NMFS Strategic Plan 

for Fisheries Research

August 2007

U.S. DEPARTMENT OF COMMERCE

National Oceanic and Atmospheric Administration

National Marine Fisheries Service

NMFS Strategic Plan

for Fisheries Research 

August 2007

U.S. DEPARTMENT OF COMMERCE

National Oceanic and Atmospheric Administration

National Marine Fisheries Service
Copies of this document may be obtained by contacting:

Office of Science and Technology, F/ST

National Marine Fisheries Service, NOAA

1315 East West Highway

Silver Spring, MD 20910

An on-line version is available at http://www.st.nmfs.noaa.gov/

The mention of trade names does not imply endorsement by the National Marine Fisheries Service, NOAA.

This publication may be cited as:

NMFS. 2007. NMFS strategic plan for fisheries research. U.S. Dep. Commer., NOAA Tech. Memo. NMFS F/SPO-80, 170 p.

Cover image of rubberlip surfperch, Rhacochilus toxotes, by David Whitting, NOAA.
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PREFACE 3

INTRODUCTION 7

LEGISLATIVE BACKGROUND 9

COMPREHENSIVE FISHERY RESEARCH PROGRAM 11

The Science Enterprise 11

Research Components 13

MAJOR FISHERY RESEARCH GOALS AND OBJECTIVES 39

NMFS FISHERIES SCIENCE CENTERS 45

Alaska Fisheries Science Center (AFSC) 46

 I. Research to Support Fishery Conservation and Management 48

 II. Conservation Engineering Research 57

 III. Research on the Fisheries 58

 IV. Information Management Research 61

Northwest Fisheries Science Center (NWFSC) 65

 I. Research to Support Fishery Conservation and Management 67

 II. Conservation Engineering Research 78

 III. Research on the Fisheries 80

 IV. Information Management Research 84

 Southwest Fisheries Science Center (SWFSC) 85

 I. Research to Support Fishery Conservation and Management 88

 II. Conservation Engineering Research 91

 III. Research On The Fisheries 92

 IV. Information Management Research 94

 Southeast Fisheries Science Center (SEFSC) 96

 I. Research to Support Fishery Conservation and Management 100

 II. Conservation Engineering Research 104

 III. Research on the Fisheries 105

 IV. Information Management Research 106

Northeast Fisheries Science Center (NEFSC) 108

 I. Research to Support Fishery Conservation and Management 110

 II. Conservation Engineering Research 118

 III. Research on the Fisheries 119

 IV. Information Management Research 126

Pacific Islands Science Center (PIFSC) 127

 I. Research to Support Fishery Conservation and Management 129

 II. Conservation Engineering Research 136

 III. Research on the Fisheries 137

 IV. Information Management Research 138

LITERATURE CITED 141

APPENDIX A: RELATIONSHIP OF THIS PLAN TO OTHER PLANS 145

Relationship Between the NOAA Strategic Plan and NMFS Programs 145

Relation of the NOAA Research Plan and This NMFS Strategic Plan for Fisheries Research 146

Relation of the NMFS Strategic Plan and This Plan for Fisheries Research 148

Overview of Planning Documents 150

 Internal Planning Documents 150

 External Reviews by the National Research Council (NRC) 151

 External Review by the Institute of Medicine 152

APPENDIX B: RESPONSE TO COMMENTS ON PUBLIC DRAFT OF THE NSPFR 155

APPENDIX C: ABBREVIATIONS AND ACRONYMS 161

APPENDIX D: GLOSSARY 165

CONTENTS

NATIONAL MARINE FISHERIES SERVICE

Mission Statement:

Stewardship of living marine resources 

through science-based conservation and management 

and the protection and restoration 

of healthy ecosystems.
2
PREFACE

The National Marine Fisheries Service (NMFS) is responsible for the science-based 

management, conservation, and protection of living marine resources within the U.S. 

Exclusive Economic Zone (EEZ). NMFS is a subagency of the National Oceanic and 

Atmospheric Administration (NOAA) within the Department of Commerce.

The U.S. EEZ is the largest in the world, encompassing an area 1.7 times greater than 

the U.S. and territorial landmass (Fig. 1). The EEZ is located from 3 to 200 nautical miles 

(n.mi.) seaward of the 48 contiguous states, Alaska, Hawaii, and U.S.-affiliated islands 

(except off Texas, the Florida Gulf Coast, and Puerto Rico, where the EEZ extends from 

9 to 200 n.mi.). The EEZ is composed of at least eight Large Marine Ecosystems (Northeast and Southeast continental shelf, Caribbean Sea, Gulf of Mexico, California Current, 

Insular Pacific Hawaiian, Gulf of Alaska, and Eastern Bering Sea). Fisheries have developed in the United States as each area was settled, either by the aboriginal peoples or by 

post-Columbian arrivals. Inshore marine fisheries are managed by states, regional Marine 

Fisheries Commissions, and even municipalities and counties in some areas. Fisheries in the 

EEZ beyond state jurisdiction (3 n.mi. in most states) are the responsibility of the Federal 

Government, specifically NMFS, as advised by eight regional Fishery Management Councils 

(FMCs). Information about this system of management is available at http://www.nmfs.

noaa.gov/councils.htm.

Alaska Region

Southeast

RegionPuerto Rico 

and U.S.

Virgin Islands

Northeast

Region

Pacific Coast Region

Pacific Island Region Midway Island

Hawaii

Palmyra Atoll and Kingman Reef

Jarvis Island

Howland and Baker Islands

Johnston Island

American Samoa

Wake Island

Northern Mariana Islands

Guam

Figure 1. The U.S. Exclusive 

Economic Zone.
4

In addition to its primary responsibilities 

within the EEZ, NMFS also plays a supportive and advisory role in the management of 

living marine resources in coastal areas under state jurisdiction, provides scientific and 

policy leadership in the international arena, 

and implements international conservation 

and management measures as appropriate.

NMFS stands at the forefront of fisheries 

research, both domestically and internationally. For example, the first of a new class of 

four 208-ft. fisheries survey vessels (FSVs), the 

Oscar Dyson, was commissioned on 28 May 

2005, and began operations in Alaska waters. 

On 25 July 2006, NOAA took delivery of 

the second new FSV, the Henry B. Bigelow,

which will be home-ported in New England. 

The Bigelow will replace the 45-year old Albatross IV and will support NOAA research 

efforts in the conservation and management 

of fisheries and marine ecosystems primarily in northeastern U.S. waters. Two other 

ships, the FSV Pisces and the FSV Bell M. 

Shimada, are currently under construction. 

These high-technology ships are among the 

most advanced fisheries research ships in the 

world. They will greatly expand the capabilities of the NOAA fleet by meeting modern 

NMFS data collection requirements, including the exacting quietness standards set by the 

International Council for Exploration of the 

Seas—to avoid influencing the survey results 

by disturbing the fish and mammals being 

studied. 

The delivery of these vessels demonstrates 

the lengthy planning and construction process. The Oscar Dyson was put in service 7 

years after the first appropriation was made by 

Congress, and several years of planning and 

justification preceded the appropriation. Although keeping the planning and budgeting 

responsive and coordinated was a challenge, 

the requirements laid out in this Plan cannot 

be met without continued availability of stateof-the-art ships. These ships provide scientists 

with the advanced research platforms required 

for at-sea data collections supporting stock 

assessments. 

Above: The FSV Henry B. Bigelow

making high-speed turns, 

without using the bowthruster, 

during its aceptance trials in 

2006. Below: the layout of the 

Bigelow’s stern. Photos: NOAA.
For more than 135 years, the agency’s long-term commitment to scientific excellence via 

internal and external peer-reviewed scientific publications has materially advanced marine 

science and policy. Since 1871, Federal fisheries scientists have collected, researched, analyzed, and published peer-reviewed data on the Nation’s living marine resources and marine 

ecosystems and on the benefits they provide. Using this peer-review process, important 

agency findings are published in many highly respected journals. NMFS uses its science 

quality assurance program to consistently monitor and review NMFS research efforts. 

Further, this program identifies gaps in infrastructure, facilities, and resources that may 

affect the productivity of NMFS scientists.

The NMFS Scientific Publications Office (SPO) and the Scientific Editor ensure the 

editorial and scientific integrity of the agency’s research products: peer-reviewed journals, 

professional papers, and technical memoranda. These products and other regional NMFS 

publication materials serve as the basis for agency scientific reports, regulatory documents, 

and technical presentations for fishery scientists and managers, commercial and recreational 

fisheries interests, environmental groups, the information community (media), and the 

public. Thus, the agency’s comprehensive scientific research and publishing efforts provide 

the foundation for developing sound policies that govern the use, protection, restoration, 

and conservation of living marine resources, marine habitats, and related aquatic environments.

The NMFS Scientific Publications Office produces the 

noted Fishery Bulletin, one of 

the top peer-reviewed marine 

science publications in the 

world, as well as other peerreviewed publications such as 

the Marine Fisheries Review and 

the NOAA Professional Paper 

NMFS series. With worldwide 

free distribution, in printed 

paper and electronic formats, 

these publications are vital 

sources for the advancement 

of marine science.
6
INTRODUCTION

This Plan represents an integration of multiple perspectives on the fisheries research 

needs of American society. The NMFS research planning process itself includes extensive 

communication with our partners (e.g., Fishery Management Councils (FMCs), the states, 

and other governmental organizations) and our constituents (e.g., fishermen and others 

who are concerned about resource conservation or seafood). NMFS research programs are 

periodically reviewed by informal and formal program reviews, with both internal and 

external participation. NMFS scientists serve on FMC scientific committees, plan development teams, and boards where research inadequacies are identified firsthand. Regulatory 

and judicial proceedings also identify information needs that are then incorporated in 

the research programs. Finally, NMFS scientists work with international counterparts to 

identify and fill information gaps that constrain management of marine resources both 

domestically and on the high seas. 

Planning takes place at multiple levels in government, and requires both awareness of 

and consistency with the goals and perspectives specific to the different levels. In response 

to the U.S. Commission on Ocean Policy, President Bush delivered the U.S. Ocean Action 

Plan to guide Federal actions to make the oceans, coasts, and Great Lakes cleaner, healthier, 

and more productive (CEQ 2004). This sets the parameters for the plans of all Federal 

agencies. At the top level within the Department of Commerce, a 5-year strategic plan 

addresses the varied responsibilities of the Department: to maximize U.S. competitiveness; 

foster science and technological leadership; and observe, protect, and manage the earth’s 

resources (DOC 2005). 

Within NOAA, a strong central Strategic Plan (NOAA 2005a) sets forth the missions, 

goals, and expectations of the organization. A companion Research Plan focuses the 

underlying research. Each NOAA line office (e.g., NMFS) has its own subordinate plan 

to outline the mission it serves and link with appropriate parts of the NOAA Strategic 

Plan. 

Within the NOAA line offices, additional plans are prepared to implement specific 

programs, such as those programs legislated by Congress. This NMFS Strategic Plan for 

Fisheries Research (NSPFR) is such a document. This Plan addresses the intent of Congress 

as expressed in legislation while maintaining consistency with the research and management framework established within NOAA. As such, this document incorporates research 

planning elements across several NOAA dimensions: from the overarching NOAA Strategic 

Plan and the NOAA Research Plan, to the NMFS Strategic Plan (NSP), and lastly, to the 

six Fisheries Science Center research plans. Lying across this planning agenda is a NOAA 

20-Year Research Vision, which presents a longer-term perspective of the environmental 

and ecological challenges our Nation faces and the technological and scientific advances 

we expect will help meet those challenges (NOAA 2005b). All these plans must comport 
8

with out-year budgets; resource, staffing, and facility plans; fleet replacement and operation 

plans; and budget and execution plans. And all of these plans are influenced by natural 

and anthropogenic events and emerging technologies.

The scope of the NSPFR is specific to the requirements of the Magnuson-Stevens Fishery 

Conservation and Management Act (MSFCMA) with respect to fisheries, habitat, and 

certain protected resources research. It does not include the regulatory and enforcement 

components of the NMFS mission, nor those research elements conducted under non-fisheries mandates, such as the Marine Mammal Protection Act (MMPA) and the Endangered 

Species Act (ESA). This Plan covers current research activities as well as strategies for 

improving data collection, analysis, and dissemination. Its relationship to other NOAA 

plans is presented in Appendix A. 
LEGISLATIVE

BACKGROUND

It is important to note that the recent 2006 reauthorization of the MSFCMA 

contains new provisions for the agency’s fisheries research enterprise, and these will 

be incorporated into its portfolio. Details on the agency’s current implementation 

efforts on the reauthorization are available online at http://www.nmfs.noaa.gov/

msa2007/implementation.htm.

Requirements for this Plan stem from the reauthorized MSFCMA as amended by the 

Sustainable Fisheries Act (SFA), on 11 October 1996. Section 404 (Fisheries Research) of 

the MSFCMA calls for the Secretary of Commerce to develop and publish in the Federal 

Register a strategic plan for fisheries research for the 5 years immediately following such 

publication. The Act stipulates that the NSPFR:

s )DENTIFYANDDESCRIBEACOMPREHENSIVEPROGRAMWITHALIMITEDNUMBEROFPRIORITYOBJECtives for research in each of the research areas specified below.

s )NDICATEGOALSANDTIMETABLESFORTHEPROGRAM

s 0ROVIDEAROLEFORCOMMERCIALlSHERMENINSUCHRESEARCHINCLUDINGINVOLVEMENTINlELD

testing.

s 0ROVIDEFORCOLLECTIONANDDISSEMINATIONINATIMELYMANNEROFCOMPLETEANDACCURATE

information concerning fishing activities, catch, effort, stock assessments, and other 

research conducted under this section.

s "EDEVELOPEDINCOOPERATIONWITHTHE&ISHERY-ANAGEMENT#OUNCILSANDAFFECTEDSTATES

and provide for coordination with the councils, affected states, and other research entities.

The MSFCMA requires the NSPFR to address the following research areas:

s 2ESEARCHTOSUPPORTlSHERYCONSERVATIONANDMANAGEMENTINCLUDINGBUTNOTLIMITED

to: 

– Biological research concerning the abundance, trends, and life history of fish stocks.

– Interdependence of fisheries or stocks of fish.

– Identification of essential fish habitat.

– Impact of pollution on fish populations.

– Impact of wetland and estuarine degradation. 

– Other factors affecting the abundance and availability of fish.
10

s #ONSERVATIONENGINEERINGRESEARCHINCLUDING

– Study of fish behavior.

– Development and testing of new gear technology and fishing techniques to minimize 

 bycatch and any adverse effects on essential fish habitat.

– Promotion of efficient harvest of target species.

s 2ESEARCHONTHElSHERIESINCLUDING

Social, cultural, and economic relationships among fishing vessel owners, crew, U.S. fish 

processors, associated shoreside labor, seafood markets, and fishing communities. 

s )NFORMATIONMANAGEMENTRESEARCHINCLUDING

Development of a fishery information base and an information management system 

under Section 401 that will permit the full use of information in the support of effective 

fishery conservation and management.
COMPREHENSIVE

FISHERY RESEARCH 

PROGRAM

THE SCIENCE ENTERPRISE

NMFS develops scientific information needed for the stewardship of the Nation’s living 

marine resources. The six NMFS regional Science Centers encompass 25 principal laboratories, employing more than 1,550 scientific and support personnel and another 380 full- or 

part-time contractors, who conduct a comprehensive, interdisciplinary science program. The 

scope of their work is multidisciplinary and broad in terms of space and time. The Science 

Centers provide the scientific knowledge base on which NMFS formulates stewardship 

policies in concert with its six Regional Offices. Research at NMFS laboratories supports 

resource management in NOAA, interstate fishery commissions, and other agencies, and 

the recommendations of the FMCs, to facilitate informed decision-making about marine 

resource management decisions for sustainable fisheries, aquaculture, protected resources, 

endangered species, and habitat. 

The NMFS science enterprise has three primary components. In addition to the laboratories and people, the third component is fisheries survey vessels. These purpose-built, 

dedicated research vessels meet primary data needs, working in cooperation with chartered 

vessels from the academic and private industry fleets. The new vessels feature acoustic 

quieting to reduce behavioral responses of species targeted in surveys and to minimize 

noise interference to hydroacoustic signals. The ships have the speed, power, and endurance to perform acoustic and trawl surveys at the shelf edge. They support a full scientific 

complement, and support laboratories, computers, and multiple gears (e.g., trawl, longline, 

and oceanographic). Dedicated to fisheries missions throughout their 30-year service life, 

the continuity of service of these ships protects the integrity of long-term resource surveys. 

These ships are critical to the mission and are the primary method for collecting fisheriesindependent data for most species. 

In addition to ships, other tools and methods used to amplify and leverage the efforts 

and intellect of scientists include a full array of sampling equipment, observation systems, 

and software and analytical systems.

Because fisheries are managed on a regional basis, the focus of NMFS research programs 

varies across Science Centers. Each Science Center develops its own annual research priorities, based on regional and national needs. The research plans are updated as necessary 
12

in consultation with the Regional Offices, 

FMCs, Program Offices in NMFS headquarters, and NOAA’s constituents. The Science 

Center research staffs are generally organized 

into teams that focus on specific issues or areas 

of expertise.

The Office of Science and Technology 

coordinates the overall NMFS integrated 

research program. The NMFS Science Board, 

composed of the six Science Center Directors 

and chaired by the Director of the Office of 

Science and Technology, is responsible for 

ensuring the integrity and quality of scientific 

research. The NMFS Science Board addresses 

national science issues and programs and 

develops science policy for the agency. All 

components of the science enterprise provide 

the agency with information that is comprehensive, objective, credible, and effectively 

communicated.

Responsibility for the total scientific effort 

lies with the Director of Scientific Programs 

and Chief Science Advisor. This Director 

reports directly to the NOAA Assistant Administrator for Fisheries and supervises the 

Science Center Directors and the Director of 

the Office of Science and Technology.

The NMFS science program collaborates 

extensively with academia, often through cooperative agreements and grants. These partnerships enhance and extend NMFS’ research capability. Many NMFS scientists serve as 

university adjunct professors, and this relationship enhances the ability of agency scientists 

to remain on the cutting edge while it expands the teaching capability of the university 

and brings NMFS expertise into the academic community. Academic scientists also play 

an important role in the periodic review and evaluation of NMFS research program quality and relevance. The Science Centers work in cooperation with other Federal and state 

agencies, international entities, nongovernmental organizations, and the private sector 

(including the recreational and commercial fishing industry).

The scale and scope of NMFS research varies. Some major research initiatives focus on 

the needs of the fishing industry and are performed jointly with industry. For instance, 

joint studies of harvesting methods and development of more effective fishing gear are 

under way to reduce wasteful bycatch. Other research initiatives focus on the needs of the 

FMCs (e.g., determination of the correct mesh size for a specific fishery or determination 

of the timing and area limits for a specific closure) and on the needs of the NMFS Habitat 

Conservation field offices to meet their scientific and management mandates under the 

Essential Fish Habitat provisions of the MSFCMA. 

A scientist in the NMFS 

NWFSC Laboratory 

checking fish tissue 

samples from the 

Hurricane Katrina area 

for harmful bacteria. 

Photo: NMFS.
The purpose of the NMFS scientific enterprise is to ensure that the science products 

produced and disseminated by the agency are of the highest possible quality. These products 

reach the decision process in various ways, including FMC meetings, technical committee meetings, written documents published in print or on the Internet, presentations to 

policymakers in other fora, and workshops convened to address specific problems.

RESEARCH COMPONENTS

The MSFCMA mandates strong action to conserve and manage fishery resources that 

contribute to the food supply, economy, and health of the Nation’s marine ecosystems. 

MSFCMA provisions require NMFS to end overfishing1

, rebuild all overfished stocks, 

and conserve essential fish habitat through research and consultations on Federal and state 

actions that may adversely affect such habitat. These are among our primary stewardship 

responsibilities.

NMFS is responsible for ensuring that management decisions are based on the highest 

quality scientific information on the biological, social, and economic status of the fisheries. 

This includes species’ responses to environmental changes, species interactions, exploitation, and other human activities that affect species and their habitat. Social, cultural, and 

economic behaviors and incentives that influence human/marine interactions are also 

addressed. The information is used not just for current management decisions, but also to 

conserve resources and anticipate future trends, ensure future utilization opportunities, 

and assess the success or failure of the agency’s management efforts. 

NMFS is also responsible for ensuring that this information and the subsequent management decisions are understood and their validity accepted by user groups and other 

constituents. To accomplish this, we provide roles for commercial fishermen in our fisheries 

research, including operating charter surveys and participating in research program reviews. 

Less visible roles include providing firsthand information and knowledge about changes 

in species abundance and distribution, ideas and testing of bycatch reduction technology, 

and reviewing assessment methods and results.

The research priorities of NMFS may be grouped into the four major areas (with several 

subareas) defined by Congress (see Legislative Background):

I. Research to support fishery conservation and management. 

II. Conservation engineering research.

III. Research on the fisheries.

IV. Information management research.

More resources are devoted to research in support of fishery conservation and management 

than all the other areas combined.

1

Definitions: A stock that is subject to overfishing has a fishing mortality (harvest) rate above the level that 

provides for the maximum sustainable yield. A stock that is overfished has a biomass level below a biological 

threshold specified in its fishery management plan. This is treated at much greater depth and with respect to 

each of the major fisheries in the Annual Reports to Congress on the Status of U.S. Fisheries, available online 

at http://www.nmfs.noaa.gov/sfa/sfweb/.
14

I. RESEARCH TO SUPPORT FISHERY

CONSERVATION AND MANAGEMENT

Living marine resources currently support extensive commercial, recreational, and subsistence uses. In 2005, commercial landings by U.S. fishermen totaled 9.6 billion pounds 

valued at $3.9 billion. The 2005 U.S. marine recreational fish catch was an estimated 423 

million fish taken on an estimated 83 million fishing trips by about 12 million anglers 

(Figure 2) (NMFS 2007a). Once the value-added benefits are calculated, the commercial 

fishing industry contributes over $33 billion annually to our economy and about $20 billion a year is spent on recreational marine fishing activities (NMFS 2007a). U.S. consumers spent about $65.2 billion for fishery products in 2005, and based on 2001–2003 data 

(most recent available), the United States is the third-ranked nation in the consumption 

of seafood. In addition to these benefits derived from the exploitation of our living marine 

resources, non-consumptive uses—such as diving on coral reefs and whale-watching—

provide additional benefits to many Americans.

Figure 2. U.S. Recreational 

Fishery Catch (includes 

releases) and Harvest 

1981–2005 (Alaska, Hawaii, 

and U.S. Territories are not 

included; surveys in Hawaii 

and Puerto Rico began in 

2003 and 2000, respectively; 

Texas harvest included for 

1983–2005, but no release 

data collected).

0

50

100

150

200

250

300

350

400

450

Atlantic & Gulf HARVEST

Atlantic & Gulf CATCH

Pacific CATCH

Pacific HARVEST
U.S. fisheries operate throughout the United States in all coastal waters, in and beyond the 

U.S. EEZ, and in many rivers and lakes. The total domestic commercial landings of finfish 

and shellfish increased from less than 3 million metric tons (MMT) in the early 1950s to over 

4 MMT in 2005 (Figure 3). Domestic landings of all commercial fishery products reached 

a record high of 4.8 MMT (10.5 billion pounds) in 1993 and 1994 at a value of $3.8 billion. Alaska pollock ranked first in terms of weight and lobster ranked first in terms of 

total revenues in 2005 (NMFS 2007a). The resulting commercial landings combined with 

aquaculture production make the United States the sixth-ranked fishing nation, with 4 

percent of the worldwide landings in 2004 (most recent year for which data are available) 

(NMFS 2007a).

NMFS has undertaken an aggressive plan of action to improve its ability to assess more 

of the 530 stocks and stock complexes that are identified and referenced in Federal fishery 

management plans. To begin implementation of this Marine Fisheries Stock Assessment 

Improvement Plan (SAIP) (NMFS 2001), the agency received an increase of $1.7 million 

in FY 2001, increasing to a total of $25.7 million in FY 2006. NMFS does not routinely 

assess the status of many of the 530 stocks and stock complexes identified in the 2005 

Status of U.S. Fisheries report (NMFS 2007b), because generally they are not targeted in 

fisheries and have a low probability of becoming overfished. Based on a ranking system, 

the SAIP indicates that stocks with the longest history of catches, or value, rank high for 

having the best data collection programs and the most comprehensive assessments. This 

ranking system demonstrates that NMFS prioritizes its allocated research dollars to conFigure 3. Commercial landings of finfish and shellfish: 

1950–2005.

Fisheries Value and Volume

0

0.5

1.0

1.5

2.0

2.5

3.0

3.5

4.0

4.5

1950 1955 1960 1965 1970 1975 1980 1985 1990 1995 2000 2005

Year

$0

$1.0

$1.5

$2.0

$2.5

$3.0

$3.5

$4.0

$4.5

$5.0

MMT Shellfish MMT Finfish Total Value
16

duct status determinations for those target 

species most vulnerable to overfishing. The 

SAIP also indicates that modernization of 

stock assessments will require expansion of 

cooperative research programs with the fishing industry and other partners. The SAIP is 

available online at http://www.st.nmfs.noaa.

gov/StockAssessment/index.html.

 NMFS scientists are also working cooperatively with the interstate marine fisheries 

commissions, state agencies, FMCs, fishing 

industries, and fishing participants to improve the way data are collected and used to 

monitor commercial and recreational fishing 

impacts on fish stocks of the United States. 

NMFS supports a number of regional fisheries 

information programs that coordinate data 

collections, data management, and data dissemination among the state and Federal partners. NMFS is working with its partners to 

better integrate the data collections conducted 

in each region into a comprehensive regional 

monitoring program that more effectively 

supports the data and statistical needs for 

stock assessments and fisheries management 

by all of the partners. NMFS works with its 

partners to gather, audit, and edit data using 

rigorous quality control protocols, and they 

participate in regularly scheduled reviews of data and statistics to identify and resolve 

possible problems. The state and Federal agencies are working to improve the integration 

of final data and statistics into regional information systems that can be readily accessed 

by stock assessment scientists and fishery managers. The cooperative regional programs 

are striving to provide statistics that stock assessment scientists and fishery managers can 

combine geographically, temporally, and spatially as needed to support their analyses for 

different species or fishery segments.

For commercial fisheries, NMFS requires participants to obtain permits and report data 

needed to assess fishing impacts. Permit data systems are essential for effective management 

of commercial fisheries, and NMFS is leading the development of an enhanced electronic 

database system that will improve the processing and issuing of commercial fishery permits 

in all regions. NMFS is designing an electronic registration system that will eliminate 

unnecessary redundancies in the entry and storage of data and allow implementation of 

operational changes that will further increase efficiency, improve data quality, and reduce 

the reporting burden for participants. NMFS also supports and enforces mandatory reporting programs for both commercial seafood dealers and commercial fishing vessel operators 

that provide the data needed to assess fishing impacts on fish stocks. Wholesale and retail 

dealers report the quantity and value of seafood products purchased on a trip-by-trip basis. 

Commercial fishing vessel operators complete and submit logbook records for each vessel trip 

that provide landings data along with area and effort information. NMFS is working with 

Top: Pacific ocean perch caught by 

an AFSC survey trawl for grounfish. 

Right: A Pacific ocean perch in the 

Gulf of Alaska. Photos: NMFS.
its partners to implement electronic reporting systems that speed the delivery of landings 

data by federally permitted dealers and vessel operators. NMFS is designing these systems 

to use unique trip identifiers that can link each dealer trip report to the appropriate vessel 

trip report. More efficient matching of dealer and vessel trip reports will help reconcile 

differences and allow further improvements in the accuracy of commercial fishing data 

provided for use in stock assessments and fishery management decisions.

NMFS is also playing a lead role in developing more effective sampling survey methods 

for the monitoring of recreational fishing impacts. Since 1979, recreational fishing effort 

and catch have been monitored primarily through a combination of shoreside surveys of 

fishing access points and telephone surveys of coastal residential households. In recent years, 

NMFS has led cooperative efforts to test and implement more efficient surveys of fishing 

effort on for-hire vessels that are based on probability sampling of vessel lists developed from 

state and Federal vessel registration programs. NMFS has also been working cooperatively 

with some states to develop more efficient surveys of shore and private boat angler fishing 

effort that are based on probability sampling of angler lists developed from state licensing 

programs. Based on recommendations received from a 2006 National Research Council 

(NRC) review funded by NMFS (NRC 2006a) and from a national assessment of the 

information needs of fishery managers and stock assessment scientists, the agency is working with the interstate fisheries commissions to initiate a formal Federal-state collaborative 

process that will reassess and redesign how recreational data are collected, analyzed, and 

used. The redesign process has been refocused to address specific requirements and timelines 

for “Recreational Fisheries Information” set in the January 2007 bill that reauthorized the 

Magnuson Stevens Fisheries Conservation and Management Act (MSA). The reauthorized 

MSA requires NMFS to implement an improved survey program by January of 2009, it 

specifies the need for a collaborative process that addresses the NRC recommendations, 

it directs NMFS to work with the states to implement Federal-state registry programs 

for marine recreational anglers, and it directs NMFS to utilize phone/address directories 

developed from the registry programs in future telephone surveys. 

Over the next two years, work will focus on resolving a number of potential problems 

with the sampling and estimation designs used in the current surveys, and on identifying 

changes needed to ensure that future surveys are appropriately designed to provide statistics 

that are readily applicable to various kinds of management decisions and that are useful 

for social and economic analyses. To ensure that a range of viewpoints and expertise will 

inform the process, NMFS will seek to establish and maintain a dialogue with those most 

involved and affected by the data, including anglers and various other constituent groups. 

Recognizing the need to implement an improved survey system in a timely fashion, NMFS 

will execute the plan at a pace that will ensure that redesign efforts are transparent, inclusive, 

and well-documented. NMFS and its partners are committed to building an improved 

recreational fisheries statistics program that will gain the confidence of scientists, fishery 

managers, and the recreational fishing community.

NMFS’ research efforts focus on understanding, protecting, and restoring fishery 

resources and the habitats on which they depend at both ecosystem and species-specific 

scales. These efforts include mapping, spatial analyses, geographic information systems 

(GIS), and fishery and ocean habitat modeling and characterization, as well as an evaluation of ecosystem approaches to focus on spatially explicit models and further research into 

food web relationships. Additionally, with the increasing need to seek new management 

approaches to enhance and conserve essential fish habitat (EFH), NMFS is conducting 
18

studies on adaptive management techniques 

through the identification and use of potential marine reserve areas or refugia (i.e., using areas closed to fishing activities for both 

recovery and research), and experiments on 

no-take and limited-take zones and time-area 

closures. NMFS is also exploring the research 

potential of Marine Protected Areas to facilitate important experiments in marine ecology 

and to support recommendations made by 

the National Research Council (NRC 2001). 

NMFS is conducting research on stock enhancement techniques (i.e., supplementing 

wild stocks with marine species raised in 

captivity) to help reduce rebuilding times for 

overfished species and recover endangered 

and threatened marine species. Further, 

NMFS is evaluating the potential impacts of 

artificial reef/habitat as well as commercial 

and recreational fishing activities on habitat 

and fisheries production. In combination with 

evaluating these impacts, public education 

plays a key role in increasing public awareness 

and support of our living marine resources.

An important aspect of NMFS’ research 

efforts is the incorporation of innovative new 

technologies and techniques. For example, 

NMFS is cooperating with other NOAA 

elements to enhance survey capabilities 

through research and development of an 

omnidirectional hydroacoustic system. Airborne LIDAR (Light Detection and Ranging) 

technology shows promise for identifying 

near-surface pelagic species. Underwater 

laserline technology is being developed to 

facilitate habitat characterization and species identification. Additionally, NMFS uses 

manned submersibles and remotely operated 

vehicles to evaluate deepwater species and 

their habitats.

NMFS provides fishery managers with the 

information needed to make scientifically 

sound decisions. To support fishery conservation and management, NMFS scientists are 

actively pursuing the research described in the 

following sections.

NMFS researchers flew over the 

school of mullet in the photo above. 

A subsequent aerial pass using LIDAR 

resulted in the graph. Photos: NMFS.
I.A. Biological research concerning the 

 abundance and life history of fish stocks 

Understanding the factors affecting the abundance and life history of fish stocks requires 

collecting catch and effort data, measuring biological characteristics, and developing biostatistical analyses for a variety of Fishery Management Plan (FMP) and non-FMP species of 

exploited fish and invertebrates. Fishery-dependent and fishery-independent (i.e., resource 

survey) sources provide age and size samples, catch composition, and indices of relative 

abundance. These data are key inputs to stock assessments, fishery management regulations, and the production of status reports for living marine resources and their fisheries. 

The biology and life history of species has taken on greater significance in managing 

the Nation’s living marine resources since passage of the MSFCMA. Describing and 

understanding migration and distribution patterns, predator-prey relationships, habitat 

use, age, growth, mortality, age structure, sex ratios, reproductive biology, and responses 

to environmental variability are key to developing harvest strategies that produce high 

yields at low risk to the long-term sustainability of the resource base. A variety of scientific methods are used, including aging with the use of otoliths (ear bones), histological 

analyses of gonads, food studies, and observations of spawning behavior. Studies of early 

life history and fishery oceanography are necessary to understand recruitment dynamics, 

with the aim of predicting incoming year-class strength. There is also an increasing need 

to identify and characterize discrete stocks. The use of molecular DNA techniques, life 

history parameter estimates, and knowledge of ecological habits can aid in determining 

stock boundaries. This will enable scientists to correctly structure stock assessments and 

design stock-specific management measures. 

The production of accurate stock assessments requires three major categories of quantitative information: 1) trends in relative abundance of the fish population, 2) total catch, 

and 3) life history data (growth, maturity, and natural mortality).

s 4HEINFORMATIONONTRENDSINRELATIVEABUNDANCECOMESPRINCIPALLYFROMHIGHLYSTANdardized, statistically designed surveys. These surveys are conducted by NOAA’s Fishery 

Survey Vessels and, in some cases, chartered vessels specially outfitted to conduct these 

surveys using a variety of case-specific methods, ranging from standardized versions 

of fishing gear to acoustics, plankton, submersibles, and other sampling tools. In some 

fisheries, the fishery catch per unit effort can be standardized to provide a relative index 

of the trend in stock abundance.

s 4HEINFORMATIONONTOTALCATCHCOMESFROMSTATEAND&EDERALPROGRAMSTOMONITORTHE

landed catch in each commercial and recreational fishery, and from the observer programs 

that monitor discarded bycatch.

s ,IFEHISTORYINFORMATIONCOMESFROMABROADRANGEOFSTATE&EDERALANDACADEMICSOURCES

and is often augmented through cooperative research between government agencies and 

the fishing industry.

These three categories of data are combined using mathematical models to derive best 

estimates of vital statistics, such as historical and recent trends in the numbers and biomass 

of the resource, recruitment levels (number of young fish entering the fishery each year), 

and the exploitation rate (the fraction of the stock alive at the beginning of the year that 

is killed by fishing). Significant gaps in any one of the three categories of information will 

compromise the quality of the assessment.
20

The SAIP defined three tiers for improving the quality of stock assessments:

Tier I: Improve stock assessments by using existing data:

a) for core species, by conducting assessments that are more comprehensive, more thorough, 

more timely, better quality controlled, and better communicated.

b) for species of currently unknown status, by mining existing databases of research vessel 

survey data and/or commercial and recreational statistics for archival information for 

new analyses to evaluate status determination criteria.

Tier II: Elevate stock assessments to new national standards of excellence by:

a) upgrading assessments for core species to at least an adequate level (today the list of core 

stocks matches the list of 230 stocks included in the Fish Stock Sustainability Index 

[FSSI]). This requires improvements in all aspects of the assessment enterprise, including ships, surveys, fishery monitoring, observers, analysis, and related components.

b) conducting baseline monitoring for all federally managed species (about 900 stocks are 

included in fishery management plans).

Tier III: Next generation assessments will:

a) assess all federally managed species or species groups at an adequate level and improve 

the accuracy and timeliness of forecasts for core stocks by including more detailed 

biological information.

b) explicitly incorporate ecosystem considerations such as multispecies interactions and 

environmental effects.

Shortly after publication of the SAIP, NOAA set a performance measure to reduce the 

number of stocks with unknown status. Between 2000 and 2006, the status of 25 major 

stocks changed from “unknown” to “known.” For 2007, this performance measure is being 

replaced by a measure designed to increase the percentage of living marine resource stocks 

with adequate assessments. This measure is tracked for the 230 core stocks also tracked 

with the FSSI. Details and updates on the FSSI performance measure are available online 

at http://www.nmfs.noaa.gov/sfa/statusoffisheries/SOSmain.htm. For these 230 stocks, an 

adequate assessment is considered to be an assessment that has enough information to make 

status determinations and track trends in stock abundance and mortality, and has been 

updated within the past 5 years. In FY 2006, 52 percent of the FSSI stocks have adequate 

assessments. Many of these assessments are required to be updated more frequently than 

every 5 years to support implementation of fishery management plans. 

Although adequate assessments can generally support the implementation of fishery 

management plans, improvements can be made by elevating more assessments to the Tier 

III level. For example, inclusion of environmental information can help explain and forecast 

fluctuations in the growth and recruitment to improve the accuracy of short-term potential 

yield and longer-term rebuilding times. Stock assessment models are being expanded to 

include interactions among species in the ecosystem, and models of ecosystem-wide food 

webs are being developed to guide fishery managers. 

By quantifying the status of assessments for each of the important species and the 

amount of resources required to raise the assessment status to the next tier, NMFS has 

been able to determine the budgetary and associated resources that are needed to improve 

stock assessments.
21

I.B.  Interdependence of fisheries or stocks of fish

	 Living and nonliving components of an ecosystem are linked

through physical and biological relationships—e.g., by food

chains or shared habitat use. Understanding these relationships

is important if we are to successfully manage our living marine

resources in a holistic manner. The status of a fish stock and the

merits of alternative harvest strategies cannot be determined in

isolation; an ecosystem-based approach is needed to take into

account the various factors that affect the status of a stock and

the importance of a stock to other components of the ecosystem,

as recommended in the Ecosystems Principles Advisory Panel’s

Report to Congress (EPAP 1999). The abundance, productivity,

and spatial distribution of a fish stock depend on a number of

factors, including environmental conditions; habitat quantity and

quality; the abundance and status of its competitors, predators,

and prey; and possible symbiotic relationships.

	 The objective of biological studies on ecosystem interdependenceis to understand thefunctional relationships among ecosystem components. To do so requires that we determine consumption rates and the functional form of feeding interrelationships

involving resources, as well as spatial and temporal variability in

abundance and habitat use. NMFS is developing recruitment and

multispecies models that incorporatefood web and environmental

information. The models can be used to help predict long-term

impacts of various harvest strategies and environmental trends on

yield potential and species composition, as well as to investigate

effects of predation and compensating biological changes on longterm stability, production, and structure of fish communities under

different harvest strategies and environmental regimes. Research

activities include:

•	 Marine food web research through field and laboratory studies

of fish consumption rates, feeding selectivity patterns, food

preference, and nutritional values of various foods.

•	 Stock size, food availability, and predator-prey dynamics.

•	 Fisheries oceanography to determine how changing environmental conditions cause changes in biological components of

ecosystems.

•	 Food-web-based dynamic mathematical models that are used to

examine how abundance of fish stocks, marine mammals, and

otherecosystem components react to changes in environmental

conditions and alternative fishery management measures.

	 Different fishing methods, whether by commercial or recreational fishermen, affect ecosystems differently and also have

different consequences for non-consumptive user groups (e.g., in

the availability of fish or mammals for tourists to view). These

An example of a food web that 

involves marine species. 

Illustration: South Atlantic 

Fishery Management Council 

Internet site.
22

different impacts, and the different values of various ecosystem attributes by different user 

groups, are important to ecosystem management. Some critical research areas include:

s 4HESUITEOFlSHINGANDNON
lSHINGACTIVITIESAVAILABLETOCOMMERCIALANDRECREATIONAL

fishermen.

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CONSUMPTIVEUSER

groups operate.

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CONSUMPTIVEUSERS

as well as those that value, from afar, the continued existence of the resource.

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POINTSPECIlCSOURCESOFPOLLUTIONONTHEECOSYSTEMEG

hypoxia in the Gulf of Mexico).

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on ecosystems, habitat, fish stocks, and their interdependence with all affected user 

groups.

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TIMElSHING

I.C. Identifying, conserving, and mapping of essential fish habitat (EFH)

The long-term viability of living marine resources depends on conservation and protection of their habitat. The effects of habitat degradation are often insidious, and some losses 

are not well understood. Other impacts are obvious. For example, we know that dams for 

hydroelectric power generation and water diversion for agriculture have restricted some 

valuable anadromous fish runs, and chemical contaminants cause tumors and reproductive dysfunction in fish (e.g., winter flounder in Boston Harbor and English sole in Puget 

Sound). We also know that habitat changes in Florida Bay and Chesapeake Bay have 

resulted in changes in fish communities, and that environmental perturbations, such as 

El Niño, change the latitudinal distribution, abundance, and recruitment dynamics of 

several species on the West Coast. Many habitat changes are not only the result of natural 

processes, but are also the direct result of human interactions with the environment.

The Sustainable Fisheries Act of 1996 requires FMCs to describe and identify EFH in 

Fishery Management Plans, to minimize to the extent practicable adverse effects of fishing activities on such habitat, and to identify other actions to encourage the conservation 

and enhancement of such habitat. The Act also requires that Federal agencies consult 

with NMFS if their actions may adversely affect habitat, and requires that the Secretary 

of Commerce initiate and maintain related research. MSFMCA defines EFH as

... those waters and substrate necessary to fish for spawning, breeding, feeding, or growth 

to maturity. For the purpose of interpreting the definition of EFH: “waters” include aquatic 

areas and their associated physical, chemical, and biological properties that are used by 

fish, and may include aquatic areas historically used by fish where appropriate; “substrate” 

includes sediment, hard bottom, structures underlying the waters, and associated biological communities; “necessary” means the habitat required to support a sustainable fishery 
and the managed species’ contribution to a healthy ecosystem; and “spawning, breeding, 

feeding, or growth to maturity” covers a species’ full life cycle. (Federal Register 2002).

NMFS will continue to conduct research and analyze data necessary to:

1. Identify freshwater, estuarine, coastal, and oceanic habitats necessary to various life 

stages of federally managed fish species.

2. Document the life history of managed fish and assess the degree to which fishing is 

adversely affecting the sensitivity and resiliency of EFH.

3. Increase NMFS’ understanding of the role of the benthic community in the overall 

ecosystem, the interaction of target fish with benthic communities, and effects of fishing on benthic communities.

4. Assess and quantify the impacts of non-fishing activities on EFH, and determine the 

best methods for conserving EFH injured by human impacts (including harmful spills, 

vessel groundings, material disposal, and fishing).

5. Develop population and habitat recovery models.

6. Describe seasonal changes in the character of the water column and seabed, megainvertebrates, and benthic infaunal communities in estuaries and nearshore waters.

7. Map EFH using remote sensing platforms (satellite, aerial, and acoustic) along with 

ground truth and algorithm development to assess habitat type and quality and environmental parameters such as temperature, turbidity, and salinity.

8. Work cooperatively with fishermen to gain information on existing fishery habitats.

9. Determine the social, cultural, and economic needs of fishing communities with respect 

to EFH designations.

Fishery managers will use the information resulting from these activities to identify, describe, conserve, and enhance EFH. 

NMFS Science Centers work closely with the regional offices, FMCs, National Ocean 

Service (NOS) research facilities, the NOAA Damage Assessment and Restoration Program, 

other Federal and state agencies, and academic and other partners to provide timely habitat 

information. NMFS works with the NOAA line offices and other agencies to develop the 

Coastal Change Analysis Program and Coastwatch to apply satellite imagery and aerial 

photography to habitat mapping, analysis of change in coastal land cover, and assessment 

of water temperature, color (for information on its content), and circulation.

These research areas and the specific EFH research described for each Science Center 

will provide information to be used by NMFS and the FMCs to: 

s $EVELOPACOMPREHENSIVEANDCOORDINATEDHABITATRESEARCHPROGRAMIN.-&3THATINteracts with and provides information to habitat managers, the FMCs, and the NMFS 

Offices of Science and Technology, Sustainable Fisheries, Habitat Conservation, and 

Protected Resources.

s )MPROVEUNDERSTANDINGOFTHEDISTRIBUTIONANDHABITATREQUIREMENTSOFEARLYLIFESTAGES

of managed species and their prey and predator species.

s )MPROVESTOCKASSESSMENTCAPABILITIESANDREDUCEUNCERTAINTY
24

s )MPROVEHABITATCONSERVATIONPROTECTIONANDENHANCEMENTCAPABILITIESANDIMPROVE

assessment of threats to EFH and managed fish stocks.

s %VALUATEANDPREDICTHOWENVIRONMENTANDCLIMATESIGNALSCHANGETHEDISTRIBUTIONAND

amount of EFH for important stocks.

s 3YNTHESIZE RESEARCH INFORMATION NEEDS NATIONALLYAND PRIORITIZE HABITAT RESEARCH AND

funding across regions to refine EFH identification, assess and minimize adverse effects 

of fishing activities, and identify actions to encourage the conservation and enhancement 

of such habitats as required by the MSFCMA.

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recovery of biodiversity and value to fisheries.

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database that will connect existing habitat information located in the Regions, Science 

Centers, and elsewhere.

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non-fishery activities (e.g., control of land-based non-point source pollution).

I.D. Impact of anthropogenic factors and 

environmental changes on fish populations

Changing conditions of the biotic and physical environment occupied by fish, whether 

natural or anthropogenic, affect population productivity through mechanisms that vary 

greatly in severity. Detecting such changes is an important task, but determining causal 

relationships is complex. Anthropogenic effects may be confounded by natural environmental changes or cycles. NMFS is conducting research to unravel these complex relationships 

to better understand their role in the sustainability of marine fish populations.

Toxic contaminant discharges to the coastal oceans can have a significant impact on the 

viability of important fish populations. For example, contaminants can disrupt an organism’s 

early life stage development and growth, which in turn can affect its reproductive potential 

as an adult. Such nonlethal effects are not easily identified or characterized, and are therefore difficult to relate to the sustainability of the fish populations. The quantification and 

identification of deleterious changes is further complicated by natural and uncontrollable 

variability within and between fish populations and their supporting food webs. 

NMFS will continue to study the potential effects of contaminants on important fish 

species as well as the sources of these contaminants. To assess the risk to fish populations 

from different combinations of stressors, a link must be made between understanding toxic 

effects of contaminants to individual organisms and the factors, both anthropogenic and 

natural, that influence fish populations. There has been growing recognition that marine 

pollution can disrupt the development and function of the reproductive, endocrine, immune, and nervous systems of marine animals, including fishes, which affects reproductive 

and growth processes critical to population stability. Because the effects are not always 
immediately visible, it is difficult to establish the impact on fish populations. 

Environmental variation at different 

temporal and spatial scales further 

complicates the picture.

NMFS is also studying social and 

economic causes of habitat degradation, from fishery and non-fishery 

sources. This research includes coordination with researchers studying 

land-based activities such as non-point 

source pollution and urban development. NMFS also engages in research 

to determine the effects of long-term 

changes in the ocean climate on living 

marine resources. This information 

helps assess the true impact of humaninduced factors.

Habitat loss and degradation affect riverine, estuarine, and coastal ecosystems. The 

primary threats come from physical destruction of wetland and other habitats, or access 

to these habitats, such as blockage by dams, alteration of freshwater flows, eutrophication, 

and destructive fishing methods. For example, logging contributes to siltation and can 

destroy salmon spawning habitat and impede migratory paths. Construction of marinas 

and docking facilities, as well as dredging and disposal of dredged material in estuaries and 

bays, also cause significant habitat impacts. Loss of aquatic habitat (e.g., coastal wetlands 

or seagrass and kelp beds) resulting from development adversely affects a variety of food 

webs important to adults and juveniles of many marine and anadromous species. Propeller damage to shallow vegetated and nonvegetated habitats not only causes a direct loss of 

habitat, but results in destabilization of these areas, resulting in increased habitat loss and 

increased sediment resuspension and turbidity. Changes in freshwater volume and flow 

rates impact nearshore ecosystems adapted to seasonal discharges of freshwater. Destructive 

fishing methods can damage EFH and live bottom, such as coral reefs.

Nutrient enrichment and eutrophication have a major impact on fish populations in 

estuarine and coastal waters. This impact is manifested by hypoxia/anoxia accompanying 

the death of phytoplankton blooms (e.g., in the Gulf of Mexico dead zone off the Mississippi River and the western portion of Long Island Sound) and loss of inshore habitat 

(e.g., replacement of eelgrass beds by macroalgae or loss of eelgrass beds due to shading by 

epiphytes or phytoplankton in Chesapeake Bay, Waquoit Bay, and Lake Pontchartrain). In 

addition, changes in nutrient dynamics can create conditions that facilitate harmful algal 

bloom events that may lead to shellfish harvest closures and mass mortalities of farmed 

salmon and wild fish in the Northwest. Fishing activities could also change the population 

dynamics of harmful algal species. A change in trophic webs that decreases grazing on 

phytoplankton is a major factor in many blooms, leading to more or longer-lasting bloom 

events. The potential effect of climate change or environmental variability on harmful 

algal blooms events is also poorly known.

NMFS is engaging in a variety of research initiatives to study the effects of natural and 

A degraded wetland on 

Staten Island, NY. Photo: 

NOAA.
26

man-made environmental changes on living marine resources and the related ecosystem, 

social, and economic causes and effects. Some of the initiatives are exploratory or at early 

stages of development. Among the initiatives are:

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sea bottom and damage fragile corals and other bottom-dwelling species.

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EFH and associated living marine resources.

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satellite remote sensing and shipboard and moored instrumentation. 

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s %STABLISHING')3DATABASESTODOCUMENTANDTRACKHABITATCHANGES

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marine fish populations.

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fishery populations.

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inputs and habitat alterations that significantly affect important fishery species.

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and habitat alterations to fishery populations.

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types and fishery populations.

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INDUCED CLIMATE

change.

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s !SSESSINGCURRENTECONOMICANDSOCIALINCENTIVESFORHABITATPROTECTIONORDEGRADATION

II. CONSERVATION ENGINEERING RESEARCH

Conservation engineering research is intended to make fishing gear more efficient and 

to reduce fishing costs, bycatch mortality, and habitat destruction. It is also intended to 

improve the data provided by scientific surveys of fish populations. This research area includes studies related to gear performance and fish behavior to be used in the development 

of selective fishing gear to reduce bycatch. Bycatch mortality decreases the sustainability 

of a fishery and the net benefits provided by that fishery in four ways (NMFS 2004):

1. If bycatch mortality is not monitored adequately, the uncertainty concerning total fishing-related mortality increases.

2. The discards themselves can have adverse effects on other species.
3. Bycatch mortality precludes some other uses of living marine resources; for example, 

juvenile fish subject to bycatch mortality will not contribute directly to the growth of 

that stock and to future catch.

4. The absence of management measures to reduce bycatch typically results in too much 

bycatch; i.e., the overall net benefit to the Nation from that fishery can be increased by 

decreasing bycatch.

Commercial discards are a significant source of fishing mortality worldwide. The United 

Nations Food and Agriculture Organization (FAO) estimates that, from 1992 to 2001, 

yearly discards worldwide averaged 7.3 million metric tons. Trawl fisheries for shrimp and 

demersal finfish account for over 50 percent of the total estimated discards while representing approximately 22 percent of total landings recorded in the study (FAO 2004).

Recreational discards are another source of fishing mortality. Information is needed to 

determine proportions of discards in different recreational fisheries and assess associated 

release mortality. Additionally, NMFS is encouraging research on ways to increase the 

survival of recreational releases. 

Bycatch reduction is particularly critical when the bycatch includes protected species. 

NMFS conducts research at several of its laboratories regarding fishing gear interactions 

with populations of species protected under the ESA and MMPA, including sea turtles, 

seabirds, and marine mammals. Such species interact with species managed under the 

MSFCMA through, for example, competition for prey species and fishing gear interactions. As such, research conducted to support requirements of the MSFCMA also makes 

an important contribution to the conservation and management requirements of the ESA 

and the MMPA. Along with incentives and other management strategies, one way to 

reduce bycatch is to design and operate selective fishing gears, using knowledge of species 

behavior, gear hydrodynamics, and fishing practices.

An important data collection method used by NMFS to conduct research on fishing 

gear and its impact on fish stocks, protected species, and habitat is the deployment of marine resource observers on commercial and recreational fishing vessels. Observers collect 

information on all aspects of fishing gear operations, including what kind of gear is used, 

how it is set, how long it is set, and how it is retrieved, as well as information on fish catch 

and bycatch and incidental takes of protected species. Observers also collect life history 

data on species of concern, collect biological samples, and support research through tagging of released animals and other activities. Observer data provide information for stock 

assessment research, for the assessment of gear efficiency, and for monitoring the relative 

impacts of various types of gear and fishing methods on fish and protected species and 

marine habitats. Currently, observers are deployed in only a fraction of the U.S. commercial and recreational fisheries managed by NMFS or required to be monitored under the 

MMPA, but initiatives are under way to expand the observer program into more fisheries 

and to more fully integrate observers into fisheries research activities. 

Bycatch levels and control measures continue to occupy the attention of most fishery 

management actions of the regional FMCs. Even when apparent solutions are found, the 

dynamics and abundance of marine species change in time and area, and this can shift the 

character of the problems and require continuous adjustments to their solutions. NMFS will 

continue to conduct studies to determine the magnitude of bycatch of overfished stocks and 

options to reduce it. The options may require the design of new types of fishing gear that 
28

are more selective for the targeted species, and NMFS is working in cooperation with the 

commercial and recreational fishing industry, tribes, states, international and environmental 

organizations, academia, and gear manufacturers to find designs that meet conservation 

needs while recognizing the financial constraints of fishermen.

To determine when gear modifications are the most appropriate response to bycatch 

problems, NMFS is studying a variety of gear technologies and fish behaviors, including: 

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fishery.

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By understanding the successes and setbacks in these and other settings, NMFS will be 

better able to coordinate gear research with the social, economic, and institutional constraints of specific fisheries.

Experimental work with selective fishing gear involves considerable fieldwork on board 

fishing vessels working under actual fishing conditions. Most trawl gear evaluation includes 

an alternative tow approach, varying which net is fishing with the experimental gear and 

comparing the catch results using statistical tests. Underwater cameras and advanced sonars allow for examination of the behavioral mechanisms and gear variations that would 

account for the catch differences. 

The MSFCMA’s EFH provisions have created a need to evaluate the impacts of fishing 

gear on EFH. Effects from fishing may include physical disturbance of the substrate and loss 

of and injury to benthic organisms, prey species and their habitat, and other components 

of the ecosystem. Recent research to evaluate fishing impacts on habitat have included:

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s !COUSTICSEABEDMAPPING

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s 4RAWLSWEEPANDFOOTROPEMODIlCATIONSTOREDUCESEAmOOREFFECTS

s 1UANTIlCATIONOFBOTTOMTRAWLEFFECTSONSOFT
BOTTOMHABITATSINNATURALLYDISTURBED

areas.

A circle hook. Offset circle 

hooks have the point bent 

off to the side. Photo: South 

Carolina Department of 

Natural Resources.
s 4HEEFFECTSOFlSHINGONTILElSHHABITATS

s (ABITATRESILIENCEANDRECOVERYFOLLOWINGCESSATIONOFBOTTOMTRAWLINGACTIVITY

s $ISTRIBUTIONOFTRAPlSHINGANDEFFECTSONHABITATSONCORALREEFECOSYSTEMS

s 0RE
CLOSUREEVALUATIONOFHABITATSANDlSHINPROPOSED3OUTH!TLANTICMARINEPROTECTED

areas.

Growing concern over the impacts of bycatch on stocks resulted in the development of 

a NMFS Bycatch Plan (NMFS 1998a). Agency experts with experience in fishery management, stock assessment, and social sciences compiled the plan, which included national 

bycatch objectives; specific recommendations concerning data collection, evaluation, and 

management actions necessary to attain the objectives; and a comprehensive assessment 

of the state of bycatch in the Nation’s marine fisheries. NMFS increased its commitment 

to addressing bycatch by issuing its National Bycatch Strategy on 11 March 2003. This 

strategy comprised six components (Benaka and Dobrzynski 2004):

1. Assess progress toward meeting the goal, objectives, and strategies of the NMFS Bycatch 

Plan.

2. Develop a national approach to a standardized bycatch reporting methodology (NMFS 

2004).

3. Implement regional bycatch implementation plans.

4. Undertake education and outreach efforts to develop effective and efficient methods to 

reduce bycatch.

5. Use existing partnerships and develop new international approaches to reduce bycatch. 

6. Identify new funding requirements to support the NMFS National Bycatch Strategy 

on an ongoing basis.

NMFS is committed to maximizing the research contribution of the commercial and 

recreational fishing industry and the other above-mentioned partners in fisheries management. Across the NMFS regions, the commercial and recreational industry and other 

important partners are providing advice in research planning, formal reviews of research 

programs, and, where possible, research operations. Examples of research involvement 

include: 

s 0ROVIDING EXPERTISE IDEAS CHARTERED VESSELS AND CREW FOR SURVEYS AND BYCATCH GEAR

development. 

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 3INCEITSINCEPTIONDECADESAGOTHE3ALTONSTALL
+ENNEDY'RANT0ROGRAMHASHADAHIStory of direct industry involvement and investment. Industry members submit proposals, 

usually with significant cost sharing, to conduct research in conservation engineering, to 

develop fisheries for underutilized species to relieve pressure on traditional species, and 

to improve the after-catch utilization of captured species. Regional programs such as the 

Marine Fisheries Initiative MARFIN Program and the Northeast Cooperative Research 

Partners Program often fund bycatch reduction research with various partners from industry, 
30

academia, states, and other nongovernmental organizations. In addition, “Research Set 

Aside” programs administered by NMFS’ Northeast Fisheries Science Center allow fishermen to harvest fish and shellfish they normally would be unable to harvest in exchange 

for the use of their vessels and other services to conduct bycatch reduction research.

III. RESEARCH ON THE FISHERIES

New management measures, based on the Sustainable Fisheries Act (Public Law 104-

297), have been successfully implemented to halt the decline in stock levels in many U.S. 

fisheries. 

The 2006 annual report to Congress on the status of the U.S. fisheries identifies 530 

marine fish stocks and stock complexes in the EEZ, an area that extends from 3 to 200 miles 

offshore and covers more than 2 million square miles, including those stocks that straddle 

international boundaries and highly migratory stocks. NMFS reviewed 530 individual 

stocks and stock complexes. Of those, 242 have known overfishing determinations: 194 

(80 percent) are not subject to overfishing and 48 (20 percent) are subject to overfishing; 

187 stocks have known overfished determinations: 140 (75 percent) are not overfished and 

47 (25 percent) are overfished (NMFS 2007b).

III. A. Social and economic research

Many of the principal threats to marine ecosystems (overfishing, habitat degradation, 

water quality degradation, etc.) are economic and social in origin. Rebuilding and maintaining marine ecosystems requires understanding the economic and social drivers at the 

root of human impacts, in addition to understanding the biological and ecological functions and constraints of marine ecosystems. The NMFS Economics and Social Sciences 

Program is tasked with understanding the economic and social motivations that generate 

impacts to marine ecosystems, as well as assessing stakeholders’ and the general public’s 

preferred status of marine ecosystems (e.g., abundance of fish stocks, marine protected 

species, etc.) and determining the outcomes that achieve the greatest benefits to society. 

To meet these mandates, the NMFS Economics and Social Sciences Program encompasses three core functions: 1) collecting information on resource users; 2) conducting 

economic and social analyses of fishery management issues; and 3) providing scientific 

advice to fishery managers. 

This emerging program has targeted its data collection efforts on meeting current management needs and building the information base to meet future challenges. For example, 

although NMFS’ goal is to establish high-quality, long-term continuous economic data 

collection programs on commercial harvesters in all federally managed fisheries, NMFS 

is currently collecting the full suite of economic data (landings revenue, trip expenditures, 

and fixed costs) only in key fisheries, with the intention of expanding these efforts to other 

fisheries in the future. However, in 2006 NMFS conducted its first national recreational 

survey of angler trip expenditures, and out-year plans call for increased use of surveys that 

directly ask anglers their preferences for proposed management options. 

Furthermore, NMFS is currently completing its initial assessment of fishing communities that includes baseline information on demographics and an inventory of marine-related 

businesses and social and cultural institutions. In the long term, continued phased growth 
of economic information collections on fishing-related industries and expanded social assessments are planned in order to provide a richer characterization of coastal economies, 

fishing communities, and fishing participants and for use in predictive modeling.

These information collections underpin the second core function of the program—

conducting economic and social analyses of fishery management issues. In particular, 

these data enable NMFS to perform rigorous economic and social assessments, including:

s $EVELOPINGECONOMICANDSOCIALINDICATORSTHATDESCRIBETHESTATUSANDTRENDSOFlSHERY

participants, marine-related businesses, and fishing communities, and that may be used 

as signals for identifying economic and social hardship in its early stages.

s $ETERMININGTHEBENElTSANDTHECOST
EFFECTIVENESSOFCURRENTlSHERIESREBUILDINGPROgrams and habitat and protected species recovery programs in an integrated ecosystem 

framework.

s !SSESSINGTHEECONOMICANDSOCIALIMPACTSANDCUMULATIVEIMPACTSOFPROPOSEDMANagement measures and existing policies on fishery participants, shoreside firms, and 

coastal communities.

s $EVELOPINGPREDICTIVEMODELSOFHARVESTBYCATCHANDENTRYEXITWHICHARECRITICALELEments in understanding fishery capacity. 

Fisheries management is undergoing two major changes, both of which suggest an expanded role for using socioeconomic research in decision-making. NMFS’ move toward 

an ecosystem approach to marine fisheries management represents a major regime shift in 

fisheries management and the science requirements underpinning management decisions. 

Fisheries economists’ ability to support ecosystem approaches has been significantly enhanced by recent advances in spatial econometric modeling, which provides an integrated 

framework for overlaying commercial harvesters’ production decisions (e.g., where to fish, 

target species choices, and whether to stay in fishing) and recreational anglers’ decisions 

(coincidentally, also location and target species decisions) against the physical, biological, 

and ecological condition on which those decisions are made. These models are already 

being used to assess the short-run costs and benefits associated with fishing ground closures. Future extensions of these models include incorporating additional biological and 

ecological information, including stock and habitat effects, that would enable scientists to 

assess the effects of localized habitat protection measures on the larger ecosystem as well as 

estimating the short- and long-run damages from environmental events (e.g., hurricanes, 

harmful algal blooms, and tsunamis), oil spills, and other exogenous factors.

The other phenomenon transforming fisheries management is the recognition of the 

importance of using market-based approaches to solving fishery management issues. The 

U.S. Ocean Action Plan and the 2005 and 2006 Economic Report of the President all 

advocate identifying market-based solutions to fishery management issues. For example, 

dedicated access privilege (DAP) programs—which include individual fishing quotas, community quotas, fishing cooperatives, and area-based quotas—are often cited as a marketbased solution for reducing overcapacity and improving the economic and environmental 

performance of commercial fisheries, as well as the long-term sustainability of the fishing 

communities that depend on these resources. Accordingly, the Administration has set a 

goal of doubling the number of Federal fisheries managed by DAPs. Increased economic 

and social monitoring and research will help ensure that the economic and social goals of 

each DAP are achieved. 
32

The data collection and research functions support the third core function of the NMFS 

economics and sociocultural program—providing scientific advice to fishery managers. 

Fisheries management is complex because decisions must reflect the values and the oftencompeting needs of many different groups, including commercial and recreational fishermen, subsistence fishing communities, non-consumptive users (e.g., non-harvest divers, 

whale watchers, etc.), Pacific Islanders, and Native American tribes, many of whom have 

treaties with the United States guaranteeing certain fishing rights. To understand the importance of economic and sociocultural information to fisheries management, one need 

only consider that a key feature of the Federal regulatory process is that it is not possible to 

simply implement a regulation to achieve a conservation goal, but instead fishery managers must consider a suite of management alternatives for achieving that outcome. Fishery 

managers’ evaluations of these options not only include weighing the trade-offs associated 

with alternative management measures at an aggregate or societal level; they also include 

evaluating the distributional effects of proposed options on various stakeholder groups. 

III.B. Seafood safety research

The Product Quality and Seafood Safety Research (PQ&S) program is the foundation 

of NMFS’ capabilities to proactively address seafood safety issues on multiple levels from 

specific shellfish or fish to human health and the broader marine environment. PQ&S has 

provided, in part, the necessary capability to respond quickly to environmental disasters 

that can affect seafood quality. The value of this capability was evident in NOAA’s rapid 

RESPONSETOPOSSIBLEHUMANHEALTHTHREATSINTHEAFTERMATHOF(URRICANE+ATRINA7ITHOUTTHISCOMPONENTOFTHE0130ROGRAM./!!SRAPIDRESPONSETO+ATRINAWOULDNOT

have been possible because the needed expertise would not have existed. The availability 

of trained and experienced staff is a critical prerequisite for a rapid, timely, and effective 

response to all seafood safety issues, which is essential to providing the public with the 

science-based assessments they need to have confidence in the quality of their seafood and 

TOUNDERSTANDANYPOTENTIALRISKS4HEPROGRAMANDTHE./!!+ATRINARESPONSEENABLED

by it, ensured public confidence in the $7 billion Gulf of Mexico fishery, demonstrating 

a sound return on NOAA’s investment in the PQ&S program. Other examples of public 

health and economic benefits involving regional fishery resources can be cited. Tangible 

benefits from NOAA’s response capabilities also occurred following the Exxon Valdez, 

North Cape, and other oil spills, as well as from surveys of mercury in Gulf of Mexico 

fishery resources and Pacific Island region resources, as well as addressing other seafood 

safety concerns.

Intra- and extramural seafood safety research and monitoring provides for the continued 

integration of trophic web research relative to fishery resource health and disease threats, 

and differential trophic-level risk evaluation effects resulting from such threats, be they to 

other fishery resources, marine mammals, or human consumers. Studies focus on identifying and determining the characteristics of marine pathogens; improving methods to detect, 

forecast, and evaluate the ecological significance of harmful algal blooms; and developing 

and applying biological and chemical analytical methods to measure toxic contaminants 

to restore living marine resources and their habitats. Additionally, when needed, specific 

highly focused research is rapidly directed to address crisis situations dealing with animal 

and human health concerns (e.g., research needed to perform a risk assessment to wild 

shrimp stocks resulting from imported aquaculture shrimp products being infected with 

various shrimp viruses, reevaluating the human exposure rate from mercury in seafood, or 

investigating the mitigating effects of selenium on mercury toxicology). Personnel associ-
ated with the program represent the agency in 

all significant national and international food 

safety forums, including those dealing with 

food safety regulatory policy development, to 

ensure that national and international food 

policy development incorporates the nuances 

associated with fishery resources being used 

as a food source. These research efforts are 

conducted primarily at the National Seafood 

Inspection Laboratory in Pascagoula, Mississippi, as well as at the Northwest, Southeast, 

and Pacific Island Fisheries Science Centers 

and Regional Offices.

III.C. Marine aquaculture

Aquaculture is defined as the propagation and rearing of aquatic organisms in controlled 

or selected aquatic environments for any commercial, recreational, or public purpose. 

NMFS has a long history in aquaculture research and development, stretching back more 

than 100 years, and has made major contributions to the progress of aquaculture both 

domestically and internationally. Research efforts span the full range of issues associated 

with the ability to culture marine species for both commercial production and as a tool in 

stock enhancement and habitat restoration. Expanded marine aquaculture production in the 

United States has the potential to reduce the pressure on wild stock harvest and help in the 

rebuilding efforts for those stocks. Research efforts include the evaluation of the impacts of 

aquaculture production and stock enhancement on marine ecosystems and, in particular, 

on wild stocks and their habitats, which is the focus of regional FMCs and NMFS under 

MSFCMA. In particular, there is a need for models, mapping tools, guidelines, protocols, 

and other research products to support NMFS and the FMCs in the review of aquaculture 

projects under MSFCMA and other authorities.

With the recent expansion of aquaculture production worldwide, and increasing interest 

in the expansion of aquaculture in the United States, NMFS laboratories can make significant contributions to public understanding of the scientific issues surrounding marine 

aquaculture and stock enhancement. Many of the issues raised in public forums are based 

on outdated or questionable studies that do not accurately reflect current industry practices, 

so it is critical for NMFS to provide up-to-date assessments based on sound science. If the 

Administration’s proposed National Offshore Aquaculture Act is enacted by Congress, 

NOAA will become the lead permitting agency for aquaculture in Federal waters of the 

EEZ, and the need will increase for science activities to support the rulemaking process, 

evaluation of aquaculture permit applications, monitoring of offshore aquaculture operations in the EEZ, and assessment of the cumulative impacts on marine ecosystems. 

National policies stated in the National Aquaculture Act of 1980, as amended, and 

in the aquaculture policies adopted by NOAA and the Department of Commerce in the 

late 1990s, support the development of sustainable aquaculture production in the United 

States. The more recent recommendations issued by the U.S. Commission on Ocean Policy 

in 2004, and in particular the support for aquaculture stated in the U.S. Ocean Action 

Plan, reaffirm the national interest in expanding aquaculture production in the United 

States. There are multiple reasons for this interest in domestic aquaculture production, 

NMFS researcher testing 

for harmful bacteria in fish 

sampled from the Hurricane 

Katrina area. Photo: NMFS.
34

including the increasing demand for seafood 

which, coupled with limited ability to increase 

harvests from wild fisheries, has resulted in a 

growing U.S. trade deficit in edible fishery 

products that currently is approaching $8 billion. Most of the increased global production 

of fisheries products during the past decade 

has come from aquaculture, so the choice for 

the United States is clear: increase seafood 

imports, which will increasingly consist of 

aquaculture products, or increase domestic 

aquaculture production.

U.S. aquaculture production in 2003 was 

about 926,000 pounds (420,000 metric tons), 

with a value of $961 million (about 20 percent 

from marine species). Aquaculture accounts 

for about 25 percent of the total U.S. landings value, and there is significant potential to 

increase U.S. marine aquaculture production. NMFS can support the expansion of marine 

aquaculture by providing sound scientific information and analyses to answer the range of 

technical, environmental, and socioeconomic questions that have been raised about aquaculture. These questions relate to the appropriate siting of aquaculture facilities, aquatic 

animal health, alternatives to the use of fishmeal and fish oil in feeds, potential genetic 

and ecological impacts of escapes, potential marketplace competition with wild products, 

and other issues. NMFS’ scientific expertise can be applied to all of these issues, as well as 

to the development of sustainable culturing techniques, design of cages and other types 

of grow-out systems, and establishment of protocols for the release of cultured stock for 

purposes of stock enhancement.

In addition to food production and stock enhancement, aquaculture can also assist in 

recovery plans for protected species, and can be used to produce nonfood products such 

as ornamental fish, baitfish, and pharmaceuticals. 

Finally, an enabling policy and regulatory framework is needed in support of aquaculture development. Regulatory complexity and uncertainty are generally recognized as the 

major reasons why domestic marine aquaculture production has not increased in recent 

years. The NOAA Aquaculture Program is addressing this barrier to domestic production by working within NOAA and with other Federal agencies to clarify and simplify 

how aquaculture is regulated under current law, and by working with NOAA’s Office of 

Legislative Affairs to obtain congressional authorization to establish and implement a 

regulatory framework for offshore aquaculture in Federal waters of the EEZ. Enactment 

of the National Offshore Aquaculture Act or similar legislation would establish NOAA 

as the lead agency for offshore aquaculture, authorize NOAA to develop regulations and 

issue permits to support a sustainable marine aquaculture industry in Federal waters, and 

pave the way for a productive offshore aquaculture industry in the United States.

Facing pages: An underwater 

aquaculture cage, called 

the Aquapod, below the 

surface (left) and at the 

surface (right) is shown in 

tests for raising a fish species 

called cobia, Rachycentron 

canadum, near Puerto Rico. 

Photo credits: NOAA.
To ensure that marine aquaculture progresses in an environmentally sound manner, 

NMFS will concentrate its aquaculture research activities in the following broad areas, 

in partnership with the broader research and 

aquaculture communities:

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husbandry technologies for new candidate 

species.

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on habitat and ecosystems.

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s $EVELOPINTEGRATEDANDEFFECTIVEENHANCEMENTRESEARCHANDMANAGEMENTSTRATEGIESFOR

aquatic species to help in the rebuilding and recovery of wild fish stocks, endangered 

species, and habitat.

s $EVELOPANDFOSTERTHEADOPTIONOFPROTOCOLSFORAQUATICANIMALHEALTHINTHEAQUACULTURE

industry. 

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working in overexploited fisheries.

s %NCOURAGECOORDINATIONANDCOLLABORATIONOFSTAKEHOLDERSTOACHIEVEREGIONALANDNATIONAL

goals by establishing frameworks for regional cooperation among the private and public 

sectors.

s !SSISTASSOCIATIONSOFPRODUCERSTOPREPAREBESTMANAGEMENTPRACTICESFORTHEIRRESPECTIVE

industries based on scientific analysis and risk assessments.

s #ONDUCTSTUDIESOFTHEENVIRONMENTALECOLOGICALSOCIALANDECONOMICIMPACTSOFAQUAculture and stock enhancement, and develop science-based strategies and guidelines for 

avoiding, minimizing, and mitigating negative impacts.

s $EVELOPDATACOLLECTIONANDANALYSISTOOLSTOMONITORANDASSESSAQUACULTUREPRODUCTION

trends.

IV. INFORMATION MANAGEMENT RESEARCH

To address important data shortcomings, MSFCMA requires the Secretary of Commerce to “develop recommendations for implementation of a standardized fishing vessel 

registration and fisheries information management system.” In December 1998, NMFS 

completed and delivered a report to Congress that outlined an approach to integrate the 

collection and management of all fisheries information required under all applicable 

NMFS statutory and regulatory requirements, including but not limited to MSFCMA, the 

Marine Mammal Protection Act, the Endangered Species Act, and the Atlantic Coastal 

Fisheries Cooperative Management Act (NMFS 1998b). It also includes all data collected 

and statistics compiled under state authority for those states willing to participate. This 

report was developed in consultation with the U.S. Coast Guard, the states, the interstate 

marine fisheries commissions, the FMCs, other key governmental and nongovernmental 

organizations, and interested stakeholders. 
36

Marine fisheries management organizations have long understood that the quantity 

and quality of fisheries information relate directly to the quality of the scientific analysis 

supporting resource management and allocation decisions. In its 1998 Report to Congress, 

NMFS made the case that significant long-term investment would be required to ensure 

that the right information of the right quality is readily available to form the basis of these 

management decisions. In that report, NOAA and its partners delivered a high-level strategy 

and an estimate of investments needed to realize a national Fisheries Information System 

(FIS). Congress began funding the agency in 2003 to initiate an FIS program that will 

improve the existing framework for partnership and collaboration with NOAA partners 

who collect, manage, and disseminate fisheries information. 

A governance structure has been developed for the program that includes an Executive Sponsorship Team, a Program Management Team (PMT), and several Professional 

Specialty Groups (PSGs). The Executive Team is composed of the agency’s Chief Science Advisor and Deputy Assistant Administrator for Regulatory Programs; it provides 

high-level guidance and advice on national and cross-regional issues and ensures that 

the FIS program operates in a manner consistent with fundamental policies and general 

principles of the agency. The PMT is composed of representatives of two headquarters 

offices (Office of Science and Technology and Office of Sustainable Fisheries), the six 

NMFS Regions, and the three interstate commissions responsible for coordinating the 

major cooperative state-Federal fisheries information network programs on the Atlantic 

coast, Pacific coast, and Gulf of Mexico. The regional state-Federal programs for which 

representation is provided include the Atlantic Coastal Cooperative Statistics Program 

(ACCSP), the Gulf of Mexico Fisheries Information Network (Gulf FIN), the Alaska 

&ISHERIES)NFORMATION.ETWORK!+&).	THE0ACIlC&ISHERIES)NFORMATION.ETWORK0ACFIN), the Pacific Recreational Fisheries Information Network (Pacific RecFIN), and the 

Western Pacific Fisheries Information Network (WPacFIN). The PMT is responsible for 

achieving the mission, vision, goals, and objectives for the program and for providing the 

tactical and operational governance needed to ensure effective planning and execution of all 

projects.

PSGs have been formed as needed to support the FIS program’s business and technical 

needs. Each PSG consists of experts from multiple disciplines brought together to address 

a specific goal, objective, or subcomponent of the FIS program. Each PSG receives approval 

and direction from the PMT for functions, tasks, and projects.

The FIS program vision of “a comprehensive, continuously updated time-series of welldocumented, high-quality, easily-accessible information on the nation’s fisheries that supports living marine resource stewardship” guides the PMT in executing the FIS program 

mission: NOAA’s FIS program delivers fisheries information collection, management, and 

dissemination solutions to improve accuracy, completeness, timeliness, and accessibility. 

The program leverages Federal-state partnerships and investments to provide the information needed to help understand the effects of fishing on living marine resources, and to 

improve the quality of resource management decisions.

The current development of the FIS program is based on linking and integrating existing 

regional state-Federal fisheries information collection and management programs around 

the country with national programs to create a “system of systems” that will satisfy information needs of Federal and state agencies, the fishing industry, and the general public.
The FIS program is working toward realizing its vision and mission by striving to achieve 

the following four goals:

1. Expand and adapt data collection to meet current and future needs for resource stewardship.

2. Build, link, and integrate information management systems within and across regions.

3. Establish regional and national standards (including minimum guidelines) for information collection, management, and dissemination to ensure high quality, completeness, 

timeliness, and accessibility.

4. Implement and maintain effective partnerships to support collaboration among stakeholders and to leverage investments across regions and throughout the Nation.

In addition, the FIS program has established certain design principles to: 

s !VOID UNNECESSARY COSTS BY REDUCING DUPLICATIVE EFFORTS AND LEVERAGING CURRENT AND

projected investments. 

s %STABLISHANOVERALL&)3PROGRAMARCHITECTURETHATINCLUDESBUSINESSANDTECHNOLOGY

perspectives, standards of measurement, and standards of quality. 

s 2EDUCEINDUSTRYANDREPORTINGBURDENS

These design principles represent guiding elements for FIS program execution. 

Recent initiatives within NOAA and with its domestic and international partners also 

illustrate the importance of an ecosystem approach to resource management. This will 

require tight integration of FIS and its products with the agency’s fishery-independent 

data collection and management programs, as well as major NOAA programs such as the 

Integrated Ocean Observing System (IOOS) and the Global Earth Observing System of 

Systems (GEOSS). 

The regional fisheries data collection and information management programs—developed by NMFS in cooperation with state agencies and interstate commissions—have progressed considerably during the past decade. The concept of a “one-stop shop” for fisheries 

information at state, regional, and national levels is achievable if funding and executive 

sponsorship continues during the next 5 to 10 years.

Initial investments have established an FIS program management plan, as well as 

governance processes for project selection and resource allocation. The PMT has also 

been developing plans for communications and outreach, program architecture, and risk 

management. The PMT is implementing program management best practices by:

s %STABLISHINGCLEARROLESANDRESPONSIBILITIESFORTHEPARTICIPANTS

s $EVELOPINGAPORTFOLIOMANAGEMENTAPPROACHTOTHEARRAYOFDIVERSEPROJECTSTOBEEXecuted.

s %NSURINGTHATPROJECTMANAGEMENTEXPECTATIONISSTANDARDIZEDANDWELL
DOCUMENTED

s %STABLISHINGTHEEXPECTATIONANDMEANSTOMONITORANDEVALUATEPROGRESSANDPERFORmance. 
38

The PMT has organized, funded, and planned projects into eight FIS program portfolios 

that represent the core areas for initial, current, and future investments:

1. FIS One-Stop Shop: Make fisheries data and statistics readily available at a regional 

or national level in a form that is easily used by fisheries managers, stock assessment 

scientists, other stakeholders, and the general public. Make all information accessible 

through a single regional or national web-enabled information portal. 

2. FIS Information Catalog: Provide a metadata catalog of all critical fisheries data holdings.

3. Information Quality: Ensure the quality of fisheries information needed to support 

stock assessments, as well as timely monitoring of FMP compliance and related fishing 

quotas.

4. Common Identifiers: Provide a unique key or identifier that can be used to link permits 

and fishing performance data for individual owners, vessels, dealers, and/or anglers for 

the purpose of effective tracking of individuals and their performance histories.

5. Establish and Meet Minimum Information Requirements: Ensure collection of 

minimum information needed to fulfill the stewardship responsibilities of NOAA, the 

FMCs, interstate fisheries commissions, and states.

6. Electronic Reporting and Registration Systems: Develop electronic systems for purchasing permits; processing and sharing permits information; and collecting, reporting, 

processing, and sharing fisheries performance information for all major fisheries.

7. Program Management Support: Maintain a well-managed program that delivers value 

to FIS program partners and customers, and is a model for program management in 

NMFS.

8. FIS Program Architecture: Develop a roadmap that describes the current state of 

business and systems elements and their use in a new FIS program state.

The PMT has developed initial high-level work plans and identified the desired outcomes 

for each portfolio. Additional analyses are establishing critical paths, interrelationships, 

and dependencies between and among these portfolios.

Development of FIS is being coordinated with the Integrated Ocean Observing System 

(IOOS), a developing, multi-agency system to routinely and continuously provide quality controlled data and information on current and future states of the oceans and Great 

Lakes. The IOOS will operate from the global scale of ocean basins to local scales of 

coastal ecosystems. It is a multidisciplinary system designed to provide data in forms and 

at rates required by decision makers to address seven societal goals. Three of these goals are 

directly relevant to fisheries research and management: reduce public health risks; protect 

and restore healthy coastal ecosystems more effectively; and enable the sustained use of 

ocean and coastal resources. The IOOS has three major components to form an end-toend system: observations, data management and communication, and data analysis and 

modeling. 

Although development of FIS predates development of the IOOS, FIS can provide the 

mechanism for bringing fishery-dependent data into the larger IOOS. For example, FIS 

can be brought into compliance with IOOS standards for data access, metadata, and data 

stewardship (e.g., quality control and archiving). 
MAJOR FISHERY 

RESEARCH GOALS 

AND OBJECTIVES 

The major fishery research goals of NMFS have a one-to-one relationship with the 

program areas identified in the MSFCMA, except that a sixth element has been added 

to help focus efforts on building partnerships. The objectives under each goal have been 

developed through many discussions with agency managers and staff and with stakeholders 

and reviewers. They generally correspond to the principal functions necessary to develop 

and disseminate information and advice for use by fisheries managers.

GOAL 1—PROVIDE SCIENTIFICALLY SOUND INFORMATION AND DATA SUFFICIENT TO SUPPORT

ECOSYSTEM-BASED FISHERY CONSERVATION AND MANAGEMENT.

Objective 1.1: Periodically assess stocks to ascertain whether changes in their status due to 

natural or human-related causes have occurred. These stock assessments require adequate 

fishery monitoring and resource surveys and knowledge of the physical environment. 

Objective 1.2: Provide stock assessments that include current and forecast abundance levels 

and trends, based on a comprehensive suite of ecosystem variables such as biological productivity, climatic and oceanographic information, ecological interactions, and economic 

and other social forces that will affect levels of fishing effort. 

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

Objective 1.4: Develop implementation strategy and annual operational plans for executing the days-at-sea requirements identified in the NMFS Data Acquisition Plan (NMFS 

1998c). 

Objective 1.5: Use stock assessment workshops, peer reviews, and other fora to ensure 

that NMFS’ information and advice are developed through an open and collaborative 

process. 

Objective 1.6: Communicate NMFS’ scientific information and advice, along with the associated uncertainties, to the Councils, other management authorities, and the public. 

Objective 1.7: Collaborate with other management authorities and the Councils to explore 

and develop fishery management regimes and alternative governance systems that will 

effectively control exploitation and promote sustainability. 
40

Objective 1.8: Provide guidelines to assist the Councils in assessing and specifying Maximum Sustainable Yield (MSY) for managed fisheries. 

Objective 1.9: Work with the Councils to develop objective and measurable criteria for 

each managed stock to determine if the stock is overfished or approaching an overfished 

condition. 

Objective 1.10: For each stock that is overfished or approaching an overfished condition, 

develop, with the advice and recommendations of the Councils, measures to eliminate or 

prevent overfishing. 

Objective 1.11: Conduct additional research to provide needed information to refine EFH 

designations (for example, to better differentiate between spawning habitats and habitats 

used occasionally) and to help the Councils minimize the adverse effects of fishing, aquaculture, and other activities on EFH, as mandated by the MSCFMA. 

Objective 1.12: Establish a continuing review of living marine resource habitats (as part of 

the Our Living Oceans series and implement measures to monitor the trends in habitat 

availability. (NMFS, in prep.). 

Objective 1.13: Support recommendations provided by the NRC (NRC 1999) and the 

Report to Congress (EPAP 1999) by establishing criteria to define and delineate marine, 

estuarine, and riverine ecosystems for management purposes, and identify indicators for 

assessing the status and detecting changes in the health of such ecosystems. 

Objective 1.14: Define the key aspects of vital habitat functions and increase our understanding of how they affect marine and anadromous species and how they are affected 

by human activities. This will involve the development of new methods of quantifying 

fishing and non-fishing impacts on habitat and evaluating the quality and productivity 

of restored habitats, as well as improved restoration and creation technologies, including 

contaminant remediation, to ensure that restored and created habitats are beneficial to 

fish populations. 

Objective 1.15: Incorporate assessments or indices of climate variability into stock assessments. 

Objective 1.16: Monitor climate change on interannual, decadal, and centennial scales and 

its impact on currently sustainable fisheries. 

Objective 1.17: Use economic and sociocultural research to predict future trends (e.g., entry 

and exit behavior from industry or community, organizational structure, cultural changes, 

etc.) of shoreside fishing-related households and firms in fishing communities. 

Objective 1.18: Use economic and sociocultural research to predict future trends in entry 

and exit of fishermen to the fishery and to assess fishing capacity. 

GOAL 2—THROUGH CONSERVATION ENGINEERING RESEARCH CONTRIBUTE TO EFFORTS TO

REDUCE BYCATCH AND ADVERSE EFFECTS ON EFH, PROMOTE EFFICIENT HARVEST OF TARGET

SPECIES, AND IMPROVE THE DATA FROM FISHERY SURVEYS.
Objective 2.1: Improve NMFS’ ability to identify and assess the magnitude of incidental 

takes of protected marine species. 

Objective 2.2: Establish sustainable levels of takes for all protected marine species and 

continue to improve the estimates of these levels through ecological research. 

Objective 2.3: Work through domestic and international cooperative relationships with 

industry and environmental groups, including take reduction teams, special task forces, 

and other needed scientific collaborations. 

Objective 2.4: Explore, develop, and implement new technologies and practices for reducing 

detrimental interactions. When such technologies could reduce detrimental effects both 

to and from protected species in other nations, these technologies will be made available 

to those nations. 

Objective 2.5: Establish a standardized reporting methodology to assess the amount and 

type of bycatch occurring in each fishery covered by an FMP. 

Objective 2.6: Work in cooperation with the fishing industry and gear manufacturers to 

improve gear selectivity, design and field test new gear designs and modifications, and 

evaluate gear regulations. 

Objective 2.7: Assess and quantify the degree of impact of existing and new gears on EFH 

and research new gear types that can reduce those impacts.

GOAL 3—THROUGH ECONOMIC AND ECOLOGICAL RESEARCH ON MARINE COMMUNITIES AND

ECOSYSTEMS, PROVIDE SCIENTIFIC DATA AND INFORMATION TO INCREASE LONG-TERM ECONOMIC AND SOCIAL BENEFITS TO THE NATION FROM LIVING MARINE RESOURCES. (THE SCOPE

CENTERS ON INFORMATION ABOUT HOW THE RESOURCES ARE USED AND ITS INTEGRATION

WITH INFORMATION ABOUT THE RESOURCES ADDRESSED IN GOAL 1.) 

Objective 3.1: For each fishery management plan, collect the complete suite of economic 

data for commercial harvesters (variable cost, annual operating cost, and revenue) and recreational anglers (expenditures on fishing boat, tackle, and other trip-related expenses). 

Objective 3.2: For each coastal state and territory, collect economic and sociocultural data 

needed for analyzing and understanding fishing, fishing-related industries, and fishing 

communities. 

Objective 3.3: Establish an inventory of non-market values for protected species, essential 

fish habitats, and ecosystems. 

Objective 3.4: Determine the costs and benefits as well as the economic and sociocultural 

impacts to fishery participants, shoreside firms, and fishing communities from proposed 

management options prior to the management decision. 

Objective 3.5: Collect data and develop integrated bioeconomic models to assess the net 

benefits to the Nation derived from living marine resources accruing to those actively en-
42

gaging in fishing-related activities, e.g., commercial harvesters, recreational users, fishing 

communities, and seafood consumers. 

Objective 3.6: Assist the Councils in reviewing optimum yield (OY) levels for consistency 

with economic theory and with the revised definition in the Sustainable Fisheries Act. 

Objective 3.7: Evaluate the impacts of climate change on biological, social, and economic 

conditions in fishing communities and commercial and recreational sectors. 

GOAL 4—PROVIDE SCIENTIFIC INFORMATION AND ASSESSMENTS TO GUIDE THE DEVELOPMENT

OF A SUSTAINABLE AND ENVIRONMENTALLY SOUND MARINE AQUACULTURE, INCLUDING RESEARCH ON ENVIRONMENTAL IMPACTS, SOCIAL AND ECONOMIC IMPACTS, AND TECHNOLOGIES

TO IMPROVE MARINE AQUACULTURE OPERATIONS.

Objective 4.1: Monitor and assess potential impacts from escapes from marine aquaculture facilities, including impacts on the genetics of wild stocks and competition from escapees.

Objective 4.2: Monitor and assess potential impacts from disease and parasite transmission 

to wild stocks.

Objective 4.3: Monitor and assess potential impacts to water quality and benthic habitats.

Objective 4.4: Provide research into developing alternative feeds for aquaculture operations 

(e.g., from plant-based proteins) to reduce reliance on fish meal and fish oil.

Objective 4.5: Study new candidate species for culture through their complete life cycle 

to determine which are economically and biologically suitable for commercial culture or 

wild stock enhancement.

Objective 4.6: Work with the aquaculture industry to develop, identify, evaluate, and transfer 

technologies that are appropriate to both economically efficient aquaculture production 

and environmental protection and sustainability.

Objective 4.7: Conduct research to evaluate local and regional economic and social impacts 

that may be expected by the introduction or expansion of marine aquaculture.

GOAL 5—IMPROVE THE FISHERY INFORMATION SYSTEM.

Objective 5.1: Integrate and link existing regional and national fisheries information systems 

so that fisheries data and statistics are readily available at a regional or national level in a 

form that is easily utilized by fisheries managers, stock assessment scientists, other stakeholders, and the general public. Make all information accessible through a single regional 

or national web-enabled information portal. 

Objective 5.2: Utilize a standard FIS web-enabled system (InPort) to compile and provide 

a metadata catalog of all critical fisheries data holdings.
Objective 5.3: Establish regional and national standards for information collection, management, and dissemination to ensure high quality, completeness, timeliness and accessibility. Implement improvements in quality control and assurance procedures for existing 

fisheries information collection, processing, and management activities as needed to assure 

the quality of fisheries information needed to support stock assessments, as well as timely 

monitoring of FMP compliance and related fishing quotas.

Objective 5.4: Develop a unique key or identifier that can be used to link permits and fishing 

performance data for individual owners, vessels, dealers, and/or anglers for the purpose of 

effective tracking of individuals and their performance histories.

Objective 5.5: Determine minimum fisheries information needs, perform gap analyses of 

current data collection programs, and assure collection of information needed to fulfill 

the stewardship responsibilities of NOAA, the Fishery Management Councils, interstate 

fisheries commissions, and states.

Objective 5.6: Develop electronic transaction systems to support “one-stop shopping” for 

fishery permits and to facilitate the processing and sharing of permits information within 

and among regions as needed.

Objective 5.7: Develop electronic systems for the collection, reporting, processing, and 

sharing of fisheries performance information for all major fisheries. 

Objective 5.8: Coordinate development of the fisheries information system with the developing Integrated Ocean Observing System. 

GOAL 6—IMPROVE THE EFFECTIVENESS OF EXTERNAL PARTNERSHIPS WITH FISHERS, MANAGERS, SCIENTISTS, CONSERVATIONISTS, AND OTHER INTERESTED GROUPS

Objective 6.1: Promote a cooperative network of partners in the coordination of fisheries 

research. 

Objective 6.2: Develop infrastructure for long-term, continuous working relationships with 

partners to address fisheries research issues. 

Objective 6.3: Sponsor symposia and conferences for partners to exchange information and 

identify major fisheries research initiatives. 

Objective 6.4: Solicit partners’ views on fisheries research needs. 

All Federal agencies operate in an environment of increasing demands competing for 

limited resources. To meet this challenge, NMFS is collaborating with other NOAA line 

offices and their programs (e.g., Sea Grant, National Undersea Research Program, Center 

for Sponsored Coastal Ocean Research); other Federal, state and local agencies; universities; Native American tribes; Pacific Islanders; the commercial and recreational fishing 

industries; environmental groups; and international organizations. NMFS is committed 

to strengthening existing relationships and building new ones. 
44

Strategic planning usually includes the use of timetables for performance of the various 

activities associated with each goal. Fisheries research has been developing for well over a 

century. Initially, it was mostly studies of fundamental life history and exploratory fishing. Routine surveys accelerated with the advent of international conservation treaties and 

became nationwide with the passage of the MSFCMA. Much of the research is operational 

in nature and will continue into the future. Issues are ever-changing, as natural and humaninduced changes to ecosystems modify species distributions and abundance, unforeseen 

ecological relationships become suspected or known, marketplace preferences change, and 

harvesting technology evolves. For example, stock assessment surveys, the analysis of the 

obtained data, and the projections of future abundance, are done according to a schedule 

(when there is sufficient funding). Other parts of this plan involve improvements to the 

science or the provision of new facilities.

Several lines of NMFS research have gained importance in recent years, reflecting 

increased levels of interest in developing management areas. One example is marine 

aquaculture. The United States has a long history in marine aquaculture, but domestic 

production has lagged behind as foreign production has substantially increased, resulting 

in a large and growing seafood trade deficit. There is growing recognition that the U.S. 

needs to increase marine aquaculture production, particularly offshore,2

 and more research 

needs to be targeted toward supporting a sustainable and productive domestic industry 

(e.g., research on new feeds, cage designs, and genetic and disease issues). NMFS is working with industry to increase the level of research required to support domestic marine 

aquaculture. Another developing line of research involves the relatively new paradigm of 

Ecosystem Area Management. In this research, all areas of an ecosystem are considered, 

from climate variability, to predator-prey relationships and changes, and multiple uses of 

the habitat areas and the resources.

2

In July 2006, the Marine Fisheries Advisory Committee unanimously approved the draft 10-Year Plan for 

the NOAA Aquaculture Program; recent statements from President Bush and Commerce Secretary Gutierrez 

strongly endorse using marine aquaculture, and offshore aquaculture in particular, to provide economic opportunities and augment commercial fishing operations.
NMFS FISHERIES 

SCIENCE CENTERS 

NMFS is a world leader in fisheries research. Each year the agency uses harvest and 

survey data to assess the status and trends of more than 200 major commercially valuable 

fish and shellfish stocks. The NMFS Science Centers provide annual stock assessment 

information and management advice to support the NOAA stewardship mission for the 

living marine resources in their regions. Increasingly, as more data and more sophisticated 

models are developed, the information and advice become better able to support ecosystembased resource management. These cross-disciplinary efforts are undertaken in cooperation 

with other Federal and state agencies, international organizations, the fishing industry, and 

academia, and are based on long-standing cooperative research agreements. In addition to 

these basic responsibilities, each regional Science Center has unique capabilities to focus 

on special research needs. The following is an overview of each of the NMFS Science 

Centers.
46

ALASKA FISHERIES SCIENCE CENTER

The Alaska Fisheries Science Center (AFSC) has research facilities in Alaska (Auke 

"AY+ODIAK)SLAND!NCHORAGEAND$UTCH(ARBOR	7ASHINGTON3EATTLE	AND/REGON

(Newport). Beginning in 2006, the Ted Stevens Marine Research Institute becomes the 

AFSC’s new home for much of the current Auke Bay Laboratory operations. Organizationally, the AFSC consists of the Resource Assessment and Conservation Engineering 

Division (RACE), the Resource Ecology and Fisheries Management Division (REFM), 

the National Marine Mammal Laboratory (NMML), the Auke Bay Laboratory, Fisheries 

Monitoring and Analysis Division, and other administrative units. The major shipboard 

platforms supporting the AFSC include the NOAA fishery survey vessels Oscar Dyson,

Miller Freeman (built in 1967), and John N. Cobb (built in 1950), as well as chartered vessels from the fishing industry. The new fishery survey vessel, the NOAA Ship Oscar Dyson,

WASCOMMISSIONEDIN-AYATHERHOMEPORTOF+ODIAK4HE!&3#HASNUMEROUS

on-going relationships with external cooperators, including state and other Federal agencies, academic institutions, foreign research institutions, the fishing industry, and resource 

conservation organizations.

The AFSC has a permanent staff of about 365 employees in support of fisheries and marine 

mammal research in the coastal and offshore waters of Alaska. This marine region of nearly 

3 million square miles includes over 50 percent of the U.S. coastline and over 70 percent 

of the U.S. continental shelf. The region supports some of the most important commercial 

fisheries in the world, particularly groundfish and Pacific salmon species, and is a popular 

destination for recreational fishing. It also hosts some of the world’s largest populations of 

marine mammals and seabirds.

A survey from a small boat in 

an icy fjord in Alaska. Photo: 

NOAA.
The AFSC focuses research on the following fishery resources that support major commercial fisheries off Alaska:

s 'ROUNDlSHINTHE"ERING3EA
!LEUTIAN)SLANDS"3!)	REGIONINCLUDINGSEPARATECATCH

quotas for 14 individual species or stocks and four species complexes. These management complexes include shortraker/rougheye rockfish, other flatfish (15 species), other 

rockfish (eight species, including thornyheads), and squid. 

s 'ROUNDlSHINTHE'ULFOF!LASKA'/!	REGIONINCLUDINGSEPARATECATCHQUOTASFOR

individual species or stocks and five species complexes. The management complexes 

include deep water flatfish, shallow water flatfish, other slope rockfish, pelagic shelf 

rockfish, and demersal shelf rockfish. 

s 4HEREMAININGGROUNDlSHSPECIESAREMANAGEDASSEPARATEhOTHERSPECIESvGROUPSINTHE

BSAI and GOA regions. These management groups include species of sculpin, skate, 

shark, and octopus. Eight species of skate, over 50 species of sculpins, three species 

of sharks, and four species of octopus are occasionally caught in groundfish fisheries. 

Commercial and scientific interest in these species continues to grow, while research 

efforts are under way to improve our knowledge of their life history, abundance, and 

interactions with commercial fisheries.

s 4HESHELLlSHSPECIESINCLUDEKINGTANNERSNOWANDHYBRIDCRABSSEVERALSPECIESOF

shrimps; and sea snails.

s 4HElVEMAJOR0ACIlCSALMONSPECIES#HINOOKCHUMSOCKEYEPINKANDCOHO	AND

steelhead have supported strong traditional salmon fisheries along the entire Alaskan 

coastline.

In addition to research on fishery resources, the AFSC is continuing to develop studies 

that will help predict how marine resources respond to climate change, the nature and 

location of habitat resources required by commercially valuable fish species, and habitat 

interactions between fish and marine mammals. Direct research on marine mammals 

includes stock assessments for most marine mammal species of Alaska, as required by 

the Marine Mammal Protection Act (MMPA) and for those species also listed under the 

Endangered Species Act (ESA). This information, in turn, is used to assess anthropogenic 

impacts, including direct (e.g., incidental take) and indirect effects (e.g., competition) of 

fisheries on those populations.

The Fisheries Monitoring and Analysis Division monitors groundfish fishing activities 

in the U.S. EEZ off Alaska and conducts research associated with sampling commercial 

fishery catches, estimation of catch and bycatch mortality, and other aspects of fishery-dependent data. The Division is responsible for training, briefing, debriefing, and oversight 

of observers who collect catch data onboard fishing vessels and at onshore processing plants 

and for quality control/quality assurance of the data provided by these observers. Division 

staff process data and make it available to the Sustainable Fisheries Division of the Alaska 

Regional Office for quota monitoring and to scientists in other AFSC divisions for stock 

assessment, ecosystem investigations, and a broad range of research investigations. 

The AFSC also conducts research on habitat use by FMP-managed fish and invertebrates, 

alterations in habitat quality through human and environmental change, and an understanding of threats to habitat in Alaska. Studies involve diverse fish habitats that range from 

eelgrass beds to benthic substrates, and wetlands to coral and sponge communities which 
48

serve as refugia, forage grounds, or nursery 

areas for managed species. Perturbations 

include fishing, oil transportation, logging, 

and development, plus natural effects on fish 

habitat such as climate, prey distribution, and 

nutritional quality.

The National Marine Mammal Laboratory (NMML) is responsible for conducting 

research on all marine mammals of the coast 

of Alaska, and pinnipeds occurring in Washington, Oregon, and California. Information 

is provided to various U.S. governmental and 

international organizations to assist in developing rational and appropriate management 

regimes for marine resources under NOAA’s 

jurisdiction. Research programs are carried 

out cooperatively with other Federal, state, 

and private sector agencies. Priorities over the next several years include:

s !SSESSINGABUNDANCEDISTRIBUTIONANDSTOCKSTRUCTUREANDESTIMATINGDIRECTANDINdirect anthropogenic impacts on all marine mammal stocks off the coasts of Alaska, 

Washington, Oregon, and California.

s #OLLECTINGINFORMATIONONTHEFOURSPECIESOFICESEALSWHICHAREVERYLIKELYTOBEHIGHLY

sensitive to projected decreases in sea ice in the Arctic.

s )NVESTIGATINGTHECAUSESOFTHEDECLINEOFPINNIPEDSINTHE"ERING3EAANDOFTHE#OOK

Inlet beluga whale stock.

s $ETERMININGTHEABUNDANCEDISTRIBUTIONANDHABITATREQUIREMENTSOF.ORTH0ACIlC

right whales in the Bering Sea and Gulf of Alaska.

RECENT ACCOMPLISHMENTS AND

RESEARCH PRIORITIES FOR FY 2007–2012

I. Research to Support Fishery Conservation and Management

Recent Accomplishments:

s -AJORRESEARCHCRUISESCONDUCTEDBYTHE!&3#INCLUDED

– The annual winter fishery acoustic surveys aboard the NOAA Ship Miller Freeman to 

estimate the biomass and distribution of pollock in the Shumagin Islands and Sanak 

Trough region of the western Gulf of Alaska, southeastern Bering Sea (including the 

"OGOSLOF)SLANDAREA	3HELIKOF3TRAITSANDALONGTHEEASTERNSIDEOF+ODIAK)SLAND

– A summer longline charter vessel survey to assess the distribution and abundance of 

sablefish, rockfish, and other commercially important groundfish resources in the 

Gulf of Alaska.

– A biennial summer bottom trawl survey in 2005 of the Gulf of Alaska shelf and continental slope groundfish, with three chartered fishing vessels, to estimate the biomass 

and distribution of groundfish and to collect other biological data.

A sculpin that was collected 

by trawl during a survey. 

Photo: NMFS.
– A biennial bottom trawl survey in 2006 of Aleutian Islands groundfish.

– A summer fishery acoustic survey aboard the NOAA Ship Oscar Dyson of the western 

and central Gulf of Alaska to further determine the feasibility of conducting a biennial summer Gulf of Alaska survey to estimate the distribution and abundance of 

pollock off bottom over the shelf.

– A biennial summer acoustic survey of eastern Bering Sea pollock in 2006.

– An annual summer bottom trawl survey of eastern Bering Sea shelf, with two chartered fishing vessels, to estimate distribution and abundance of crab and groundfish 

stocks.

– Support to the Alaska Department of Fish and Game to continue the annual bottom 

trawl survey for shrimp in Pavlof Bay.

– Spring, summer, and fall surface trawl surveys by the NOAA Ship John N. Cobb to 

determine abundance, migration patterns, ecology, bioenergetics, and carrying capacity for juvenile salmon in Southeast Alaska waters.

– Fall surface trawl surveys of the eastern Bering Sea shelf and basin with chartered 

vessels to determine distribution, relative biomass, habitat, and ecology of western 

Alaskan salmonids.

s 4HE!&3#S&ISHERIES-ONITORINGAND!NALYSIS$IVISIONRUNSANOBSERVERPROGRAMTO

collect information from the federally regulated fisheries of Alaska. The observer program collected valuable data on the target fishery resource for the purpose of stock 

assessment and fishery management. In addition, the observer program provided the 

information used to estimate the levels of direct, incidental takes of all protected species 

in Alaska’s federally regulated fisheries, including seabirds, prohibited species of fish, 

and marine mammals. The scope of this program is extensive. For example, in 2005, 

366 individual observers collected over 35,000 data collection days from 304 vessels 

and 24 shoreplants. 

s 4HE!&3#HADTHELEADRESPONSIBILITYFORANALYZINGTHEPOPULATIONDYNAMICSANDSTATUS

of most of the groundfish species managed by FMPs in the Bering Sea-Aleutians and 

the Gulf of Alaska regions. For effective management, hypotheses on different complex 

population dynamics (including environmental and inter-species interactions) are being 

tested relative to current harvest guidelines. For example, management strategy evaluations are currently being conducted for Gulf of Alaska Pollock. Extensive data analyses 

from observer data are continuing. Specifically, for the eastern Bering Sea Pollock fishery the salmon bycatch levels have increased in recent years. Studies on causes for these 

increased levels are under way and advice revisions to the FMP have been provided.

s 4HE!&3#S2ECRUITMENT0ROCESSES0ROGRAMINCOOPERATIONWITHTHE0ACIlC-ARINE

Environmental Laboratory (PMEL), conducted a number of research cruises to support 

studies of environmental and biological factors affecting the spatial distribution and 

relative abundance of larval and juvenile pollock in the Gulf of Alaska and the Bering 

Sea, particularly with respect to their role in the ecosystem and importance as prey for 

Steller sea lions. These studies were supported by the Steller sea lion research program, 

the North Pacific Research Board, and appropriated funding for the North Pacific Climate Regime and Ecosystem Productivity studies. 

s 4HE!&3#CONDUCTEDSTUDIESONSALMONOCEANECOLOGYSPECIESLIFEHISTORIESANDHIStorical data patterns to increase our understanding of how marine and anadromous 

species are affected by natural and human activities.

s 4HE !&3# IN COOPERATION WITH THE .ORTH 0ACIlC !NADROMOUS &ISH #OMMISSION
50

(NPAFC), will continue its role in the Bering Aleutian Salmon International Survey 

(BASIS), an international research program encompassing the entire Bering Sea epipelagic ecosystem, to understand the mechanisms underlying the effects of climate 

change, environmental variation, and density-dependence on salmon carrying capacity 

in the Bering Sea for sustainable conservation of salmon stocks.

s !FTERTHEDISCOVERYOFDENSEAGGREGATIONSOFDEEPWATERCORALSANDSPONGEINTHE

Aleutian Islands, AFSC scientists conducted further mapping and Remotely Operated 

Vehicle (ROV) and submarine work in 2003 and 2004. Data are currently being processed to better understand coral and sponge distributions and biology.

s )NTHE!&3#CONDUCTEDA
DAYSURVEYINTHE"ERING3EAWITHUNIVERSITYPARTNERS

to develop methods for assessing forage species. Methods included adaptive sampling 

with midwater trawls, acoustics, LIDAR, as well as nearshore sampling and assessment 

of energy content.

s #OOPERATING WITH THE )NTERNATIONAL 0ACIlC (ALIBUT #OMMISSION AND INDUSTRY THE

AFSC expanded the collection of sablefish logbook data and included them within the 

annual sablefish stock assessment.

s 4HE!&3#ADDEDSEVERALNEWAGE
STRUCTUREDSTOCKASSESSMENTSINCLUDINGROUGHEYEAND

dusky rockfish, raising these assessments to Tier III.

s 4HE!&3#CONTINUESRESTORATIONSTUDIESSTEMMINGFROMTHEExxon Valdez oil spill in 

Prince William Sound, particularly those relating to the abundance and biological 

availability of lingering oil. 

s 4HE!&3#HASCONDUCTEDSYNTHESISSTUDIESONTHEEFFECTSOFTHEExxon Valdez oil spill, 

either from the initial impacts or lingering oil, on various species ranging from marine 

mammals to herring (long-term population depressed state).

s !&3#SCIENTISTSINCOOPERATIONWITHTHE3TATEOF!LASKAANDOTHERSPARTICIPATEDIN

technical fora under auspices for implementation of the Pacific Salmon Treaty to help 

sustain fisheries among healthy stocks while rebuilding weaker stocks within jurisdictional regions of the treaty. 

s 4HE!&3#INCOLLABORATIONWITHTHE"ERING3EA&ISHERIES2ESEARCH&OUNDATIONCONducted a number of studies in 2004–2006. The collaborative efforts included expansion of the standard eastern Bering Sea annual survey effort to the north to examine 

abundance of snow crab in the northern areas of the Bering Sea and, in 2005, included 

a pilot survey of Bristol Bay red king crab using an alternative trawl and survey station 

design. Cooperative research was conducted with a number of segments of the Alaska 

fishing industry to reduce the bycatch of salmon and halibut in trawl fisheries. The 

research focused on the development of fishing gear modifications and modification of 

fishing practices to reduce bycatch. 

s !&3#SCIENTISTSHAVEMADETHEDATAPROVIDEDBYTHEATLASOFICHTHYOPLANKTONABUNdance and distribution patterns in the northeast Pacific Ocean and the Bering Sea 

ecosystems available to the public through the web. The Ichthyoplankton Information 

System (IIS) provides data on the early life history of fishes from the northeast Pacific 

Ocean and Bering Sea to identify unknown fish eggs and larvae by using known data 

such as meristics, distribution, and illustrations of developmental stages or as a source 

of original data on the early life history stages of fishes of the Northeast Pacific Ocean 

and Bering Sea. 
s 4HE.--,CONDUCTEDRESEARCHTODETERMINETHESTATUSCONSERVATIONNEEDSANDPOtential impacts of fishing activities on marine mammals of Alaska. Based on data collected by the AFSC’s observer program, federally regulated fisheries are not considered 

to have a direct, incidental take level of marine mammals high enough to warrant 

management action. However, indirect interactions between some commercial fisheries and some species of marine mammals (e.g., Steller sea lions and northern fur seals) 

may potentially occur. Research to resolve whether and to what extent these interactions occur has included surveys of marine mammal forage fish and the collection of 

detailed foraging information. The NMML worked closely with the Alaska Scientific 

Review Group (ASRG) to determine the status of marine mammal stocks in Alaska. 

The ASRG includes representatives from Alaskan universities, the Alaska Native community, and the commercial fishing industry.

s 4HE !&3#S !UKE "AY ,ABORATORY COMPLETED RADIO
TAGGING STUDIES ON 9UKON 2IVER

Chinook and fall chum salmon that documented spawning location, migration rates, 

and estimated numbers crossing the border into Canada. Genetic baseline information 

on salmonids was assembled to identify stocks or country of origin. AFSC scientists 

are key partners in Coastal Fish Habitat Restoration design, application of new aquatic 

habitat restoration technologies, and in developing the database needed to test the effectiveness of those restoration designs.

Research Priorities, FY 2007–2012:

I.A. Biological research concerning the 

abundance and life history of fish stocks

The following surveys are planned by the AFSC:

s #ONDUCTANANNUALSUMMERBOTTOMTRAWLSURVEYONGROUNDlSHANDCRABSINTHEEASTERN

Bering Sea shelf with chartered fishing vessels.

s #ONDUCTSUMMERMIDWATERTRAWL
ACOUSTICSURVEYSTOASSESSTHEOFF
BOTTOMCOMPONENT

of pollock stock in the Bering Sea every 2 years (2008, 2010, 2012) and the Gulf of 

Alaska (2007, 2009) from the NOAA Ship Miller Freeman and the new NOAA Ship 

Oscar Dyson.

s 2EINSTATETHEBIENNIALEASTERN"ERING3EASLOPESURVEYFORGROUNDlSH	

with a chartered fishing vessel that was discontinued in 2006 due to lack of funding.

s #ONDUCTTHEANNUALWINTERSURVEYSONSPAWNINGPOLLOCKSTOCKSINTHESOUTHEASTERN"ERing Sea, Bogoslof Island area (biennial schedule), Shumagin Islands, Shelikof Straits, 

ANDALONGTHEEASTSIDEOF+ODIAK)SLANDUSINGTHE./!!3HIPMiller Freeman and/or 

the new NOAA Ship Oscar Dyson.

s #ONDUCTTHEBIENNIALSUMMERBOTTOMTRAWLSURVEYONGROUNDlSHINTHE'ULFOF!LASKA

with chartered fishing vessels every 2 years (2007, 2009, 2011).

s #ONDUCTTHEBIENNIALSUMMERBOTTOMTRAWLSURVEYONGROUNDlSHINTHE!LEUTIAN)SLANDS

region with chartered fishing vessels every 2 years (2008, 2010, 2012).

s #ONDUCTANNUALSUMMERLONGLINESURVEYSONSABLElSHANDOTHERlSHERYRESOURCESIN

the Gulf of Alaska by a chartered vessel and in the Bering Sea and Aleutian Islands on 

alternate years. 
52

s #ONDUCTANNUAL2ECRUITMENT0ROCESSES&/#)	RESEARCHCRUISESFORLARVALPOLLOCKPLANKton productivity and ecosystem status, and juvenile pollock ecology from the NOAA 

Ship Miller Freeman and/or the new NOAA Ship Oscar Dyson and chartered UNLOS 

(University-National Oceanographic Laboratory System) vessels.

s #ONDUCTSEASONALACOUSTICANDBIOLOGICALSAMPLINGOFPRE
SPAWNINGEULACHONINSOUTHEAST

Alaska and observe associated Steller sea lion feeding aggregations. 

s 3URVEYSOFSEASONALTEMPORALANDHABITATRELATEDVARIATIONINNUTRITIONALQUALITYOFPREY

consumed by Steller sea lions and other apex predators.

s #OMPLETETHREEESTUARINESURVEYSINSOUTHEAST!LASKATODELINEATEHABITATSANDlSHASsociations.

s #ONDUCTANNUALFALLSURFACETRAWLSURVEYS"!3)3	ON0ACIlCSALMONECOLOGYANDASSOCIated marine fish species (e.g., age-0 pollock) in the Bering Sea using the NOAA research 

vessel Oscar Dyson and chartered fishing vessels (2007–2012).

s #ONDUCTANNUALSUMMERSURFACETRAWLSURVEYSON0ACIlCSALMONINTHE'ULFOF!LASKA

using a chartered fishing vessel (2007–2012). 

s #ONDUCTANNUAL3OUTHEAST#OASTAL-ONITORING3%#-	SURFACETRAWLCRUISESWITHTHE

NOAA research vessel John N. Cobb to study the habitat use and early marine ecology 

of juvenile Pacific salmon. 

In addition to the above traditional baseline surveys, the AFSC has a Fishery Interaction 

Team that develops and implements surveys to study the interactions among the component 

species of the ecosystem, the environment, and fisheries. The research includes: 

An adult male Steller sea lion 

on a rocky shoreline. Photo: 

NMFS. 
s 4AGRELEASEANDRECOVERYCRUISEFOR!TKAMACKERELINTHE!LEUTIAN)SLANDSTOASSESSTHE

impact of commercial fishing on the local distribution and abundance of Atka mackerel 

inside and outside Steller sea lion critical habitat. 

s -APTHEDISTRIBUTIONANDSIZEOF0OLLOCKAGGREGATIONSINTHE!LEUTIAN)SLANDSWITHACOUSTIC

data collected on commercial vessels.

s $EVELOPASTATISTICALMODELFORESTIMATING0ACIlCCODMOVEMENTRATESFROMTAGGING

data.

s 6ERIFYVISUALKEYSOF0ACIlCCODMATURITYSTAGESWITHHISTOLOGICALDATAANDCALIBRATEGROSS

maturity data collected by observers.

s %XAMINESPATIALANDTEMPORALPATTERNSIN0ACIlCCODREPRODUCTION

s 2ELATELARGE
SCALEPATTERNSIN!TKAMACKERELFOODHABITSTOGROWTHANDUSEFOODHABITS

data to assess small-scale habitat utilization.

The AFSC is conducting research cruises in 2006 and 2007 to inter-calibrate the scientific acoustic survey systems between the NOAA Ship Miller Freeman and the new NOAA 

Ship Oscar Dyson 1) to ensure the standardization of the surveys over time series; 2) to 

estimate the selectivity and catchability of standard mid-water and bottom trawl survey 

nets; 3) to conduct experiments with trawling procedures in order to confirm or revise 

AFSC trawl survey standards relative to ensuring that the national trawl protocols are met; 

and 4) to continue research on essential fish habitat determination and to measure the 

effects of fishing on it. The inter-calibration work may need to be continued beyond 2007 

depending on the results of research completed in 2006 and 2007. During all standard 

surveys, biological specimens of fish and invertebrates will be collected to identify new 

species, estimate biological rates, and study prey-predator relationships and genetic stock 

structure.

Each year, observers will be deployed on commercial fishing vessels and at shoreside 

processing plants to meet the following coverage requirements (as specified in the groundfish 

FMPs for the Gulf of Alaska and Bering Sea/Aleutian Islands regions):

s PERCENTOBSERVERCOVERAGEOFlSHINGANDPROCESSINGVESSELSLONGERTHANFEET

s PERCENTOBSERVERCOVERAGEOFMOSTlSHSHORESIDEPROCESSINGPLANTS

s PERCENTOBSERVERCOVERAGEOFlSHINGVESSELSnFEETLONG

s PERCENTOBSERVERCOVERAGEWITHMULTIPLEOBSERVERS	OFSPECIALCATEGORYVESSELSTHAT

engage in community development quota (CDQ) and American Fisheries Act (AFA) 

fishing operations.

The AFSC will assess trends in Alaskan salmon populations and the environment 

through: 

s /PERATIONOFATWO
WAYlSHWEIRTORELATECLIMATICCHANGESWITHLONG
TERMVARIABILITYIN

freshwater and marine survivals for seven anadromous salmonids.

s 2ETROSPECTIVEANALYSESANDMONITORINGPROGRAMSFOCUSINGONTHECOVARIANCEBETWEEN

climate, ocean conditions, and Alaskan salmon populations at various time and spatial 

scales. 
54

s 0ROCESS
ORIENTEDSTUDIESONINTER
ANNUALVARIATIONSINMARINECARRYINGCAPACITYANDBIOenergetics of juvenile salmon, including trophic interactions with predators and competitors.

s #OOPERATIVEOPERATIONOFTHE&ISH%NERGETICS$IETSAND:OOPLANKTON&%$:	,ABOratory to analyze, maintain, and correlate biophysical databases for food habits, zooplankton prey densities and composition, condition assessed as energy density, and associated oceanographic data.

s $ETERMINATIONOFTHESTOCKORIGINOFTHESALMONBYCATCHINTHE"ERING3EAGROUNDlSH

fishery using new DNA-based genetic methods.

s 5SEOFTHENEW$.!
BASEDGENETICMETHODSTODETERMINETHENUMBERSOF#ANADIAN


origin sockeye salmon harvested in the southeast Alaska fishery.

The AFSC will assess the status of Alaskan groundfish and Bering Sea crab stocks and 

document their management requirements in annual Stock Assessment and Fishery Evaluation (SAFE) documents. The SAFE documents will define estimates of stock biological 

production potential (Maximum Sustainable Yield (MSY) or proxy thereof), recommend 

levels of acceptable biological catch (ABC), overfishing levels, bycatch requirements, and 

other harvest control rules for the setting of fishery regulations. The stocks covered are:

s !LL"ERING3EA
!LEUTIAN)SLANDSGROUNDlSHSTOCKSORSTOCKCOMPLEXESINCLUDING%"3

pollock, AI pollock, Bogoslof pollock, Pacific cod, yellowfin sole, rock sole, arrowtooth 

flounder, flathead sole, Greenland turbot, Alaska plaice, other flatfish, Pacific ocean 

perch, other rockfish, other red rockfish (including shortraker, rougheye, and northern 

rockfish), Atka mackerel, and sablefish. 

s !LL '/! GROUNDlSH STOCKS OR STOCK COMPLEXES INCLUDING WESTERN CENTRAL POLLOCK

southeast pollock, Pacific cod, arrowtooth flounder, flathead sole, other flatfish (including rex sole, deepwater flatfish, and shallow water flatfish), Pacific ocean perch, 

northern rockfish, other slope rockfish (including shortraker, rougheye rockfish), pelagic shelf rockfish, Atka mackerel, and sablefish. The Alaska Department of Fish and 

Game will assess the demersal shelf rockfish complex. 

s 4HE!&3#WILLWORKCOOPERATIVELYWITHTHE!LASKA$EPARTMENTOF&ISHAND'AMETO

assess the status of king, Tanner, and snow (opilio) crab stocks in the eastern Bering Sea. 

s #ONCERNSFOR3TELLERSEALIONRECOVERYCONTINUES)NADDITIONTODIRECTMONITORINGOF

populations, fishery and ecosystem interaction research continues. 

s &ISHBONESWILLBEUSEDTORECONSTRUCT3TELLERSEALIONDIETSANDIDENTIFYSEASONALCHANGES

in their principal sources of energy by combining diet data with seasonally adjusted 

energetic equivalents.

s &ORAGElSHSPECIESCOLLECTEDSEASONALLYINSOUTHEAST!LASKAWILLBECOMPAREDWITHTHOSE

FROM+ODIAKTHE!LEUTIAN)SLANDSAND"ERING3EATOUNDERSTANDBASIN
WIDEPROCESSES

that affect their nutritional value. 

s 2ESULTSOFTHECOMPARATIVESURVEYSOFFORAGElSHABUNDANCEANDDISTRIBUTIONOFF+ODIAK

Island and Southeast Alaska will be analyzed.

I.B. Interdependence of fisheries or stocks of fish

s #OLLECTANDANALYZESTOMACHCONTENTSOFGROUNDlSHTODETERMINEECOLOGICALLINKAGES

between species.
s $EVELOPANDMAINTAINMULTISPECIESANDECOSYSTEMMODELSTHATQUANTIFYPREDATOR
PREY

interactions between species. Models will be developed into a predictive framework for 

management policy, climate, and cumulative effects analysis and used in ecosystemlevel projections presented in the Ecosystem Assessment section of the annual SAFE 

report. Analysis will include indices of foraging habitat for key groundfish as it changes 

with time, space, and season, and indices of forage fish abundance for augmentation of 

assessments.

s %MPIRICALLYDERIVEBIOENERGETICMODELSDESCRIBINGTHELIFEHISTORIESOFFORAGElSHSPECIES

to better understand energetic limitations on their survival and reproduction. 

s #OLLECTBIOLOGICALSPECIMENSOFPRE
SPAWNINGEULACHONTHROUGHOUTITSRANGEFOR$.!


based genetic marker.

s !NALYZESURVEYANDOBSERVERDATATODETERMINESPATIALDISTRIBUTIONSOFDIFFERENTSPECIES

clusters that would indicate separation or interdependence of stocks.

s $EVELOP$.!
BASEDGENETICBASELINEINFORMATIONONSALMONIDSTOIDENTIFYSTOCKSOR

area of origin.

s $EVELOP$.!
BASEDGENETICBASELINEDATAFORSELECTEDSPECIESOFGROUNDlSHANDFORAGE

fish to establish stock structure and stock boundaries.

s #ONTINUETHEDEVELOPMENTOFANEWMOVEMENTMODELFOR!LASKASABLElSHBASEDONTIME

series of tag returns. 

s $ETERMINE INCIDENCE OF CODED
WIRE TAGGED SALMONIDS IN COMMERCIAL AND RESEARCH

catches in the North Pacific Ocean and Bering Sea and report annually to Pacific States 

Marine Fish Commission and North Pacific Anadromous Fish Commission. 

s %VALUATETHEIMPORTANCEOFRESIDENTRAINBOWTROUTFORUSEINPROTECTEDSPECIESRECOVERY

programs for a large number of ESA-listed salmonids. 

s $ETERMINEGENETICDOMESTICATIONANDBEHAVIORALEFFECTSFROMMULTIPLEGENERATIONSOF

hatchery culture in two stocks of Chinook salmon compared with their pristine founder 

populations. 

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

s #ONDUCTSTUDIESONTHEIMPACTSOFLOGGINGURBANIZATIONANDMININGONCOASTALHABItats; information will provide a basis for mitigation or restoration strategies

s #ONDUCT RESTORATION STUDIES RELATED TO THE %XXON 6ALDEZ OIL SPILL IN 0RINCE 7ILLIAM

Sound. Studies will focus on long-term persistence and long-term effects.

s #ONDUCTBOTTOMTYPINGANDMAPPINGSURVEYSUSINGACOUSTICTECHNIQUESSIDESCANSOnar and multibeam) to characterize and identify bottom type and map the habitats of 

the continental shelf and slope off Alaska.

s #ONDUCTPILOTMAPPINGOFlSHINGGROUNDSANDESSENTIALlSHHABITATASSOCIATEDWITH

those grounds; describe benthic habitats, community structure of the habitats, and the 

basic life histories of corals, sponges, and other benthic invertebrates. 

s %XPANDGEOSPATIALHABITATDATAFORTHE!LASKACOASTLINETHROUGHCONTINUED3HORE:ONE

videography, habitat classification, and ground-truthing.

s %STABLISHEELGRASSMONITORINGSITESINVARIOUSPARTSOFCOASTAL!LASKATOTRACKLONG
TERM
56

and large-scale changes in fish communities and habitat that may result from shoreline 

development or global climate change. 

s 5SE lSH BIOENERGETICS AND BIOCHEMICAL INDICATORS OF GROWTH TO DEVELOP METRICS FOR

quantifying fish habitat quality; emphasis will be on seasonal changes, particularly on 

habitats that support critical life stage bottlenecks for survival and growth. 

s $EVELOPMODELSDESCRIBINGBASICMETABOLICREQUIREMENTSOFFORAGElSHTOCOMBINEWITH

empirical observations of energy allocation to understand how climate change will affect forage fish distributions. 

s -APSEASONALANDTEMPORALSHIFTSINTHEUSEOFKELPANDEELGRASSHABITATBYNEARSHORE

fish assemblages in Southeast Alaska.

s %XPANDMODELSOFlSHINGIMPACTSANDIMPROVEINPUTSUCHASGROWTHREPRODUCTIONAND

recovery rates of sessile invertebrates.

I.D. Impact of anthropogenic factors and 

environmental changes on fish populations 

s )NVESTIGATETHEROLEOFPATHOGENSANDPARASITESINVITALITYOFMARINElSHANDSHELLlSH

populations and as biomarkers of anthropogenic and environmental change on stock 

health.

s #ONDUCT2ECRUITMENT0ROCESSES&ISHERIES/CEANOGRAPHY#OORDINATED)NVESTIGATIONS

(FOCI)) studies, a cooperative research program with the Pacific Marine Environmental Laboratory of NOAA’s Oceanic and Atmospheric Research Office to investigate the 

causes of variation in annual recruitment in fish stocks and investigate the ecological 

interactions and relationships relevant to the productivity of the ecosystem and ecosystem-based management.

s !SSESSEFFECTSOFlSHINGON%&(ANDDEVELOPWAYSTOMINIMIZEADVERSEIMPACTS

s !SSESSIMPACTSOFNATURALANDANTHROPOGENICFACTORSONTHEPRODUCTIONDISTRIBUTION

and abundance of Alaskan groundfish stocks. Products are included in contributions to 

the ecosystem considerations chapter of the SAFE documents, peer-reviewed publications, and stock assessment advice. 

s !NALYZETHERESPONSEOFlSHPOPULATIONSTOCHANGESINCLIMATEANDTHEECOSYSTEM

s $EVELOPEVALUATEANDUPDATEINDICATORSOFCLIMATEEFFECTSON.ORTH0ACIlCSTOCKSAND

ecosystems and incorporate these into predictive assessments. This will take the form of 

an enhanced ecosystem assessment section of the SAFE report.

s %VALUATE HATCHERYWILD STOCK INTERACTIONS OF JUVENILE CHUM SALMON IN INSHORE AND

coastal marine habitats of Southeast Alaska to rebuild and maintain sustainable, economically viable fisheries.

s #ONDUCT/CEAN#ARRYING#APACITY/##	INVESTIGATIONSACOOPERATIVEECOSYSTEM

research program with the North Pacific Anadromous Fish Commission and other Federal, state, and university partners to investigate the factors affecting distribution and 

survival of Pacific salmon and associated marine species in the Gulf of Alaska and Bering Sea. 

s #ONDUCT RESTORATION STUDIES RELATED TO THE Exxon Valdez oil spill in Prince William 

Sound. The research will focus on the long-term effects of lingering oil on intertidal 

organisms. This is part of an interagency study examining transfer of oil from intertidal 

organisms to bird and otter predators.
s $EVELOPMODELSDESCRIBINGBASICMETABOLic requirements of forage fish to combine 

with empirical observations of energy allocation to understand how climate change 

will affect forage fish distributions. 

s -ONITOR ORGANOCHLORINE LEVELS IN FORAGE

fish species to understand spatial and temporal patterns to food web contamination 

in Alaskan waters. 

s 5SESATELLITEANDOTHEROCEANOGRAPHICDATA

within groundfish stock assessments.

II. Conservation Engineering 

Research

Recent Accomplishments:

s 4HE!&3#CONTINUESTOCONDUCTRESEARCH

cruises and to analyze results of recent surveys to measure the direct effects of bottom trawling on seafloor habitat in the eastern and central Gulf of Alaska, eastern 

Bering Sea, and the Aleutian Islands. Some of the major accomplishments were:

– Assessment of changes to the seafloor caused by chronic long-term trawling in softbottom areas in the Gulf of Alaska.

– Examination of possible adverse effects of bottom trawls on soft-bottom benthos in 

the eastern Bering Sea.

– Evaluation of acoustic technology for seabed classification.

– Assessment of impacts to habitat areas of particular concern (HAPC), such as gorgonian corals.

– Documentation of the effects of trawling on hard bottom habitat in the Aleutian 

Islands and Gulf of Alaska.

– Mapping of the areas by sediment types.

s 4HE!&3#WORKEDCOOPERATIVELYWITHTHEPOLLOCKMIDWATERlSHINGVESSELSTODESIGN

and evaluate a bycatch reduction device to reduce the bycatch of salmon in their midwater trawls. Prior work supported by the North Pacific Research Board provided the 

first observations of the capture behavior of salmon in a midwater trawl targeting on 

pollock. Based on these results, fishermen working with AFSC scientists developed and 

evaluated a number of possible salmon excluder designs. Testing of these designs with 

industry cooperation is continuing. A similar project working with Alaskan fishermen 

and funded by Cooperative Research and Reducing Bycatch funding is designed to 

reduce the bycatch of Pacific halibut in trawl fisheries in the Gulf of Alaska for Pacific 

cod and flatfishes. Current excluder designs being tested look promising for reducing 

bycatch in these fisheries. 

s !&3#SCIENTISTSCARRIEDOUTLABORATORYEXPERIMENTSONLIVElSHATTHE(ATlELD-ARINE

Science Center in Newport, Oregon, to determine the impact of stress from capture 

processes on the behavior and survival of important bycatch species in trawl and longline fisheries. This research has provided insights on the key principles that control 

bycatch fish mortality by integrating analysis of behavioral and physiological assays and 

observed mortality. Recent published research on the measurement of bycatch mortalSorting groundfish from a 

research trawl in Alaskan 

waters. Photo: NMFS.
58

ity has shown the value of the use of the measurement of easily observable behavioral 

reactions in predicting bycatch mortality.

s 4HE!&3#RESPONDEDTOACRITICALNEEDTOCONDUCTRESEARCHONMETHODSTOREDUCESEAbird incidental take on groundfish trawl vessels. Three types of seabird deterrent devices 

were chosen by industry as having potential for large catcher processor vessels, including paired streamer lines, side-boom arrays, and third wire control devices. Seabirds 

interact with the trawl warp cables and third wire sonar cables, sometimes resulting in 

mortalities. The experimental deterrent devices were designed to keep seabirds away 

from these cables. Additional research is being conducted to examine the risk of interactions between groundfish trawl components and the endangered short-tailed albatross 

and to characterize the trawl fleet regarding seabird interactions.

s !TTHEREQUESTOF!LASKALONGLINERSTHE!&3#DEVELOPEDSAMPLINGPLANSFORADEVELOPmental “shrimpfly” rockfish fishery that will experiment with fishing gear capable of 

catching rockfish without bycatch of salmon, halibut, and other valuable groundfish.

Research Priorities, FY 2007–2012:

s #ONTINUETOCONDUCTRESEARCHTOMEASUREDIRECTEFFECTSOFBOTTOMTRAWLINGONSEAmOOR

habitat according to a 5-year research plan.

s #ONDUCTlSHINGGEARPERFORMANCEANDlSHBEHAVIORALSTUDIESTOREDUCEBYCATCHANDBYcatch mortality of prohibited, undersized, or unmarketable species, and to understand 

performance of survey gear. 

s 7ORKWITHINDUSTRYANDTHE#OUNCILTODEVELOPBYCATCHREDUCTIONTECHNIQUES

s #ONTINUEWORKTOCHARACTERIZETHETRAWLGROUNDlSHmEETSINTERACTIONSWITHSEABIRDS

s #ONTINUERESEARCHTODEVELOPAPPROPRIATEMITIGATIONGEARUSINGEXPERIENCEFROMRECENT

work. Identify which component of the trawl fleet is the most likely to have seabird interaction issues and develop directed research to take place during the fishing season.

s !NALYZEVESSEL
SPECIlCEFFECTSOFSEABIRDINCIDENTALTAKEINTHELONGLINElSHERYANDDEvelop means to work with those individual companies and vessels to further reduce 

seabird takes.

III. Research on the Fisheries

Recent Accomplishments:

The AFSC conducted economic and social research to support fishery conservation and 

management actions, particularly those recommended by the North Pacific Fishery Management Council. In terms of that research and data programs to support such research, 

the principal accomplishments included the following:

s #OLLABORATEDWITHTHE.ATIONAL/VERCAPACITY7ORKING'ROUPTODEVELOPAMETHODOLogy to estimate overcapacity in all federally managed fisheries in order to satisfy an 

obligation in the National Plan of Action on Overcapacity in Fisheries.

s #OMPLETEDTHISYEARS%CONOMIC3TATUSCHAPTERFORTHEGROUNDlSH3!&%REPORT4HE

SAFE report was expanded to include a broad range of research topics, in response to 

the Council’s Scientific and Statistical Committee requests.
s 0UBLISHEDORSUBMITTEDFORPUBLICATION	SEVERALPAPERSINVARIOUSAREASINCLUDINGRECreational demand modeling, regional economic modeling, fisher behavior, productivity 

and fishing capacity measurement, quantitative methods for evaluating knowledge, and 

community profiling.

s $EVELOPINGAJOINTECOLOGICALANDREGIONALECONOMICMODELWITHRESEARCHERSATTHE5NIversity of Wyoming.

s #OMPLETEDANDDISSEMINATEDALARGECOMMUNITYPROlLINGDOCUMENTTHATSUMMARIZES

the cultural and economic relationships between the fishing industry and over 100 

Alaskan communities. The profile of each individual community will be available soon 

on the web.

s #ONDUCTEDASTUDYTHATANALYZESTHEEFFECTSOF)NDIVIDUAL4RANSFERABLE1UOTAS)41	

programs on emigration from remote Alaska fishing communities.

s $EVELOPEDNEWMETHODSFOREVALUATINGSPATIALLYCOMPLEXAREACLOSURESUSINGANIMproved discrete location choice model for the Bering Sea pollock fishery. This model 

measures the impacts on profits of boats traveling to more distant locations and/or 

experiencing lower levels of catch in alternative fishing areas. The model also provides 

ex-ante and ex-post welfare estimates of the economic impacts of the Steller sea lion 

Conservation Area (SCA). Extensions of the model will allow the prediction of the 

economic impact of future closures, such as marine reserves.

s $EVELOPEDASURVEYTOESTIMATETHEECONOMICVALUEOFSPORTHALIBUTlSHINGIN!LASKA

and the public’s value for Steller sea lion protection measures, and contributed to a national survey on the public’s value for over 20 protected species.

s 7ORKEDWITH.ORTH0ACIlC&ISHERY-ANAGEMENT#OUNCILECONOMISTSTODEVELOPANEW

economic data collection program for freezer-longliner head and gut fleet (as part of 

Amendment 80). Developed a draft economic survey, and the Council recently voted 

to have this data collected as part of mandatory regulations for the fleet. 

s ,EDINTHEDEVELOPMENTIMPLEMENTATIONANDMANAGEMENTOFTHE"3!)#RAB2ATIONALization Data Collection Program. This collection is the most detailed economic data collected in Alaska fisheries and will be used to assess the effects of this novel program. 

s )MPLEMENTEDTWOPROJECTSTOCOLLECTPRIMARYDATAONSEAFOODINDUSTRYEXPENDITURESIN

the Gulf and Southwest Regions of Alaska for our regional economic model. Collaborating with the Alaska Department of Labor to have them compile additional information for use in the regional economic model.

s 0ERFORMEDANANALYSISOFMULTISPECIES)NDIVIDUAL&ISHING1UOTA)&1	SYSTEMSTHAT

looks at multispecies IFQ fisheries in Iceland, New Zealand, Australia, and Canada. 

The AFSC assessed the design and use of catch-quota balancing mechanisms, with an 

eye on applications to the West Coast and Alaska.

s $EVELOPEDACAP
AND
TRADESYSTEMFORREGULATINGHABITATIMPACTSOFlSHERIESWITHTHE

goal of developing a cost-effective approach for protecting habitat. This work proposes 

and explores a rights-based system to manage fishery impacts on habitat using individual habitat quotas (IHQ). Also compared the performance of the IHQ system with 

more conventional fixed or rotating Marine Protected Areas (MPA).

s %XAMINED COMMERCIAL lSHING CREW DEMOGRAPHICS AND TRENDS USING THE COMMERCIAL

crew license database of the Alaska Department of Fish and Game. This database in-
60

cludes information on age, gender, citizenship, and residency and covers 272,000 crew 

licenses (1993 to 2003). The crew demographics were discussed and analyzed in terms 

of crew population, license tenure, age and gender distribution, and geographic distribution.

s 0UBLISHEDRESEARCHDOCUMENTINGDRAMATICSIZECHANGESINSALMONINRELATIONTOCLIMATE

change and population density.

s 0UBLISHEDRESEARCHONNORTHWARDMIGRATIONOFlSHINTHE"ERING3EAINRESPONSETO

changing ocean conditions.

s )DENTIlED SINGLE NUCLEOTIDE POLYMORPHISMS 3.0	 USEFUL FOR STOCK IDENTIlCATION OF

salmon and forage fish bycatch in the GOA and BSAI.

Research Priorities, FY 2007–2012:

III.A. Social and economic research

s !SSISTINIMPLEMENTINGANDIMPROVINGDATACOLLECTIONPROGRAMSTHATSUPPORTECONOMIC

and social research.

s $EVELOPANDCONTINUETOMAINTAINSOCIALANDECONOMICINFORMATIONDATABASESONTHE

fisheries and fisheries-dependent communities of GOA and BSAI in order to evaluate 

the impacts of Council actions intended to improve the long-term net benefits derived 

from fisheries. This information is required for establishing a baseline for use in 1) 

identifying stakeholders to be included in the distribution of dedicated access privileges 

(e.g., harvesting quotas and processing quotas), 2) projecting the likely consequences of 

alternative management measures, and 3) conducting retrospective analysis of management actions that have been taken.

s 0REPARETHEECONOMICSTATUSREPORTOF!LASKASGROUNDlSHlSHERIESASPARTOFTHEANNUAL

Groundfish SAFE reports. 

s !NALYZECURRENTDETERMINANTSOFEX
VESSELWHOLESALEINTERNATIONALANDRETAILDEMANDS

for principal seafood products from the GOA and BSAI.

s %STIMATETHEPRE
ANDPOST
IMPLEMENTATIONBENElTSANDCOSTSANDDISTRIBUTIONOFBENEfits and costs, associated with changes in management regimes (e.g., changes in product 

markets, characteristics of quota share markets, changes in distribution of ownership, 

and changes in crew compensation as a consequence of the introduction of dedicated 

access privileges in the halibut/sablefish, pollock, and crab fisheries). 

s !NALYZETHEROBUSTNESSANDRESILIENCEOFALTERNATIVEMANAGEMENTSTRATEGIESUNDERVARYing environmental and ecological conditions.

s !NALYZECHANGESINTHESPATIALANDTEMPORALDISTRIBUTIONOFlSHINGEFFORTINRESPONSE

to management actions (e.g., time/area closures, marine reserves, bycatch restrictions, 

co-ops, IFQs).

s %VALUATETHEEVOLUTIONOFCOMMUNITYSOCIALANDECONOMICSTRUCTUREINRESPONSETOALternative management actions; the benefits and costs, and the distribution of benefits 

and costs, associated with consumptive and non-consumptive uses of resources supported by the North Pacific and Eastern Bering Sea ecosystems; and evolving seafood 

markets.

s $EVELOPLONGITUDINALDATASETSOFEX
VESSELWHOLESALEANDRETAILPRICESDAILYORWEEKLY
firm-scale data on production by species and product form; trip-scale data on variable 

costs for catcher vessels, catcher-processors, and sportfishing charters; daily or weekly 

plant-scale data on variable processing costs for shore-based and floating processors; annual vessel- or plant-level data on fixed costs; trip-scale information about the location 

and duration of fishing; weekly or monthly data on patterns of expenditures associated with harvesting, processing, and sportfishing charters; pay-period scale, vessel- and 

plant-level data on employment and income of fishery participants; socioeconomic and 

demographic data for fishery-dependent communities; and community- and regionalscale annual data on the distribution and magnitude of tax receipts and transfer payments associated with commercial and sport fishing.

s %XPAND SOCIOLOGICAL AND ECONOMIC RESEARCH AND INCORPORATE RESULTS INTO THE lSHERY

management process. The process will include the acquisition of data, and development 

and analysis of socioeconomic models that are compatible with, and can be integrated 

with, ecosystem models.

s #ONDUCTRESEARCHONVESSELOVERCAPITALIZATIONANDIMPACTSOFTHEIRlSHINGEFFORTLEVELS

on fisheries.

s #OMPILEANDANALYZEDATAONHARVESTINGANDPROCESSINGSECTORBEHAVIOR

III.B. Seafood safety research 

This item is not applicable.

III.C. Marine aquaculture

s #ONDUCTSTOCK
ENHANCEMENTAQUACULTURERESEARCHON#HINOOKSALMONATTHE!&3#S

Little Port Walter Marine Station to determine strategies that result in increased contribution of Alaska-origin fish in Alaska fisheries to help achieve an improved harvest 

balance under Pacific Salmon Treaty oversight. 

s #ONDUCTPARENTAGEANALYSISOFMULTI
GENERATIONALHATCHERY#HINOOKSALMONANDWILD

stock cohorts using DNA micro-satellites to determine relative biological and fishery 

contribution performance measures. 

s -EASURETHEEFFECTSOFYEARSOFFRESHWATERSEQUESTRATIONONGENETICVARIABILITYGROWTH

survival, maturation, juvenile behavior, and adult spawning behavior on normally anadromous steelhead trout with protected species implications for successful restoration of 

ESA-listed stocks.

s $ETERMINEEFFECTSOFDIFFERENTFOUNDERREGIMESONGENETICVARIATIONINHATCHERYBROOD

stocks of salmon.

IV. Information Management Research

Recent Accomplishments:

The AFSC communicates its scientific information and advice, along with the associated 

uncertainties, to NMFS staff, other management authorities, the Councils, and the public. 

For example, survey results of the AFSC were disseminated to the user groups through 

the participation of experts at meetings and submission of technical reports and published 

papers. On a yearly basis, the AFSC publishes roughly 100 scientific papers as well as over 

a dozen NOAA Technical Memorandums and Center Processed Reports.
62

The AFSC’s Auke Bay Laboratory is developing protocols and formats to comply with 

Federal Geospatial Data Committee (FGDC) 

requirements for web-accessible metadata sets 

of fisheries-related biophysical and oceanographic information. A full FGDC-compliant 

metadata record has been constructed for a 

large data set (Southeast Coastal Monitoring 

[SECM]) consisting of fish catches and associated biological and physical oceanographic 

data. In addition, a data dictionary has been 

constructed for the entire data set. The complexity of the SECM data set makes it likely 

that its metadata record and data dictionary 

can serve as the example for most other data 

sets within the AFSC. When all active Auke 

Bay Lab data sets are FGDC-compliant (by 

the end of FY 2007), the information will be 

ready for access via the Internet.

s 4HE!&3#HASBEENPROACTIVEINPROVIDINGPUBLICACCESSTORESEARCHINFORMATIONVIATHE

web. Projects include:

– AFSC scientists have conducted ichthyoplankton cruises in 1972 and yearly from 

1977 until the present. The results are now in a web-enabled database, the Ichthyplankton Information System, that allows users to search for information and data on 

the early life history of fishes from the northeast Pacific Ocean and Bering Sea. 

– AFSC scientists and researchers gather thousands of digital images on the various 

scientific cruises. The AFSC has web-enabled access to nearly 10,000 images through 

the deployment of an image management database system.

– Geographic Information Systems (GIS) play a key role in the analysis of data. The 

AFSC annually conducts training programs for AFSC scientists and researchers on 

how to use the various GIS tools available to them.

– A GIS habitat and fish use database was established in 2006 for nearshore habitats. 

Nearshore surveys of habitat and fish species use was combined with a ShoreZone 

GIS database, and includes data from 1998 to present over thousands of kilometers of 

Alaska shoreline. Data can be accessed online and queried by location or species, and 

will give managers and researchers quick access to information. Periodic updates are 

conducted as new information is gathered. 

– The AFSC is the host for the NMFS publication FishNews—an automated e-mail 

newsletter that provides electronic notification of important actions, rules, policies, 

and programs that may be of interest to the public.

– The AFSC hosts the scientific editor position for 2005-2008 for the NMFS publication Fishery Bulletin, publishing peer-reviewed scientific manuscripts of the highest 

caliber. 

– The AFSC is developing a Internet-accessible longline survey database.

s 4HE!&3#ANDOTHERRESEARCHUNITSOF.-&3USEDSTOCKASSESSMENTWORKSHOPSPEER

reviews, and other forums to ensure that our information and advice are developed 

through an open and collaborative process. The stock assessment process of the AFSC 

undergoes periodic review internally and externally throughout the years. 

The NOAA vessel John N. 

Cobb on a research cruise in 

Alaskan waters.
s !&3#SCIENTISTSPARTICIPATEDASSCIENTIlCADVISORSTOBILATERALPANELSANDBILATERALTECHnical committees in various international salmon forums, including the U.S.-Canada 

Pacific Salmon and Yukon Treaty accords and NPAFC.

s 4HE!&3#DATABASEFORBOTTOMTRAWLSURVEYSISUNDERGOINGAMAJORRESTRUCTURINGTO

include all the catch, haul, specimen, and effort data that are routinely collected. The 

design is complete and populating the new database is continuing. 

s 4HE!&3#PROVIDEDGUIDELINESTOASSISTTHE#OUNCILSINASSESSINGANDRECOMMENDING

MSY for managed fisheries. The AFSC’s Resource Ecology and Fisheries Management 

Division (REFM) has the lead role for defining and estimating the MSY levels for all 

the groundfish stocks managed in the BSAI and GOA area. The information helps 

the NPFMC determine the relative status of the stocks to historical levels. The AFSC 

also has the lead role in defining and estimating the overfishing levels for each of the 

groundfish stocks managed in the BSAI and GOA area. These maximum fishing levels 

guide the NPFMC to recommend management measures to maintain the exploitation 

of the stocks within biologically safe levels.

s 2%&-PROVIDEDTHETECHNICALLEADROLETODEVELOPOBJECTIVEANDMEASURABLECRITERIAFOR

stocks that are overfished or approaching an overfished condition. The definitions were 

used as uniform applications throughout NMFS. These definitions would standardize 

the criteria for determining depleted stocks due to fishing and other causes throughout 

the Nation. 

s 4HE!&3#PROVIDEDTECHNICALEXPERTISEANDANALYSISINENVIRONMENTALIMPACTSTATEments involving Alaska groundfish fisheries. Most notably, AFSC scientists contributed 

substantially to the successful completion of two key Environmental Impact Statements 

(EISs): 1) the Alaska Groundfish Fisheries Final Programmatic Supplemental Environmental Impact Statement, and 2) the Final Environmental Impact Statement for 

Essential Fish Habitat Identification and Conservation in Alaska. 

s 4HE!&3#ISDEVELOPINGECOSYSTEM
BASEDINDICATORSANDASSESSMENTS4HISINFORMATION

is being integrated into documents provided to fishery managers in support of ecosystem-based management. Time-series data on climate, fishing, and status and trends of 

species and ecosystem-level characteristics are being collected from diverse sources and 

consolidated into a central place to facilitate integrated ecosystem assessments.

s 4HE!&3#PROVIDEDTHETECHNICALLEADROLEFORDEVELOPINGTHE-ARINE&ISHERIES3TOCK

Assessment Improvement Plan for Alaska groundfish. Research activities include a 

broad spectrum of field research and data analyses that involves other divisions within 

the AFSC and partnerships with three universities.

s 4HE!&3#2%&-	CONTINUESTOPROVIDETHETECHNICALLEADTOFURTHERDElNEOVERlSHing for uniform applications throughout NMFS. The role also extends into a National 

Committee tasking to establish new for listing under ESA.

s 4HE!&3#HASWORKEDCOOPERATIVELYWITHSTAFFFROMTHEOTHER.-&33CIENCE#ENTERS

and NOAA’s Office of Marine and Aviation Operations in the design, development, 

and implementation of the Fisheries Scientific Computer System on NMFS research 

vessels. This system provides for improved collection and recording of data collected 

at sea through the use of improved data collection and computer technology. Work is 

now continuing to extend these same advances for use on vessels chartered by NMFS to 

conduct stock assessment surveys.
64

Research Priorities, FY 2007–2012:

s $EVELOPPROCESSESANDPROCEDURESTOENHANCETHECOMMUNICATIONOFSCIENTIlCINFORMAtion generated by the AFSC, with emphasis on web-enabled access to its data.

s #ONTINUETOBUILDDATAINFRASTRUCTUREANDRESOURCESFOREASYACCESSANDDATAPROCESSING

The AFSC’s key databases are its survey data bases from the 1950s (or earlier) and the 

scientific observer database that extends back to the foreign fishing days of the 1960s.

s #ONTINUETOPROVIDEINFORMATIONPRODUCTSBASEDONEXPERTSANDTECHNICALDATATHATSUPport NMFS, the Regional Office, the Councils, international scientific commissions, 

and the overall research and management community. 
NORTHWEST FISHERIES SCIENCE CENTER

The Northwest Fisheries Science Center (NWFSC) conducts research to support the 

management, conservation, and sustainable use of the Pacific Northwest region’s anadromous and marine fishery resources and their habitats. The NWFSC carries out its research 

from its Montlake Laboratory headquarters in Seattle, Washington, and from five research 

stations in Manchester, Mukilteo, and Pasco, Washington, and in Newport and Pt. Adams, 

Oregon. The NWFSC’s more than 320 Federal employees and 200 non-Federal employees 

conduct both field and laboratory research in coastal, ocean, and estuarine environments, 

as well as in inland freshwater habitat used by anadromous species, such as salmon.

The NWFSC has several small vessels for conducting studies. The R/V Harold Streeter

serves Puget Sound, and the R/V Murrelet, R/V Siliqua, and R/V Quinnat serve Columbia 

River Basin projects. The Center does not have a dedicated research vessel, but one is currently being planned. Center scientists currently rely on the NOAA FSV Miller Freeman

and the NOAA vessel McArthur II, as well as on privately chartered vessels and academic 

research ships to supplement the Center’s research capability and to conduct critical surveys.

The NWFSC’s research brings together a number of disciplines, including fisheries science, marine biology and ecology, genetics, biochemistry, molecular biology, oceanography, 

mathematics, and physiology. Organizationally, the Center consists of the Conservation 

Biology Division, the Environmental Conservation Division, the Fish Ecology Division, 

the Fishery Resource Analysis and Monitoring Division, and the Resource Enhancement 

and Utilization Technologies Division. In addition, the Center has Socioeconomics, and 

Science Synthesis and Coordination programs. Across these five divisions and programs, 

NWFSC scientists and staff conduct research in several primary areas:

An adult male killer whale 

breaches the surface. Photo: 

NMFS.
66

s 3TATUSOFSTOCKS#ENTERSCIENTISTSCONDUCTANDCOORDINATESTOCKASSESSMENTSFOR7EST

Coast groundfish and salmon stocks in the Pacific Northwest by conducting surveys to 

monitor trends in stock abundance and biological characteristics, and analyzing these 

data with mathematical models of the populations. These assessments are the primary 

tool used by managers to set biologically sustainable harvest levels for healthy stocks 

and to identify and guide the monitoring and rebuilding of overfished and threatened 

stocks.

s (UMAN
#AUSED3TRESS2ISKS#ENTERSCIENTISTSCONDUCTRESEARCHTOBETTERUNDERSTAND

how salmon, marine fish, and marine mammals react to anthropogenic stresses and 

to quantify, assess, and minimize associated risks. The Center’s research provides the 

underpinning for management decisions.

s %COSYSTEMAND#LIMATE#HARACTERISTICS#ENTERSCIENTISTSCONDUCTRESEARCHONPHYSIcal and biological processes that influence aquatic, marine, and estuarine ecosystems 

in the Pacific Northwest, as well as the effects of invasive species, toxic phytoplankton, 

pathogenic bacteria, climate change, and natural environmental fluctuations.

s 2ECOVERAND2EBUILD3PECIES#ENTERSCIENTISTSSTUDYGENETICVARIATIONANDCONDUCTREsearch on the population structure of salmon, marine fish, and killer whales. The Center also develops innovative recovery tools like captive broodstock programs to propagate salmon species, new techniques for rearing hatchery fish, and culture techniques to 

rear marine fish. In addition, Center scientists provide scientific leadership for salmon 

recovery planning efforts on the West Coast.

s )NNOVATIONAND4ECHNOLOGY#ENTERSCIENTISTSARETAKINGALEADROLEINDEVELOPINGAND

applying technologies, techniques, and tools to support conservation and recovery of 

the Pacific Northwest’s living marine resources. Over the years, the Center’s innovative 

and original research has helped establish new aquaculture endeavors, seafood processing techniques, dam passage equipment and techniques, methods to detect and evaluate 

harmful algal blooms, and technology to integrate and track important fisheries dependent data, as well as to identify and monitor marine and anadromous fish populations.

s 0RODUCT1UALITYAND3EAFOOD3AFETY#ENTERSCIENTISTSCONDUCTRESEARCHONSEAFOODTO

reduce risks and demonstrate benefits from the Nation’s seafood supply. The primary 

objectives are improving our understanding of, monitoring for, and mitigating the possible adverse human health effects of pathogens (bacteria and viruses), algal toxins, and 

chemical contaminants in fish and shellfish; understanding human health benefits; and 

supporting environmentally sound production of marine aquaculture species.

NWFSC research supports critical management decisions. The Center has lead responsibility in the region to study and provide state-of-the-art scientific information on the 

following primary living marine resources. 

s 0ACIlC 3ALMON&IFTY
TWO GROUPS OF POPULATIONS EVOLUTIONARILY SIGNIlCANT UNITS

[ESUs]) of salmon and steelhead exist on the West Coast, 26 of which are listed as 

endangered or threatened under the Endangered Species Act.

s 7EST#OAST'ROUNDlSH4HE7EST#OASTGROUNDlSHlSHERYINCLUDESSOMECOMmercially fished stocks and supports millions of dollars in economic activity and many 

livelihoods. The Center coordinates the NMFS’ Groundfish Program on the West 

Coast.

s +ILLER7HALES4HE3OUTHERN2ESIDENTKILLERWHALEPOPULATIONWASRECENTLYLISTEDAS
endangered under the ESA and depleted under the Marine Mammal Protection Act. 

The Center has developed a research plan to address possible causes for the killer whale 

decline and gain a better understanding of the physiology, ecology, and behavior of 

these whales.

The NWFSC develops and maintains strong collaborative partnerships with state and 

Federal agencies, industry, environmental groups, Native American tribes, individual fishermen, universities, and other research and academic institutions. The Center also provides 

opportunities for students in marine research, technology, and library science through 

cooperative research agreements with regional universities and councils.

RECENT ACCOMPLISHMENTS AND

RESEARCH PRIORITIES FOR FY 2007–2012

I. Research to Support Fishery Conservation and Management

Recent Accomplishments:

s -AJORSURVEYCRUISESCONDUCTEDBYTHE.7&3#INCLUDED

– The biennial acoustic survey aboard the NOAA Ship Miller Freeman to estimate the 

biomass and distribution of hake off the coasts of California, Oregon, and Washington.

– A summer bottom trawl survey on board chartered commercial fishing vessels to assess the distribution and abundance of commercially important groundfish resources 

off the coasts of Washington, Oregon, and California and to collect other biological 

data.

– In collaboration with the Pacific Whiting Conservation Cooperative, a juvenile 

groundfish survey that extends from the Washington border to central California.

– In collaboration with fishing industry, a pilot acoustic survey of widow rockfish off 

the coast of Oregon.

– A pilot survey to assess abundance and distribution of groundfish in untrawlable 

areas using autonomous underwater vehicle (AUV) technology.

– A pilot survey of vermillion and bocaccio rockfish in the southern California Bight. 

s 4HE.7&3#CONDUCTEDTWOOBSERVERPROGRAMSTOCOLLECTINFORMATIONFROMTHEFEDERally regulated groundfish fisheries off the West Coast, including limited entry trawl 

and fixed gear fleets, the at-sea hake fleet, and the open access fleet. The observer programs collect valuable data on the bycatch and discard of groundfish. In addition, the 

observer program data are used to estimate the levels of direct, incidental takes of all 

protected species, including seabirds, prohibited species of fish, and marine mammals. 

The observer program is also testing the application of electronic monitoring systems to 

cut costs while still collecting essential at-sea data. The systems are being tested on the 

entire hake fleet that processes their catch shoreside—the first full fleet in the Nation to 

be monitored with this method.

s 4HE#ENTERHADLEADRESPONSIBILITYFORANALYZINGTHEPOPULATIONDYNAMICSANDSTATUSOF

most of the groundfish species managed by the Pacific Fishery Management Council. 

It coordinated the groundfish stock assessment and review process for the Council and 

conducted 12 of the 23 stock assessments during the last biennial management cycle. 

In 2005 Stock Assessment team members completed assessments of Pacific hake, sablefish, darkblotched rockfish, canary rockfish, Pacific ocean perch, longspine thornyhead, 
68

shortspine thornyhead, English sole, petrale sole, cabezon, blackgill rockfish, and 

yellowtail rockfish. Rebuilding analyses 

were conducted for canary rockfish, darkblotched rockfish, and Pacific ocean perch. 

Details on these and other West Coast 

groundfish assessments conducted in 2005 

are available online at www.pcouncil.

org. These assessments form the basis for 

Council recommendations for Allowable 

Biological Catches and Optimum Yields 

for these species for 2007–2008, which 

were finalized at the June 2006 Council 

meeting.

s4HE.7&3#COORDINATEDTHEPEERREVIEW

process (STAR panels) for these assessments and also organized several pre-assessment workshops, including one on data

 issues, one on modeling methods (including introduction of the new Stock Synthesis 2 modeling platform), and another on the 

use of recreational catch per unit effort (CPUE) data, which was co-sponsored with the 

Southwest Fisheries Science Center. 

s 4HROUGHACOOPERATIVEAGREEMENTBETWEEN.-&3ANDTHE0ACIlC3TATES-ARINE&ISHERies Commission, the NWFSC hosted the cooperative Ageing Lab based at Hatfield Marine Science Center. The Ageing Lab produced ages to support assessments on Pacific 

hake, Pacific ocean perch, sablefish, Dover sole, canary rockfish, darkblotched rockfish, 

and English sole. 

s 4HE.7&3#HASALSOEXPANDEDITSSTOCKASSESSMENTSBYINCORPORATINGENVIRONMENTAL

INDICES+EYOCEANOGRAPHICVARIABLESHAVEBEENIDENTIlEDANDCORRELATEDWITHANNUAL

variations in sablefish recruitment success. This work was formally incorporated into 

the 2005 sablefish stock assessment. 

s )NCOOPERATIONWITH/REGON3EA'RANT#ENTERSTAFFDESIGNEDAPROJECTTOCOMPENSATE

fishermen who participate in research planning and data collection. As part of this 

project, port liaisons—local leaders in West Coast communities—have been selected to 

help match fishermen with research projects, and the fishermen are then compensated 

for their time spent assisting in research and research planning.

Other accomplishments by the NWFSC include:

s 3TATISTICALLYEVALUATEDTHERELATIONSHIPOFCLIMATEWITHRECRUITMENTOFBOCACCIOANDTHE

interaction of fishing and climate impacts on groundfish and on rebuilding of overfished groundfish. 

s 5PDATEDMODELSANDDATAINPUTSUSEDFORESTIMATINGDISCARDSINDIRECTEDGROUNDlSH

fisheries off Washington, Oregon, and California.

s #ONDUCTEDSTUDIESINGROUNDlSHECOLOGYSPECIESLIFEHISTORIESANDHISTORICALDATAPATterns. This included the development of a new program to collect information on trophic dynamics of key groundfish during the bottom trawl surveys.

Yellowtail rockfish. Photo: 

Timothy Nesseth, NOAA.
s $EVELOPEDACOUPLEDBIOLOGICAL
OCEANOGRAPHIClSHERIESMODELOFTHE#ALIFORNIA#URrent that can be used to test sensitivity of ecosystem indicators to natural and humaninduced environmental perturbations, to evaluate the effects of management strategies 

on ecosystem attributes, and to forecast changes in the California Current LME as a 

result of climate oscillations or climate change. 

s 5SED ACTIVE AND PASSIVE ULTRASONIC TELEMETRY TO CHARACTERIZE THE DAILY AND SEASONAL

movements of groundfish and apex predators. These data have been used to parameterize models of movement that allow us to evaluate habitat preferences, movement rates, 

and responses to fishing. Such models also allow us to estimate the number, size, and 

location of marine reserves necessary to achieve specific fisheries or conservation goals.

s $EVELOPEDSPECIES
AREARELATIONSHIPSFOR7EST#OASTGROUNDlSH4HERELATIONSHIPSALlow us to evaluate trade-offs between fisheries yield and conservation goals, the value 

of a few large Marine Protected Areas versus several small ones, and mechanisms maintaining fish biodiversity in the California Current.

s !UTHOREDTHE7EST#OASTCOLDWATERCORALCHAPTERFORTHENATIONALREPORTONCOLDWATER

corals, and provided a summary of cold water coral information off Washington, Oregon, and California to be used during analyses and discussion of areas to be proposed 

for EFH designations. 

s !PPLIEDINDUCTIVELYCOUPLEDMASSSPECTROMETRYANDLASERABLATIONTOCHARACTERIZETHE

chemical composition of water masses as well as the otoliths of juveniles to identify 

essential nursery habits for English sole. Examined the juvenile portion of adult otoliths to determine whether different habitats contributed disproportionately to the adult 

population. Results indicate that fish from regions within 10 km of urban centers grow 

slower and die at a greater rate than in areas distant from urban centers, even when 

habitat structure is identical.

s $EVELOPEDFRAMEWORKSTOPROVIDEMANAGEMENTOPTIONSSPECIlCTOCOMMUNITYPROTECtion and community quota to include as alternatives for the Trawl Individual Quota 

System. The Pacific Fishery Management Council was able to select specific community options for future impact analysis in an environmental impact statement process.

s #ONDUCTEDANDPUBLISHEDAN%3!STATUSREVIEWFOR#HERRY0OINT0UGET3OUND	0ACIlC

herring.

s #ONDUCTEDRESEARCHONPRESPAWNMORTALITYINADULTCOHOSALMONFROMURBANSTREAMS

The Center documented rates of 60 to 90 percent pre-spawn mortality over the past 3 

years and developed population models based on these results.

s #ONDUCTEDRESEARCHTOESTIMATEGROWTHCONDITIONOFJUVENILESALMONDURINGEARLYPHASes of ocean entry. Physiological indicators of growth status (plasma insulin-like growth 

factor I) of juvenile coho salmon off the coast of Washington were related to long-term 

survival.

s #ONTINUEDRESEARCHDESIGNEDTOESTIMATETHERELATIVEREPRODUCTIVESUCCESSOFNATURALLY

spawning hatchery salmon and initiated a new long-term research project to study the 

genetic effects of hatchery rearing on the fitness of wild salmon populations.

s #ONTINUEDTOCHAIRTHREESALMON4ECHNICAL2ECOVERY4EAMS424S	0UGET3OUND

Lower Columbia River and Willamette River, and Interior Columbia River Basin—

and co-chaired the Oregon and Northern California Coast TRT. These teams are describing the biological conditions necessary for recovery of listed populations and are 
70

providing technical support to policymakers to help evaluate alternative strategies for 

meeting recovery goals. In conjunction with the Northwest Regional Office, Southwest 

Regional Office, and Southwest Fisheries Science Center, the NWFSC developed the 

original TRT concept, purpose, and goals. 

s $EVELOPEDAFRAMEWORKFORANALYZINGTHEECONOMICIMPACTSOFCRITICALHABITATDESIGNAtion under the ESA. This framework was successfully applied to critical habitat designations for 12 West Coast salmon and steelhead ESUs, and to Southern Resident killer 

whales.

s $EVELOPEDANUNDERSTANDINGOFTHEROLEOFESTUARIESASCRITICALHABITATTOENHANCEPOPUlation productivity and resilience needed to support recovery of endangered salmon 

stocks.

s $EVELOPEDANUNDERSTANDINGOFTHEROLEOFRIVERPLUMESASTHEYINTERACTWITHTHE#ALIfornia Current as critical habitat for salmon and coastal pelagic species.

s $EVELOPEDECONOMICGUIDANCEFORESTIMATIONOFCOSTSOFRECOVERYACTIONSFOR7EST#OAST

salmon and steelhead recovery planning. 

s $EVELOPEDlNALORDRAFTBIOLOGICALVIABILITYCRITERIAFORLISTEDSALMON%35SIN0UGET

Sound, the Lower Columbia River, Interior Columbia River, and Oregon Coast. 

s $EVELOPEDMETHODSFORASSESSINGHUMANIMPACTSONSTREAMHABITATSINTRIBUTARIESTO

the Columbia and Snake Rivers, and completed analyses of habitat change in the Columbia River basin. These analyses helped identify populations where habitat restoration is likely to improve salmon populations, and also where there are few opportunities 

to increase salmon abundance through habitat restoration.

s )NITIATEDMODELDEVELOPMENTTOQUANTIFYTHEPOPULATIONANDGENETICEFFECTSOFCONSERVAtion-type hatcheries for rockfish stocks.

s )NITIATEDRESEARCHTOESTIMATETHEEARLYMARINESURVIVALOFSTEELHEADANDIDENTIFYNEARshore habitats important for survival.

s ,ED A MULTI
AGENCY PROJECT THAT CREATED A STANDARDIZED GENETIC DATASET FOR #HINOOK

salmon sampled from California to Alaska. The dataset is being used for estimating 

fishery impacts, and for understanding the ocean distribution of salmon stocks.

s /RGANIZEDANDSPONSOREDA3YMPOSIUM7ORKSHOP-ARCHIN3EATTLE	ONDESIGnation of conservation units of Pacific salmon and steelhead, with special emphasis on 

complex units that might include both resident and anadromous populations and/or 

both hatchery and natural populations. The objective was to review the state of the 

science underlying complex legal and policy issues that NMFS must address under the 

ESA. The symposium was attended by over 150 people, and the report of the Science 

Panel outlines scientifically defensible options for NMFS to consider in listing determinations.

s 0RODUCEDAlNALGUIDANCEDOCUMENTFORDEVELOPINGMONITORINGANDEVALUATIONPLANS

for ESA-listed salmon stocks.

s 0UBLISHED A BOOK SPONSORED BY THE !MERICAN &ISHERIES 3OCIETYENTITLED Monitoring 

Stream and Watershed Restoration. The book, consisting of 12 chapters authored primarily by NWFSC scientists, provides comprehensive guidance on how to monitor and 

evaluate habitat restoration projects for salmon and other fish species that are important 

in the Pacific Northwest. The book synthesizes much of the important innovations in 
monitoring and restoration science made 

by Center scientists in the past several 

years. Additionally, this publication provides guidance on the cost-effectiveness 

(i.e., hundreds of millions of dollars being 

spent annually on habitat restoration for 

salmon) of habitat restoration on improvements in habitat conditions as well increases in salmon abundance. The book is 

being used extensively by local watershed 

groups, scientists, and restoration practitioners to quantify physical and biological response to various stream restoration 

techniques at various scales.

s $EVELOPED RECOVERY PLANS FOR  LISTED

salmon and steelhead populations in four 

geographic domains under the Center's jurisdiction.

s ,EDTHE)NTERIOR#OLUMBIA424SEFFORTTODEVELOPADRAFTPOPULATIONVIABILITYDOCUment. This document describes key parameters related to population viability (abundance, productivity, spatial structure, and diversity) and is a critical step for developing 

biological recovery goals. These goals are also useful in determining when listed salmon 

populations will no longer be considered threatened or endangered.

s #ONDUCTEDCOOPERATIVESAMPLINGEFFORTIN0UGET3OUNDNEARSHOREENVIRONMENTSTOBETter understand life history patterns of six Skagit River Chinook populations. The sampling program filled important life history data gaps and greatly improved our ability 

to model potential effects of restoration on various life history patterns. The findings 

of this study have led to an expanded Puget Sound-wide sampling program being conducted by scientists with the NWFSC, U.S. Geological Survey, and local tribes, with 

monetary support from Seattle City Light, U.S. Army Corps of Engineers, and the Port 

of Bellingham.

s (OSTEDANINTERNATIONALCONFERENCEON"ACTERIAL+IDNEY$ISEASE"+$	WITHPRESENtations on the history, current research, and future needs and directions in the study 

of Renibacterium salmoninarum. The R. salmoninarum Genome Project was also publicly unveiled during the conference. Microbiologists, fisheries biologists, and resource 

MANAGERSFROMTHE5NITED3TATES#ANADA)CELAND.ORWAYANDTHE5NITED+INGDOM

attended the conference. A conference website with most of the scientific presentations 

and future needs summaries is hosted by the NWFSC.

s (OSTEDAWORKSHOPTOIDENTIFYNEEDSANDFUTUREDIRECTIONSFORA7EST#OASTPROGRAM

using marine mammals as sentinels of ocean change impacting human health. Veterinarians, biologists, and epidemiologists working with marine mammals attended, a 

West Coast network is proposed, and website for communication among attendees will 

be hosted by the NWFSC.

s 3AMPLED#ALIFORNIASEALIONSONTHE#HANNEL)SLANDS3AN-IGUEL)SLANDAND3AN.ICOlas Island) and in Seattle for the incidence of different zoonotic fecal bacteria. A high 

prevalence of Salmonella spp. and Campylobacter spp. was identified on the islands; 

Salmonella decreased northwards, and Salmonella isolates from the islands showed no 

A chinook salmon in spawning 

colors. Photo: USGS.
72

antibiotic resistance. Presence of both these bacteria in gulls suggests these birds may be 

important vectors of these enteric bacteria.

s )NVESTIGATEDTHEPREVALENCEOFDIFFERENTZOONOTICFECALBACTERIAINELEPHANTSEALSAND

areas of high Salmonella and Campylobacter spp. prevalence were identified.

s #HAIREDA"IOLOGICAL2EVIEW4EAMTOREVIEWTHESTATUSOFTHE3OUTHERN2ESIDENTKILLER

whale population. The team evaluated whether these whales were a distinct population of the global killer whale species, examined why the whale population has been 

declining, and estimated the risk of extinction of this stock. The report led to a listing 

as endangered.

s #O
HOSTEDWITHTHE7ASHINGTON$EPARTMENTOF&ISHAND7ILDLIFEANDTHE#ANADIAN

Department of Fisheries and Oceans, a killer whale research symposium to review recent research accomplishments and identify future priorities.

s #ONDUCTEDRESEARCHON3OUTHERN2ESIDENTKILLERWHALESINCLUDINGSTUDIESTODETERMINE

what species and stocks of fish they prey upon. 

s 3AMPLEDEIGHTADULT#ALIFORNIASEALIONSWITHDOCUMENTEDUROGENITALCANCERlVENON


cancerous sea lions for DNA adduct analyses, and 14 fresh dead late-term sea lions for 

additional analyses.

s %STABLISHEDADETAILEDPOSTMORTEMSAMPLINGPROTOCOLIEUROGENITALTRACTOTHERPArenchymal tissues) for both cancerous and non-cancerous sea lions. Tissue samples for 

both DNA adduct analysis and future caricinogenesis studies were obtained.

s $ETERMINEDTHEANTIMICROBIALRESISTANCEINEscherichia coli isolated from rectal swabs 

using broth microdilution from free-ranging elephant seals on their natal beaches and 

stranded seals at admission and release from the Marine Mammal Center. These results 

indicate antibiotic resistant E. coli are acquired by elephant seals in coastal waters rather 

than on the beach from other seals.

s -EASUREDCHEMICALSIGNALSFATTYACIDPROlLESCARBONANDNITROGENSTABLEISOTOPERAtios, and persistent organic pollutants (POPs) concentrations, patterns, and ratios—in 

blubber biopsy samples and used this data to provide information about prey species 

of killer whale groups called “ecotypes.” In North Pacific waters, two ecotypes have 

been identified—the “transients” (thought to prey solely on marine mammals) and the 

“residents” (believed to principally consume marine fish). Because of possible predation 

by Alaskan transients on protected Alaskan marine mammal populations, more information is needed about the specific diet of this ecotype. In the current study, carbon 

and nitrogen stable isotope ratios, supported by field observations of the transient diet, 

found that it is unlikely that Steller sea lion pups represent a substantial proportion 

the overall diet for Alaska transients. In addition, Alaskan resident killer whales were 

found to be consuming a fish diet, based on both field observations and their chemical 

signatures compared to those of other resident populations. A third ecotype—the “offshores”—had fatty acid profiles in the blubber most similar to those of the fish-eating 

resident ecotype. POP concentrations and ratios suggested these whales are consuming 

contaminated, predatory species that are distinctly different from those of sympatric 

resident and transient killer whales.

s $EVELOPEDASTATUSREPORTONTHESTATEOFTHE#ALIFORNIA#URRENTTOBEUSEDBYlSHERIES

managers. 

s )NITIATEDAMULTI
AGENCYCOLLABORATIVEPROCESSTODEVELOPASCIENTIlCFRAMEWORKFORAN
ecosystem approach to management in 

Puget Sound. 

s )NITIATED PROJECTS TO STUDY THE EFFECTS OF

climate change on salmon population viability.

s ,EDANINTER
INSTITUTIONALEFFORTTODEVELOP

new tools for ecosystem-based management, including efforts with University of 

Washington to include climate cycles and 

climate change scenarios in rebuilding 

models.

s "ECAME A ./!! /CEANS AND (UMAN

Health Initiative Center of Excellence to 

investigate linkages between ocean processes and human health—specifically the 

impacts of pathogens, marine biotoxins, 

and toxic chemicals on both seafood and sentinel species. 

s 7ITHCOLLABORATORSATTHE.ATIONAL2ESEARCH#OUNCIL#ANADA5NIVERSITYOF7ASHINGton, and University of Maine, determined the molecular basis for resistance to paralytic 

shellfish toxins in clams. Determined that a mutation in the sodium channel of nerves 

in clams from areas that have records of paralytic shellfish poisoning (PSP) results in a 

single amino acid change in these channels, conferring over 1000x resistance of clams 

to saxitoxins. This is the first demonstration of a harmful algal bloom (HAB) as a 

natural selection agent in the marine environment, resulting in greater rates of toxin 

accumulation in exposed clams, thereby increasing the risk of PSP to humans. This 

understanding of shellfish adaptation to toxins will serve as a model for improved characterization of the effects of oceans on human health.

s ,EDAMULTI
INSTITUTIONALSTUDYOFTHEECOLOGYOFHARMFULALGALBLOOMSALONGTHE7EST

Coast of the United States. Scientists successfully identified a potential “bloom initiation site” and correlated storm activity with the arrival of toxic blooms on the coast. The 

use of drifter buoys to track blooms also has provided insight into the conditions that 

favor the movement of HABs toward shore, where shellfish beds may be contaminated. 

In addition, the biophysical models resulting from this project will be applicable to 

other coastal regions around the world that are affected by similar toxic events.

s 0ARTICIPATED IN TWO (!" SAMPLING CRUISES TO COLLECT BACTERIAL SAMPLES FROM PHYTOplankton bloom areas off the Washington coast in order to begin studies on the relationship of Vibrio parahaemolyticus with algal blooms. These samples will be analyzed 

for V. parahaemolyticus by qPCR, and the presence/absence compared to sample data 

already available, including species of phytoplankton and salinity/temperature/depth 

data for each sample and sample site.

s )DENTIlEDKEYFACTORSEXPRESSEDBYPATHOGENICVibrios that contribute to shellfish colonization and ability to cause disease in human hosts. Understanding the mechanisms 

used by the bacteria to persist in the environment holds promise toward development of 

methods to eliminate them from shellfish prior to market.

s !NALYZEDTHERISKOFZOONOTICDISEASEINTEGRATINGLANDSCAPEECOLOGYCOMMUNITYTHEOry, and epidemiology in Bayesian relational models.

Microscopic view of 

Pseudo nitzschia plankton, 

prominent in harmful algal 

blooms (HABs) and which 

accumulate in shellfish and 

are potentially lethal to 

humans. Photo: NMFS.
74

s #HARACTERIZEDTHEIMPACTOFPOLYCYLICAROMATICHYDROCARBONS0!(	EXPOSUREONTHE

kinetic expression of both innate and adaptive immune system genes in rainbow trout. 

s %STABLISHEDAZEBRAlSHMODELSYSTEMASANEWEXPERIMENTALSYSTEMFORINVESTIGATING

the impacts of chemical contaminants on fish development. Studies showed that the 

developing heart is the most likely target of PAH toxicity, and that deformities in PAHexposed embryos can be attributed to cardiac arrhythmia and circulatory failure. These 

findings hold considerable promise for developing new cardiovascular biomarkers that 

can be used to monitor the health of at-risk fish species in the coastal waters of the 

United States. 

s )MPLEMENTEDASERIESOFINNOVATIVEIMPROVEMENTSTOTHEMETHODSUSEDTOANALYZEFOR

persistent organic pollutants in environmental samples. The new procedures have improved quality assurance results significantly, so that now more than 90 percent of 

analyses in standard reference material agree with certified values (70 percent is the 

minimum allowable). Furthermore, costs for the analyses have been lowered by 43 percent. Finally, safety has been improved considerably by reducing solvent consumption 

by 60 percent and hazardous waste by 40 percent.

s -ONITORED CONTAMINANT CONCENTRATIONS IN WATER SEDIMENTS AND JUVENILE #HINOOK

salmon from five sites along the Columbia from Bonneville to the mouth of the estuary, 

and from local hatcheries, and are using the data to model potential impacts on salmon 

health and survival. Results indicate toxicants are widespread in the system, with particularly high concentrations in the Portland area. In addition, salmon are being exposed to other environmental stressors (i.e., estrogenic compounds and brominated fire 

retardants [PBDE]). These data were used to develop a population dynamic model to 

assess the incidence and corresponding significance of delayed disease-induced mortality in outmigrant salmon populations associated with environmental stressors.

s $EPLOYEDSEVERALDATABASESTOSUPPORTRESEARCHINVOLVEDWITH%3!
LISTEDSALMONSPECIES

for abundance, artificial propagation release and spawner, age structure, harvest fraction, bird predation, and habitat data tied to ArcInfo IMS mapping software available 

online. These efforts are aimed at bringing together disparate data sources, integrating 

where feasible, and providing a centralized corporate repository that will be managed 

over the data and application life cycle tied to geospatial locations for query and analysis. 

s $EPLOYEDACENTRALIZED')3REPOSITORYWITHOVERCORPORATEGEOSPATIALLAYERSAND

individual project layers and serving over 30 GIS users within the Center. Efforts are 

expanding to share the NWFSC GIS infrastructure and technical support with the 

Northwest Regional Office users for ESA-listed salmon recovery efforts. 

s 7ORKEDCLOSELYWITHTHE.ORTHWEST2EGIONAL/FlCETODEVELOPACENTRALIZEDWEB
ENabled database to track funds from the Pacific Coastal Salmon Recovery Fund (PCSRF) 

with five states and 10 tribal groups. This database is tracking $462 million in funding 

for over 5,857 projects and has been used to generate data needed for the PCSRF Annual Report to Congress.

s )NCOLLABORATIONWITH/REGON3TATE5NIVERSITYCREATEDA'EOLOGICAND'EOPHYSICAL"OTtom Character Database and GIS for U.S. West Coast groundfish. The database and 

GIS project for West Coast Essential Fish Habitat is a joint effort between the NWFSC 

and the Active Tectonics and Seafloor Mapping Laboratory at Oregon State University.

s $EVELOPEDANACCESSDATABASEOFHABITATUTILIZATIONOFGROUNDlSHTOSUPPORTANALYSISOF

Essential Fish Habitat information.
s -ERGEDTHE.ORTH0ACIlC-ARINE3CIENCE/RGANIZATION0)#%3	(ARMFUL!LGAL"LOOM

(HAB) Section harmful algal event database (HAE-DAT) with the ICES/IOC database. The goal is to enroll countries in the creation of worldwide maps that will document harmful algae events on a yearly basis. This marked the first year of PICES 

member country HAB data submission to HAE-DAT.

s !PPLIEDINNOVATIVETECHNOLOGIESSUCHASTHEUSEOF!56STOSURVEYROCKlSHANDTHEUSE

of biopsy hooks to assess groundfish abundance of rockfish by genetic identification on 

individuals for “tag recapture” assessments. 

s #ONDUCTEDANINTEGRATEDSTUDYUSINGRADIOTELEMETRYAND0)4
TAGTECHNOLOGYTOEVALUate total project survival, route-specific survival, and fish passage behavior at Ice Harbor 

and Lower Monumental Dams for yearling and sub-yearling Chinook salmon. 

s #ONDUCTED ANALYSES IN SUPPORT OF THE #OLUMBIA 2IVER &EDERAL (YDROPOWER 3YSTEM

Biological Opinion, including analyses of the survival changes necessary to reach the 

population viability goals set by the Technical Recovery Teams.

Research Priorities, FY 2007–2012

I.A. Biological research concerning the 

abundance and life history of fish stocks

The following surveys are planned:

s #ONDUCT AN ANNUAL BOTTOM TRAWL SURVEY ON GROUNDlSH ACROSS THE ENTIRE #ALIFORNIA

Current LME with chartered fishing vessels.

s #ONDUCTTHEBIENNIALMIDWATERTRAWLACOUSTICSURVEYSTOASSESSTHEABUNDANCEOFHAKE

off the West Coast using the NOAA FSV Miller Freeman. This survey will be conducted in collaboration with the Department of Fisheries and Oceans Canada. 

s #ONDUCTTHEANNUALGROUNDlSHJUVENILEPRERECRUITSURVEYFROMTHE#ANADIANBORDERTO

central California.

In addition, in response to GAO recommendations, the Center will continue to develop 

new surveys for groundfish to address needs for additional information on species not 

surveyed by traditional bottom trawl surveys. These surveys include:

– An annual survey using AUV platforms developed by Woods Hole Oceanographic to 

survey species in untrawlable areas

– An annual survey of widow rockfish in cooperation with the fishing industry.

– An annual hook and line survey of vermillion and bocaccio rockfish in the Southern 

California bight.

s 4HEFOLLOWINGOBSERVERPROGRAMSAREPLANNEDFORTHEGROUNDlSHlSHERIESTHATOCCUROFF

California, Washington and Oregon:

– 25 percent observer coverage of permitted trawl fleet.

– 25 percent observer coverage of permitted fixed-gear fleet.

– 100 percent observer coverage of fishing vessels at-sea processor fleet.

– 5 percent observer coverage of the open-access groundfish fleet.

s 4HE.7&3#WILLCOORDINATETHEASSESSMENTANDREVIEWOFTHESTATUSOF7EST#OAST

groundfish stocks. The NWFSC will coordinate and organize pre-assessment workshops, including workshops on modeling, data, and trawl survey data use and standards. 
76

s 3TOCK ASSESSMENT SCIENTISTS WILL 	 ASSESS THE STATUS OF 0ACIlC OCEAN PERCH SABLElSH

Pacific hake, darkblotched rockfish, canary rockfish, English sole, arrowtooth flounder, 

and longnose skate; and 2) test and improve the capability of assessment software to use 

available ecological indicators and correctly estimate pertinent fishery parameters.

s 4HE.7&3#COOPERATIVEAGEINGLABORATORYWILLPRODUCEAGEINFORMATIONTOSUPPORT

assessments of Pacific hake, Pacific ocean perch, sablefish, Dover sole, canary rockfish, 

darkblotched rockfish, arrowtooth flounder, and English sole. 

s 4HE.7&3#STAFFWILLIMPROVETHERELIABILITYOFlSHAGESUSEDINASSESSMENTSTHROUGH

further age validation research.

s 4HE.7&3#WILLCONTINUETOPROVIDEANALYSESTOSUPPORTBIOLOGICALLYBASEDDELISTING

goals for listed salmon and steelhead. This work will be carried out by the Puget Sound, 

Willamette/Lower Columbia River, Columbia River Basin, and Oregon and Northern 

California Coast Technical Recovery Teams (TRTs). TRTs will apply extinction risk estimates to salmonid populations to establish rationally based priorities for recovery goals.

s #ENTERSTAFFWILLCONDUCTRESEARCHTOEVALUATENEWLYDEVELOPEDMETHODSFORTHEANALYsis of population genetic data and their applicability to real-world problems in natural resource management (these methods and evaluations are applicable to all species 

under NMFS’ jurisdiction). Genetic Stock Identification studies will be continued to 

determine stock allocation under the Pacific Salmon Treaty, help elucidate the ocean 

migration patterns of listed salmon stocks, and compare different methods of stock 

identification.

The NWFSC will also:

s )NITIATERESEARCHPROJECTSTOMEASURETHELONG
TERMEFFECTSOFHATCHERYSUPPLEMENTATION

on the abundance, productivity, and diversity of wild salmon populations. 

s #ONTINUEANDINITIATENEWRESEARCHONTHEPREDICTEDEFFECTSOFCLIMATECHANGEON.ORTHwest ecosystems, particularly with regard to ESA-listed Pacific salmon.

s !SSESSCONDITIONOFJUVENILESALMONDURINGEARLYOCEANENTRYIN0UGET3OUNDAND7ASHington coast.

s !SSESSTHEDISTRIBUTIONANDRELATIVEABUNDANCEOFRESIDENTRAINBOWTROUT	ANDANADROmous (steelhead) Oncorhynchus mykiss to help determine population status.

s $EVELOPANOCEANCONDITIONINDEXOFTHE#ALIFORNIA#URRENTECOSYSTEM

s $EVELOP MORE EFlCACIOUS VACCINES OR CHEMOTHERAPEUTANTS TO TREAT "ACTERIAL +IDNEY

Disease in salmon.

I.B. Interdependence of fisheries or stocks of fish

NWFSC staff will:

s $EVELOP BIOENERGETICS MODELS FOR Sebastes species, and use these models to examine 

various issues, such as per capita prey demand of different species, the influence of temperature anomalies (e.g., PDO shifts, El Niño) on fish growth and reproductive potential, and habitat-specific prey allocation across different life history stages of rockfish.

s #OLLECTANDANALYZESTOMACHCONTENTSOFGROUNDlSHTODETERMINEECOLOGICALLINKAGES

between species.
s $EVELOPANDMAINTAINANECOSYSTEMMANAGEMENTMODELFORTHE#ALIFORNIA#URRENT

LME.

s !NALYZESURVEYANDOBSERVERDATATODETERMINESPATIALDISTRIBUTIONSOFDIFFERENTSPEcies.

s $EVELOPGENETICBASELINEDATAFORSELECTEDSPECIESOFGROUNDlSHTOESTABLISHSTOCKSTRUCture and stock boundaries.

s $ETERMINE INCIDENCE OF CODED
WIRE TAGGED SALMONIDS IN COMMERCIAL AND RESEARCH

groundfish catches. 

s #ONDUCTlELDOBSERVATIONSONHOMERANGESOFROCKlSHANDLINGCODANDDEVELOPMODEL

to link these data to Marine Protected Area design.

s $EVELOPBIOPHYSICALMODELSTOQUANTIFYTHEECOLOGICALLINKAGESOFJUVENILESALMONDIStribution, growth, and survival in Pacific Northwest estuarine and coastal marine waters.

s )MPROVEUNDERSTANDINGOFTHEIMPACTOFFUTURECLIMATECHANGEONOCEANCONDITIONSOF

the California Current ecosystem.

s )NPARTNERSHIPWITHTHE-ARINE-AMMAL#ENTERDEVELOPTOOLSTOMEASURETHEPRESENCE

of and effects of domoic acid and chemical contaminants in California sea lions, which 

serve as a model for human heath impacts and a proxy for ecosystem condition.

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

The NWFSC will:

s #ONDUCTACOUSTICSURVEYSOFOCEANmOORTOCHARACTERIZEANDIDENTIFYBOTTOMTYPEAND

map groundfish habitats off the West Coast.

s #ONDUCTPILOTMAPPINGOFAREASCLOSEDASGROUNDlSHESSENTIALlSHHABITAT

s $ESCRIBEBENTHICHABITATSCOMMUNITYSTRUCTUREOFTHEHABITATSANDTHEBASICLIFEHISTOries and distributions of corals, sponges, and other benthic invertebrates in the California Current LME.

s $EVELOPTOOLSFORRECOVERYPLANNINGTHATMELDECONOMICCOSTSWITHBIOLOGICALBENElTS

to ensure that conservation planning is responsive to both economic considerations and 

biological needs

I.D. Impact of anthropogenic factors and 

environmental changes on fish populations

The NWFSC will:

s !SSESSEFFECTSOFlSHINGON%&(ANDDEVELOPWAYSTOMINIMIZEADVERSEIMPACTS

s !NALYZETHERESPONSEOFGROUNDlSHPOPULATIONSTOCHANGESINCLIMATEANDTHEECOSYStem.

s !SSESSTHEEVOLUTIONARYCONSEQUENCESOFANTHROPOGENICCHANGESONSALMONPOPULATIONS

(previous assessments have focused almost entirely on demographic effects). 

s $EVELOPBIOENERGETICMODELSANDAPHOTOGRAPHICKEYFORLARVALROCKlSH
78

s %VALUATEPOTENTIALLONG
TERMEFFECTSOFSHORT
TERMEXPOSUREOFJUVENILESALMONTOENDOcrine disrupting contaminants that are present in sewage waste water effluent.

s %VALUATEPOTENTIALENDOCRINEDISRUPTINGACTIVITYOFmAMERETARDANTCHEMICALS0OLYbrominated diphenyl ethers (PBDEs)—in fish.

s !NALYZEEFFECTSOFMULTIPLESTRESSORSONSALMONANDMARINElSHPOPULATIONSTHROUGHUSE

of next generation population dynamic models.

s $ETERMINERELATIONSHIPSBETWEENLANDUSESTORMWATERmOWSWATERQUALITYlSHHEALTH

survival/reproduction, and population viability for Pacific salmon in urbanizing areas.

s $EVELOP METHODS FOR ASSESSING DEVELOPMENTAL PROCESSES IN WILD SALMON AND MARINE

fishes.

s )MPLEMENTAFORECASTINGCAPABILITYFORDETECTINGANDRESPONDINGTOHARMFULALGALBLOOM

events on the Northwest coast.

s 5SINGCHEMICALSIGNATURESEVALUATETHELIFEHISTORYANDFEEDINGECOLOGYECOTYPESFOR

killer whale populations on a global scale.

s ,INKHABITATCHARACTERISTICSTOSALMONPRODUCTIVITYINAQUANTITATIVEMANNERFORFRESHwater and estuarine systems of the West Coast.

s $ESCRIBETHERELATIONSHIPBETWEENIMPAIREDREPRODUCTIVEPROCESSESANDCONTAMINATION

of urban bays for marine groundfish species. 

s %VALUATETHELONG
TERMEFFECTSOFSUPPLEMENTATIONHATCHERIESONTHEABUNDANCEGENETIC

and demographic characteristics of salmon populations in the Pacific Northwest.

s $ETERMINEIMPACTOFENVIRONMENTALCHANGETEMPERATURESALINITYZOOPLANKTONQUALity/quantity, etc.) on growth and development of larval marine fish. Develop a predictive model based on results.

II. Conservation Engineering Research

Recent Accomplishments:

s .7&3#STAFFCONTINUEDTOWORKWITHTHE3TATEOF/REGONTOTESTANDDEVELOPGEAR

to reduce the capture of overfished groundfish. Initiated in 2004, this project used a 

state-of-the-art ultrasonic camera (DIDSON, or dual frequency identification sonar) in 

conjunction with conventional in situ video to document and categorize fish behavior 

during the sequence of capture in bottom trawls with an emphasis on a selective flatfish 

trawl—an experimental net being used in West Coast groundfish fisheries. 

s 4HE.7&3#CONDUCTEDRESEARCHTOPRODUCE#HINOOKSALMONFROMARTIlCIALPROPAGAtion programs with age of maturity similar to that of fish rearing in their native habitat. 

Juvenile salmon rearing conditions and growth regimes that reduce proportions of males 

maturing at age 2 have been developed. This information is being used to control age 

of maturity in fish reared in captive broodstock programs to aid recovery of ESA-listed 

stocks of Pacific salmon. Spawning locations for hatchery and wild spring Chinook 

salmon in the Yakima River were characterized and the efficacy of acclimation ponds for 

improving homing fidelity of hatchery fish determined. Center staff initiated a large-scale, 

long-term experiment to quantify the demographic and genetic effects of supplementation-type hatcheries, and developed a method of detecting natural spawning of salmon 

by implanting electromyogram transmitters and monitoring muscle activity.
s #ENTERSTAFFDEVELOPEDBIOlLMANDCHITINBINDINGASSAYSFORV. parahaemolyticus and 

V. vulnificus. These assays will be used to assess the role of the type IV adhesins in 

environmental persistence. Center staff also demonstrated that the V. vulnificus type 

IV fimbrial adhesin encoded by PilA is required for biofilm formation, epithelial cell 

adherence, virulence, and persistence in oysters, confirming that the PilA adhesin is an 

important colonization factor. This is the first study to show that a specific bacterial 

protein structure contributes to colonization of shellfish. They also confirmed that PilA 

and MshA are highly conserved among all strains of V. parahaemolyticus isolated from 

many geographical areas (like V. vulnificus). This suggests that adherence and colonization factors identified for one strain will be applicable to all, an important consideration 

for development of a universal colonization inhibitory factor. 

s #ENTERSTAFFALSOCONSTRUCTEDIN
FRAMEDELETIONMUTANTSINTHE0IL!GENEINBOTHV. 

parahaemolyticus and V. vulnificus. In order to study the role of the PilA and MshA 

adhesins, it is necessary to construct mutants unable to express these proteins without 

affecting expression of adjacent genes. This was a significant hurdle requiring considerable 

empirical experimentation. Development of the method will now allow us to construct 

similar mutants deficient in expression of MshA, as well as strains defective in expression 

of both adhesins. 

s .7&3#STAFFDEVELOPEDCYTOMETRICCRITERIAFORTRACKING(!"S)DENTIlCATIONOFFUNCtional phytoplankton groups is now possible. A single cell immunofluorescent assay for 

domoic acid was developed through a jointly sponsored study between the University 

of Washington’s Pacific Northwest Center for Human Health and Ocean Studies and 

NOAA's West Coast Center for Oceans and Human Health.

s 4HE.7&3#DEVELOPEDMETHODSTOCHARACTERIZETHEDIVERSITYOF6$AND*REGIONSWITHIN

salmon lymphocytes that will be used to assess the potential impact of contaminants 

on antibody diversity, and thereby provide a fundamental underpinning for observed 

population level effects.

s )NITIALIMMUNOHISTOCHEMISTRYWASCOMPLETEDONVARIOUSTISSUESFROMSIXSEALIONSTO

DETERMINEWHETHERANTIBODIESTOPESTROGENRECEPTORPROGESTERONERECEPTOR+I

and E-cadherin will cross-react with formalin fixed paraffin embedded sea lion tissue. 

Initial results indicate good cross reactivity between sea lion tissues and all the antibodies 

except anti p53. Interestingly, an estrogen receptor was identified in genital epithelium 

in males and females.

s .7&3#STAFFCONTINUEDDEVELOPINGANDTESTINGACOUSTICTECHNOLOGIESDESIGNEDTOMEASURE

survival and behavior of anadromous salmonid juveniles at Columbia River hydroelectric 

projects and in the river’s estuary and plume environment.

Research Priorities, FY 2007–2012:

NWFSC staff will:

s #ONDUCTSURVEYSOFHABITATTOMEASUREDIRECTEFFECTSOFBOTTOMTRAWLINGONSEAmOOR

habitat. 

s #ONDUCTlSHBEHAVIORALSTUDIESINlELDTOASSISTINDEVELOPMENTOFGEARTOREDUCEBYcatch and bycatch mortality of prohibited, undersized, or unmarketable species.

s 7ORKWITHINDUSTRYANDTHE#OUNCILTODEVELOPBYCATCHREDUCTIONTECHNIQUES
80

s$EVELOP GROUNDlSH INFORMATION FOR NAtional reports on bycatch.

s#ONTINUETOFUNDINDUSTRYCOOPERATIVEREsearch projects that propose the development of bycatch reduction methods.

s#ONTINUETODEVELOPANACOUSTICTELEMETRY

receiver array in Puget Sound and Hood 

Canal to track the movements and estimate survival of numerous marine species, 

monitor species interactions, and identify 

important habitats.

s#ONTINUETODEVELOPUNDERSTANDINGOFHOW

and why pathogenic Vibrio bacteria persist 

in the environment and develop methods 

to remove them from harvested shellfish 

prior to market.

s#ONTINUETOSTUDYV. parahaemolyticus association with marine phytoplankton, zoo

plankton, and various climatic and ocean conditions in order to develop and refine risk 

assessment models for the shellfish industry and public health agencies.

s 5SERADIOTELEMETRYAND0)4
TAGTECHNOLOGYTOEVALUATETHEPERFORMANCEOFREMOVABLE

spillway weirs as a surface-oriented passage route for yearling and sub-yearling Chinook 

salmon at Ice Harbor and Lower Monumental Dams.

s #ONTINUEADVANCING0)4
TAGANDACOUSTICTECHNOLOGIESTOPROMOTESAFEANDEFlCIENT

fish passage through hydropower systems and other unnatural barriers, and to gain 

understanding of migration patterns.

III. Research on the Fisheries

Recent Accomplishments:

The NWFSC developed and began fielding a survey to collect cost information from 

the West Coast groundfish trawl fleet. Phase 1 of this effort, covering Oregon trawlers, 

has yielded a positive response rate of over 65 percent. A recreational valuation survey of 

Washington and Oregon recreational anglers was also developed and initiated. A new 

economist was hired to coordinate data collection and model development for analyzing 

regional income impacts associated with West Coast fisheries. Center staff developed objectives and methodology for a cost-earnings data collection program covering West Coast 

groundfish fisheries and ocean troll salmon fisheries. A pilot research project on methods 

for enumerating and profiling Washington coast communities involved in West Coast and 

North Pacific fisheries, including the West Coast groundfish and salmon fisheries, was 

conducted. Frameworks to discuss communities in quota systems were also developed. The 

Pacific Fishery Management Council (PFMC) was able to select specific community options 

for future impact analysis in an environmental impact statement process. NWFSC staff 

conducted collaborative research to gain a greater understanding of management measures 

that have been incorporated into global individual quota systems with the specific goals of 

protecting or addressing community impact and issues under a quota system.

Quillback rockfish. Photo: 

Timothy Nesseth, NOAA.
In 2005–2006, NWFSC staff provided critical responses (cruises on the R/V Nancy Foster

and Gordon Gunter) through sampling of seafood species (i.e., mollusks, crustaceans, and 

fish) and measured chemical contaminant levels to provide information for determining 

SUITABILITYFORCONSUMPTIONASARESULTOF(URRICANE+ATRINA)NADDITIONPATHOGENSWERE

measured in water, sediment, and tissues to assess risks to humans.

Salmon-related accomplishments included:

s )NITIATEDRESEARCHTOESTIMATERATESOFEARLYMALEMATURATIONOFSPRING#HINOOKSALMON

in Columbia Basin production hatcheries.

s #ONDUCTEDRESEARCHTOMAXIMIZETHElTNESSOFSALMONREAREDANDRELEASEDFROMARTIlcial propagation programs aimed at conserving depleted salmon and steelhead populations.

s #ONTINUEDCOOPERATIVEACTIVITIESUSING#ENTER
DEVELOPEDCAPTIVEBROODSTOCKTECHNOLogy, to spawn sockeye and Chinook salmon captive broodstock for use in stock restoration activities in Idaho and Oregon. This effort returned more than 350 sea run sockeye 

salmon adults to the Stanley Basin Lakes over the past 8 years (1999–2006). This is 

more than a 20-fold increase over the number of fish returning to the Lakes during the 

prior 8 years (1991–1998). 

s &ROMINCEPTIONOFRESEARCHPROGRAM	TO.7&3#STAFFHAVEDEVELOPEDAND

improved the technology to rear 10 species of local marine organisms from the egg to 

the juvenile stage. Five species had never been reared before. The capacity to produce 

small numbers of juvenile marine fish for laboratory study allows development of bioenergetic models to improve models used for management, and opens the door for smallscale stock enhancement and commercial aquaculture experiments with those species. 

Specific studies have focused on optimizing environmental conditions and nutritional 

quality of early life stages of a variety of marine organisms. Genetic studies and smallscale releases (less than 25 fish) of two species have occurred. Additionally, experiments 

designed to commercialize the culture of two species of local marine fish (sablefish and 

lingcod) were conducted. Studies included development of hatchery and grow-out technology, feeds development, and final product quality evaluation. Sablefish is now being 

reared commercially, and lingcod is being considered by industry.

s #ENTER STAFF CO
AUTHORED THE #ODE OF #ONDUCT FOR 2ESPONSIBLE !QUACULTURE IN THE

United States Exclusive Economic Zone (EEZ) and the Draft National Offshore Aquaculture Act now before Congress.

s 4HE.7&3#PROVIDED./!!WITHTHElRST!QUACULTURE-ATRIX-ANAGER!DDITIONAL

staff served and still serve as a part of the NOAA Aquaculture Matrix team and provide 

written and verbal technical information to the NOAA Aquaculture Matrix Manager.

s .7&3#(!"STAFFCONDUCTEDAPILOTlELDSTUDYONTHEEFFECTSOF(!"SONPLANKtivorous fish and assessed the potential for risk by consumption of HAB-contaminated 

seafood using a cruise of opportunity (leveraged from PNW ECOHAB). 

s 4HE .7&3# DEMONSTRATED THE UTILITY OF THE ZEBRAlSH MODEL FOR CROSS
DISCIPLINARY

research with applications to both human and fish health.

s 4HE.7&3#AQUACULTURETEAMDEVELOPEDANDDEMONSTRATEDAlSHMARINEALGAECO


culture aquaculture system. The algae portion has been commercialized.

s 4HE#ENTERWORKEDWITHPARTNERSTODEVELOPANDAPPLYHATCHERYREFORMPROTOCOLSAS
82

part of the congressionally established Puget Sound Hatchery Scientific Review Group 

and the U.S. Fish and Wildlife Service Hatchery Review Team for service facilities in 

the Columbia River Basin. 

s 4HE.7&3#LEDTHEEFFORTTOSEQUENCETHEGENOMEOFTHEPREDOMINANTBACTERIALPATHOgen of ESA-listed salmon stocks, Renibacterium salmoninarum, and the causal agent of 

"ACTERIAL+IDNEY$ISEASE"+$	4HERESULTSANDDATAGENERATEDWILLAIDSTUDIESONTHE

development of more efficacious therapeutic treatments or vaccines, increasing broodstock and hatchery fish survival. 

s 4HE#ENTERPUBLISHEDASERIESOFREVIEWPAPERSONTHERISKSOFSALMONCULTURETOTHE

Pacific Northwest marine ecosystem and human health. 

s 4HE#ENTERORGANIZEDANDHOSTEDAN)NTERNATIONAL7ORKSHOPONTHE2ISK!SSESSMENT

of Marine Fish Aquaculture on behalf of the United States and the European Union 

for the FAO Committee on Fisheries (COFI), Sub-committee on Aquaculture (April 

2005). 

Research Priorities, FY 2007–2012:

III.A. Social and economic research

s %XPAND SOCIOLOGICAL AND ECONOMIC RESEARCH AND INCORPORATE RESULTS INTO THE lSHERY

management process by collecting cost earnings data from fleets and coastal communities, and developing models that can integrate with ecosystem models for evaluating the 

socioeconomic effects of management or stock abundance changes. 

s #ONDUCTRESEARCHONTHEVALUATIONOFRECREATIONALlSHERIESANDDEVELOPMODELSFOREVALuating the effects of management or stock abundance changes.

s #OMPILEANDANALYZESOCIOECONOMICDATATOBEADDEDTOECOSYSTEMMANAGEMENTMODels.

s $EVELOPANDANALYZEINFORMATIONTOBEUSEDINDEVELOPMENTOF)&1ALTERNATIVESFORTHE

West Coast groundfish fishery.

s )NVESTIGATETHEINTERDEPENDENCEOF7EST#OASTCOMMUNITIESINVOLVEDINlSHINGAND

their social and economic dependence on North Pacific and other non-West Coast fisheries.

s $ESCRIBEANDENUMERATE7EST#OASTENVIRONMENTALJUSTICECOMMUNITIESDEPENDENTON

or engaged in fishing.

s $EVELOPMETHODSANDCOLLECTDATATOFACILITATETHEEVALUATIONOFTHECOST
EFFECTIVENESSOF

actions for the implementation of recovery planning for endangered species.

s $ESCRIBECHARACTERIZEANDQUANTIFYNON
CONSUMPTIVESOCIALANDECONOMICVALUESASSOciated with Northwest marine mammal populations, specifically the Southern Resident 

killer whales of the Greater Puget Sound.

s #LARIFYANDDESCRIBECOMMUNITIESTHATAREDEPENDENTONENGAGEDINOROTHERWISEIMpacted by the West Coast Groundfish Trawl fleet. Data will be used in the future analysis of impacts on communities under a quota management system. 

s $EVELOPBEHAVIORALMODELSOFECONOMICINCENTIVESAFFECTINGTHELEVELANDALLOCATIONOF

fishing effort in fisheries with FMPs.
s %XPAND SOCIOLOGICAL AND ECONOMIC RESEARCH AND INCORPORATE RESULTS INTO THE lSHERY

management process. 

s #OMPILEANDANALYZEADDITIONALDATAONHARVESTINGANDPROCESSINGSECTORBEHAVIOR

s %XPAND SOCIOLOGICAL AND ECONOMIC RESEARCH AND INCORPORATE RESULTS INTO THE lSHERY

management process.

s )NVESTIGATELOCALKNOWLEDGESOITMAYBEINCORPORATEDINTOTHEDESIGNANDMANAGEMENT

of marine protected areas and quota systems.

s )NVESTIGATEHUMANINSTITUTIONALATTRIBUTESASSOCIATEDWITHSUCCESSFULEFFORTSTORESPOND

to watershed flow conditions, and that are consequently linked to the implementation 

of water flow controls to support salmon recovery.

III.B. Seafood safety research

s )MPROVEMETHODSTOELIMINATEPATHOGENICVibrio bacteria from harvested shellfish prior 

to market.

s $EVELOPAREALTIME0OLYMERASE#HAIN2EACTION0#2	ASSAYTOTESTFORACORRELATION

between Vibrio parahaemmolyticus and algal blooms in marine waters, which may be 

useful for the development of new risk assessment tools for the presence of this pathogen in shellfish.

s $EVELOPMETHODSTORAPIDLYASSESSPATHOGENPRESENCEINCOASTALWATERSANDESTIMATERISK

of exposure through recreational water use or shellfish consumption.

s $EVELOPBIOSENSORSFORIDENTIlCATIONOFPHYTOPLANKTONRELATEDTOHUMANHEALTHRISKS

s $EVELOPMODELSFORPREDICTINGCARDIOVASCULAREVENTSINHUMANSEXPOSEDTOURBANPOLlutants, and methods to mitigate such effects.

s )MPROVEMODELSOFDISEASETRANSMISSIONPROCESSESINHUMANPOPULATIONSWHICHTAKE

into account factors such as chemical exposure and age.

s $EVELOPPORTABLEBIOSENSORSFORRAPIDDETECTIONOFMICROBIALCONTAMINANTSINCOASTAL

waters.

s $EVELOPMETHODSFORROUTINEMOLECULARSURVEILLANCETOMONITORFORTHEPREVALENCEOF

influenza—and other diseases with potential human health impacts—in marine vertebrates.

III.C. Marine aquaculture

s $ETERMINEEFFECTSOFGROWTHDURINGEARLYJUVENILEREARINGONADULTFEMALEREPRODUCTIVE

fitness characteristics of spring Chinook salmon to improve hatchery technology for 

ESA-listed stocks of Pacific salmon.

s )NITIATEGERMCELLCRYOPRESERVATIONPROGRAMFOR2EDlSH,AKESOCKEYESALMONTOREDUCE

risk of extinction.

s !SSESSTIMINGOFOLFACTORYIMPRINTINGINJUVENILESOCKEYESALMONTOIMPROVEHATCHERY

technology for ESA-listed stocks of Pacific salmon.

s !SSESSANDRElNEHATCHERYREFORMPROTOCOLSTOHELP0ACIlCSALMONHATCHERIESACHIEVE

conservation and sustainable fisheries goals.
84

s $EVELOPANDTESTCONSERVATIONHATCHERYTECHNOLOGYTOAIDRECOVERYOFDEPLETEDSTOCKSOF

Pacific cod and rockfish.

s %VALUATEANDDEVELOPMETHODSFORTHEPRODUCTIONOFHIGHLYNUTRITIOUSSEAFOODHIGHN


fatty acid, low contaminant) through aquaculture.

s $EVELOPCONSERVATIONHATCHERYTECHNOLOGYTOAIDRECOVERYOF%3!
LISTEDSTOCKSOF0ACIlC

salmon. 

s %VALUATETHEPOTENTIALFORSUSTAINABLEMARINElSHAQUACULTUREFORCONSERVATIONANDCOMmercialization. This work would focus on: sustainable feeds based on non-fish-meal/oil 

feedstuffs, energy and impact modeling for aquaculture systems, multitrophic and 

monotrophic systems design, environmental risk assessment modeling, and hatchery 

technology.

IV. Information Management Research

Recent Accomplishments:

s )NFORMATIONDEVELOPEDFORTHE%SSENTIAL&ISH(ABITAT%)3ISBEINGUSEDDIRECTLYTODEvelop a new West Coast Marine Habitat Server—an interactive mapping tool providing 

access to various marine habitat data through an online mapping service (ArcIMS map 

server). This is part of the Pacific Ocean Observation System (PaCOOS) and is funded 

by NOAA’s Integrated Ocean Observation Program.

s 4HE .7&3# HAS DEVELOPED STANDARDIZED ROUTINES FOR EXTRACTING AND SUMMARIZING

data for use in 2005 assessments, including survey, landings, and logbook data.

s .7&3#STAFFHASACQUIRED7ASHINGTON3TATEDATAONPARALYTICSHELLlSHTOXINLEVELS

and have begun dataset development and data exploration.

Research Priorities, FY 2007–2012:

s $EVELOPAWEB
ACCESSIBLEDATABASEFORBOTTOMTRAWLSURVEYDATA

s %XPANDANDMAINTAINELECTRONICARCHIVEOF7EST#OASTGROUNDlSHSTOCKASSESSMENTS

s !DDDATATOTHE7EST#OAST-ARINE(ABITAT3ERVER
SOUTHWEST FISHERIES SCIENCE CENTER

The Southwest Fisheries Science Center (SWFSC) headquarters is located in La Jolla, 

California, and research is conducted at laboratories in La Jolla, Santa Cruz, and Pacific 

Grove, California. The current staffing level involved in MSFCMA-related activities is at 

about 95 full-time equivalents (FTEs). An estimated 55 percent of total SWFSC resources 

are assigned to MSFCMA activities. NOAA research vessels assigned to fisheries research in 

the SWFSC are the NOAA FSV David Starr Jordan, which has San Diego as its homeport, 

and approximately two-thirds of the time of the NOAA vessel McArthur II. The Center 

also charters in excess of 100 sea days annually aboard fishing and research vessels.

The SWFSC is a world-class research organization that conducts integrated, multidisciplinary research programs in biology, mathematics, oceanography, and economics to 

develop scientific technology and provide information to support the management and 

allocation of Pacific coastal and high-seas fishery resources. These activities support the 

scientific, statistical, and economic needs of the Pacific Fishery Management Council 

(PFMC) and international commissions for large pelagic fishes and Antarctic resources. 

Center programs also support efforts directed toward the reduction of protected species 

interactions, fishery-related porpoise mortality, and a better understanding of the biological 

and environmental factors affecting the marine resources exploited by U.S. commercial and 

recreational fisheries. The Center provides the scientific information necessary to conserve 

and manage the following important fisheries in the Pacific and Antarctic regions:

s ,ARGEPELAGIClSHESOFTHE0ACIlC/CEANTUNABILLlSHSHARKANDSWORDlSH	

s 'ROUNDlSHESOFTHE7EST#OAST0ACIlCHAKEROCKlSHESLINGCODANDCOWCOD	

s 3MALLCOASTALPELAGICSPECIESOFTHE7EST#OASTNORTHERNANCHOVYSARDINEMACKEREL

and squid).

A school of yellowfin tuna. 

Photo: William L. High, NMFS.
86

s 3ALMONOFTHE7EST#OAST

s !NTARCTICKRILLCRABSANDlNlSHINCLUDING0ATAGONIANTOOTHlSH	

The SWFSC specializes in fisheries of the California Current, Pacific Oceanic, and 

Antarctic regions. Research is carried out on the ecology, population dynamics, fisheries, 

and stock assessment of small coastal pelagic species, West Coast groundfishes, Pacific 

billfish, tunas and sharks (in collaboration with the Pacific Islands Fisheries Science Center), and California salmon. The Center maintains and uses the largest database on tuna 

and tuna-related fisheries in the world. The Center makes extensive use of biological and 

fisheries data, which are collected by observers placed on fishing vessels by the Southwest 

Region, to monitor interactions with protected resources to achieve goals related to the 

MSFCMA. It is also considered a leader in fish survey design, conducting surveys to 

monitor early recruitment success of economically important fish stocks along the U.S. 

West Coast. It is a co-founder and co-participant in the Pacific Coast Ocean Observing 

System (PaCOOS) an extension of the much cited state-Federal California Cooperative 

Fisheries Investigations (CalCOFI), a comprehensive long-term study of the biology and 

oceanography of the California Current. In the Pacific, the Center is the leading source of 

stock assessment expertise on tunas, sharks, and billfishes for international commissions 

and for the PFMC. In the Antarctic, the SWFSC leads U.S. research directed at gathering 

ecological information to prevent overexploitation of fish and krill and to protect Antarctic 

living marine resources. The SWFSC provides oceanic environmental data and indices 

to the rest of NMFS as well as to other Federal, state, academic, and foreign fisheries scientists. Center scientists are leaders in the research and development of fisheries-relevant 

environmental data products. The SWFSC is home to a NOAA CoastWatch node at its 

Environmental Research Division in Pacific Grove, California.

Organizationally, the SWFSC consists of the Fisheries Research Division, Fisheries 

Ecology Division, Environmental Research Division, Protected Resources Division, the 

Antarctic Ecosystem Research Division, and the Operations, Management and Information 

Division. Nine research programs are conducted across these divisions: Coastal Pelagic 

Species, Highly Migratory Species, California Demersal Species, California Anadromous 

Species, Marine Mammals, Marine Turtles, Abalone, Antarctic Marine Living Resources, 

and Strategic Research. The SWFSC also has eight programs oriented around the following 

disciplines: 1) Population Assessment; 2) Resource Surveys; 3) Ecosystem and Climate; 4) 

Ecology and Ecosystem; 5) Biology and Life History; 6) Life History, Demographics & 

Movement; 7) Economic and Social Monitoring and Assessment; 8) Data Management; 

and 9) Administration and Infrastructure. These Discipline Programs cut across all Divisions and Research Programs.

SWFSC scientists have taken the lead in characterization of large- and small-scale habitats that support white abalone, groundfish, and bottomfish populations in deep water off 

California. This work requires an interdisciplinary approach from fishery biologists, geologists, and ecologists and couples the use of GIS with remote-sensing visual and acoustic 

tools, in-situ survey techniques using remotely operated vehicles, submersibles, and spatial 

analyses. This approach is being applied to the identification of EFH for various species, 

the improvement of stock assessment surveys, development of endangered species recovery 

plans, and the evaluation of MPAs as an effective supplement to traditional fishery management. The National Ocean Service’s MPA Center is cooperatively co-located with the 

SWFSC’s Santa Cruz Laboratory.
The SWFSC maintains an active communications network with constituents, colleagues 

in the scientific professions, and the public to receive input for research planning, execution, 

and results. The network includes frequent dialogue with commercial and recreational fishermen, leaders of environmental groups, participants of FMCs, state and Federal research 

agency staff, and outside scientists in the United States and foreign countries. Supporting 

this network is an infrastructure that includes cooperative agreements to support collaborative work with researchers in state agencies, universities, and foreign governmental agencies 

for collecting logbook and other types of fisheries data and for shared research projects; 

arrangements for data exchange; and contracts for charters of research vessels and specialty 

expertise. The SWFSC and its laboratories maintain up-to-date Internet sites that provide 

a range of information, including scientific reports and summary databases available to 

other researchers as well as the general public.

The SWFSC provides scientific and research support for U.S. commitments resulting 

from the following international arrangements and agreements in the Pacific region:

s #ONVENTIONFORTHE#ONSERVATIONOF!NTARCTIC-ARINE,IVING2ESOURCE##!-,2	

which manages the marine living resources of the Antarctic.

s )NTER
!MERICAN4ROPICAL4UNA#OMMISSION)!44#	WHICHDEALSWITHTUNAANDTUNA


like fishes, and the tuna-dolphin issue of the eastern Pacific Ocean.

s 3OUTH0ACIlC4UNA4REATY3044	WHICHPROVIDESTUNAlSHINGACCESSTOTHEWESTERN

Pacific Ocean.

s .ORTH0ACIlC)NTERIM3CIENTIlC#OMMITTEEFOR4UNAAND4UNA
LIKE3PECIES)3#	WHICH

promotes research on tuna and tuna-like species of the North Pacific Ocean.

s 3TANDING#OMMITTEEON4UNAAND"ILLlSHOFTHE3ECRETARIATOFTHE0ACIlC#OMMUNITY

(SCTB), which facilitates collaborative research on tuna and billfish of the western Pacific 

Ocean.

s -%853
0ACIlCOWHICHPROMOTESJOINT53
-EXICORESEARCHPROJECTSOFMUTUALINTERest.

s .ORTH0ACIlC!LBACORE7ORKSHOP.0!,"	WHICHPROMOTESSTOCKASSESSMENTRESEARCH

for North Pacific albacore.

s #OMMISSIONONTHE#ONSERVATIONOF(IGHLY-IGRATORY&ISH3TOCKSINTHE7ESTERNAND

Central Pacific Ocean, which will manage the highly migratory fish resources of the 

western and central Pacific Ocean.

s )NTERNATIONAL 7HALING #OMMISSION )7#	 WHICH PROMOTES CONSERVATION OF WHALE

stocks.

In addition, SWFSC scientists periodically work with other scientists on joint projects 

sponsored by international organizations such as the FAO, Global Ecosystem Dynamics 

(GLOBEC), and the North Pacific Marine Science Organization (PICES). 

The SWFSC maintains an exceptional and growing fisheries economic research capability. Special studies are undertaken to help explain and evaluate the potential impacts of 

various management options on components of the fishery or on the public. In addition, 

economic data collection and analyses are carried out to evaluate the economic health of 

fisheries or components of the fisheries.
88

RECENT ACCOMPLISHMENTS AND

RESEARCH PRIORITIES FOR FY 2007–2012

I. Research to Support Fishery Conservation and Management

Recent Accomplishments:

s !NECOSYSTEM
BASEDSYNOPTICSARDINESURVEYALONGTHEENTIRE7EST#OASTFROM"RITISH

Columbia to Baja California, was conducted onboard the NOAA ships Oscar Dyson

and the David Starr Jordan. Biological and physical data were collected using pelagic 

trawls and acoustics, CUFES (Continuous Underway Fish Egg Sampler) and plankton 

tows, and in situ sensor packages to obtain vertical profiles of water properties. Data 

from this survey is especially important for the production of sardine assessments. This 

was an extension of CalCOFI (California Cooperative Fisheries Investigation), one of 

the longest-running ecosystem approaches to monitoring living marine resources and a 

collaboration among academia and state and Federal agencies. 

s 3TOCKASSESSMENTSFOR0ACIlCSARDINEANDMACKERELWEREPROVIDEDTOTHE0&-#ALONG

with economic analyses of Pacific sardine harvest guidelines and Coastal Pelagic Species performance measures. Economic analyses were used to redesign the distribution 

of Total Allowable Catch for Pacific sardines on the West Coast for a more equitable 

allocation. 

s 37&3#SCIENTISTSBEGANDEVELOPING'ENETIC3TOCK)DENTIlCATION'3)	TECHNIQUESFOR

Pacific salmon using microsatellite DNA. This quick turnaround technique will be 

USEDTOCONDUCTMIXEDSTOCKlSHERYANALYSISREDUCEIMPACTSON+LAMATH"ASIN#HInook, and maximize harvest of Central Valley fall Chinook salmon. Results of a quick 

turnaround-time genetic stock identification analysis of Chinook salmon port sampled 

in Monterey Bay were presented to the PFMC. The SWFSC, in collaboration with the 

NWFSC, developed a population genetics database of several California salmonid stocks 

for determining stock structure and to use as a baseline for future monitoring efforts. 

Molecular genetic data are collected from salmonids to identify genetic population 

structure and demographic units for management and conservation, to estimate relatedness of individuals and populations, and to estimate life-history and population-genetic 

parameters. Novel analytical methods will also be developed and employed to estimate 

population-genetic parameters, such as effective population size, probability of parentage, 

demographic trajectory, new ways to use genetic methods for tagging individual salmon, 

and manage breeding of salmonids in hatcheries for conservation purposes.

s 4HE#ALIFORNIA$EMERSAL3PECIES0ROGRAMPROVIDEDTHE0&-#WITHSTOCKASSESSMENTS

for shortbelly rockfish, bocaccio, cowcod, California scorpionfish, California sheepshead, 

starry flounder, widow rockfish, gopher rockfish, kelp greenling, and vermilion rockfish, 

as well as rebuilding analyses for boccacio, widow rockfish, and cowcod. 

s 4HE#ALIFORNIA!NADROMOUS0ROGRAMPROVIDEDTHE0&-#WITHAHARVESTRATEMODELFOR

+LAMATH2IVERFALL#HINOOKSALMONA+LAMATH2IVER/CEAN(ARVEST-ODELA#ALIfornia coastal Chinook ocean harvest jeopardy standard, hook-and-release mortality in 

California's ocean recreational fishery, and a Phase I recovery plan through participation 

in Take Reduction Teams for all listed salmon stocks. 

s 37&3#RESEARCHERSINTHE(IGHLY-IGRATORY3PECIES0ROGRAMPROVIDEDSTOCKASSESSMENTS

for North Pacific Ocean Striped Marlin and North Pacific Ocean Albacore, which the 

ISC used to recommend management action to the Western and Central Pacific Fisheries 
Commission. Annual Stock Assessment and 

Fishery Evaluation reports were provided to 

the PFMC on recreational and commercial 

Highly Migratory Species fisheries, including albacore and bluefin tunas. 

s 4HE !NTARCTIC -ARINE ,IVING 2ESOURCES

(AMLR) program developed a prey-based 

ecosystem model for the Commission for 

the Conservation of Antarctic Marine 

Living Resources (CCAMLR) to use in 

managing the Antarctic krill fishery. The 

model was populated with data directly 

from the AMLR program. CCAMLR will 

use the model to set krill harvest guidelines 

by area.

Research Priorities, FY 2007–20012:

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

of fish stocks

s #ONDUCTBIOLOGICALRESEARCHBYTHE53!NTARCTIC-ARINE,IVING2ESOURCE0ROGRAM

concerning abundance and life history parameters of fish stocks.

s 0LANCONDUCTANDPRESENTRESULTSOFANNUALPREDATOR
PREYINTERACTIONSTUDIESINWATERS

around the South Shetland Islands, Antarctica.

s $EVELOP A NEW "AYESIAN METHOD OF STOCK ASSESSMENT FOR APPLICATION TO DATA
POOR

groundfish species.

s $EVELOPANADVANCEDTECHNOLOGY
BASEDGROUNDlSHSURVEYUSINGOPTICALTECHNOLOGIES

and sonar for the Southern California Bight.

s #ONTINUEDEVELOPINGAPOPULATIONGENETICSDATABASEOFANADROMOUS#ALIFORNIASALMOnid stocks for determination of stock structure and as a baseline for future monitoring 

efforts. 

s 0ROVIDEQUANTITATIVEESTIMATESOFTHETAKEOFLISTEDSALMONINTHE#ALIFORNIASALMON

harvest and evaluate proposals to minimize listed species take. 

s %XPANDTHEARCHIVALTAGGINGPROGRAMFOR.ORTH0ACIlCALBACOREINCOOPERATIONWITH

the albacore fishing industry, Japanese fishery agencies, and other groups to trace albacore movements between fisheries and countries.

s $ElNE UNIT STOCKS USING GENETICS AND OTOLITH CHEMISTRY IN HIGHLY MIGRATORY SPECIES

(albacore, thresher shark, and striped marlin), in coastal pelagic species (sardine), and 

in groundfishes.

s #ONDUCT PEER
REVIEWED ASSESSMENTS AND STATISTICAL ANALYSES ON STOCKS OF GROUNDlSH

coastal pelagics, tunas, sharks, swordfish, salmon, and other species.

s $EVELOPANEWGENERATIONOFSTOCKASSESSMENTMODELSFORHIGHLYMIGRATORYSPECIESAND

coastal pelagic species stocks of the Pacific and the state-of-the-art software to support 

them, using modern statistical optimization techniques, Bayesian methods, and objectoriented programming languages.

A vermillion rockfish swims 

in the dark depths of the 

Pacific Ocean. Photo: NMFS.
90

s 5SEPOP
UPSATELLITETAGSTOIDENTIFYFORAGEANDMIGRATIONHABITATSOFEXPLOITEDSHARK

species in the California Current.

I.B. Interdependence of fisheries or stocks of fish

s #ONTINUERESEARCHPROGRAMUNDERTHE)NTERNATIONAL$OLPHIN#ONSERVATION0ROTECTION

Act to determine whether the chase-and-encirclement practice by the fishery is having 

a significant adverse impact on depleted dolphin populations in the eastern tropical 

Pacific.

s $ESIGNSAMPLINGSURVEYSTOANALYZETHEIMPACTOFMARINEMAMMALSONLISTEDSALMON

s $EVELOPINTEGRATIVEOCEANICENVIRONMENTALINDICESTOIMPROVEUNDERSTANDINGOFHOW

environmental variability affects fish stocks.

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

s 0ARTICIPATEINSALMON%&(IDENTIlCATIONANDPROTECTION

s $EVELOPANDPRODUCEDIGITALMOSAICSOFSEAmOORHABITATSFROMELECTRO
OPTICIMAGESINTO

a format compatible with other geo-referenced data sets used in GIS.

s $EVELOPAPPROACHESTOEVALUATEESSENTIALHABITATOFPELAGIClSHESBASEDONSATELLITEREmote sensing and applications of archival and pop-up satellite tags.

s %VALUATE%&(ANDMONITORMARINERESOURCESINhNO
TAKEvMARINERESERVESINTHE#HANnel Islands National Marine Sanctuary.

s $ElNEESSENTIALSPAWNINGHABITATOFMARKETSQUIDANDTHEEFFECTSOFlSHINGGEARONTHAT

habitat and the survivorship of demersal egg capsules.

I.D. Impact of anthropogenic factors and 

environmental changes on fish populations

s )NVESTIGATE RELATIONSHIP OF JUVENILE SALMON ABUNDANCE AND PHYSIOLOGICAL STATUS WITH

respect to oceanographic features (e.g., estuary plumes, upwelling centers, coastal jets, 

eddies, and fronts).

s $ETERMINETHEEFFECTSOFHATCHERYANDAQUACULTUREOPERATIONSONINDIGENOUSSALMON

and steelhead stocks in California by molecular genetic analysis of museum specimens 

and previously collected scale samples.

s %VALUATETHEEFFECTSOFCLIMATECHANGEOFINTERANNUALDECADALANDCENTENNIALSCALESON

fisheries and fish habitat.

s $EVELOPMODELSOFTHEIMPACTSONSALMONPOPULATIONSOFNATURALDISTURBANCESDUETO

climatologies.

s )MPROVEMETHODSTOIDENTIFYPATHWAYSINESTUARINEECOSYSTEMSFORTHEBIO
ACCUMULAtion of contaminants in salmon.

s %XAMINETHEASSOCIATIONOFRECRUITMENTOFYOUNGROCKlSHESANDCLIMATICANDOCEANOgraphic variables off central California.

s )NVESTIGATEUSEOFSMALLESTUARIESONTHECENTRAL#ALIFORNIACOASTBYJUVENILESALMONIDS

s !SSESSTHEEFFECTSOFENVIRONMENTALVARIABILITYPARTICULARLYSANDBARDYNAMICSANDWAter quality—on growth, development, and survival.
s )NVESTIGATE THE LINKAGE BETWEEN THE DYNAMICS OF OCEANIC FEATURES INCLUDING EDDIES

fronts, and boundary currents, and the dynamics of highly migratory fishes (tunas and 

billfishes) in the central and western Pacific.

II. Conservation Engineering Research 

Recent Accomplishments:

The SWFSC completed research to improve our understanding of fisheries impacts on 

marine ecosystems by developing equipment, methods, and protocols to survey abundance 

and distribution of demersal fish associated with offshore rocky habitats using advanced 

technologies. One study pioneered the use of the combination of acoustic techniques, fishing 

information, and direct submersible research to directly evaluate deepwater fisheries habitat. 

Research considered the potential of multibeam sonar, multi-frequency echosounder, and 

a Remotely Operated Vehicle (ROV) to estimate rockfish distributions and abundance in 

the Southern California Bight, suggesting that this type of direct observation is a promising independent approach to evaluate fishing effects on a scale consistent with commercial 

fishing activities. Species identification algorithms for acoustic surveys were also developed 

for bocaccio rockfish.

The Center conducted the first workshop to develop alternative gear for reducing bycatch of dolphins, turtles, and other species in the Eastern Tropical Pacific (ETP) tuna 

purse-seine fisheries. This workshop identified three research proposals that showed the 

most conservation promise and were the most cost-effective for review and evaluation at 

a future workshop. These were proposals to reduce fishery mortality of sharks, examine 

historical fishery data to establish time-area closures, and modify fish aggregating devices 

(FADs) to reduce sea-turtle entanglement.

Launching the SWFSC’s 

remotely operated vehicle 

(ROV) for surveying 

deepwater rockfish and 

abalone. Photo: NMFS.
92

Research Priorities, FY 2007–2012:

s 5NDERTAKESTUDIESTODETERMINETHEMOSTEFFECTIVEMETHODSTOINCREASESURVIVALOFSEA

turtles on nesting beaches in the eastern and western Pacific.

s $ETERMINEHOWTOINCREASESURVIVALINTHEECONOMICREGULATORYDISCARDSOFUNDERSIZED

tunas, sharks, and other fishes.

s #REATEANDTESTNEWTRAPDESIGNSFORJUVENILEOUT
MIGRANTSALMONTHATWILLMINIMIZE

predation on juveniles from larger salmonids (in cooperation with Humboldt State 

University).

s $EVELOPADVANCEDSURVEYTECHNOLOGYFORMONITORINGABUNDANCEOFlSHESINCLUDING	

use of LIDAR for monitoring the abundance of CPS species, 2) remote monitoring of 

FAD fish aggregations, and 3) testing an Autonomous Underwater Vehicle for monitoring groundfish species. 

s 0ARTICIPATEINSECOND%40BYCATCHWORKSHOPTODEVELOPBESTOPTIONFORBYCATCHREDUCTION

s $EVELOPMETHODTOREDUCESHARKBYCATCHINTUNAPURSE
SEINElSHERIESAROUND&!$S

s $EVELOPADVANCEDTECHNOLOGYFORAUTOMATICSHIPBOARDDATALOGGINGOFBIOACOUSTICAND

environmental data from standard equipment on commercial fishing vessels and logging of catch. Develop algorithms for processing and analysis of these data.

III. Research On The Fisheries

Recent Accomplishments:

The SWFSC initiated and led the efforts to evaluate MPAs as a supplemental tool for 

groundfish management on the West Coast. The Center provides scientific advice to the 

Master Plan Team for California’s Marine Life Protection Act, which develops recommendations for Marine Protected Area Networks to California’s Fish and Game Commission. 

The Center also participates in a National Center for Ecological Analysis and Synthesis 

an (NCEAS) working group, “Development of Tools for the Practical Design of Marine 

Reserves.” The National Marine Protected Area Center (NMPAC) Science Institute is colocated at the SWFSC laboratory in Santa Cruz, California. The Science Institute provides 

coordination and support of MPA research, design, monitoring schemes, and management 

strategies. Center staff work on several MPA-related projects for the NMPAC and NMFS 

on sea-floor mapping using GIS and distribution associated with habitat using ROV technology. Currently the SWFSC is leading efforts to develop a NMFS strategy to integrate 

MPAs into conventional fisheries science and management. 

The SWFSC analyzed buybacks of tuna purse-seine vessels in the Eastern Pacific Ocean 

and determined the feasibility of routinely collecting input data for the Data Envelopment 

Analysis and for performing industry surveys of tuna fishing capacity utilization for the 

FAO. The SWFSC developed economic models for three different fishing capacity or productivity analyses. The projects will measure total factor productivity of tuna purse seine 

vessels accounting for catches of undesirable outputs, measure total factor productivity of 

U.S. tuna purse seine vessels in the Western and Central Pacific Ocean accounting for 

environmental influences, and analyze standardization of fishing effort. Data are being 

collected for the high seas tuna fleets and the longline fleet; computer code has been written for the high seas tuna fleet. 
SWFSC researchers met in Bellagio, Italy, with international economists, marine life 

policy experts, legal scholars, fishing industry and fisheries professionals, conservation, sea 

turtle and natural resource management specialists, and development assistance researchers 

from governmental, nongovernmental, and private institutions to provide a scientific and 

policy basis to develop elements of a model treaty to conserve and promote recovery of Pacific 

sea turtles. The group concluded that a blueprint for sea turtle conservation must address 

1) protecting all nesting beaches, 2) reducing turtle take in at-sea and coastal fisheries, 3) 

stimulating pan-Pacific policy actions, and 4) encouraging sustainability of traditional use 

of sea turtles. The first point recognizes that protecting nesting beaches has been proven 

to work in restoring sea turtle populations. In addition, SWFSC economists developed a 

model for predicting leatherback interactions with the drift gillnet fishery, estimated the 

costs of leatherback beach protection in the western Pacific, and estimated costs of bycatch 

reduction to California drift gillnet fisheries.

Research Priorities, FY 2007–2012:

III.A. Social and economic research

s )NITIATEECONOMICEVALUATIONOFSALMONHATCHERYREFORMACTIONS

s $EVELOPAUTOMATEDANALYTICALTEMPLATESINTEGRATEDWITHCURRENTlSHERYPERFORMANCE

cost, and price information for completing Regulatory Flexibility Act analyses in an efficient and timely manner. Augment these templates to include the basic demographic 

information required to initiate preliminary Social Impact Assessments.

s #ONDUCTRESEARCHTOSUPPORTTHE5NITED.ATIONS)MPLEMENTING!GREEMENTOR0ROVIsion of the United Nations Convention on the Law of the Sea [UNCLOS] Relating to 

the Conservation and Management of Straddling Fish Stocks and Highly Migratory 

Fish Stocks).

s 2ESEARCHINTRA
INDUSTRYLINKAGESANDDEVELOPINPUT
OUTPUTRELATIONSHIPSTODESCRIBEAND

model the employment, income, and economic impacts of potential management actions on each of the FMP fisheries and fishing communities.

s !NALYZERECREATIONALECONOMICSFOR(-3#OMMERCIAL0ASSENGER&ISHING6ESSELSAND

private sport fishermen targeting tuna, marlin, and billfish.

s )NITIATEANECONOMICSURVEYOFTHE3OUTHERN#ALIFORNIA(IGHLY-IGRATORY3PECIESRECreational fishery.

s %NHANCE EXISTING SALMON HARVEST MODELS TO BETTER PREDICT lSHING EFFORT RESPONSE TO

changes in sport and commercial fishery regulations.

s #ONDUCT2EGULATORY)MPACT2EVIEWSAND2EGULATORY&LEXIBILITY!NALYSESFORMANAGEment actions being considered for all fisheries with FMPs.

s %VALUATEGROWTHINPRODUCTIVITYFORPURSESEINEVESSELSHARVESTINGTUNAINTHEWESTERN

and central Pacific, paying special attention to the effects of fish aggregating devices 

(FADs).

III.B. Seafood safety research 

This item is not applicable.
94

III.C. Marine aquaculture

s $EVELOPTECHNIQUESFORCULTUREOFWHITEABALONEANDOTHERABALONESPECIESFORRECOVERY

of endangered stocks, stock enhancement, and commercial production.

IV. Information Management Research

Recent Accomplishments:

The SWFSC has been a leader within NOAA in providing data to a broad spectrum of 

users, using methods consistent with emerging NOAA Global Earth Observation—Integrated Data Environment and Integrated Ocean Observing System (IOOS) Data 

Management and Communication (DMAC) standards for data access and transport providing interoperability with other NOAA data and data servers. The SWFSC continues 

to develop a suite of fisheries-relevant data that cover the entire spectrum of the ocean 

environment, from surface or near-surface wind and pressure data to surface and subsurface 

measurements of important oceanographic parameters. A key focus is the integration of 

these oceanographic and atmospheric data with biological data in support of a regional 

ecosystem-based management and to make these data sets readily accessible to scientists, 

managers, and the general public to support research on fisheries, marine mammals and 

protected species, and for studies in climate change and environmental variability.

In cooperation with the West Coast Regional Node of Coastwatch, over 4 terabytes 

of data are available online, and the amount is increasing every month. The data can accessed, subsetted, visualized, and downloaded in a variety of methods designed to reduce 

the time users need to spend preparing the data, and allowing users to acquire only the 

desired data rather than an entire dataset. The SWFSC has developed Thematic Real-time 

Environmental Distributed Data Services (THREDDS) catalogs, including OPeNDAP 

and Open Geospatial Consortium standard Web Coverage Services; provided access to a 

variety of near real-time and science quality satellite data; developed a variety of data delivery and integration tools for the Tagging of Pacific Pelagics (TOPP) program; developed 

Dapper/dchart applications for accessing aggregated in situ information; and developed 

data transport and access applications for the Central California Ocean Observing System 

(CeNCOOS) and the Pacific Coast Ocean Observing System (PaCOOS). 

The SWFSC developed several software and hardware systems to modernize and standardize data collection and management for HMS biological, physical, and fisheries data 

through collaboration with the National Fisheries Information System and the SWFSC/

PIFSC Data Coordination Team. The Data Coordination Team developed an Oracle data 

system integrating all types of fishery data, and a data portal to display HMS data, metadata, and data policies. Electronic calipers were field tested that will enable port samplers 

to more efficiently collect data from HMS fisheries and allow SWFSC data technicians to 

more efficiently process the data. The Data Coordination Team also continued to collect 

data from and monitor HMS fisheries in the Pacific for stock assessments and in support 

of WCPFC, PFMC, and the International Scientific Committee for Tuna and Tuna-Like 

Species.

The SWFSC began developing IOOS-compatible software that will allow CalCOFI 

biological and physical data to be accessed on the Internet by interested academic, government, and research partners. The SWFSC began long-term planning and design for an 
integrated PaCOOS data management system. This system will ensure that physical and 

biological data from a wide variety of sources and PaCOOS partners will be available and 

easy to access for scientists and managers.

Research Priorities, FY 2007–2012:

s !UTOMATEQUARTERLYANDANNUALCOMPILATIONOFlSHERIESSTATISTICSANDANNUALREPORTSON

FMP fisheries.

s $EVELOPANDMAINTAINWEB
BASEDCOASTALSALMONABUNDANCEDATABASE

s !DVANCE APPROACHES OF DATA FUSION TO COMBINE lSHERIES DATA AND ASSESSMENT MODEL

outputs with environmental data from ship, satellite, and physical models.

s $EVELOPELECTRONICALBACORETROLLBAITBOATlSHINGLOGBOOKANDMAKEITAVAILABLETOTHE

fishing fleet to modernize data collection.

s $EVELOPAPPLICATIONSTOCAPTURE(-3DATAWITHELECTRONICCALIPERSANDTRANSMITDIrectly to HMS Oracle system.

s 0ROVIDEELECTRONICCALIPERSTOALL(-3PORTSAMPLERS

This southern elephant seal 

has been fitted with nonpermanent tracking apparatus on it’s head so that data 

can be collected via satelllite. 

Satellite tracking tags allow 

researchers to collect data 

on migration routes, diving 

depths, and other aspects of 

behavior. Photo: Mike Goebel, NOAA.
96

SOUTHEAST FISHERIES SCIENCE CENTER

The Southeast Fisheries Science Center (SEFSC) with headquarters in Miami, Florida, 

implements and manages a multidisciplinary science and research program that provides 

technical information for conserving and maintaining the sustainability and health of 

living marine resources and their environments. The SEFSC is responsible for the eight 

southeastern states, Puerto Rico, and the U.S. Virgin Islands, and research is conducted 

at laboratories located in Miami and Panama City, Florida; Beaufort, North Carolina (a 

joint NOS-NMFS facility); Galveston, Texas, with a lab facility in Lafayette, Louisiana; 

and Pascagoula, Mississippi, with a field station at the Stennis Space Center, Mississippi. 

In addition, numerous field offices provide additional information for research along the 

coast of the southeastern United States. The SEFSC has two fishery research vessels berthed 

at Pascagoula, Mississippi—the NOAA vessels Oregon II and Gordon Gunter—as well as 

numerous smaller research craft located at individual laboratories.

In general, the SEFSC develops the scientific information required for: 1) fishery resource 

conservation, 2) fishery development and utilization, 3) habitat conservation, and 4) the 

protection of marine mammals and endangered species. Impact analyses and environmental 

assessments for fishery management plans and international negotiations are also prepared, 

and research is pursued to address specific needs in population dynamics, fishery biology, 

fishery economics, engineering and gear development, and protected species biology. The 

SEFSC’s current staffing level is 276 FTEs. Approximately 80 percent of all SEFSC resources are devoted to MSFCMA activities.

The SEFSC provides scientific support for NMFS’ fishery management activities and 

the recommendations of the South Atlantic Fishery Management Council (SAFMC), the 

A spiny lobster crawling out 

of a crevice. Photo: Doug 

Harper, NMFS.
Gulf of Mexico Fishery Management Council (GMFMC), and the Caribbean Fishery 

Management Council (CFMC) that involve 17 fishery management plans covering the following major fisheries: spiny lobster, snapper-grouper, reef fish, red drum, coastal migratory 

pelagic species, coral, shrimp, stone crab, queen conch, and golden crab. The SEFSC also 

has significant interactions with the Gulf States Marine Fisheries Commission (GSMFC), 

which administers the Fisheries Information Network (FIN) statistics effort; and the 

Atlantic States Marine Fisheries Commission (ASMFC), which administers the Atlantic 

Coastal Cooperative Statistics Program and exercises fishery management responsibilities 

through the Atlantic Coastal Fisheries Cooperative Management Act. In addition, the 

SEFSC maintains close ties with state fishery programs and has funded the state-Federal 

cooperative statistics program since 1983. Researchers at the SEFSC collaborate extensively 

with other Federal agencies and academia.

Internationally, the SEFSC provides scientific leadership to, and support for U.S. participation in, 1) the International Commission for the Conservation of Atlantic Tunas 

(ICCAT), which manages Atlantic Ocean-wide fisheries for tunas and billfishes; and 2) 

the International Oceanographic Commission for the Caribbean (IOCARIBE), which 

coordinates fishery oceanography studies among the approximately 30 islands and continental countries in the region. SEFSC scientists also work jointly with the Government 

of Mexico on projects of mutual interest in the Gulf of Mexico under the M%853-Gulf 

research working group.

Constituents have the opportunity to provide input to the SEFSC’s research programs 

through representation on FMCs, participation in Council public hearings, and service on 

Council advisory committees. Input to the SEFSC research program is also received via the 

activities of interstate fishery commissions (the Atlantic and Gulf States Marine Fisheries 

Commissions), joint agency planning groups, and cooperative programs with state fishery 

agencies (GulfFIN). The SEFSC responds to the information needs of FMCs and has a 

formal procedure (Council Operations Plan) for matching its research program to fishery 

management plan requirements.

The SEFSC’s high caliber of research is maintained through periodic program reviews 

by teams that include officials from industry, councils, state agencies, universities, and other 

constituents. The Center also works diligently to be responsive to the results of program 

reviews.

Each SEFSC laboratory is responsible for conducting research in specific subject areas 

and also tend to have specific geographic focuses. However, there is extensive cooperative 

research between SEFSC laboratories. Research activities conducted by the various laboratories are as follows:

Beaufort Laboratory: 

s #ONDUCTSRESEARCHONBIOLOGYANDlSHERYFORREEFlSHINCLUDINGHEADBOATLANDINGS

fishing effort, age and growth, reproduction, and assessment of abundance—to support 

the management of territorial sea, EEZ, and highly migratory resources.

s #ONDUCTSRESEARCHONPROCESSESAFFECTINGTHEDISTRIBUTIONABUNDANCEANDUSEOFNATURAL

and restored habitats by fishery organisms, and develops techniques and methodologies 

to evaluate natural and anthropogenic impacts on fishery organisms and their habitat.
98

s 3UPPORTSCONSERVATIONANDRECOVERYEFFORTSTHROUGHEVALUATIONSOFMARINEPROTECTEDAREAS

and also provides scientific recommendations to FMCs.

s #ARRIESOUT.-&3MANDATESFORTHERECOVERYANDCONSERVATIONOFPROTECTEDSPECIES

under the MMPA, the ESA, and related legislation. 

Miami Laboratory:

s 0ERFORMSSTOCKASSESSMENTSFORSPECIESSUCHASTHESNAPPER
GROUPERCATEGORYMACKERELS

and highly migratory species (e.g., sharks, swordfish, tunas, and billfish). 

s #OLLECTSANDANALYZESCATCHANDEFFORTDATAASWELLASSCIENTIlCINFORMATIONUNDERTHE

Fishery Observer Program for addressing issues such as bycatch of protected species, the 

assessment of bycatch mitigation techniques, and discard mortality of targeted species.

s 3UPPORTSCOOPERATIVERESEARCHSCIENCEPROJECTSWITHCONSTITUENTSSTATESANDLOCALGOVERNments, and conducts economics and social science research to evaluate the socioeconomic 

impacts of existing and proposed fishery management actions.

s )MPLEMENTSRESEARCHTOSUPPORTTHECONSERVATIONANDRECOVERYOFDEPLETEDTHREATENED

and endangered species of marine mammals, sea turtles, and seabirds by: conducting 

species-population assessment surveys; research on stock structure including genetics, 

radio tagging, photographic identification, and morphological studies; and assessing 

strandings and unusual stranding events. 

s 0ERFORMSRESEARCHONhNO
TAKEvMARINERESERVESASAlSHERYMANAGEMENTTOOLTOSUPPORT

sustainable fisheries and protect marine biodiversity; ecosystem structure and function; 

coral reefs; essential fish habitat; habitat restoration; the effectiveness of artificial reefs; 

fishing gear effects on populations and habitat; biological research to support stock 

assessments; fishery-independent assessments; and the early-life history and early-life 

ecology of southeastern species. 

s 0ERFORMSRESEARCHTOMEASUREMONITORUNDERSTANDCONSERVEANDRESTOREMARINEBIOLOGIcal diversity in ecosystems essential for fishery productivity. Research focuses on corals, 

invertebrates, and fishes in coral reefs, estuaries, and mangroves with complex biological diversity. Specific research goals are to improve ecosystem-based stock assessments; 

maintain healthy stocks; eliminate overfishing; restore habitat damaged by human or 

natural disturbances and rebuild overfished stocks important to commercial, recreational, 

and subsistence fisheries.

s #OLLABORATESWITHSTATEANDOTHER&EDERALAGENCIESINRESEARCHMODELINGANDMONITORING

programs to support more effective management of watersheds and freshwater flows to 

coastal waters in order to restore and protect coastal fishery habitat by ensuring appropriate 

quantity, quality, timing, and location of freshwater inflows. Other goals are to increase 

long-term economic and social benefits to the nation from living marine resources by 

reducing fishery conflicts that involve protected species; by protecting, conserving, and 

restoring habitat and marine ecosystem goods and services, including biological diversity, 

connectivity, and resilience.

s #ONDUCTSRESEARCHTOENSURETHATCOASTALECOSYSTEMSAREIMPROVEDANDARENOTHARMED

by the Comprehensive Everglades Restoration Project, which will modify freshwater 

inflow to estuaries and nearshore areas in southern Florida.
Panama City Laboratory:

s #ONDUCTSRESEARCHONREEFlSHESANDMACKERELSASRELATEDTOlSHERYBIOLOGYLIFEHISTORY

recruitment dynamics, ecology, essential fish habitat, fisheries, stock assessment/population modeling, and fishing gear selectivity patterns.

s 0ERFORMS RESEARCH ON SPATIAL VARIABILITY AT VARIOUS SCALES IN POPULATION TRAITS OF REEF

fishes.

s 3TUDIESlSHCOMMUNITYSTRUCTUREOFNEAR
SHOREANDMID
SHELFHARDBOTTOMROCKYREEF

habitats, including fishery-independent estimates of relative abundance and demographics 

of reef fishes on these habitats.

s #ONDUCTSRESEARCHONCORALANDROCKYREEFHABITATSASTHEYRELATETOlSHERYSPECIESOF

interest.

s -ONITORSPROPOSEDANDENACTEDMARINEPROTECTEDAREASRESERVESWITHRESPECTTOTHEEXTENT

and nature of reef habitat, to abundance and composition of reef fishes, and to impacts 

of fishing activity.

s #ONDUCTSSTOCKASSESSMENTSANDPOPULATIONMODELINGOFPELAGICLARGECOASTALANDSMALL

coastal sharks, as well as sharks for which harvest is prohibited. 

s #ONDUCTSRESEARCHTODEVELOPAlSHERY
INDEPENDENTINDEXOFJUVENILESHARKABUNDANCE

Performs studies on several aspects of elasmobranch life history, delineation of Essential 

Fish Habitat, and ecosystem modeling.

s #OORDINATESOBSERVERPROGRAMSTOMONITORCATCHANDBYCATCHINDIRECTEDSHARKlSHERIES

and fishery interactions with whales and sea turtles.

s #ONDUCTSCOLLABORATIVENATIONALANDINTERNATIONALPROJECTSANDACTIVELYPARTICIPATESIN

international scientific fora such as ICCAT and CITES. 

s #ONDUCTSRESEARCHONANDMONITORINGOFENDANGEREDANDTHREATENEDSPECIESSUCHAS

sturgeon, sawfish, marine mammals, and Johnson’s seagrass, participates in the development and implementation of their recovery plans, and participates in stranding networks 

for marine mammals and sea turtles.

Mississippi Laboratories:

s $EVELOPlSHERY
INDEPENDENTESTIMATESFOR&-0SPECIESABUNDANCESVIATRAWLPLANKTON

trap/video and longline surveys.

s -ONITORSSTATUSOFlNlSHANDINVERTEBRATESANDENVIRONMENTALVARIABLESUSINGTHESE

surveys.

s #ONDUCTVISUALANDACOUSTICASSESSMENTSURVEYSOFCETACEANSTOCKS

s #ONDUCT RESEARCHANDDEVELOPMENTOFNEWGEARTECHNOLOGY ANDlSHINGPRACTICESTO

reduce bycatch, including Turtle Exclusion Devices (TEDs), trawl Bycatch Reduction 

Devices (BRDs), and longline fishing practices.

s $EVELOPADVANCEDTECHNOLOGYAPPROACHESTOIMPROVINGDATACOLLECTIONATSEA

s 0ARTICIPATEINREMOTESENSINGPROGRAMSINCLUDINGDISTRIBUTIONOF#OAST7ATCH/CEANWatch operational data.
100

Galveston Laboratory:

s #ONDUCTSRESEARCHONESSENTIALlSHHABITATSANDTHEUSEOFLANDSCAPETECHNIQUESTOIDENtify Essential Fish Habitat by integrating GIS tools into assessments of habitat value; 

habitat modifications caused by sea level rise, subsidence, changes in freshwater inflow, 

coastal eutrophication, and broad scale hypoxia; habitat restoration research; wetland 

restoration; and ecosystem models for estuarine and coral reef systems.

s #ONDUCTSRESEARCHTODETERMINEMONITORANDDESCRIBESHRIMPPOPULATIONCHARACTERISTICS

as well as associated effort trends.

s -ONITORSTEMPORALANDSPATIALlNlSHANDPROTECTEDSPECIESBYCATCHLEVELSFROMCOMmercial shrimp trawl and reef fish vessels using fishery observers.

s 5SINGOBSERVERSMONITORSANDDOCUMENTSSEATURTLEANDMARINEMAMMALINTERACTIONS

during petroleum platform removal operations in the Gulf of Mexico.

s #ONDUCTSCAPTIVEREARINGOFLOGGERHEADSEATURTLESFORUSEINTURTLEEXCLUDERDEVICE4%$	

certification trials and other fishery-related studies (e.g., turtle responses to longline fishing gear).

RECENT ACCOMPLISHMENTS AND

RESEARCH PRIORITIES FOR FY 2007–2012

I. Research to Support Fishery Conservation and Management

Recent Accomplishments:

s 4HE3%&3#HASFULLYSUPPORTEDTHE&-#
LED3OUTHEAST$ATA!SSESSMENTAND2EVIEW

(SEDAR) process for conducting stock assessments. SEDAR was initiated in 2002 to 

improve the quality and reliability of fishery stock assessments in the South Atlantic, 

Gulf of Mexico, and U.S. Caribbean. SEDAR emphasizes constituent/stakeholder participation and an independent scientific review of stock assessments, and benefits greatly 

from the expertise of existing stock assessment-related committees and panels of Councils and Commissions. The SEDAR Steering Committee—composing of representatives from the CFMC, GMFMC, SAFMC, ASMFC, GSMFC, and NMFS—meets 

regularly and schedules stock assessments.

s !SSESSMENTANDINDEPENDENTSCIENTIlCREVIEWOFCRITICALSTOCKSFROMTHEREGIONHAVE

been completed using this process, which requires from 9 months to several years to 

accomplish. The stocks thus far assessed using the SEDAR process include stocks of red 

porgy, Atlantic vermilion snapper, black seabass, Florida yellowtail snapper, Atlantic 

menhaden, croaker, tilefish, snowy grouper, king mackerel, goliath grouper, hogfish 

snapper, gulf red snapper, Caribbean yellowtail snapper, spiny lobster, gulf vermilion 

snapper, greater amberjack, gray triggerfish, Atlantic and gulf gag grouper, large coastal 

sharks, and blacktip and sandbar sharks. 

s 4HE3%&3#HASSUCCESSFULLYINCORPORATEDhRISKASSESSMENTvhUNCERTAINTYvANDTHENEW

SFA guidelines on “overfished” and “overfished status” into stock assessment methodologies for numerous species in the Gulf of Mexico, Atlantic, and Caribbean. 

s 2EBUILDINGPLANSFOROVERlSHEDSTOCKSINCLUDINGREDSNAPPERANDANUMBEROFTHOSE

noted above, have been developed based on SEFSC scientific efforts.
s 4HE 3%&3# CONTINUES ITS NATIONAL AND

international leadership roles in the provision of scientific advice for fisheries management.

s 4HE3%&3#INSTITUTEDSEVERALMECHANISMS

for training and recruiting the next generation of quantitative fisheries scientists 

to support increasing demands for fisheries management advice.

s 4HE3%&3#ISRECOGNIZEDFORITSEXPERTISE

in the fields of habitat research and restoration and has successfully developed criteria to define and assess areas of EFH.

s 4HE 3%&3# RECENTLY COMPLETED THE lFTH

and sixth annual assessments of fish populations at the Madison-Swanson and 

Steamboat Lumps Marine Protected Areas 

in the northeastern Gulf of Mexico as part 

of the planned 10-year baseline required 

by the GMFMC for a decision on reauthorization.

In addition, the SEFSC:

s #ONDUCTEDAWORLDWIDEREVIEWOFTHENURSERYVALUEOFSALTMARSHESANDMANGROVESFOR

fishery species in comparison with other estuarine habitat types.

s #ONDUCTEDSURFACELONG
LINElSHERYEXPERIMENTSINTHE.ORTHEAST$ISTANT.%$	WAters to improve hook design to reduce bycatch of protected species while maintaining 

catch of targeted fishes.

s 7ITHTHElSHINGINDUSTRYDEVELOPEDIMPROVEDTOOLSANDPROCEDURESTOMINIMIZEINJURY

and release protected species hooked in long-lines.

s #ONDUCTEDRESEARCHINDICATINGTHATSEASONALITYTIDALCYCLESANDhINTERNALTIDESvMOVEments of sub-surface ocean waters that occur at or near tidal periods, play a significant role in the supply of pink shrimp, a valuable commercial species in the southwest 

Florida fisheries economy.

s #OMPLETEDAREVIEWOF"ISCAYNE"AY&LORIDACOMMERCIALPINKSHRIMPBAITANDFOOD

fisheries showing the influence of salinity and freshwater flow on landings.

s $EVELOPED NON
DESTRUCTIVE lSHERY
INDEPENDENT LENGTH
BASED METHODS FOR lSHERY

stock assessment. 

s #ONDUCTEDECOSYSTEM
BASEDMULTISPECIESREEFlSHSTOCKASSESSMENTSFORTHE&LORIDA

+EYSAND$RY4ORTUGASREGIONSOF&LORIDA

s 7ITHPARTNERSIMPROVEDMAPPINGCLASSIlCATIONANDEVALUATIONOFREEFHABITATINTHE

southeast United States.

s #OMPLETEDAMETA
ANALYSISANDREVIEWOFFACTORSTHATCONTRIBUTETOCATCHANDRELEASE

mortality by recreational angling.

A snowy grouper in rocky 

reef habitat off North 

Carolina. Photo: NMFS.
102

s %VALUATEDTHEIMPORTANCEOFMANGROVESASJUVENILEGOLIATHGROUPERHABITATINSOUTHERN

&LORIDAANDTHE+EYS

s 0UBLISHEDIDENTIlCATIONGUIDESANDDESCRIPTIONSOFlSHEGGSLARVAEANDJUVENILESOF

2,285 species and all 214 families with pelagic early life history stages known to inhabit 

FAO Fishing Area 31, which includes the western central North Atlantic, Caribbean 

Sea, and Gulf of Mexico. The two-volume Early Stages of Atlantic Fishes: An Identification Guide for the Western Central North Atlantic includes over 2,600 pages and 3,000 

illustrations with contributions of over 70 authors. 

s #ONDUCTEDRESEARCHONCORALREEF%&(TODETERMINECAUSESOFCORALDISEASEASSESSPOPulation genetic structure, and coral reef restoration possibilities.

s #OMPLETEDANDPUBLISHEDMANYlSHERYBIODIVERSITYSTUDIESTOPROVIDEDATAANDRESOURCE

understanding necessary to manage fishery resources in the southeast United States.

s #OLLECTEDDATAANDCONDUCTEDMODELINGEFFORTSTOSUPPORTTHE#OMPREHENSIVE%VERglades Restoration Program (CERP). 

Research Priorities, FY 2007–2012:

I.A. Biological research concerning the 

abundance and life history of fish stocks

s 5NDERSTANDANDMODELTHELINKAGESBETWEENHABITATSENVIRONMENTALCHARACTERISTICS

and fishery productivity in order to implement ecosystem-based management.

s $EVELOPINNOVATIVETECHNIQUESTOASSESSGENETICDIVERSITYANDHABITATUTILIZATIONOFMANaged fish and invertebrate stocks.

s $EVELOPANDMAINTAINHIGH
QUALITYlSHERY
DEPENDENTANDlSHERYINDEPENDENTLONG


term data sets for stock assessments. A main component of this effort will be the expanded use of at-sea observers on commercial and recreational fishing vessels to report 

on catch and bycatch. Emphasis will be on collecting a wide range of information, 

including biological and environmental data, gear type deployed, and method of deployment.

s )NCORPORATEMARINEECOSYSTEMSDATAINTOCONCEPTUALMODELSOFFOODWEBSTOLINKHABITAT

to productivity and increase the Center’s ability to survey, inventory, and understand 

the dynamics of marine systems and their biota.

s #ONTINUETOASSESSANDMONITORPROTECTEDlSHSPECIESEGGOLIATHGROUPERAND.ASSAU

grouper, dusky and night sharks, smalltooth sawfish, and gulf sturgeon).

s #ONDUCTRESEARCHON(-3STOCKSPARTICULARLYINTHEAREASOFSTOCKIDENTIlCATIONLIFE

history, and precautionary approach methodologies.

s $EVELOPBASICLIFEHISTORYINFORMATIONANDCONDUCTASSESSMENTSONlSHANDINVERTEBRATE

stocks in support of management for the Commissions (ASMFC, GSMFC) and management recommendations of the Councils (SAFMC, GMFMC, and CFMC).

s #ONDUCTRESEARCHTOIMPROVEMETHODSOFSTOCKASSESSMENTANDIMPROVEMODELINGOFTHE

effects of fishery management on stocks.

s )MPROVE THE EFFECTIVENESS OF lSHERY RESOURCE MANAGEMENT PROGRAMS BY RElNING THE

definition of stocks (including the “management unit” within species).
s #ONDUCTRESEARCHTOMONITORANDEVALUATEEFFECTIVENESSOFlSHERYREGULATIONSTOSUPPORT

sustainable fisheries.

s #ONDUCTRESEARCHTOMOVEECOSYSTEM
BASEDMANAGEMENTPRINCIPLESFROMTHEORYINTO

practice.

s #ONDUCTRESEARCHTOASSESSANDREDUCEBYCATCHFROMVARIOUSlSHERIESINCLUDINGSHARK

drift gillnet, bottom long-line, and surface long-line fisheries in the Southeast Region.

s #ONTINUEPROVIDINGNATIONALANDINTERNATIONALSCIENTIlCLEADERSHIPINDEVELOPMENTAND

provision of fishery management advice while accounting for uncertainties in stock 

abundance and productivity. 

I.B. Interdependence of fisheries or stocks of fish

s %VALUATETHECATCHOFNON
TARGETSPECIESBYRECREATIONALANDCOMMERCIALlSHERIESUSING

applicable programs including the observer program, particularly in cases where the 

population status of non-target species, and the community dynamics of important 

southeast U.S. marine ecosystems, stand to be impacted.

s )NCREASE OUR UNDERSTANDING OFTHEINTERACTIONS OFPROTECTED SPECIESEGSEATURTLES

marine mammals [bottlenose dolphin and large whales]), dusky shark, night shark, and 

fish candidate species (e.g., smalltooth sawfish, goliath grouper, and Nassau grouper) 

with ongoing fisheries in the Southeast Region, including research to assess marine 

mammal interactions with the menhaden fishery.

s 0REVENTTHEEXTINCTIONANDPROMOTETHERECOVERYOFMARINESPECIESANDAT
RISKPOPULAtions through interventions and the continued development of recovery strategies.

s $EVELOPSCIENTIlCMETHODOLOGYFORMULTISPECIESORECOSYSTEMAPPROACHESTOWARDTHE

management of fishery resources, and where appropriate, transition from single-species 

approaches.

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

s $ElNEANDCHARACTERIZE%&(ANDDEVELOPANUNDERSTANDINGOFNATURALANDANTHROPOgenic threats.

s $EVELOPMAPPINGTECHNIQUESFORMOREPRECISEPOSITIONINGOFBOUNDARIESANDFOREVALUation of fishery values of existing and proposed marine reserves.

s )NVESTIGATEDOWNSTREAMANDCOASTALIMPACTSOFAGRICULTURALANDURBANACTIVITIESAND

provide the technical basis for designing and implementing programs for ensuring sustainable coastal communities.

s 'AINABETTERUNDERSTANDINGOFTHESTRUCTUREANDFUNCTIONOFESTUARINECOASTALAND

marine systems to enhance the conservation and restoration of wetland, benthic, and 

aquatic areas of EFH.

s %XPLOREINNOVATIVETECHNIQUESTODETERMINETHEFUNCTIONALVALUEOFNATURALHABITATSAND

to evaluate the restoration success relative to the fish and invertebrate community rather 

than solely to the plant community. 

s $EVELOPRESTORATIONTECHNIQUESFOR%&(INCLUDINGCORALSSALTMARSHESANDSEAGRASSES

and determine whether habitats created or restored with such techniques are ecologically functional.
104

s )NTEGRATE%&(RESEARCHWITHSTOCKASSESSMENTSTODEVELOPANECOSYSTEMAPPROACHFOR

managing fisheries.

I.D. Impact of anthropogenic factors and 

environmental changes on fish populations

s #ONTINUETOENGAGEINJOINTEFFORTSWITHSTATEANDOTHER&EDERALAGENCIESTORESTORETHE

ecological integrity and water quality in regional estuaries upon which fish depend. 

s #ONTINUERESEARCHEFFORTSUNDERTHE3OUTH&LORIDA2ESTORATION%FFORTPARTICULARLYINTHE

areas of modeling fishery dynamics, recovery of protected resources, restoring EFH. 

s $ETERMINETHEIMPACTSOFlSHINGONREEFlSHPOPULATIONSTRUCTUREGENETICDIVERSITY

and resilience. 

s $ERIVEMOREACCURATEASSESSMENTSOFlSHINGANDOTHERANTHROPOGENICIMPACTSONLIVING

marine resources by incorporating risk and uncertainty into models used to predict 

natural living marine resource variations.

s $EVELOPTECHNIQUESANDSCIENTIlCDATANECESSARYTOSUPPORTTHEEFFECTIVEAPPLICATIONOF

precautionary approaches to fisheries management.

s #ONTINUETOEVALUATETHEEFlCACYOFMARINERESERVESNO
TAKEANDLIMITED
TAKEZONES

and time closures as fishery management tools.

II. Conservation Engineering Research

Recent Accomplishments:

s )NNOVATIVEAPPROACHESTOBYCATCHREDUCTIONDEVICE"2$	DESIGNHAVEBEENDEVELOPED

For example, the SEFSC has conducted in-situ observations of red snapper behavior 

during shrimp trawling to aid in the design of more effective BRDs, and has successfully 

led efforts to significantly reduce the bycatch of non-target species such as red snapper 

in the Gulf of Mexico shrimp fishery.

s 4HEDEVELOPMENTANDUSEOFIMPROVED4%$SISCONTRIBUTINGTOTHERECOVERYOFSEATURTLES

ESPECIALLY+EMPSRIDLEYINTHE3OUTHEASTERN2EGION

A nesting sea turtle. Photo: 

Ben Higgins, NMFS.
s !RECOVERYMODELFORIMPACTEDSUBTROPICALSEAGRASSHABITATSWASDEVELOPEDANDHASBEEN

used successfully in court to demonstrate impacts to sanctuaries.

Research Priorities, FY 2007–2012:

s #ONTINUEINVESTIGATIONSONTHEIMPORTANCEOFENVIRONMENTALCUESINTHESPATIALORIENTAtion and migration behavior of sea turtles. 

s $EVELOPANDTESTNEWGEARTECHNOLOGYANDlSHINGTECHNIQUESTOMINIMIZEBYCATCH4HE

SEFSC continues to explore options to reduce bycatch and mitigate mortality of sea 

turtles and other non-target species captured in the distant water longline fisheries.

s $EVELOPANDTESTNEWGEARTECHNOLOGYANDlSHINGTECHNIQUESTOMINIMIZEADVERSEIMpacts on EFH. The Center will continue to document the extent and assess the impact 

of various fishing gears on EFH in support of conservation and management activities. 

s 0ROMOTEEFlCIENTHARVESTOFTARGETSPECIES4HE#ENTERWILLCONDUCTINVESTIGATIONSINTO

limited access options (e.g., Individual Transferable Quotas [ITQs]) as resource management alternatives to aid increased harvest efficiency. 

III. Research on the Fisheries

Recent Accomplishments:

s 0ROVIDED ECONOMIC INFORMATION ANALYSES AND EVALUATIONS FOR NUMEROUS PROPOSED

southeast fishery management actions.

s )MPLEMENTEDAPROGRAMINCONJUNCTIONWITHEXISTINGLOGBOOKREPORTINGREQUIREMENTS

to collect operating and ownership costs from boats in the Atlantic snapper-grouper and 

mackerel fisheries and in the Gulf of Mexico reef fish and mackerel fisheries.

s #OLLECTEDANDSUMMARIZEDECONOMICDATAFROMASAMPLEOFCOMMERCIALTRAPlSHERMEN

in the Caribbean. Results were published in Agar et al (2005).

s $EVELOPEDAMODELTOESTIMATETHEEFFECTOFCLIMATICVARIABLESONlSHINGEFFORTAND

landings for red snapper by the headboat fishery in the Gulf of Mexico.

s 7ORKEDWITHCONTRACTORSANDTHE3OUTHEAST2EGIONAL/FlCE3OCIAL3CIENCE"RANCHSTAFF

to identify and describe fishing communities in the Caribbean, Gulf of Mexico, and 

South Atlantic. Final reports for the Gulf of Mexico and South Atlantic are available 

online at http://sero.nmfs.noaa.gov/economics/economics.htm.

s 7ORKEDWITHCONTRACTORSTODOCUMENTTHEEFFECTSOFTHEHURRICANESEASONONTHE

charterboat industry in the Gulf of Mexico.

s 7ORKEDWITHCONTRACTORSTODOCUMENTTHEEFFECTSOF(URRICANE+ATRINAONlSHINGCOMmunities in the Gulf of Mexico.

s $EVELOPED AND IMPLEMENTED THE 'ULF 3HRIMP 6ESSEL AND 'EAR #HARACTERIZATION

Form.

s 7ORKEDWITHTHE'ULF#OUNCILS!D(OC3HRIMP%FFORT#OMMITTEETOHELPDEVELOP

theory and methods for estimating MSY, MEY, and socially optimal levels of fishing 

effort and harvest in the Gulf shrimp fishery.
106

Research Priorities, FY 2007-2012:

III.A. Social and economic research

s %XPANDTHECOLLECTIONOFECONOMICDATATOINCLUDEALLMAJORCOMMERCIALlSHERIESMANaged with FMPs in the southeast.

s $EVELOPIMPROVEDMODELSOFCOMMERCIALANDRECREATIONALlSHERIESTOEVALUATEPROPOSED

management alternatives.

s %STIMATEECONOMICRELATIONSHIPSSUCHASDEMANDCURVESPRODUCTIONFUNCTIONSANDRECreational benefit functions needed to support the evaluation of management decisions.

s #OLLABORATE WITH 3OUTHEAST 2EGIONAL /FlCE 3OCIAL 3CIENCE "RANCH STAFF TO CONDUCT

ethnographic research to develop community profiles for fishing communities in the 

southeast, and incorporate resulting information into FMPs.

s #OLLABORATEWITH3OUTHEAST2EGIONAL/FlCE3OCIAL3CIENCE"RANCHSTAFFTOEVALUATEAND

improve baseline data for research about the Gulf and south Atlantic shrimp fisheries, 

and incorporate resulting information into FMPs.

III.B. Seafood safety research

s 3UPPORTRESEARCHAIMEDATIDENTIFYINGANDCHARACTERIZINGMARINEPATHOGENSESPECIALly viruses, in aquaculture shrimp products, and the extent of viruses in wild shrimp 

stocks.

s #ONTINUETODEVELOPBIOLOGICALANDCHEMICALANALYTICALMETHODSFORTOXICCONTAMINANTS

(e.g., mercury), assess their presence in seafood, and define their impacts on marine 

ecosystems.

s )MPROVEMETHODSTODETECTFORECASTANDEVALUATETHEECOLOGICALSIGNIlCANCEOFHARMful algal blooms and their impact on fish stocks, marine mammals, and other protected 

species.

III.C. Marine aquaculture

s $EVELOPTHESCIENTIlCFOUNDATIONANDTECHNICALGUIDELINESFORESTABLISHINGECOLOGICALLY

responsible marine aquaculture.

s #ONTINUETOINVESTIGATETHENATURALOCCURRENCEOFSHRIMPVIRUSES

IV. Information Management Research

Recent Accomplishments:

s #OMPLETEDMIGRATIONOFOVERPERCENTOFOURTEXT
BASEDAPPLICATIONSTOWEB
BASEDAPplications that are SSL-enabled, to provide secure access by constituents and the public 

to SEFSC information resources via web-based technologies.

s 2EDESIGNEDOURSYSTEMSINFRASTRUCTURETOIMPROVEPERFORMANCEANDFACILITATEIMPROVED

continuity of operations.

s $EVELOPEDGLOBALINFORMATIONSYSTEMSCAPABILITYTOPROVIDEENHANCEDABILITYTOANALYZE

and distribute scientific data.
Research Priorities, FY 2007–2012:

s &ULLY SUPPORT THE &ISHERIES )NFORMATION

System, a fishery database and information 

management system that will allow the full 

use of information in support of effective 

fishery conservation and management.

s %NHANCE ACCESSIBILITY TO DATA COLLECTIONS

by migrating existing metadata to the FIS 

InPort metadata catalog,

s %XPANDOURCAPABILITYANDUSEOF')3APplications to enhance access to and understanding of fisheries information with spatial characteristics.

s %NHANCETHEUTILITYOFCURRENTANDHISTORIcal data collections through implementation of Oracle Datawarehouse and other 

database-driven, web-enabled applications.

Tagging sharks yields valuable data for NMFS 

researchers. Top, a blacktip shark is being 

tagged. Bottom, an Atlantic sharpnose shark 

with an acoustic tag. Photos: NMFS.
108

NORTHEAST FISHERIES SCIENCE CENTER

The Northeast Fisheries Science Center (NEFSC) has facilities in Woods Hole, Massachusetts; Narragansett, Rhode Island; Milford, Connecticut; Highlands, New Jersey; and 

Orono, Maine, and the National Systematics Laboratory (NSL) is housed at the Smithsonian Institution in Washington, D.C. The NOAA FSVs Albatross IV and Delaware II along 

with the R/V Gloria Michelle are berthed in Woods Hole and support the majority of the 

Center’s fisheries survey and research cruises. Commercial fishing vessels and academic 

research ships have been used periodically to support ecosystem surveys on the northeast 

continental shelf. Two smaller vessels, the R/V Nauvoo and the R/V Victor Loosanoff, support inshore research activities in the Center and are berthed in Highlands and Milford, 

respectively. The R/V Gloria Michelle supports cooperative research between the NEFSC, 

Massachusetts Division of Marine Fisheries, and the University of Massachusetts School 

of Marine Science and Technology.

The FSV Henry B. Bigelow, delivered during summer 2006, is the second new fisheries 

survey ship to be built by NOAA, representing a significant achievement in NOAA’s efforts 

to modernize its fleet of fisheries, oceanographic, and hydrographic survey ships. The primary objective of the ship will be to study, monitor, and collect data on a wide range of sea 

life and ocean conditions in the waters from Maine to North Carolina. It will also observe 

weather, sea state, and other environmental conditions; conduct habitat assessments; and 

survey marine mammal and marine bird populations. All missions support the application 

of ecosystem principles to fishery management. The FSV Bigelow is a state-of-the-art, 40-

day endurance, research ship with multiple science mission capabilities, including bottom 

trawling, midwater trawling, hydroacoustic surveying (the ship’s “quiet” hull minimizes 

underwater sound made by the ship), and oceanographic and hydrographic operations. 

In addition, it has capabilities for handling specialized gear such as MOCNESS frames, 

The FSV Henry B. Bigelow

after being lauched from the 

shipyard where it was built. 

Photo: NOAA.
floating and moored buoys, towed vehicles, dredges, and bottom corers. Also available are 

marine mammal and bird observation stations to track and identify protected species such 

as North Atlantic right whales, humpback whales, and harbor porpoises.

The NEFSC research activities range from assessments of finfish populations during 

trawl surveys conducted annually since the 1960s, to process-oriented research projects 

such as studying the impacts of global climate change on the coupling of zooplankton to 

cod and haddock larval distributions and predation on Georges Bank. Surveys are also 

conducted for ocean quahogs, surfclams, and sea scallops. In addition, grants are provided 

to support surveys of Gulf of Maine northern shrimp and finfish surveys in state waters. 

Aquaculture research focuses on mollusks and finfish, including the development of efficient systems by improving biological and physical rearing parameters. Interdisciplinary 

research in husbandry, physiology, genetics, immunology, chemical ecology, and nutrition 

is conducted to optimize growth and production in culture systems. Projects extend to 

include study of harmful algal blooms (HABs) and exploration of aquaculture-based stock 

enhancement strategies.

Long-term changes in the ecosystem supporting fisheries are monitored through surveys 

of that ecosystem; research is under way to convert these data into indices on the health 

of the ecosystem. Additional process-oriented research projects focus on the effects of 

pollution on coastal species (e.g., winter flounder and bluefish); biological characteristics 

of selected shark species in the North Atlantic; field investigations on the effects of trawling on seabed habitats; and descriptions of essential fish habitat (EFH) for most finfish 

species. The Center also conducts social and economic research in support of the fishery 

management process. The NSL provides taxonomic expertise on finfish, crustaceans, and 

squids for all of NMFS.

Reliable information—critical to the development of regional FMPs, subsequent amendments, and ultimately to the maintenance of sustainable fisheries—is produced through the 

Northeast Regional Stock Assessment Workshop (SAW) process. This cooperative effort 

is guided by the Northeast Regional Coordinating Committee composed of the directors 

of the NEFSC, Northeast Regional Office (NERO), New England Fishery Management 

Council (NEFMC), Mid-Atlantic Fishery Management Council, and Atlantic States Marine Fisheries Commission (ASMFC). The Northeast Regional Stock Assessment Review 

Committee (SARC) is an important part of the SAW process, which includes peer-assessment development (SAW Working Groups or ASMFC technical committees), assessment 

peer-review, public presentation, and document publication. The process has been in place 

since 1985, and has provided a forum for preparing, peer reviewing, and reporting on stock 

assessments of over 40 species/stocks in the region. The SAW is the oldest such process for 

review of assessments by peers in the Nation and has been used as a model in developing 

similar protocols around the United States and in Europe. All meetings are open to the 

public and widely announced. As currently constituted, the SAW has three parts: 1) SAW 

working group meetings where the assessments are developed (or ASMFC technical/stock 

assessment groups when stock assessment are prepared by the ASMFC), 2) a high-quality peer review of the assessments by an independent panel of assessment/management 

experts, and 3) presentation of results/reports from the SARC meeting to the FMCs and 

ASMFC. The Plan Development Teams and Technical Committees of the FMCs use the 

Stock Assessment Reports and the peer reviewers’ reports to develop management advice 

for the FMCs that is consistent with existing FMPs.
110

The Northeast Cooperative Research Partners Program (NCRPP)—NMFS’ largest 

cooperative research program in the northeast—was established in 1999 in conjunction 

with the New England Fishery Management Council. The NCRPP is one of six regional 

cooperative research programs nationwide. The program has funded more than $26 

million in cooperative research projects both large and small, and just over $1 million 

in 2005. Cooperative research programs promote trust and understanding among fishermen, scientists, and managers; provide a way for fishermen to contribute their empirical 

knowledge of the sea and marine life to the scientific process; and can strengthen both the 

information underlying fishery management decisions and the decisions themselves.

Much recent gear research in the Northeast has been accomplished through grants, 

with Northeast Regional Office (NERO) oversight. These grants have gone to fishermen, 

or to organizations such as states and universities, which carry out the research with the 

help and cooperation of the fishing industry. The NERO Fisheries Engineering Group is 

also involved with data analysis for exempted fishery permits and fishway engineering for 

anadromous fish. Conservation engineering activities in the NERO have recently been 

concentrated on the problem of entanglement of large whales in fixed fishing gear (e.g., 

lobster traps and gillnet gear). The fishing industry aided this effort through its participation in the Gear Advisory Group to the Atlantic Large Whale Take Reduction Team 

by devising solutions and by volunteering vessels and time for observations and testing. 

Also, NERO and the NEFSC are collaborating on experiments using pingers and acoustic 

reflective nets as deterrents to marine mammal entrapment in gillnets.

RECENT ACCOMPLISHMENTS AND

RESEARCH PRIORITIES FOR FY 2007–2012

I. Research to Support Fishery Conservation and Management

Recent Accomplishments:

s !TWO
VOLUMETAXONOMICATLASOFEGGSANDLARVAEOFlSHESOFTHEWESTERN.ORTH!TLANTIC

has been completed.

s 4HEDISTRIBUTIONABUNDANCEANDBASICBIOCHEMISTRYOFANINVASIVETUNICATESEASQUIRT	

Didemnum sp. on eastern Georges Bank has been documented; as of August 2005, the 

species was present over at least 82 n.mi.2

 of the productive gravel bottom on the eastern 

bank. 

s ,EDTHEMONITORINGFORACOMMUNITY
BASEDOYSTERRESTORATIONINTHE.AVESINK2IVERIN

New Jersey. The project led to the first successful oyster spawning and setting in the 

river in over a decade.

s !PEERREVIEWOFALTERNATIVE%&(DESIGNATIONMETHODOLOGIESWASCONDUCTED

s %&( DOCUMENTS WERE COMPLETED FOR THE  SPECIES FOR WHICH MANAGEMENT RECOMmendations are provided by the Mid-Atlantic and New England Fishery Management 

Councils.

s 5PDATED%&(INFORMATIONONSPECIESOFSHARKSTUNASANDBILLlSHESUSEDDATAFROM

observer and tagging databases for the Draft Consolidated Atlantic Highly Migratory 

Species Management Plan.

s 2ESISTANCETO0#"SWASDEMONSTRATEDINANANADROMOUSlSHTOMCOD	COLLECTEDFROM
throughout the Hudson River estuary. This is the most widespread occurrence of such 

resistance found to date.

s -ETHODSWEREDEVELOPEDFORDETECTINGTHEEFFECTOFCONTAMINANTSONGENEEXPRESSION

and regulation in winter flounder.

s 4HE#ENTERDEMONSTRATEDTHATDIETINmUENCESCONTAMINANTCOMPOSITIONINYOUNG
OF


the-year bluefish.

s 4HE#ENTERDEMONSTRATEDTHATCONTAMINANTCOMPOSITIONPATTERNINYOUNG
OF
THE
YEAR

bluefish uniquely identifies individuals to nursery estuary with a resolution of less than 

15 km.

s 4HECONCENTRATIONOFMANGANESEACCUMULATEDONGILLSOF!MERICANLOBSTERSWASFOUND

to be an indicator of exposure to hypoxia in estuaries with degraded habitat quality. A 

paper in the Journal of Shellfish Research may help us understand the vulnerability of 

lobsters in marginal estuaries to events such as the recent mass mortality in Long Island 

Sound. 

s 4HE.%&3#DEMONSTRATEDRAPIDACCUMULATIONOF0#"SINYOUNG
OF
THE
YEARBLUElSH

in the Hudson River estuary with an indication of dilution by exponential growth.

s 4HE.%&3#DEMONSTRATEDTHEINADEQUACYOFEXISTINGBATHYMETRICMAPSINTHE(UDSON

Canyon for purposes of habitat definition.

s 4HEOCEANOGRAPHICCONDITIONSONTHE.ORTHEAST3HELFWEREMEASUREDANDTHEINTERANnual variability was documented in a report each year. The data were used in stock 

assessment activities and available to the scientific community via the web.

s 3HELF
WIDESURVEYSOFECOSYSTEMCONDITIONSFROM#APE(ATTERASTOTHE'ULFOF-AINE

were completed, along with monthly continuous plankton recorder transects of the 

Gulf of Maine and across the Middle Atlantic Bight using ships of opportunity in cooperation with NOAA’s Global Ocean Observing Program. These activities contribute 

to our understanding of the role of plankton for fish recruitment and demonstrate the 

success of the program. 

s !NANALYSISOFTHEDEMOGRAPHICSOFTHECalanus finmarchicus population in the MidAtlantic Bight was completed and published.

s $RIFTERDEPLOYMENTSWERECONDUCTEDINSUPPORTOFMONITORINGTHEREDTIDEEVENTIN

New England waters during spring 2005. The drifter location data were made available 

in real-time via a web page display.

s 4HE#ENTERCOMPLETEDSTUDIESEXAMININGTHEHABITATDYNAMICSOFJUVENILEWINTERmOUNder predation in a shallow coastal nursery area.

s 3TUDIESOFSPECIES
SPECIlCPREDATOR
PREYINTERACTIONSAFFECTEDBYCHANGESINSTRUCTURAL

refuge were completed, supporting previous field research that complex seafloor habitats contribute to juvenile fish survival. 

s 4HEOCCURRENCEANDPOSSIBLEECOLOGICALROLEOFTHINLAYERFORMATIONINTHEWATERCOLUMN

in the New York Bight was examined, revealing layers of varied community composition and dynamic habitat interactions. 

s %VIDENCE OF !TLANTIC MENHADEN SPAWNING AT LOWER TEMPERATURESTHAN PREVIOUSLY REcorded was documented in the New York Bight Apex. 
112

s !NACOUSTICTAGGINGSTUDYSHOWEDTHATBLACKSEABASSANDSUMMERmOUNDERWEREPATCHily distributed in a disturbed coastal environment with higher occurrences in shallow, 

complex habitats and little evidence of long-term residency.

s 4HEPREDATORSURVIVALBEHAVIORSOFTHREEYOUNG
OF
THE
YEARTEMPERATEREEFlSHSPECIES

were characterized.

s 3TUDIESWERECONDUCTEDTHATDEMONSTRATEDLOWWINTERTEMPERATURESANDSALINITIESINTHE

Hudson-Raritan estuary do not harm adult female blue crabs. 

s )NITIATED THE ECOSYSTEM PROJECT ENTITLED h%NERGY -ODELING AND !NALYSIS E8ERCISEv

%-!8	THATAPPLIESAFOODWEBMODELTOFOURSUBREGIONSOFTHENORTHEAST53CONTInental shelf. Completed initial report describing baseline conditions in the ecosystem.

s $EVELOPEDCONSUMPTIONESTIMATESOFALLMAJORPREDATORSOF!TLANTICHERRINGCOMMERcially targeted forage fish), and translated values into preliminary estimates of predation 

mortality.

s !SSISTEDINTHEDEVELOPMENTINITIALIZATIONANDPARAMETERIZATIONOFA-ULTI
SPECIES6IRtual Population Analysis (MSVPA) for the mid-Atlantic species complex. Emphasis 

was on menhaden as focal species with major predators including those stocks that are 

recreationally important.

s !SSISTEDINTHEDEVELOPMENTOFAMULTI
SPECIESECOSYSTEMMODELTOOLBOX

s 0ROVIDEDPREYlELDINFORMATIONTOASSISTWITHTHEDESIGNATIONOF%&(FORALLSPECIESFOR

which management recommendations are provided by the NEFMC. Diet compositions 

of all managed stocks and location of prey distribution (using stomachs as samplers) 

have been calculated.

s )NTHE26Gloria MichelleSAILEDTO+INGS0OINT53-ERCHANT-ARINE!CADemy to conduct fisheries training for NOAA Corps’ Basic Officer Training Class 106.

s 4HE26Gloria Michelle has conducted acceptance testing of the Macartney towed 

underwater vehicle. The multibeam sonar head can be operated on this vehicle to further extend its abilities. In addition, the task of using the multibeam sonar for sea floor 

habitat mapping the waters of Massachusetts has begun.

s $EVELOPEDAMETHODTOESTIMATETHEAGEOFBUTTERlSHFROMOTOLITHWEIGHTS

s $EVELOPEDSTANDARDIZATIONMETHODSTOESTIMATETHEACCURACYANDPRECISIONOFAGEDATA

to monitor Quality Assurance/Quality Control (QA/QC) and provide estimates of aging error for assessment models.

s #ONVENEDORPARTICIPATEDIN!GING7ORKSHOPSFOR!TLANTICCODHADDOCKPOLLOCK!Tlantic herring, and surfclam to ensure consistency in conventions, methodologies, and 

age interpretations between Federal, state, academic, and international aging laboratories.

s %VALUATEDCHANGESINMEANWEIGHTSATAGEGROWTHRATESANDSEXRATIOSFORlVECOMmercially important species of flatfish.

s 0UBLISHEDVALIDATEDAGEESTIMATESFORTHESHORTlNMAKOSHARKIN!TLANTICWATERS

s #OMPLETEDBLUESHARKSTOCKSTRUCTUREANALYSESBASEDON#OOPERATIVE3HARK4AGGING

Program mark/recapture data detailing size composition and movements between Atlantic regions.
s #OMPLETEDANEXAMINATIONOFTHEPREDAtor-prey relationships between the shortfin 

mako and bluefish (its primary prey), to 

compare contemporary and historic levels 

of predation on bluefish.

s #OMPLETED SURVIVAL RATE ESTIMATES FOR

shortfin mako shark in the Atlantic using 

the Cooperative Shark Tagging Program 

mark/recapture data.

s 0RODUCEDAPICTORIALlELDGUIDETOSHARKS

tunas, and billfishes of the U.S. Atlantic 

and Gulf of Mexico for identifying large 

pelagics.

s 0RODUCEDAPICTORIALlELDGUIDEANDDICHOTOMOUSKEYFORIDENTIFYINGSHRIMPANDDECApod species of the Georges Bank-Gulf of Maine region.

s !UTHOREDTAXONOMICPAPERSINCLUDINGSEVERALBOOKCHAPTERS4HESEPUBLICATIONSIMprove our knowledge of the diversity of marine organisms and contribute critical baseline information required in decisions involving marine ecosystem management.

s !#ENTERSYSTEMATICSSCIENTISTWASACO
RECIPIENTOFMILLIONGRANTAWARDEDBYTHE

National Science Foundation to support systematic research on cnidarians. This collaborative research effort, “Assembling the tree of life—An integrative approach to investigating cnidarian phylogeny,” is funded through NSF’s Assembling the Tree of Life 

Program, 2005–2009. 

s 0ROVIDEDLEADERSHIPANDTECHNICALADVICEINTHEDEVELOPMENTOFTHENEW/CEANS(ALL

Exhibit, co-sponsored by NOAA, at the Smithsonian’s Natural History Museum.

s #OMPLETEDAREPORTONTHESTATUSOFDEEPWATERCORALSINNORTHEAST53MARINEWATERS

s #ONTINUEDDEVELOPMENTOFDEDICATEDRESEARCHPROGRAMONDEEP
SEACORALECOSYSTEMS

and associated fauna on the U.S. southeast continental shelf. A Center scientist was 

co-Principal Investigator on two NOAA Ocean Expedition projects to examine deep 

coral reefs in the South Atlantic Bight and co-authored a chapter on deep-sea corals 

in the Southeast Region for NOAA’s Status of Corals report, and participated in two 

USGS/MMS-funded deep coral research expeditions in the Gulf of Mexico. 

s #OMPLETEDASTUDYOFSELECTEDFAUNAOF"EAR3EAMOUNT.EW%NGLAND3EAMOUNTCHAIN	

providing baseline information on seamount ecosystems from the field program on the 

mount. 

s #OMPLETEDASERIESOFSPECIESCHECKLISTSFORFAMILIESOFlSHESPUBLISHEDBYTHE#ALIFORNIA

Academy of Sciences, which included evaluations of all valid species and all of the scientific names used for members of the families Scombridae, Belonidae, Scomberesocidae, 

and Hemiramphidae.

s *UVENILELOBSTERHAVEBEENCAPTUREDMARKEDANDRELEASEDONANATURALCOBBLEREEFIN

Long Island Sound, Connecticut. A recapture rate of approximately 7 percent has enabled the determination of movement, site fidelity, growth, and estimated population 

size.

s !lELDECOLOGICALSTUDYOFTHEINTRODUCED!SIANSHORECRABHASQUANTIlEDTHEIRIMPACT

A great white shark, one of 

the large pelagic species of 

shark. Photo: NOAA.
114

on natural settlement of recruiting barnacles in Long Island Sound, Connecticut. Information on predator density effects and diet preference has been identified.

s %XPERIMENTAL CALIBRATIONS HAVE BEEN CONDUCTED THAT WILL ENABLE USE OF 2.!$.!

measurements of muscle tissue of finfish to estimate growth potential. This increases 

confidence in using this biochemical method to evaluate wild-caught and aquaculturally reared fish.

s 4HE.%&3#HADTHELEADROLEINANINTERNATIONALINTERCALIBRATIONSTUDYOFBIOCHEMICAL

methods for measuring RNA/DNA ratios in larval and juvenile fish. These methods 

are used to determine recent growth and condition of the organisms. 

s !PRELIMINARYEXPERIMENTTOEVALUATESTOCKENHANCEMENTPOTENTIALOFBLACKSEABASSWAS

conducted: approximately 2,000 laboratory-reared and fin-clipped fish were released on 

a rock reef in Long Island Sound, Connecticut. Some recaptured fish were at liberty for 

up to 3 months.

s !STUDYOFTHEDIETOFJUVENILETAUTOGHASIDENTIlEDSIZE
RELATEDSHIFTSINFOODPREFERences.

s 4HE#ENTERINTRODUCEDVALIDATEDANDAPPLIEDNOVELmOW
CYTOMETRICAPPLICATIONSIN

marine science, including: immunological analysis of invertebrate hemocytes, live-sorting of bivalve hemocytes, determination of nutrient status in individual phytoplankton 

cells, quantification and size-distribution analysis of phytoplankton and other particles 

in seawater, isolation of microorganisms using flow-cytometric sorting, and quantification of grazing activity of filter-feeding mollusks on phytoplankton.

s #OMPLETED AREPORT PROVIDING GUIDANCE FORDETERMINING WHETHERTHE%ASTERNOYSTER

should be listed as an endangered or threatened species. This work was conducted as 

part of the activities of an agency-supported Biological Review Team for Eastern oyster. 

s 0ARTICIPATEDINANEXTENSIVERESEARCHPROGRAMONTOMCODANIMPORTANTCOMPONENTOF

the Hudson River ecosystem and a compressed-life model for research on gadid fishes. 

Staff coauthored "Evidence of spatially extensive resistance to PCBs in an anadromous 

fish of the Hudson River” and "Characterization of the aryl hydrocarbon receptor repressor and a comparison of its expression in Atlantic tomcod from resistant and sensitive populations."

s %STABLISHEDAPARTNERSHIPWITHTHE5NITED.ATIONS%NVIRONMENTAL0ROGRAM5.%0	

wherein the LME projects and their Strategic Action Programs under way in the 19 

UNEP Regional Seas areas around the globe will, through agreed-upon transboundary ministerial actions, constitute the principal assessment and management authorities for recovering depleted fish stocks, restoring degraded habitats, and reducing and 

controlling coastal pollution through the introduction of ecosystem-based practices for 

sustaining marine resources and their environments.

s )NCOOPERATIONWITHTHE'LOBAL%NVIRONMENT&ACILITYANDITSMILLIONINGRANTAID

to 121 countries in Africa, Asia, Latin America, and eastern Europe, provided scientific 

and technical assistance in the introduction of ecosystem-based management practices 

framed around five ecosystem assessment and management modules: 1) productivity, 

2) fish and fisheries, 3) pollution and ecosystem health, 4) socioeconomics, and 5) governance.
s !SSISTEDINTRAININGSCIENTISTSFROMDEVELOPINGCOUNTRIESIN	MODELINGOFTHECARRYING

capacity for maximum sustainable fisheries, 2) modeling of nitrogen and phosphorus, 

and 3) modeling of particle spectra as indicators of ecological condition of LMEs.

s )SSUEDTHElRSTADVISORYONTHEECOLOGICALCONDITIONOFTHE.ORTHEAST3HELF,ARGE-Arine Ecosystem, based on an analysis of two decades of time series measurements of 

chlorophyll, primary productivity, zooplankton, and temperature that described the 

plankton component of the ecosystem as robust with no significant change in average 

annual primary. 

s .%&3#SCIENTISTSCO
EDITEDASPECIALISSUEOFDeep Sea Research reporting results of the 

U.S. GLOBEC Georges Bank program, which investigated the influence of environmental variability on the physics, plankton, and fish populations of the bank. NEFSC 

scientists were also lead authors or co-authors on 7 of the 18 contributions in the volume.

s 0UBLISHEDANATLASOFlSHEGGDISTRIBUTIONSON'EORGES"ANKDURINGTHE53',/"%#

Georges Bank Program (1995–1999).

s $EMONSTRATED THE PALATABILITY OF THE INVASIVE COLONIAL TUNICATE SEA SQUIRT	 TO THREE

common marine invertebrates: the purple sea urchin, common spider crab, and Asian 

shore crab. Cunner, a local wrass, did not ingest the tunicate.

s !NALYZEDFOODVALUEOFACOLONIALTUNICATESEASQUIRT	COLLECTEDFROMAVARIETYOFLOCAtions in New England, revealing that the squirt contained a high and variable content 

of indigestible matter for potential animal consumers.

Research Priorities, FY 2007–2012:

I.A. Biological research concerning the 

abundance and life history of fish stocks

s )MPLEMENTANIMAGE
ANALYSIS
BASEDMETHODTOGENERATEPRODUCTIONFECUNDITYESTIMATES

for numerous species.

s %XPANDRESEARCHINTHEDEVELOPMENTOFMICRO
CONSTITUENTCHEMICALANALYSISTECHNIQUES

for stock identification.

s $EVELOPTESTANDIMPLEMENTMULTISPECIESANDECOSYSTEM
BASEDMODELSINCLUDINGNEW

approaches for dynamic ecosystem modeling, resulting in assessments for groups of 

stocks or entire systems and decision analysis tools for fishery managers and ecosystem 

committees.

s 5SINGTHE"ARCODEOF,IFEMETHODSADOPTEDBYTHE#ENSUSOF-ARINE,IFEDEVELOPA

DNA barcode library for species of interest and their prey (e.g., fish, plankton, protected species), and combine this information with emerging technologies to develop 

the next generation of species-specific sensors for use in ecosystem surveys, ecosystem 

research, and regulatory enforcement.

s $ETERMINEDISTRIBUTIONANDABUNDANCEOFYOUNGlNlSHANDLOBSTERINNEARSHORECOASTAL

habitats and nursery areas, through sampling over multiyear time series.

s ,OCATEANDDESCRIBEHABITATCHARACTERISTICSOFWINTERmOUNDERPseudopleuronectes americanus, spawning areas by sampling of demersal eggs.
116

s#ONDUCT COMPREHENSIVE HEALTH ASSESSMENTS

of bivalve mollusks, including nutritional, 

physiological, immunological, histological, 

and bacteriological variables, with the overall objective of detecting and identifying 

sources of sub-lethal stress that impact production by slowing growth or increasing 

susceptibility to parasites and pathogens.

s%NHANCE CONSUMPTION RATE ESTIMATES FOR

commercially valuable stocks utilizing the 

NEFSC's food habits data. This effort will 

calculate consumption for a wide range of 

species which can then be used to track 

both changes in growth and changes in 

mortality.

s3AMPLEHADDOCKCUSKEELPOUTANDREDlSH

on boulder reefs inside and outside the 

Western Gulf of Maine Closure by means

of fish pots, determine diet composition and utilize stable isotopes to assess feeding 

habitats and effective trophic level; expand the food web study into deep mud habitats, 

using trawl sampling; obtain further data from a previously sampled gravel-bottom 

habitat; and make fuller use of food web (stable isotope and stomach) samples from 

shoal habitats.

s $EVELOPCALIBRATIONAPPROACHESTOCOMPARESURVEYRESULTSFORCURRENTMULTISPECIESBOTtom trawl surveys conducted on the RV Albatross IV using a Yankee 36 trawl, with 

new bottom trawl surveys conducted on the FSV Henry B. Bigelow using an improved 

4-seam, 3-bridle trawling system.

s $EVELOPCALIBRATIONAPPROACHESTOCOMPARESURVEYRESULTSFORCURRENT3EA3CALLOPDREDGE

surveys conducted on the RV Albatross IV using a standard NEFSC scallop dredge to 

surveys conducted on a leased University-National Oceanographic Laboratory System 

(UNOLS) vessel utilizing an improved scallop dredge design developed in conjunction 

with industry stakeholders.

s $EVELOPCALIBRATIONAPPROACHESTOCOMPARESURVEYRESULTSFORCURRENT3URF#LAMAND

Ocean Quahog dredge surveys conducted on the RV Delaware II using a standard 

NEFSC clam dredge, to surveys conducted on a leased commercial vessel platform utilizing an improved clam survey dredge design developed in conjunction with industry 

stakeholders.

s #ONTINUETOASSESSTHESTATUSOFMARINEMAMMALSANDTURTLESINTHE.ORTHWEST!TLANtic Ocean through a three-pronged approach—stock identification, abundance estimation, and mortality assessment—thereby providing a better understanding of the 

spatial/temporal overlap between protected species and fisheries.

I.B. Interdependence of fisheries or stocks of fish

s %STABLISH -ARINE )NTEGRATED %COSYSTEM !SSESSMENTS -)%!S	 FOR ALL 53 REGIONAL

LMEs following the process of 1) National Workshop for identifying, compiling, and 

vetting ecological indicators; 2) Regional Working Groups for culling National StanJuvenile haddock from a trawl 

sample collected on the NOAA 

ship Albatross IV. Sampling is an 

essential part of fisheries research. 

Photo: NMFS.
dard Ecological Indicators; 3) National Ecosystem Modeling Workshop; 4) Regional Ecosystem Modeling Working Groups; 5) Regional Ecosystem Plan Assimilation 

Teams; and 6) National Ecosystem Assessment Reporting Group.

s $ElNEFOODHABITSANDPREDATOR
PREYRELATIONSHIPSOFMARINElNlSHINNEARSHORECOASTAL

nursery areas.

s 5SE2.!$.!RATIOSINMUSCLETISSUEOFlNlSHASABIOCHEMICALINDICATOROFGROWTH

in wild-caught and aquaculturally reared fish.

s $EVELOPTHECAPACITYFORQUANTITATIVEINTEGRATEDECOSYSTEMASSESSMENTSINCLUDINGDEvelopment, culling, and vetting of a wide range of ecological indicators, including the 

ability to quantitatively model major ecosystem processes, tracking the major forcing 

functions of key ecosystem indicators.

s $EVELOPMULTISPECIESMODELSTOPROVIDETHEANALYTICALFRAMEWORKFOREVALUATINGMANagement decision tradeoffs. A wide range of multispecies models—including MSVPA, 

MSYPR, MSProd, MSFore, Network Analysis, and Atlantis—are under development 

and parameterization. The Center will explore their utility in the management context 

to simulate various decisions.

s %NHANCEESTIMATESOFFACTORSTHATINmUENCESTOCKMORTALITYPARTICULARLYASRELATEDTO

species interactions, by incorporating factors into stock assessments beyond fishing 

mortality that have the potential to alter stock abundance, structure, and production. 

The particular emphasis is to examine the role of predation mortality on stocks that are 

important forage for many other species and are also targeted themselves. 

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

s #ONDUCTSTUDIESTODOCUMENTANDUNDERSTANDTHEBEHAVIORANDMOVEMENTOFlSHIN

areas of critical habitat.

s )DENTIFYANDPROVIDE%&(INFORMATIONASREQUIREDBYTHE-3&#-!FOR&-0S

s #ONTINUETOCONDUCTRESEARCHTODETERMINETHEFUNCTIONALVALUEOFESTUARINEANDNEARshore habitats, including restored sites, to the sustainability of fishery resources.

s #ONTINUETOIMPROVE')3CAPABILITIESINORDERTOMAPSEABEDHABITATSANDINDICATE%&(

with respect to various human activities.

s 5SElNE
SCALESEABEDMAPPINGAND')3TOIDENTIFYDISTRIBUTIONOFlNlSHACROSSDIFFERent habitat types.

s $EVELOPAQUICKANDCOST
EFFECTIVEMETHODFORTHEBROAD
SCALECHARACTERIZATIONOFMArine habitats, initially in the Gulf of Maine, using existing hydrographic and geological 

data; define sensitive habitats; and help to predict changes to ecosystems as a result of 

climate change.

s $ETERMINEHABITATUSEOFlNlSHANDLOBSTERUTILIZINGTAGGINGANDTRACKINGTECHNIQUES

(both internal sonic tags and external tags), focusing on defining growth-rates, site 

fidelity, movement, and population estimates.

I.D. Impact of anthropogenic factors and 

environmental changes on fish populations

s $ETERMINEBIOLOGICALENVIRONMENTALANDHABITATPROCESSESCONTROLLINGTHEREPRODUCtive success of important fishery resources.
118

s #ONTINUElELDANDMODELINGRESEARCHACTIVITIESTOBETTERUNDERSTANDTHEINmUENCEOF

environmental variability and climate change on lower trophic level productivity and 

fish recruitment.

s #ONTINUETOMONITOROCEANOGRAPHICANDBIOLOGICALCONDITIONSONTHE.ORTHEAST3HELF

and document ecosystem variability in order to determine its role in the recovery and 

sustainability of depressed fish stocks.

s %STABLISHA.ORTHEAST3HELF%COSYSTEMANALYSISCENTERASARESEARCHGROUPFOCUSEDON

the relationship between resource species and the environment, examining the relationship between climate and recruitment, the impact of climate change on the reproduction and yield of species, and the variation in ecosystem and food web interactions.

s 5NDERSTANDHOWHIGHDENSITIESOFORGANISMSEGCOPEPODS	WHICHAREAPRIMARYFOOD

source for right whale populations frequenting the Gulf of Maine region, are maintained through physical and biological processes. This understanding will lead to improved capabilities to forecast the locations of whales and their prey.

s 0ARTNERWITH.3&TOJOINTLYUNDERTAKELONG
TERMECOLOGICALRESEARCHINTHECOASTALOCEAN

under the Long-Term Ecological Research (LTER) program, focusing on coastal ocean 

and estuarine effects of global warming, eutrophication, or other stressors, thereby supporting improved ecosystem management capabilities. 

s )NVESTIGATEEFFECTSOFHYPOXIAINTHE-IDDLE!TLANTIC"IGHTANDITSESTUARIESTHROUGHCOordinated modeling (coupled physical-NPZ), field, and laboratory studies resulting in 

a modeling capability to support ecosystem management that would address resourcelevel effects and sampling criteria for improved monitoring to support the operational 

modeling, as part of the IOOS.

s $EVELOPANDDEPLOYAN%COSYSTEM0RODUCTIVITY/BSERVING3YSTEM%0/3	TORAPIDLY

map 3-dimensional patterns of ocean productivity across an LME and provide integrated 3-dimensional assessments of the health and productivity of the lower trophic levels 

by synergistically combining several state-of-the-art sampling technologies, including 

in situ platforms and satellites.

s )NVESTIGATESKELETALANOMALIESINlNlSHASPOSSIBLEINDICATORSOFENVIRONMENTALQUALity.

II. Conservation Engineering Research

Recent Accomplishments:

s 4HE lRST SURVIVABILITY STUDY ON ELASMOBRANCHS AND MORE SPECIlCALLY JUVENILE SPINY

dogfish (Squalus acanthias) that included stress measurements and survival assessment 

in the Atlantic trawl fishery. In addition, research investigated short- and long-term 

survivorship following trawl exposure and discard. 

s -ORPHOMETRICMEASUREMENTSOFKEYGROUNDlSHSPECIESCOLLECTEDDURINGSTANDARDlSHing operations on commercial fishing vessels in the Gulf of Maine. Variability of body 

measurements for each length class of fish was calculated and a simple model formulated to estimate the mesh size and configuration through which commercial fish species 

of any size will be most likely to escape. The model enables managers and the fishing 

industry to predict potential retention rates of major commercial fish species for a range 

of mesh sizes and configurations. 
s 4HEEFFECTIVENESSOFTWOCOD
AVOIDINGTRAWLNETDESIGNSTHEh2IBASvANDh4OPLESSv

trawls—has been tested and verified, using larger versions of the designs and including 

nighttime testing.

s !3OUTHERN.EW%NGLAND7ORKING'ROUPTHATFOCUSEDONBYCATCHANDGEARCONSERVAtion engineering was established to share knowledge and skills of fishermen and gear 

researchers for the development of collaborative efforts in conservation gear engineering 

projects.

s -ESHSIZESELECTIVITYSTUDIESABOARDALARGECOMMERCIALlSHINGVESSELWERECONDUCTED

and results integrated into the study of yield-per-recruit (YPR) and spawning-stock 

biomass-per-recruit (SSBPR) models evaluating the effects of incrementally increasing 

mesh sizes. Specifically, 1) mesh selectivity studies were conducted using an alternate 

tow method aboard commercial fishing vessels, 2) selectivity analyses on resulting data 

were conducted and selectivity curves generated for each species by mesh size and shape, 

and 3) YPR and SSBPR analyses were conducted and isopleths generated.

s "LUESHARKBEHAVIORTOWARDAVARIETYOFBAITSBOTHNATURALANDARTIlCIALWERECARRIED

out to learn which bait characteristics are distasteful to the species. During 10 sea trials 

offshore, blue sharks were presented with a series of natural and artificial baits. Shark 

responses were recorded and comparisons made between reactions to artificial baits and 

control baits that are widely used by pelagic longliners for tunas and swordfish.

s $EVELOPEDGEAR
BASEDSOLUTIONSTOSEATURTLEBYCATCHIN6IRGINIAPOUNDNETGEARAND

partial solution to turtle bycatch in scallop trawl gear. Research is continuing on ultimate gear modifications to reduce turtle bycatch in dredge and trawl gear.

s $EVELOPEDANDTESTEDANEW-ARINER3HUTTLE3YSTEM-33	FORMONITORINGPRIMARY

productivity in near-real time. The MSS towed body undulates in the upper 50m of the 

water column and carries a payload of additional sensors for chlorophyll, zooplankton, 

temperature, salinity, oxygen, and light.

Research Priorities, FY 2007–2012:

s #OORDINATEWITHTHE0ACIlC/CEAN3HELF4RACKING0/34	PROGRAMOFTHE#ENSUSOF

Marine Life to deploy an acoustic array on the Northeast Shelf to track fish movements 

and stock mixing, not only along the coast but also in the significant inshore and offshore components.

s $EVELOPANDTESTCALIBRATIONPROCEDURESFORMULTIBEAMSYSTEMSTOENSUREDATAACCURACY

to develop data acquisition and analytic processes as well as new database structures, 

to rapidly provide post-processed data to analysts, and to upgrade current underwater 

remote sensing capability, in order to estimate species composition and target strengths 

of water column organisms, benthic organisms, and habitat types.

s 5NDERTAKEACOLLABORATIVERESEARCHSTUDYTOASSESSTHEDISCARDSURVIVABILITYANDESCAPE

vent efficiency in the deep-water red crab fishery off the New England continental shelf, 

in addition to quantifying bycatch composition of this fishery.

III. Research on the Fisheries

Recent Accomplishments:

s #ONDUCTED BENCHMARK ASSESSMENTS OF  lSH STOCKS THROUGH THE 3TOCK !SSESSMENT
120

 Review Committee (SARC: http://www.

nefsc.noaa.gov/nefsc/saw/) peer-review

process. An additional 19 groundfish stocks 

 were assessed at the Groundfish Assessment 

 Review Meeting in August 2006. 

s#ONTRIBUTED EXTENSIVELY TO THE BENCHmark assessment of American lobster by 

the ASMFC. Center scientists regularly 

provide updates on the status of several 

species, including summer flounder, spiny 

dogfish, and sea scallops, among others.

s)NTERNATIONALLY CONDUCTED ASSESSMENTS OF

Georges Bank yellowtail flounder, Georges 

Bank cod, haddock, and Atlantic herring 

as part of the Transboundary Resource Assessment Committee (TRAC). 

s!SSESSMENTSOFNORTHEAST53MARINE

mammal stocks were completed and reviewed by the Atlantic Scientific Review

Group. Assessments were updated for five large whale, 21 small cetacean, and four pinniped stocks.

s #ENTERSCIENTISTSHAVELEDTHEDEVELOPMENTANDIMPLEMENTATIONOFPROGRAMSFORSTOCK

assessment in the NMFS Toolbox—a software package comprising classical and modern estimation methods, forecasting tools, and advanced simulation testing programs. 

s #ENTERSCIENTISTSDEVELOPEDMETHODSTOCOMPREHENSIVELYEVALUATETHEPRECISIONANDACcuracy of aggregate discard estimates in the groundfish, monkfish, and fluke-scup-sea 

bass fisheries and used optimization methods to improve the allocation of observer days 

to fleets. 

s 3IGNIlCANTADVANCESINTHETHEORYOFROTATIONALlSHERIESMANAGEMENTHAVEBEENDEVELoped and implemented as part of the Atlantic sea scallop FMP. 

s &IELD RESEARCH ON !TLANTIC SALMON FOCUSES ON OBTAINING SMOLT PRODUCTION ESTIMATES

telemetry studies of emigrating hatchery and wild smolts, fishery-independent sampling 

through marine smolt trawling surveys, and monitoring of fishery removals on the high 

seas. Smolt production in various rivers is monitored through the use of in-river traps. 

Annual monitoring of the biological characteristics of Atlantic salmon in West Greenland fishery continued as well.

s #ONTINUEPROTECTEDSPECIESBYCATCHMITIGATIONPROGRAMTHOUGHACOMBINATIONOFAT
SEA

monitoring of fisheries through the Fishery Sampling Branch’s observers, estimation 

of bycatch in observed fisheries, research on the environmental conditions and fishery 

practices associated with this bycatch, development of gear-based solutions to bycatch 

reductions, and assessment of economic alternatives to and impacts of mitigation measures. The NEFSC staff will continue to advise MMPA Take Reduction Teams, Turtle 

Expert Working Groups, and Regional/National Protected Resources managers on bycatch mitigation.

s $EVELOPEDMARINEMAMMALPASSIVEACOUSTICSRESEARCHPROGRAMINTHE.ORTHEAST"Egan multiyear program using passive acoustics to monitor presence of large whales in 

Scallops on the sea floor of 

Georges Bank at a depth of 

94 meters. Photo: NMFS and 

USGS.
Northwest Atlantic waters; hired full-time permanent acoustician; co-hosted (with the 

NMFS Office of Science and Technology) first NMFS national passive acoustics workshop; and developed multiyear funding initiative with the NOS, NMFS Office of Science and Technology, and PIFSC to implement a national passive acoustics monitoring 

program.

s !REPORTWASCOMPLETEDWITH.%2/AND.EW%NGLAND&ISHERY-ANAGEMENT#OUNCIL

staff) on characterizing fishing gears used in northeast U.S. marine waters, and potential effects on EFH.

s #OOPERATIVERESEARCHEFFORTSBETWEENTHElSHINGINDUSTRYAND#ENTERSCIENTISTSINCLUDE

extensive tagging programs for yellowtail flounder, black sea bass, and scup. 

s !3TUDY&LEETPROGRAMHASBEENDEVELOPEDFORCOMMERCIALVESSELSIN3OUTHERN.EW

England and the Gulf of Maine to provide high-resolution (temporal and spatial) selfreported data on catch, effort, and environmental conditions. An advanced electronic 

logbook system (ELB) has been developed to acquire the information. In the past 2 

years the logbook has been deployed on 33 fishing vessels and has been used to record 

over 1,100 fishing trips.

s #ENTERANTHROPOLOGISTSHAVEESTABLISHED.ATIONAL3TANDARDPROTOCOLSFORSHORTAND

extended community profiles, published a “Practitioners’ Manual” for work under National Standard 8, organized a “Social Impacts Assessment” workshop, and published a 

series of articles on the nature of community dependence on fishing, on defining Magnuson Fishing Communities, on the use of diversification indices for communities, and 

on the use of GIS to visualize land/sea connections.

s #ENTERECONOMISTSANDANTHROPOLOGISTSHAVEUNDERTAKENEFFORTSTOFACILITATE#OUNCIL

consideration of market-based institutions to facilitate efficient fisheries management. 

These include establishing of days-at-sea (DAS) categories of effort units, modeling 

DAS trading and pricing with the University of Rhode Island and developing draft 

guidelines for the establishment and operation of sectors.

s $EVELOPEDANDUSEDEXTENSIVE)NPUT/UTPUTMODELSOFlSHERYREGULATORYIMPACTSON

the marine economy with county level impacts for New England, Mid-Atlantic, and 

New England linkages, recreational fisheries components, forward linked impacts to 

processing and wholesaling, and published “On the Use of I/O in Marine Fisheries.”

s #ENTERECONOMISTSAREENGAGEDINANATIONALEFFORTTOMEASUREEXCESSANDOVERCAPACITY

in U.S. fisheries using Data Envelopment Analysis (DEA) and other models developed 

at the NEFSC. In addition, designed and assessed a series of buy-back programs over 

the past 5 years.

s #ENTER ECONOMISTS HAVE WORKED JOINTLY WITH #ANADAS $EPARTMENT OF &ISHERIES AND

Oceans (DFO) to estimate models of U.S.-Canada haddock trade in response to varying joint harvest strategies for eastern Georges Bank haddock.

s 5NDERECOSYSTEMAPPROACHESTOMANAGEMENTDEVELOPEDASURVEYPROGRAMTOMEASURE

the public’s valuation of marine protected area (MPA) ecological reserves in the Northeast Region. In addition, published manuscripts on fishery zoning, national asset valuation of living marine resources, the utility of portfolios in the appropriate exploitation 

of the marine ecosystem, and the value of rents in several fisheries.

s #ONDUCTEDANNUALBROADSCALEMULTISPECIESBOTTOMTRAWLSURVEYSCOVERINGNMI2

along the continental shelf of the northwest Atlantic Ocean. Data produced included 
122

biomass and abundance indices, size distributions, age distributions, maturation data, 

and diet information. The survey data provide an essential fishery-independent component to the population assessment for 45 stocks of finfish and invertebrates.

s #ONDUCTEDANNUALSEASCALLOPDREDGESURVEYSALONGTHECONTINENTALSHELFOFTHENORTHwest Atlantic Ocean covering approximately 17,000 n.mi.2

 and 500 stations. The survey data provided an essential fishery-independent component to the population assessment of the Atlantic sea scallop (Pacopecten magellanicus). In 2005, sea scallops 

were the most valuable commercial landings in the northeastern United States, finally 

eclipsing American lobsters, which has been the region’s perennial front runner. Since 

2000, New Bedford, Massachusetts, has been the top-grossing U.S. fishing port, mostly 

because of sea scallop landings. The fishery is also the largest harvest of wild scallops in 

the world.

s #ONDUCTEDATRIENNIALDREDGESURVEYTOASSESSTHESTATUSOFSURFCLAMSSpisula solidisima,

and ocean quahogs, Arctica islandica, covering approximately 31, 900 n.mi.2

 along the 

continental shelf of the northwest Atlantic Ocean. The survey data provided an essential fisheries-independent component to the population assessment of these two species, 

which, along with sea scallops, represent the three primary offshore bivalves targeted by 

industry in the northeast U.S. coast. 

s #ONDUCTED BIANNUAL lSHERY
INDEPENDENT SURVEY OF !TLANTIC LARGE AND SMALL COASTAL

sharks to monitor the species composition, distribution, and abundance of sharks and 

to collect biological samples for life history studies.

s )NCOOPERATIONWITHSTATEAGENCIESCONDUCTEDANNUALSURVEYSOFSHARKNURSERYAREASIN

major coastal Atlantic states to identify shark species utilizing coastal zones as pupping 

and nursery grounds, gauge the relative importance of these areas, and determine migration and distribution patterns of neonate and juvenile sharks.

s #ONDUCTEDANNUALSHARKLONGLINESURVEYTOASSESSANDMONITORTHEJUVENILESANDBAR

shark population during the nursery season in Delaware Bay to provide the only youngof-the-year and juvenile sandbar shark relative indices of abundance.

s #ONDUCTEDANNUALSURVEYSOFNORTHERNSHRIMPINTHE'ULFOF-AINETOPRODUCEBIOMASS

and abundance indices, as well as size, age, and sex distributions. This information is the 

primary input for the population assessment of Gulf of Maine stock of northern shrimp. 

s #ONDUCTEDANNUALFALL.%&3#(ERRING(YDROACOUSTIC3URVEYSANDDERIVEDESTIMATES

of spawning population biomass for Atlantic herring in the Georges Bank and Gulf of 

Maine regions, which are used in the U.S./Canadian TRAC Assessment for Atlantic 

herring.

s $EVELOPEDANONLINE)NTRANETSYSTEMOFDIGITALVIDEOANDPHOTOSAUDIOANDTEXTINformation providing age structure, maturation, and diet dissection techniques for 40 

species of finfish and invertebrates. This information, now available on board NOAA 

research vessels on stations during data collection, is designed to improve performance 

and consistency during at-sea sampling.

s )MPROVED ROUTINE ACOUSTIC SURVEY OPERATIONS USING THE %+ AND %+ 3CIENTIlC

Echosounders through a variety of field and laboratory experiments in collaboration 

WITHOTHER.-&3#ENTERSANDEXTRAMURALCOLLABORATORSINCLUDINGAN%+CALIBRATION

workshop sponsored by the NMFS Advanced Sampling Technology Working Group.

s $EVELOPEDACOUSTICCAPABILITIESWITHTHEMULTIBEAMSONARMODELS%-ON26
Gloria Michelle, EM70 on FSV Bigelow, and SM2000 scheduled to be installed aboard 

FSV Delaware II) through various training workshops and hands-on field trials. These 

multibeam systems will provide water-column and seafloor backscatter measurements 

that will potentially improve NEFSC stock assessment, conservation engineering, and 

EFH research.

s $EVELOPEDOPTICALTECHNOLOGYCAPABILITIESANDINFRASTRUCTURETHATAREROUTINELYIMPLEmented aboard NEFSC cruises involved with trawl and dredge performance tests, seabed classification, and acoustic target recognition.

s ! RECENTLY CONSTRUCTED PORTABLE lBER
OPTIC !DVANCED &ISHERIES 4ECHNOLOGY 6EHICLE

(AFTV) provides the NEFSC with a universal towfish platform (with 2000 m depth 

capability) for deploying advanced technologies (integrated acoustic-optic-environmental sensors) to support various strategic missions (SAIP, EFH, IOCM).

s 4HE.%&3#CREATEDTHE.ORTHEAST&ISHERIES/BSERVER0ROGRAM4RAINING#ENTER3INCE

May 2005, eight 3-week training classes as well as numerous refresher classes for specific sampling issues have been held. The Training Center represents a commitment to 

professionally training and preparing observers in order to collect high-quality fisheriesdependent data.

s 4OLERANCESOFYOUNGBAYSCALLOPSTOUN
IONIZEDAMMONIAANDOTHERNITROGENCOMPOUNDS

have been quantified in bioassay procedures. The study found that the pH plays an important role in determining toxicity and is important in properly maintaining optimal 

conditions in re-circulating aquaculture systems.

s !SERIESOFEXPERIMENTSHAVEALLOWEDAGENERALASSESSMENTOFTHEAQUACULTUREPOTENTIAL

of black sea bass. Some experiments were conducted at a local aquaculture-themed high 

school with the help of students, as part of the Center’s outreach and education activities.

s 'ENERATEDNEWKNOWLEDGEONSEVERALTOPICSRELEVANTTOIMPROVINGTHEEFFECTIVENESSOF

hatchery production of bivalve mollusc seed for aquaculture, including: determination 

of sterol nutritional requirements in bivalves, development of probiotic bacteria for 

hatchery use, clarification of light and nutrient interactions in microalgal feed cultures, 

development of selected genetic lines of bay scallops, and risk analysis of transferring 

non-native harmful algal blooms during transplant of bivalve seed.

s "ASEDONNATIONALTEMPLATEESTABLISHEDREGION
SPECIlCPROTOCOLFORDESCRIBINGCOMMUnities involved in fishing and completed 130 profiles of key coastal communities in the 

Northeast Region using that protocol.

s ,EDTHEWORKINGGROUPFORDEVELOPMENTOFANATIONALPROTOCOLUSINGQUANTITATIVEINdicators (primarily from existing secondary data sources) for identifying fishing communities relative to MSFCMA National Standard 8 requirements.

s )NVESTIGATEDTHROUGHINTERVIEWSANDCASESTUDIESTHEGROWINGINTERESTINANDPOLICYENvironment for development of community and sector-based collaborative management 

initiatives; co-authored two related peer-reviewed journal articles.

s 4HROUGHCASESTUDIESFOCUSGROUPSANDINTERVIEWSELUCIDATEDTHEDIFFERENTIALVULNERabilities of varied populations in the region’s fisheries and co-authored final report.

s )NVESTIGATEDMETHODSFORDElNINGlSHINGCOMMUNITIESTHATBOTHADDRESS-3&#-!

requirements and are grounded in sociocultural theory. Recommended key topics for 

investigation in order to identify fishing communities (including indicators from sec-
124

ondary sources and ethnographic data to provide context) and published results as a 

peer-reviewed journal article.

s 0ARTICIPATED IN THE DEVELOPMENT OF A NATIONAL SOCIAL
IMPACT ASSESSMENT CONCEPTUAL

model and co-authored resulting peer-reviewed journal article.

s %DITEDANDWROTESELECTEDARTICLESFORATHEMEISSUEOFAMAJORPEER
REVIEWEDAPPLIEDANthropology journal on the topic of research and resource management in North American fisheries.

Research Priorities, FY 2007–2012:

III.A. Social and economic research

s $EVELOPMETHODSTOALLOWDECISIONMAKERSTOEVALUATETHEBENElTSANDCOSTSOFALTERnative ecosystem outcomes, to compare ecosystem-wide mixes of uses employing, for 

example, spatially defined methods and zone-defined portfolios. Develop methods to 

determine ecosystem services and stock valuations focusing on national asset accounting methods.

s #OLLECTSOCIOECONOMICINFORMATIONTHROUGHSURVEYSWITHPREPARATIONASSISTANCEFROM

a Stakeholder Steering Committee. The survey will be followed by a series of meetings 

throughout Maine, New Hampshire, and Massachusetts to report and interpret resulting data with stakeholders.

s 4RAINlSHERMENINSAFETYDAMAGECONTROLRESCUEPROCEDURESANDlRSTAIDTOIMPROVE

their knowledge and skills; increase interaction between the Coast Guard and fishermen to improve communication and collaboration; work closely with the New Bedford 

Safety Task Force and the Coast Guard to develop a long-term program that will provide ongoing opportunities for and participation in safety training for fishermen; and 

explore potential for lowering the costs of safety equipment and/or insurance in part 

through active participation in safety training. 

s !COMPREHENSIVESTRATEGYFOREXPERIMENTALRESOURCEENHANCEMENTTRIALSWILLBEIMPLEmented considering both risks and benefits, using mathematical population models. 

This will result in testable hypothesis-based experimental design to determine success 

and return on investment.

s 0ERFORMMULTIVARIATESTATISTICALANALYSESOFOBSERVERAND3TUDY&LEETDATATOIDENTIFY

species assemblages and appropriate strata for estimation of landings and discards to lay 

the groundwork for subsequent ecosystem modeling for Ecosystem-based Approaches 

to Fisheries (EAF) and Ecosystem-based Approaches to Management (EAM), resulting 

in refinements and new methods for estimation of fishing effort and fishing mortality.

s $ElNESTRATEGIESFORSTOCKRESTORATIONORENHANCEMENTOFTHEBAYSCALLOPArgopecten 

irradians, by cooperating with many local activities in New England.

s $EVELOPREGIONALECOSYSTEMMANAGEMENTPROCEDURESSETTINGUPA-ANAGEMENT3TRATegy Evaluation framework to simulate and explore properties of various management 

decisions before they are enacted. This effort will particularly elucidate a holistic and 

integrated view of all living marine resources, be they targeted, protected, or otherwise. 

s #ONTINUETOPRODUCEANDUPDATEBASELINECOMMUNITYPROlLESPERTHE
TO
YEARUPdating cycle implemented nationally.
s "ROADEN SOCIAL AND CULTURAL INVESTIGATION

beyond fishermen, to include more women 

and those involved in fishing-related industries (such as processing workers). 

s #ONTINUE TO EXPLORE USE OF ')3 TO ASSIST

in describing and analyzing the social and 

cultural dimensions of fisheries and fishing communities.

s #ONTINUETOmESHOUTTHESOCIALANDGOVernance aspects of Northeast fisheries, to 

facilitate expanded use of ecosystem management.

s #ONDUCT STATISTICAL ANALYSIS OF lXED
COST

and trip-cost data to develop cost and/or 

profit functions to be used in regulatory 

analysis of management actions.

s 0ERFORM STATISTICAL ANALYSIS OF CHANGES IN

marine industries in regional economies 

over time, and investigate the relationships 

between these changes and resource conditions.

III.B. Seafood safety research 

This item is not applicable.

III.C. Marine aquaculture

s $EVELOPHATCHERYTECHNOLOGIESTOPROVIDELARGEQUANTITIESOFSHELLlSHORlNlSHhSEEDv

animals for stocking grow-out systems in an environmentally conscientious manner. 

s 1UANTIFYTRANSFEROFBIOLOGICALLYIMPORTANTELEMENTSFROMAQUACULTUREOPERATIONSTO

the marine food web.

s $EVELOPAQUACULTUREMETHODSFORTHEBLACKSEABASSANDBAYSCALLOPSINRECIRCULATING

aquaculture systems by experimentally establishing optimal nutritional, physical, and 

chemical rearing conditions.

s $ETERMINEPHYSIOLOGICALRESPONSESOFMARINEINVERTEBRATESTODIFFERENTREARINGCONDItions in aquaculture systems, by measuring animal and molecular health and growth 

performance. 

s -AKEPROGRESSINTHEDOMESTICATIONOFFARMEDBIVALVESPECIESBYSELECTIVELYBREEDINGFOR

desired traits and identifying the genetic and proteomic bases for successful phenotypes 

for aquaculture production in different environments. 

s #OMPLETEDEVELOPMENTOFANDlELDTESTASUITEOFENVIRONMENTALMEASUREMENTSTOQUANtify interactions between shellfish farming practices and the ecosystems in which they 

are contained. 

An adult black sea bass. 

Photo: Karen Roeder, NOAA.
126

IV. Information Management Research

Recent Accomplishments:

s 0ROVIDEDTECHNICALSUPPORTFORDATABASESUSED BY#ENTERSCIENTISTS INCLUDING AT
SEA

Fisheries Scientific Computing System (FSCS), Biological Sample Monitoring Data 

Base System (BSMDBS), Commercial Fisheries Data Base System (CFDBS), Food 

Habits Data Base System (FHDBS), Observer/Sea Sampling Data Base System (OBDBS), Northeast Survey Database System (SVDBS), and Mark/Recapture Database 

System (MRDBS).

s #ONTINUEDIMPLEMENTATIONOFTHEALLOCATIONSCHEMEFORnCOMMERCIALlSHERies, which uses vessel logbook data to allocate effort to trip-level catch data.

s 3UPPORTEDTHE.%2/INTHEIREFFORTSTOIMPLEMENTMANDATORYCOMMERCIALlSHERIES

processor (dealer) and vessel electronic reporting by providing programming and database management services. 

s #ONTINUEDTODESIGNDEVELOPANDIMPLEMENTNEWSYSTEMSTOSUPPORTELECTRONICCAPture of data at sea using Personal Digital Assistants (PDA) technology and rugged PC 

tablets. These systems are used by observers and scientists aboard commercial and research vessels to collect scientific data electronically.

s )MPLEMENTEDTHE)NDUSTRY
"ASED3URVEYWEBSITEWHICHISACCESSIBLEFROMTHE.%&3#

and NERO public websites. Atlantic cod, yellowtail flounder, and monkfish surveys are 

currently available.

s )MPLEMENTEDANINTERACTIVEWEBPAGETHATPROVIDESPUBLICACCESSTOALLOFITSHYDROgraphic data sets. This activity is in support of the Regional Associations of the IOOS 

for the Middle Atlantic Bight and Gulf of Maine regions.

s /PENED#ENTERWIDEE
LIBRARYPROVIDINGVIRTUALLYALL.%&3#STAFFWITHDESKTOPACCESS

to core journals, citation databases, reference works, and search instruments.

s -ANAGEDINTERNALTECHNICALANDPEERREVIEWSANDTRACKEDPUBLISHINGHISTORYFORAPproximately 600 staff-authored publications including manuscripts, websites, posters, 

abstracts, and presentations, and distributed a list of publications annually.

s $EVELOPEDANDPRODUCED.%&3#gSONLINEPUBLICMAGAZINEThe Ffiles, profiling Center 

research, researchers, and community involvement.

Research Priorities, FY 2007–2012:

s )NCOOPERATIONWITHREGIONALPARTNERSCONTINUEACTIVITIESTOPROMOTETHEREGIONAL)//3

and to develop web-based tools for easy access to IOOS data in support of management 

needs.
PACIFIC ISLANDS

FISHERIES SCIENCE CENTER

The Pacific Islands Fisheries Science Center (PIFSC) conducts multidisciplinary basic 

and applied research on insular and pelagic living marine resources and fisheries of the 

Pacific Islands and central and western Pacific. The PIFSC is located in Honolulu, Hawaii, 

adjacent to the University of Hawaii at Manoa campus. The PIFSC maintains a Honolulu 

SHORESIDERESEARCHFACILITYAT+EWALO"ASINANDASATELLITEOFlCEINWEST/AHUWHEREITS

primary wet laboratory facilities are located. These facilities house over 170 people, including Federal employees as well as collaborating staff of the NOAA-University of Hawaii 

Joint Institute of Marine and Atmospheric Research, University of Hawaii students, and 

visiting scientists. The primary platform supporting PIFSC field activities in fisheries is 

the NOAA FSV Oscar Elton Sette and the NOAA ship Hi‘ialakai, with additional support 

from chartered, contracted, and cooperating commercial fishing vessels. 

Fisheries research activities at the PIFSC support the scientific information and advice 

needs of NOAA Fisheries Pacific Islands Regional Office; the Western Pacific Fishery Management Council; the Papahānaumokuākea Marine National Monument; other federally 

managed marine resources; and the marine resource management agencies of the State of 

Hawaii, the Territories of American Samoa and Guam, and the Commonwealth of the 

Northern Mariana Islands. They also contribute to U.S. scientific support of international 

organizations concerned with the management and conservation of tunas, billfishes, and 

other highly migratory pelagic species in the central and western Pacific. Such organizations include the Western and Central Pacific Fisheries Commission and its scientific and 

technical committees and the International Scientific Committee for Tuna and Tuna-like 

Species in the North Pacific Ocean. Highly migratory species research at the PIFSC is 

often collaborative and coordinated with the Southwest Fisheries Science Center. Other 

Mokumanamana, the second 

island in the Northwest 

Hawaiian Island chain, 

approximately 460 miles 

from Honolulu. Photo: NOAA.
128

collaborative and cooperative research partners include Federal and State of Hawaii agencies; 

academic institutions; foreign research institutions; the government agencies of American 

Samoa, Guam, and the Commonwealth of the Northern Mariana Islands; and the public 

sector, including the commercial fishing industry, seafood markets, and recreational and 

environmental interests. 

The PIFSC conducts biological, ecological, and socioeconomic research on the following living marine resources that fall under existing FMPs for this region:

s ,ARGEPELAGIClSHESOFTHE0ACIlC/CEANINCLUDINGTUNASBILLlSHESSHARKSANDA

number of other incidentally caught but commercially important species).

s #RUSTACEANSOFTHEINSULARHABITATSLOBSTERSANDSHRIMP	

s "OTTOMlSHSNAPPERSGROUPERSANDJACKS	ANDSEAMOUNTGROUNDlSHOFTHEDEEPSLOPE

and seamount areas.

s 0RECIOUSCORALS

s #ORALREEFECOSYSTEMS

In addition, from a marine ecosystem perspective, many PIFSC research programs rely 

on information about the physical environment in the central and western Pacific Ocean. 

The Center uses satellite remotely sensed ocean and atmospheric data, including the 

CoastWatch/Ocean Watch station with the National Environmental Satellite, Data, and 

Information Service; ocean circulation models; a comprehensive physical and biological 

Coral Reef Ecosystem Integrated Observing System; information from research cruises; 

and fisheries data to advance our understanding of the dynamic physical and biological 

ecosystems found in the Pacific region. The PIFSC also makes extensive use of biological and 

fisheries data collected by observers placed on fishing vessels by the Pacific Islands Regional 

Office’s Observer Program. These observers monitor fishery interactions with protected 

species to achieve goals related to the MSFCMA, Endangered Species Act, Marine Mammal 

Protection Act, and Migratory Bird Treaty Act.

Organizationally, marine ecosystem and fisheries research at the PIFSC primarily is 

carried out by four of the Center’s research divisions: the Coral Reef Ecosystem Division 

(CRED), the Ecosystems and Oceanography Division (EOD), the Fish Biology and Stock 

Assessment Division (FBSAD), and the Fisheries Monitoring and Socioeconomics Division 

(FMSD):

s #2%$CONDUCTSMULTIDISCIPLINARYECOSYSTEM
BASEDRESEARCHMONITORINGANDHABITAT

mapping that provides the scientific basis for effective management and conservation 

of coral reef ecosystems in the U.S.-affiliated islands of the central and western Pacific 

Ocean. Specific research activities include: 1) ecological assessment and monitoring to 

quantify and document spatial and temporal changes in the health of coral reef living 

resources resulting from either natural or human-induced impacts; 2) detailed taxonomic 

surveys of reef-associated organisms to assess conservation of biodiversity in using ecosystem approaches to management; 3) habitat mapping and characterization to define 

and understand the dynamics of habitat-ecosystem-resource linkages; 4) monitoring 

of oceanographic processes affecting reefs to identify conditions that influence coral 

reef ecosystem health; and 5) reef restoration through the assessment, monitoring, and 

mitigation of the effects of marine debris on coral reef ecosystems. Complementary applied research includes evaluating the effectiveness of marine protected areas, developing 
non-extractive fishery-independent methods to assess and study bottomfish and their 

habitat associations, and development of active and passive acoustic technologies to 

improve capabilities to remotely monitor indicators of ecosystem health.

s %/$CONDUCTSRESEARCHTOADVANCEOURUNDERSTANDINGOFTHESTRUCTUREANDDYNAMICSOF

marine ecosystems in the Pacific Islands region and the broader North Pacific. Research 

focuses on: 1) the role of living resources in the ecosystem and 2) how these resources 

might respond to change, both on the local scale (e.g., predators or prey availability) 

and on broader temporal and spatial scales (e.g., ocean climate change). EOD’s multidisciplinary projects address ecosystem, environmental, and anthropogenic effects on a 

range of species, including the Hawaiian monk seal, several species of sea turtles, highly 

migratory target species such as tunas and billfishes, and incidentally harvested species 

such as marlins.

s &"3!$CONDUCTSSTATE
OF
THE
ARTRESEARCHONTHEPOPULATIONBIOLOGYSTOCKASSESSMENT

ecology, and life history of exploited marine resources and associated species (e.g., prey, 

bycatch, and protected species) in the central and western Pacific. FBSAD integrates 

biological, ecological, oceanographic, and economic data to advance stock assessments 

and to advise resource management at both the species and ecosystem levels while addressing mandates for conservation and management objectives. Activities undertaken by 

FBSAD research programs include population modeling, resource survey cruises, fishing 

experiments, determination of vital rates and other life-history parameters, characterization of environmental physiology, research on distributional ecology, and development 

of methods to mitigate fishery interactions with protected species.

s 4HE&-3$ISTHEFOCALPOINTFORMUCHOFTHElSHERYDATACOLLECTIONANDALLOFTHESOCIOeconomic research for the PIFSC. This Division collects, quality-controls, and processes 

fishery-dependent information (i.e., logbooks); issues quarterly and annual reports on 

federally managed fisheries (including the pelagic longline, bottomfish, and crustacean 

fisheries); and conducts socioeconomic research on federally managed fisheries. Also 

residing in FMSD is the Western Pacific Fisheries Information Network (WPacFIN), 

which collects and processes data from Pacific island agencies (i.e., Territories of Guam 

and American Samoa, Commonwealth of the Northern Mariana Islands, and State of 

Hawaii). FMSD also provides technical support to develop and implement data collecting, processing, summarizing, analyzing, and report-generating systems for these island 

agencies.

RECENT ACCOMPLISHMENTS AND

RESEARCH PRIORITIES FOR FY 2007–2012

I. Research to Support Fishery Conservation and Management

Recent Accomplishments: 

s Stock Assessment and Fish Biology.

– Stock assessment research includes conducting baseline assessments of key species 

and regular updates for fishery management and conservation purposes. Baseline 

assessments include a metapopulation stock assessment model completed for lobsters 

in the Papahānaumokuākea Marine National Monument, which will become a complete population assessment in 2007. Pursuant to Proclamation 8031 establishing 

the Monument and its codifying regulations, lobsters in the Monument are subject 

to a zero harvest guideline. The assessment of Hawaiian archipelago bottomfish was 
130

updated using a new standardized time-series of catch per unit effort in 2006. An 

independent assessment of bottomfish was also contracted, confirming the previous 

baseline approach and results, and providing an alternative model for future analyses. 

An updated stock assessment of Pacific swordfish was conducted that indicates the 

resource can well sustain exploitation at the highest levels of fishing effort that have 

been exerted to date without becoming overfished. In addition, an updated stock assessment on blue sharks was conducted which indicated that, since the 1990s drift net 

ban, biomass has increased well above minimum levels needed to sustain maximum 

yield. In collaboration with the Oceanic Fisheries Program of the Secretariat of the 

Pacific Community, stock assessments of yellowfin and bigeye tuna were also updated, 

which indicated that overfishing is now occurring on both stocks. Working group 

meetings of the International Scientific Committee on Tuna and Tuna-Like Species 

in the North Pacific were held to foster cooperative international stock assessments 

of blue shark, striped marlin, and swordfish. 

– In addition, several analyses of fish biology were completed or are under way. PIFSC 

scientist Bruce Mundy published a 704-page book entitled, Checklist of the Fishes of 

the Hawaiian Archipelago, which describes the known diversity, biogeographic origins, 

behaviorally defined habitats, and conservation status of the 1,250 fish species known 

from the area. An age and growth study based on growth rings on hard parts was 

completed on swordfish, and similar studies are under way on targeted bottomfish 

species as well as on bycatch species in the longline fishery (snake mackerel and lancet 

fish). 

– Using ocean models to describe larval transport, the PIFSC also developed a metapopulation dynamics model of larval movement within the Hawaiian Archipelago. 

This work included specimen collections and laboratory analyses of trace elements 

in otoliths, which are used to characterize the pelagic environments experienced by 

individual larvae during the planktonic dispersal stage. Completion of this work 

will ultimately provide a series of case studies elucidating connectivity and dispersal 

among main Hawaiian Island and Papahānaumokuākea Marine National Monument 

metapopulations of representative species of shallow-water reef fishes.

– A multi-year cooperative tag and release study of lobster growth and mortality is being 

conducted with chartered commercial fishing operations in the Papahānaumokuākea 

Marine National Monument. Annual lobster survey cruises are also conducted in 

the Monument. In addition, PIFSC scientists published a new morphometric method 

for estimating body size at sexual maturity in slipper and spiny lobster populations. 

These studies also provide insight to the health of the Monument ecosystem, and 

the annual lobster survey provides a long-term time-series of both lobster abundance 

and the abundance of other shallow-water demersal species.

s International Cooperation on Resource Management.

– The PIFSC hosted or attended meetings and conferences that brought together Pacific-wide delegations to coordinate marine resource conservation and management. 

The PIFSC led the U.S. delegation to the annual meeting of the North Pacific Marine 

Science Organization (also known as PICES) in Yokohama, Japan; NOAA scientists 

from four science centers and several other NOAA research offices participate in the 

PICES working groups. PICES serves as a vehicle for enhancing ecosystem research 

coordination in the North Pacific, with an increasing emphasis on living marine 

resource conservation and management. The PIFSC also represented the United 
States on the Scientific Committee of the Western and Central Pacific Fisheries 

Commission (WCPFC), and PIFSC scientists conducted stock assessment and related 

research in conjunction with the WCPFC’s Scientific Committee and also with the 

advisory working groups of the ISC. The Center also sponsored the 3rd Northwestern 

Hawaiian Islands Science Symposium, presenting the results of over 20 years of living 

marine and terrestrial research throughout the Northwestern Hawaiian Islands. A 

wide variety of agencies and universities participated in the symposium, which also 

drew large public participation.

s Habitat Characterization and Remediation.

– Several habitat mapping projects were completed. PIFSC scientists surveyed 3000 km2

of seafloor during multibeam mapping operations on the NOAA ship Hi‘ialakai and 

the 25-ft PIFSC survey launch AHI. Major surveys were conducted at French Frigate 

3HOALS-ARO2EEF0EARLAND(ERMES!TOLLAND+URE!TOLLINTHE0APAHānaumokuākea 

Marine National Monument, and at Niihau and Penguin Bank in the main Hawaiian Islands. Using these data, accurate delineation of 25-, 50-, and 100-fm isobaths, 

an important management need for the Monument, was completed. The PIFSC 

collaborated with the University of Hawaii’s Hawaii Mapping Research Group, the 

Hawaii Undersea Research Laboratory, and other key NOAA partners to produce the 

Bathymetric Atlas of the Northwestern Hawaiian Islands. 

– In addition, high-resolution bathymetric data for coral reef habitats in the Commonwealth of the Northern Mariana Islands, Guam, and the Territory of American Samoa 

were published. Surveys were conducted by the 25-foot survey launch AHI, equipped 

with a Reson 8101ER multibeam echosounder. PIFSC scientists also used multibeam 

and video validation data to characterize benthic habitat for anchorage at Saipan, in 

the Commonwealth of the Northern Mariana Islands, for the U.S. Navy. 

– The first Pacific Reef Assessment and Monitoring Program cruises were conducted in 

the main Hawaiian Islands aboard the NOAA ships Oscar Elton Sette and Hi‘ialakai.

The Pacific RAMP cruises are multidisciplinary research cruises to conduct assessments 

and monitoring of fish, corals, other invertebrates, and algae in the context of their 

benthic and oceanographic habitats in coral reef ecosystems. The second Marianas 

Archipelago Reef Assessment and Monitoring Program (MARAMP) cruise—to the 

Commonwealth of the Northern Mariana Islands, Guam, and Wake Atoll—was 

conducted in partnership with University of Guam Marine Lab; the Commonwealth 

of the Northern Mariana Islands’ Divisions of Fish and Wildlife, Environmental 

Quality, and Coastal Resources Management; U.S. Army; and Guam Division of 

Aquatic and Wildlife Resources. 

– The PIFSC also participated in a multiagency expedition led by the Scripps Institution 

OF/CEANOGRAPHYTOTHENORTHERN,INE)SLANDS530ALMYRAAND+INGMAN!TOLLS

+IRIBATI#HRISTMASAND&ANNING!TOLLS7ASHINGTON)SLAND	INAMULTIDISCIPLINARY

assessment of the effects of human exploitation on fishery resources and related aspects 

of their coral reef ecosystems.

– The PIFSC also completed Pacific RAMP surveys of coral reef ecosystems around 

all islands of American Samoa (ASRAMP) in 2002, 2004, and 2006 and the U.S. 

Line and Phoenix Islands in 2000, 2001, 2002, 2004, and 2006. Surveys included 

quantitative spatial and temporal monitoring of biological populations of fish, coral, 

algae, macroinvertebrates, and important oceanographic processes of ecosystem function. Using monitoring surveys, PIFSC scientists documented that the ecosystem
132

impact of a foreign longline fishing vessel grounding (1993) to the reef at Rose 

Atoll has now persisted for over a decade, 

as characterized by a significantly greater 

abundance of algae/cyanobacteria and 

greater density of herbivorous fishes at the 

site of impact.

– In 2005, the Center’s Marine Debris Team 

completed a 5-year large-scale marine 

debris removal effort from the coral reefs 

and beaches of the Northwestern Hawaiian Islands (now the Papahānaumokuākea 

Marine National Monument) after removing about 550 metric tons of primarily 

derelict fishing gear. With the conclusion 

of the large-scale debris removal effort, the 

Marine Debris Team initiated a “maintenance mode” removal by collecting 19 tons of debris in 2006 and completed a detailed

debris accumulation study that documents average annual accumulation in the Monument of greater than 52 metric tons. 

– PIFSC scientists made several key findings regarding the role of algae in the Pacific 

Islands marine environment. The PIFSC reported in Status of Coral Reefs of the World: 

2004 that macro algae, not corals, dominate many healthy subtropical reef systems 

in the Northwestern Hawaiian Islands. Center scientists also published discovery of 

two algal species new to science from the Northwestern Hawaiian Islands in 2004: 

Acrosymphtyon brainardii and Scinaia huismannii. To foster algal research in the Pacific Islands, PIFSC scientists entered into collaborative partnerships with molecular 

researchers from the University of Ghent, Belgium, and the University of Louisiana, 

Lafayette, to understand molecular population structure of select algal species in 

the tropical Pacific, and also published a rapid ecological assessment algal sampling 

protocol designed specifically for remote tropical islands.

– In support of NOAA’s emphasis on Habitats of Particular Concern within Essential 

Fish Habitat, PIFSC scientists published a paper in 2004 documenting the importance of sheltered habitats at Northwestern Hawaiian Island atolls as juvenile reef fish 

nursery habitats, and a second paper also in 2004 documenting the disproportionate 

abundance of endemic species in shallow reef fish assemblages of the Northwestern 

Hawaiian Islands.

– Other habitat-related accomplishments included: completion of a cooperative NOAA 

and State of Hawaii survey of black (deep sea) corals; completion of an in-depth 

fisheries oceanography survey of the American Samoa tuna fishing grounds; and 

collaboration with the National Ocean Service to develop an on-line encyclopedia of 

marine plants in the Papahānaumokuākea Marine National Monument.

Abandoned fishing nets such 

as these are prime examples 

of marine debris. Photo: 

USCG.
Research Priorities, FY 2007–2012:

I.A. Biological research concerning the diversity, abundance, 

distribution, and life history of living marine resources

s #ONDUCT PEER
REVIEWED ASSESSMENTS AND STATISTICAL ANALYSES ON STOCKS OF INSULAR AND

pelagic species.

s #ONDUCTRESEARCHTOBETTERUNDERSTANDTHESTOCKDYNAMICSANDINmUENCEOFENVIRONMENTAL

conditions on pelagic stocks (North Pacific and around American Samoa) and insular 

stocks of the Papahānaumokuākea Marine National Monument.

s #ONTINUEDEVELOPMENTOFNON
EXTRACTIVElSHERY
INDEPENDENTMETHODSTOASSESSANDSTUDY

bottomfish and their habitat associations.

s #ONDUCTCOMPREHENSIVEBIODIVERSITYSURVEYSOFUNDERSTUDIEDINVERTEBRATESALGAEAND

microbes throughout the U.S.-affiliated Pacific Islands to improve ability to implement 

ecosystem approaches to fisheries management.

s $EVELOPACOMPREHENSIVEINSULARRESOURCESURVEYUSINGCHARTEREDCOMMERCIALlSHING

and research vessels for the Hawaiian Archipelago. 

s !SSESSTHECONNECTIVITYOFSPATIALLYSTRUCTUREDINSULARPOPULATIONSINTHE(AWAIIAN!Rchipelago.

s $EVELOPANDIMPLEMENTANINTERNATIONALTAGGINGPROGRAMFORHIGHLYMIGRATORYSPECIESIN

the Pacific Ocean to trace their movements between fisheries and countries, and provide 

biological data to advance stock assessments.

s $EVELOPANEWGENERATIONOFSTOCKASSESSMENTMODELSFORSTOCKSOFHIGHLYMIGRATORYAND

coastal pelagic species in the Pacific Ocean and state-of-the-art software to support them, 

using modern statistical optimization techniques, Bayesian methods, and simulation.

s 5SEPOP
UPSATELLITETAGSTOIDENTIFYFORAGEANDMIGRATIONHABITATSOFEXPLOITEDSPECIES

and protected resources in the central and western Pacific.

s #ONTINUEANALYSISOFLONGLINEEXPERIMENTSTOUNDERSTANDHIGHLYMIGRATORYSPECIESHABITAT

requirements and options for bycatch reduction.

s $EVELOPASPATIALANDTEMPORALMODELTOPREDICTTHECATCHOFBIGEYEANDYELLOWlNTUNA

in the Palmyra region.

s !SSISTLOCALRESOURCEMANAGEMENTAGENCIESTODEVELOPSYSTEMSOFMARINEPROTECTEDAREAS

appropriate for each island’s marine ecosystems.

s $EVELOPMETHODSTOASSESSTHEEFlCACYOFVARIOUSMARINEPROTECTEDAREASECOSYSTEMPREserves, and other time-area closures in restoring fish stocks and increasing sustainable yields. 

s %XAMINETHEROLEOFOCEANCIRCULATIONONLARVALTRANSPORTANDRECRUITMENTOFlSHCORALS

algae, and crustaceans with the goal of improved understanding of ecosystem dynamics 

and an ability to evaluate the effectiveness of no-take marine protected areas as refugia 

and replenishment areas.

I.B. Interdependence of fisheries or stocks 

of fish with other ecosystem components

s $EVELOPINTEGRATIVEOCEANICENVIRONMENTALINDICESTOIMPROVEUNDERSTANDINGOFHOW

environmental variability affects fish stocks.
134

s %XTENDANALYSISOFFACTORSAFFECTINGLONGLINE
TURTLEANDLONGLINE
SEABIRDINTERACTIONSTO

include more detailed oceanographic, tagging, and behavioral analysis.

s )NTEGRATECENTRAL0ACIlCPELAGICANDINSULARECOSYSTEMMONITORINGWITHSTOCKASSESSments. 

s $EVELOPECOSYSTEMMODELSTODESCRIBEECOSYSTEMSTRUCTUREANDDYNAMICSFORPELAGICAND

insular ecosystems. 

s #ONDUCTlSHERYDYNAMICSRESEARCHONTHE!MERICAN3AMOALONGLINElSHERY

s #ONTINUEWORKONDEVELOPINGBETTERMETHODSFORESTIMATINGTHEINCIDENTALTAKEOFPROtected species.

s %XPANDTHESURVEYSOFTHEDEEPWATERCORALCOMMUNITYTHROUGHOUTTHE0ACIlCREGION

using archival instruments to characterize environment.

s %XPAND%#/0!4(PARAMETERSBEYONDTHE&RENCH&RIGATE3HOALSREGION

s #ONTINUEWORKASSOCIATEDWITHIDENTIFYINGANDUNDERSTANDINGECOLOGICALLINKSBETWEEN

deep slope and shallow ecosystems with a focus on habitat aspects, particularly for fishery 

and protected species. 

s #ONDUCTSTUDIESONDEEPSLOPEBLACKCORALFORAGINGHABITATOFMONKSEALSANDJUVENILE

snappers in the main Hawaiian Islands.

I.C. Identifying, restoring, and mapping of essential fish habitat 

s #ONTINUESTUDYINGTHEBANKSUMMITHABITATECOLOGYANDSPECIlCALLYSTUDYSEASONALITY

and growth of algal meadows using archival technology.

s #ONTINUETHERESEARCHONDEEPSLOPEHABITATECOLOGYANDSPECIlCALLYEXPLORETHEUSEOF

acoustics technology to assess deep slope species.

s #ONTINUEANDIMPROVEPROGRAMTORAPIDLYCHARACTERIZEANDMAPBENTHICHABITATSOF

coral reef ecosystems around Hawaii, American Samoa, Guam, Commonwealth of the 

Northern Mariana Islands, and the Pacific remote island areas.

s $ETERMINE THE SPATIAL DISTRIBUTIONS COMPOSITION EXTENT AND HEALTH OF THE BENTHIC

substrates.

s $ETERMINEANDDElNETHE%SSENTIAL&ISH(ABITATAND(ABITAT!REASOF0ARTICULAR#ONCERN

for the coral reef areas.

s !SSOCIATEIDENTIlEDHABITATSWITHDISTRIBUTIONSOFTHEBIOLOGICALCOMPONENTSOFTHEECOsystem, including fish, invertebrates, and algae.

s $ETERMINEDEPTHORHABITAT
BASEDBOUNDARIESTOSUPPORTMARINEPROTECTEDAREASANDTHE

Coral Reef Ecosystem Fishery Management Plan.

s 0ROVIDEHIGH
RESOLUTIONIN
SITUDATATOASSIST.ATIONAL/CEAN3ERVICEINGROUND
TRUTHING

remote sensing-based mapping data of shallow water areas.

s %XAMINECHANGESOVERTIMEOFTHEDISTRIBUTIONANDHEALTHOFSELECTEDHABITATSPARTICULARLY

corals, algae, and sand.

s #ONTINUEDEVELOPMENTANDIMPLEMENTATIONOFAMULTI
PLATFORM#ORAL2EEF%COSYSTEM

Integrated Observing System to monitor the key physical and biological parameters 
likely to affect coral reef ecosystem health, including expanded use of passive acoustic 

technologies.

s #ONTINUETHEDEVELOPMENTOFPASSIVEACOUSTICTECHNOLOGIESTODETECTVESSELACTIVITIESIN

marine protected areas.

s %XAMINETHEROLEOFOCEANCIRCULATIONONTRANSPORTDISTRIBUTIONANDACCUMULATIONOF

marine debris and continue development of technologies, including remote sensing and 

use of Unmanned Aerial Vehicles, to significantly improve capabilities for efficiently and 

cost-effectively removing debris at sea.

s $EVELOPGEOGRAPHICINFORMATIONSYSTEMAPPLICATIONSFORIDENTIFYINGTHEINTERRELATIONSHIP

of precious (gold) coral and Hawaiian monk seal habitat. 

s )NVESTIGATE0ALMYRA!TOLLASANECOSYSTEMHOTSPOT

I.D. Impact of anthropogenic factors and 

environmental changes on fish populations

s %VALUATETHEEFFECTSOFCLIMATECHANGEOFINTERANNUALDECADALANDCENTENNIALSCALESON

fisheries and fish habitat.

s %XAMINEASSOCIATIONSBETWEENTHERECRUITMENTOFJUVENILEINSULARSPECIESANDCLIMATIC

and oceanographic variables in the Hawaiian Archipelago.

s )NVESTIGATE THELINKAGEBETWEENTHEDYNAMICS OFOCEANIC FEATURES INCLUDING EDDIES

fronts, and boundary currents) and the dynamics of highly migratory fishes (tunas and 

billfishes) in the central and western Pacific.

s $EVELOPANDUTILIZEACOMBINATIONOFREMOTELYSENSEDOBSERVATIONSOFWINDSTEMPERATURE

sea surface height, and ocean color to define regions of oceanic convergence and the 

likely accumulation of marine debris, and then develop methods to track and interdict 

marine debris at sea before it damages coral reef ecosystems.

s )DENTIFYDERELICTlSHINGGEARANDITSPROBABLESOURCESBASEDONGEARTYPEMATERIALOF

construction, and construction methods used.

s !SSESSTHEAMOUNTOFANDEVALUATETHEIMPACTSOFMARINEDEBRISPRESENTONTHECORALREEFS

of the U.S. Pacific Islands.

s 2EMOVEMARINEDEBRISFROMCORALREEFSANDBEACHESTOPREVENTFURTHERDAMAGETOTHE

coral reef ecosystem and to mitigate entanglement hazards to the animals within the 

ecosystem.

s #ONTINUE TO DEVELOP A CAMPAIGN THAT PROMOTES PUBLIC AWARENESS AND EDUCATION OF

marine debris affecting the U.S. Pacific Islands, focusing on educating the commercial 

fishing and maritime industries regarding the damage to coral reef ecosystems caused 

by marine debris and on efforts to minimize future damage by reducing or eliminating 

the sources.

s )NITIATE BASIC FISHERIES BIOLOGY WORK FOR BOTTOMFISH FISHING AREAS OTHER THAN THE

Papahānaumokuākea Marine National Monument (e.g., main Hawaiian Islands), including otolith studies.
136

II. Conservation Engineering Research

Recent Accomplishments:

PIFSC scientists have made several advances in protected species bycatch reduction. The 

Hawaii-based longline fishery has reduced seabird takes from thousands per year and sea 

turtle takes from hundreds per year during the late 1990s to only a few dozen per year in 

2005. This was accomplished using bycatch reduction measures developed by scientists at 

the PIFSC and the NMFS Southeast Fisheries Science Center working with the fishery 

councils and conservation groups. In addition, 

PIFSC scientists are collaborating in on-going experiments to reduce sea turtle bycatch 

with longline fisheries in Hawaii, Japan, 

+OREATHE0HILIPPINES-EXICO#OSTA2ICA

Guatemala, Ecuador, Peru, Brazil, Uruguay, 

Spain, and Italy, and are developing logistics 

for similar experiments in Indonesia, Papua 

New Guinea, and Vietnam. 

Scientists also are working to identify protected species hot spots to support efforts to minimize protected species-fisheries interactions. Bottom-mounted high-frequency acoustic recording packages were placed in strategic 

locations to provide acoustic information where marine mammal/fishery interactions (false 

killer whales and longline fishing vessels) are known to occur in the Pacific Islands Region. 

In addition, using satellite telemetry of 43 juvenile loggerhead turtles (Caretta caretta) in 

the western North Pacific together with satellite remotely sensed oceanographic data, the 

+UROSHIO%XTENSION"IFURCATION2EGIONWASIDENTIlEDASIMPORTANTLOGGERHEADTURTLEFORAGEHABITAT)NTHE+UROSHIO%XTENSION"IFURCATION2EGIONJUVENILELOGGERHEADSRESIDEDIN

+UROSHIO%XTENSION#URRENTMEANDERSANDTHEASSOCIATEDANTI
CYCLONICWARMCORE	AND

CYCLONICCOLDCORE	EDDIESDURINGTHEFALLWINTERANDSPRINGWHENTHE+UROSHIO%XTENSION

Current water contains high surface chlorophyll. This work was conducted jointly with 

the Port of Nagoya Public Aquarium in Japan.

With respect to recreational fisheries in the main Hawaiian Islands, PIFSC scientists 

have developed a successful outreach, education, and data collection program for shoreline and near-shore fishermen in Hawaii to investigate the use of barbless circle hooks 

to increase survival of fish caught in tag and release programs and to reduce injury to 

protected species such as green sea turtles and Hawaiian monk seals when accidentally 

hooked.

Research Priorities, FY 2007–2012:

s #ONTINUESTUDIESTODETERMINETHEBESTMETHODSTOREDUCEINTERACTIONSANDINCREASE

survival of protected, prohibited, or sensitive species caught by longline and troll vessels 

and make this information widely available to fishery managers both domestically and 

internationally.

s $ETERMINE WAYS TO REDUCE INCIDENTAL CAPTURE OF SEA TURTLES IN LONGLINE lSHING GEAR

through various sensory physiology experiments on sea turtles and targeted fish species 

Seabirds on a Hawaiian 

shore. Photo: NOAA.
(e.g., swordfish and tuna) to determine mechanisms used to attract (and eventually deter) 

both fish and turtles to bite baited hooks.

s $ETERMINEEFFECTIVElSHINGGEARMODIlCATIONSFORREDUCINGLONGLINEINTERACTIONSWITHSEA

turtles, including performing at-sea experiments with the commercial longline fleet. 

s #ONTINUERESEARCHONTHEUSEOFBARBLESSHOOKSINNEARSHORElSHERIESTOMINIMIZEINJURY

to incidentally hooked species (e.g., Hawaiian monk seals and green turtles).

III. Research on the Fisheries

Recent Accomplishments:

PIFSC researchers have made substantial progress in characterizing the socioeconomic 

structure of the Hawaii longline fishery. One key accomplishment was the implementation 

of a successful economic data collection system for the fishery through cooperation with 

the Pacific Islands Regional Office’s Observer Program and longline fishery participants. 

Another key accomplishment was completion of a study of the socio-cultural dynamics 

and characteristics of longline participants. Using the data collected, PIFSC scientists 

prepared a number of socioeconomic analyses of this fishery. The results of these analyses, 

including a detailed look at the use of contract foreign labor in the fishery, were presented 

at international conferences.

Research Priorities, FY 2007–2012:

III.A. Social and economic research

s %XPAND SOCIOLOGICAL AND ECONOMIC RESEARCH AND INCORPORATE RESULTS INTO THE lSHERY

management process (e.g., National Environmental Policy Act analysis).

s $EVELOPBEHAVIORALMODELSOFECONOMICINCENTIVESAFFECTINGTHELEVELANDALLOCATIONOF

fishing effort in federally managed fisheries.

s %VALUATETHEREGULATORYIMPACTSOFRECENTANDPOTENTIALTIME
AREACLOSURESINTHE(AWAII

domestic longline fishery using an updated economic programming model with the latest catch, effort, and price data. 

s $EVELOPAUTOMATEDANALYTICALTEMPLATESINTEGRATEDWITHCURRENTlSHERYPERFORMANCE

cost, and price information for completing Regulatory Flexibility Analyses in an efficient and timely manner. Augment these templates to include the basic demographic 

information required to initiate preliminary Social Impact Analyses.

s #ONTINUETORESEARCHANDUPDATEINTRAINDUSTRYLINKAGESANDDEVELOPINPUT
OUTPUTRElationships to describe and model the employment, income, and economic activity impacts of management actions being considered for each of the federally managed fisheries and fishing communities.

s $EVELOPMETHODSTOCOMPAREANDASSESSTHESOCIOECONOMICIMPACTSOFVARIOUSMANAGEment options, including marine protected areas, ecosystem preserves, and other timearea closures designed to restore fish stocks and increase sustainable yields.

s $EVELOPMETHODSANDMODELSTOASSESSTHEEFFECTSOFVARIOUSMANAGEMENTOPTIONSON

the recreational and subsistence fisheries in the island areas.
138

s 2ESEARCHTHESOCIALANDECONOMICRAMIlCATIONSOFTHEVARIOUSMANAGEMENTOPTIONSON

the recreational and subsistence fisheries in the island areas.

s 3TUDYSMALL
BOATANDCHARTER
BOATANGLERSTOELICITEXPLICITNON
MARKETECONOMICVALUES

for blue marlin using standard contingent valuation techniques.

s 2ESURVEYTHE(AWAII
BASEDDOMESTICLONGLINEmEETTOPROVIDEANUPDATEDDATABASEFOR

conducting regulatory impact analyses on forthcoming regulations.

s $EVELOPALONG
TERMMONITORINGPROGRAMTOPROVIDEDATAONTRENDSINECONOMICAND

social conditions for use in making fisheries management decisions. 

s $EVELOPANECONOMICDATACOLLECTIONPROGRAMTHATWILLCOVERlSHINGCLUBMEMBERSAND

tournament participants in Hawaii.

s $EVELOPPROlLESOFlSHINGPORTSANDCOMMUNITIESIN(AWAII'UAM!MERICAN3AMOA

and Commonwealth of the Northern Mariana Islands, to support analysis of patterns 

of engagement in and dependency on fishing and associated activities.

s %XAMINETHEECONOMICVALUESANDPOLICYTRADEOFFSASSOCIATEDWITHCONSERVATIONAND

protection of threatened and endangered sea turtles in the Pacific. 

s %NHANCETHEEMPIRICALMODELANDEXTENDTHEAPPLICATIONTOINCLUDEOTHERlSHERIESTROLL

handline, and recreational fishing), which could enable an estimation of the change in 

the tradeoff value between small boats and longline fishery due to regulations. 

s #ONDUCT2EGULATORY)MPACT2EVIEWSAND2EGULATORY&LEXIBILITY!NALYSESFORMANAGEment actions being considered for all federally managed fisheries. 

s %VALUATE ALTERNATIVE SPECIlCATIONS OF THE ECONOMIC PROGRAMMING MODELS TO TEST THE

impact of critical assumptions concerning longline fishing industry behavior.

s )NITIATERESEARCHINTOAGENT
BASEDMODELING!"-	ASAMETHODTOCHARACTERIZEAND

understand fishing effort.

III.B. Seafood safety research 

This item is not applicable.

III.C. Marine aquaculture

This item is not applicable.

IV. Information Management Research

Recent Accomplishments:

The PIFSC has implemented projects that improve both data collection procedures 

and access to data holdings. One key accomplishment was the implementation of major 

shoreline-based creel surveys in American Samoa and the Commonwealth of the Northern 

Mariana Islands to improve monitoring of coral reef fisheries resources in cooperation with 

local fisheries agencies. 

In addition, PIFSC personnel have developed detailed metadata describing the Center’s 

collections and holdings of fisheries statistics and fisheries research survey data. These 

metadata have been packaged into a Data Catalog for posting on the Center’s Intranet, 
making the information readily available to all Center staff. In a related effort, the PIFSC 

developed, refined and beta-tested the web-enabled InPort Data Catalog prototype for the 

FIS Program. The InPort system has been approved and accepted as the standard for the 

FIS Program and is now in use for the entry of metadata on current fisheries information 

holdings in all regions. InPort is designed to maintain and search a “who, what, where, 

and when” catalog of fisheries data holdings. InPort provides capabilities to: 1) share data 

across NMFS; 2) search and study existing data for use in fisheries science, management, 

and regulation; and 3) ensure the quality and 

understandability of our data in support of 

ecosystem-based management. InPort also 

stores details on the quality and completeness 

of data, its confidentiality policies, research 

models, data collection protocols, methodologies, and usage constraints.

Research Priorities, FY 2007–2012:

s )MPLEMENTACOMPREHENSIVE/RACLE
BASED

integrated system for storing and distributing, via the Internet, appropriate PIFSC 

data holdings, including fisheries-dependent, research cruise, remote sensing, laboratory, and video data.

s $EVELOP')3TECHNOLOGYFORMAPPINGAND

spatial analysis of fisheries, oceanographic, 

and habitat information.

s !DVANCEAPPROACHESOFDATAFUSIONTOCOMbine fisheries data and assessment model 

outputs with environmental data from ship, satellite, and physical models.

s !UTOMATEQUARTERLYANDANNUALCOMPILATIONOFlSHERIESSTATISTICSANDANNUALREPORTSON

federally managed fisheries.

s -AINTAINANDIMPROVETHEWEB
BASEDACCESSTONON
CONlDENTIALDATA)NVESTIGATENEW

avenues for public access to data. 

s 2ESEARCHDEVELOPANDIMPLEMENTELECTRONICDATAREPORTINGPROGRAMSFORALLAREASAND

technology for fisheries-dependent information, i.e., electronic logbooks, seafood dealer 

reporting systems, etc.

s 2ESEARCHANDDEVELOPALTERNATEDATAREPORTINGINSTRUMENTSANDWAYSOFARCHIVINGDATA

to fulfill the Paperwork Reduction Act requirements. 

s $EVELOPAUTOMATEDSYSTEMSFORINTEGRATINGDATASETSWITHCOMMONlELDSEGLONGLINE

logbook and observer reports, NOAA research vessel cruise data, and satellite oceanographic remote sensing).

s #ONTINUETOIMPROVEDATASECURITYANDDATAQUALITYPRACTICES

s %NHANCEANDIMPROVETHElSHERIESMONITORINGINPUTANDOUTPUTPROGRAMSOFISLAND

areas.

s 3UPPORT)N0ORTMIGRATIONTO(EADQUARTERSANDMETADATAGATHERING

A map showing Hawaiian 

locations where marine 

debris has been found and 

requires removal. Mapping 

systems such as GIS greatly 

enhance the ability of 

researchers and managers 

to study marine life and 

habitat. Image: NOAA.
140

s #OMPLETEMODULARIZATIONOF(AWAII,ONGLINE/BSERVER$ATA3YSTEM

s )MPROVEANDPACKAGE$ATA)SSUES-ANAGER4OOL$ATA6ALIDATION-ANAGEMENTAND

Workflow Management.

s #ONTINUESUPPORTOFREGIONALNATIONALANDINTERNATIONALINFORMATIONSYSTEMS

s 7ORKWITHSTAKEHOLDERSTOIDENTIFYEMERGINGRESEARCHNEEDSANDIDENTIFYRESOURCESTHAT

can be reprogrammed to address those needs.

s 7ORKWITHSTAKEHOLDERSTOEXPEDITEDISSEMINATIONOFDATAANDANALYSESBYPROVIDING

them in formats other than final publications while still meeting Information Quality 

Act (IQA) requirements.
LITERATURE CITED

!GAR**-3HIVLANI*27ATERS-6ALDES
0IZZINI4-URRAY*+IRKLEYAND$3Uman. 2005. U.S. Caribbean fish trap fishery costs and earnings study. NOAA Technical 

Memorandum NMFS-SEFSC-534, 127 p.

Benaka, L.R., and T.J. Dobrzynski. 2004. The National Marine Fisheries Service’s National 

Bycatch Strategy. Marine Fisheries Review 66(2) 8 p.

Council on Environmental Quality (CEQ). 2004. U.S. Ocean Action Plan. Available 

online at http://ocean.ceq.gov/actionplan.pdf.

Department of Commerce (DOC). 2005. Department of Commerce Strategic Plan for 

FY 2004–FY 2009. Available online at http://www.osec.doc.gov/bmi/budget/Strategic04-

1002.htm.

Ecosystems Principles Advisory Panel (EPAP). 1999. Ecosystem-based fishery management: A report to Congress by the Ecosystems Principles Advisory Panel, as mandated by 

the Sustainable Fisheries Act amendments to the Magnuson-Stevens Fishery Conservation 

and Management Act of 1996. NMFS, Silver Spring, MD, 54 p. Available online at www.

nmfs.noaa.gov/sfa/EPAPrpt.pdf.

Food and Agriculture Organization of the United Nations (FAO). 2004. The state of 

world fisheries and aquaculture, 2004. Rome, 154 p. Available online at http://www.fao.

org/sof/sofia/index_en.htm.

Federal Register. 2002. Magnuson-Stevens Act Provisions; Essential Fish Habitat, Final 

Rule. Federal Register 67(12):2343, Thursday, January 17, 2002.

Institute of Medicine (IOM). 2006. Seafood choices: balancing benefits and risks. National 

Academies Press, Washington, DC, 608 p. Available online at http://www.nap.edu/openbook/0309102189/html/index.html.

National Marine Fisheries Service (NMFS). 1998a. Managing the nation’s bycatch. Programs, activities, and recommendations for the National Marine Fisheries Service. Silver 

Spring, MD, 174 p. Available online at http://www.nmfs.noaa.gov/bycatchplanonline.

pdf.

NMFS. 1998b. Proposed implementation of fishing vessel registration and fisheries information system. Report to Congress submitted to the Committee on Resources of the House 

of Representatives and the Committee on Commerce, Science, and Transportation of the 

Senate. Available online at http://www.nmfs.noaa.gov/sfa/401.pdf.
142

NMFS. 1998c. NOAA Fisheries Data Acquisition Plan. Silver Spring, MD, 28 p.

Available online at http://www.st.nmfs.gov/st4/DataAcquisitionPlan.html.

NMFS. 2001. Marine Fisheries Stock Assessment Improvement Plan. NOAA Technical 

Memorandum NMFS-F/SPO-56. Available online at: http://www.st.nmfs.noaa.gov/

StockAssessment/index.html.

NMFS. 2004. Evaluating bycatch: a national approach to standardized bycatch monitoring 

programs. NOAA Tech. Memo. NMFS-F/SPO-66, 108 p. Available online at http://spo.

nmfs.noaa.gov/tm.

NMFS. 2005. New Priorities for the 21st Century: National Marine Fisheries Service 

Strategic Plan Updated for FY 2005–FY 2010. Available online at http://www.nmfs.noaa.

gov/mb/strategic/.

NMFS. 2007a. Fisheries of the United States, 2005. Curr. Fish. Stat. 2005, 110 p. Available online at http://www.st.nmfs.gov/st1/fus/fus05/index.html.

NMFS. 2007b. Annual Report to Congress on the Status of U.S. Fisheries–2006. Available online at http://www.nmfs.noaa.gov/sfa/statusoffisheries/SOSmain.htm#roc06.

NMFS. In prep. Our living oceans. Report on the status of U.S. living marine resources. 

Silver Spring, Md.

NOAA. 2005a. The NOAA Strategic Plan: New Priorities for the 21st Century. Available 

online at http://www.ppi.noaa.gov/pdfs/STRATEGIC%20PLAN/Strategic_Plan_2006_

FINAL_04282005.pdf.

NOAA. 2005b. NOAA 20-Year Research Vision. Available online at http://www.nrc.

noaa.gov/plans.html.

NOAA. 2005c. Research in NOAA: Toward understanding and predicting earth’s environment. Available online at http://www.nrc.noaa.gov/plans_docs/research_cover.pdf.

National Research Council (NRC). 1998. Improving fish stock assessments. National Academies Press, Washington, DC, 188 p. Available online at www.nap.edu/books/0309057256/

html/.

NRC. 1999. Sustaining marine fisheries. National Academies Press, Washington, DC, 184 

p. Available online at www.nap.edu/books/0309055261/html/.

NRC. 2000. Improving the collection, management, and use of marine fisheries data. 

National Academies Press, Washington, DC, 236 p. Available online at www.nap.edu/

books/0309070856/html/.

NRC. 2001. Marine protected areas: tools for sustaining ocean ecosystems. National Academies Press, Washington, DC, 288 p. Available online at www.nap.edu/books/0309072867/

html/.
NRC. 2006a. Review of Recreational Fisheries Survey Methods. National Academies Press, 

Washington, DC, 202 p. Available online at http://fermat.nap.edu/catalog/11616.html.

NRC. 2006b. Dynamic Changes in Marine Ecosystems. National Academies Press, Washington, DC, 153 p. Available online at http://newton.nap.edu/catalog/11608.html.
144
APPENDIX A:

Relationship of This Plan to Other Plans

RELATIONSHIP BETWEEN THE NOAA 

STRATEGIC PLAN AND NMFS PROGRAMS

The NOAA Strategic Plan (NOAA 2005a) comprehensively addresses the NOAA mission: To understand and predict changes in Earth’s environment and conserve and 

manage coastal and marine resources to meet our Nation’s economic, social, and 

environmental needs. The Plan’s focus through 2011 is on five goals:

1. Protect, restore, and manage the use of coastal and ocean resources through an ecosystem 

approach to management.

2. Understand climate variability and change to enhance society’s ability to plan and 

respond.

3. Serve society’s needs for weather and water information.

4. Support the Nation’s commerce with information for safe, efficient, and environmentally 

sound transportation.

5. Provide critical support for the above four Mission Goals.

To build on its core strengths, NOAA has selected five essential activities called “CrossCutting Priorities” that are closely allied and essential to support its goals: 

s $EVELOPINGVALUINGANDSUSTAININGAWORLD
CLASSWORKFORCE

s )NTEGRATINGGLOBALENVIRONMENTALOBSERVATIONSANDDATAMANAGEMENT

s %NSURINGSOUNDSTATE
OF
THE
ARTRESEARCH

s 0ROMOTINGENVIRONMENTALLITERACY

s %XERCISINGINTERNATIONALLEADERSHIP

Virtually all of the NMFS programs, including the research programs, are encompassed 

within NOAA’s Mission Goal 1, focused on coastal and ocean resources. The NOAA 

program areas included in this goal are: Aquaculture; Coastal and Marine Resources; 

Corals; Ecosystem Observations; Ecosystem Research; Enforcement; Fisheries Management; Habitat; and Protected Species. A small NMFS component, within the Climate and 

Ecosystems program, is encompassed within NOAA’s Mission Goal 2, and other NMFS 

climate-related research on ecosystem productivity is closely associated with this goal. Many 

NMFS programs have outputs that also serve the Cross-Cutting Priorities. For example, to 

advance research capabilities, NMFS is active in developing and applying state-of-the-art 

tools including computational models, survey ships, and sensing instruments. By being attuned to broader needs, program managers can ensure additional benefits are obtained.

NOAA has identified two desired outcomes under Goal 1: 1) Healthy and productive 

coastal and marine ecosystems that benefit society; and 2) a well-informed public that acts 
146

as a steward of coastal and marine ecosystems. The associated performance objectives are 

the following:

s )NCREASENUMBEROFlSHSTOCKSMANAGEDATSUSTAINABLELEVELS

s )NCREASENUMBEROFPROTECTEDSPECIESTHATREACHSTABLEORINCREASINGPOPULATIONLEVELS

s )NCREASENUMBEROFREGIONALCOASTALANDMARINEECOSYSTEMSDELINEATEDWITHAPPROVED

indicators of ecological health and socioeconomic benefits that are monitored and understood.

s )NCREASENUMBEROFINVASIVESPECIESPOPULATIONSERADICATEDCONTAINEDORMITIGATED

s )NCREASENUMBEROFHABITATACRESCONSERVEDORRESTORED

s )NCREASEPORTIONOFPOPULATIONTHATISKNOWLEDGEABLEOFANDACTINGASSTEWARDSFORCOASTAL

and marine ecosystems.

s )NCREASEENVIRONMENTALLYSOUNDAQUACULTUREPRODUCTION

s )NCREASENUMBEROFCOASTALCOMMUNITIESINCORPORATINGECOSYSTEMANDSUSTAINABLEDEvelopment principles into planning and management.

The NOAA Strategic Plan is available at: 

http://www.ppi.noaa.gov/pdfs/STRATEGIC%20PLAN/Strategic_Plan_2006_FINAL_

04282005.pdf.

RELATION OF THE NOAA RESEARCH PLAN AND

THIS NMFS STRATEGIC PLAN FOR FISHERIES RESEARCH

To focus the research efforts necessary to accomplish the NOAA Strategic Plan, NOAA 

has a companion research plan, called Research in NOAA: Toward Understanding and Predicting Earth’s Environment (NOAA 2005c). It covers all research undertaken in support 

of NOAA’s various mission as described in the NOAA Strategic Plan. Its planning horizon 

is FY 2007–2011 and is undergoing revision with a similar schedule as this update of the 

NMFS Strategic Plan for Fisheries Research (NSPFR). It has a somewhat different goal 

structure than the NSPFR because it is based on broad themes designed to bring all of the 

NOAA resources together in an integrated fashion to address societal needs. The NSPFR, 

on the other hand, follows a legislatively driven outline guiding the much narrower suite of 

programs designed to achieve the research objectives of NMFS necessary to implement the 

Magnuson-Stevens Fishery Conservation and Management Act (MSFCMA) as amended 

by the Sustainable Fisheries Act (SFA). Thus, the NSPFR encompasses much of NMFS 

research activities regarding fisheries and habitat issues and includes specific Fisheries Science Center plans as well. Research on marine mammals, turtles, and protected species of 

fish is included, but only when it is directed at MSFCMA requirements. The NSPFR is 

more comprehensive and goes into much greater detail regarding NMFS MSFCMA-related 

research than does any other strategic planning document in NOAA.

Nearly all of the NMFS research program falls under the NOAA Ecosystem Goal and its 

supporting research program, which has five themes: supporting collaborative approaches 

to science and management at the regional level, understanding the impacts of climate on 

ecosystems, enhancing social and ecological resilience to hazards, protecting marine and 

coastal resource security, and developing a more robust ecosystem modeling capability to 

serve current and future management information needs. These research priorities can be 
organized in an end-to-end portfolio that covers advancing the understanding of ecosystems; providing new insight into the oceans through discovery and identification of new 

resources; forecasting biological events or consequences of natural and human-induced 

changes in the environment; and developing scenarios to simulate potential impacts on 

marine and coastal resources.

Except for climate-related research on ecosystem productivity that resides in the NOAA 

Climate Goal, most of the NOAA Research Plan milestones for the Ecosystem Goal are 

all related to this NSPFR. The exceptions are several milestones related to the NOAA 

Ocean Exploration Program of NOS and the Ecosystem Forecasting work of OAR. The 

NSPFR-related milestones of the NOAA Research Plan, by NOAA Goal are as follows: 

Ecosystem Mission Goal: 

Protect, Restore, and Manage Use of Coastal and Ocean 

Resources through Ecosystem Approach to Management

Research Milestones For Advancing Understanding 

of Ecosystems to Improve Resource Management

s $ElNETHEPRIMARYFORCINGFACTORSANDTIMEANDSPACESCALESTHATAFFECTlSHRECRUITMENT

and fisheries production for selected regions.

s -EASURETHENATURALSCALESOFVARIABILITYREGARDINGPHYSICAL
BIOLOGICALCOUPLINGFOOD

web dynamics and ecosystem production in selected ecosystems.

s %XPANDECOSYSTEMMODELSTOADVANCETHESCIENTIlCFRAMEWORKFORTHEPROVISIONOFADVICE

through integrated ecosystem assessments.

s 0ROVIDEINTEGRATEDECOSYSTEMASSESSMENTSTHATEVALUATETHEECOLOGICALRESPONSETOVARIOUS

anthropogenic stressors. 

s )DENTIFYECOSYSTEMCARRYINGCAPACITYFORCRITICALPROTECTEDSPECIESASASTEPINPROVIDING

more efficient recovery strategies.

s -APANDEVALUATEHABITATEXISTINGANDRESTORABLE	ANDIDENTIFYKEYHABITATFUNCTIONS

evaluate the function/health of habitat. 

s %STIMATEAMBIENTNOISEBUDGETSINREGIONALECOSYSTEMSBYCHARACTERIZINGTHENOMINAL

acoustic environments.

s $EVELOPENVIRONMENTALLYSOUNDAQUACULTURETECHNOLOGIESFORMARINESPECIES

Research Milestones For Forecasting Our Ecosystems

s $EVELOPFORECASTSFORTHEECOLOGICALEFFECTSOFVARYINGWEATHERPATTERNSANDEXTREME

physical events.

s $EVELOPFORECASTSFORTHEECOLOGICALEFFECTSOFSEALEVELRISEANDCLIMATECHANGE

s $ElNETHEPRIMARYFORCINGFACTORSANDTIMEANDSPACESCALESTHATCAUSE(!"SANDANOXIA

for selected coastal, ocean, and Great Lakes regions. 

s $ElNETHEPRIMARYFORCINGFACTORSANDTIMEANDSPACESCALESTHATAFFECTWATERQUALITY

and quantity for selected coastal and Great Lakes regions.

s )DENTIFYSENTINELSPECIESANDOTHERPROXIESFOREARLYDETECTIONOFPATHOGENANDMICROBIAL

contaminants.
148

s $ElNETHEPRIMARYFORCINGFACTORSANDTIMEANDSPACESCALESTHATAFFECTlSHRECRUITMENT

and fisheries production for selected coastal and Great Lakes regions.

s 3TUDYAQUATICBIODIVERSITYANDHOWANTHROPOGENICSTRESSESEXTREMEENVIRONMENTALEVENTS

and climate influence population dynamics of coastal and marine ecosystems.

Research Milestones For Developing Scenarios and 

Building Capacity to Support Regional Management

s %VALUATE THE RISKVALUE OF ALTERNATIVE ECOSYSTEM
BASED MANAGEMENT STRATEGIES USING

integrated ecosystem assessments.

s 2ESEARCHTOIMPROVEOURUNDERSTANDINGOFTHEFACTORSAFFECTINGTHREATENEDSPECIESAND

the potential success of alternative remediation/management strategies.

s $EVELOPMETHODOLOGIESANDTOOLSFORESTIMATINGNON
MONETARYECOSYSTEMVALUETHATCAN

be translated into decision support tools for stewardship of coastal and marine ecosystems.

s %XPANDEXTENSIONANDEDUCATIONAPPROACHESTOPROVIDESCIENTIlCINFORMATIONINADVANCE

of actions and regulations and to assist NOAA in fostering increased understanding 

and partnerships among fishermen, conservation and environmental groups, coastal use 

communities, and scientists.

s 0ROVIDECOST
BENElTFORECASTSANDRISKANALYSESOFMANAGEMENTDECISIONSANDHUMANUSE

of coastal and Great Lakes ecosystems.

Climate Mission Goal: Understand Climate Variability 

and Change to Enhance Society’s Ability to Plan and Respond

Research Milestones For Understanding 

Impacts Of Climate Variability And Change On Marine 

Ecosystems To Improve Management Of Marine Ecosystems

s $EVELOPMENTOFAMODELTOINCORPORATETHEEFFECTSOFCLIMATEINTOLIVINGMARINEREsource assessments for the Bering Sea. 

RELATION OF THE NMFS STRATEGIC PLAN

AND THIS PLAN FOR FISHERIES RESEARCH

The NMFS Strategic Plan (NMFS 2005), guides NMFS activities in support of NOAA’s 

mission and its underpinning goals and objectives. It interweaves with the NOAA Strategic 

Plan by establishing indicators of progress, and their associated performance measures and 

metrics primarily in the context of NOAA’s Strategic Goal 1. Details regarding the NMFS 

Strategic Plan are available at http://www.nmfs.noaa.gov/mb/strategic/.

The NMFS Strategic Plan requires the support of research to meet most of its objectives. As an agency-wide strategic plan, it must address all relevant legislative mandates, 

and closely correspond to the NOAA Strategic Plan. However, this NMFS Strategic Plan 

for Fisheries Research (NSPFR) has a somewhat different structure that is specific to the 

content mandated by the Magnuson-Stevens Fishery Conservation and Management Act 

(MSFCMA). 
Table 1. Corresponding 

elements of the NMFS 

Strategic Plan and the NMFS 

Strategic Plan for Fisheries 

Research.

This NSPFR guides the suite of programs that address the research objectives of NMFS 

necessary to implement the MSFCMA as amended by the Sustainable Fisheries Act (SFA). 

This encompasses much of NMFS research activities regarding fisheries and habitat issues 

and includes specific Fisheries Science Center plans as well. Research on marine mammals, 

turtles, and protected species of fish, is included but only when it is directed at MSFCMA 

requirements.

Table Comparing the NMFS Strategic Plan 

and the NMFS Strategic Plan for Fisheries Research

Table 1 presents the outline of the NMFS Strategic Plan goals and elements in the left 

column and corresponding elements of this MSFCMA-required NMFS Strategic Plan for 

Fisheries Research in the right column.

NMFS Strategic NMFS Strategic Plan

Plan Outline for Fisheries Research

NOAA Mission Goal 1: Protect, 

Restore, Manage 

PROGRAMS

 s %COSYSTEM/BSERVATIONS )! "IOLOGICALRESEARCHCONCERNINGSTOCKABUNDANCE

 I.B. Interdependence of fisheries or stocks of fish

 I.C. Identifying, restoring, and mapping essential fish habitat

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

 II. Conservation engineering research

 III.A. Social and economic research

 s %COSYSTEM2ESEARCH )" )NTERDEPENDENCEOFlSHERIESORSTOCKSOFlSH

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

 s &ISHERIES-ANAGEMENT .OT&ISHERIES2ESEARCH

 s 0ROTECTED3PECIES )! "IOLOGICALRESEARCHCONCERNINGSTOCKABUNDANCE

 I.B. Interdependence of fisheries or stocks of fish

 II. Conservation engineering research

 s %NFORCEMENT .OT&ISHERIES2ESEARCH

 s (ABITAT )# )DENTIFYINGRESTORINGANDMAPPINGOFESSENTIALlSHHABITAT

 s #ORAL2EEF#ONSERVATION )! "IOLOGICALRESEARCHCONCERNINGSTOCKABUNDANCE

 I.B. Social and economic factors affecting abundance levels

 I.B. Interdependence of fisheries or stocks of fish

 I.C. Identifying, restoring, and mapping of essential fish habitat

 s !QUACULTURE )))# -ARINEAQUACULTURE

NOAA Mission Goal 2. Understand I.B. Interdependence of fisheries or stocks of fish

 Climate Variability and Change I.D. Impact of anthropogenic factors and environmental changes on fish populations 

NOAA Support Goal: Provide Critical IV. Information management research 

 Support for NOAA’s Missions Indirect support across all programs

Not Specifically Included III.B. Seafood safety research
150

OVERVIEW OF PLANNING DOCUMENTS

Over the past several years there have been numerous outside reviews of Federal ocean 

and fisheries programs. NMFS research programs and plans have been developed to implement the recommendations of these reviews. Both broad and program-specific reviews and 

planning efforts have had significant impact on NMFS research and are reflected in this 

present Plan. Overviews of the more important reviews and plans are presented below.

Internal Planning Documents:

s 53/CEAN!CTION0LAN

In response to the U.S. Commission on Ocean Policy, President Bush delivered the 

U.S. Ocean Action Plan to guide actions to make the oceans, coasts, and Great Lakes 

cleaner, healthier, and more productive. It calls for management strategies that ensure 

continued conservation of coastal and marine habitats and living resources while at 

the same time ensuring that the American public enjoys and benefits from those same 

resources. The Plan lays out an approach to obtain the best science and data to inform 

decision-making, based on an ecosystem approach in making decisions related to water, 

land, and resource management in ways that do not erode local and state authorities 

and are flexible to address local conditions. It envisions stronger partnerships between 

Federal, state, tribal, and local governments, the private sector, international partners, 

and other interests. The Plan is available at http://chartmaker.ncd.noaa.gov/ocs/hsrp/

admin/mar2005/oceanactionplan.pdf.

s .-&3-ARINE&ISHERIES3TOCK!SSESSMENT)MPROVEMENT0LAN3!)0	

(October 2001)

The Marine Fisheries SAIP is the report of the NMFS National Task Force for Improving 

Fish Stock Assessments. This report is part of a series of plans for enhancing and modernizing NMFS programs for data collection, information technology, data management, 

stock assessments, scientific research, and fisheries management. The report includes 

specific recommendations for improving the quality of NMFS’ stock assessment programs 

and emphasizes the need for the agency to foster partnerships and cooperative research 

programs with other Federal agencies, state agencies, private foundations, universities, 

commercial and recreational fishing organizations and individuals, environmental groups, 

and others with a vested interest in collecting similar types of data. Recommendations 

from the SAIP have formed the basis for successful budget initiatives to augment funding for improving stock assessments. The SAIP is available at: http://www.st.nmfs.noaa.

gov/StockAssessment/index.html (NMFS 2001). 

s .-&33TRATEGIC0LANFOR&ISHERIES2ESEARCHAND	

Originally released in 1998 as a requirement of the Sustainable Fisheries Act of 1996, 

these Plans are consistent with contemporaneous planning initiatives, yet with a more 

detailed focus on NMFS research activities. In particular, the Plans function as a subset 

of the NSP. The objectives found under the “Major Fishery Research Goals and Objectives” section of the Plans can be matched with strategies in the counterpart NSPs. 

s ./!!&ISHERIES$ATA!CQUISITION0LAN	

This September 1998 document represents a strategy for meeting NMFS’ rapidly growing 

at-sea data requirements. The Plan provides an overview of the existing data acquisition 

program, describes anticipated growth and changes to data requirements in the future, 
details options available, and presents a suite of recommendations for meeting these 

challenges, including the construction of a fleet of modern Fisheries Research Vessels. 

Recommendations from the Plan have formed the basis for budget decisions relative to 

the acquisition of at-sea data. This Plan is available from the NMFS website at http://

www.st.nmfs.gov/st4/documents/DataPlan.pdf.

External Reviews by the National Research Council (NRC)

s 2EVIEWOF2ECREATIONAL&ISHERIES3URVEY-ETHODS)

This 2006 report commissioned by NOAA reviewed NOAA recreational fisheries survey 

methods used to estimate catch per unit effort and effort in NOAA and state/Federal 

cooperative programs. The study examined representative survey types, but did not 

evaluate every regional or state survey method. It also considered the match or mismatch 

between options for collecting recreational fisheries data and alternative approaches for 

managing recreational fisheries. The report recommended that the current survey programs be redesigned to improve sampling and estimation procedures, their applicability 

to various kinds of management decisions, and their usefulness for social and economic 

analyses. The report also emphasized that state and Federal agencies must work together 

to provide ongoing technical evaluation and modification of survey programs to meet 

emerging management needs and to achieve much greater degree of standardization 

among state and Federal surveys. It recommended treating the For-Hire fishing sector 

as a “commercial” sector, and proposed that mandatory timely reporting of all catch 

and effort by that sector be required. The report also called for NOAA to set a firm 

deadline linked to sufficient program funding to implement the recommendations (NRC 

2006a).

s $YNAMIC#HANGESIN-ARINE%COSYSTEMS	

This 2006 report commissioned by NOAA reviews the many recent scientific papers 

about the effects of fishing on marine food webs and the productivity of species. The 

objective of the review was to evaluate these effects in the context of relevance to fisheries 

management, future research and stewardship. Recommendations in this report call for 

a more comprehensive ecosystem-based approach to fisheries management, rather than 

the species-by-species approach currently being used. It calls for supporting research 

on the extent of fishing effects on ecosystems and the development of comprehensive 

models suitable for portrayal of different management scenarios. These models should 

include food webs and species interactions within the ecosystems and the intertwining 

social and economic factors (NRC 2006b).

s -ARINE0ROTECTED!REAS4OOLSFOR3USTAINING/CEAN%COSYSTEMS	

Published in 2001, this NOAA-commissioned report evaluates marine protected areas 

(MPAs) as a tool to supplement conventional fishery management. The report recommended networks of MPAs, some for fishery management, embedded within broadly 

zoned management areas in the coastal ocean. Additionally, the study indicated that the 

basic knowledge gained through monitoring and evaluation of MPAs on the structure, 

function, and variability in marine ecosystems would enhance the design of reserves and 

allow more accurate evaluations of their ecological and socio-economic consequences. 

Reserves would also allow more accurate estimation of parameters such as natural mortality rates—an essential variable in stock assessment models. This report can be read 

online or purchased at www.nap.edu/ (NRC 2001). While this report was not a specific 

review of NMFS science and management efforts, it sought and made recommendations 
152

on how MPAs should be used and is thus useful in guiding NMFS research programs 

(NRC 2001). 

s )MPROVING THE #OLLECTION -ANAGEMENT AND 5SE OF -ARINE &ISHERIES $ATA

(2000)

This 2000 NRC-commissioned report assesses methods for improving data for stock 

assessments and fisheries management. The summer flounder fishery was used as a case 

study in this report because it supported a fishery that spanned state and Federal waters 

over a vast geographic area, both recreational and commercial fishermen targeted the species, and there was an abundance of data available for assessments. The report analyzed 

summer flounder stock assessments and implicit and explicit modeling assumptions that 

affected modeling outcomes. The study also examined data collection and use and made 

40 recommendations to Federal and state fishery agencies, Congress, regional FMCs, 

interstate commissions, and commercial and recreational fishermen with the objective 

of improving fisheries data and management. (NRC 2000).

s 3USTAINING-ARINE&ISHERIES	

Published in 1999, this NRC-commissioned report explores the nature of marine ecosystems and the complex interacting factors that shape their productivity. The book documents the condition of marine fisheries in 1999, highlighting species and geographic areas 

that were under particular stress. Challenges to achieving sustainability are discussed, and 

shortcomings of existing fisheries management and regulation are examined. The report 

calls for fisheries management to adopt a broader ecosystem perspective that encompasses 

all relevant environmental and human influences, but also emphasizes that the first step 

towards ecosystem-based management is to reduce fishing mortality on individual stocks 

to optimal levels. It can be read on-line or purchased at the National Academy Press 

Web site at www.nap.edu/ (NRC 1999). While this report was not a specific review of 

NMFS science and management efforts, it sought and made recommendations on how 

the ecosystem approach should be used and is thus useful in guiding NMFS research 

programs (NRC 1999).

s )MPROVING&ISH3TOCK!SSESSMENTS	

This 1998 report commissioned by NMFS reviews the agency’s stock assessment methods 

and models and makes recommendations for alternative approaches. The report authoritatively documented the strengths and limitations of stock assessment methods relative to 

the diversity of available data and types of fisheries management systems (NRC 1998).

External Review by the Institute of Medicine

s 3EAFOOD#HOICES"ALANCING"ENElTSAND2ISKS	

This 2006 report commissioned by NOAA reviewed evidence on the benefits and risks 

associated with seafood consumption to recommend ways to guide U.S. consumers 

in making seafood selections to meet their needs. Seafood contributes to a variety of 

nutritious benefits to the American diet. Contamination of marine resources, however, 

whether naturally occurring or anthropogenic is a concern to U.S. consumers. Because of 

the potential for adverse health effects, consumers—particularly subpopulations, which 

may be at increased risk—need authoritative information to make informed choices that 

provide desired nutrients balanced against exposure to potential toxicants. The study 

is being used a centerpiece of information for the agency to focus its extensive fishery 

food science expertise to assist other Federal agencies and the U.S. consumer to develop 
a decision path to balance seafood choices to obtain needed nutritional benefits while 

minimizing exposure. The study is also being used to identify data gaps and recommendations for future research. The NAS report has been published and reaffirms the 

benefits of seafood consumption and makes specific recommendations to encourage 

increased seafood consumption by the public, including those specific subpopulations 

that may be at risk (IOM 2006).

All of these external reports can be read online or purchased at www.nap.edu/.
154
APPENDIX B:

RESPONSE TO COMMENTS

ON THE PUBLIC DRAFT OF THE NSPFR

Comment: Numerous comments noted the need for more information and research into 

a variety of topics to address potential concerns related to marine aquaculture, including 

but not limited to: genetics, disease, competition from escapes, feeds (including use of fish 

meal and oil), economic impacts, water quality, and benthic impacts. Other comments 

recommended that the plan be restructured consistent with the topic areas described in 

the report of the Woods Hole Marine Aquaculture Task Force (Task Force).

Response: NMFS agrees with these comments, and has revised the plan accordingly. The 

intent of the NSPFR was to include all of the research topics described by the Task Force, 

but NMFS agrees they were unnecessarily grouped together and therefore not adequately 

addressed individually. The Plan was revised to more explicitly address the key research 

topic areas as described by the Task Force by breaking out a single objective in the draft 

plan into four individual objectives. It should be noted, however, that some of the Task 

Force’s recommendations are for regulatory matters and therefore were not included in 

this research plan.

Comment: Instead of having a rigid calendar period assigned to the time when fishing is 

allowed, NMFS could allow some flexibility in the schedule for bad weather.

Response: This is a regulatory suggestion and not within the scope of the NSPFR.

Comment: The Plan acknowledges the need to manage fisheries within an ecosystem context, 

but fails to focus on this issue and to develop it as a focus of strategic research.

Response: NMFS has strengthened the concept of ecosystem-based science throughout the 

document, but note that this is a research plan that must provide the information necessary 

for resource management. The first two elements of the first research area (Research to 

support management) treat ecosystem research intensively, demonstrating its importance 

as a strategic focus to NMFS. Additionally, specific wording has been added to the NSPFR 

for GOAL 1 and its first two objectives to show that research must provide scientifically 

sound information and data sufficient to support ecosystem-based fishery conservation 

and management.

Comment: The present document fails to articulate the vital role of research partnerships 

in realizing a strategic research vision for the national fisheries.

Response: NMFS recognizes the need for partnerships in conducting the research mission 

and had already included improvement in this area as a sixth goal to help focus efforts 

on building partnerships. Also, the introductory sentence of the Science Centers section 
156

discusses these cooperative relationships. We believe that the present treatment is adequate 

for the purposes of this document.

Comment: To ensure the progression to ecosystem-based management stays on course, 

NMFS should design a research program specifically geared toward the recommendations 

of the Ecosystems Principles Advisory Panel (EPAP) Report to Congress, with schedules 

and milestones to gauge progress. 

Response: The EPAP recommendations are useful for measuring progress towards providing information to support ecosystem-based management. The Plan addresses the EPAP 

recommendations in section I.B. Interdependence of fisheries or stocks of fish.

Comment: The Plan notes that an ecosystem-based approach is needed to take into account 

the various factors that affect the status of a stock and the importance of a stock to other 

components of the ecosystem, but omits a comprehensive initiative that would serve to 

implement the first step toward an ecosystem-based approach recommended by the Ecosystems Principles Advisory Panel Report to Congress—that fishery managers consider 

how fishing affects predator-prey interactions.

Comment: While the NSPFR does not directly address regulatory matters, NMFS notes 

(as explained in the prior ecosystems-related comment) that the agency has increased its 

emphasis on a holistic approach to resource management. By bringing ecosystem-wide information and advice to resource managers, NMFS helps to ensure that managers will be in 

a better position to consider predator-prey and all other relevant ecosystem interactions.

Comment: NMFS should direct the Science Centers to investigate the ecological roles of 

commercially important forage species in each region so that these roles can be qualitatively 

and quantitatively described.

Response: The role of forage species is a fundamental aspect of ecosystem research, and is 

a high priority addressed in section I.B. Interdependence of fisheries or stocks of fish.

Comment: This Plan reflects an inherent bias towards research that contributes to managing and maximizing fishery yields over that for protected species.

Response: The NSPFR, as mandated by Congress, deals with only fisheries conservation 

and management. It includes only protected species issues that are derived from interactions with recreational or commercial fisheries. Otherwise, protected species research is 

not part of this Plan, as is explained in the Introduction. When there is known bycatch or 

entanglement problems due to fishing gear, these issues are addressed through gear research 

(such as turtle excluder devices or dolphin/tuna net innovations), and through regulatory 

measures (such as closed fishing areas or seasons when protected species are present). There 

is considerable effort identified for gear research concerning protected species in this Plan’s 

Goal 2 and corresponding Objectives (pages 40–41) as well as the six individual Science 

Center sections devoted to conservation engineering research (starting on pages 57, 78, 

91, 104, 118, and 136).

Comment: The Plan should not promote expansion of open-ocean aquaculture. 

Response: NMFS does support development of open-ocean aquaculture (OOA) in a manner 
that is sustainable and minimizes environmental impacts. It is important to note that no 

commercial aquaculture currently is ongoing offshore (i.e., in Federal water), and very little 

open ocean aquaculture is currently underway. Therefore, even a small industry would represent “expansion.” NMFS will conduct an environmental impact statement, using the best 

available science, to help determine appropriate locations and permit conditions for OOA, 

taking into account environmental and other impacts, including cumulative impacts.

Comment: Strongly agree with research Objective 1.11 (Conduct additional research to 

provide needed information to refine EFH designations). Many of the EFH descriptions 

and designations are now effectively fish habitat descriptions and fail to identify any particular areas that are truly EFH. Research should be conducted to better distinguish 

between “essential” fish habitat and fish habitat generally.

Response: NMFS has changed the wording of Objective 1.11 to further clarify the intent 

of the objective.

Comment: The work of the fisheries aspect of NOAA is outstanding and should be fully 

funded by Congress. NOAA should include Great Lakes waters in its Fisheries studies 

and request adequate funding for that work from Congress.

Response: NOAA has responsibility for some aspects of research in the Great Lakes, but 

not that related to fisheries stewardship. That role falls to the states and Canadian provinces that border the Lakes. Coordination of fisheries research and stewardship occurs 

through the Canadian/U.S. Convention on Great Lakes Fisheries as implemented by the 

Great Lakes Fishery Commission. A similar arrangement exists along the ocean coastal 

states where federally chartered Coastal States Marine Fisheries Commissions coordinate 

state roles in research and stewardship. The research addressed in this Strategic Plan for 

Fisheries Research is primarily that in support of stewardship in Federal waters and on 

the high seas.

Comment: The greatest threat to the coastal environment right now is the influx of raw 

and treated sewage, and increased amounts of farm fertilization and waste runoff being 

discharged into the fragile back bay and tributary environments instead of being piped a 

few miles offshore. Also, the industrial waste and byproducts which are causing increased 

risk of cancer or other disease to humans should be immediately eliminated everywhere.

Response: Nutrient loading through sewage, land runoff, and other causes is a major problem 

leading to eutrophication of many estuaries and coastal waters. NMFS works with the U.S. 

Army Corps of Engineers, the Environmental Protection Agency, the states, and others to 

reduce pollution, for the benefit of both the resources and their human and other users. 

The research-related aspects of this comment are already included in the Plan.

Comment: Mass catching methods (such as purse seining and long-lining are causing complete and utter shutdown of certain populations within our marine habitat.

Response: Fish removals must not be disruptive to ecosystems. The agency works internationally with regional fisheries organizations, with the United Nations fisheries organization, and with individual nations, to coordinate research and stewardship of high seas 

fisheries. In such work we address such concerns as long lining, bycatch of fish and turtles 

in shrimp trawls, taking of dolphins in tuna purse seines, and unregulated fishing by fleets 
158

from non-participating nations. Domestically, we work with the states and Fishery Management Councils to focus our research and stewardship actions on the most important 

problems affecting resource conservation. The research-related aspects of this comment 

are already included in the Plan.

Comment: 1) Ban all genetically modified organism (GMO) species and manipulation, so 

marine species are not altered in any way, 2) Coordinate national and international regulation of fisheries, and 3) Continue qualitative and quantitative research.

Response: NMFS believes that: 1) unintended release of (GMOs) into the marine environment is to be avoided, 2) that fisheries regulations need to be coordinated, and 3) that 

qualitative and quantitative research needs to continue to develop a basis for decisions.

NOAA policy (http://govdocs.aquake.org/cgi/reprint/2003/514/5140040.pdf) with respect 

to GMOs is that regulations and decisions regarding the risk to biodiversity, particularly 

from introduction of aquatic organisms and use of genetically altered organisms, should 

be guided by internationally accepted codes of practice, existing Federal regulations and 

procedures and, where appropriate, by approaches and regulations in use at the state level. 

The same protocols should be used as tools in any evaluations of impact subsequent to 

the agency’s decisions. This Plan will assist decision makers by making the best science 

available so that appropriate decisions can be made.

With respect to coordination of fisheries regulations, we work internationally with regional 

fisheries organizations, with the United Nations fisheries organization, and with individual 

nations, to coordinate the research underlying regulatory regimes and the stewardship of 

high seas fisheries. In such work we address such concerns as long lining, bycatch of fish 

and turtles in shrimp trawls, taking of dolphins in tuna purse seines and unregulated 

fishing by fleets from non-participating nations. Domestically we work with the states 

and Fishery Management Councils to focus our research and stewardship actions on the 

most important problems affecting resource conservation. The need for continuation and 

strengthening of our research program is evidenced throughout the Plan. 

Comment: Somewhere in this extensive NOAA NMFS document there should be a credible discussion of overfishing.

Response: Much of NMFS’ scientific work is devoted to assessing and monitoring the 

fish stocks, including the scientific basis for determining whether they are overfished or 

experiencing overfishing. NMFS agrees that overfishing and overfished should be better 

defined and has included the operational definitions used by this agency. A stock that is 

subject to overfishing has a fishing mortality (harvest) rate above the level that provides 

for the maximum sustainable yield. A stock that is overfished has a biomass level below 

a biological threshold specified in its fishery management plan. This is treated at much 

greater depth and with respect to each of the major fisheries in the Annual Report to 

Congress on the Status of U.S. Fisheries, available on the NMFS site at http://www.nmfs.

noaa.gov/sfa/sfweb/.

Comment: Greater effort needs to be put into direct manipulation of Bering Sea commercial fisheries to better determine their role and impacts in areas where there are ongoing 

declines in marine mammals. 
Response: NMFS recognizes that the effects of indirect interactions between commercial 

fisheries and marine mammals will not be understood solely by studying marine mammals. To this end, the AFSC has designed and supported a suite of studies directed at both 

Steller sea lions and their prey, including commercially important forage fish. Studies that 

involve manipulation of the commercial fishery have not been pursued due to operational 

and logistic difficulties, and because fishery management measures taken to protect Steller 

sea lions effectively provided the changes in fishing effort that could aid in assessing responses in Steller sea lion survival, reproduction, or foraging patterns. However, studies 

that involve manipulations in fishing effort in some areas might be appropriate in the 

future should indirect interactions continue to be a serious issue for marine mammals in 

the Bering Sea.

Comment: Clearly the discussion in the Plan focuses on salmon recovery. Indeed many 

species of salmon are listed under the ESA and are still declining. While there is an impressive list of activities, it is clear that either research is not properly focused or management 

action arising from the research is inadequate, since the fish continue to decline. NMFS 

should examine whether the interplay between its research and management actions is 

logical and robust.

Response: NMFS concurs that many salmon stocks remain threatened or endangered. 

NMFS supports the need to ensure that the science to inform management is the best 

possible given the funding constraints to meet all mandates for the agency. To achieve this 

end in regard to salmon science, the NWFSC has conducted both internal and external 

peer reviews of our science plans to achieve a credible effort that can inform management 

in critical areas in as timely a manner as possible. Moreover, multistakeholder-authored 

recovery plans and targets now exist for nearly all listed ESU’s from which measured gains 

in relation to management actions can be documented. In many cases, improvements in 

the status of many stocks have been observed, although delisting has only been achieved 

for one stock at this time. 

Comment: NMFS should shift the focus of the Northwestern Hawaiian Islands lobster 

assessment from establishment of harvest guidelines to use as an indicator of ecosystem 

health.

Response: Lobster in the Papahānaumokuakeā Marine National Monument are subject 

to a zero harvest guideline pursuant to Proclamation 8031 and its codifying regulations. 

NMFS believes that the data gathered in these assessments is useful as an indicator of the 

ecosystem health of the Monument, and has modified text accordingly.

Comment: NMFS should initiate collection of age-length data for central Pacific non-pelagic (i.e., bottomfish) species from otolith reading, to support examination of the impacts 

of fishing on age structure and to estimate mortality rates. Given that the Proclamation 

establishing the Papahānaumokuakeā Marine National Monument restricts fishing activity, 

NMFS should focus on main Hawaiian Islands bottomfish stocks.

Response: NMFS agrees that more basic fisheries biology work is important for the other 

bottomfish fishing areas, and has revised text accordingly.

Comment: Development of tagging programs for highly migratory species in the central 
160

and western Pacific seems more in the realm of international fishery management agencies 

than a NMFS-specific responsibility.

Response: NMFS agrees that such tagging programs should be developed in conjunction 

with regional fishery management organizations, and has modified the text accordingly.

Comment: NMFS should ensure that studies examining the impacts of gear modifications 

on longline fisheries are performed and that the results of the studies be analyzed, reviewed, 

and made available to fishery managers.

Response: NMFS agrees that dissemination of the results of such studies is extremely important, and has worked assiduously both domestically and internationally to disseminate 

these results. The text has been modified to reflect this.

Comment: NMFS should use agent-based modeling to analyze how the participation of 

individual fishermen in small boat fisheries in the western Pacific region can affect catch 

rates and, in turn, stock assessments that rely on catch rates as a measure of biomass.

Response: NMFS agrees that agent-based modeling (ABM) is a potentially fruitful approach 

towards understanding fishing effort from both a biological and economic perspective, and 

has initiated research in this direction. The text has been modified accordingly.
APPENDIX C:

ABBREVIATIONS AND ACRONYMS

ABC acceptable biological catch 

ABL Auke Bay Laboratory

ACCSP Atlantic Coastal Cooperative Statistics Program

AFA American Fisheries Act

AFSC Alaska Fisheries Science Center

AI Aleutian Islands

AKFIN Alaska Fisheries Information Network

AOP Annual Operating

ASMFC Atlantic States Marine Fisheries Commission

ASRG Alaska Scientific Review Group

BASIS Bering Aleutian Salmon International Survey

BRDs bycatch reduction devices

BSAI Bering Sea and Aleutian Islands

BSMDBS Biological Sample Monitoring Data Base System

CAGEAN catch-age analysis

CalCOFI California Cooperative Fisheries Investigations

CCAMLR Commission for the Conservation of Antarctic Marine Living Resources

CDQ community development quota

CFDBS Commercial Fisheries Data Base System

CFMC Caribbean Fishery Management Council

CPS coastal pelagic species

CPUE catch-per-unit-of-effort

CRED Coral Reef Ecosystem Division

DNA deoxyribonucleic acid

DOC Department of Commerce

EBS Eastern Bering Sea

EEZ Exclusive Economic Zone

EFH essential fish habitat

EIS Environmental Impact Statement

EOD Ecosystems and Oceanography Division

EPA Environmental Protection Agency

ESA Endangered Species Act 

ESU evolutionarily significant unit

FAD fish aggregating device

FAO Food and Agriculture Organization of the United Nations

FBSAD Fish Biology and Stock Assessment Division

FHDBS Food Habits Data Base System

FIN Fisheries Information Network

FMC fishery management council

FMP fishery management plan

FOCI Fisheries Oceanography Coordinated Investigations
162

FSCS Fisheries Scientific Computer System

FTE full-time equivalent

GIS geographic information system

GLOBEC Global Ocean Ecosystems Dynamics

GMFMC Gulf of Mexico Fishery Management Council

GOA Gulf of Alaska

GSMFC Gulf States Marine Fisheries Commission

GulfFIN Gulf of Mexico Fisheries Information Network

HAB harmful algal bloom

HAPC habitat areas of particular concern

HMS highly migratory species

IATTC Inter-American Tropical Tuna Commission

ICCAT International Commission for the Conservation of Atlantic Tunas

ICES International Council for the Exploration of the Seas

IFQ Individual Fishing Quota

IOCARIBE International Oceanographic Commission for the Caribbean

ISC Interim Scientific Committee for Tuna and Tuna-like Species in the North 

Pacific Ocean

ITQ individual transferable quota

IWC International Whaling Commission

LIDAR light detection and ranging

LME large marine ecosystem

LMR living marine resource

MMPA Marine Mammal Protection Act

MPA marine protected area

MSFCMA Magnuson-Stevens Fishery Conservation and Management Act

MSY maximum sustainable yield

NEFMC New England Fishery Management Council

NEFSC Northeast Fisheries Science Center

NEPA National Environmental Policy Act

NERO Northeast Regional Office

NSP NMFS Strategic Plan

NMFS National Marine Fisheries Service

NMML National Marine Mammal Laboratory

NOAA National Oceanic and Atmospheric Administration

NODC National Oceanographic Data Center

NOS National Ocean Service

NPAFC North Pacific Anadromous Fish Commission

NPALB North Pacific Albacore Workshop

NPFMC North Pacific Fisheries Management Council

NRC National Research Council

NSL National Systematics Laboratory

NSPFR NMFS Strategic Plan for Fisheries Research 

NWFSC Northwest Fisheries Science Center

NWHI Northwestern Hawaiian Islands

OBDBS Observer Data Base System

OCC ocean carrying capacity

OMB Office of Management and Budget

OY optimum yield

PacFIN Pacific Coast Fisheries Information Network
Pacific RecFIN Pacific Recreational Fisheries Information Network

PCR polymerase chain reaction

PFMC Pacific Fishery Management Council

PICES North Pacific Marine Science Organization

PIFSC Pacific Islands Fisheries Science Center

PIT passive integrated transponder

PMEL Pacific Marine Environmental Laboratory

RACE Resource Assessment and Conservation Engineering Division, AFSC 

RecFIN Recreational Fisheries Information Network 

REFM Resource Ecology and Fisheries Management Division, AFSC

ROV remotely operated vehicle

SAFE stock analysis and fishery evaluation

SAFMC South Atlantic Fishery Management Council

SAIP Stock Assessment Improvement Plan

SARC Stock Assessment Review Committee

SAW stock assessment workshop

SCTB Standing Committee on Tuna and Billfish

SEDAR Southeast Data Assessment and Review

SEFSC Southeast Fisheries Science Center

SFA Sustainable Fisheries Act of 1996

SPO NMFS Scientific Publications Office, Seattle, WA

SPTT South Pacific Tuna Treaty

SWFSC Southwest Fisheries Science Center

TED turtle excluder device

TRT technical recovery team

UN United Nations

UNCLOS United Nations Convention on the Law of the Sea

URI University of Rhode Island

WPacFIN Western Pacific Fisheries Information Network

WPRFMC Western Pacific Region Fishery Management Council
164
APPENDIX D:

GLOSSARY

Acceptable biological catch (ABC): The ABC is a scientific calculation of the sustainable 

harvest level of a fishery as determined by Federal fisheries biologists.

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

Anthropogenic: Human caused; usually used in reference to risks created to fish stocks by 

human activities.

Aquaculture: The propagation and rearing of aquatic organisms in controlled or selected 

aquatic environments for any commercial, recreational, or public purpose. 

Atlantic Coastal Cooperative Statistics Program (ACCSP): A cooperative state-Federal marine 

and coastal fisheries data collection program. The goal of the program is to cooperatively 

collect, manage, and disseminate fishery statistical data and information for the conservation 

and management of fishery resources of the Atlantic coast and to support the development 

and operation of a national data collection and data management program. 

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

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

BMSY: 1) Long-term average biomass that would be achieved if fishing at a constant fishing mortality rate equal to FMSY. 2) The weight (biomass) of a group of fish necessary to 

produce maximum sustainable yield (MSY).

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

Bycatch: The Magnuson-Stevens Fishery Conservation and Management Act defines bycatch as “fish which are harvested in a fishery, but which are not sold or kept for personal 

use, and includes economic discards and regulatory discards... [But not] fish released alive 

under a recreational catch and release fishery management program.”

Bycatch reduction device (BRD): Any of a number of implements that have been certified to 

reduce the likelihood of capturing nontarget species.

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

gear is used.

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

recreational fishing.
166

Commercial fishing: Fishing in which the fish harvested, either in whole or in part, are 

intended to enter commerce or enter commerce through sale, barter, or trade.

Conservation engineering: The practice of determining the modification in gear design that 

will meet conservation objectives, such as decreasing bycatch and bycatch mortality by 

increasing the selectivity of gear and increasing the survival of fish and other living marine 

resources that fishing gear encounter inadvertently.

Continental shelf: Submerged margin of continent from low-tide line to a point (generally 

between the 50- and 100-fathom isobaths) at which there is a marked increase of slope 

(i.e., the continental slope) to greater depth.

Delisting criteria: Determination as to what indicators need to exist before stocks can be 

taken off the list of endangered species. Typically, delisting criteria are elaborated by policy 

decisions regarding various recovery activities, such as reforming hatchery practices, reducing harvest, eliminating impacts of dams or restoring habitat.

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

Fish Aggregating Device: Artificial or natural floating objects placed on the ocean surface, 

often anchored to the bottom, to attract schooling fish species underneath, thus increasing 

their catchability.

Endangered species: A species is considered “endangered” if it is in danger of extinction 

throughout a significant portion of its range; it is considered “threatened” if it is likely to 

become an endangered species.

Endangered Species Act (ESA): The Federal law, enacted by Congress in 1973, to provide 

protection for, and promote recovery of, animal and plant species considered as threatened 

or endangered because of natural or anthropogenic conditions.

Essential fish habitat (EFH): The Magnuson-Stevens Fishery Conservation and Management Act defines essential fish habitat as “those waters and substrate necessary to fish for 

spawning, breeding, feeding, or growth to maturity.”

Evolutionarily significant unit (ESU): An ESU is a distinctive group of Pacific salmon, steelhead, or sea-run cutthroat trout that is uniquely adapted to a particular area or environment 

and cannot be replaced. 

Exclusive Economic Zone (EEZ): The zone contiguous to the territorial sea of the United 

States, the inner boundary of which is a line coterminous with the seaward boundary of 

each of the coastal states and the outer boundary of which is a line drawn in such a manner 

that each point on it is 200 nautical miles from the baseline from which the territorial sea 

is measured. This zone was established by Proclamation Numbered 5030, dated March 

10, 1983. 

Exploitation rate: The proportion of a population at the beginning to a given period that 

is caught during that time period (usually expressed on a yearly basis). For example, if 

720,000 fish were caught during the year from a population of 1 million fish alive at the 

beginning of the year, the annual exploitation rate would be 0.72.
Ex-vessel value: The amount paid to vessel’s owner or operator for its catch, excluding any 

value added by at-sea processing.

Fishery: a) One or more stocks of fish which can be treated as a unit for purposes of conservation and management and which are identified on the basis of geographical, scientific, 

technical, recreational, and economic characteristics; and b) any fishing for such stocks.

Fishery Management Council (FMC): One of eight regional groups established under Section 

302 of the Magnuson-Stevens Fishery Conservation and Management Act to prepare and 

oversee fishery management plans for fisheries conducted principally within the Exclusive 

Economic Zone.

Fishery management plan (FMP): A plan developed by a regional Fishery Management 

Council, or the Secretary of Commerce under certain circumstances, to manage a fishery 

resource in the U.S. EEZ pursuant to the Magnuson-Stevens Fishery Conservation and 

Management Act. Includes data, analyses, and management measures for a fishery. 

Gillnet: A flat net suspended vertically in the water used to capture fish which entangle 

themselves in the net, usually by the forward part of the body near the gills. 

Groundfish: Any species of fish, usually finfish that live on or near the sea bottom part of 

the time.

Juvenile: A young fish, usually resembling an adult in appearance, but which has not yet 

become sexually mature.

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

Landings: The number or poundage of fish unloaded at a dock by commercial fishermen 

or brought to shore by recreational fishermen for personal use. Landings are reported at 

the points at which fish are brought to shore.

Marine Mammal Protection Act (MMPA): The MMPA is a statue which was enacted in 1972 

to protect marine mammals and their habitat. These species include whales, dolphins, 

seals, seal lions, walruses, and others.

Maximum Fishing Mortality Threshold (MFMT, Fthreshold): One of the status determination 

criteria (SDC) for determining if overfishing is occurring. It will usually be equivalent to 

the fishing mortality (F) corresponding to the maximum sustainable yield (MSY) control 

rule. If current fishing mortality rates are above Fthreshold, overfishing is occurring

Maximum Sustainable Yield (MSY): A management goal specifying the largest long-term average catch or yield (in terms of weight of fish) that can be taken, continuously (sustained) 

from a stock or stock complex under prevailing ecological and environmental conditions, 

without reducing the size of the population.

Metapopulation: A group of partially isolated populations (or subpopulations) belonging to the same biological species (or subspecies) and connected by migratory pathways. 

These partially isolated populations or subpopulations can exchange individuals, which 
168

are potentially able to recolonize sites within the metapopulation from which the species 

or subspecies recently became extinct.

Minimum Stock Size Threshold (MSST, Bthreshold): A status determination criteria (SDC). The 

greater of: a) 1/2 BMSY, or b) the minimum stock size at which rebuilding to BMSY will 

occur within 10 years while fishing at the maximum fishing mortality threshold (MFMT). 

MSST should be measured in terms of spawning biomass or other appropriate measures of 

productive capacity. If current stock size is below Bthreshold, the stock is overfished.

Optimum yield (OY): a) The amount of fish which will provide the greatest overall benefit 

to the Nation, particularly with respect to food production and recreational opportunities, 

and taking into account the protection of marine ecosystems; b) is prescribed as such on 

the basis of the maximum sustainable yield from the fishery, as reduced by any relevant 

economic, social, or ecological factor; and c) in the case of an overfished fishery, provides 

for rebuilding to a level consistent with producing the maximum sustainable yield in such 

fishery.

Overfished: 1) An overfished stock or stock complex “whose size is sufficiently small that 

a change in management practices is required to achieve an appropriate level and rate of 

rebuilding.” A stock or stock complex is considered overfished when its population size 

falls below the minimum stock size threshold (MSST). A rebuilding plan is required for 

stocks that are deemed overfished. 2) A stock is considered “overfished” when exploited 

beyond an explicit limit beyond which its abundance is considered ‘too low’ to ensure safe 

reproduction. In many fisheries fora the term is used when biomass has been estimated to 

be below a limit biological reference point that is used as the signpost defining an “overfished condition.” This signpost is often taken as being FMSY, but the usage of the term 

may not always be consistent. (see Minimum Stock Size Threshold) Comment: The stock 

may remain overfished (i.e., with a biomass well below the agreed limit) for some time 

even though fishing pressure might be reduced or suppressed.

Overfishing: 1) According to the National Standard Guidelines, “overfishing occurs 

whenever a stock or stock complex is subjected to a rate or level of fishing mortality that 

jeopardizes the capacity of a stock or stock complex to produce maximum sustainable yield 

(MSY) on a continuing basis.” Overfishing is occurring if the maximum fishing mortality 

threshold (MFMT) is exceeded for 1 year or more; 2) In general, the action of exerting 

fishing pressure (fishing intensity) beyond the agreed optimum level. A reduction of fishing 

pressure would, in the medium term, lead to an increase in the total catch. 

Pinger: High-frequency acoustic devices that may keep marine mammals from entering 

and becoming entangled in fishing nets.

PIT-tag: The passive integrated transponder (PIT) tag is an electronic tag 10 mm long by 

2.1 mm in diameter that can be coded with one of 35 billion codes. The tag can be automatically detected and decoded in situ and eliminates the need to sacrifice, anesthetize, 

handle, or restrain fish during data retrieval. The tag has been developed as a research and 

management tool for monitoring the movement of juvenile and adult fish species. 

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

also components of the plankton community.

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

area.

Quota: The maximum amount of fish that can be legally landed in a time period. It can 

apply to the entire fishery, an individual fisher’s share under an individual fishing quota 

(IFQ) system, or refer to the size of fish.

Recreational Fisheries Information Network (RecFIN): A cooperative state-Federal effort among 

marine fisheries agencies to improve collection and management of marine recreational 

fisheries statistical information.

Recruitment: A measure of the weight or number of fish which enter a defined portion of 

stock, such as the fishable stock or the spawning stock. 

Regulatory impact review (RIR): The part of a Federal fishery management plan that describes 

impacts resulting from the plan.

Relative abundance: An index of fish population abundance used to compare fish populations 

from year to year. This does not measure the actual numbers of fish, but shows changes 

in the population over time.

Saltonstall-Kennedy Grant Program: A competitive program that provides funds through 

grants or cooperative agreements for research and development projects to benefit the U.S. 

fishing industry. The Saltonstall-Kennedy Act, as amended [15 U.S.C. 713 (c) (3)], is the 

program’s statutory authority.

ShoreZone: A coastal habitat mapping and classification system in which geo-referenced 

aerial imagery is collected specifically for the interpretation and integration of geological 

and biological features of the intertidal zone and nearshore environment. Additional information is available at: http://www.shorezone.org/

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

Stock: A more-or-less discrete and identifiable unit of fish or other exploited species, often 

referring to a management unit.

Stock assessment: The biological assessment of the status of the resources. This analysis 

provides the official estimates of stock size, spawning stock size, fishing mortalities, recruitment, and other parameters.

Stock assessment workshop (SAW): A cooperative stock assessment activity in which scientists 

from various agencies evaluate the status of fish stocks.

Subsistence fishing: Fishing for personal consumption or traditional/ceremonial purposes.
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Technical Recovery Team (TRT): A panel of scientists set up to define “delisting criteria” in 

specific geographic domains for endangered salmon and steelhead species on the west 

coast.

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

Turtle excluder device (TED): An implement that has been certified to reduce the likelihood 

of capturing turtles.

Yield-per-recruit: The average weight of fish ultimately harvested for each fish that enters 

the fishery.

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

sustained by those age-classes.