarters of other NOAA elements), other
NMFS Regions and Centers (consultation on fates and effects
of contaminants, peer review and product development), NOS’s
OAD (identification of sources, levels, and fates of toxic
chemicals, nutrients, and pathogens in coastal waters and
sediments; identification of environmental factors associated
with pathogen occurrence and disease outbreaks), and Sea
Grant (cooperative studies).

Significant participation is also expected from FWS and
the National Cancer Institute (NCI; cooperative studies), the
Food and Drug Administration (FDA; assistance in analyzing
tissue samples, regional surveys of pathogen occurrence and
disease outbreaks), EPA (identification of contaminant
sources, cooperative studies of effects, and assessment of
alternative strategies for clean-up), state agencies
(cooperative studies, assistance in survey design and sample
collection), the academic sector (cooperative studies), and
the private sector (participation in regional surveys,
contracts for sample processing). Many of these entities
will participate in peer review and product development.

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Table 1. Inshore Research Projects of the Northeast
Fisheries Center in FY87.

Center
Brief Project Title Sitel Cooperator? Lead}
Emergency Striped Bass Study Regional FWS cuUD
o Maturity of Striped Bass States
o Discrimination of Stocks
o Stock Assessment
Assessment of Effects of Pollutant Regional EPA, FWS cuD
Exposure on Estuarine Populations States
Cooperative Fisheries Statistics Regional States cuD
Program
Juvenile Winter Flounder Age & Regional FVSC cuD
Growth Based on Otoliths
Life History Studies of Molluscs LIs NURP FED
Occurrence of Bacterial Pathogens LIS FED
of Oyster Larvae
Cytogenetic Effects of Pollution LIS, BH FED
on Development of Fish & Shellfish
Algal Population Studies LIS FED
Chemical Composition of Seston LIS FED
Growth & Reproduction of LIS EPA, OAD FED
Winter Flounder
Growth & Reproduction of Lobster LIS,BB EPA, OAD FED
Effects of Contaminants on Growth, NB EPA FED
Reproduction, and Metabolism of
Winter Flounder
Comparative Pathobiology -- Regional FED
Disease & Environmental Effects
o Comparative Invertebrate
Pathology
o Fish Pathology
Effects of Estuarine Cultural RB, HRE EPD

Eutrophication & Hypoxia in
Coastal Habitats



Assembly, synthesis, and evaluation of information that
defines inshore habitat requirements and use by important
living marine resources will receive the next highest
priority. Undertaking these tasks is a logical step in the
evolution of the RAP process. The initial product of this
effort, a matrix of the status of habitat-use knowledge, will
be used to formulate a coastwide cooperative research program
on the effects of habitat alteration, loss, and mitigation.

2.0 Ongoing Projects

Biological effects research and joint State/Center
fisheries statistics collections and stock assessments are
two research areas identified in the Framework where the
Center already has significant ongoing involvement. FED has
launched a "case study" on winter flounder in Northeast
inshore waters; this study focuses on the population-level
effects of contaminants. CUD has begun conducting stock
assessment workshops on a biannual basis; scientists from the
Center, states, and academia exchange information and jointly
develop advice for fishery managers. The Center is also
participating in a joint program with the states, under the
auspices of the ASMFC, for a shared network of fisheries
statistics data. It _is important that these activities
continue, with an emphasis on the population- and fishery-
level effects of contaminants on the reproductive success of
winter flounder and lobster.

D. RECOMMENDED ACTIONS

1. Prepare a Center budget initiative for FY89 that
expands the capability of the Center and Region to address
the objectives of the Framework for Inshore Research. The
initiative should be for a five-year cycle, should identify
products from each year’s activities and relate them to the
Framework’s objectives, and should include allowances for
changes based on short-term findings. The Center should use
the initiative funding to build upon its current base level
expenditures, rather than depend on the new monies to support
the entire inshore research program.

2. Immediately begin to enhance the ongoing inshore
research activities being conducted by the Center by drawing
them into a more focused program. Other Divisions within the
Center should align their activities, to the extent possible,
with the winter flounder studies recently initiated by FED.
Reimbursable funding should be used to help establish new
areas of inshore research, summarize information to satisfy
the needs of the Center’s user groups, and complete inshore
projects currently being undertaken that are beyond the scope

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(continued from inside front cover)

39. USA Historical Catch Data, 1904-82, for Major Georges Bank Fisheries. By
Anne M. T. Lange and Joan E. Palmer. May 1985. iii + 21 p., 12 figs., 2
tables. NTIS Access. No. PB85-233948/AS.

40. Indexing the Economie Health of the U.S. Fishing Industry's Harvesting
Sector. By Virgil J. Norton, Morton M. Miller, and Elizabeth Kenney. May
1985. v + 42 p., 44 figs., 25 tables, 1 app. NTIS Access. No. PB85-217958/AS.

41. Calculation of Standing Stocks and Energetic Requirements of the Cetaceans
of the Northeast United States Outer Continental Shelf. By Robert D. Kenney,
Martin A. M. Hyman, and Howard E. Winn. May 1985. iv + 99 p., 1 fig., 5
tables, 1 app. NTIS Access. No. PB85-239937/AS.

42. Status of the Fishery Resources Off the Northeastern United States for
1985. By Conservation & Utilization Division, Northeast Fisheries Center.
August 1985, iii + 137 p., 46 figs., 49 tables. NTIS Access. No. PB86-
125473/AS.

43, Status of the Fishery Resources Off the Northeastern United States for
1986. By Conservation & Utilization Division, Northeast Fisheries Center.
September 1986. iii + 130 p., 45 figs., 48 tables. NTIS Acces. No. PB87-
122115/AS.

44. NOAA's Northeast Monitoring Program (NEMP): A Report on Progress of the
First Five Years (1979-84) and a Plan for the Future. By Robert N. Reid, Merton
C. Ingham, and John B. Pearce, eds., and Catherine E. Warsh (water quality),
Robert N. Reid (sediments & bottom organisms), Adriana Y. Cantillo (trace
contaminants in tissues), and Edith Gould (biological effects), topic coords.
May 1987. xi + 138 p., 13 figs., 1 table, 9 app.

45. Food and Distribution of Juveniles of Seventeen Northwest Atlantic Fish
Species, 1973-1976. By Ray E. Bowman, Thomas R. Azarovitz, Esther S. Howard,
and Brian P. Hayden. May 1987. xi + 57 p., 10 figs., 19 tables.

46. Influence of Freshwater Inflows on Estuarine Productivity. By James G.
Turek, Timothy E. Goodger, Thomas E. Bigford, and John S. Nichols. May 1987.
iii + 26 p.

47. MARMAP Surveys of the Continental Shelf from Cape Hatteras, North Carolina,
to Cape Sable, Nova Scotia (1977-1984). Atlas No. 2. Annual Distribution
Patterns of Fish Larvae. By Wallace W. Morse, Michael P. Fahay, and Wallace G.
Smith. May 1987. viii + 215 p., 27 figs., 2 tables.

48. Indexed Bibliography of the Bay Scallop (Argopecten irradians). By Barbara
D. Sabo and Edwin W. Rhodes. May 1987. iii + 85 p.


II. THE CENTER’S FRAMEWORK FOR INSHORE RESEARCH

A. THE ROLE OF THE CENTER IN INSHORE WATERS

The Center is obligated to develop a basic understanding
of the productivity of living resources of the Northwest
Atlantic, and to predict the effects on fishery yields of
natural and man-induced changes to the ecosystem. In meeting
its obligation, the Center must, first and foremost, respond
to the information requirements of the Northeast Region and
the New England and Mid Atlantic Regional Fishery Management
Councils.

To realize the full potential productivity of the
nation’s fishery resources, fishery managers must develop
strategies, impose management regimes and regulations, and
monitor progress. As an integral part of this process, the
Center’s "Core emphasis" must, at a minimum, be able to
determine the restraints that resource productivity impose on
management. Therefore, the "Core emphasis" of the Center’s
research program is to define the limits of fishing and
habitat degradation in the Northwest Atlantic that still
assure living resource populations can sustain themselves at
levels consistent with prevailing fishery management policies
and goals.

Based on this emphasis, the Center’s role in inshore
waters is to integrate scientific information and conduct
research necessary to support fishery conservation and
management goals and objectives for species that move between
inshore (within three miles) and offshore habitats, or that
occur alongshore over a major portion of the Northeast U.S.
coast.

In such a large, comprehensive endeavor, coordination
and cooperation with others is imperative. Thus, although
the Center’s inshore research program maintains a regional
perspective of the status and condition of living resources
that depend on inshore habitats, the success of the program
is highly dependent upon cooperation with state and local
institutions, academia, public and private organizations
other NOAA elements, and other federal agencies.

Conservation and management of "“inshore-dependent"
living marine resources involves addressing multiple-use
conflicts that frequently arise between those who wish to

2 “fhe Purpose and Direction of the Northeast Fisheries
Center Research Program." Manuscript. RPAC, Northeast
Fisheries Center, Woods Hole, MA.

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