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 
OOI\A TECHNICAL MEK)RANUJM ~-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, 

developinq, 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 Memorandwn NMFS-F/NEC 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 NOAA TechnicaL Memorandum NMFS-F/NEC are noted below: 

35. AnnuaL NEMP Report on the Health of the Northeast CoastaL Wateps, 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. GZ'OL1th and Su:PvivaL of LaPvaL Fishes in ReLation to the TPophodynamics of 

Geopges 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/AS. 

n. RegionaL Action PLan: Northeast RegionaL Office and Northeast Fisheries 

Centep. 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 Fpont South of Nantucket ShoaLs and Geopges Bank as 

DeLineated by SateLLite Infrared ImagepY and Shipboard Hydpographic and PLankton 

ObseZ'Vations. 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) 
NOAA Technical Memorandum NMFS-F /NEC-49 

This TM series IS used for documentation and timely communication of 

preliminary results. 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 

Malcolm 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 

TABLE OF CONTENTS 

EXECUTIVE SUMMARy .•........................................ v 

I. INTRODUCTION ......................................... 1 

II. 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 ............ 9 

1.0 Inshore Data and Information Management 

System (IDIMS) ............................. 11 

2.0 Inshore Habitat Requirements and Use ....... 14 

3.0 Biological Effects of Inshore 

Habitat Degradation •......•................ 16 

3.1 Effects of Contaminants .•••........... 19 

3.1.1 Effects of Toxic Chemicals ..... 22 

3.1.2 Effects of Nutrient 

Overenr ichment ....•••••........ 23 

3.1.3 Effects of Pathogens 

and Disease ..•••••....••..•.... 24 

3.2 Effects of Physical Habitat 

Alteration •.•..•.•.•••..........•..... 25 

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 ..••.•••••.....••...•.... 34 

III. IMPLEMENTATION OF THE INSHORE RESEARCH PROGRAM ...... 36 

A. IMPLEMENTATION OPTIONS ........•................. 36 

B. IMPLEMENTATION SCHEDULE ..........•.............. 37 

C. PROGRAM PRIORITIES .............................. 42 

1.0 New Proj ects ............................... 42 

2.0 Ongoing Projects ..•...........•............ 43 

D. RECOMMENDED ACTIONS ............................. 43 

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-
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-
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. 1 

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-
I 

N 

I 

r-------r---r-----tl CENTER DIRECTOR I t--~-~----, 

PROGRAM SUPPORT 

FISHERIES ECOLOGY 

DIVISION (FED) 

Ecosystem Dynamics 

Experimental Biology 

Marine Pathology 

Manned Undersea Research 

and Fishery 

Engineering (MURFE) 

I 

ENVIRONMENTAL PROCESSES 

DIVISON (EPD) 

Chemical Processes 

Physical Oceanography 

Environmental Assessment 

DATA MANAGEMENT 

SUPPORT (DMS) 

CONSERVATION AND 

UTILIZATION 

DIVISION (CUD) 

Fishery Statistics 

Population Dynamics 

Population Biology 

Resource utilization 

RESEARCH PLANNING AND 

COORDINATION STAFF 

(RPAC) 

NATIONAL SYSTEMATICS 

LABORATORY (NSL) 

Figure 1. Organization of the Northeast Fisheries Center 
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) i 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 MFCMAi the inshore research program became a 

-3-
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-
Table 1. Inshore Research Projects of the Northeast 

Fisheries Center in FY87. 

Brief project Title 

Emergency Striped Bass Study 

o Maturity of striped Bass 

o Discrimination of Stocks 

o Stock Assessment 

Assessment of Effects of Pollutant 

Exposure on Estuarine Populations 

Cooperative Fisheries statistics 

Program 

Juvenile winter Flounder Age & 

Growth Based on otoliths 

Life History Studies of Molluscs 

Occurrence of Bacterial Pathogens 

of Oyster Larvae 

Cytogenetic Effects of Pollution 

on Development of Fish & Shellfish 

Algal population Studies 

Chemical Composition of seston 

Growth & Reproduction of 

winter Flounder 

Growth & Reproduction of Lobster 

Effects of Contaminants on Growth, 

Reproduction, and Metabolism of 

winter Flounder 

Comparative Pathobiology --

Disease & Environmental Effects 

o Comparative Invertebrate 

Pathology 

o Fish Pathology 

Effects of Estuarine Cultural 

Eutrophication & Hypoxia in 

Coastal Habitats 

-5-

Center 

Sitel cooperator2 Lead3 

Regional FWS CUD 

States 

Regional EPA,FWS CUD 

States 

Regional States CUD 

Regional FVSC CUD 

LIS NURP FED 

LIS FED 

LIS,BH FED 

LIS FED 

LIS FED 

LIS EPA,OAD FED 

LIS,BB EPA,OAD FED 

NB EPA FED 

Regional FED 

RB,HRE EPD 
Table 1. (Cont'd). 

Brief Project Title 

Coastal Habitat Assessment, 

Research, & Mensuration 

(CHARM) Program 

Historical Trends in Benthos 

Biomass 

Limits to Production of 

Estuarine Shellfish 

Behavior of Marine Fishes & 

Invertebrates 

Chesapeake Bay Stock Assessment 

Program 

NOAA Status & Trends -- National 

Benthic Surveillance Project: 

o Analysis of Extractable 

organic Compounds 

o Histopathological Analysis 

o Heavy Metals Analysis 

o Benthos Studies 

Cytogenetic Effects of 

contaminants on Mackerel Eggs 

Massachusetts Inshore Survey 

Northern Shrimp Survey 

Maine Herring Survey 

Center 

Site1 Cooperator2 Lead3 

Regional ORNL EPD 

NYB,HRE, LIS EPD 

Middle Atlantic EPD 

Regional OSU,EPA EPD 

CB MD,VA,DC, RPAC 

PSU 

S&T sites OAD 

CUD 

FED 

EPD 

EPD 

Regional EPD 

MA MA FED, 

CUD 

Gulf of MA,NH,ME FED, 

Maine CUD 

ME ME FED, 

CUD 

1BH: Boston Harbor, BB: Buzzards Bay, NB: Narragansett Bay, LIS: 

Long Island Sound, HRE: Hudson River Estuary, RB: Raritan Bay, 

NYB: New York Bight, CB: Chesapeake Bay, S&T: Status and Trends 

2FWS: Fish and wildlife 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-
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. 

-7-
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. 2 

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 "The Purpose and Direction of the Northeast Fisheries 

Center Research Program." Manuscript. RPAC, Northeast 

Fisheries Center, Woods Hole, MA. 

-8-
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 tne 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. 

-9-
, 

~ 

o 

, 

,--------111. Identify problems 

and select species « - ~ 

1\ - USER GROUPS 

2. Assemble and evaluate 

available information 

~ , , , 

", 

, 

", 

, , " RESEARCH 

7 COOPERATORS 

-11\\ 

I \ 

" 

« 

"'1 .1\ 

" " 8. Feedback to I Iplanning process 

"'1 

" " " " 

... ... ... ... 

13 • 

L'" 

Develop research Plan~ I 

I 

, 

, 

\ 

\ E Develop and distribute productsl 

I \ 

I \ 

\ I 

\ 

4A. Modify ongoing I 14B. Conduct additional 

studies ~ research 

\ 

\ 

\ 

\ 

, 

v ...J 

15. Combine and interpret 1 16. Record on data base 

results management system 

Figure 2. General study approach to inshore research. 
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-
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. 

IOIMS 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 in a 

relational data base. 

IOIMS, 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, IOIMS 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. IOIMS 

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 IOIMS is that information 

produced in response to one request (e.g., habitat requirements 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). IOIMS 

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 IOIMS is 

compatible with its eventual offshore counterpart; (6) 

develop tutorials for NMFS staff and other users; and 

-12-
(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-
2.0 Inshore Habitat Requirements and Use 

Effective conservation and management of inshoredependent 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 wellbeing 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-
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. 

o 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-
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. Sourcespecific 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-
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 longterm 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 costeffectiveness 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-
Biological effects studies should be conducted using the 

following guidelines: 

1. Focus on relationship of laboratory experiments to 

in-situ field observations, especially macrocosm/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 longterm 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-
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 nqrmally 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-
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-
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. 

-21-
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--microbiology, 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-
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-
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-
base and software, and prepare data for IDIMSi 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. 

o 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-
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 techniques for ameliorating habitat 

loss. 

Resource and habitat managers need quantitative causeand-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 1,833 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 suitable habitat 

remains in the Northeast each year to 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 infot~ation 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 att:eIl1pt.ing to develop 

mitigation and enhancement approaches to ameliorate habitat 

loss through the COE's regulatory program for proposed 

construction and dredge-and-fill activities in coastal and 

inland waters. However, the degree to, and rate at which, 

-26-
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-
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. 

o 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 aoal 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-
anthropogenic mortality: (5) create a relational data base 

and software, and prepare data for IDIMSi 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 inshoredependent 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 ecosystem, 

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-
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: 

o 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-
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-
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. 

o 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-
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 I 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-
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. 

-35-
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 

and beyond could follow one of three possible options: 

reduce or eliminate involvement in inshore research in 

FY88 

(1) 

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 (Option 3b). Coordination and cooperation 

among federal agency line offices is desired, but the oneyear 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-
research program. Therefore, the option for a center basefunded 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 anyone 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 anyone 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-
I 

W 

00 

I 

Table 2. Major Research Activities Included in the Framework for Inshore Research 

AREA 

IDIMS 

HABITAT 

REQUIREMENTS 

PHASE I 

Obtain, evaluate, 

and summarize aVaiLable information 

Design IDIMS 

Develop data base 

format 

specify interim system 

to archive data and 

information 

Select speci es 

Obtain, evaluate, and 

summarize available 

information 

Develop matrix of 

status of habitat 

requirements and use 

knowledge 

PHASE II 

Procure hardware 

Develop software 

Develop tutorials 

Define habitat use, 

essential habitat 

areas, and requirements, based on 

available information 

Develop plans and 

conduct research to 

fill information gaps 

PHASE III 

Begin loading data 

on system 

Make modifications 

and adjustments 

Develop interim 

products 

Develop relational 

data base and software 

package 

Make input to IDIMS 

Make input to Physical 

Habitat Alteration and 

Loss research, and 

other projects 

Develop interim products 

.--------------------------------------

PHASE I V 

Complete "userfriendly" system 

Develop maps, atlases, 

inventories, etc. 

PHASE V 

Develop and disseminate 

integrated products 

Modify system, as 

necessary 

Develop and disseminate 

integrated products 
I 

W 

~ 

I 

Table 2 (Cent'd). 

AREA PHASE I PHASE II PHASE III PHASE IV PHASE V ... --- ........ -- ................ -...... -.............. __ .. _ ....... ------ ...... _--_ .... --------- ...... -_ .... _-------_ .... -..... -_ ............... _ ..... _---- .. ---------_ .. -.................. __ ......... _ ........ _---_ .......... --

TOXIC 

CHEHICALS 

NUTRIENTS 

Obtain, evaluate, and 

summarize available 

information 

Develop research plan 

Choose study sites and 

target species 

Rank chemicals 

Conduct regional 

survey of concen- tratiQn of contaminants in target species 

Summarize regional 

distribution of 

toxic chemicals 

Conduct biological 

effects studies 

Obtain, evaluate, and 

summarize available 

information 

Survey scope of problem 

Develop research plan 

Conduct biological 

effects studies 

Continue biological 

effects stud i es 

Develop relational data 

base and software 

Develop summary of 

effects on reproduction, 

development, genetics, 

behavior, feeding, etc. 

Summarize exposure and 

retention in organisms 

Summarize biological 

effects on target 

species 

Develop relational data 

base and software 

Continue biological 

effects studies 

Hake input to IDIHS 

summarize relationship 

of contamination to 

concentrations in the 

environment 

Determine mortality 

rates 

Determine relationship 

of disease and 

abnormalities to toxic 

chemicals 

Hake input to 

cumulative effects 

studies 

Hake input to IDIMS 

Make input to cumulative effects studies 

Determine mortality 

rates 

Continue biological 

effects studies 

Develop interim 

products 

Develop interim 

products 

Determine relationship 

of nutrient enrichment to target species 

productivity and 

distribution 

Develop and disseminate 

integrated products 

Evaluate alternative 

management strategies 

Develop and disseminate 

integrated products 

Evaluate alternative 

management strategies 
I 

.+:» 

o 

I 

Table 2 (Cent'd). 

AREA PHASE I PHASE II PHASE III PHASE IV PHASE V ....... ~ .............................................................................. _ ............... w ....... _ ............. _ .............. _ ....................... __ ........................................................... "' ................ __ ................................ _ ...................................... .. 

PATHOGENS 

PHYSICAL 

HABITAT 

ALTERATION 

AND LOSS 

Obtain, evaluate, and 

summarize available 

information 

Develop research plan 

Conduct biological 

effects studies 

Obtain, evaluate, and 

summarize available 

information 

Specify product needs 

to NOAA/OAD 

Summarize life cycles 

of pathogens 

Summarize conditions 

that favor disease 

outbreaks 

Develop relational data 

base and software 

Continue biological 

effects studies 

Make input to IDIMS 

Make input to 

cumulative effects 

studies 

Determine mortality 

rates 

Develop interim 

prodUcts 

Determine relationship 

of disease occurrence to other sources of 

organism stress 

Develop and disseminate 

integrated products 

Evaluate alternative 

management strategies 

---------------------------------------- Summarize availability 

of habitat types and 

rates of gain or loss 

Develop valuation of 

habitat types for 

selected species 

Integrate output 

from HABITAT REQUIREMENTS AND USE studies 

Develop research plan 

Make input to IDIMS Specify impacts of loss 

of habitat types on Conduct planned studies selected species 

Evaluate relative 

importance of sources of 

mortality by habitat type 

Make recommendations for 

mitigation and enhancement 

techniques 
I 

~ 

...... 

I 

Table 2 (Cent/d). 

AREA 

CUMULATIVE 

EFFECTS OF 

HABITAT 

DEGRADATION 

FISHERY 

STATISTICS 

AND STOCK 

ASSESSMENTS 

PHASE I 

Obtain, evaluate, and 

summarize available 

information 

Evaluate available 

methodologies and 

develop new ones, 

if necessary 

Obtain, evaluate, and 

summarize available 

information 

Implement fishery 

statistics network 

Conduct biannual 

Stock Assessment 

IJorkshops 

Conduct studies on stock identification, 

surveys, and special 

studies 

PHASE II 

Develop population 

modelling techniques 

Conduct inshore 

species assessments 

Develop inshore - offshore relational 

software 

Continue biological 

studies 

PHASE I II 

Evaluate and 

integrate output 

from other biological 

effects studies 

Make input to IDIMS 

Hake input to IDIMS 

Conduct inshore - offshore comparisons 

for selected species 

Continue biological 

studies 

PHASE IV 

Develop research plans 

and begin cumulative 

effects studies 

Develop relational data 

base and software 

Develop interim products 

Develop interim 

products 

Continue biological 

studies 

PHASE V 

Determine mortality rates 

Develop and disseminate 

integrated products 

Develop and disseminate 

integrated products 

Continue biological 

studies 
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 comDletion of the tasks associated with creation 

and use of IDIMS. Development and implementation of IDIMS is 

key to the program's success. IDIMS is important to the 

entire RAP effort, and to more fully implementing NMFS's 

Habitat Conservation Policy in the Northeast. 

IDIMS will link all areas of the Center's inshore 

research program by functioning as the mechanism by which 

data and information produced by the program are assembled, 

retrieved, and evaluated. Once IDIMS is operational, it will 

facilitate interactive analyses of inshore data and 

information, and development of integrated products such as 

maps, atlases, inventories, and characterizations. It will 

also provide information useful to scientists conducting 

studies under any particular program element, and RPAC and 

others involved in research planning, evaluation, and 

coordination. 

-42-
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 II 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 fisherylevel 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 

-43-
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 longterm implications of inshore fishing mortality to recreational and commercial fisheries. 

5. Develop operational approaches for accomplishing the 

Framework's objectives, with or without additional fundinq. 

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-
(continued from inside front cover) 

39. USA HistoricaL Catch Data, 1904-82, for Major Georges Bank Fishel~es. 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 Economic Health of the U.S. Fishing Industry's Harvesting 

Sector. By Virgil J. Norton, Morton M. Miller, and Elizabeth Kenney. Hay 

1985. v + 42 p., 44 figs., 25 tables, 1 app. NTIS Access. No. PB85-2l7958/AS. 

41. CaLcuLation of Standing stocks and Energetic Requirements of the Cetaceans 

of the Northeast United States Outer ContinentaL SheLf. By Robert D. Kenney, 

r1artin A. M. Hyman, and Howard E. Winne 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-

l25473/AS. 

43. Status of the Fish.~y Resources Off the North@aste~ United Stat.s fo~ 

1986. By Conservation & Utilization Division, Northeast Fisheries Center. 

September 1986. iii + 130 p., 45 figs., 48 tables. NTIS Acces. No. PB87-

l22115/AS. 

44. NOAA's Northeast Monitoring Program (NEMP): A Report on Progress of the 

First Fit). real's (2979-84) and a PLan for the Future. By Robert N. Reid, Merton 

C. Inqham, 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 Nort~est 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 Fres~ter InfLObJs on Estuarine Productivity. By James G. 

Turek, Timothy E. Goodger, Thomes 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 SooUop (Argopecten irradians). By Barbara 

D. Sabo and Edwin H. Rhodes. May 1987. iii + 85 p. 
Information Services Section 

Northeast Fisheries Center 

National Marine Fisheries Service, NOAA 

Water St. 

Woods Hole, MA 02543 

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